/***************************************************************************** ****************************************************************************** ***** ***** ***** RSTYPES.H v1.1 ***** ***** Copyright (c) 1990 by Joyce C. Miller. All Rights Reserved. ***** ***** ***** ***** This header file contains TYPE DEFINITIONS and SYMBOLIC CONSTANTS ***** ***** required by the RESTSITE programs, which analyze restriction site ***** ***** and fragment data. ***** ***** ***** ****************************************************************************** *****************************************************************************/ /***************************************************************************** ** SYMBOLIC CONSTANTS ** *****************************************************************************/ #define MAXSTRLEN 255 /* maximum length of text line */ #define FILELEN 50 /* maximum length of a file name */ #define PREWORDS 8 /* number of items on line before frag data */ #define IDLEN 9 /* max. length of ID number */ #define KEYLEN 21 /* max. length of genus/species */ #define PRBLEN 9 /* max. length of probe name */ #define ENZLEN 9 /* max. length of enzyme name */ #define NUMFS 50 /* max # fragments or sites per individual */ #define MAXFS 50 /* max # frags or sites per prb/enz combination */ #define MAXOTU 200 /* max # OTUs allowed */ #define MAXPEC 500 /* max # probe/enzyme combinations allowed */ #define MAXRVS 10 /* max # of enzyme classes (diff sized restr sites */ #define TEST 0.000001 /* test value for iterative equations */ #define BOOTSTRAP 200 /* number of bootstrap cycles */ #define FLLMT 1000 /* maximum number of files made by program WRITETXT */ #define CALCG sqrt(sqrt(F*(3-2*G1))) /* function to compute G2 */ #define prbmatch ((strcmp(t.prb,d.prb)) == NULL) /* do probes match? */ #define enzmatch ((strcmp(t.enz,d.enz)) == NULL) /* do enzymes match? */ #define rvmatch (t.rv == d.rv) /* do site sizes match? */ #define treatmatch (prbmatch && enzmatch && rvmatch) /* treatments match? */ /***************************************************************************** ** TYPE DEFINITIONS ** *****************************************************************************/ /********************* RECORD STRUCTURE FOR THE DATABASE ********************/ typedef struct { /* structure that contains all info: */ char id[IDLEN]; /* ID number */ char key1[KEYLEN]; /* sorting key 1 */ char key2[KEYLEN]; /* sorting key 2 */ char key3[KEYLEN]; /* sorting key 3 */ char key4[KEYLEN]; /* sorting key 4 */ char prb[PRBLEN]; /* probe */ char enz[ENZLEN]; /* enzyme */ float rv; /* size of recognition site */ float f[NUMFS]; /* number of fragments or sites found */ } fragdat; /* TOTAL SIZE: 316 bytes */ /*********** RECORD STRUCTURE FOR FRAGMENT/SITE AND ITS FREQUENCY ***********/ typedef struct { /* structure that holds pooled info about frags/sites */ float f; /* fragment or site */ int no; /* number of occurrences of that frag/site */ } fragsite; /* TOTAL SIZE: 6 bytes */ /******************* RECORD STRUCTURE FOR THE POOLED DATA *******************/ typedef struct { /* structure that contains pooled data: */ char otu[KEYLEN]; /* OTU */ char prb[PRBLEN]; /* probe */ char enz[ENZLEN]; /* enzyme */ float rv; /* size of recognition site */ fragsite fs[MAXFS]; /* info on different fragments or sites found */ long tn; /* total number of sites/fragments found in this OTU */ int ni; /* number of individuals */ } pooldat; /* TOTAL SIZE: 350 bytes */ /******************** RECORD STRUCTURE FOR THE OTU NAMES ********************/ /* List of all of the OTU names found in the datafile(s) */ typedef char otuname[KEYLEN]; /* TOTAL SIZE: 21 bytes */ /************ RECORD STRUCTURE FOR THE PROBE/ENZYME COMBINATIONS ************/ typedef struct { /* structure containing "treatment" */ char prb[PRBLEN]; /* probe */ char enz[ENZLEN]; /* enzyme */ float rv; /* size of recognition site */ } treatment; /* TOTAL SIZE: 22 bytes */ /***************** RECORD STRUCTURE FOR THE ENZYME CLASSES ******************/ typedef struct { /* structure with info for each OTU/OTU comparison */ float rv; /* size of enzyme's recognition site */ int nt; /* # of treatments w/in this enzyme class */ float xmx; /* Within-population Nx for OTU X */ float xmy; /* Within-population Ny for OTU X */ float xmz; /* Within-population Nxy for OTU X */ float ymx; /* Within-population Nx for OTU Y */ float ymy; /* Within-population Ny for OTU Y */ float ymz; /* Within-population Nxy for OTU Y */ float mx; /* # of frags/sites in OTU X */ float my; /* # of frags/sites in OTU Y */ float mz; /* # of frags/sites in common */ } rclass; /* TOTAL SIZE: 42 bytes */ /***** ARRAY TO HOLD m-HAT AND Mxy FOR EACH PEC, FOR USE IN JACK & BOOT *****/ typedef struct { float rv; /* r for this treatment */ float xmxy; /* (Mx + My) for within-OTU X for this PEC */ float xmz; /* (Mxy) for within-OTU X for this PEC */ float ymxy; /* (Mx + My) for within-OTU Y for this PEC */ float ymz; /* (Mxy) for within-OTU Y for this PEC */ float mxy; /* (Mx + My) for OTU X vs. OTU Y for this PEC */ float mz; /* (Mxy) for OTU X vs. OTU Y for this PEC */ } bjtrt; /* TOTAL SIZE: 16 bytes */ /***************** TEMPORARY STRUCTURE USED TO HOLD RESULTS *****************/ typedef struct { /* structure to hold results from both analysis */ float rv; /* r for each enzyme class, or "0" for weighted results */ float xm; /* for OTU X: m-hat for each enzyme class, or weighted m-hat */ float ym; /* for OTU Y: m-hat for each enzyme class, or weighted m-hat */ float zm; /* for X-Y: m-hat for each enzyme class, or weighted m-hat */ float xS; /* within-population S or F for OTU X */ float yS; /* within-population S or F for OTU Y */ float zS; /* between-population S or F for X-Y comparison */ float AS; /* corrected between-population S or F for X-Y comparison */ float xSse; /* standard error for within-population S or F for OTU X */ float ySse; /* standard error for within-population S or F for OTU Y */ float zSse; /* standard error for between-population S or F for X by Y */ float ASse; /* s.e. for corrected between-population S or F for X by Y */ float xp; /* within-population p or d for OTU X */ float yp; /* within-population p or d for OTU Y */ float zp; /* between-population p or d for X-Y comparison */ float Ap; /* corrected between-population p or d for X-Y comparison */ float xpse; /* standard error for within-population p or d for OTU X */ float ypse; /* standard error for within-population p or d for OTU Y */ float zpse; /* s.e. for between-population p or d for X-Y comparison */ float Apse; /* se for corr'd between-population p or d for X-Y comparison */ float xJC; /* within-OTU X Jukes-Cantor distance */ float yJC; /* within-OTU Y Jukes-Cantor distance */ float zJC; /* between-OTU X & Y Jukes-Cantor distance */ float AJC; /* corrected between-OTU X & Y Jukes-Cantor distance */ float xJCse; /* s.e. for within-OTU X Jukes-Cantor distance */ float yJCse; /* s.e. for within-OTU Y Jukes-Cantor distance */ float zJCse; /* s.e. for between-OTU X & Y Jukes-Cantor distance */ float AJCse; /* se for corrected between-OTU X & Y Jukes-Cantor distance */ float xNL; /* within-OTU X Nei-Li distance */ float yNL; /* within-OTU Y Nei-Li distance */ float zNL; /* between-OTU X & Y Nei-Li distance */ float ANL; /* between-OTU X & Y Nei-Li distance */ float xNLse; /* s.e. for within-OTU X Nei-Li distance */ float yNLse; /* s.e. for within-OTU Y Nei-Li distance */ float zNLse; /* s.e. for between-OTU X & Y Nei-Li distance */ float ANLse; /* s.e. for between-OTU X & Y Nei-Li distance */ } results; /* TOTAL SIZE: 144 bytes */ /************** STRUCTURE TO HOLD # OF TREATMENTS IN EACH S.E. **************/ typedef struct { float xSnt; /* # treatments that go into the OTU X S-hat s.e. */ float ySnt; /* # treatments that go into the OTU Y S-hat s.e. */ float zSnt; /* # treatments that go into the OTU X by Y S-hat s.e. */ float ASnt; /* # treatments that go into the corrected S-hat s.e. */ float xpnt; /* # treatments that go into the OTU X p-hat s.e. */ float ypnt; /* # treatments that go into the OTU Y p-hat s.e. */ float zpnt; /* # treatments that go into the OTU X by Y p-hat s.e. */ float Apnt; /* # treatments that go into the corrected p-hat s.e. */ float xJCnt; /* # treatments that go into the OTU X d-hat s.e. */ float yJCnt; /* # treatments that go into the OTU Y d-hat s.e. */ float zJCnt; /* # treatments that go into the OTU X by Y d-hat s.e. */ float AJCnt; /* # treatments that go into the corrected d-hat s.e. */ float xNLnt; /* # treatments that go into the OTU X d-hat s.e. */ float yNLnt; /* # treatments that go into the OTU Y d-hat s.e. */ float zNLnt; /* # treatments that go into the OTU X by Y d-hat s.e. */ float ANLnt; /* # treatments that go into the corrected d-hat s.e. */ } bjnt; /* TOTAL SIZE: 64 bytes */ /****************************************************************************/