- Maintenance update to preserve ability to connect with calhoun database.
- Genome Map fits its window better and the image export works as expected (Christina).
- "File > Open File Sequence Tree" menu item added that brings up the initial sequence tree
when opening up multiple sequence files.
- Added location of selected feature on contig if the contig track is present (Qian).
- BAM files can be loaded remotely (Brian).
- Multiple Alignment: Line is drawn create more distinction between multiple alignment tracks (James).
- Removed internal UCSC option, since it wasn't working anyway as the database has been disabled.
- Turned off continuity renderer for multi-conservation alignments (Sharda).
- Export entire genome map when saving image (Christina).
- Genome Map's line graph is shaded like in the feature map.
- Genome map scores can be non-integer (Christina).
- Multiple Alignment: change gap color to light blue (James).
- Pending feature insert will be filled with edit color instead of just outlined (Teena).
- Plus and minus features are colored slightly differently when in combined mode (Teena).
- In auto-sized feature mode, the track size can vary independently of strand.
- Added remote BAM support (Brian).
- Added a status popup window for when data is being loaded.
- Feature density plot is created when loading in GTFs.
- Multiple Alignment: selected feature's frame will be used to calculate and show codons if zoomed in to base level (James).
- Multiple Alignment: changed non-synonymous to be a shade of blue instead of magenta (James).
- Multiple Alignment: group and ungroup projected features available to remoting.
- Fixed bug where feature on the minus strand weren't clickable when in auto-sized track mode (Allison Griggs).
- Chromo Map legend displays error if no tracks can be displayed and improved layout (Christina Cuomo).
- Multiple Alignment: Reference features will show codon markup (James Galagan).
- Multiple Alignment: Alignment track order can be set with xml (James Galagan).
- Sequence ruler shows structural features (contigs) as alternating bands of gray (Qiandong Zeng).
- Added tooltips for features (Tom Walk).
- Sizing of genome view adjusted to fit in the window; this eliminated the scrollbar when unneeded.
- Fixed ordering of track table ("view?" and "count" were flipped).
- Added group and ungroup options for multiple alignment projected features (Qiandong Zeng).
- Ends of multiple alignment projected features can be locked and unlocked independently (Qiandong Zeng).
- Moved track size menu item out of submenu (Tom Walk).
- QA Results window lists genome and updated look (Michael Koehrsen).
- Linkage Group scaffold colors can be changed (Li-Jun Ma).
- Fixed bug where Argo would continue to exit even if the user clicked "no" after closing the window (Tom Walk).
- List of sequences is limited to 100; users can select the "see more" item to show the next 100. (Brain Haas).
- Fixed bug where pinned track features would disappear when crossing from graph to feature display.
- 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).
- Multiple Alignment: Releases saved in new location (fixes bug with conflicting releases).
- Multiple Alignment: Saving, Updating, and Deleting to Calhoun added.
- Changed default sort order from Blast features (Matt Pearson)
- Remember track label divider bar location in preferences (Tom Walk)
- Fasta file indexing: fixed sporadic windows bug
- Improved feature and graph sizing/positioning
- Multiple alignment mode: show internal calhoun database feautures.
- Mutliple alignment mode: show alternating congiguous regions with thatched/unthatched texture.
- Multiple alignment mode: numerous performance enhancements.
- Fixed some resizing cosmetic issues
- Fixed codon drawing for negative stranded features
- Addded mfa/maf independent stacked conservation/diversity bar view and data manager (Patrick Charlebois)
- Fixed Featurize highlights (Jon Goldberg, Paul Godfrey)
- Graph bounds can now be explicitly set (and normalized).
- Splash screen closed after initialization
- Fixed accuracy of drag indicator
- Lots of multiple alignment stuff which the curious can admire here:
- Generic Features: display dynamic properties regardless of ontology term (Edward Freedman)
- Added Analyze -> GC% by Frame action (Allison Griggs, Qian Zeng)
- Updated help links to point to argo2 docs. (Edward Freedman)
- Fixed wiggle graph rounding when less than bin size.
