Broad: Annotation: Argo: Internal: Download

Note: This is out of date. Please refer to: Argo2

Argo Internal Download

Install/Update Instructions

Just download and double click. No install required.

STABLE! Run Argo1 via webstart.

BETA! run Argo2 via webstart. Argo2 uses a google maps style binning approach to allow seamless navigation of much bigger sequences. It's still officially in "beta," but we think it should be suitable for most single sequence view tasks. Combo and Genome Map view don't work yet. Please give it a try and let us know what you think.

Requirements

  1. You must have java 1.5 installed (JRE). Email help@genome to request this.
  2. You must have an appropriately permission oracle account. Email Reinhard to request this.

Don't forget to update regularly!

Updates happen about once a week and are posted on this page. Registered users will receive update alerts via email. The splash screen will tell you what version you're running and how old it is on startup. You can also check this through the "About" menu.

If you run argo through the webstart link above (right click and save link as to your desktop for easy access), argo will automatically be kept updated to the lastest version.

Release History

If you registered interest in a certain change, your name will appear after it in parentheses.

Argo2 Release History

2009-08-142009-08-14
Release Number Release Date Changes
74 2010-05-26
  1. Fixed bug where feature on the minus strand weren't clickable when in auto-sized track mode (Allison Griggs).
  2. Chromo Map legend displays error if no tracks can be displayed and improved layout (Christina Cuomo).
  3. Multiple Alignment: Reference features will show codon markup (James Galagan).
  4. Multiple Alignment: Alignment track order can be set with xml (James Galagan).
73 2010-05-11
  1. Sequence ruler shows structural features (contigs) as alternating bands of gray (Qiandong Zeng).
  2. Added tooltips for features (Tom Walk).
  3. Sizing of genome view adjusted to fit in the window; this eliminated the scrollbar when unneeded.
  4. Fixed ordering of track table ("view?" and "count" were flipped).
  5. Added group and ungroup options for multiple alignment projected features (Qiandong Zeng).
  6. Ends of multiple alignment projected features can be locked and unlocked independently (Qiandong Zeng).
72 2010-05-03
  1. Moved track size menu item out of submenu (Tom Walk).
  2. QA Results window lists genome and updated look (Michael Koehrsen).
  3. Linkage Group scaffold colors can be changed (Li-Jun Ma)
    4. .
71 2010-04-16
  1. Fixed bug where Argo would continue to exit even if the user clicked "no" after closing the window (Tom Walk).
  2. List of sequences is limited to 100; users can select the "see more" item to show the next 100. (Brain Haas).
  3. Fixed bug where pinned track features would disappear when crossing from graph to feature display.
  4. Added auto-sized feature layout (a.k.a. squishy tracks), which will resize features to fit in the track. Turn this on in the Feature Map Options and changing the Track Layout to "Auto Sized Feature" (Lots of People).
  5. Multiple Alignment: Releases saved in new location (fixes bug with conflicting releases).
  6. Multiple Alignment: Saving, Updating, and Deleting to Calhoun added.
70 2010-03-19
  1. Changed default sort order from Blast features (Matt Pearson)
  2. Remember track label divider bar location in preferences (Tom Walk)
  3. Fasta file indexing: fixed sporadic windows bug
  4. Improved feature and graph sizing/positioning
  6. Multiple alignment mode: show internal calhoun database feautures.
  7. Mutliple alignment mode: show alternating congiguous regions with thatched/unthatched texture.
  8. Multiple alignment mode: numerous performance enhancements.
  9. Fixed some resizing cosmetic issues
  10. Fixed codon drawing for negative stranded features
68 2010-01-27
  1. Addded mfa/maf independent stacked conservation/diversity bar view and data manager (Patrick Charlebois)
67 2010-01-22
  1. Fixed Featurize highlights (Jon Goldberg, Paul Godfrey)
  2. Graph bounds can now be explicitly set (and normalized).
  3. Splash screen closed after initialization
  4. Fixed accuracy of drag indicator
  5. Lots of multiple alignment stuff which the curious can admire here: (tb) http://www.broadinstitute.org/annotation/argo/internal/preview/ and here: (staph) http://www.broadinstitute.org/annotation/argo/internal/preview/staph/argo2-preview.jnlp
66 2009-12-10
  1. Generic Features: display dynamic properties regardless of ontology term (Edward Freedman)
65 2009-12-08
  1. Added Analyze -> GC% by Frame action (Allison Griggs, Qian Zeng)
  2. Updated help links to point to argo2 docs. (Edward Freedman)
  3. Fixed wiggle graph rounding when less than bin size.
  4. Fixed graph size bug.
64 2009-11-30
  1. Wicked cool splash screen (thanks Christian!)
  2. Don't freak out with new feature types (Edward Freedman)
  3. Load gtf2 subfeature properties and show . strand features (David Borenstein)
  4. Lots of multiple alignment stuff you can preview here
63 2009-10-27
  1. Editing: fixed right click deselecting feature bug (Tom Walk).
62 2009-10-22
  1. Multiple Alignment Display: added convergence "diversity" mode with two color maps. Previous mode is "divergence" diversity mode.
  2. Zooming: fixed zoom click expands track bug.
  3. Editing: fixed unnecessary restacking.
61 2009-10-02
  1. Tracks: added combined strand track option. (James Galagan, Brian Haas, Paul Godfrey)
  2. Editing: fixed 0 rowsize expanded tracks (Tom Walk).
60 2009-09-27
  1. Editing: fixed stacking bugs that were caussing mouse position errors with overlapping edited features and sodd behavior with strand switches (Tom Walk).
  2. Row size: fixed just introduced minimum track size/row size confusion.
59 2009-09-23
  1. Graphs: graph size now separate from row size.
  2. Track right click options: feature and graph specific options organized into submenus.
  3. Calhoun Database: blast cluster queries much faster, especially on big sequences. (Matt Pearson, Brian Haas)
  4. Calhoun Database: vastly fewer tracks selected by default. Might be too few -- let me know if there's anything else that should be turned on. (David Borenstein, Brian Haas).
  5. Broad public database: argo can take authentication cookie from jnlp to display protected data.
  6. Numpad +/- on windows: I really think I got it this time. Allison?
58 2009-09-21
  1. Graphs: toggle log mode. Show actual values on mouseover even in log mode. (David Borenstein, James Galagan)
  2. Calhoun Database: move blast cluster queries to separate connection. Still slow, but they don't block everything else. (Matt Pearson, Brian Haas)
  3. Calhoun Database: restored "connecting..." indicator in status bar.
  4. Calhoun Database: get sequence groups on initial connect rather than first featuremap open (same wait, more appropriate time)
  5. Calhoun Database: default threshold for blast cluster back to regular features -- too much overhead per query.
  6. Numpad +/- on windows: another stab... plus some debugging output.
57 2009-09-18
  1. Graph Style: Line graph is now way cooler looking (shaded google finance style). Now the default graph style. (David Borenstein)
  2. Sequence Ruler: raw sequence requests are now done in separate thread and binned like features so you can scroll smoothly without the UI locking. "?" indicates loading.
  3. Calhoun Database: made a number of performance tweaks. Blast clusters are still pretty horrid -- working on it. (Matt Pearson, Brian Haas)
  4. Numpad plus on windows resizing instead of zooming fixed (I think -- Tom and Allison please let me know)
56 2009-09-16
  1. BAM: fixed bookmarking of multi sequence bam files when bam sequence id does not match sequence id of the sequence it is imposed upon (David Borenstein)
  2. Broad Public Sequences: added rudimentary file based cacheing. (James Galagan)
55 2009-09-11
  1. BAM coverage plots: plot log of values. Fixed coverage plot bug in multi sequence bam files. Should be faster as well as accurate. (David Borenstein, Brian Haas, James Galagan)
  2. BAM short read support: added max short read rows filter to deal with massive stacks better. Default is 250 reads, you can configure this in Options -> Feature Map Options. Set to 0 to turn off. (James Galagan)
  3. Divergence mode: fixed case sensitivity bug.
  4. Multi fasta support: crude first cut. Track associations are still by individual sequence, which is inconvenient. Also bookmarks don't quite work. These will be fixed shortly.
  5. Track Table: fixed strange bug that was only (but consistantly!) happening on Sharvari's machine. (Sharvari Gujja)
54 2009-09-08
  1. Multiple alignment view: first cut at showing multiple alignment data in argo (from mfa file). Shows coverage for each alignment at distant zoom, and color coded "diffs" at close zoom. (Jared White, James Galagan)
  2. BAM coverage plot: dynamically calculate single nucleotide BAM short read coverage as a separate track (combined strands, but shown on the positive strand). It can take a while to calculate (several minutes for a multi-gigabyte bam file) but doesn't lock the ui and you can zoom in to view individual reads while it's calculating. (David Borenstein, James Galagan)
  3. BAM file support: much more tolerant of crappy input files (why are there so many of these????). Smarter default association of multi sequence bam file seqeunces with reference on which it is imposed (match by id or label). (David Borenstein)
  4. Track Management: fixed row height being remembered in preferences.
  5. Ruler Tracks: fixed "expand" option being available and then behaving strangely.
  6. Calhoun Database Editing: fixed bug that was causing pending insertion tracks to blip out (Tom Walk).
51 2009-08-28
  1. Fixed step/span Wiggle Rulers: added dynamic rebinning down to single nucleotide resolution. This is all done in memory, so eventually you'll run out. But you can load up to 5 single base step/span wiggle files with the default argo memory onto TB and it's quite fast once loaded. Note that this currently works only with fixed step/span wiggle rulers. (Brian Haas, James Galagan, Danny Park)
  2. Crude Navigation Panel: so it's more obvious to new users how to do basic zoom and pan. (James Galagan)
  3. Track Tooltips: to make it clear that collapsed tracks can be clicked to be expanded, and show score/min/max of graphs. (James Galagan)
  4. Track Management: single click expands collapsed track instead of having to double click.
50
  1. Cleaned up some wasteful debug.
49
  1. Keyboard Shortcut cheat sheet: contains most shortcut information (hit ? to see it or use the Help menu)
  2. Tracks: row resize: fixed so that expansion toggle isn't triggered.
  3. Tracks: arrow: fixed no longer showing up when set to size 5px (James Galagan)
  4. Tracks: row resize: changed bigger/smaller keyboard shortcut to control/command + and - to be more consistent with other apps
  5. Divergence Base Renderer: show for single row colapsed tracks so you don't have to expand (Sean Sykes)
  6. Tracks: expand to expands collapse rows even if only to 1
48 2009-08-11
  1. Wiggle and Tab value tracks: fixed recent screw up.
  2. Help: keyboard shortcut "cheat sheet" now has some information.
47 2009-08-08
  1. MAQ conversion tweaks: problems remain, but was able to process Brian's data. (Brian Weiner)
46 2009-08-06
  1. Divergence Renderer: show Ns and other non-ATGCs. Fixed recently broken deletions not showing.
  2. Tracks: set rows visible shortcut is alt-r instead of control-r because the latter was already taken./li>
  3. Help: first cut at keyboard shortcut "cheat sheet." Looks gorgeous -- now we just have to fill it in with the actual information.
45 2009-08-05
  1. Calhoun Feature Store: convert from file no longer shows negative total feature count with files over 2 GB (David Borenstein)
  2. RNA sequence panel: pass on calculated ORFS for viewing in feature map (Tom Walk)
  3. Divergence Base Renderer: colors consistent with sequence ruler. Show (crude) "diff mode" heatmap in collapsed state (Mike Koehrsen)
  4. Tracks: added explanatory tooltips over expansion state widgets (James Galagan)
  5. Tracks: fixed explicitly save number of tracks rows even if matches current setting
  6. Tracks: "r" keyboard shortcut is now control r to prevent accidental value clobbering in manage visible rows window. Value is default selected so you don't have to take your hand off the keyboard to overwrite. Expansion values always saved to prefs even if they match current. (Qian Zeng)
  7. Tracks: fixed load tracks causing top level menus to disappear.
44 2009-07-29
  1. Tracks: argo now remembers the number of expanded visible track rows you explicitly set for each track/strand in the manage visible rows window. (Qiandong Zeng, Everyone)
  2. Tracks: added an "r" keyboard short cut to bring up the manage visible rows window. Hitting return presses OK button.
  3. Tracks: you can now rename tracks from the right click track menu.
  4. Tracks: Track table now lets you filter by track name substring.
  5. Sequence Tree: now lets you filter by sequence group substring
  6. RNA Sequence Panel: fixed non-editable features not showing reset ORFs in feature map. (Tom Walk)
  7. Genome Map: works again. (Mia Champion)
43 2009-07-24
  1. Tracks: added (+) or (-) to track label for extra clarity
  2. Tracks: added set row size to track right click menu. The only reason you should now ever need to use the track table is to add new tracks.
  3. Editing: restored auto scroll when dragging evidence (Tom Walk)
  4. Editing: Progene: added "transpose" as a suggested name in the drop down (Qian Zeng)
  5. Editing: Progene: fixed truncate whitespace around gene name (Qian Zeng)
  6. Editing: Progene: give focus to gene name rather than symbol (Qian Zeng)
  7. RNA Sequence Panel: auto set ORFs after selection instead of making this a confusing 2 step process (Qian Zeng, Jon Goldberg)
  8. Calhoun PolyLocus Tracks: removed Solexa filtering that was hiding critical tracks (Sean Sykes)
  9. Calhoun PolyLocus Tracks: show simple single strain substitions. Some remaining issues with more complex divergences that will have to wait for David Borenstein's enlightening presence. (Sean Sykes)
  10. Calhoun Feature Store: added compress action. Bundled all CFS actions into Calhoun Feature Store submenu.
  11. Calhoun Feature Store: compression no longer default at least until we sort out cfz memory and performance issues. You can explicitly compress if you want.
  12. Zoom Scrollbar: fixed some recetly introduced cosmetic issues with the control point lines
  13. Feature Map Desities: fixed positive strand not respecting minimum track height.
42 2009-07-21
  1. Tracks: Pin to Ruler now supports multiple tracks. (Allison Griggs, Jon Goldberg)
  2. Genbank Format: tracks show up. (Anjan Purkayastha)
  3. Wiggle Format: fixed min and max set to rebinned values rather than native data scale.
41 2009-07-17
  1. BAM: show human releable sequence name in problem for multi sequence BAM files. (Rob Nicols)
  2. Feature Map Options: show hex color code in color buttons.
  3. Start/Stop Codons: Added Feature Map Options to set colors (Tom Walk)
  4. Sequence Ruler: Added Feature Map Option to set Sequence Ruler Style to Base (default) or Codon (like in argo1) (Sharvari Gujja)
  5. Feature Map: Density Drawing bounded by minimum track size if less than row size so you can safely set row size to something tiny
  6. Calhoun Feature Store: added uncompress option to deal with problematic compressed files.
40 2009-07-16
  1. Calhoun Feature Store: add feature names to CFS export. (Sean Sykes)
39 2009-07-14
  1. BAM: fixed not being able to process non paired read features (Sean Sykes)
  2. MAQ: fixed duplicated id error./li>
38 2009-07-14
  1. Tracks: raised minimum track size so you can collapse big stacks without making track labels illegible. (James Galagan)
  2. Calhoun Feature Store: Added File-> Export Track to Calhoun Feature Store to allow (inefficient, but useful) export to CFS from any format argo can load. Ecporting Tracks with too many features will make argo run out of memory, but up to 100K or so should be no problem. (Carsten Rus, Sean Sykes).
  3. Tracks: fixed bug with minimum density value being set to 0 if only one track of data.
37 2009-07-09
  1. Keyboard Shortcuts: fixed . zoom to selected (Chandri Yandava)
  2. BAM: added direct support for viewing bam files. Note: index is required. You'll have to zoom in to individual features to see anything. (Mike Koehrsen, David Borenstein, David Jaffe)
  3. BAM to CFS conversion: fixed multi sequence BAM conversions running out of memory (Michael Koehrsen)
  4. MAQ to CFS conversion: fixed SNP bug (no single base features) (Michael Koehrsen)
  5. Filed Features: changed the way threading works so it's one thread per file. Necessary for BAM. Think it might be a slight improvement for other formats as well. Complain if you don't think so.
  6. Clearer in-featuremap error messages. Like "Zoom in to see SAM features" instead of "ERROR"
36 2009-07-06
  1. Calhoun Open by Feature Id: provide context when re-using open map. (Allison Griggs)
  2. Calhoun Feature QA Analysis: more concise error messages instead of full stack trace (Allison Griggs)
  3. Menu Shortcuts: fixed double action firing bug with some of these -- in particular, double + and - zoom. (Tom Walk)
  4. Calhoun Sequence Tree: fixed sorting so it's case insensitive. Show the id that's being used to sort first. (Tom Walk)
35 2009-07-02
  1. Memory: Garbage Collect after every feature map close (and open). If nothing else, should make it clearer what is going on. (Tom Walk)
34 2009-07-02
  1. Analyze: added Cumulative GC Skew (Paul Godfrey)
  2. CFS Converter: fixed compression bug. Rudimentary support for MAQ SNP and MAQ Map formats. Faster approximate feature counting for BAM.
33 2009-07-01
  1. Wiggle Format: fixed density display bug (Paul Godfrey)
32 2009-07-01
  1. Calhoun Feature Id Dialog: added checkbox to indicate whether or not existing feature map should be re-used (Chandri Yandava)
  2. Feature Arrow Renderer: made more symetrical. Got rid of unintentional "3D" effect. Labels no longer obscure strand indicators.(Teena Mehta)
  3. Feature RoundRect Renderer: labels no longer obscure strand indicators. (Teena Mehta)
  4. BAM to CFS converter: split multi sequence BAM files into multiple single sequence CFS files. (David Borenstein)
  5. Track Label: enforce minimum size even if feature rows are smaller than this. Minimum is still illegibly small right now, but we will adjust and make configurableshortly.
  6. GC Percent: added action to generate but something seems off for this and GC skew on some sequences. Investingating... (Paul Godfrey)
31 2009-06-26
  1. Divergence String Base Renderer: deletions now show. Fixed mousevers. Minor performance enhancements. (David Borenstein)
  2. (rare) "Future" error: suppressed this since it doen't seem to matter. (David Borenstein)
  3. Tracks: fixed track control widget not initially realizing it needs to show expansion stuff when zoomed exactly to 1 px = 1 base.
  4. Wiggle Format: added basic support (Paul Godfrey, Brian Haas)
  5. GC Skew: works again except no rebinning yet -- percent and cumulative will be next. (Paul Godfrey, Brian Haas)
30 2009-06-25
  1. Divergence String Base Renderer: more memory efficient. (David Borenstein)
  2. Feature/Raw Sequence Loader: got rid of preloading bins (premature and counterproductive optimization) and reduced cache size to save memory.
29 2009-06-25
  1. Divergence String Base Renderer: much faster and better display. Only diffs are displayed instead of everying. Diffs are color coded. Base renderer mode kicks in earlier, at 1 base per pixel. Insertions are indicated with a + sign instead of clumsy, obscuring thick line. (David Borenstein)
  2. Zoom to Coordinates: undocumented shortcut is # keystroke (David Borenstein)
  3. Zoom to Feature: ROLLED BACK fixed rounding bug that sometimes contract view when zooming to tiny features. Broke more than it fixed.
28 2009-06-23
  1. BAM Format: File -> Create Calhoun Feature Store lets you create a file argo can efficiently handle from gigantic BAM files.
  2. Broad Public Data: More clearly indicated that this is public data vs. internal (Mike Zody)
  3. Feature Map: fixed mousewheel focus being set on new window when it opens.
  4. Feature Map: really fixed (again?) highlight column size bug
  5. Zoom to Feature: fixed rounding bug that sometimes contract view when zooming to tiny features
27 2009-06-19
  1. Feature Map: fixed sporadic unnessessary track bin reloads (aka "spaz loading bug")
  2. Feature Map: fixed minor locking issue that might make UI a little more responsive under heavy load.
  3. Feature Map: fixed key and mouse listeners not initially having focus when new tab/window is opened. Still an issue with mousewheel not having inital focus in new window.
  4. Feature Map: cancel pending densitty plot loads if map is closed
  5. Tracks: expanding an already expanded track now sets to max visible rows if not there already.
  6. Tracks: added expanded all tracks (shift-e) and collapse all tracks (shift-c) shortcuts (Chandi Yandava)
26 2009-06-16
  1. Feature Map: fixed feature map memory not being de-allocated on tab or window close (Tom Walk)
  2. Feature Map: fixed selection highlight column being truncated (Jon Goldberg)
  3. Calhoun Database: fixed BLAST feature links (Tom Walk)
  4. Calhoun Feature Store (CFS): convert CIGAR strings and Read sequence into Divergence Strings (James Galagan)
  5. Tracks: fixed alt-space shortcut to select all tracks
25 2009-06-12
  1. Multitouch Trackpad Horizontal Scrolling Support: to enable this, go to Options -> Feature Map Options and untick "Shift to Zoom?". It's not enabled by default because this would require switching the zoom and grab/pan modifiers (shift and alt keys) and that's a little too shocking for now I think. But as more people get multitouch trackpads, this might become the default. It's a very quick and intuitive way to navigate. (Brian Haas)
  2. Tracks: fixed track label mouseclicks not being received with very large number of tracks (Brian Haas)
  3. Tracks: added "Pin to Ruler" track label right click option. This lets you pin any track, fully zoomed out to the top level ruler. It doesn't zoom, so you can see 2 levels of zoom at the same time (3 if you could the sequence inspector panel). At the moment, only one track at a time can be pinned, but support for multiples will come soon. (Michael Koehrsen)
24 2009-06-08
  1. Webstart: support for isInternal flag
  2. Feature map: fixed repaint issue with scroll zoom on some machines
  3. Feature Map: fixed expanded tracks not redrawing until scroll if partially offscreen (Michael Koehrsen)
23 2009-06-05
  1. Calhoun Database: lowered default BLAST feature threshold to 100 from 300 to mitigate performance problems with massive stacks on Strept_sp_2_1_36FAA. There still seems to be some locking if the database is in a bad mood, but less because it's much less data. Further investigations pending. (Clint Howarth, Narmada Shenoy)
  2. Edit: restored drag and drop cursors (Jon Goldberg)
  3. Feature Map: fixed scroll bar sizing bug on windows (Allison Griggs)
  4. Feature Map: switched shift page up and page down panning to make down downstream and up upstream.
  5. Tracks: Sort and Filter are now right click options on track label.
  6. Feature Map: fixed sorting of non-calhoun features
  7. Feature Map: P selects parent feature (Allison Griggs)
22 2009-05-29
  1. GTF2/GFF3: show ORFs in feature map by default (Jared White)
  2. Feature Map: fixed obscure stack size reporting bug
    3. File -> Load Tracks: fixed isEnabled bug that was preventing enabling when feature selected
  3. Feature Map: removed misleading + from zoom cursor (misleading because it also - zooms with right click) (Jared White)
  4. Edit: fixed rollback refresh issues (Jon Goldberg)
  5. Edit: edge dragging in featuremap works again (Jared White, Tom Walk)
  6. Edit: removed edit caching for now. More trouble than it was worth. Will reconsider later (Jared White)
  7. Edit: fixed pending update mousever/stacking bug.
21 2009-05-27
  1. Tracks: random colors can be chosen for tracks (Brian Haas)
  2. Feature Map: - feature map opened initially to center strand (Paul Godfrey
    3. )
  3. Feature Map: Shift + page up will pan up (right), shift + page down will pan down (left) (Allison Griggs))
  4. Feature Map: changed many of the keyboard shortcuts so that they're stranded, rather than affecting both tracks, and only the stranded track that the mouse is over will be highlighted (boxed).
20 2009-05-25
  1. Edit: edit dialogs are now non modal so you can click on other stuff while they are open (Allison Griggs)
  2. Edit: fixed track resizing after insert (Allison Griggs)
  3. Feature Map: fixed resizing (Tom Walk)
  4. Feature Map: got rid of goofy big hand on windows for alt drag
  5. Tracks: indicate expansion state more clearly with darker gray background
  6. Tracks: indicate mouseover track with border.
  7. Feature Map: fixed graph mouseovers working like in argo1
19 2009-05-20
  1. Feature Map: fixed individual feature mouseovers working like in argo1 (Jon Goldberg)
  2. Edit: Fixed keyboard shortcut for save not always working (Allison Griggs)
  3. Feature Stacking: fixed concurrent modification exception with non-bitmap stacker. Also use sligntly faster lists instead of rangemaps.
  4. Graph Renderers: fixed sporadic array out of bounds when zooming out with mouse scroll.
18 2009-05-19
  1. Feature Map Navigation: mouse scroll wheel now zooms (shift+scroll) and pans left and right (alt+scroll) in addition to vertical scrolling (scroll without holding modifier key) (Brian Haas)
  2. Tracks: keyboard shortcut '0' will hide empty tracks/rows for selected tracks. Quick way to compact your featuremap without losing data..
  3. Tracks: fixed selection indication showing in featuremap even for hidden tracks.
  4. Edit Keyboard Shortcuts: fixed insert, update, and delete keyboard shortcuts not always working. Make backspace also delete. (Allison Griggs)
  5. Edit: fixed convert to single exon gene action nullpointer
  6. Edit: Edit Windows are now modal dialogs so you can't accidentally bring up multiple ones and/or lose track of them behind other windows (Tom Walk, Jon Goldberg)
  7. Calhoun Database: support for SAMPSTAT features (Jared White)
17 2009-05-18
  1. Feature Selection: fixed single subfeature click so it selects parent. Also made select child/parent actions update inspector. (Sharvari Gujja, Chandri Yandava, Clint Howarth, )
  2. Feature Selection: fixed collapsed subfeatures not being selectable (Zehua Chen, Tom Walk)
  3. Tracks: selected tracks now highlighted in feature map (Allison Griggs)
  4. Tracks: space bar in feature map now selects track. Alt space selects all tracks.
  5. Tracks: feature map 'e' (expand) and 'c' (collapse) keyboard shortcuts now apply to selected / mouseover tracks intead of all tracks. If you want all tracks, just alt space to select all first.
  6. Calhoun Database: Open Calhoun by Calhoun Feature Id now reuses current map instead of opening new map if possible (Tom Walk)
16 2009-05-15
  1. Feature Map: Right click popup menu restored (Tom Walk)
  2. Pending Inserts: fixed disappearing in expanded mode (Tom Walk, Zehua Chen)
  3. Track Label: Added rest of styles, also added track table menu item (Allison Griggs)
  4. Feature Style: added argo1-like arrow style.
  5. Feature Label Positions: added option to set to NONE or CENTER (TOP pending).
  6. Feature Map Options: set default styles for feature, graph, and base styles. Also label position.
  7. Insert Progene: fixed isEnabled logic
15 2009-05-13
  1. Tracks: track order is now saved to preferences after drag and drop
  2. Tracks: positive strand track label now positioned at bottom
  3. Track Table: fixed null pointer if feature selected when track table opened (Clint Howarth)

Argo1 Release History

Release Number Release Date Changes
325 2009-07-13
  1. Fixed right click.
  2. Made "segregated" track style the default.
324 2009-07-02
  1. Calhoun Feature Store: updated to argo2 level. Support for multi sequence BAM files, etc.
322 2009-05-19
  1. Calhoun Database: support for SAMPSTAT features (Jared White)
321 2009-05-10
  1. Sequence Inspector Panels: don't load sequence for gigantic features. You can specify how gigantic in featuer map options (default is 100k) (Qian Zeng)
320 2009-05-06
  1. Fixed smarter (was actually dumber, last time) cutting over to bitset alternative for stacking with tons of rows (Narmada Shenoy)
319 2009-04-03
  1. Smarter cutting over to sparse bitset for stacking with tons of rows (Sharvari Gujja)
318 2009-04-27
  1. Make argo not freak out quite so badly when it sees bad orfs. (Allison Griggs)
317 2009-04-21
  1. Removed ORF validation for partials (Jon Goldberg, Clint Howarth, Allison Griggs)
  2. aster (debugged) feature stacking (James Galagan, Mike Zody)
  3. Batch ruler operations (James Galagan)
  4. Incremental load Calhoun Feature Store (CFC) file support (James Galagan)
  5. Smarter (less frequent) Feature Map data reload after track table updates (James Galagan)
  6. Divergence track style for viewing calhoun and cfc divergence strings (James Galagan)
  7. UCSC fixes (internal sequence tree going to external, problem with "galaxy") (Mike Zody)
316 2009-02-18
  1. BED format: restored partial BED support (Moran Cabili)
315 2009-02-17
  1. Fasta: more improvements from Bil for handling large files. (Lijun Ma)
  2. Calhoun Database: fixed Blast parameters (they were the opposite of what they were supposed to be). (Alison Griggs)
314 2009-02-13
  1. BED format: added support for stranded features and strand, fixed offset, do not require track header line (Moran Cabili)
  2. Calhoun Database: added alt_sequence_group default filter (Matt Pearson)
  3. Fasta Format: small improvement in (recently degraded) handling of large files. Slow and requires a ton of memory, but possible. More pending. (Lijun Ma)
313 2009-01-26
  1. Calhoun Database: added basic support for Aligned Short Reads, operon, epitope,called region.
312 2009-01-08
  1. Feature Map: Turned on anti-aliasing. Don't ask me why I didn't do this years ago.
  2. Combo: added right click heat map legend (Lijun Ma)
  3. Combo: allow min and max to be set in alignment track table (Lijun Ma)
311 2009-01-07
  1. Combo: fixed max valued alignment being colored improperly. (Lijun Ma)
310 2009-01-07
  1. Combo: fixed alignments not drawing on Leopard. Turned on anti-aliasing for more attractive dotplot. (Lijun Ma)
309 2008-12-22
  1. Transcript Edit: fixed null pointer bug for no name evidence (Jon Goldberg)
308 2008-12-22
  1. Transcript Edit: remove non ascii characters from transcript name (Jon Goldberg)
307 2008-11-13
  1. Calhoun Database: option to use explicit database parameters for connection (Bil Lewis)
  2. Calhoun Database: default button in the Insert Annotation Transcript window is now the OK button (Tom Walk)
  3. Combo: changed "shade by" to (even more poorly named, I now notice) "heat map" to use complementary color mix instead of heat map (Lijun Ma)
  4. mRNA Inspector: make intronic now works here directly as well as in DNA panel (Tom Walk)
  5. DNA Inspector: frame 1 NTGs are highlighted in 5 prime context (Qian Zeng)
306 2008-10-05
  1. Feature Map Status Bar: Report parent, exon, intron locations sizes and positions along with 5 prime seq start frame and mrna start frame. (Jon Goldberg, Brian Haas)
    2. .
  2. DNA Sequence Panel Status Bar: report selection size and mod3 (Jon Goldberg)
305 2008-09-24
  1. Load Tracks: you can now select multiple tracks in the load tracks file chooser using control/apple/shift click. (Mike Zody)
  2. Track Table: Renamed Binary Map Track style to Opaque (Christina Cuomo)
  3. Feature Map: fixed color of Bar Graph track style
304 2008-09-18
  1. Combo: added Calhoun, Broad, and UCSC sequence data source options to load dialog (Lijun Ma)
  2. Calhoun Database: load and show orfs with initial featuremap load for automatically generated transcipts (Brian Haas)
  3. GFF Track Format: fixed (rolled back) compound feature bug in partial file loading. Simple features fine.
303 2008-09-16
  1. GFF Track Format: support for partial file loading (Mike Zody)
302 2008-08-28
  1. Calhoun Database: fixed generic (sub)feature issues (Brian Haas)
  2. Calhoun Database: use gapstrings ONLY for PROTDOM subfeatures
301 2008-08-26
  1. Calhoun Database: don't use gapstrings for transcript subfeatures (Zehua Chen)
300 2008-08-15
  1. mRNA Panel: NTG codons are now highlighted in lighter green for bacterial genomes (Qiandong Zeng)
299 2008-08-14
  1. Sequence Panels: new and improved superimpose overlapping features. You can now choose individual features to superimpose instead of being limited to entire tracks, and you can see the overlaps in the mRNA and protein panels as well as DNA.
298 2008-08-08
  1. Genome View: added right click rebin option to rebin density plots to current zoom level (Rays Jiang)
297 2008-08-01
  1. Calhoun Database: fixed bug that prevented deletions of features updated in two hours subsequent to creation (Sharvari Gujja, Tom Walk)
  2. Calhoun Database: PROTDOM gapstrings now used as basis for subfeatures (Edward Freedman, Michael Koerhsen)
  3. Track Table: Added "Overlapping" Track Style (Michael Fischbach))
296 2008-07-16
  1. Finder Panel: limit sequence search by frame (Jonathan Goldberg)
  2. Alignment Track Style: fixed mouseover so that it shows gaps again (Mike Koehrsen)
  3. Edit Menu: added convert to single exon gene actin (Brian Haas)
295 2008-07-07
  1. Genbank/NCBI: fixed clobbering of gene property. (Andrea Hoerster)
294 2008-07-02
  1. Genbank/NCBI: added more criteria. (Andrea Hoerster)
293 2008-06-24
  1. Edit: Drag resize transript/exon boundaries in featuremap when zoomed in to 1 or more pixels per base (Tom Walk)
  2. Edit: automatically regenerate orf when location changes (start,stop of transcript or exons)
292 2008-06-12
  1. Windows: added manage (rename) windows option (Edward Freedman)
  2. Bookmarks: Added "Open All" option in folders (Andrew Roberts)
291 2008-06-07
  1. BED Format: fixed to handle tabs and multiple spaces (Malcolm Cook)
290 2008-06-04
  1. File->Open Recent Sequence: increased number of sequences from 14 to 25 (Chinnappa Kodira)
289 2008-04-11
  1. Combo: simplified combo file dialog.
  2. Combo: fixed segment size in parallel view
  3. NCBI/Genbank: feature links to NCBI from genbank file db xrefs (James Galagan)
  4. Calhoun Database: support for PolyLocus features (Paul Godfrey)
  5. Calhoun Database: Removed "partial..." error message on save. (Paul Godfrey)
288 2008-03-04
  1. Combo: toggle lock aspect ration (Paul Godfrey, Qian Zeng)
  2. Error Handling: added a "Hide" option for dealing with situations in which you get a million consecutive error messages. Added a firefox style error manager widget in the status bar to review errors.
  3. Preferences: fixed export bug on windows jre 1.6 (Chinnappa Kodira)
287 2008-02-28
  1. Calhoun Database: fixed open generic feature by id bug (Brian Haas)
  2. Zoom: fixed * and . shortcuts so you don't have to use the numpad. (Michael Fischbach)
  3. Zoom: changed zoom to selected shortcut to be = (more in line with + - * .)
  4. Valued Feature: fixed line graph render bug and mouseover nullpointer
  5. Error handling: added "Details" button which gives stack trace (Alistair Rust)
286 2008-02-25
  1. Calhoun Database: fixed just introduced transcript insert bug (sorry!) (Sharvari Gujja, Zehua Chen)
    2. .
285 2008-02-23
  1. Calhoun Database: Added support for Excluded Regions. Edit -> Insert Excluded Region. The first time you do this for a sequence group you'll have to DB -> Clear Cache for it to show up (I'll fix this, but for now it's what you have to do). (Paul Godfrey, Narmada Shenoy)
  2. Feature Map: Scroll featuremap when dragged out of bounds (Tom Walk)
  3. Feature Map: Scroll vertically to control-N selected feature (Tom Walk)
  4. Calhoun Transcript Update: Fixed pointless reload on transcript update.
  5. Inspector Properties Panel: Don't show alt location etc. if it's null.
284 2008-02-15
  1. Edit: Added Trim To Orf option in Edit menu (Brian Haas)
283 2008-02-13
  1. Calhoun Database: Allow saving of bacterial orfs (Paul Godfrey)
  2. Calhoun Database: Default blast rank filter for blast clusters (had been just for alignments)
282 2008-02-01
  1. Calhoun Database: Select -> Group now Select -> Gene. Works with autocalled transcripts. (Chinnappa Kodira)
  2. Calhoun Database: Show signal P tool evidence properties (Michael Koehrsen, Jared White, Christina Cuomo)
281 2008-01-23
  1. Genemark Track Manager: added basic support (Mandanda Sassanfar)
  2. Glimmer Track Manager: fixed help meta data (Mandanda Sassanfar)
280 2007-01-09
  1. Genome View: fixed chromo map legend so it shows up for calhoun tracks (Lijun Ma)
  2. Workspaces: sequence tree window will refresh the list of group when opened, removed caching of the sequence group and composite group ids from workspaces (Sharvari Gujja)