- Fixed graph size bug.
- Wicked cool splash screen (thanks Christian!)
- Don't freak out with new feature types (Edward Freedman)
- Load gtf2 subfeature properties and show . strand features (David Borenstein)
- Lots of multiple alignment stuff you can preview here
- Editing: fixed right click deselecting feature bug (Tom Walk).
- Multiple Alignment Display: added convergence "diversity" mode with two color maps. Previous mode is "divergence" diversity mode.
- Zooming: fixed zoom click expands track bug.
- Editing: fixed unnecessary restacking.
- Tracks: added combined strand track option. (James Galagan, Brian Haas, Paul Godfrey)
- Editing: fixed 0 rowsize expanded tracks (Tom Walk).
- Editing: fixed stacking bugs that were caussing mouse position errors with overlapping edited features and sodd behavior with strand switches (Tom Walk).
- Row size: fixed just introduced minimum track size/row size confusion.
- Graphs: graph size now separate from row size.
- Track right click options: feature and graph specific options organized into submenus.
- Calhoun Database: blast cluster queries much faster, especially on big sequences. (Matt Pearson, Brian Haas)
- 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).
- Broad public database: argo can take authentication cookie from jnlp to display protected data.
- Numpad +/- on windows: I really think I got it this time. Allison?
- Graphs: toggle log mode. Show actual values on mouseover even in log mode. (David Borenstein, James Galagan)
- Calhoun Database: move blast cluster queries to separate connection. Still slow, but they don't block everything else. (Matt Pearson, Brian Haas)
- Calhoun Database: restored "connecting..." indicator in status bar.
- Calhoun Database: get sequence groups on initial connect rather than first featuremap open (same wait, more appropriate time)
- Calhoun Database: default threshold for blast cluster back to regular features -- too much overhead per query.
- Numpad +/- on windows: another stab... plus some debugging output.
- Graph Style: Line graph is now way cooler looking (shaded google finance style). Now the default graph style. (David Borenstein)
- 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.
- Calhoun Database: made a number of performance tweaks. Blast clusters are still pretty horrid -- working on it. (Matt Pearson, Brian Haas)
- Numpad plus on windows resizing instead of zooming fixed (I think -- Tom and Allison please let me know)
- 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)
- Broad Public Sequences: added rudimentary file based cacheing. (James Galagan)
- 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)
- 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)
- Divergence mode: fixed case sensitivity bug.
- 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.
- Track Table: fixed strange bug that was only (but consistantly!) happening on Sharvari's machine. (Sharvari Gujja)
- 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)
- 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)
- 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)
- Track Management: fixed row height being remembered in preferences.
- Ruler Tracks: fixed "expand" option being available and then behaving strangely.
- Calhoun Database Editing: fixed bug that was causing pending insertion tracks to blip out (Tom Walk).
- 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)
- Crude Navigation Panel: so it's more obvious to new users how to
do basic zoom and pan. (James Galagan)
- Track Tooltips: to make it clear that collapsed tracks can be clicked to
be expanded, and show score/min/max of graphs. (James Galagan)
- Track Management: single click expands collapsed track instead of
having to double click.
- Cleaned up some wasteful debug.
- Keyboard Shortcut cheat sheet: contains most shortcut information (hit ? to see it or use the Help menu)
- Tracks: row resize: fixed so that expansion toggle isn't triggered.
- Tracks: arrow: fixed no longer showing up when set to size 5px (James Galagan)
- Tracks: row resize: changed bigger/smaller keyboard shortcut to control/command + and - to be more consistent with other apps
- Divergence Base Renderer: show for single row colapsed tracks so you don't have to expand (Sean Sykes)
- Tracks: expand to expands collapse rows even if only to 1
- Wiggle and Tab value tracks: fixed recent screw up.
- Help: keyboard shortcut "cheat sheet" now has some information.
- MAQ conversion tweaks: problems remain, but was able to process Brian's data. (Brian Weiner)
- Divergence Renderer: show Ns and other non-ATGCs. Fixed recently broken deletions not showing.
- Tracks: set rows visible shortcut is alt-r instead of control-r because the latter was already taken./li>
- Help: first cut at keyboard shortcut "cheat sheet." Looks gorgeous -- now we just have to fill it in with the actual information.
- Calhoun Feature Store: convert from file no longer shows negative total feature count with files over 2 GB (David Borenstein)
- RNA sequence panel: pass on calculated ORFS for viewing in feature map (Tom Walk)
- Divergence Base Renderer: colors consistent with sequence ruler. Show (crude) "diff mode" heatmap in collapsed state (Mike Koehrsen)
- Tracks: added explanatory tooltips over expansion state widgets (James Galagan)
- Tracks: fixed explicitly save number of tracks rows even if matches current setting
- 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)
- Tracks: fixed load tracks causing top level menus to disappear.
- 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)
- Tracks: added an "r" keyboard short cut to bring up the manage visible rows window. Hitting return presses OK button.
- Tracks: you can now rename tracks from the right click track menu.
- Tracks: Track table now lets you filter by track name substring.
- Sequence Tree: now lets you filter by sequence group substring
- RNA Sequence Panel: fixed non-editable features not showing reset ORFs in feature map. (Tom Walk)
- Genome Map: works again. (Mia Champion)
- Tracks: added (+) or (-) to track label for extra clarity
- 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.
- Editing: restored auto scroll when dragging evidence (Tom Walk)
- Editing: Progene: added "transpose" as a suggested name in the drop down (Qian Zeng)
- Editing: Progene: fixed truncate whitespace around gene name (Qian Zeng)
- Editing: Progene: give focus to gene name rather than symbol (Qian Zeng)
- RNA Sequence Panel: auto set ORFs after selection instead of making this a confusing 2 step process (Qian Zeng, Jon Goldberg)
- Calhoun PolyLocus Tracks: removed Solexa filtering that was hiding critical tracks (Sean Sykes)
- 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)
- Calhoun Feature Store: added compress action. Bundled all CFS actions into Calhoun Feature Store submenu.
- 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.
- Zoom Scrollbar: fixed some recetly introduced cosmetic issues with the control point lines
- Feature Map Desities: fixed positive strand not respecting minimum track height.
- Tracks: Pin to Ruler now supports multiple tracks. (Allison Griggs, Jon Goldberg)
- Genbank Format: tracks show up. (Anjan Purkayastha)
- Wiggle Format: fixed min and max set to rebinned values rather than native data scale.
- BAM: show human releable sequence name in problem for multi sequence BAM files. (Rob Nicols)
- Feature Map Options: show hex color code in color buttons.
- Start/Stop Codons: Added Feature Map Options to set colors (Tom Walk)
- Sequence Ruler: Added Feature Map Option to set Sequence Ruler Style to Base (default) or Codon (like in argo1) (Sharvari Gujja)
- Feature Map: Density Drawing bounded by minimum track size if less than row size so you can safely set row size to something tiny
- Calhoun Feature Store: added uncompress option to deal with problematic compressed files.
- Calhoun Feature Store: add feature names to CFS export. (Sean Sykes)
- BAM: fixed not being able to process non paired read features (Sean Sykes)
- MAQ: fixed duplicated id error./li>
- Tracks: raised minimum track size so you can collapse big stacks without making track labels illegible. (James Galagan)
- 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).
- Tracks: fixed bug with minimum density value being set to 0 if only one track of data.
- Keyboard Shortcuts: fixed . zoom to selected (Chandri Yandava)
- 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)
- BAM to CFS conversion: fixed multi sequence BAM conversions running out of memory (Michael Koehrsen)
- MAQ to CFS conversion: fixed SNP bug (no single base features) (Michael Koehrsen)
- 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.