  3. Workspaces: removed the rename button in the manage workspaces window.
  4. Input Dialogs: trim whitespace (James Galagan)
  5. Valued Features: no longer insist on ontology term 701 (Phil Montgomery)
279 2007-12-20
  1. Calhoun Database: set open by feature id feature tracks visible if not already (Matthew Pearson)
278 2007-12-18
  1. Calhoun Database: new connection information.
  2. Calhoun Database: add/remove/rename workspaces.
277 2007-12-14
  1. Calhoun Database: for clarity, workspaces now separate menu ("WS: Current workspace name"). Ability to add and remove sequence groups, composite sequence groups, and tracks from workspace (select sequence group or track,then right click for optin).
  2. Calhoun Database: added Composite Sequence Groups menu item. Renamed "Sequence Tree" to "Sequence Groups".
  3. Calhoun Database: drastically reduced number of queries when opening sequence group in sequence group window (Brian Haas)
  4. Calhoun Database: added default RANK_ORDER <= 5 for blast features (Brian Haas)
  5. Calhoun Database: in properties window, hyperlink ALT_SEQUENCE (Tom Walk)
  6. Calhoun Database: recognize ProteinDomain features (Tom Walk)
276 2007-12-06
  1. Calhoun Database: use the DB -> workspaces menu to filter sequence groups and tracks by calhoun database workspaces. Local workspaces depricated (but still around for now). (Phil Montgomery)
275 2007-11-21
  1. Calhoun Database: fixed display of calhoun 3 prime partial orfs. (Sinead O'leary)
  2. Feature Map / Combo Dotplot: keyboard zooming now also centers on mousepoint. Especially useful for "." zoom to bases.
  3. Combo: partial alignment glyph highlighting now supported, like in the web dotplot.
  4. Combo: constrain aspect ration of dot plot so that width = height (Paul Godfrey).
274 2007-11-06
  1. Feature Map, Perpendicular Combo View: Shift-click zoom now keeps the point that was clicked in the same location.
  2. Feature Map, Combo View: Panning uses new grab and grabbing mouse icons.
  3. Zoom Menu: "Zoom to Bases" shortcut is now "."
  4. Zoom Menu: Zoom In, Out, Full, and to Bases, are clustered together.
  5. Protein Sequence Panel: fixed highlight projection to feature map.
273 2007-10-30
  1. Feature Map: * zooms to full, changed wording of zoom menu items: zoom to 100% is now zoom to full, zoom to sequence is now zoom to bases.
  2. Workspace: Adding and removing of workspaces are immediately updated (Chinnappa Kodira).
  3. mRNA/Protein Sequence Panel: For exons, show mRNA markup and protein sequence with respect to parent transcript (Mike Zody).
272 2007-10-18
  1. Calhoun Database: Added checkbox to allow test database connection (Bil Lewis, Danny Park)
271 2007-10-10
  1. Rulers: fixed codon panel ruler caching sequence, messing up drawing on reload with different boundaries. (Bob Handsaker)
  2. Track Table: fixed recently introduced nullpointer when loading color preferences.
270 2007-10-04
  1. Crude "workspace" in db menu shows sequence groups that you have marked by right clicking and choosing "add to workspace." (Chinnappa Kodira)
269 2007-10-03
  1. Genome Map Track Table: fixed min being set to -1 for new tracks loaded from files causing very strange drawing (Lijun Ma)
268 2007-09-14
  1. Thresholds: you can now specify "Line" as well as default "Bars" style (Mark Borowsky)
  2. Track Table: fixed unsaved options getting clobbered with multiple "add tracks from file" clicks (Mark Borowsky)
  3. Genome Map: fixed chromo map legend columns (Lijun Ma)
  4. Web Browser Launch: use new BrowserLauncher library for faster (and Linux friendly) browser launching (Alistair Rust)
267 2007-09-05
  1. Genome Map: chromo map legend works for gff features. (Lijun Ma)
  2. Genome Map: chromo map legend lets you change colors. Colors are saved to prefs. (Lijun Ma)
266 2007-08-30
  1. Genome Map: you can now upload gff files with altLinkageGroup attributes and display in Chromo Map track style. (Lijun Ma)
  2. Genome Map: fixed mouseover tooltip coordinates.
265 2007-08-10
  1. Edit: fixed transcript name not being saved (Lucia Alvarado)
264 2007-08-08
  1. Calhoun DB: point to new db.
263 2007-08-01
  1. Edit: fixed label being stuck in name field (Chinnappa Kodira)
  2. Feature Map: draw border around all selected features (Chinnappa Kodira)
  3. Feature Map: fixed zoom to sequence position off by one that was messing up xml zoomStart/stop at sequence boundaries. Constrain zoom to boundaries. (Matthias Boeck)
262 2007-07-13
  1. Start XML: added support for zoomStart and zoomStop sequence paramenters. (Matthias Boeck)
  2. Start XML: added support for Empty sequences (Jim Robinson)
261 2007-06-25
  1. Combo: restored scroll bars.
  2. Combo: added start file support to go directly to parallel mode.
  3. Combo: fixed parallel adding offset to queries at 100% zoom from perpendicular.
260 2007-06-13
  1. Select Menu: add ability to select evidence for autocalled transcripts (Chinnappa Kodira, Qian Zeng)
259 2007-06-12
  1. Analyze: Show Multiple Alignment: made non modal so you can zoom around on the feature map with one of these open.
  2. Analyze: Show Multiple Alignment: force all caps.
  3. Analyze: Show Multiple Alignment: project highlights to feature map (Mike Zody)
  4. Feature map: fixed display of features with strand NONE (Alison Ziesel)
258 2007-05-27
  1. Track Table: added "is/is not" to criteria (Chinnappa Kodira)
257 2007-05-21
  1. UCSC: Connect to internal database. (Mike Zody)
256 2007-05-18
  1. Webstart: highlight feature, force track visible, select parent feature if child, show some surrounding sequence like with regular feature id open (Clint Howarth)
255 2007-05-18
  1. Thresholds: you can now specify operator instead of always having it be >= (Lijun Ma)
  2. Genome View: you can now set valued feature thresholds in the genome map. Click on the last column in the track table. (Lijun Ma)
254 2007-05-16
  1. Combo: made Pad Query Sequences? remembered in prefs (Paul Godfrey)
  2. Analyze: GC Skew fixed divide by zero if not Gs or Cs in span (Paul Godfrey)
  3. Genome View: fixed Bar Graph (Centered) protruding too far in both directions
  4. Genome View: fixed mouseover score reporting off by one interval
  5. Genome View: fixed track table being confused if a segment view is open.
253 2007-05-04
  1. Webstart: made some tweaks so you can now open argo on calhoun feature internal ids with this url template: http://www.broad.mit.edu/cgi-bin/annotation/argo/calhoun/webstart.cgi?f=7000001150322060 (Matthew Pearson)
  2. Combo: added Pad Query Sequences? option to Feature Map Options (Paul Godfrey)
  3. Genome View: added "Heatmap (Complementary)" track style. (Lijun Ma)
  4. Genome View: added "Bar Graph (Centered)" track style. (Lijun Ma)
  5. Genome View: Track table now shows editable info for min/max/center.
  6. Genome Map: fixed gff files being reloaded constantly.
  7. Segment View: removed space in front of feature ids in open by feature id (Qian Zeng)
  8. Segment View: track table count column now only shows info for currently selected feature map instead of more confusing entire loaded features in sequence group (Narmada Shenoy, Qian Zeng, Chinnappa Kodira)
252 2007-04-26
  1. Wiggle Fixed Span Format: parse scientific notation (Paul Godfrey)
  2. Segment View: added "Heatmap (Complementary)" track style. Values less than "center" (default 0) are drawn in complementary color. (Lijun Ma)
  3. Segment View: added "Bar Graph (Centered)" track style. Bars are centered on specified value (default 0) (Paul Godfrey)
  4. GC Skew: round values to 3 decimal places.
  5. Combo: fixed terrible performance of vertical valued feature drawing -- was redrawing entire component even when zoomed in. (Paul Godfrey)
251 2007-04-20
  1. Combo: fixed invisible 0 px width/height alignment highlights by rounding up to 1 (Paul Godfrey)
  2. Inspector: indicated STORED_ORF (when present) in addition to ORF in properties panel. Added right click copy option to proterties panel. (Narmada Shenoy)
250 2007-04-18
  1. GC Skew Action: fixed string out of bounds with stretched vertical sequences (Paul Godfrey)
  2. Calhoun Database: open by feature id opens one feature map per feature if features for given identifier fall on more than one sequence. (Lucia Alvarado, Sinead O'Leary, Chinnappa Kodira)
  3. Combo: explicit right click option to use gaps for projections (Lucia Alvarado)
  4. Combo: more compact properties
  5. SNP Track Style: case insensitive (Mark Borowsky, Phil Montgomery)
  6. Inspector Panel: restored superimpose overlapping features, adjusted transparancy so that nucleotides are not obscured (Mark Borowsky)
249 2007-04-16
  1. Calhoun Database: added support for RNAGene features (Jared White, Sinead O'Leary)
248 2007-04-12
  1. Combo: fixed windows only perpendicular glyph drawing bug (Lucia Alvarado)
247 2007-04-10
  1. Calhoun Database: added support for VSNPS (Danny Park)
246 2007-04-09
  1. Genome Map: added support for gff scores. (Lijun Ma)
245 2007-04-09
  1. Edit: Make Highlighted columns selectable action ingnores existed selected columns. Removed semi-redundant create selectable column action. (Paul Godfrey)
  2. Combo: fixed vertical valued feature plotting.
  3. Analyze: added GC Skew action. (Paul Godfrey, Kalai Mathee)
  4. Filed valued features: fixed smoothing bugs
244 2007-04-02
  1. Inspector: workaround for sequence link wrap on windows JRE 1.5.0_10 and up. (Chinnappa Kodira, Qian Zeng)
  2. Inspector: Show codon boundaries disabled by default. Show codon boundaries action repaints immediately.
  3. Combo: fixed sporadic right click menu redraw bug in dna and rna inspector panels.
  4. Combo: fixed vertical feature map min 1 px highlight columns
243 2007-03-23
  1. IMPORTANT! Argo calhoun login is no longer based on oracle account, it uses calhoun web credentials instead. I created an annotguest web account so if you've been using that you don't have to do anything differently.
  2. Calhoun Feature Id Open: tolerate spaces (Chinnappa Kodira)
    3. >
  3. Combo: calhoun combo bookmarks and alignment uris now work
  4. Combo: highlight color changes depending on source (like web dot plot. imitation is the finest form of flattery, right Phil?)
  5. Combo: made dot plot alignment glyphs less "sausage like" (James Galagan)
  6. Combo: highlight does not extend beyond originating alignment glyph (like web dot plot)
  7. Combo: report dot plot size in status bar
242 2007-03-21
  1. Inspector Panel: show track and location for "no name" evidences (Qian Zeng)
  2. Inspector Panel: got rid of red table cell borders on windows JRE 1.6.0
  3. Insert Calhoun Transcript: default name is "hypothetical protein" for transcripts based on "no name" primary evidence. (Qian Zeng)
  4. Insert Calhoun Transcript: show track and location for "no name" primary and secondary evidences (Qian Zeng)
241 2007-03-16
  1. Inspector Panel: codon boundaries for selected frame in RNA panel line up (Qian Zeng)
  2. Inspector Panel: toggle on/off display codon boundaries for selected frame in RNA panel (Qian Zeng)
  3. Feature Map Options: default integrated row limit set to 1000 from 250 (Chinnappa Kodira)
  4. Feature Map Sequence Columns: fixed off by 1 pixel (Jared White)
  5. About: report memory usage.
240 2007-03-08
  1. Inspector Panel: indicated codon boundaries for selected frame in RNA panel (Qian Zeng)
  2. Genome Map: you can set the spacing between linkage groups in the Genome Map Options Window (Lijun Ma)
  3. Feature Map: no border for less than 3 px long so you can see identifying color for tiny features instead of just black border.
  4. Feature Map Ruler: dragging across position ruler creates highlight column instead of selectable sequence column (Dave Decaprio, Heidi Kuehn)
  5. Feature Map Ruler: fixed right click also creating column.
  6. Custom Data Ruler: fixed recently introduced null id bug that was preventing more than one ruler at a time from being loaded (Michael Freitag)
  7. Tab Value Track data: tolerate comments with # prefix (Michael Freitag)
  8. GFF3: tolerate duplicate feature ids (Michael Freitag)
  9. Sequence View: renamed to Segment View. Less confusing when contrasted with Genome View, Sequence Panels, etc.
  10. Combo: added legend to properties panel when dot plot clicked. (Kalai Mathee)
239 2007-03-02
  1. Calhoun Database: fixed open by multipe feature ids not prompting for sequence range every time (Mike Zody)
  2. Window Menu: fixed crash when all windows close and you scroll across the iwndow menu (Mike Zody)
238 2007-03-01
  1. Calhoun database: removed problematic "promote transcript" option (Phil Montgomery)
  2. Genome Map: fixed recently introduced bug where min and max of density plost were not being set (resulting in some very ugly drawing)
237 2007-02-26
  1. Wiggle BED format: added support. (Tarjei Mikkelsen)
  2. Wiggle VariableStep format: added support. (Tarjei Mikkelsen)
  3. Wiggle fixedStep format: respect span declaration instead of making equals to step.
  4. Valued Features: treat gaps as gaps and not as zeros.
  5. UCSC: finally really fixed stubborn session bug (Amir Karger)
  6. GFF3: support for representing fixed step and range map valued features as gff3 records
  7. Argo Archive: exports and imports valued features (as gff3)
236 2007-02-16
  1. Valued Features: fixed colored threshold values being drawn 1 px too high
  2. Valued Features: colored threshold values now associated with tracks, not features (Lijun Ma)
  3. Valued Features: threshold values now remembered in preferences file (Lijun Ma)
  4. Valued Features: min and max now associated with tracks, not features.
  5. Valued Features: threshold values now drawn against bar graph track style too
  6. Valued Features: you can now load custom data ruler tab delimited input as a valued ruler. This is nicer for a number of reasons, including smoothing. Eventually I'd like rulers and tracks to be completely interchangable: a ruler should just be a track in the columnheader that doesn't scroll.
  7. Calhoun Database: plugged some more unclosed statements and resultSets that were causing maximum cursors exceeded message.
  8. Feature Map: SNP and alignment track styles: draw nucleotides same size as regular features. Looks cleaner. Less surprising when you zoom in.
235 2007-02-09
  1. Feature Map: right click menu now only shows active menu items. Was getting too crowded. This also means I can add more context specific stuff. (James Galagan)
  2. Valued Features: you can now click and inspect them (Lijun Ma)
  3. Valued Features: should now stack properly like regular features.
  4. Valued Features: you can set the min and max as a right click option like you can with data rulers.
  5. Valued Features: in the line graph, you can set values at which to draw an mlagan style colored column (Lijun Ma)
234 2007-02-06
  1. Calhoun Database: multi calhoun valued feature support in feature map (Lijun Ma)
  2. Calhoun Database: calhoun valued feature support in genome map (Lijun Ma)
  3. Calhoun Database: fixed sporadic maximum cursors exceeded message in property search (I hope)
  4. Genome Map: report min and max in graph track mousevers
233 2007-01-31
  1. Wiggle Format: added basic support for fixedStep wiggle format track files (Manuel Garber)
  2. Line Graph Track Style: fixed repaint issue with scrolling.
  3. Calhoun Database: search ap_euk_gene.ap_locus for feature identifiers (Lucia Alvarado)
  4. Properties Panel: hide meaningless ids
  5. Genbank: show note and db_xref fields in properties
  6. Genbank: recognize gbf file extension (Leah Reshef)
  7. Genbank: fix db_xref being used as unique idenfifier and hiding features (Leah Reshef)
232 2007-01-26
  1. Blast Track Files: fixed blast specific criteria not showing up for sorting and filtering. (Charlie Whittaker)
  2. Blast Track Files: recongize .blastx, .blastn, .blastz, .blastp file extensions (Charlie Whittaker)
  3. Vertical Zoom: restored this functionality (Charlie Whittaker)
  4. Calhoun Database: added ad hoc feature support (Bob Handsaker)
  5. Calhoun Database: fixed wording on default progene names in combobox (Qian Zeng)
  6. Calhoun Database: fixed repleat cluster info being hidden behind long property "click to view"
  7. Calhoun Database: fixed inspector panel sequence group link to calhoun website.
231 2007-01-22
  1. Genome Map: fixed nullpointer that was preventing track table from opening (Lijun Ma)
230 2007-01-19
  1. Properties panel: instead of struggling to display enormous properties values in html on click, link to a new window if they are too long. Was causing freezes with large blast alignments in combo. (Antonis Rokas, James Galagan)
  2. Combo: fixed scroll to strand boundary on all featuremaps after bookmark open (Antonis Rokas, James Galagan)
  3. Select Marked: fixed action enabling. Was only being enabled if the currently selected feature was marked.
  4. GFF3: clearer error reporting with file name and offending record (Bob Handsaker)
  5. Sequence columns: fixed off by one nucleotide mouseover detection (Jared White)
  6. Insert Generic Compound feature: fixed action enabling so that you don't have to select a template feature (Jared White)
  7. UCSC Sequence Manager: another band aid for raw sequence retrieval. Works for now, but must properly fix.
229 2007-01-10
  1. Custom Data Rulers: added right click "Set Bounds" action that lets you specify the minimum and maximum score range. (Qian Zeng, Steve Johnson)
228 2007-01-08
  1. Feature Map: fixed sneaky preferences bug that was causing row drawing to be slightly off for integrated track style. It only happened the first time you open the current version of argo on a machine that has never run a previous version of argo (it was looking for a preference setting for row height, and setting it to 0 if it can't find it, but at the end of the session that value gets written to the preferences as something sensible). Existing argo users would probably never have noticed this, only new users (and only the first time). This bug was introduced in release 223. (Charlie Whittaker)
  2. NCBI: added caching for much faster performance (Antonis Rokas)
  3. GFF3: generate id based on row and filename if no explicit id attribute given (Antonis Rokas)
  4. Combo: fixed subtle Blast specific bug where blast track files would not load to reference feature map via track table (Antonis Rokas)
  5. Error handling: removed some colorful error messages (Charlie Whittaker)
227 2007-01-03
  1. Track Labels: fixed not rendering properly (Qian Zeng)
  2. UCSC Sequence Manager: fixed raw sequence error due to UCSC site change.
226 2006-12-29
  1. Track Table: added track offset column. Use case: you select a subsequence in argo to paste into the glimmer website for analysis. The coordinates of that output will be relative to that subsequence. The track offset lets you adjust the coordinates back to those of the parent sequence. (Antonis Rokas)
  2. Progene Edit: added default Hyothetic ORF and Conserved Hypothetical ORF options to the Gene Name drop down (Qian Zeng)
  3. Genome Map: fixed track order updating after track table refresh (James Galagan)
  4. Subversion: calhoun project is now argo! And cruiseControl acknowledges this!
225 2006-12-21
  1. Glimmer: added GLIMMER track support (Antonis Rokas)
  2. Webstart: fixed so it doesn't barf under java 1.4
224 2006-12-21
  1. Blast: fixed labeling, allow scientific notation score. Fixed query label property being stored as start. (Antonis Rokas)
223 2006-12-18
  1. Export Image: now (more) reliably produces vector (pdf/ps/eps/svg) output on mac and windows. Luck had a lot to do with this. A new (less buggy) freehep vector graphics library was released december 7 -- this would have been very hard otherwise (java printing api is not fun). Note: powerpoint seems to like pdf best for me. It doesn't like the freehep eps files. (Giri Narasimhan)
223 2006-12-14
  1. Blast: fixed parsing of problematic blast output (Antonis Rokas)
  2. Feature Map: you can now specify track size on a per track basis in the track table. The number means the number of pixels in the shaft of the feature arrow. Density plots will be drawn at this size + the label size (label size is still global in options -> feature map options). If you have integrated style and different track sizes for component tracks, it will look odd because integrated row size will not change (it should change to largest component size but I haven't implemented that yet) (Matt Henn, Kalai Mathee)
  3. Webstart: you can now specify broad db url in the start.xml file (Michael Koehrsen)
  4. Webstart: toFront works on windows (but not mac) (Michael Koerhsen)
  5. Webstart: smaller obfuscated jar lives here: http://www.broad.mit.edu/annotation/argo/webstart/broad/argow.jar See working examples here: http://www.broad.mit.edu/annotation/argo/webstart/broad/ (Michael Koehrsen)
222 2006-12-08
  1. Calhoun Database: fixed multi alignment bug if more than one track to explode per sequence group (Tim Ledlie)
  2. QA Report Message: stuck in scrollpane (Lucia Alvarado, Qian Zeng)
221 2006-12-05
  1. Properties Panel: show compact alt feature strand, start, stop, length as ALT_LOCATION (Giri Narasimhan)
  2. Properties Panel: show detailed, hyperlinked repeat cluster information for repeats. Click on cluster id to highlight all contained repeats in feature map (you may have to zoom out again to see them). Click on individual listed repeat to highlight if in current map or open new map if not in current map (Kalai Mathee)
  3. GFF3: uri decode attribute key names (was just doing values).
220 2006-11-30
  1. Track Table: added string IN LIKE operator for filter criteria (Lijun Ma)
  2. Track Table: trim spaces for string IN and IN LIKE (Lijun Ma)
  3. Genome Map: refresh density plot data after track table filter criteria change (Lijun Ma)
  4. Combo: fixed parallel drag select highlights propagating.
219 2006-11-29
  1. Finder: added results panel. Click row to highlight feature in feature map. Only shows feature results right now (sequence results pending). (James Galagan)
  2. Finder: report some more info to the "OK".
  3. Finder: fixed sporadic concurrent modification error
  4. Combo: fixed de-highlighting in query maps.
  5. Combo: keep glyph color when selected in perpendicular combo map instead of changing to selection color.
  6. Combo: fixed slighly off window placement for perp combo window
  7. Track Table: added string IN operator for filter criteria (Lijun Ma)
  8. Calhoun Database: added support for hmmer FAM accession filtering (Lijun Ma)
218 2006-11-21
  1. Genome Map: fixed null pointer error when uploaded gff data is missing data for some supers (Lijun Ma)
  2. Feature Map: for alignment track style, draw smaller mismatches and gaps so they fit inside feature glyph (James Galagan)
  3. Webstart: no more prompt for sequence boundaries.
  4. Webstart: pass start file as argument rather than property so singleton picks it up.
  5. Start XML: Broad Alignment uris work.
  6. Start XML: prompt for broad login if missing or insufficient credentials.
  7. Broad Login: catch http login failure and reprompt
  8. Broad Login: remember login in preferences
  9. Broad login: show login status in connection window and in status bar
  10. Broad Login: no quit (Mark Borowsky)
  11. Broad Login: added wwwdev checkbox
  12. Broad Alignment Manager: alignments should theoretically work from features urls with alt_start and alt_stop
  13. Bookmarks (and recent sequences): indicated sequence manager by default as first part of label (James Galagan)
  14. Bookmarks menu: added separator between control actions and bookmarks (James Galagan)
  15. File Menu: removed "Public" from Broad file menu options (because it might not be).
  16. Options Menu: added Options menu for all optiony stuff (James Galagan)
  17. View/Rulers Menu: moved Rulers menu to View menu (James Galagan)
  18. Link Menu: renamed Show Smart Domains -> Find Smart Domains. (James Galagan)
217 2006-11-17
  1. Combo: oops. Fixed mistake of removing horizontal scroll bar instead of vertical from reference (James Galagan).
216 2006-11-17
  1. Combo: I made the JSplitPanes thinner in perpendicular combo (I left them in regular feature map because the minimize/maximize widgets, which are useful there, get squished if it's too smaller)
  2. Combo: I got rid of all feature map JScrollbars in perpendicular combo. They are unnecessary. The dot plot scroll bars are sufficient.
  3. Combo: I fixed the sporadic query -> reference gap mapping bug (made faulty assumption that all alignment span features have alt features). This would cause an hql query where feature id = null that hung the whole app.
  4. Combo: Multi perpendicular query maps now get more screen real estate by default (1/3 of screen width vs. matching reference's 1/3 of height).
216 2006-11-16
  1. Genome View: stack smallest ranges on top for contig and chromo map track styles so no data loss (Dave DeCaprio)
  2. Genome View: show range stack depth for contig and chromo track styles
  3. Genome View: show info for all mouseover ranges in contig and chromo map track styles
  4. Feature Map: (default) polymorphic track style no longer includes nice but slow nqs bit map coverage. To get that choose new Polymorphic+coverage track style. (Dave DeCaprio)
215 2006-11-14
  1. Genome View: contig/chromo map mouseover tooltip gives contig/chromo information. (Dave DeCaprio)
  2. Genome View: only draw visible region. Marginally snappier scrolling. (Dave DeCaprio)
214 2006-11-14
  1. Genome View: fixed just added negative line graph bug
  2. Broad Web Services: added optional login (Mike Koehrsen)
  3. Broad Web Services: multi level tree (Mike Koehrsen)
  4. Combo: fixed projection when feature selection overflows alignment bounds
  5. Combo: fixed multi parallel feature recycling getting the right perpendicular map
213 2006-11-08
  1. Genome View: got rid of auto rebucketing because of horrendous performance. Buckets stay at initial resolution. Will add mechanism to manually rebucket. Performance could still pretty easily be improved by drawing only visible window instead of whole thing. (Dave DeCaprio)
  2. Genome View: added "Contig map" track style to color features by alt contig. Will add legend and mouseover info. (Dave DeCaprio)
  3. Genome View: added support for viewing of polymorphic tracks both by combined run and by strain. Warning: strain is slow because it uses a more complex kind of query.
  4. Genome View: fixed unnecessary and slow track preferences update (an issue when there are hundreds of snp tracks)
  5. Genome View: fixed heat map alpha out of bounds bug
  6. Genome View: theoreticaly, valued features should now work but I haven't actaully tried this (Phil Montgomery)
  7. Calhoun DB: added support for TRANSCRIPT_ADJUSTMENT tracks (Jared White)
212 2006-11-02
  1. Combo: use database gap information to map coordinates across alignments. Warning: This will be slow if you drag select a bunch of features. (Chandri Yandava, Phil Montgomery, Chinnappa Kodira)
  2. Webstart: argo now runs as singleton instead of firing up a new instance with every webstart invocation (Mike Koerson, Dave DeCaprio, James Galagan)
  3. Feature Map: added support for "sticky tracks." These are track files that argo tries to load up against any open sequence. Features will only be loaded if the sequence identifier matches the current sequence. Sequence identifiers must be either absolute file paths or calhoun uris (eg: calhoun://sequence/7000000033067269). This only works for gff files right now. The sequence idenfifier is in column 1. To make a track sticky, load it on a sequence, then right click and choose "Make Sticky." The track label cell will turn pink. To make it unsticky, right click and chose "Make Unsticky." It's a little bit like having your own local version of ap_feature. Don't add to many or too large sticky tracks or it will take a while to open every feature map. (Bob Handsaker)
  4. Inspector: report file for filed sequences in properties panel
211 2006-10-31
  1. Combo: recycle perpendicular map features in parallel maps instead of reloading (Dave DeCaprio)
  2. Open File: fixed class cast error (Thomas Sharpton)
  3. Start XML: added ability to specify calhoun sequences and tracks. (Bob Handsaker)
210 2006-10-30
  1. Combo: alignment track selector fixed nullpointer if no cluster set on reference.
  2. Combo: no default max overlaps (confusing in general and in particular with .combo archive dumps)
  3. Combo: fixed negative feature map highlight projection (James Galagan)
  4. Combo: show only dual overlaps in parallel panel (had been showing overlaps in either dimension) (James Galagan)
  5. Archive Files: fixed saving to current directory which tends to have more premissions problems. Save to home diretory instead.
  6. Feature Map: mouseover gives sequence label in status bar. Particularly useful for easy identification of vertical combo query maps.
209 2006-10-25
  1. Genome Map: fix infinite loop if too many colors (Lijun Ma)
208 2006-10-20
  1. Genome Map: fixed infinite loop if too many colors (Lijun Ma)
  2. Genome Map: fixed null pointer on get polymorphic tracks
207 2006-10-20
  1. Argo Archive File: .combo files now work.
  2. Argo Archive File: fixed entire sequence fasta being exported instead of just visible segment (James Galagan)
  3. Argo Archive File: preserves feature sort within track
  4. Combo: calhoun combo alignment tracks limited to those where query is on Genome Assembly (Dave Decaprio)
  5. Combo: calhoun combo alignment tracks default sorted by reference length desc
  6. Combo: fixed nullpointer on cancel calhoun combo alignment track selection window
  7. Genome Map: right click to open Chromo Map Legend (Lijun Ma)
  8. Genome Map: no more white as chromo map color (Lijun Ma)
  9. Genome Map: chromo cycles through up to 80 colors instead of just the java named standards.
  10. Polymorphic Site Tracks: mouseover now gives track (strain) info status bar (Phil Montgomery)
  11. Polymorphic Site Tracks: default (nqsb) color is now gray instead of distracting black (and you can change in track table) (Dave DeCaprio)
206 2006-10-17
  1. Argo Archive File: fixed windows path issue (Chinnappa Kodira)
  2. Feature Map: fixed reverse feature map coordinates off when segment doesn't start at 1. (Qiandong Zeng)
  3. Combo Parallel Feature Map: fixed feature map highlights inappropriately being drawn crossed (Qiandong Zeng)
  4. Feature Map: replaced sluggish and distracting tooltip (particularly bad with valued features) with status bar string.
  5. Polymorphic Tracks: hide SNP matches (Dave DeCapio)
  6. Polymorphic Tracks: use heat map instead of line graph to show NQS bitmap (Dave DeCaprio)
  7. Polymorphic Tracks: set max for NQS bitmap to 2 to deemphasize spikes. (Dave DeCaprio)
  8. Polymorphic Tracks: only get selected track data. Still slow, but less so. (Dave DeCaprio)
  9. Alignment Track Style: fixed last reference gap not being shown (Dave DeCaprio)
205 2006-10-11
  1. Combo: added right click action to calhoun sequence tree (Dave Decaprio)
  2. Combo: open combo on calhoun sequence faster because skip useless EST alignments (Dave DeCaprio)
  3. Combo: open combo on calhoun sequence now shows sortable jtable with length and other info instead of jlist. (Dave DeCaprio, Phil Montgomery)
  4. Combo: fixed vertical feature map border colors not matching alignment glyphs
  5. Calhoun Sequence Tree: replaced raw sequence action with more flexible sequence export. Got rid of not quite working and presumably unused gene feature map right click option.
  6. Sequence export: fixed trailing "-"s.
204 2006-10-10
  1. Export/Import argo feature map archive: lets you take a single file data snapsot of the featuremap you are looking at for easy sharing. Just a (.argo) zip fill with gff, fasta, and a meta.xml with preferences info. .combo files coming soon....
  2. Sequence Export: (new) lets you export feature map as raw fasta.
  3. Feature Export: made dialog instead of internal frame that confusingly floats arount forever.
  4. Inspector: alphabetize non standard properties (Tim Ledlie)
  5. Combo: fixed ruler highlight messed up for horizontal reverse and vertical forward.
  6. Combo: fixed vertical feature highlight messed up
  7. Track Table: show absolute path in track table mouseover for filed features
203 2006-09-25
  1. Calhoun Database: find by parent assigned id works (Chinnappa Kodira)
  2. Polymorphic Sites: much faster track retrieval (Dave DeCaprio, Phil Montgomery)
  3. Polymorphic Sites: superimpose onto NQSB bitmap valuedfeature tracks. (Dave DeCaprio, Phil Montgomery)
  4. Polymorphic Sites: hide duplicated track info (nqsb tracks, "query" polymorphictracks)
  5. Calhoun Valued Features: use stored min/max instead of expensively regenerating each time
202 2006-09-21
  1. Feature Map: fixed reverse feature map.
  2. Broad External: fixed track prefs not sticking
  3. Track Table: fixed set limit broken.
  4. Combo: fixed jerky mouse click zoom in
  5. Combo: fixed reload (Heidi Kuehn)
  6. Combo: moved reload combo action and filter to top level combo menu. (Heidi Kuehn)
  7. Combo: fixed dynamic enabling of top level combo menu.
201 2006-09-19
  1. Feature Map: fixed just introducted sort by criteria bug
  2. Feature Map Right Click menu: moved tabular dump next to new feature map (Heidi Kuehn)
  3. Feature Map Options: removed alignment style (Heidi Kuehn)
  4. Feature Map Options: fixed ok button not working on external version (Heidi Kuehn)
200 2006-09-18
  1. Polymorphic Sites: explode polymorphic tracks into one track per alt sequence sample (warning: slow. Can take over a minute). Draw mismatches as red, conficts orange. Show sequence in feature map if zoomed in enough. Mouseover shows reference and alt sequence and alt sample (Dave DeCaprio)
  2. Track Table: fixed prefs updating on tracks so it only happens when something has actually changed. Was getting very expensive now that we can have hundreds of multi alignment and snp tracks per sequence group.
  3. Feature Map: fixed mouseover/click off by one sp. Not really noticeable unless you're mousing SNPs.
199 2006-09-13
  1. Calhoun Database: added Promote Transcript action to edit menu. (Qiandong Zeng)
  2. Alignment Track Style: added "Diff" style that just highlights differences from reference. Made this default. To revert to old color by nucleotide style, go to View -> Feature Map Options -> Alignment Track Style and select "Nuclotide". (Dave Decaprio)
  3. Alignment Track Style: show diffs even when zoomed all the way out. (Dave Decaprio)
  4. Alignment Track Style: fixed some bugs with reference gap display (don't display if query is also gapped on multi, now displays on normal non multi alignments) (Dave Decaprio)
  5. View Menu: got rid of mysterious hide ocntained evidence action (Heidi Kuehn)
  6. Edit: Got rid of typo in gene id != transcript id validation (Heidi Kuehn)
  7. Combo: removed baffling and buggy select all overlapping alignments (Heidi kuehn)
  8. View menu: moved reverse feature map action here (Heidi Kuehn)
198 2006-09-06
  1. Calhoun Database: Fixed hibernate error on save (Chinnappa Kodira)
    2. Feature Map Options: sanity check feature height and label height (Niall Lennon)
  2. Feature Map options: removed sub height, super height complementary subfeatures.
  3. Feature Map: lots of gory refactorings to enable smaller feature representation. So far only calhoun database subfeatures take advantage of this.
197 2006-08-29
  1. Genetic Code: treat genetic code 111 like 11 (Lucia Alvarado).
  2. Webstart: should work internally, jarsigning part of build.
  3. Alignment Track Style: fixed old tooltips being displayed.
196 2006-08-28
  1. Multi Alignment Tracks: fixed bug that prevented opening several reference feature maps.
  2. Calhoun DB: fixed bug with clear cache. bean was trying to save valued features for some reason. session.clear() seemed to fix this. (Tim Ledlie)
  3. Analysis: Alignment: replaced "Standard Local" (aka ZIMMER) with JAligner Smith Waterman and Needleman Wunsch. Still hogs just as much memory, but runs much faster as is more familiar.
  4. Analysis: Alignment: fixed BLAT url
  5. Feature Map Options: hid some internal only options from external versions: "Pending Review Color." Renamed "Max Segment Length" to "Warn if DB Sequence Length >". Removed "track space."
  6. Menu: added Combo menu. Removed user menu (prefs stuff moved to File). Moved editing related stuff from File to Edit. Got rid of mysterious and buggy align and create selectable column drag modes. (Heidi Kuehn)
  7. Feature Map: removed some internal only options from external version. (Heidi Kuehn)
195 2006-08-23
  1. Alignment Sequence display: now works for regular alignmentspans (not just multis). Select track style ALIGNMENT and zoom in. If for some reason I can't get the alignment I show question marks. (Dave DeCaprio)
  2. Alignment Track Style: show features using Segregated style at distant zoom (Dave DeCaprio, Tim Ledlie))
  3. EMBL Sequence/Track File support: basically works. Let me know if it doesn't on your files or if there are any finesses you'd like me to add. (Eshwar Mahenthiralingam)
  4. Featurize Highlight: fixed. was breaking when compound featuer was the source of the highlight (Heidi Kuehn)
  5. GFF2/GTF2: tolerate # signs in source column. Decode url encoded pound signs. (Stacey Luoma, Phil Montgomery)
  6. Calhoun DB: added clear cache menu item. Now when new tracks are added to the database you don't have to restart argo, just click this (Tim Ledlie)
  7. Tabbed Browsing: fixed longstanding mac only bug that broke the little arrow drop down when there are too many tabs to attractively display (Matt Pearson)
  8. Editing: added option to removed cached edit when unable to restore instead of giving you irritating message every time you start forever (Matt Pearson, Chinnappa Kodira)
194 2006-08-16
  1. DB: Open feature by id: surrounding sequence context size can now be set in Feature Map Options window (Qiandong Zeng)
  2. DB: Open feature by id: opens one feature map per id, not one map per feature (a gene id can map to several features) (Matt Pearson)
  3. Multi Alignment Sequence display: much faster generation -- thanks Phil. (Dave DeCaprio)
  4. Multi Alignment Sequence display: gaps on query shown instead of repeating last matched nucleotide
  5. Multi Alignment Sequence display: gaps on reference indicated by black line. Mouseover shows query sequence in status bar. (Dave DeCaprio)
  6. Multi Alignment Sequence display: some indication that something is happenning at distant zoom (Tim Ledlie)
  7. Multi Alignment Sequence display: contrastier colors (Tim Ledlie)
  8. Multi Alignment Sequence display: fixed redraw bug at end of sequence
  9. Multi Alignment Sequence display: centered nucleotides
  10. Multi Alignment Sequence display: Alignment is default track style for multi alignment tracks
193 2006-08-11
  1. Added basic support for Multiple Alignment sequence display. Open any DENGUE or DENGUE_S2 sequence. Open the track table. You'll see circa 100 multiple alignment tracks. Set the track style to alignment (this should be the default but I forgot to do this before kicking off the build). If you select a lot of tracks, you will have to wait a long time for the alignment strings to calculate but you can view all 100ish. Zoom to sequence. It's colorized by nucleotide. Gaps in the reference are not yet indicated. (Tim Ledlie, Dave DeCaprio, Phil Montgomery)
192 2006-08-08
  1. Added support for Genetic Code 111 (Chandri Yandava, Clint Howarth)
191 2006-08-07
  1. Applet: fixed stubborn raw sequence bug (Mike Zody)
  2. Feature Map: got rid of irritating mouseover (Sinead O'Leary, Chinnappa Kodira)
  3. Track Table: rename Dynamic track Temporary Track (Heidi Kuehn)
  4. File Menu: moved Broad to top (Heidi Kuehn)
  5. File Menu: NCBI explicit that it's DNA sequence (Heidi Kuehn)
  6. Select Menu: select all columns activation fixed (Heidi Kuehn)
  7. View Menu: add Genome Maps options externally. (Heidi Kuehn)
  8. View Menu: got rid of mysterious mark contained evidence action (Heidi Kuehn)
  9. Link: you can now create feature links with interpolated sequence with $dna, $mrna, and $protein (Heidi Kuehn)
  10. Link: got rid of mysterious UCSC browser link. (Heidi Kuehn)
  11. Zoom Menu: Scroll to strand boundard action greyed out if starnds not segregated (Heidi Kuehn)
190 2006-07-28
  1. Valued Feature density plots: fixed completely broken in last night's release and added smoothing.
189 2006-07-27
  1. Feature Map: tweaks mouseover data (Heidi Kuehn)
  2. Combo: fixed feature map highlights propagating to parallel alignmentglyph .
  3. Broad Public: fixed feature links.
  4. Broad Public: warn if sequence big (Heidi Kuehn)
  5. Broad Public: locus uses new more efficient web services api (thanks Mike)
  6. Broad Public: fixed bookmarks (was broken with new web services because we now need to save sequence group to prefs)
  7. Blast Files: fixed features being marked as pending inserts (Hiedi Kuehn)
188 2006-07-25
  1. Generic Features: 8 dynamic value field inputs instead of 2, field names no longer case sensitive, list numeric and string operators (Tim Ledlie, Dave DeCaprio)
187 2006-07-21
  1. Fixed drawing of valued features, scale matches stored interval instead of rescaling to pixel, mouseover gives sequence position score and some other info. (Tim Ledlie)
186 2006-07-20
  1. Calhoun DB: fixed index -1 error for value features (Tim Ledlie)
185 2006-07-19
  1. Calhoun DB: fixed "unable to load dynamic features" message on subfeature click (Chinnappa Kodira)
  2. Combo: fixed recently broken partial alignment projection
  3. Combo: fixed recently broken vertical top row not visible
  4. Combo: fixed recently broken vertical feature map density plots completely broken
184 2006-07-17
  1. Calhoun DB: added support for ValuedFeatures. Example: feature id 7000000714450483 (Phil Montgomery, Dave DeCaprio)
  2. Calhoun DB: added support for GenericFeatures with dynamic properties. Example: feature id 7000000607967911 (Phil Montgomery, Dave DeCaprio)
  3. Calhoun DB: fixed recently introduced virtual tracks preferences not being restored bug
183 2006-07-13
  1. Sequence Panel: DNA Quality is now a checkbox remembered across feature selections (Qiandong Zeng)
  2. Sequence Panel: DNA Quality Threshold can be configured from default 50. (Qiandong Zeng)
  3. Sequence Panel: highlight projection to feature map removed when no sequence selection
  4. Sequence Panel: RNA status bar exon indicator fixed
182 2006-07-11
  1. Feature Map: removed slow auto rescale for heat map, line graph, and bar graph track rendering styles.
  2. Sequence Panel: made projected feature map highlights darker again (Tim Ledlie)
  3. Genome Map: got rid of unnecessary rescale on scroll (still rescales with zoom) (Dave Decaprio)
  4. Calhoun Database: LEGACY tracks are are not visible by default (Chinnappa Kodrira)
  5. Broad Sequennce Tree (Calhoun Web Services): updated to use the new web site so we get current data (and faster) (Christina Cuomo)
181 2006-06-27
  1. Feature Map: added support for heat map, line graph, and bar graph track rendering styles.
  2. Analysis: Codon Usage window added to Analysis menu. Select features whose orfs you want to analyse then choose this. (Chinnappa Kodira)
  3. Calhoun Database: fixed really expensive isEnabled check fo calhoun combo action in DB Menu (Dave Decaprio)
  4. Calhoun Database: merged locus search into feature id search. You can also now type in multiple comma or space delimited identifiers to open multiple feature maps (Matt Pearson)
  5. Calhoun Database: added contains in frame stops curation flag to progene list (Lucia Alvarado)
180 2006-06-23
  1. Fasta Track Manager: added this to read a multi fasta file and impose exact matches onto currently opened sequence (Manuel Garber, Carsten Russ)
179 2006-06-22
  1. Calhoun Database: changed login to lowercase to jive with web login stuff. (Lucia Alvarado)
  2. Genome Map: fixed orientation of tracks on scaffolds.
178 2006-06-21
  1. Genome Map: you can now impose gff tracks onto the genome map. Open a genome map and then use the File -> Load Track file (or use the Load File button in the track table). Column 1 must contain the (1 based) scaffold number or sequence id. You can prefix the scaffold number with 'scaffold_' for readablity. The attribute column is ignored, so all gff formats are treated the same. (Lijun Ma)
177 2006-06-13
  1. Calhoun DB: fixed attempted database lookup of pending subfeatures when clicked (Chinnappa Kodira, Lucia Alvarado)
  2. Calhoun DB: fixed alt sequence action enabling
  3. Calhoun DB: fixed show stored alignments so that it adjusts coordinates for gaps (Dave DeCaprio)
  4. Edit Menu: fixed enabling of featurize/columnize highlights
  5. Finder: sequence now has BOTH strands option (Carsten Russ)
  6. Analyze: fixed multialignment broken for selected column glyphs (Dave DeCaprio)
  7. GFF1: moderated gff field 10 color hack so it doesn't freak out if there's some other non-color hack there instead (Manuel Garber)
  8. GFF2: fixed field 10 color hack not workign at all here.
  9. Combo: fixed perpendicular/parallel map so that featuremap highlights are projected to opposite featuremaps again. Still a couple of highlight problems that will be fixed in another release this week (needed to get this other stuff out).
176 2006-06-07
  1. Feature Map: Features and highlights now drawn by renderers rather than as components. Makes a big performance different with lots of features -- 50% fewer biggish objects to store in memory and container.add(Component) was often slower than stacking and database retrieval combined for feature rich areas. It also makes it easy to swap in alternate feature rendering code. This required huge code changes and there is a greater than usual chance that something is broken in this release. You may wish to keep around a copy of release 175.
  2. Feature Map: integrated tracks now have a default max rows of 250. You can change this in the feature map options window.
  3. Feature Map: more efficient stacking (rows represented as RangeMaps instead of Lists and some cheating with huge stacks of features).
  4. Menus: should be less sluggish because a single FeatureMapActionEnabler is consulted and updated only when necessary. Before each menu item did its own redundant and potentially expensive isEnabled checking.
175 2006-05-26
  1. View: Show/Hide Features: added "show selected" action (Jared White)
  2. Combo: added support for tabular blast format alignment files (Thomas Sharpton, Lijun Ma)
  3. Combo: made "Open Combo on Sequence..." and "Open Combo on Feature" separate actions.
  4. Bookmarks: prompt for name on creation (Chinnappa Kodira)
  5. Calhoun DB: Edit: added curation flag to progenes (Lucia Alvarado)
  6. Applet: fixed annother prefs related null pointer
174 2006-05-23
  1. Fixed feature link for virtual tracks and for blast cluster superfeatures (just turned latter off because subfeatures are all that should have links). (Lucia Alvarado)
  2. Calhoun DB: Edit: ProGene: fixed erroneous "Missing 5' End" curation flag validation error (thanks Mike) (Lucia Alvarado)
173 2006-05-18
  1. Genome View: fixed chromo map color allocation array out of bounds. View actual data AN1 vs AF2! (thanks Phil)
  2. Progene Edit: fixed drag and drop inserting introns. Fixed name getting clobbered. Maybe fixed curation flag bug. (Lucia Alvarado)
172 2006-05-15
  1. Feature Map: Edit: Pending edits are segregated.
  2. Genome View: linkage group information is cached to it doesn't take forever to load this info (just a really long time)
  3. Genome view: top level track table menu item now available when you select genome in sequence tree so you don't have to load data before filtering.
  4. Feature Map: Track Labels: added track label for "Integrated." Show strand info. Foreground black and background transparant track color for increased clarity.
171 2006-05-07
  1. Calhoun DB: support new progene storage as transcript. old progenes no longer editable. Do not hesitate to bug me if you are confused or something doesn't work.
  2. Genome Map: added rudimentary chromo map support. Red if no query sequence, black if no linkage group, semi random other color if linkage group (haven't found one yet so not sure if this actually works) (Dave DeCaprio)
  3. Alignment Panel: catch out of memory error.
170 2006-05-03
  1. Calhoun DB: updated spelling of Covarient -> Covariant
  2. Calhoun DB: progene edit ui elements labeled "old" in prep for new to be release friday.
  3. Combo: fixed vertical redraw bug on windows for post initial dialog open on single query sequence (it worked with multi since last fix)
  4. Inspector: Properties Panel: Sequence/Segments: show genetic code, sequence group (with calhoun web link), editablity, and link sequence id to calhoun web ui
169 2006-04-27
  1. Calhoun DB: warn instead of error for unknown cell type.
  2. Calhoun DB: added new subclass CMHIT
  3. Calhoun DB: Combo feature map track table broken (Chinnappa Kodira)
  4. Combo: added track table right click link to parallel
  5. Combo: parallel: sort alignments so smallest are on top (so they aren't smothered by bigger ones and you can click them)
  6. Combo: track table: shade by score: added "none" option so you can go back to normal
  7. Virtual Tracks: fixed freak out if you hit cancel (Chinnappa Kodira)
  8. Feature Map: made it marginally more memory efficient by getting rid of some unnecessary members (got rid of drag and drop align as part of this, which I don't think anybody was using).
168 2006-04-21
  1. Feature Map Track Table: added suport for "Virtual Tracks." Select a track. Right click. Choose "create virtual track." You'll see a copied track appear in the track table. You can give this new track separate criteria and colors etc (like taxid). It is saved between sessions. When you get tired of it, right click and choose clear virtual tracks. Only works with calhoun tracks right now. Labels are not editable after initial virtual track creation. Both these will be fixed soon. (Chinnappa Kodira)
  2. Help: added direct links to specific, current documentation to rna, dna, protein, and properties panels (had all been linking to old vague inspector doc). (James Galagan).
  3. Calhoun: ProGene Edit: fixed strange bug with GeneMark evidences (Lucia Alvarado, thanks Phil for helping me track this down)
  4. Combo: fixed just introduced nucleotide level alignment sequence out of bounds error.
  5. Combo: fixed vertical redraw bug on windows for post initial dialog open
  6. Calhoun Web UI Links: updated to point to new server
167 2006-04-11
  1. RNA Panel: fixed bad label for "Longest Start-Stop Codon" right click action (Chinnappa Kodira)
  2. Combo: added Alignment Track Table. You can set: alignment track color, visibility, order (=z-order), shade, filter; and see: count, label, (James Galagan)
  3. Combo: shade by score: remove border, min alpha still visible, fixed null pointer if no score. (James Galagan)
  4. Combo: multi query map border goes around whole feature map window instead of just scrollpane view (James Galagan).
  5. Feature Track Table: more concise headers (to make room for more)
  6. Calhoun Database: fixed missing transcript type message when using genemark evidences (Lucia Alvarado)
  7. UCSC: added links to UCSC feature detail pages, fixed to parse as GTF2 instead of GFF2 (Mike Zody)
166 2006-04-06
  1. DNA panel: added superimpose overlapping features option. Useful (among other things) for projecting SNPs onto a transcript. (Amanda Lukens, Sarah Volkman)
  2. Feature finder: added search by curation flag with drop down (Amanda Lukens, Sarah Volkman, Dave DeCaprio). execute cheap queries to limit results before expensive ones. Made feature length search much faster by querying against method instead of named property.
  3. UCSC: fixed sequence tree. Was missing hg17 due to html parsing error (Mike Zody)
  4. Combo: added show nucleotide level alignment for selected alignment glyph with right click option (James Galagan)
  5. Combo: added alignmentglyph shade by score as right click option. This works but would be much more useful with ability to choose alignment glyph colors and remove borders and limit to one set of alignments at a time. Coming soon... (James Galagan)
  6. Combo: multi query feature maps given border color of corresponding alignment glyphs in dot plot (James Galagan)
  7. Help: added blue right click help links to inspector panels, feature map, finder window, combo panels and blank sequence view. Added right click open sequence file and open recent to blank sequence view. (James Galagan)
  8. Track Table: default sort is now by label instead of by rank. Should have done this ages ago...
  9. Calhoun DB: added connect action in db menu so you don't have to restart the app to do this. Also lets you toggle print sql without restart.
  10. Misc: fixed a bunch of errors in sequence and finder panels where code assumed features would be at least 1 codon long.
165 2006-04-03
  1. Feature Map: fixed sort of mixed floatin point/int values (Lucia Alvarado)
  2. Genome Map: can now be opened on any sequence group. Sequences are just glommed together into one big make believe linkage group. (Phil Montgomery, Dave Decaprio)
  3. Combo: can now be opened on selected alignment span track/queries instead of prompting to choose from list (Dave DeCaprio)
  4. RNA Sequence Panel: longest start codon for right click "" now matches NTG instead of ATG for genetic code 11 (Chinnappa Kodira)
  5. Feature Map Options: fixed highlight color changing with selection color.
  6. Track Table: stuck designed label jlist in scrollpane because too long on some monitors (Dave DeCaprio)
  7. Combo: Parallel: made glyphs transparant so overlap info not lost (Phil Montgomery, Matthew Crawford)
  8. Combo: input window: fixed simple alignment format being listed as "null" in file prompt. Tolerate Empty second query(James Galagan)
  9. Error Handling: out of memory error gives url to FAQ describing how to run argo with more RAM. All java messages are hiden from prompts in external argo (internal still shows them) (James Galagan)
  10. General: replaced "philosophical sounding" (and long) "Perspective" terminology with "View." (James Galagan)
164 2006-03-23
  1. Calhoun DB: fixed featurelink bug with some blast cluster features (Lucia Alvarado)
  2. Genome Map: added genome map options to view menu and right click menu. Allow setting of alternating scaffold colors and width. Added "Binary Map" style to track table (useful for SNPs).
163 2006-03-21
  1. Calhoun DB: Open by Feature Id: find features even if they are not part of a registered track type (Lucia Alvarado)
  2. GTF2: show exons,cds, and codons in export/save (Chinnappa Kodira)
162 2006-03-20
  1. Calhoun DB: set default host to francium. Fixed calhoun db connect reprompt (Clint Howarth). Delete calhoun transcripts (not just annotated) (Clint Howard, Matt Pearson)
  2. Genbank file parser: handle single nucleotide subfeatures
  3. NCBI: link to ncbi website from feature gis. Fixed no tracks visible until reload. Only CDS tracks are default visible. Added too large sequence warning a la calhoun. Fixed raw sequence bug.
161 2006-03-07
  1. Calhoun Database: include new oracle jar so it works.
  2. Finder Panel: Feature Finder: fixed null pointer property search. Fixed protein search (Stacey Luoma)
  3. Genome Map: fixed primary sequence group bug (Dave Decaprio)
160 2006-03-07
  1. Calhoun Database: Combo: added DB "Open Combo on Sequence..." action that looks for all visible alignments on selected sequence, uses these to build alignment groups based on track and query sequence, orders by alignment feature count and presents user with list to select from, then draws multi-combo perspective on these. For efficiency, no tracks are selected by default in the resulting combo view. (Dave DeCaprio)
  2. Calhoun Database: Show Stored Alignment: added positions (Mike Koehrson, Dave DeCaprio)
  3. Calhoun Database: Editing: fixed extra curation flags bug (thanks Phil) (Chinnappa Kodira). fixed "Gene extends past transcripts' starts" bug (thanks again Phil) (Sinead O'Leary)