- Clearer in-featuremap error messages. Like "Zoom in to see SAM features" instead of "ERROR"
- Calhoun Open by Feature Id: provide context when re-using open map. (Allison Griggs)
- Calhoun Feature QA Analysis: more concise error messages instead of full stack trace (Allison Griggs)
- Menu Shortcuts: fixed double action firing bug with some of these -- in particular, double + and - zoom. (Tom Walk)
- Calhoun Sequence Tree: fixed sorting so it's case insensitive. Show the id that's being used to sort first. (Tom Walk)
- Memory: Garbage Collect after every feature map close (and open). If nothing else, should make it clearer what is going on. (Tom Walk)
- Analyze: added Cumulative GC Skew (Paul Godfrey)
- CFS Converter: fixed compression bug. Rudimentary support for MAQ SNP and MAQ Map formats. Faster approximate feature counting for BAM.
- Wiggle Format: fixed density display bug (Paul Godfrey)
- Calhoun Feature Id Dialog: added checkbox to indicate whether or not existing feature map should be re-used (Chandri Yandava)
- Feature Arrow Renderer: made more symetrical. Got rid of unintentional "3D" effect. Labels no longer obscure strand indicators.(Teena Mehta)
- Feature RoundRect Renderer: labels no longer obscure strand indicators. (Teena Mehta)
- BAM to CFS converter: split multi sequence BAM files into multiple single sequence CFS files. (David Borenstein)
- 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.
- GC Percent: added action to generate but something seems off for this and GC skew on some sequences. Investingating... (Paul Godfrey)
- Divergence String Base Renderer: deletions now show. Fixed mousevers. Minor performance enhancements. (David Borenstein)
- (rare) "Future" error: suppressed this since it doen't seem to matter. (David Borenstein)
- Tracks: fixed track control widget not initially realizing it needs to show expansion stuff when zoomed exactly to 1 px = 1 base.
- Wiggle Format: added basic support (Paul Godfrey, Brian Haas)
- GC Skew: works again except no rebinning yet -- percent and cumulative will be next. (Paul Godfrey, Brian Haas)
- Divergence String Base Renderer: more memory efficient. (David Borenstein)
- Feature/Raw Sequence Loader: got rid of preloading bins (premature and counterproductive optimization) and reduced cache size to save memory.
- 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)
- Zoom to Coordinates: undocumented shortcut is # keystroke (David Borenstein)
- Zoom to Feature: ROLLED BACK fixed rounding bug that sometimes contract view when zooming to tiny features. Broke more than it fixed.
- BAM Format: File -> Create Calhoun Feature Store lets you create a file argo can efficiently handle from gigantic BAM files.
- Broad Public Data: More clearly indicated that this is public data vs. internal (Mike Zody)
- Feature Map: fixed mousewheel focus being set on new window when it opens.
- Feature Map: really fixed (again?) highlight column size bug
- Zoom to Feature: fixed rounding bug that sometimes contract view when zooming to tiny features
- Feature Map: fixed sporadic unnessessary track bin reloads (aka "spaz loading bug")
- Feature Map: fixed minor locking issue that might make UI a little more responsive under heavy load.
- 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.
- Feature Map: cancel pending densitty plot loads if map is closed
- Tracks: expanding an already expanded track now sets to max visible rows if not there already.
- Tracks: added expanded all tracks (shift-e) and collapse all tracks (shift-c) shortcuts (Chandi Yandava)
- Feature Map: fixed feature map memory not being de-allocated on tab or window close (Tom Walk)
- Feature Map: fixed selection highlight column being truncated (Jon Goldberg)
- Calhoun Database: fixed BLAST feature links (Tom Walk)
- Calhoun Feature Store (CFS): convert CIGAR strings and Read sequence into Divergence Strings (James Galagan)
- Tracks: fixed alt-space shortcut to select all tracks
- 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)
- Tracks: fixed track label mouseclicks not being received with very large number of tracks (Brian Haas)
- 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)
- Webstart: support for isInternal flag
- Feature map: fixed repaint issue with scroll zoom on some machines
- Feature Map: fixed expanded tracks not redrawing until scroll if partially offscreen (Michael Koehrsen)
- 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)
- Edit: restored drag and drop cursors (Jon Goldberg)
- Feature Map: fixed scroll bar sizing bug on windows (Allison Griggs)
- Feature Map: switched shift page up and page down panning to make down downstream and up upstream.