  4. Calhoun Database: added DB -> alt sequence action
  5. Calhoun Database: alt feature action doesn't freak out if selection is missing alt feature
  6. Genome Map: Treat null orientation as positive (Dave DeCaprio)
  7. Combo: fixed dot plot panel click bug with overlapping alignments.
  8. Custom Data Ruler: don't draw markers on heat map. Report correct score on mouseover. Added support for null values or gaps (Bob Handsaker, Alan Derr)
  9. Track Table: Fixed recently introduced Filter bug (Lucia Alvarado). Designer Labels: alphabetized (Dave DeCaprio)
159 2006-02-24
  1. Genome Map: added scale rulers. Added ability to set track width in track table. Added line graph and bar graph styles and abitlity to choose in track table. Heat map automatically decides alpha instead of using arbitrary or user specified. Added track and score information to mouseover. Added "Genomes..." as right click option. (James Galagan, Dave DeCaprio)
  2. Bookmarking: fixed unncecessarily slow bookmark folder updates (including recently open sequences folder). Saves about 5 seconds per feature map open on my mac.
  3. XML Start File: added support for ruler size and ruler markers (Bob Handsaker)
158 2006-02-16
  1. Genome Map: Added zoom to 100% right click menu option. Added Density Track table. Darkened default alpha. Filter citeria now applied. Scaffold glyphs expand to accomodate tracks. Track rank works. Don't show any tracks by default. Moved scaffold labels to left.
  2. Calhoun Database: fixed filter by ap_length. Replaced synteny link with alt feature link (Dave Decaprio)
  3. Track Table: fixed bug where filed tracks were being loaded on wrong sequence through track table under some circumstances.
  4. XML Start File: added support for rank and arrangement track options. Added suport for segregate_strands feature map option. Added ruler support (Bob Handsaker)
157 2006-02-10
  1. Genome Map: Restored "Genomes" menu item. Stuck "unmapped" scaffolds on right. Display goes bottom up instead of top down. Fixed keyboard zooming. Fixed right click so you don't have to left click first. Show linkage group and scaffold sequence position on mouseover. Round feature map coordinates to nearest 1000 and handle boundaries better. Handle negative orientation scaffolds correctly. Grey box starts above linkage group label. (Dave DeCaprio)
  2. Genome Map: Preliminary feature densities: hard coded for now to ap_subclasses ANTRS and SNP, uses colors specified in track table, overlaps get darker because of alpha, based on entire feature not just starts. (Dave DeCaprio)
  3. Genome Map: fixed relative zoom centering, made absolute zoom work, drag zooms works.
  4. Calhoun Database: cache tracks by sequence group instead of sequence. Should make loading multiple sequences in the same sequence group faster (plus I needed it for the genome perspective).
  5. Inspector: MRNA Sequence Panel: fixed search by protein (Stacey Luoma)
  6. Calhoun Database: drag and drop edit now truncates progenes (Chinnappa Kodira)
  7. Rulers: custom data rulers now share default directory with tracks (Jade Vinson)
156 2006-02-01
  1. Genome Perspective (alpha): mapped assemblies are blue in the Sequence Tree. Right click and choose "Genome Perspective." All it does right now is show you the ordered scaffolds by linkage group and let you zoom in/out. Click on a scaffold to open a feature map. Tabbing works. Let me know what's a priority to see here. These first steps were obvious, I can think of a lot of possible next steps. (Dave DeCaprio, Lisa Larsen)
  2. Export Image: removed obscure and buggy output formats. Change Map export to export visible map plus rulers instead of entire map minus rulers. Added Perspective export. Catch and display errors. (Dave DeCaprio, Michael Freitag)
  3. Added gff3 link field (Martin Korb)
  4. Map Options: added option to turn off ORF autogeneration (Matt Pearson, Bob Handsaker)
155 2006-01-23
  1. Calhoun Database: fixed accession search for accessions not matching old pattern (Sinead O'Leary)
  2. GFF1: throw error on load if file contains overlapping subfeatures (Jade Vinson).
  3. GTF2: now recognizeds .gtf extension files as well as .gtf2 by default (Jade Vinson).
  4. GFF2 and GFF3: fixed these files not loading as mutably editable (Michael Freitag)
  5. DNA Panel: clearly indicate that something is wrong when clicked on feature with overlapping subfeatures. (Dave DeCaprio)
  6. Genbank: unnamed features default to track name.
  7. Genbank: recognize features with hytpens in track name (Alex Mallet)
154 2006-01-17
  1. Calhoun Database: fixed feature link from blast cluster subfeatures on ms-windows (Chinnappa Kodira)
  2. Inspector Window mRNA Sequence Panel: fixed last codon not displaying on os x/unix.
153 2006-01-17
  1. Inspector Window Sequence Panels: fixed ms-windows off by one for displayed base. Fixed related but less serious bug on mac/unix. (Dave DeCaprio)
  2. Feature Map: fixed right click setting selected on mac (was making it impossible to get right click menu options for single subfeature feature subfeatures) (Dave DeCaprio)
152 2006-01-11
  1. Calhoun Database: restored correct disciminators to keep subfeatures from showing up as separate tracks (Dave DeCaprio)
  2. Sequence Perspective: fixed bug of "null" tab showing when you click outside of a tab on the tab bar (Bob Handsaker)
  3. Sequence Perspective: fixed tab label update for feature map on map/shift refresh (was always showing initial map boundaries).
  4. Finder Sequence Panel: made search case insensitive (Lisa Larson)
  5. Feature Map: "done loading" message now gives number of top level features loaded.
151 2006-01-05
  1. Calhoun Database: added support for blast cluster subfeature to ncbi www links (Chinnappa Kodira)
  2. Calhoun Database: added ability to search for progenes by accession (Lucia Alvarado)
  3. Combo: added right click finder window option to combo feature maps (Dennis Knudson)
  4. Track Table: Criteria Filter: broke into two columns (Lucia Alvarado)
150 2006-01-05
  1. Calhoun Database: added support for tandem repeat subclass (Dave Decaprio)
  2. Combo: fixed parallel bookmarks reseting query start to 1 and showing alignments that cross but don't overlap either sequence. (Mark Borowsky)
  3. Bookmarks: fixed export/import of subfolders
149 2005-12-29
  1. Calhoun Database: fixed display of progene names (Lucia Alvarado)
  2. Command line: argo can be give startfile as system property (among other things, makes for more straightforward webstart launch)
  3. Startfile: fixed track labeling
148 2005-12-18
  1. Calhoun Database: only apply oracle hint to blast features because was slowing down other feature queries (Chandri Yandava)
  2. Calhoun Database: show old style labels for blast features (Chinnappa Kodira)
  3. Calhoun Database: re-enable blast filter by taxid (Lucia Alvarado, Chinnappa Kodira)
147 2005-12-16
  1. Calhoun Database: added oracle hint as band aid to make blast feature queries go faster (Chandri Yandava)
  2. Calhoun Database: use new feature_track table for much faster determination of tracks by not sequence, but sequence group. Faster and better. (Chandri Yandava)
  3. Combo: added reload right click menu option (Mark Borowsky)
  4. Combo: parallel perspectives can be bookmarked (Mark Borowsky
  5. Calhoun database: assigned ids are now included in feature labels if available (Christina Cuomo)
  6. Multiple Alignment Window: resize now works normally on windows (David Decaprio)
  7. Calhoun database: fixed calhoun web urls.
146 2005-12-08
  1. Calhoun Database: fixed dispaly of ap_concensus and ap_alignemnt fields. (Lijun Ma)
145 2005-12-08
  1. Calhoun Database: catch preference caching error when too many subfeatures. Also catch error if location invalid. Also catch missing transcript type freak out. (Sinead O'Leary)
  2. Error messages: fixed width to 600 px. Add scrollbars if too long.
144 2005-12-06
  1. Calhoun Database: fixed validation errors caused by other transcripts in gene not being repaired by "save anyway." (Sinead O'Leary)
  2. Inspector Window: fixed update of column segments (Dave DeCaprio)
  3. Custom Rulers: fixed handling of negative scores (Bob Handsaker)
143 2005-12-02
    Calhoun Database: fixed gene accession search (broken in 142 and horribly slow in 141).
142 2005-12-02
  1. Calhoun Database: took advantage of new database schema to make feature map loading significantly faster and more memory efficient (I loaded over 100K top level features in less than 2 minutes). For very large regions, rendering is now slower than db retrieval (until I optimize this, use "segregated stacking" and max rows for quicker navigation of such regions). Disclaimers: getting the initial list of tracks per sequence is still slow. Some Finder panel queries will be prohibatively slow because data has not been preloaded and will be retrieved feature by feature. Some (not much) view specific criteria is no longer available for filtering. Let me know if you miss it. Regions with large numbers of annotated transcripts are slower than they could be because of some per transcript queries.
  2. Calhoun Database: use new transcript validation. Better QA panel formatting for long error messages.
  3. Multiple Alignment Window: pad with gaps set to false (Dave DeCaprio)
141 2005-11-27
  1. Calhoun Database: works with new schema
  2. Calhoun Database: fixed feature id link in properties panel
  3. Calhoun Database: fixed partial orf setting error (Lucia Alvarado)
140 2005-11-18
  1. XML start file: handles combo.
  2. XML start file: explicit sequence_perspective node.
  3. Complain less vociferously about tduplicate feature ids (Mark Borowsky)
  4. Multiple Alignment Window: added scrollbars (this fixes big windows freezing ms-windows) (Dave DeCaprio)
  5. Multiple Alignment Window: color nucleotides (Dave DeCaprio)
  6. Multiple Alignment Window: catch and display model errors.
  7. Multiple Alignment Window: resize resizes content (Dave DeCaprio)
139 2005-11-14
  1. Fixed simple segment constructor offset error.
  2. Command line: Simple startup file with -x option can open argo on specified sequence and tracks. You can set the track color and feature link. See documentation here. (Martin Korb)
  3. Command line: -p and -x options now support taking a url instead of a file
  4. Combo: fixed vertical zoom scrolling to start of sequence (Mark Borowsky)
  5. GFF3: allow subfeatures without space between them (Bob Handsaker)
  6. GFF3: complain if duplicate or missing feature ids (Bob Handsacker)
  7. Edit: fixed listing of "pending" tracks in track table. Also fixes double feature bug if when this was unticked (Lucia Alvarado)
138 2005-11-02
  1. X11: fixed sizing (Jonathan Butler)
  2. Calhoun Database: don't load big files anyway after "are you sure?" cancel (Lucia Alvarado)
  3. Track Table: fixed file uploading onto wrong sequence if feature in another map selected.
  4. Finder: Feature Finder: added Generic Properties search. (Dave DeCaprio)
  5. Combo: control arrows work for vertical feature map feature selection (Mark Borowsky)
  6. Feature Map: fixed longstanding super annoying sproradic y axis jumpiness on zoom.
137 2005-10-24
  1. Calhoun Database: view store multiple alignments for selected alignment spans. Select sequence column and then menu to Analyze -> View Multiple Alignment. Alignments for all overlapping alignment spans will be displayed for the span of the selected column. Alternately, select individual features and then menu as above. Alignments for these spans in the area of overlap will be shown. (Dave DeCaprio)
136 2005-10-14
  1. Calhoun Database: override evidence validation with "Save Anyway." Also added corresponding analysis to the menu "Analyze -> Run Feature QA Analysis". (Chinnappa Kodria, Lucia Alvarado)
135 2005-10-07
  1. Calhoun Database: got rid of error window if no evidence found for transcript (Mark Borowsky)
  2. GFF1: made color hack work on subfeature vs. feature level (Alan Derr)
134 2005-10-06
  1. Calhoun Database: added properties panel links to analysis run, features and sequence. Condensed. (Dave Decaprio)
  2. GFF1: added extra column color hack. Stick a hex color value to set. (Alan Derr)
133 2005-09-23
  1. Calhoun Database: validate bypass support -- thanks Phil! (Sinead O'Leary)
  2. Calhoun Database: Gene/Transcript accession searches about 50 times faster -- thanks again Phil! (Lucia Alvarado).
  3. Calhoun Database: Generic Features have better names (Dave DeCaprio)
  4. Calhoun Database: no more exon, egene, and alignment spans in generic (Dave DeCaprio)
132 2005-09-13
  1. REQUIRES JAVA 1.5
  2. Calhoun Database: genewise select evidence works (Chinnappa Kodira)
  3. Calhoun Database: curation flags shown for all features (Dave DeCaprio)
  4. Calhoun Database: argo works with test database (Dave DeCaprio)
  5. Calhoun Database: sequence quality information can be shown in inspector window dna sequence panel with right click -> show quality. (Dave DeCaprio)
  6. Custom Data Ruler: mouse over shows value (Lijun Ma, Bob Handsaker)
  7. Custom Data Ruler: right click to specify ruler name (Bobo Handsaker)
  8. Custom Data Ruler: added mean and median options to "Add Marker..." (Lijun Ma)
  9. Custom Data Ruler: sp highlighted on mouseover
  10. Feature Map: restored darker yellow highlight for better visibility (Clint Howarth)
  11. GTF2 Handling: handle CDS features properly -- was treating them as exons (Dave DeCaprio)
  12. Inspector Window: fixed orf setting of selected column (was insisted on always going back to best atg-stop (Mark Borowsky)
131 2005-08-26
  1. Calhoun Database: fixed progene update and delete (Lucia Alvarado)
130 2005-08-26
  1. Map Options: take effect immediately on all open maps (Charlie Whittacker)
  2. Calhoun Database: Build orf based on (Phil Mongtomery)
  3. Calhoun Database: force db stored partial orfs to be in frame for visualization (Lucia Alvarado)
  4. Calhoun Database: tracks with no matching ap_track_type table entries will be treated as being of a generic track type (Dave DeCaprio)
  5. Calhoun Database: mouseover tracks to see analysis event notes (Dave Decaprio)
  6. Calhoun Database: annotated transcript standard transcript names in drop down are lowercase (Sinead O'Leary, Dave DeCaprio)
  7. Combo: fixed repaint problem when combo opened from bookmark
  8. Calhoun Database: fixed HQL console (Dave DeCaprio)
129 2005-08-15
  1. Combo: Perpendicular: fixed zoom, hand cursor going back to pointer when over glyph. (James Galagan)
  2. Combo: Perpendicular: fixed sporadic drag scroll jumpiness (James Galagan)
  3. Combo: perpendicular: fixed drag scroll getting messed up when drag scrolling over glyph (James Galagan)
  4. Combo: perpendicular: fixed status bar message giving absurdly large number (system time) as time to load.
  5. Combo: perpendicular: fixed vertical map not painting right away.
  6. Combo: parallel: fixed selections being cleared across maps
  7. Combo: parallel: fixed highlight in featuremap transferring to connection panel. (James Galagan)
128 2005-08-02
  1. Custom Data Rulers: added Heat Map (David Twomey, Gad Getz)
  2. Custom Data Rulers: added bar graph options -- single sp and sp to sp(Bob Handsaker)
  3. Custom Data Rulers: black boundaries instead of data color (Bob Handsaker)
127 2005-07-27
  1. Calhoun DB: complain but don't freak out if genetic code is 0. Set to 1 (Chinnappa Kodira)
  2. Calhoun DB: by default, tracks which are marked non admissible evidence are not visible. Note that if you have already opened such a track in the track table, you may have saved it as visible in your preferences. (Matt Pearson)
  3. Bookmarks: import and export works. (James Galagan)
  4. Preferences: can be loaded from command line with -p option
  5. Preferences: default behavior is no clobber. Clear explicitly if you want to clobber.
126 2005-07-25
  1. Calhoun DB: made locus id search work for SN (Chinnappa Kodira, Qian Zeng)
  2. Calhoun DB: refresh tracks after first transcript insert on sequence so new track shows up (Lucia Alvarado)
125 2005-07-22
  1. Applet: javascript urls now work as feature doubleclick actions (Yanxia Liu)
  2. Applet: added splitStrands param option to control whether or not to split strands. Set to 0 to not split strands. Anything else (or absense of this param) means do split (Yanxia Liu)
  3. Applet: fixed sequence offset bug (Yanxia Liu)
  4. Applet: display out of bounds sequence as "-" (Yanxia Liu)
  5. Combo: registers in File -> Recently Opened
124 2005-07-19
  1. Calhoun Database: faster loading of transcript evidences. This was inefficient and very slow for regions with many transcript supplemental evidences. (Chinnappa Kodira)
123 2005-07-15
  1. Combo: fixed reverse feature map in parallel mode (James Galagan, Alan Derr)
  2. Combo: fixed (by preventing) parallel bookmarking
  3. Combo: fixed selection on drag zoom.
  4. Combo: added selected highlighted right click action to dot plot (James Galagan)
122 2005-07-14
  1. Fixed single sequence perspective window not reopening after close (Lucia Alvarado, Chinnappa Kodira)
  2. Track Table: redid columns to allow more room for track label and renamed others for brevity and clarity. (Chinnappa Kodira)
  3. Admissible evidence filtering works again (Matthew Pearson)
  4. Fasta locking error fixed on windows -- last fix only did it for macs. (Qian Zeng)
  5. Added Reverse Feature Map Right Click option. Note: Does not yet behave properly in parallel combo. (James Galagan, Alan Derr)
  6. Combo load data dialog: prompt for alignment file interpretation up front like sequence files. No more cancel looses everything (Alan Derr, James Galagan)
121 2005-07-08
  1. Calhoun Database Tracks: now based on anaylsis event + ontology term + ap_feature.ap_subclass instead of ap_subtype. This required many changes under the hood. I've spent a long time trying to iron everything out, but I'm sure something is still broken (or at least oddly different) and am braced to have to do a quick release 122, so please don't be shy about reporting anything funny. The upside of the new tracking system is that you can now manipulate tracks at a finer granularity, and that they don't have to be manually registered in the database. The downside is that you have to manipulate them at that finer granulatity. By default, only the latest version of an anaylsis event is visible.
  2. Inspector: RNA: fixed select click point to stop codon (Chinnappa Kodira)
  3. Annotated Transcript Insert: fixed slow and unncecessary query on opening of insert window. (Chinnappa Kodira)
  4. Fasta Files: Matt P fixed file locking bug (Qian Zeng)
120 2005-06-17
  1. Annotated Transcript Edit: fixed new gene always assigning same gene accession number. (Chinnappa Kodira, Lucia Alvarado)
119 2005-06-16
  1. File: added "open recent edit" submenu (Chinnappa Kodira, Chandri Yandava)
  2. Combo: Parallel: whitespace click deselects featuremap highlights.
  3. Combo: Parallel: open only on zoomed perpendicular view subsequence. Used to show entire thing. (James Galagan)
  4. Combo: Parallel: non-overlapping alignments for at least 1 featuremap not shown. (James Galagan)
  5. Applet: Custom Ruler: can now specify multiplicity (if it operates on 1 or multiple features). Can limit to specified tracks. Can apply to column segment. Fixed template url parsing bug with multiple fields. (Yanxia Liu)
  6. Applet: added refresh map data right click and file menu option (Yanxia Liu)
  7. Applet: fixed width % bug in html. (Yanxia Liu)
  8. Segment Column: added toggle strand right click action. (Yanxia Liu)
  9. Edit: Featurize: fixed nullpointer on cancel.
  10. Tabbed Browsing: added "Close All" right click option.
118 2005-06-08
  1. Combo: added parallel view (James Galagan, Dave DeCaprio)
  2. Calhoun Annotated Transcript Editing: use beans instead of stored procedure (Mike Koerson, Dave Decaprio, Phil Montgomery)
  3. Edit Cache: fixed attempt to restored cached edits before db connect (Lucia Alvarado)
  4. Track Table: fixed bug where criteria were being applied to all tracks sharing a view (Matt)
  5. Track Table: allow comma delimited IN criteria (Christina Cuomo, Chinnappa Kodira)
117 2005-05-18
  1. Calhoun Annotated Transcript: fixed exon subtype naming (Philip Montgomery, Shawn Samuel, Chinnappa Kodira, Sinead O'Leary)
116 2005-05-16
  1. Applet: now includes inspector and finder panels. No more textDisplayApplet.
  2. Applet: support for distinct subfeature tracks with their own colors and doubleclick urls (Menng Wang)
  3. Track Table: fixed bug causing infinite loop on set criteria click (Chinnappa Kodira, Qian Zeng, Lijun Ma)
  4. Calhoun XML: open up Synteny Anchor records and load first and second features (Miriam Averbuch).
115 2005-05-11
  1. Sporadic Startup Freeze: should no longer happen.
  2. Calhoun Connection: Moved to after window creation for better visual feedback that something is happening. Slightly faster startup time.
  3. Status Bar: consistenly show caller on left, message in middle. Message color coded orange for wait, yellow for select.
  4. Tabbed Browsing: added open tab in new window action.
  5. Dense Stacking: gives warning on feature click (Sinead O'Leary)
  6. Track Labels: no longer block feature clicks (Sinead O'Leary)
114 2005-05-05
  1. Comparative Perspective: track table shows for last clicked on feature map (was insisting on always showing for vertical). (Mark Borowsky)
  2. Comparative Perspective: fixed sizing to show status bar at bottom on windows.
  3. Tabbed Browsing: right click options to close, close all, move left, move right. Disambiguated close window and close tab in File menu. (Sinead O'Leary)
  4. Single Sequence Perspective: you can open additional windows through the file menu.
  5. Window activation: set selected on new open.
113 2005-05-03
  1. Fixed Sizing of Single Sequence Perspective so status bar shows on windows
  2. Fixed align against query (Chinnappa Kodira)
  3. Command line launch can optionally take http urls instead of filenames (Alistair Rust).
  4. Image export works again.
  5. Calhoun XML: loading from File -> Load track file only loads requested file, not whole filebase. (David DeCaprio)
112 2005-05-02
  1. Single Sequence Perspective Reopenable after close (Heather Hood, Lucia Alvarado)
  2. Really no default load of calhoun xml (Chinnappa Kodira)
111 2005-04-28
  1. Tabbed Feature Map Browsing: new feature maps now open in new tab instead of new window. (David DeCaprio)
  2. Split Panes: now separate single sequence perspective components (they used to be separate windows). (David DeCaprio)
  3. Shared Status Bar: instead of cluttery one per panel.
  4. Calhoun Database: fixed a couple of bugs with Show Stored Alignments (Alexandre Buer, Chandri Yandava)
  5. Calhoun XML: only loads if specifically requested for that session (Chinnappa Kodira)
110 2005-04-20
  1. Calhoun Database: Show Stored Alignments (using GapUtil). Available from the DB menu or as a right click option (Dave DeCaprio, Chinnappa Kodira, Alexandre Buer)
  2. Cahhoun Database: fixed Open by Sequence id when sequence id is not part of a genome assembly (important for lots of these query sequences for stored alignments).
109 2005-04-19
  1. Calhoun DataBase: show Ns when no raw sequence available (Miriam Averbuch)
  2. Inspector: DNA Sequence Panel: fixed make intronic/exonic after setting five prime context. Was off by context length (Matthew Henn)
  3. Track Table: fixed batch set criteria and sort criteria (Mathew Henn)
  4. Custom Data Ruler: fixed nullpointer
  5. GFF: fixed pending insert label
108 2005-04-11
  1. Custom Data Ruler: fixed a bunch of bugs (Lijun Ma)
107 2005-04-06
  1. Image export: allows dump of active panel to postscript, png, jpeg, svg and more. Replaces less functional and more mysterious print. (Jade Vinson, April Cook)
  2. Combo: added pattern hunter alignment file format support (James Galagan, Alan Derr)
  3. Combo: fixed Jamesian alignment manager bug when alignment stop extends to sequence boundary. (Alan Derr)
  4. Map options: added track spacing (April Cook)
  5. Track Labels: now respect rowspacing.
  6. GFF 3: fixed ORF editing.
  7. GFF 1/2 and GTF2: use "exon" instead of misleading "CDS" in export. (Chinnappa Kodira)
106 2005-03-29
  1. Fixed max zoom shifting around (Mike Zody)
  2. GTF2 Edit/Export: fixed stop codon bug.
  3. GFF3 Edit/Export: fixed stop codon bug.
  4. GFF3 Edit: fixed transcript and gene id showing up in update dialog
  5. Inspector Window: mRNA panel: fixed highlight orf off by one codon
  6. File Menu: Broad Sequence Tree: fixed sequence branches
  7. Cached Edit: fixed restore error if not connected to calhoun database.
105 2005-03-29
  1. Inspector Window: Protein Panel: fixed display of proteins that extend to 3 prime mrna boundary (Heather Hood)
  2. File Menu: Added broad locus action
104 2005-03-23
  1. GFF3 (and others): treat stop codon as part of CDS, not 3 prime UTR. (Dave DeCaprio)
  2. DB Menu: added open by locus menu item (Heather Hood).
103 2005-03-21
  1. CalhounXML: Fixed "Pending" label being attached to no-named xml features (labelled "unnamed" instead). (Qiandong Zeng)
  2. FileBase: FileBase works on mac with script
  3. Delete: Fixed delete of pending inserts (they were lingering, without pending flag).
  4. Drag Mode: fixed copy selection to clipboard drag mode highlighting features in drag rectangle.
  5. Splice Site Profile: fixed highlight in sequence panel being short by 1.
102 2005-03-17
  1. Track Labels: they now float without leaving artifacts all over teh screen (Dave DeCaprio)
  2. Finder Window: Sequence Panel: negative strand searching fixed (Chinnappa Kodira)
101 2005-03-16
  1. GFF: Fixed seqid criterion filtering (Qiandong Zeng)
  2. Feature Map: Fixed positive strand background not painting (Lucia Alvarado)
100 2005-03-15
  1. Feature Map: fixed bad orf handling so browser doesn't crash. Will show error and temporarily correct. Edit feature to permanently fix. (Lucia Alvarado)
  2. Fixed annoying long standing jerky double paint bug on zoom in.
99 2005-03-10
  1. Genbank: Fixed superslow genbank file parsing (Alan Derr)
  2. Track Table: Subsort by previously clicked column. Among other things, makes it easier to get calhoun xml files out of the way.
  3. Track Table: highlight calhoun xml files in grey to discourage accidental selection. (Chinnappa Kodira, Lucia Alvarado)
  4. Calhoun XML: catch out of memory error ( Chinnappa Kodira, Lucia Alvarado)
98 2005-03-04
  1. Inspector: RNA Sequence Panel: fixed just introduced bug of frame 1 always being shown by default instead of frame containing selected orf (Lucia Alvarado)
97 2005-03-04
  1. Inspector: RNA Sequence Panel: fixed error when no default orf was detected in selected feature (Chinnappa Kodira, Lucia Alvarado)
96 2005-03-03
  1. Inspector: Properties: Complementary track color on track color background for easier reading of track field.
  2. Edit: Calhoun Transcript: Removed error message when using evidence transcripts with missing genes to insert new annotated transcripts (Lucia Alvarado, Chinnappa Kodira)
  3. Feature Map: No more drawing orfs of subfeatures.
  4. DB: Sequence Id: Fixed sequence group (space) group order. It was just broken before, now it works.
  5. Fixed editablity of new oragnism sequences not being set except when opened through sequence tree (Lucia Alvarado, Chinnappa Kodira)
  6. Command line: when run from command line on specified files ignores previous track associations.
  7. Calhoun XML: Filesession: added label (Shawn Samuel).
  8. Track Table: it now resizes with the window.
95 2005-03-01
  1. Fixed sequence offset.
  2. Removed superslow orf drawing for now.
  3. Fixed occassional inaccurate UTR generation.
  4. Detect transcripts with impossible ORFs and complain (but not too often)
  5. Treat genbank files as multi tracked.
94 2005-02-16
  1. Inspector Sequence Panel: instead of intrusive tooltip mouseover reporting, use status bar at bottom of inspector. It's a little unattractive at the moment, but I'll tart it up over the next couple of releases. Start/Stop codons are color coded in mrna mouseover. (Chinnappa Kodira)
  2. Bookmarks: added Move to bookmark edit window. Added help link to bookmark edit window. Made bookmarks scrollable. (Lijun Ma)
  3. Track Table: fixed global view not showing. Changed title from "Track Options" to "Track Table" for consistancy. Restored help link.
  4. File -> Open Sequence File: clearer error messages when improperly formatted files are opened. Restricted sequence size warning to calhoun and UCSC sequences. (James Galagan)
  5. Combo: renamed Jamesian Alignment manager to Simple Alignment Manager (James Galagan)
  6. Drag Scroll: use hand cursor instead of arrow. The default swing hand cursor has an annoyingly pointy finger, but better than arrow. I'll look into getting grabbier hand. (James Galagan)
93 2005-02-14
  1. Track table: one panel for all data sources instead of on panel per data source. Data source is listed in column.
  2. Combo: added overlap filtering for viewing of large, repeat heavy alignment files. Default is 3. Right click dot plot to set to another value. This is a litle clunky, but should let you view your enormous files now. Ideally we'll have a "track table" type widget for filtering and displaying alignments.(Lijun Ma)
  3. Transcript Edit: added default names (Sinead O'Leary)
92 2005-02-09
  1. Open by Feature Id: fixed for gene ids (Chinnappa Kodira)
91 2005-02-07
  1. Inspector: RNA Sequence Panel orf setting by highlight now works (Lucia Alvarado)
  2. Combo: you can now start up argo with combo data to load at the command line. -q flat precedes query sequence plus optional track files, -a flag precedes alignemnt file, -r flat precedes reference sequence file plus optional track files. To specify multiple query sequences, use additional -q and -a args. The first -q sequence will be associated with the first -a alignment, the second with the second, etc. Some examples of the syntax: 
    java -jar argo.jar -q query.fasta -a alignment.blast -r reference.fasta
java -jar argo.jar -q query.fasta queryFeatures.gff3 moreQueryFeatures.gff3 -a alignment.blast -r reference.fasta referenceFeatures.gff3
java -jar argo.jar -q query1.fasta -a alignment1.blast -q query2.fasta -a alignment2.blast -r reference.fasta
    (James Galagan)
90 2005-02-04
  1. Alt-mouse-drag can now be used for scrolling in both the feature map and the combo alignment dot plot. An intuitive way to scroll diagonally, among other things. (James Galagan)
  2. Calhoun XML: Argo now checks for filesession files. It will locate them but not load them by default. Just go to the calhounxml tab in the track table and click on "visible" to load any available files. (Dave DeCaprio)
  3. Combo: added right click select by criteria option (Lijun Ma, James Galagan)
  4. Combo: Support for BLAST alignment files in Combo (James Galagan)
  5. Finder: Show finder result count as popup window (Charlie Whittaker)
89 2005-02-01
  1. Fixed nullpointer on NC3 contig 1 (Alan Derr)
  2. Export: mrna to file fixed (Charlie Whittaker)
  3. Featurize: delete dynamic feature fixed (Charlie Whittaker)
  4. Featurize: fixed labeling (Charlie Whittaker)
  5. Feature Edit: Fixed minimum width of structure box (Charlie Whittaker)
88 2005-01-31
  1. Annotated Transcript: fixed single exon transcript drag and drop edit not working. (Sinead O'Leary)
  2. Analyze: added "Featurize UTRs" option. Creates temporary, inspectable features based on selected transcript UTRs. (Chinnappa Kodira)
  3. Progene: made Gene name box bigger (Chinnappa Kodira)
87 2005-01-28
  1. Annotated Transcript: fixed "the gene associated with this transcript..." error message when updating pending insert and also "nnew gene" getting clobbered and replace with best overlapping in this situation. (Lucia Alvarado)
  2. Splice Site Profile: added intron length in parentheses before coordinates (Qiandong Zeng)
  3. Edit: Featurize Highlights: you can now specify strand, color and label.
  4. Start Codons: fixed bug when they spanned exons (Lucia Alvarado).
86 2005-01-25
  1. Annotated Transcript: fixed save of negative orf coordinates (Chinnappa Kodira)
  2. Fixed gff3,gtf2,bed help links
85 2005-01-24
  1. Annotated Transcript: Fixed nullpointer on transcript insertion (Lucia Alvarado, Chinnappa Kodira)
  2. Annotated Transcript: frixed UTRs and ORFs from only being show for editable transcripts, now shown for all.
  3. Inspector: Show gene accession for progenes in sequence fasta headers (Chinnappa Kodira)
  4. Inspector: beefed up mouseover in rna sequence panel.
  5. Argo now takes optional command line arguments specifying sequence file and one or more track files (Alistair Rust)
  6. GFF3: edit and export works.
  7. GFF3: supports "canonical" 3 tier gene models per the spec. Build orf from UTR rows.
  8. GTF2: added explicit track manager separate from GFF1 and GFF2 to avoid confusion. GTF2 and GFF3 are editable, GFF1 and GFF2 are not.
  9. Feature Map: added max zoom in (Dave Decaprio)
  10. Export: fixed null pointer on to file -> cancel
  11. Progene: lowercase first character of gene symbol in edit dialog (Chinnappa Kodira)
  12. Fixed nullpointer in select primary evidence action
84 2005-01-12
  1. Progene: Show progene database error messages instead of silently failing. (Sinead O'Leary, Chinnappa Kodira, Lucia Alvarado)
  2. Progene: Fixed sporadic progene insert/update error. (Sinead O'Leary, Chinnappa Kodira, Lucia Alvarado)
  3. Inspector: fixed showing sequence info for features in top of properties panel instead of feature label. (Lucia Alvarado)
  4. Inspector: show codon and frame info on mouseover in RNA panel. (Chinnappa Kodira)
  5. Progene: Remove extra whitespace in progene edit windows (Qian Zeng ).
  6. Progene: Added valid start/stop codon test. (Chinnappa Kodira)
  7. Progene: Prokaryotic drag and drop extension now prompts for direction (Chinnappa Kodira)
  8. HQL console: better sized and added scrollbars
  9. BED track format: added support for it (Peter Rogan)
  10. Feature map: restored clicking on single subfeature feature selects parent instead of subfeature.
  11. Calhoun XML: fixed properties error (Shawn Samuel)
  12. Handle longs as sort keys so certain NC3 tracks can be displayed. (Shawn Samuel)
83 2004-12-10
  1. Calhoun DB: added hql console that allows feature and sequence search (easy to add support for other return types if desired). Click on results to open feature map. Removed old find features window that no one seemed to be using. (Dave DeCaprio)
  2. Menu: moved calhoun db stuff from overcrowded File to new DB menu
  3. Applet: standard ruler menu now works (Yanxia Liu)
  4. Applet: custom data rulers can now be added using the "rulers" parameter. See applet home page for details. (Yanxia Liu)
  5. General UI: Super annoying lingering zoom mode bug fixed. Note: there are now only two click modes: select and shift zoom. P,G,Z click no longer work. Use menu or keyboard shortcuts to select parent or group. I have created more intuitive keyboard shortcuts for select parent, children, group and track (see select menu). If lack of direct click really annoys you let me know and I'll reconsider. (Chinnappa Kodira)
  6. Combo: Jamesean alignment parser now skips blank lines instead of throwing array out of bounds error (Alan Derr).
  7. Inspector: sequence id reported again for selected segments (Qian Zeng)
  8. Inspector: report feature track id and show track color
82 2004-12-03
  1. Rulers: custom: right click to set "limits." Sorry this doesn't work in the applet yet. (Yanxia Liu)
  2. Rulers: custom/GC/Codon: vertical now works in combo (Lijun Ma).
  3. Rulers: custom/GC: plot size and color now configurable (Charlie Whittaker)
  4. Rulers: custom: fixed highlight clobbering plot.
  5. Rulers: cutsom: mouseover now reports sequence position and plot value
  6. Rulers: applied to one map at a time instead of global on/off
  7. Rulers: added remove ruler right click action.
81 2004-11-22
  1. Applet: added support for multiple feature files. (Yanxia Liu)
  2. Applet: added support for custom menus. (Charlie Hatton)
  3. Progene: added insert to right click menu (Chinnappa Kodira)
  4. Progene: more compact properties display in inspector window. (Chinnappa Kodira)
  5. Progene: supplemental evidence grouped and colored by track in edit window. Sorted by selected sort criteria (Chinnappa Kodira)
  6. Progene: gene accession numbers added and displayed. (Chinnappa Kodira)
  7. Progene: known orf is default.
  8. BlastX: more compact properties display in inspector window (Chinnappa Kodira)
80 2004-11-09
  1. You can now add ProGenes to Prokaryotic sequences (Chinnappa Kodira).
  2. Disabled buggy printing to gui console for now to isolate performance trouble.
  3. Fixed nullpointer on new gene insertion that resulted in red properties window and possibly put argo into some messed up invalid (and slow) state.
  4. Complain if too many fields in gff file. (Sinead O'Leary).
  5. ProGene track automatically added to pro gene sequence tracks even if none inserted yet (ditto Annotated Transcripts for euk sequences). You used to have to restart after inserting first feature on sequence to get new track to show up.
79 2004-10-29
  1. Combo: hide selected/others and unhide works for dot plot alignment glyphs as with regular features.
  2. Synteny jump works. Select a syntenic anchor and then File -> Open Syntenic Feature. (Chinnappa Kodira)
  3. Code 11 set orf to entire mrna. (Chinnappa Kodira)
  4. Protein Sequence Panel: show stop codons in red (Chinnappa Kodira)
  5. Genetic code taken from ap_bio_sequence instead of by chasing down ap_taxid. Complains if none set. (Dave DeCaprio)
  6. UTRs drawn in feature map. Red line for 3 prime and green line for 5 prime. Green is kind of hard to see. I'll mess around until I find the right balance between clarity and unobtrusiveness. (Chinnappa Kodira)
  7. gff1,gff2: displays stored start and stop codons (Sinead O'Leary)
  8. gff2: labels fixed to take up less space like gff1 (Sinead O'Leary)
78 2004-10-25
  1. Added "Gene Feature Map" right click option to sequence tree. Opens feature map showing annotated genes as only features. Good for higher level overview. (Chinnappa Kodira)
  2. Rudimentary GFF3 track manager.
  3. Clear selections action also clears highlight columns
  4. Feature Map now sizes to desktop frame instead of screen (Shawn Samuel)
  5. Combo: fixed vertical sequence ruler not showing (Alan Derr)
  6. Combo: fixed out of bounds error for raw sequence in scaled multicombo.
  7. Select Group works with gff (Sinead O'Leary)
  8. Calhoun XML: handle childless features (Miriam Averbuch)
  9. Calhoun XML: handle HmmerRun objects (Miriam Averbuch)
  10. Load calhoun bean db connection up front instead of at first request.
  11. Sequence tree built from GenomeAssembly. Sequence order taken from ap_bio_sequence ap_group_order. (Dave DeCaprio)
77 2004-10-18
  1. Combo: scale query maps to common coordinate frame (Alan Derr)
  2. Combo: change Z order of alignment glyphs based on which query map is active (James Galagan)
  3. Combo: added select overlapping alignment glyphs action (James Galagan)
  4. Combo: added relative zoom actions
  5. Combo: add absolute zoom actions
  6. Combo: added zoom to selection aciton
  7. Fixed positioning of right click menu in inspector sequence panels (Chinnappa Kodira)
76 2004-10-07
  1. Comparative: added bookmarking and "open recent". (Alan Derr, Mike Kamal)
  2. Comparative: added rudimentary support for multiple query sequence/alignments. Alignment files will be overlayed in dot plot and a vertical feature map is opened for each query sequence. The horizontal sequence is the reference. (Alan Derr, James Galagan, Christina Cuomo)
  3. Comparative: added link to html help page from input dialog.
  4. Comparative: load all Jamesian File Format properties
  5. Calhoun XML: errors consolodated into one message. (Shawn Samuel)
  6. Printing: basic scaled active feature map printing and save to file postscript (Jade Vinson).
75 2004-09-24
  1. Comparative: fixed double sequence tree.
  2. Comparative: added calhoun sequence tree (Mark Borowsky)
  3. Comparative: shift zoom now works (Alan Derr)
  4. Export: option to export selections in all open feature maps (Alan Derr)
  5. Select Menu -> Added "Select Overlapping Features" action (Alan Derr)
  6. Select Menu -> Added "Select Contained Features" action (Alan Derr)
  7. Select Menu -> Added "Clear Selections" action
  8. Genbank Files: fixed horrendously slow incessant reloading (Alan Derr)
  9. Genbank Files: take id from db_xref if available (Alan Derr)
  10. File based editing: allow update of transcript id (Sinead O'Leary)
  11. Console: fixed size getting messed up.
  12. Splice site profile: fixed bolded first entry that has been driving me crazy for years
  13. Splice site profile: no longer freaks out with tiny introns (Sinead O'Leary)
  14. Editing: fixed totally unncessary full feature refresh after save. (Sinead O'Leary)
74 2004-09-20
  1. Tamara Yu's comparative browser beta integrated (Mike Kamal, James Galagan, Dave DeCaprio, Jade Vinson, Li-jun Ma, Mark Borowsky). Doesn't do anything beyond what tamara's could yet, but should behave normally in both comparative and regular modes. Really limited documentation, including short term todo list, which I encourage you to fight with me about, available here: http://www.broad.mit.edu/annotation/argo/help/comparative.html
  2. Added Analyze -> Console window so you can see error/debug/jython output without having to run from command line (Shawn Samuel)
  3. Add option to force quite to unsaved edits dialog (Qiandong Zeng)
  4. Added Zoom -> scroll to strand boundary.
  5. More compact gtf2 labeling (Sinead O'Leary)
  6. Added Analyze -> run Feature QA Tests (Chinnappa Kodira)
  7. Added splice junction feature QA test (Chinnappa Kodira)
  8. Fixed multi feature QA results output (Sinead O'Leary)
  9. Fixed width values in properties panel. Had been working on mac but not windows. (Chinnappa Kodira)
  10. Got rid of turquoise matching intronic edge color (Sinead O'Leary)
  11. Remaining track managers now also like gff2 just load features for segment instead of whole file.
  12. Fixed properties panel turning red when null values were present.
73 2004-09-13
  1. Fixed click point to stop codon (Chinnappa Kodira)
  2. No more hard to see yellow default track color.
  3. Added really primitive Jython Interpreter window. Launch from Analyze Menu. (Shawn Samuel)
  4. Calhoun XML: handle 3 level gene -> transcript -> exons features (Shawn Samuel)
  5. Got rid of obsolte pref check code with spewed lots of nasty command line junk.
  6. Fixed track sort for file based tracks (Sinead O'Leary)
  7. Bumped defaul sequence complaint length from 200k -> 500k (Sinead O'Leary)
  8. Got rid of UCSC strand parse error for GC percent track (Sinead O'Leary)
  9. Feature QA results window now shows something meaningful (Sinead O'Leary)
  10. Fixed no repaint after select marked
  11. Added Rollback action to File Menu (more convenient that going through unsaved edit screen)
  12. Fixed new filed track feature inserts not being loaded right away (Sinead O'Leary)
72 2004-08-27
  1. Added Calhoun XML Track Manager. Can handle big files without running out of memory, but very slow. (Alan Derr, Dave DeCaprio)
  2. Gff2 track manager now only loads features for viewed segment so you can feed it enormous files (April Cook)
  3. FINALLY fixed shift arrow sticks you in zoom mode bug (Chinnappa Kodira)
  4. Fixed nullpointer on markaction isEnabled (Mark Borowsky)
  5. Added search MRNA using protein for mRNA sequence panel (Chinnappa Kodira)
  6. Added Link Menu -> open ucsc web browser on selected region in browser action (Chinnappa Kodira)
  7. Fixed Finder Window track criterion always being boolean "NOT."
71 2004-08-20
  1. Added Analyze Menu Align against Query Action (Chinnappa Kodira)
  2. Added BLAT as Aligner option (Chinnappa Kodira).
  3. Added very rudimentary JALVIEW launch from alignment text panel.
  4. Added Link Menu Smart Domain Action. (Chinnappa Kodira)
  5. Complain if edited transcript coordinates are out of sequence bounds (Dave DeCaprio)
  6. Fixed slow repaint after select others action
  7. Fixed Genewise -> NCBI site click (Chinnappa Kodira)
70 2004-08-13
  1. Added Featurize highlighted column action. Useful in combination with sequence search.
  2. Added select all columns action.
  3. N is kept N in complement. Was messing up negative strand sequence search.
  4. Alignment window automatically shift to text panel when alignment is complete (Charlie Whittaker)
  5. Fixed loading of files after new generic feature inserts (Sinead O'Leary).
  6. Fixed export of all features in sequence matching criteria.
  7. Single child compound features have the parent selected on click instead of child (Sarah Calvo).
  8. Added select children action.
69 2004-08-03
  1. Added select all evidence action.
  2. Added highlight to column action.
  3. Added plain text sequence manager.
  4. Inspector window no longer pops to front.
  5. Fixed problem with hst66628 not being updatable because number of suplemental evidence caused edit cache record to exceed java preferences max length (Chinnappa Kodira)
  6. Fixed insert feature on column
  7. Finder Window: Added negative criteria to Feature panel.
  8. Fixed drag and drop edits not working for filed features (Charlie Whittaker)
68 2004-07-27
  1. 5prime and 3prime sequence context can now be displayed in dna sequence panel. Right click to select size of each. Context sequence is colored orange. (Dave DeCaprio)
  2. Added Track Table button to open feature map dialog (Mark Borowsky, Dave DeCaprio)
  3. Properties window properties categorized and clustered. The stuff most of you want to see most of the time should now be visible without scrolling. Let me know if this isn't the case, or if I've overcompacted and you don't immediately understand what each line means. I've replace the JTable implementation which was buggy and required thousands of lines of hacky code to support variable height rows with a simpler, less buggy html textpane. (Chinnappa Kodria, Sinead O'Leary, Mark Borowsky)
  4. Zoom actions stay enabled even when you click on another window besides the feature map (you can use keyboard shortcuts to zoom the featuremap while youre in the inspector)
  5. Added zoom to highlight action. This means you can select a stretch of sequence in the inspector (or finder) and easily zoom to it.
  6. Fixed really slow feature map repaint after selection of many features (map repaint was unnecessarily being done for each selected feature)
  7. Fixed recently introduced bug that made gff file un-unloadable onto calhoun database sequences.
  8. Fixed broad/applet feature sort (Sarah Calvo)
67 2004-07-09
  1. Batch Update: "new gene" now an option.
  2. Finder: added Sequence Finder panel for regex sequence search. (Charlie Whittaker, Dave DeCaprio)
  3. Finder: added status window with cancel button.
  4. Finder: much better performance. Relevent data is preloaded.
  5. Finder: added ID, Transcript, Gene. (Chinnappa Kodira)
  6. Open Calhoun Sequence Id: now also takes sequence group and sequence number in the format "SEQUENCE_GROUPSEQUENCE_NUMBER." Example: "HUMAN_CHR17 1" (Dave DeCaprio)
  7. Calhoun Track Criteria: Strand is now an option (had been buggily left out because it's a char not varchar).
66 2004-07-02
  1. Batch Update. Select multiple transcripts and hit "update." Instead of seeing the regular transcript edit form come up multiple times, a single batch edit form comes up. This shows the two properties (gene and name) you're likely to want to change for multiple transcripts. Changing them here changes them for all selected. Leave either blank to keep current transcript values. Let me know if you want me to add other batch edit fields. (Chinnappa Kodira)
  2. Transcript Edit Form: modified supplemental evidence and curation flag panels so that accidental setting is less likely. Only items associated with transcript are listed. To remove, select and hit delete. To add, click "add..." and a popup selection window will list options to add. (Chinnappa Kodira)
  3. Fixed error when assigning "new gene" to updated transcript (Chinnappa Kodira)
  4. Default negative strand color now yellowish instead of gray because of problems with label visibility.
  5. Fixed nullpointer error if transcript saved with no primary evidence.
  6. Hide confusing and misleading selected sequence column from inspector window (Mark Borowsky)
  7. Argo (external) only: Added Registration to app instead of web site.
65 2004-06-29
  1. Supplemental evidence now editable. You can explicitly set or unset it in the transcript edit form. Drag and drop will also add the dragged evidence (or its parent, if it's a subfeature) to the supplemental evidence list. (Chinnappa Kodira)
  2. Fixed missing scroll bars on sequence tree (Sarah Calvo, Charlie Whittaker)
  3. Fixed transcript retirement dialog coming up for exon deletes (Charlie Whittaker)
  4. Applet jar size reduced from 8 MB to 300 KB.
64 2004-06-17
  1. Applet data renamed to "Broad Data." Sequence tree now available.
  2. Fixed broad (=applet) sort and criteria filtering.
  3. view UCSC through file menu -> UCSC Sequence Tree. UCSC tracks are not visible by default because there are so many of them. (Dave DeCaprio)
  4. Sequence trees remain open until shut (Chinnappa Kodira)
  5. Sequence ids may now contain spaces.
  6. Configurable/Overridable max sequence length warning (default is 200 kb, change this in view -> map options. This prevents you from opening an unloadably large feature map by accident.
  7. Track table automatically comes up when you try to open a segment without any associated tracks (like UCSC or file data)
  8. Got rid of Exit on mac. Just standard aqua Quit.
  9. Improved raw sequence caching. Features now share sequence when they overlap. Cache trims itself.
  10. Fixed annoying flash on sequence tree startup.
  11. Default negative grey instead of black in app
  12. Fixed genes showing up as features (Chinnappa Kodira)
63 2004-06-02
  1. The Applet data on the website is now viewable in the desktop application. This isn't very exciting for internal users, but might be to external ones. At the moment you need to know the sequence id. Sequence tree pending.
  2. The Applet has been modified so that it can easily be used on arbitrary data sets. Other groups can now stick the applet on their sites to view their data. Instructions and download here.
62 2004-05-21
  1. Added File -> Close and File -> Close All (Dave DeCaprio)
  2. Fixed genbank database bookmarks/open recent
  3. Fixed genbank database not properly loading features.
  4. Got rid off space wasting toolbar. Drag mode is now settable via select menu. Traffic lights are now in thinner status bar on bottom of feature map. Use shift-click to toggle to zoom mode. Parent and group select shortcuts have been added to right click menu.
  5. Fixed problems with editing gff features (not loading new file after save and deleting whole transcript on exon delete). (Charlie Whittacker)
  6. Fixed track table help url.
  7. Applet can now get its own data instead of relying on pregenerated files (Dave DeCaprio,Charlie Hatton).
  8. Feature map right click menu: added select options and removed clutter. Let me know if it wasn't clutter to you.
61 2004-05-14
  1. The applet now works with current codebase. Argo app users probably don't care much about this, but a lot of code has been mucked with under the surface to get this to work, so you may wind up caring in a negative sort of way. Let me know immediately if you notice anything.
  2. Raw sequence is now only loaded when it is needed. This means you can now look at much bigger sequence files without running out of memory (as long as you don't load too many features). (Christian Weinel)
  3. Fixed a bug involving feature validation being run on deletes (Sinead O'Leary)
  4. List transcript accession numbers in unsaved edits window (Sinead O'Leary).
  5. Right click copy option in sequence panels (Charlie Whittaker).
  6. Shift key toggles to zoom mode. I'm keep z,p,g click for the moment but want to retire them.
  7. Strands are segregated by default.
  8. Delete key (aka backspace) now deletes on mac.
60 2004-04-28
  1. Moved load track and track table menu items into File menu, show track label into map options (makes sense and were too many top level menus).
  2. Fixed Preferences error after clear and insert (Charlie Whittaker).
  3. Fixed blast parser query id not handled properly for files with multiple query sequences (Christian Weinel).
  4. Got rid of pointless spacewasting non spinning helix.
  5. Genbank input: collapse whitespace in various fields. Was ugly.
  6. Added Link menu and feature link editing capability. Lets you specify a template url for sending selected feature property to web site via browser launch. (Charlie Hatton)
  7. Show selected feature count in status bar. Particularly useful for Finder.
  8. Added +/- buttons to Finder panel instead of strange hyperlinks.
59 2004-04-13
  1. Added Finder window to replace Select Menu -> Select by Criteria and fill former sequence tree real estate. Please play around with this and let me know what you think. (Dave DeCaprio)
  2. Fixed genscan files not reloading once they had been unloaded (Charlie Whittaker)
  3. Fixed Select Menu -> Select Left/Select Right for top level features.
  4. Fixed release 57 introduced bug preventing generic edits.
  5. Added Select Menu -> Select Others action.
58 2004-04-07
  1. File -> Open Calhoun sequence replaces sequence tree. For now we just have a really wide inspector. Ugly, especially for properties, but I'll find a better use for the space shortly.
  2. File -> Open Genbank Database Sequence now retrieves sequences and tracks staight from ncbi website if you know the gi. (Dave DeCaprio)
  3. Fixed p-click (Charlie Whittaker)
  4. Added status indicator bar at bottom of feature map.
  5. Fixed yellow highlights clobbering subfeature labels (Andrew Zimmer)
  6. Fixed bookmarks not remembering start and stop.
  7. Fixed bookmark hyperhelp link disappearing.
  8. Fixed genbank file bookmarks not working.
  9. Fixed lingering gebo reference in meta info (Mark Borowsky)
57 2004-03-31
  1. Gebo is now Argo. The jar file and all end user exposed references within the program have been changed.
  2. Added File Menu -> Open Sequence File. (Dave DeCapio)
  3. Added File Menu -> Open Recent Sequence that lists last 10 feature map segments.
  4. Replaced "favorites" with "bookmarks" menu that works pretty much like a web browser bookmarks menu (a little simpler). Instead of bookmarking sequence groups, you now bookmark feature maps (segments, actually). This is more sensible. (Charlie Whittaker, from a long time ago)
  5. GFF Frame column now consulted when determining ORF. If a 0,1, or 32 is in this column, that entire frame will be used as the ORF. If you do not want this to happen, leave the column empty (with a '.'). (Charlie Hatton)
  6. Added explicit set orf to entire frame options to mrna sequence panel right click menu (Charlie Hatton)
  7. "Zimmer Aligner" renamed to "Standard Local Aligner". Properly registered for argo as well as argoc. Sim4 is now hidden from external. (Charlie Whittaker, Andrew Zimmer)
  8. Added help links from map options panel and track panel (Dave DeCaprio).
  9. Fixed freezing when you click to other apps and then back again in mid dialog (Charlie Whittaker, Dave DeCaprio)
  10. Replaced zoom to specific percent menu items with zoom to arbitrary percent menu item. Default is current map size. I kept zoom to 100%.
  11. Feature/sequence selection color now configurable via map options. It now also applies to feature map selections. I think the new default yellow is much clearer than the old pale blue. If you don't like it, override it.
  12. Feature map actions now active when map is first opened (formerly you had to click the map first).
  13. Select by criteria now has beefier ui. Same as find features ui.