- Tracks: Sort and Filter are now right click options on track label.
- Feature Map: fixed sorting of non-calhoun features
- Feature Map: P selects parent feature (Allison Griggs)
- GTF2/GFF3: show ORFs in feature map by default (Jared White)
- Feature Map: fixed obscure stack size reporting bug
- File -> Load Tracks: fixed isEnabled bug that was preventing enabling when feature selected
- Feature Map: removed misleading + from zoom cursor (misleading because it also - zooms with right click) (Jared White)
- Edit: fixed rollback refresh issues (Jon Goldberg)
- Edit: edge dragging in featuremap works again (Jared White, Tom Walk)
- Edit: removed edit caching for now. More trouble than it was worth. Will reconsider later (Jared White)
- Edit: fixed pending update mousever/stacking bug.
- Tracks: random colors can be chosen for tracks (Brian Haas)
- Feature Map: - feature map opened initially to center strand (Paul Godfrey)
- Feature Map: Shift + page up will pan up (right), shift + page down will pan down (left) (Allison Griggs))
- 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).
- Edit: edit dialogs are now non modal so you can click on other stuff while they are open (Allison Griggs)
- Edit: fixed track resizing after insert (Allison Griggs)
- Feature Map: fixed resizing (Tom Walk)
- Feature Map: got rid of goofy big hand on windows for alt drag
- Tracks: indicate expansion state more clearly with darker gray background
- Tracks: indicate mouseover track with border.
- Feature Map: fixed graph mouseovers working like in argo1
- Feature Map: fixed individual feature mouseovers working like in argo1 (Jon Goldberg)
- Edit: Fixed keyboard shortcut for save not always working (Allison Griggs)
- Feature Stacking: fixed concurrent modification exception with non-bitmap stacker. Also use sligntly faster lists instead of rangemaps.
- Graph Renderers: fixed sporadic array out of bounds when zooming out with mouse scroll.
- 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)
- Tracks: keyboard shortcut '0' will hide empty tracks/rows for selected tracks. Quick way to compact your featuremap without losing data..
- Tracks: fixed selection indication showing in featuremap even for hidden tracks.
- Edit Keyboard Shortcuts: fixed insert, update, and delete keyboard shortcuts not always working. Make backspace also delete. (Allison Griggs)
- Edit: fixed convert to single exon gene action nullpointer
- 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)
- Calhoun Database: support for SAMPSTAT features (Jared White)
- Feature Selection: fixed single subfeature click so it selects parent. Also made select child/parent actions update inspector. (Sharvari Gujja, Chandri Yandava, Clint Howarth, )
- Feature Selection: fixed collapsed subfeatures not being selectable (Zehua Chen, Tom Walk)
- Tracks: selected tracks now highlighted in feature map (Allison Griggs)
- Tracks: space bar in feature map now selects track. Alt space selects all tracks.
- 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.
- Calhoun Database: Open Calhoun by Calhoun Feature Id now reuses current map instead of opening new map if possible (Tom Walk)
- Feature Map: Right click popup menu restored (Tom Walk)
- Pending Inserts: fixed disappearing in expanded mode (Tom Walk, Zehua Chen)
- Track Label: Added rest of styles, also added track table menu item (Allison Griggs)
- Feature Style: added argo1-like arrow style.
- Feature Label Positions: added option to set to NONE or CENTER (TOP pending).
- Feature Map Options: set default styles for feature, graph, and base styles. Also label position.
- Insert Progene: fixed isEnabled logic
- Tracks: track order is now saved to preferences after drag and drop
- Tracks: positive strand track label now positioned at bottom
- Track Table: fixed null pointer if feature selected when track table opened (Clint Howarth)