  14. New file based features are no longer gray. They are assigned colors from a rotating list. This way you don't have to muck with the track table settings if you don't have strong feelings about what color a track should be. (Dave DeCaprio)
  15. Blast properties are now also criteria.
  16. MRNA right click menu now broken into submenus. Was getting cumbersome. (Dave DeCaprio)
  17. New shorcut for hide others. Was buggily the same as hide feature.
56 2004-03-15
  1. BLAST: remember what user decided about query and subject prefs. Unload track to make it forget.
  2. BLAST: fixed pipe cutting off query label (Charlie Whittaker)
  3. BLAST: handles stupid "header" thing at the top of some BLAST files. (Charlie Whittaker)
  4. BLAST: show text alignments
  5. BLAST: "user subject coordinates IN THIS FILE" and list file (Charlie Whittaker)
  6. Edit cache works for non-oracle features. This means that if your program dies before you've saved your non-oracle edits, it will be able to restore them like it does with oracle edits.
  7. Generic edit more intuitive because of track = file assumption. Select track/file from drop down or "add new track." Validate that transcript id is unique to track/sequence.
  8. Help: added help hyperlinks to most menus.
  9. Labels now shown for strandless features (Charlie Whitaker)
  10. Menus: Hide remaining menus that don't make sense in external jar. "insert generic feature" becomes "insert" and takes control i shortcut. Moved some menus around from "select" to "view" and "view" to "zoom" because they make more sense there (plus select was way too long).
  11. Imposed tracks remembered accross sessions and automatically reloaded so you don't have to reload the same old files every time. If file not where expected, silently remove the association.
  12. File based tracks now tracked by file name. This simplifies a lot of code and ui, is is more likely what users expect. (Mark Borowsky, Charlie Whitaker)
  13. Track files may now be unloaded via track table (Charlie Whittaker)
  14. Track table: Renamed "Selected?" column to "Visible?" to get rid of ambiguity between ui selection of table row with and ticking the checkbox for display in featuremap.
  15. Fixed selectable sequence columns being removed on refresh. (Charlie Whittaker)
  16. DNA Sequence Panel: got rid of false error message after every exon boundary edit (Charlie Whittaker)
  17. Ids only have to be unique within track. Important because many generated gffs don't column 9 cluster ids that are likely to be unique (Charlie Whitaker. Mark Borowsky)
55 2004-02-27
  1. Added Genscan file track manager -- very vanilla, just does structure. Let me know what else you'd like to see. (Charlie Whittaker)
  2. BLAST: prompt user to use subject or query coords for drawing feature instead of very weirdly just using query coords (Charlie Whittaker)
  3. BLAST: Show query and subject ids (Charlie Whittaker)
  4. BLAST: Fixed parsing of e-values (Charlie Whittaker)
  5. BLAST: Fixed parsing of score (Charlie Whittaker)
  6. BLAST: fixed handling of start > stop (Charlie Whittaker)
  7. Remove spaces from track criteria (Chinnappa Kodira, Dave DeCaprio)
  8. User can determine how gff is tracked. Choose between file name and two fields that potentially make sense. (Mark Borowsky)
  9. File dialogs: show extensions for supported file types (Mark Borowsky)
  10. File dialogs: remember if filters turned off (Mark Borowsky)
  11. File dialogs: prefs specific to type instead of same for all.
  12. Load track files: prompts user to specify file type because can be ambiguous.
  13. Track table: show editablity for each track. Read only mostly, but read/write for gff.
  14. Fixed vertical zoom resetting map prefs (Dave DeCaprio)
  15. GFF2 files editable/exportable
54 2004-02-13
  1. Added BLAST track manager. Please bang on this. I'm not even sure which versions of blast it supports, since I borrowed most of the code. It assumes the sequence you are imposing it on is the query sequence. Maybe this should be configurable? (Charlie Whittacker, Mark Borowsky)
  2. Added GFF2 TrackManager. Renamed old GFF Track Manager to GFF1 Track Manager to minimize future confusion. (Charlie Whittaker)
  3. Added contextual help links for gff1 and gff2 (Charlie Whittacker)
  4. Fixed slashes in gff problem (Charlie Whittaker)
  5. Fixed strandless features misbehaving (no count in track label, drawn on negative strand, always using "full" arrangement). (Charlie Whittaker)
  6. Fixed track options max row cancel complaining "Integer Please!" (Miriam Averbuch)
  7. Fixed nullpointers when called from genepattern (Ted Liefeld)
  8. Added OS and java version to meta info.
  9. All blue urls now really open browser
  10. Meta info is now selectable and copyable for easy paste into support email (so you can send me exactly what version, os, java version you have when something goes wrong)
53 2004-02-05
  1. Alignment: you can now input fasta headers with your raw sequence and it won't freak out. (Charlie Whittaker)
  2. Alignment: fixed sim4 featurize working for odd (but presumably legit) header produced by aligning "Human Chr17 Second Assemble contig 1.3 (1321561 - 19243743):3582501-3637082" with ">gi|27436918|ref|NM_170663.2| Homo sapiens misshapen/NIK-related kinase (MINK), transcript variant 2, mRNA" (Charlie Whittaker)
  3. Genbank: Fixed serious performance problem with opening non-tiny Genbank files (Charlie Whittaker).
  4. Alignment: now it complains if you try to align using a blank raw sequence (Charlie Whittaker)
  5. Both gebo and geboc link to their respective home pages in the help menu (Dave DeCaprio)
  6. Open new map on feature by exon id (Dave DeCaprio)
  7. Browserlauncher works on mac osx.
  8. Fixed file load dialogs still loading on "cancel."
  9. Fixed feature table windows getting null featuremap except for the first track.
  10. Fixed features being drawn with rectangles slightly skinnier than polygon heads if borders turned off.
  11. Removed unused EdgeFrameAction
  12. GFF/GBK features are default selected (must have broken this in 52).
  13. Fixed activity indicator spinning for no reason on gebo.jar startup.
52 2004-01-26
  1. smaller prefs files. Don't record defaults and cluster properties in nodes instead of flat.
  2. Plugged missing genetic codes. If you were looking at something with a code higher than 6, you may have been looking at errors.
  3. Build info from anthill included in about and login screen. Gebo (not geboc) also takes anthill version.
  4. Fixed problem with designer labels getting garbled on prefs import/export because of tab delimiter.
  5. Genetic code is now more discreetly asked for. And it's remembered in prefs.
  6. Sequence offset may be specified for looking at mid-sequence fasta files without having to translate feature coordinates. (Dave DeCaprio)
  7. Added post tracking to startup. (Dave DeCaprio)
  8. Fixed prefs export (wasn't working at all last few releases though no one seems to have noticed)
  9. Got rid of open by protein id because no one uses anymore and it's just clutter. (Dave DeCaprio)
  10. Alignment window can now take sequence ids as arguments (Dave DeCaprio)
  11. Fixed Transcript retire dialog dissappearing (Charlie Whittaker)
51 2004-01-15
  1. Select by criterion now takes transcript and gene accession (Shunguang Wang).
  2. Select by criterion default button is "ok"
  3. Added drag mode: copy image to clipboard. Useful for quick copy and paste into powerpoint, etc. (Shunguang Wang, Mike Kamal)
  4. Fixed annotdbo hard coding in view metadata retrieval so it works with annotdev (Shunguang Wang)
  5. "Designer Labels." You can now decide exactly what fields and text to use to label features in each track. Open up the track table and click on the cell at the intersection of the "Designer Label" column and the row of the track you want. You'll see a window with two lists and a bunch of buttons. The list on the left lists all the fields of the track. Use the "add" button to move them to the chosen list. If you want some text between each field, use the "Add text" button to enter it. You can then move the fields from the chosen list around or remove them altogether using the other buttons. Note: there is a price to pay for this: memory, and db load up front. You can now, for example, show qstart and qstop in the label (and therefore mouseover tooltip) for BLAT features. (Chinnappa Kodira)
  6. Fixed extra bad fields being returned for track meta data due to wildcard confusion. If you've ever tried to search or sort by a criterion and gotten a "no such descriptor" error, this was why. (Shunguang Wang).
50 2004-01-07
  1. Show percent id of SIM4 exons (Chinnappa Kodira)
  2. Fixed nullpointer when gff feature is edited and track is changed
  3. Fixed repaint glitches in columnheader after sequence column drag resize (ruler whould get all splotchy blue)
  4. Fixed rows doubling for show hidden features.
  5. Fixed show hidden features being enabled when no active feature map
  6. Ram tracks sort to center, not ends. Segregated arragement. This makes it easier to keep track of new generic features.
  7. Got rid of windows only backing store exception.
  8. Editable transcript name drop down instead of text field. Lists primary evidence name and names of all transcripts in currently selected gene. Selecting a new gene dynamically updates the list (Mark Borowksy)
  9. Track and TrackManager specific reload in feature map. Example: When you use the Tracks -> Load Track File to load a gff track it won't reload all the oracle tracks. Faster. There are a few other places in the code I should stick this to speed them up that I haven't yet. Let me know if you think you have a suspect and I might get to it quicker. (Shunguang Wang)
  10. hide others option in select menu. Opposite of hide. This hides all the features except the ones you have selected. (Charlie Whittaker)
  11. Open new map on feature/sequence dialog now wide enought to show title.
  12. generated alignment features are now deletable. (Chinnappa Kodira)
49 2003-12-19
  1. Fixed (I hope) Sim4 parsing and featurization. Tested on the folling target-query pairs: hst39060 and gi:4507010; HsT39945 and gi:28838611 (Chinnappa Kodira)
  2. Fixed repaint glitch after column glyph delete
  3. Added 10 item history for open by feature/sequence id/accession. I think this is going to be a big time saver. Let me know if you want a longer history and/or keyboard shortcuts.
  4. Added tooltip for selected primary evidence and made combobox slightly wider to deal with truncated long labels. (Charlie Whittaker)
  5. Structure textarea in transcript edit window now dynamically sizes to accomodate big sequence positions (Charlie Whittaker)
  6. Position ruler now shows position in tooltip on mouseover (like sequence ruler has always done)
  7. Fixed horrible sequence ruler performance on osx panther by using non anti aliased font.
  8. Show columnglyph coordinates in tooltip while dragging (James Galagan, from ages ago)
  9. Moved alignmentpanel target on top when just a single selection. It's possible this may be more confusing than it was before under certain circumstances. Let me know (Chinnappa Kodira)
  10. Set tooltip delay to 0 and doubled duration. This should make it feasible to turn feature labels off completely for spartans who crave that slight rendering boost.
  11. Genewise style gff files (space delimited instead of tab) can now be read. (Charlie Whittaker)
  12. Fixed red dna label in dna sequence panel tab lingering after other features selected.
48 2003-12-12
  1. Featurize generated alignments (Chinnappa Kodira)
  2. De-minimize inspector window on feature selection (Shunguang Wang)
  3. Fixed inserts pending all over the place
  4. Remember selected aligner (Chinnappa Kodira)
  5. Only auto fix orfs if out of bounds (Mark Borowsky)
  6. Faster drag rect selection
  7. Fixed highlighted codons in sequence ruler in reverse view.
47 2003-12-03
  1. Do not display calculated fields in generic edit panel.
  2. Added rememeber password option to login screen (Mark Borowsky)
  3. On transcript update, check whether orf has included stop codons and alert user (Chinnappa Kodira)
  4. Feature diff now works across track managers.
  5. Added score to gff criteria
  6. Crash protection properly handles special characters in records
  7. Find features now lets you search on all track criteria. I think this is going to actually make this a useful feature. Please play around with it a bit and let me know whether you think it's worth improving further and if so what's most important.
  8. Find features searches now case insenstive.
  9. Fixed delete of pending insert. Just rolls back.
  10. Fixed gff no refresh after rollback
  11. Fixed refresh after editing crash restored edited features.
  12. Improved delete speed by getting rid of double screen refresh
  13. Single feature rollback properly refreshes screen.
  14. set default button in retire transcript dialog so you can just hit enter for ok.
46 2003-11-25
  1. Limited threading in featuremap to feedback dialog. This should get rid of the nasty sporadic UI freezes people were seeing while still keeping you informed that the browser is doing something. (Mark Borowsky, Charlie Whittaker)
  2. Added drag and drop overlap options to replace right and replace left. Ask me if you are confused about how this is different from extend right and extend left. (Chinnappa Kodira).
  3. Added scroll to sequence position zoom option with control g (James Galagan)
  4. Standard rulers now apply to all open feature maps, not merely selected. Was confusing because sometimes it looks like a feature map is selected when it's not, and adding a ruler does nothing.
  5. Select evidence now highlights evidence in ruler instead of transcript (Mark Borowsky).
  6. Restored drag rectangle(Mark Borowsky).
  7. Fixed open by gene accession (Chinnappa Kodira)
45 2003-11-18
  1. Edit Features from feature table (Chinnappa Kodira)
  2. Select features rather than highlight columns from feature table (Chinnappa Kodira)
  3. Refresh mrna/protein window after edit (Shunguang Wang)
  4. Select supplmental evidence action (Shunguang Wang)
  5. Review and retire multiple selected transcripts with a single dialog (Chinnappa Kodira)
  6. Choose track file manager allows new file for generic inserts.
  7. Quick search for features matching selected feature qsequence id or repeat cluster (Lijun Ma)
  8. Slightly faster find features by skipping view.
  9. Got rid of sporadic painting of featuremap over toolbar (Chinnapa Kodira, Mark Borowsky)
44 2003-11-07
  1. Faster review: was doing unnecessary refresh from db. (Chinnappa Kodira).
  2. Added transcript and protein length to annotated transcript properties (Mark Borowsky, Chinnappa Kodira)
  3. Status indication for featuremap data refreshes. Used to just mysteriously freeze while it was getting data.
  4. Control L shortcut for load tracks
  5. Track Table: critera and sort criteria defaults restored (was blanking out even if there were existing settings) (Chinnappa Kodira)
  6. Sequence tree more reliable. I wish I could say perfectly reliable but still does odd stuff occassionally.
  7. Color selected colors subfeatures of selected too.
  8. Faster getTracks by sequenceid (thanks Dave D)
  9. Choose track file manager for inserts: fixed blank labels
  10. Choose track file manager: default to only open file if just one.
  11. api change: db -> api where appropriate
  12. api change: teased apart export and edit
  13. Genbank is viewable/exportable. Disabled direct editablity because hard and buggy and no one seems interested.
  14. Feature level success/failure with commit (Mark Borowsky)
  15. Track labels show feature counts instead of row counts (Chinnappa Kodira)
43 2003-10-30
  1. Clear error message when you try to view feature with overlapping exons in dna panel. I think this is what was causing the strange hst33574 issues you were seeing (Chinnappa Kodira).
  2. Fixed sim4 malformed url error (Chinnappa Kodira)
  3. Fixed find feature criteria boxes being tiny on mac
  4. Reverse orientation checkbox works again in map options
  5. Sort criteria/criteria/login dialogs are centered.
  6. Batch edit sort criteria in the tracks table. It figures out the common criteria for the tracks you have selected and lets you edit those.
  7. Batch edit criteria in the tracks table. Works like the sort criteria.
  8. Select bad splice site features added to select menu. You can then easily mark or hide selected. (Mark Borowsky)
  9. Clear error in update transcript window if transcript refers to gene that does not exist (Charlie Whittaker, Mark Borowsky)
  10. Control-o shortcut for review (Mark Borowsky)
  11. GFF/GBK criteria filtering now work.
  12. GFF/GBK sort now works
  13. Alt-m shortcut for select marked. I find this really useful.
  14. Option to sort by NONE for performance.
  15. Fixed some hide feature display issues on mac (and pc to smaller degree).
42 2003-10-24
  1. Crash recovery of unsaved edits (Mark Borowsky, Sinead O'Leary)
  2. No longer possible to update pending review (Mark Borowsky)
  3. Added Track menu. Renamed tools menu -> analysis, because of hot key contention (and because it's a slightly better name).
  4. Track menu: load files.
  5. Track menu: view track labels. Extremely ugly at the moment. Only works for segregated tracks. Shows label, visible rows, total rows. Proof of concept. I'll make it prettier next week.
  6. Track menu: autosave switch that you can turn off when you are happy with your settings and don't want further changes saved.
  7. Tracks table: added feature counts column.
  8. Tracks table: added max rows column. Only works with segregated. I think this might make segragated a much more useful way of looking at evidence.
  9. Tracks table: Select multiple track rows to right click and batch edit settings. Batch edit works for all but last 2 columns (criteria and sort criteria). They'll be batch editable soon too.
  10. Tracks table: fixed sort jump after a setting is edited. This has been driving me crazy for almost a year, and probably everyone else.
  11. Fixed nullpointer on filed load cancel.
  12. Fixed sort bug for calhountracks. Sort works again.
41 2003-10-17
  1. Fixed null file displayed for gff pending edits in unsaved edit panel.
  2. Fixed map options segregate by strand not allowing changes.
  3. Yellow highlight color in sequence panel for greater clarity/logical association with featuremap sequence highlight (Chinnappa Kodira).
  4. Hitting enter/return will press the OK button on the following screens: sequence range input, login, track options. Let me know if there are any other screens you would like me to add this to. It's easy. (Chinnappa Kodira)
  5. Larger scrolling increments with alt-arrow (James Galagan)
  6. Login to calhounDB through sequence tree works again (was causing problems when you tried to open a feature map)
  7. Make intronic/exonic fixed for gff (Charlie Whittaker)
  8. Got rid of extra space in gff export/save
  9. PolyA signal view fixed for sequence regions (Mark Borowsky)
  10. Clear error message if you try to control n to features on different sequences (Mark Borowsky)
  11. Recenter feature map on strand boundary after shift
  12. You can highlight multiple polyA signals, tabular dump features, and splice site profiles in the feature map (Everyone)
  13. Got rid of "halloween" effect when you tried to delete an exon from a gff feature (Charlie Whittaker)
  14. New jar is much more mac friendly. Faster and fewer weird glitches.
40 2003-10-02
  1. Genbank export works for some definition of the term 'works.' If you're lucky, you'll produce a file that gebo can read back in again. Direct editing should theoretically work also, but I had no time to test this.
  2. Unsaved edits indicator (4 button traffic light, 1 light for each kind of edit) (Sinead O'Leary)
  3. Gebo insists that you commit or rollback unsaved edits before closing. The menu exit will be disabled if there are unsaved edits. If you close using the window x, gebo will complain and redirect you to the view unsaved edits window (Sinead O'Leary).
  4. Drag and drop editing works for editable file features (Charlie Whittaker)
  5. Export complete popup no longer appears for screen dumps
  6. Only GFF records with proper GTF2 gene_id and transcript id are editable. With genbank, it's gene and db_xref. This is both to reduce bugs by insisting on a unique identifier, and to keep you from accidentally modifying your evidence (Charlie Whittaker, Mark Borowsky).
39 2003-09-25
  1. GFF features now editable.
38 2003-09-16
  1. Make intronic/exonic in dna panel pends properly (Charlie Whittaker)
  2. Delete single exon transcripts works with pending.
  3. Review works with pending.
  4. Drag and drop edit works on pending updates/inserts.
  5. Features resize properly after drag and drop edit.
  6. Diff detects start/stop codon changes.
  7. Save selected orf -> Set selected Orf (Chinnappa Kodira)
37 2003-09-12
  1. Editing and saving decoupled. You have to use File -> Save to push your edits to the db. Pending edits will show up violet for inserts and orange for updates. You can examine tabular view of pending edits in File -> View Unsaved Edits. You can rollback edits from this screen, and compare updates against database originals. Please note: diff doesn't detect start and stop codon changes. Also, it is possible to delete last exon of a single exon transcript and have an exonless transcript. Also, review doesn't pend like the rest of the edit actions. These will be fixed in next release. Annotators please test carefully -- lots of under the hood changes to support this.
  2. Minor File menu changes.
  3. Fixed GFF exons click bug (James Galagan)
  4. History table now sorts on column header click
  5. Tabular dump now lets you chose fields to dump (Charlie Whittaker)
  6. Tabular dump now sorts on column header click
  7. View -> Map Options -> Show coords in label option so people who like to see this still can when I take it out of the views today (Lijun Ma)
  8. Handle null feature labels (Sinead O'Leary)
  9. Sort bug on refresh editable features (Mark Borowsky)
  10. Give focus back to last feature map after closing edit/tools dialogs (Mark Borowsky)
36 2003-09-03
  1. Reload map now gives option to change boundaries (Mark Borowsky)
  2. Shift arrow up/down extends/focuses map (Mark Borowsky)
  3. Control-e now selects primary evidence instead of export (Mark Borowsky)
  4. Fixed tabular dump sometimes missing curation flag values (Charlie Whittaker)
  5. Updated polyA hexamer table (Chinnappa Kodira)
  6. Alignment sequence panel gives 3 options for each sequence: genbank gi, raw, or selected feature (Chinnappa Kodira)
  7. SIM4 can now be selected as alignment method (Chinnappa Kodira)
35 2003-08-28
  1. Fixed horrible slowness with big start-stop regions.
  2. Restored font in properties window so alignents display properly.
34 2003-08-21
  1. Transcript retirement comment now optional (Chinnappa Kodira)
  2. In properties window, if you select text in a value cell and then click on another feature, it now gets updated (Mark Borowsky, Chinnapp Kodira)
  3. Alignment textarea now removes whitespace (Mark Borowsky, Chinnappa Kodira)
  4. Manual shift arrow override (Chinnappa Kodira)
  5. Fixed big poly A bug (Mark Borowsky)
  6. Shift arrow refreshes sequence ruler as well as map.
  7. Alignment testarea now shows error messages if there's a problem (Mark Borowsky, Chinnappa Kodira)
  8. Added scrollbars to alignment panel (Mark Borowsky)
  9. Fixed longstanding weird font switch when you click into a value field in the properties window
  10. Multi polyA insert with right click (Charlie Whittaker, Chinnappa Kodira)
  11. Cache tracks for each sequence for better performance (Shunguang Wang, Chinnappa Kodira)
  12. Fixed release 33 introduced nullpointer for track options ok
33 2003-08-19
  1. Fixed triple refresh after track options ok (yes, the was taking 3 times as long as it should simply because it was being called three times).
  2. Got rid of mysterious duplicate criteria for blastx views (for reasons I don't understand, this seems to make a big difference for those blast queries. Why it never did before, I don't know)
  3. Removed unnecessary sort by type in getfeatures (I don't know if this makes much performance difference but it was totally unnecessary and distracting)
32 2003-08-14
  1. Alignment: select gene and use tools menu -> align to align against pasted sequence (Chinnappa Kodira)
  2. DNA sequence Panel: fix font color of intronic so it shows up better accross monitors (Chinnappa Kodira)
  3. Sequence Panel Search: is now case insensitive (Chinnappa Kodira)
  4. Custom Data Ruler: Handle Negative numbers (James Galagan)
  5. Custom Data Ruler: new color for each graph (Mike Kamal)
  6. Custom Data Ruler: option to clear from memory (Mike Kamal)
  7. Custom Data Ruler: Flip graph (Mike Kamal)
  8. Custom Data Ruler: more efficient rendering
  9. Custom Data Ruler: lines to show min, max, and middle (or 0, if negative). (Mike Kamal)
  10. Custom Data Ruler: o and + instead of line for y1,y2 data when sufficiently zoomed in (Mike Kamal)
  11. Genbank File Display: use note field for label if available (Tamara Yu)
  12. GFF File Display: tracks are now applicable to multiple sequences (bug fix).
  13. GFF File Display: gff tracks may now be cleared to free up memory (Mike Kamal, James Galagan)
  14. GFF File Display: use comment field, then group for label (James Galagan, Mike Kamal)
31 2003-08-08
  1. Created external jar with no calhoun database login prompt. If you don't connect to the calhoun database, the genome browser will start up faster and be less cluttered if you use this jar.
  2. Favorites no longer freak out if not connected to calhoun database.
  3. Added "All Frames" radio button to RNA panel (Chinnappa Kodira)
  4. On open new sequence, if you specify out of bounds range it just sets it within bounds instead of complaining (Mark Borowsky)
  5. Select by Criteria lets you select genes in a feature map by their properties. Please note that this is currently very inefficient for large featuremaps of calhoun database features, since the database is queried for each feature. The name/label field does not query the db, and limiting by track queries only features of that track (Sarah Calvo)
  6. Right click in the properties panel of a feature to select by criteria on the clicked on property (Chinnappa Kodira)
  7. Restored vertical zoom in/out, but made it work better. It's no longer a click mode. Use the zoom menu. I also renamed Expand/Collapse to "Restore" and "Zoom to Fit," which are more accurate descriptions of what they do. (Mark Borowsky).
  8. Deleting the last exon in a transcript now deletes the transcript (Mark Borowsky)
  9. File extension filters are applied everywhere there is a file dialog (Mike Kamal)
  10. Genbank and Fasta files may now be added to favorites. Side effect: you'll have to reset your current calhoun favorites -- sorry to do this yet again. (Mike Kamal)(
  11. Slightly faster gettypes by sequence sql. This is still too slow.
30 2003-07-30
  1. Fixed vertical zoom to fit sizing (now renamed 'collapse').
  2. Fixed negative codon ruler start/stop detection.
  3. Fixed codon ruler null pointer exception when column segment selected.
  4. Fixed custom data ruler nullpointer exception when featuremap deactivated.
  5. Fixed feature highlighting obscuring sequence ruler.
  6. Added relative and genomic coordinates to splice site profile (Chinnappa Kodira)
  7. Fixed g-click bug where transcripts of different genes were being selected in some cases (Mark Borowsky)
  8. Sequence and codon ruler now detect start/stop codons case insensitvely.
  9. Custom data ruler now added to ruler after load instead of requiring explicit second step. Dialog disappears automatically.
  10. Tools -> Show Edge Frames (Jade Vinson)
  11. Poly A window no longer resizable. Smartly sizes up to 20 rows, then scrollpane (Mark Borowsky)
29 2003-07-25
  1. Fixed custom data ruler sp -> px. Was displaying loaded x coordinates wrong. (Mike Kamal)
  2. Fixed GC percent ruler breaking on small sequences.
  3. Fixed selectable column creation by dragging on ruler when you are on segments that don't start at 1 (Charlie Whittaker)
  4. G clicking an exon now selects the gene. You used to have to g click the transcript. (Mark Borowsky)
  5. Border is drawn on 1 px selected features to make them stand out better.
  6. Selecting a glyph now highlights it in *all* rulers.
28 2003-07-25
  1. Added new top level menu: Rulers
  2. Custom Data Rulers basically work. If you have an input file in x tab y1 tab y2 *or* x tab y format, where x is the nucleotide position a y is a score of some kind, Rulers->Custom Data Rulers->Edit->Load will load it onto the current sequence. Check the checkbox that appears to add the ruler to the column header. (Mike Kamal)
  3. Export -> FASTA trascript defline sometimes null bug fixed (Charlie Whittaker)
  4. Export -> Protein FASTA now is orf instead of entire MRNA (Charlie Whittaker)
  5. Fixed selectable column height bug (Charlie Whitacker)
  6. Create Selectable Column Drag Mode now works (Elia Stupka)
  7. When you export features to a file, the file filter now always shows directories, even if files are filtered by some criteria (James Galagan)
  8. +/- keys now zoom without control chord (James Galagan)
  9. GFF labels are cobbled together from type and location (James Galagan)
  10. Menu Arrow key order fixed (James Galagan)
  11. Fixed Map Options save bug
  12. GFF/GBK segment filtering
  13. Nicer names for Track Managers ("BlahBlahTM" -> "Blah Blah Track Manager")
27 2003-07-09
  1. Added control E accelerator for Export
  2. Added mRNA and protein fasta feature export (Charlie Whittaker, Chinnappa Kodira)
  3. Export features now give option to export to file or screen (Charlie Whittaker, Chinnappa Kodira)
  4. Fixed minimizing removing window from windows menu (Chinnappa Kodira)
  5. Fixed create selectable column for subfeatures being off (James Galagan)
  6. Directory of last file opened in file chooser is remembered (James Galagan)
  7. Yellow highlighted column may be made selectable from sequence panels (James Galagan)
  8. Fixed global tracks not listing bug (Serge Smirnov)
  9. Assign proper GFF ids (so mark feature among other things works with them) (Mike Kamal)
  10. Fixed GFF feature track filter (was showing all tracks, even if not selected) (Mike Kamal)
  11. GFF . for strand read as Strand.NONE and displayed properly (Mike Kamal)
  12. Made translation case insensitive to handle soft masked sequences (Mike Kamal)
  13. Fixed last sequence in fasta file being ignored bug (Mike Kamal)
  14. Set minimum selectable sequence column width to 1 px
26 2003-06-30
  1. Replaced vertical zoom click mode with vertical collapse, expand and zoom to fit zoom menu items (James Galagan)
  2. Moved track attachment ui from sequence tree to track options dialog (much clearer) (James Galagan, Mike Kamal).
  3. Custom Sequence Manager takes a custom trackmanager in constructor (necessary because of above UI change)
25 2003-06-27
  1. Hide/Mark all "contained" evidences (Mark Borowsky)
  2. Standard, more sensible arrangement of properties in inspector window (standard come first) (Chinnappa Kodira)
  3. Fixed broken track sort (Sinead O'Leary)
  4. Genbank -- fixed features display multiple times in map.
  5. Genbank/GFF -- fixed track color not updating in session.
  6. Genbank: smarter about taking default colors from calhoun
  7. Genbank: fixed subfeature inspection null pointer error
  8. Genbank: grab label from 'gene' field is no name.
  9. Genbank: remove quotes from properties.
  10. Genbank: ignore features with locations outside of current sequence. (James Galagan)
  11. Show segment bounds rather than sequence bounds in feature map.
  12. Got rid of last biojava/xerxes dependencies. Smaller jar means faster download and startup.
  13. Fixed sort of curation flag groups (Chinnappa Kodira)
  14. Transcript strands may now be updated (gene will change too) (Mark Borowsky)
24 2003-06-23
  1. Fixed delete transcripts (Charlie Whittaker)
  2. Fixed save selected Orf (Charlie Whittaker)
  3. Seq Path Data Manager works again (Shuli Yang)
  4. Fixed strange loading of polyA and selection after save selected orf
  5. Fixed add polyA signal nullpointer exception (Charlie Whittaker)
  6. API change: added open/close DataManager registries (so you can prevent the defaults from loading). Added AnotherCustomWrapper to show how to do this.
  7. Clear indication when open by sequence id/accession does not find anything (Chinnappa Kodira)
  8. Fixed don't connect to calhoun option.
  9. Fixed select evidenced.
  10. Control click deselects selected features (Mark Borowsky)
  11. Fixed local track listing overriding global.
23 2003-06-16
  1. Added FastA Sequence Manager.
  2. Removed DAS on the broken windows principle.
  3. Only tracks which are relevant for given sequence are shown in track options for calhoun track manager (Shunguang Wang)
  4. Only tracks which are relevant to given sequence are queried (should result in a performance boost for those who don't tweak their tune their track options to every sequence)
  5. When no feature map is open and a sequence is selected in the sequence tree, show track options for that sequence when track options are opened (formerly showed global tracks).
  6. Obsolete preferences are removed up import (current prefs are cleared). This makes for less junk in prefs file.
  7. References to oracle changed to calhoun, in anticipation of other oracle based data sources.
  8. Tabbed pane in track options makes it easier to deal with multiple track managers.
  9. Sequence to track manager association unobtrusively and generically done by right click menu in sequence tree UI (was formerly hard coded for gff in track options)
  10. API change: bio concept classes moved from db package to model package. db package is for now just classes that handle persistance. Model suffix removed (long and now redundant)
  11. API change: globally accessibly static TrackManager and SequenceManager instances make it easy for custom wrapper classes to add track and sequence managers to applicaiton (Sarah Calvo, Mike Zody, Mike Kamal).
  12. API change: all remaining references to 'type' changed to 'track'.
  13. API change: unclear and over specific 'Annotation' renamed to more generic sounding 'Property.'
  14. API change: monolithic DataManager interface broken into 3 parts: TrackManager, SequenceManager, and (very rough) FeatureFinder. Why? Because some data sources only provide features (GFF) and others only provide sequence (fasta). You can still have a single class that implements both, or (to keep class size small, as I prefer) feed your sequence manager to your track manager in the constructor if the tracks don't make sense apart from the sequence. FeatureFinder is where I tucked to calhoun oracle search code for now. I wouldn't recommend implementing that interface. It will change. At the moment it's very sql specific.
  15. Skeletal wrapper class and data managers provided as examples for people who want to write their own data managers and plug them in (documentation and some more meat on the bone to follow this afternoon)
22 2003-06-05
  1. Shift Map Action is Cancelable (Chinnappa Kodira)
  2. Shift Map Action presents english direction rather than numeric key code (Chinnappa Kodira)
  3. Select Transcript from PolyA (same way as with primary evidence)
  4. Select PolyAs for transcript
  5. GFF import: fixed no such element error.
  6. GFF import: get type from source rather than method.
  7. GFF import: now supports eukarotic features (creates virtual transcript features based on group field)
  8. Feature Table off by FASTA header (Mark Borowsky)
  9. PolyA insert checks to see if in same location (Chinnappa Kodira)
  10. Fixed polyA deletion refresh (Chinnappa Kodira)
21 2003-05-29
  1. Added drop down list of transcript retirement codes (Mark Borowsky).
  2. Fixed polyA signal off by fasta header bug (Chinnappa Kodira)
  3. Fixed GFF output format bugs. Can now be fed to gff2ps.
  4. Fixed initial zoom jump (was drag zooming on minimal drag)
  5. Fixed hide/unhide mark/unmark so that they do not mess up matching intronic edges view. Mark/unmark hide/unhide is also faster. (Mark Borowsky)
  6. Transcript accession is now shown at top of update dialog
  7. Click zoom in alignment plot rather than slider zoom
20 2003-05-15
  1. Edit exon boundaries in dna sequence panel. Highlight and right click to make intronic/exonic. (Chinnappa Kodira)
  2. Added select marked action to select menu.
  3. File -> Export option. Only supported output format is gtf2. Note that the frame column is always 0 right now because I wasn't sure what this meant. I called pretty much everything a CDS, which I don't think is right. Exons that are not annotated genes have their parent id as transcipt id, and 'NA' as gene id. Simple features are done in vanilla gff, which I assume is OK in a GTF2 file. (Chinnappa Kodira).
  4. Sequence input window now handles spaces and other non integers more gracefully (Chinnappa Kodira)
  5. Select primary evidence for selected transcript and vice versa. It's in the select menu. (Chinnappa Kodira)
  6. Delete option only shows up when deletable selections are selected (was showing up when anything was selected before, even if you couldn't actually delete it).
  7. Exons can be deleted in the featuremap (Chinnappa Kodira)
19 2003-05-08
  1. Sequence Panel reading frame checkboxes are now radio buttons. Defaults to default selected orf frame. (Mark Borowsky)
  2. Alignments: got in map subfeature drawing to work (Shuli Yang)
  3. Major menu overhaul: all featureMap right click and keyboard actions are now available through the top menu. All menu items have mnemonics, frequently used have keyboard accelerations. I thought a lot about the organization, but if something strikes you as irrational, please let me know. Please note: some keyboard shortcuts and menu item descriptions have changed.
  4. SequencePanel: tooltip coordinates were off by fasta header lenght. Save highlighted off by header length. Select click to stop off by header length. Fixed. (Charlie Whittaker, Mark Borowsky))
  5. Preference import: got favorites to refresh without restart.
  6. Fixed center selected wiggling (Charlie Whittaker, Mark Borowsky)
18 2003-04-28
  1. Preferences can now be imported without restart (Mark Borowsky)
  2. Added rowSpacing to Style (Shuli Yang)
  3. Login dialog, X quits instead of acting like "Don't" option (Shunguang Wang)
  4. Prettier Alignment plot: zoom using slider, show aligned sequences as row/column headers, scrollbars.
  5. Alignment parameters are (marginally) prettier, can be set, are stored to prefs.
  6. Segment lengths are no longer stored to prefs on open by feature accession (Charlie Whittaker)
  7. Fixed splice site profile bug introduced last release. Yellow display in featuremap was off by fasta header length. (Charlie Whittaker)
  8. Added 50% buffer to feature map segment opened by feature accession number (Charlie Whittaker)
  9. Shift arrow navigation works more consistantly (keyevents were being ignored before under some circumstances)
  10. Drag and drop alignments are drawn in featuremap. Note that this works for simple features and compound features but NOT yet for subfeatures (thanks Shuli Yang!)
17 2003-04-18
  1. Intron edge grouping (Mark Borowsky)
  2. Fixed case sensitve gene accession type in (Charlie Whittaker)
  3. FASTA headers in sequence panel (Mark Borowsky, Chinnappa Kodira)
  4. Fixed right click featuremap bug on mac
  5. Alignment wrapper code to give sequencemodel + alignment info (Shuli Yang)
  6. The world's simplest alignment dot plot (Everybody)
  7. The world's ugliest alignment parameter display
  8. Open gene correctly from accession number (Chinnappa Kodira)
  9. Alphabetize evidence features in transcript edit panel (Chinnappa Kodira)
  10. Fixed scroll jump after insert/update transcript (Charlie Whittaker, Chinnappa Kodira)
16 2003-04-09
  1. View Session history (features selected) with control-H (Mark Borowsky) or via Go menu. Note this is currently very ugly you have to reopen the window for it to refresh). What do we want to happen when you select a feature?
  2. Hide/Unhide Features for session(via History panel) (Mark Borowsky)
  3. Mark/Unmark Features for session(via History panel) (Mark Borowsky)
  4. Use genetic code associated with sequence in rulers (was hard coded). (Shuli Yang, Chinnappa Kodira)
  5. Catch Alignment errors and display message instead of silently failing (Andrew Zimmer, Mike Kamal)
  6. Alignment compares transcripts of compound features rather than compound start-stop (Chinnappa Kodira, Andrew Zimmer, Mike Kamal)
  7. Ruler highlighting now works again at distant zoom (was only working when sequence alphabet became visible)
  8. Keyboard zoom shortcuts. 1-9 zooms to absolute 100-900%. 0 zooms to sequence. +/= key zooms in. -/_ key zooms out. ~/` key zooms to selection
  9. Shift featureMap along sequence by 50% of length using shift left and right arrow. Note that this reloads all data. Not terribly efficient. (Chinnappa Kodira, Sarah Calvo)
  10. Explicitely closed all remaining statments and resultsets to prevent sporadic "Maximum Number of Cursors Exceeded" error. (Chinnappa Kodira)
  11. Feature Table looks much better with horizontal scrollbar. Columns aren't so squished (Chinnappa Kodira)
  12. S-click works as advertised (did nothing before, now will normal click if clickmode is other than normal selector)
  13. Newly opened featuremaps scroll to strand divide instead of staying at top. There is an awkward pause while it jumps. Working on it. (Chinnappa Kodira)
15 2003-04-01
  1. Fixed nullpointer error when you clicked on non-oracle features (Shuli Yang)
  2. Drag and drop features to align them. Note: for now, stick with small features or you'll run out of memory. Pretty much just proof of concept right now. (Andrew Zimmer, Mike Kamal)
  3. Select (and report) click mode and drag and drop mode on toolbar (before was just a toggle button that showed 2 of 5 clickmodes). The icons need some work.
  4. Added scroll bar in splice site profile when there are more than 20 (Charlie Whittaker)
  5. Feature Table right click option dumps inspector properties for all selected features into table. One table for each type. Select row to highligh sequence in map. Easy copy and paste into excel. (Chinnappa Kodira)
  6. Keyboard feature navigation. If you select a subfeature, left arrow and right arrow select the next left/right subfeature. It wraps when you get to the end. If you select a regular feature, left/right arrow will move you to the next (by start position) feature of that type on that strand. No features are skipped, so this can be slow going. If you want to go a bit faster, control arrow click to skip to next non-overlapping feature of strand/type. As with exons, it overlaps when you get to the end of the map. Up arrow selects parent if you are on an exon. Downarrow selects the leftmost exon if you are on a parent. (Mark Borowsky)
  7. Better positioning of internal frames (no more overlap).
14 2003-03-21
  1. Fixed drag rectangle rendering (wasn't looking very rectangular)
  2. Fixed accidental drag and drop with right click zoom (Charlie Whittaker).
  3. Fixed splice site profile offset error (Mark Borowsky)
  4. Fixed curation flag loss during drag and drop and orf set updates (Charlie Whitaker, Mark Borowsky)
  5. PolyA Signal View/Insert/Delete. Right click option opens view on selections. Click on polyA in view to highlight in featuremap. If you're on an editable transcript, double click to create and insert poly A signal feature into the database. They can be deleted like other editable features. (Chinnappa Kodira)
  6. Drag and drop now works over exons (Chinnappa Kodira)
13 2003-03-13
  1. Explicit Gene assignment for annotated transcripts. Here's how it works: all genes on the currently visible segment and strand are shown. Overlapping genes are colored blue, the rest are black. Genes are sorted by start position and their coordinates are shown next to them in parentheses. By default, the first overlapping gene is selected. This is usually right because there is usually only one. For updates, the previously saves gene is selected. Both updates and inserts have a "new gene option."
  2. New right click option: open selections in new featuremap.
  3. DataSourceModel class now called SequenceGroup. NOTE: your favorites will be lost and must be reassigned as a result of this change. I could have done something smart to save them, but it should just take you a minute and it would have taken me much more than that. (Shuli Yang)
  4. Only refresh editables after insert/update/delete
  5. Keep previously selected feature selected on refresh (including update)
  6. Newly inserted features are set selected.
  7. Fixed delete cancel bug (somewhat shockingly, glyph was erased)
  8. Inspector window refreshes on feature update.
12 2003-03-07
  1. Fixed a bunch of performance issues. I think it's even better now than before last release. You can comfortably browse a megabase (though data refreshes will be painful). RAM should be the first thing you run out of.
  2. Added overlap handling option to drag and drop editing. If there are overlaps, user is prompted to choose replace or merge (Chinnappa Kodira)
  3. No more unnecessary database refresh when sequence region is deleted (Chinnappa Kodira)
  4. Fixed drag and drop permissions bug
11 2003-03-02
  1. Drag and Drop transcript editing. Drag evidence exons or simple features to an annotated transcript to insert them as exons (transcript will be extended if necessary, overlapping exons will be merged). Drag evidence transcripts/spans to annotated transcript to insert all exons, or just right or left extending exons. (Chinnappa Kodira)
  2. Minimum feature size is now 1 pixel. This provides a ton more information at distant zoom, but there is a performance hit. I'm working on it, but let me know if and how much it annoys you. Hardest hit: Scrolling is choppier for big/full regions, and drag multi selection crawls. (Charlie Whittaker,Chinnappa Kodira)
  3. p-click selects parent features instead of error prone label click (Charlie Whittaker)
  4. g-click selects genes for clicked transcript (Chinnappa Kodira)
  5. Fixed yellow highlight in negative strand (Charlie Whittaker)
  6. Transcript edit panel exon textbox is now scrollable so mega-exon genes can be accomodated (Charlie Whittaker)
  7. Fixed save ORF bug (Chinnappa Kodira)
  8. Orfs from template feature are used for new inserts (Chinnappa Kodira)
  9. Matching intronic edges are shown for both strands (Sinead O'Leary)
10 2003-02-15
  1. Refresh at vertical scrollpoint (Chinnappa Kodira)
  2. Vertical Zoom using the v key and right/left mouseclick for larger/smaller (vertical zoom is a fancy way to say adjust feature and label height) (Chinnappa Kodira)
  3. z key and right/left mouseclick zooms in and out (Charlie Whittaker) )
  4. Fixed nullpointerexception in trackoptions onOK when no segment selected.
  5. Show new primary evidence column in properties panel (Chinnappa Kodira).
  6. Fixed control is pressed highlight bug on control keyboard shortcuts (James Galagan, from a long time ago).
9 2003-02-07
  1. You can now turn feature borders on or off in Map Options. I find it looks better without (less cluttered), especially if you use the new options below.
  2. You can control label font size in map options. Setting it to 0 turns them off entirely, which reduces clutter, gets more features into a screen, and you can still easily get the label by mouseover.
  3. Feature width settings in Map Options now actually affect component width (before the invisible space alloted to the feature was constant, so if it got too big you just would see part of it anymore, etc.), so setting them tiny (and setting labels to 0) can give you a great overview of a large stretch of sequence.
  4. You can control strand background colors. Foreground (labels and feature outlines) will be complementary. This is useful because it makes it easy to see what strand you are in in segregated strand view. Default colors are white for positive/mixed, black for negative.
  5. MouseOver tooltip display for subfeatures now displays relative position followed by parent label (Chinnappa Kodira, sort of)
  6. FeatureMap now always refreshes on OK from Track options window (it wasn't before if you had a feature selected).
  7. No more FeatureMap refresh on right click Track Options cancel.
  8. Fixed subffeature positioning bug which was causing border to lose a side in negative features.
  9. Turned off sequence highlighting in Ruler for Protein sequence (Sarah Calvo, from a long time ago)
  10. DAS track color generation now a bit more sensible (they don't all look the same)
8 2003-01-30
  1. Fixed single intron splice profile bug (Chinnappa Kodira).
  2. If you try to open the splice profile on a feature without any introns, it tells you you can't, and why, instead of spewing out mysterious error messages to STDERR.
  3. If you try to go -> to protein id in a non-oracle datamanager, it tells you you can't, and why, instead of spewing as above.
  4. DasDataManagers are now actually grouped instead of merely seeming so (in other words, they kindasorta work again -- ensemble server is best) (Sarah Calvo)
  5. DAS types are now recognized. They are all colored the same by default (actually, imperceptably differently based on an idiotic algorithm involving id string length) but you can change the colors by right clicking and choosing "Feature Type Options" and set the arrangement etc.
  6. DAS feature strands are now recognized.
  7. DAS features that stretch the whole sequence are not displayed.
  8. Javadoc beefed up a bit and available here.
7 2003-01-22
  1. Left exon border is drawn again for positive start exons.
  2. Added Import/Export Preferences (as java prefs API xml file).
  3. Arranged Menus more sensibly. More intuitive hot keys.
  4. Segregated strands are now sorted towards the center instead of from the top (Chinnappa Kodira).
  5. Subsequence dialog remembers what you chose last time (Chinnappa Kodira)
  6. Better titles for many windows so they are easier to recognize in the Window menu.
  7. "Feature Options" split into "Map options" and "Track options".
  8. Fixed 1000 parent id bug in OracleDataManager. Was a problem looking at big sequences with lots of features of a given type. (Chinnappa Kodira)
6 2003-01-15
  1. Fixed >2 clicks ignored bug in Feature Map. Should reduce incidence of "what happened? I clicked, didn't I?"
  2. Find Feature Results navigation buttons now initially disabled when resultset is smaller than number to display.
  3. Feature Map right click menu now placed higher to accomodate smaller monitors (Sinead O'Leary)
  4. In transcript edit panel, made curation flag list larger (10 at a time vs 5) (Chinnappa Kodira)
  5. Changed references to "Stacked" arrangement to "Segregated." (James Galagan, Chinnappa Kodira)
  6. Cut eggregious cruft from feature map right click menu (Chinnappa Kodira)
  7. In Find Features dialog, no tracks selected by default instead of mirroring feature options preferences (Chinnappa Kodira)
  8. Find features search makes double helix activity indicator spin (Chinnappa Kodira)
  9. Sequences in sequence tree UI now properly sorted by sequence number.
  10. Find Feature dialog now doesn't list irrelevent track columns in track criteria panel.
  11. Find feature results no longer display ugly feature/sequence ids, instead they display sequence number (Chinnappa Kodira)
  12. Yellow highlighted sequence is unhighlighted when you left click somewhere else on the feature map (Sinead O'Leary)
  13. Fixed Find Feature Results copy and past bug with NULL data fields.
  14. In insert transcript panel, default transcript type is "Known" (Chinnappa Kodira)
  15. In the find feature dialog, you can now search by sequence number. You can specify a single number, multiple comma delimited numbers, a hyphenated range of numbers, or a > or < number.
  16. Sequence groups are now alphabetized.
  17. Find Feature Panel now forces you to select one or more tracks (just too slow otherwise) (Chinnappa Kodira)
  18. Find Feature dialog has combo box for strand selection instead of ambiguous text field (Chinnappa Kodira)
  19. Find Feature common criteria panel more compactly laid out.
5 2003-01-08
  1. Reverse orientation of genomic axis via Feature Options panel (it's a little checkbox at the bottom). The only thing that I can tell doesn't work properly with reverse orientation is the codon rulers. (Chinnappa Kodira)
  2. Find Feature search runs in separate cancellable thread. So you don't have to be afraid that a slow query (i.e., most of them) will take the browser hostage.
  3. Find Feature search comlumn widths and table size preserved on navigation with next/previous buttons.
  4. Insert Eukaryotic Transcript now populates name field with template feature's label if no transcript name or feature name is found. (Chinnappa Kodira)
4 2003-01-02
  1. Rudimentary Find features lets you search for features and see results in tabular format. Clicking on row opens feature in new Feature map. Note that queries will be very slow unless limited to a single sequence group. Track specific criteria are currently ignored. I'm aware that the current results table is a little ugly.
  2. Splice Site Profile available as feature map right click open as well as from DNA panel. (Chinnappa Kodira)
  3. Fixed width fonts for splice site profile.
  4. Splice site profile part of desktop pane, so you can jump to it using the window menu
  5. Splice site profile shows 3 more intronic nucleotides on each side (Chinnappa Kodira)
  6. Numered splice site profile entries (Chinnappa Kodira)
  7. Hightlight matching intronic edges as right click option in feature map (Chinnappa Kodira)
3 2002-12-17
  1. Can be run using java web start (Seth Purcell)
  2. Genetic code defaults to 1 (Cherylyn Smith)
  3. Splice Site Profile option for DNASequencePanel (Chinnappa Kodira)
  4. Open by feature id now takes gene/transcript accessions (Chinnappa Kodira)
  5. Fixed subsequence subfeature rendering bugs
  6. Graceful cancel of open by feature and sequence id
  7. Open by feature id now highlights features and defaults to their boundaries with option to enlarge
  8. Password field gets initial focus in oracle logon
  9. Fixed protein alphabet detection in desktop app (was ok in applet)
2 2002-12-05
  1. Runs on Mac OS X with beta java 1.4 (Mike Zody).
  2. Fits in a single jar file, just download and double click.
  3. Won't attempt to complement protein sequences. (Sarah Calvo)
  4. jar file lightened of various cruft.
  5. Inspector window displays curation flag, transcript type, and primary evidence labels for annoted transcripts. (Chinnappa Kodira)
  6. Oracle sql stopwatch matches stops to starts (was strange with threading before)
  7. Fixed coordinate bug in applet (Sarah Calvo)
1 2002-11-27
  1. Show version info and other meta data on startup.
  2. Fixed subfeature coordinates (now they line up better with sequence regions and yellow highlights).
  3. Show sequence editablity in inspector window (was formerly just shown for sequence groups).
  4. Show only sequence groups that have been marked fit for human consumption in ap_sequence_group_description (thanks Chris Seaman)
  5. Fixed right click type options freak out for non-Oracle features.
  6. Got rid of annoying jump of right click menu on first open.
  7. Got rid of distracting but otherwise harmless nullpointer exception on zoom to sequence/out fully.
  8. When feature options are opened on "Favorites," default to oracle rather than null.
0 2002-11-21
  1. You can specify the primary and secondary sort columns (and their sort directions) for features of each type.

Known Bugs

Known bugs (and new feature requests) are on display at Reinhard's desk (7 CC,7029G). The yellow ones are Genome Browser bugs.

Last modified: Mon Oct 24 14:38:36 EDT 2005