static void prettyplot_fillinboxes(ajint numseq, ajint length, ajint seqstart, ajint seqend, ajint start, ajint end, ajint numres, ajint resbreak, AjBool boxit, AjBool boxcol, AjBool consensus, float ystart, float yincr, const AjPSeqCvt cvt) { ajint count = 1; ajint gapcount = 0; ajint countforgap = 0; ajint table[16]; ajint i; ajint j; ajint k; ajint w; ajint oldfg = 0; ajint oldcol = 0; ajint l; float y; char res[2]=" "; AjPStr strcon = NULL; char numberstring[10]; float defcs = 0.; float curcs = 0.; /* ajDebug("fillinboxes numseq: %d length: %d\n", numseq, length); ajDebug("fillinboxes start: %d end: %d seqstart: %d seqend; %d\n", start, end, seqstart, seqend); ajDebug("fillinboxes numres: %d resbreak: %d\n", numres, resbreak); ajDebug("fillinboxes boxit: %B boxcol: %B consensus: %B \n", boxit, boxcol, consensus); ajDebug("fillinboxes xmid: %.3f ystart:%.3f yincr: %.3f\n", xmid, ystart, yincr); */ ajStrAppendC(&strcon,"Consensus"); ajStrTruncateLen(&strcon,charlen); if(boxit && boxcol) { y = ystart-(float)6.0; for(k=start; k< end; k++) { if(countforgap >= resbreak) { gapcount++; countforgap = 0; } if(count >= numres+1 ) { y = y-(yincr*((float)numseq+(float)2.0+((float)consensus* (float)2))); if(y<yincr*((float)numseq+(float)2.0+((float)consensus* (float)2))) { y = ystart-(float)6.0; } count = 1; gapcount = 0; } count++; countforgap++; /* thiscol = ajGraphicsGetColourFore(); Unused */ for(j=seqstart,l=0;j<seqend;j++,l++) if(seqboxptr[j][k] & BOXCOLOURED) { ajGraphicsDrawposRectFill((float)(count+gapcount-(float)1)+ (float)1.0, y-(yincr*((float)l+(float)0.5)), (float)(count+gapcount-(float)1), y-(yincr*((float)l-(float)0.5))); } } } oldcol = ajGraphicsSetFgcolour(BLACK); /* DO THE BACKGROUND OF THE BOXES FIRST */ count = 0; gapcount = countforgap = 0; y = ystart-(float)6.0; ajGraphicsGetCharsize(&defcs,&curcs); if(shownames) { for(i=seqstart,l=0;i<seqend;i++,l++) ajGraphicsDrawposTextAtstart((float)-charlen,y-(yincr*l), ajStrGetPtr(seqnames[i])); if(consensus && (numseq==seqend)) ajGraphicsDrawposTextAtstart( (float)-charlen, y-(yincr*((seqend-seqstart)+(float)1)),ajStrGetPtr(strcon)); } for(k=start; k< end; k++) { if(countforgap >= resbreak) { gapcount++; countforgap = 0; } if(count >= numres ) { if(shownumbers) { for(j=seqstart,l=0;j<seqend;j++,l++) { sprintf(numberstring,"%d",seqcount[j]); ajGraphicsDrawposTextAtstart( (float)(count+numgaps)+(float)5.0, y-(yincr*(float)l),numberstring); } if(consensus && (numseq==seqend)) { sprintf(numberstring,"%d",k); ajGraphicsDrawposTextAtstart( (float)(count+numgaps)+(float)5.0, y-(yincr*((float)l+(float)1)), numberstring); } } y = y-(yincr*((float)numseq+(float)2.0+((float)consensus* (float)2))); if(y<yincr*((float)numseq+(float)2.0+((float)consensus*(float)2))) { y = ystart-(float)6.0; } count = 0; gapcount = 0; if(shownames) { for(i=seqstart,l=0;i<seqend;i++,l++) ajGraphicsDrawposTextAtstart((float)-charlen,y-(yincr*l), ajStrGetPtr(seqnames[i])); if(consensus &&(numseq==seqend)) ajGraphicsDrawposTextAtstart( (float)-charlen, y-(yincr*((seqend-seqstart)+1)), ajStrGetPtr(strcon)); } } count++; countforgap++; if(boxit) { for(j=seqstart,l=0; j< seqend; j++,l++) { if(ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])) seqcount[j]++; if(seqboxptr[j][k] & BOXLEF) ajGraphicsDrawposLine((float)(count+gapcount),y- (yincr*((float)l+(float)0.5)), (float)(count+gapcount), y-(yincr*((float)l-(float)0.5))); if(seqboxptr[j][k] & BOXTOP) ajGraphicsDrawposLine((float)(count+gapcount),y- (yincr*((float)l-(float)0.5)), (float)(count+gapcount)+(float)1.0, y-(yincr*((float)l-(float)0.5))); if(seqboxptr[j][k] & BOXBOT) ajGraphicsDrawposLine((float)(count+gapcount),y- (yincr*((float)l+(float)0.5)), (float)(count+gapcount)+(float)1.0, y-(yincr*((float)l+(float)0.5))); if(seqboxptr[j][k] & BOXRIG) ajGraphicsDrawposLine((float)(count+gapcount)+(float)1.0,y- (yincr*((float)l+(float)0.5)), (float)(count+gapcount)+(float)1.0, y-(yincr*((float)l-(float)0.5))); } } else if(shownumbers) /* usually set in the boxit block */ { for(j=seqstart,l=0; j< seqend; j++,l++) { if(ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])) seqcount[j]++; } } if(consensus && (numseq==seqend)) { res[0] = constr[k]; /* start -> mid */ ajGraphicsDrawposTextAtmid((float) 0.5 + (float)(count+gapcount), y-(yincr*((seqend-seqstart)+1)),res); } } if(shownumbers) { for(j=seqstart,l=0;j<seqend;j++,l++) { sprintf(numberstring,"%d",seqcount[j]); ajGraphicsDrawposTextAtstart((float)(count+numgaps)+ (float)5.0,y-(yincr*l), numberstring); } if(consensus && (numseq==seqend)) { sprintf(numberstring,"%d",k); ajGraphicsDrawposTextAtstart((float)(count+numgaps)+(float)5.0, y-(yincr*(l+(float)1)), numberstring); } } ajStrDel(&strcon); for(i=0;i<16;i++) table[i] = -1; for(i=0;i<numseq;i++) for(k=0; k< length; k++) table[seqcolptr[i][k]] = 1; /* now display again but once for each colour */ /* for(w=0;w<15;w++)*/ for(w=0;w<16;w++) { /* not 16 as we can ignore white on plotters*/ if(table[w] > 0) { oldfg = ajGraphicsSetFgcolour(w); count = 0; gapcount = countforgap = 0; y = ystart-(float)6.0; for(k=start; k< end; k++) { if(countforgap >= resbreak) { gapcount++; countforgap=0; } if(count >= numres ) { y=y-(yincr*((float)(seqend-seqstart)+(float)2.0+ ((float)consensus*(float)2))); count = 0; gapcount = 0; } count++; countforgap++; for(j=seqstart,l=0; j< seqend; j++,l++){ if(seqcolptr[j][k] == w) { if(ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])) res[0] = seqcharptr[j][k]; else res[0] = '-'; /* start -> mid */ ajGraphicsDrawposTextAtmid((float) 0.5 + (float) (count+gapcount), y-(yincr*l),res); } } } } oldfg = ajGraphicsSetFgcolour(oldfg); } oldfg = ajGraphicsSetFgcolour(oldcol); start = end; return; }
AjPPatlistSeq ajPatlistSeqRead (const AjPStr patspec, const AjPStr patname, const AjPStr fmt, AjBool protein, ajuint mismatches) { AjPPatlistSeq patlist = NULL; AjPStr line = NULL; AjPStr name = NULL; AjPFilebuff infile = NULL; AjPRegexp mismreg = NULL; AjPStr patstr = NULL; AjPStr pat = NULL; ajuint mismatch = 0; ajint ifmt = 0; ajuint npat = 0; AjPStr namestr = NULL; ajStrAssignS(&namestr, patname); ajStrAssignEmptyC(&namestr, "pattern"); ajStrAssignS(&patstr, patspec); patlist = ajPatlistSeqNewType(protein); ifmt = patternSeqFormat(fmt); ajDebug("ajPatlistSeqRead patspec: '%S' patname: '%S' " "protein: %B mismatches: %d\n", patspec, patname, protein, mismatches); if(ajStrGetCharFirst(patstr) == '@') { ajStrCutStart(&patstr, 1); infile = ajFilebuffNewNameS(patstr); if(!infile) { ajErr("Unable to open pattern file '%S'", patstr); return NULL; } line = ajStrNew(); name = ajStrNew(); if(!ifmt) { ajBuffreadLineTrim(infile,&line); if(ajStrPrefixC(line, ">")) ifmt = 2; else ifmt = 1; ajFilebuffReset(infile); } switch(ifmt) { case 1: while (ajBuffreadLineTrim(infile,&line)) { npat++; ajStrAppendS (&pat,line); ajFmtPrintS(&name, "%S%u", namestr, npat); ajPatternSeqNewList(patlist,name,pat,mismatches); ajStrSetClear(&pat); } break; default: mismreg = ajRegCompC("<mismatch=(\\d+)>"); while (ajBuffreadLineTrim(infile,&line)) { if (ajStrGetCharFirst(line) == '>') { if (ajStrGetLen(name)) { ajPatternSeqNewList(patlist,name,pat, mismatch); ajStrSetClear(&name); ajStrSetClear(&pat); mismatch=mismatches; } ajStrCutStart(&line,1); if (ajRegExec(mismreg,line)) { ajRegSubI(mismreg,1,&name); ajStrToUint(name,&mismatch); ajStrTruncateLen(&line,ajRegOffset(mismreg)); ajStrTrimWhiteEnd(&line); } ajStrAssignS (&name,line); ajStrAssignEmptyS(&name, patname); } else ajStrAppendS (&pat,line); } ajStrAssignEmptyS(&name, patname); ajPatternSeqNewList(patlist,name,pat,mismatch); ajRegFree(&mismreg); break; } ajFilebuffDel(&infile); } else { ajStrAssignS(&name, namestr); ajPatternSeqNewList(patlist,name,patstr,mismatches); } ajStrDel(&name); ajStrDel(&line); ajStrDel(&pat); ajStrDel(&namestr); ajStrDel(&patstr); return patlist; }
int main(int argc, char **argv) { ajint i; ajint numseq; ajint j = 0; ajint numres; ajint count; ajint k; ajint kmax; float defheight; float currentscale; AjPStr shade = NULL; AjPFloat pair = NULL; AjPGraph graph = NULL; AjPMatrix cmpmatrix = NULL; AjPSeqCvt cvt = NULL; AjPStr matcodes = NULL; AjBool consensus; AjBool colourbyconsensus; AjBool colourbyresidues; AjBool colourbyshade = AJFALSE; AjBool boxit; AjBool boxcol; AjBool portrait; AjBool collision; ajint identity; AjBool listoptions; ajint alternative; AjPStr altstr = NULL; AjPStr sidentity = NULL; AjPStr ssimilarity = NULL; AjPStr sother = NULL; AjPStr sboxcolval = NULL; AjPStr options = NULL; /* ajint showscore = 0; */ ajint iboxcolval = 0; ajint cidentity = RED; ajint csimilarity = GREEN; ajint cother = BLACK; float fxp; float fyp; float yincr; float y; ajint ixlen; ajint iylen; ajint ixoff; ajint iyoff; char res[2] = " "; float *score = 0; float scoremax = 0; float *identical = NULL; ajint identicalmaxindex; float *matching = NULL; ajint matchingmaxindex; float *colcheck = NULL; ajint **matrix; ajint m1 = 0; ajint m2 = 0; ajint ms = 0; ajint highindex = 0; ajint myindex; ajint *previous = 0; AjBool iscons = ajFalse; ajint currentstate = 0; ajint oldfg = 0; float fold = 0.0; ajint *colmat = 0; ajint *shadecolour = 0; /* float identthresh = 1.5; */ /* float simthresh = 1.0; */ /* float relthresh = 0.5; */ float part = 0.0; const char *cptr; ajint resbreak; float fplural; float ystart; float xmin; float xmax; float xmid; AjPTime ajtime; ajint gapcount = 0; ajint countforgap = 0; ajint boxindex; float max; ajint matsize; ajint seqperpage = 0; ajint startseq; ajint endseq; ajint newILend = 0; ajint newILstart; void *freeptr; ajint itmp; embInit("prettyplot", argc, argv); seqset = ajAcdGetSeqset("sequences"); numres = ajAcdGetInt("residuesperline"); resbreak = ajAcdGetInt("resbreak"); ajSeqsetFill(seqset); /* Pads sequence set with gap characters */ numseq = ajSeqsetGetSize(seqset); graph = ajAcdGetGraph("graph"); colourbyconsensus = ajAcdGetBoolean("ccolours"); colourbyresidues = ajAcdGetBoolean("docolour"); shade = ajAcdGetString("shade"); pair = ajAcdGetArray("pair"); identity = ajAcdGetInt("identity"); boxit = ajAcdGetBoolean("box"); ajtime = ajTimeNewTodayFmt("daytime"); ajSeqsetTrim(seqset); /* offset = ajSeqsetGetOffset(seqset); Unused */ ajGraphAppendTitleS(graph, ajSeqsetGetUsa(seqset)); if(boxit) { AJCNEW(seqboxptr, numseq); for(i=0;i<numseq;i++) AJCNEW(seqboxptr[i], ajSeqsetGetLen(seqset)); } boxcol = ajAcdGetBoolean("boxcol"); sboxcolval = ajAcdGetString("boxuse"); if(boxcol) { iboxcolval = ajGraphicsCheckColourS(sboxcolval); if(iboxcolval == -1) iboxcolval = GREY; } consensus = ajAcdGetBoolean("consensus"); if(consensus) { AJCNEW(constr, ajSeqsetGetLen(seqset)+1); constr[0] = '\0'; } shownames = ajAcdGetBoolean("name"); shownumbers = ajAcdGetBoolean("number"); charlen = ajAcdGetInt("maxnamelen"); fplural = ajAcdGetFloat("plurality"); portrait = ajAcdGetBoolean("portrait"); collision = ajAcdGetBoolean("collision"); listoptions = ajAcdGetBoolean("listoptions"); altstr = ajAcdGetListSingle("alternative"); cmpmatrix = ajAcdGetMatrix("matrixfile"); ajStrToInt(altstr, &alternative); matrix = ajMatrixGetMatrix(cmpmatrix); cvt = ajMatrixGetCvt(cmpmatrix); matsize = ajMatrixGetSize(cmpmatrix); AJCNEW(identical,matsize); AJCNEW(matching,matsize); AJCNEW(colcheck,matsize); numgaps = numres/resbreak; numgaps--; if(portrait) { ajGraphicsSetPortrait(1); ystart = (float) 75.0; } else ystart = (float) 75.0; /* pair is an array of three non-negative floats */ /* identthresh = ajFloatGet(pair,0); Unused */ /* simthresh = ajFloatGet(pair,1); Unused */ /* relthresh = ajFloatGet(pair,2); Unused */ /* ** shade is a formatted 4-character string. Characters BLPW only. ** controlled by a pattern in ACD. */ if(ajStrGetLen(shade)) { AJCNEW(shadecolour,4); cptr = ajStrGetPtr(shade); for(i=0;i<4;i++){ if(cptr[i]== 'B' || cptr[i]== 'b') shadecolour[i] = BLACK; else if(cptr[i]== 'L' || cptr[i]== 'l') shadecolour[i] = BROWN; else if(cptr[i]== 'P' || cptr[i]== 'p') shadecolour[i] = WHEAT; else if(cptr[i]== 'W' || cptr[i]== 'w') shadecolour[i] = WHITE; } colourbyconsensus = colourbyresidues = ajFalse; colourbyshade = ajTrue; } /* ** we can colour by consensus or residue but not both ** if we have to choose, use the consensus */ if(colourbyconsensus && colourbyresidues) colourbyconsensus = AJFALSE; sidentity = ajAcdGetString("cidentity"); ssimilarity = ajAcdGetString("csimilarity"); sother = ajAcdGetString("cother"); if(colourbyconsensus) { cidentity = ajGraphicsCheckColourS(sidentity); if(cidentity == -1) cidentity = RED; csimilarity = ajGraphicsCheckColourS(ssimilarity); if(csimilarity == -1) csimilarity = GREEN; cother = ajGraphicsCheckColourS(sother); if(cother == -1) cother = BLACK; } else if(colourbyresidues) { matcodes = ajMatrixGetCodes(cmpmatrix); if(ajSeqsetIsProt(seqset)) colmat = ajGraphicsBasecolourNewProt(matcodes); else colmat = ajGraphicsBasecolourNewNuc(matcodes); } /* output the options used as the subtitle for the bottom of the graph */ if(listoptions) { ajStrAssignC(&options,""); ajFmtPrintAppS(&options,"-plurality %.1f",fplural); if(collision) ajStrAppendC(&options," -collision"); else ajStrAppendC(&options," -nocollision"); if(boxit) ajStrAppendC(&options," -box"); else ajStrAppendC(&options," -nobox"); if(boxcol) ajStrAppendC(&options," -boxcol"); else ajStrAppendC(&options," -noboxcol"); if(colourbyconsensus) ajStrAppendC(&options," -colbyconsensus"); else if(colourbyresidues) ajStrAppendC(&options," -colbyresidues"); else if(colourbyshade) ajStrAppendC(&options," -colbyshade"); else ajStrAppendC(&options," -nocolour"); if(alternative==2) ajStrAppendC(&options," -alt 2"); else if(alternative==1) ajStrAppendC(&options," -alt 1"); else if(alternative==3) ajStrAppendC(&options," -alt 3"); } AJCNEW(seqcolptr, numseq); for(i=0;i<numseq;i++) AJCNEW(seqcolptr[i], ajSeqsetGetLen(seqset)); AJCNEW(seqcharptr, numseq); AJCNEW(seqnames, numseq); AJCNEW(score, numseq); AJCNEW(previous, numseq); AJCNEW(seqcount, numseq); for(i=0;i<numseq;i++) { ajSeqsetFmtUpper(seqset); seqcharptr[i] = ajSeqsetGetseqSeqC(seqset, i); seqnames[i] = 0; ajStrAppendS(&seqnames[i],ajSeqsetGetseqNameS(seqset, i)); ajStrTruncateLen(&seqnames[i],charlen); previous[i] = 0; seqcount[i] = 0; } /* ** user will pass the number of residues to fit a page ** therefore we now need to calculate the size of the chars ** based on this and get the new char width. ** 'charlen' maximum characters for the name (truncated above) */ ajGraphicsGetCharsize(&defheight,¤tscale); xmin = -charlen - (float)2.0; xmax = (float)numres+(float)11.0+(float)(numres/resbreak); xmid = (xmax + xmin)/(float)2.0; ajGraphOpenWin(graph, xmin, xmax, (float)0.0, ystart+(float)1.0); ajGraphGetParamsPage(graph, &fxp,&fyp,&ixlen,&iylen,&ixoff,&iyoff); if(portrait) { itmp = ixlen; ixlen = iylen; iylen = itmp; } ajGraphicsGetCharsize(&defheight,¤tscale); ajGraphicsSetCharscale(((float)ixlen/((float)(numres+charlen+1)* (currentscale * (float) 1.5)))/ currentscale); /* ajGraphicsSetCharscale(((float)ixlen/((float)(numres+charlen)* (currentscale+(float)1.0)))/ currentscale); */ ajGraphicsGetCharsize(&defheight,¤tscale); yincr = (currentscale + (float)3.0)*(float)0.3; /* ** If we have titles (now the standard graph title and subtitle and footer) ** leave 7 rows of space for them */ y=ystart-(float)7.0; if(ajStrGetLen(options)) { fold = ajGraphicsSetCharscale(1.0); ajGraphicsDrawposTextAtmid(xmid,2.0, ajStrGetPtr(options)); ajGraphicsSetCharscale(fold); } /* if sequences per page not set then calculate it */ if(!seqperpage) { seqperpage = prettyplot_calcseqperpage(yincr,y,consensus); if(seqperpage>numseq) seqperpage=numseq; } count = 0; /* ** for boxes we need to set a foreground colour for the box lines ** and save the current foreground colour */ if(boxit && boxcol) oldfg = ajGraphicsSetFgcolour(iboxcolval); /* ** step through each residue position */ kmax = ajSeqsetGetLen(seqset) - 1; for(k=0; k<= kmax; k++) { /* reset column score array */ for(i=0;i<numseq;i++) score[i] = 0.0; /* reset matrix character testing arrays */ for(i=0;i<matsize;i++) { identical[i] = 0.0; matching[i] = 0.0; colcheck[i] = 0.0; } /* generate a score for this residue in each sequence */ for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); for(j=0;j<numseq;j++) { m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]); if(m1 && m2) score[i] += (float)matrix[m1][m2]* ajSeqsetGetseqWeight(seqset, j); } if(m1) identical[m1] += ajSeqsetGetseqWeight(seqset, i); } /* find the highest score */ highindex = -1; scoremax = INT_MIN; /*ajDebug("Scores at position %d:\n", k);*/ for(i=0;i<numseq;i++) { /*ajDebug(" seq %d: '%c' %f\n",i,seqcharptr[i][k],score[i]);*/ if(score[i] > scoremax) { scoremax = score[i]; highindex = i; } } for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if(!matching[m1]) { for(j=0;j<numseq;j++) { m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]); if(m1 && m2 && matrix[m1][m2] > 0) matching[m1] += ajSeqsetGetseqWeight(seqset, j); } } } /* find highs for matching and identical */ matchingmaxindex = 0; identicalmaxindex = 0; for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if(identical[m1] > identical[identicalmaxindex]) identicalmaxindex = m1; } for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if(matching[m1] > matching[matchingmaxindex]) matchingmaxindex = m1; else if(matching[m1] == matching[matchingmaxindex]) { if(identical[m1] > identical[matchingmaxindex]) matchingmaxindex= m1; } } iscons = ajFalse; boxindex = -1; max = -3; ajDebug("k:%2d highindex:%2d matching:%4.2f\n", k, highindex, matching[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])]); if(highindex != -1 && matching[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])] >= fplural) { iscons = ajTrue; boxindex = highindex; } else { for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if(matching[m1] > max) { max = matching[m1]; highindex = i; } else if(matching[m1] == max) { if(identical[m1] > identical[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])] ) { max = matching[m1]; highindex = i; } } } if(matching[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])] >= fplural) { iscons = ajTrue; boxindex = highindex; } } if(iscons) { if(!collision) { /* check for collisions */ if(alternative == 1) { /* check to see if this is unique for collisions */ for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if(identical[m1] >= identical[identicalmaxindex] && m1 != identicalmaxindex) iscons = ajFalse; } /*ajDebug("after (alt=1) iscons: %B",iscons);*/ } else if(alternative == 2) { for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if((matching[m1] >= matching[matchingmaxindex] && m1 != matchingmaxindex && matrix[m1][matchingmaxindex] < 0.1)|| (identical[m1] >= identical[matchingmaxindex] && m1 != matchingmaxindex)) iscons = ajFalse; } } else if(alternative == 3) { /* ** to do this check one is NOT in consensus to see if ** another score of fplural has been found */ ms = ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k]); for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if(ms != m1 && colcheck[m1] == 0.0) /* NOT in the current consensus */ for(j=0;j<numseq;j++) { m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]); if( matrix[ms][m2] < 0.1) { /* NOT in the current consensus */ if( matrix[m1][m2] > 0.1) colcheck[m1] += ajSeqsetGetseqWeight(seqset, j); } } } for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); /* if any other matches then we have a collision */ if(colcheck[m1] >= fplural) iscons = ajFalse; } /*ajDebug("after alt=2 iscons: %B", iscons);*/ } else { for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if((matching[m1] >= matching[matchingmaxindex] && m1 != matchingmaxindex && matrix[m1][matchingmaxindex] < 0.1)) iscons = ajFalse; if(identical[m1] >= identical[matchingmaxindex] && m1 != matchingmaxindex && matrix[m1][matchingmaxindex] > 0.1) iscons = ajFalse; } if(!iscons) { /* matches failed try identicals */ if(identical[identicalmaxindex] >= fplural) { iscons = ajTrue; /* ** if nothing has an equal or higher match that ** does not match highest then false */ for(i=0;i<numseq;i++) { m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]); if(identical[m1] >= identical[identicalmaxindex] && m1 != identicalmaxindex) iscons = ajFalse; else if(matching[m1] >= matching[identicalmaxindex] && matrix[m1][matchingmaxindex] <= 0.0) iscons = ajFalse; else if(m1 == identicalmaxindex) j = i; } if(iscons) highindex = j; } } } } if(identity) { j = 0; for(i=0;i<numseq;i++) if(seqcharptr[highindex][k] == seqcharptr[i][k]) j++; if(j<identity) iscons = ajFalse; } } /* ** Done a full line of residues ** Boxes have been defined up to this point */ if(count >= numres ) { /* check y position for next set */ y=y-(yincr*((float)numseq+(float)2.0+((float)consensus*(float)2))); if(y<yincr*((float)numseq+(float)2.0+((float)consensus*(float)2))) { /* full page - print it */ y=ystart-(float)6.0; startseq = 0; endseq = seqperpage; newILstart = newILend; newILend = k; while(startseq < numseq) { /* AJB */ /*if(startseq != 0) ajGraphNewpage(graph, AJFALSE);*/ /*ajDebug("Inner loop: startseq: %d numseq: %d endseq: %d\n", startseq, numseq, endseq);*/ if(endseq>numseq) endseq=numseq; prettyplot_fillinboxes(numseq,ajSeqsetGetLen(seqset), startseq,endseq, newILstart,newILend, numres,resbreak, boxit,boxcol,consensus, ystart,yincr,cvt); startseq = endseq; endseq += seqperpage; ajGraphNewpage(graph, AJFALSE); } } count = 0; gapcount = 0; } count++; countforgap++; for(j=0;j<numseq;j++) { /* START OF BOXES */ if(boxit) { seqboxptr[j][k] = 0; if(boxindex!=-1) { myindex = boxindex; if(matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])] [ajSeqcvtGetCodeK(cvt, seqcharptr[myindex][k])] > 0) part = 1.0; else { if(identical[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])] >= fplural) part = 1.0; else part = 0.0; } if(previous[j] != part) /* draw vertical line */ seqboxptr[j][k] |= BOXLEF; if(j==0) { /* special case for horizontal line */ if(part) { currentstate = 1; /* draw hori line */ seqboxptr[j][k] |= BOXTOP; } else currentstate = 0; } else { /* j != 0 Normal case for horizontal line */ if(part != currentstate) { /*draw hori line */ seqboxptr[j][k] |= BOXTOP; currentstate = (ajint) part; } } if(j== numseq-1 && currentstate) /* draw horiline at bottom */ seqboxptr[j][k] |= BOXBOT; previous[j] = (ajint) part; } else { part = 0; if(previous[j]) { /* draw vertical line */ seqboxptr[j][k] |= BOXLEF; } previous[j] = 0; } if(count == numres || k == kmax || countforgap >= resbreak ) { /* last one on the row or a break*/ if(previous[j]) { /* draw vertical line */ seqboxptr[j][k] |= BOXRIG; } previous[j] = 0; } } /* end box */ if(boxit && boxcol) if(boxindex != -1) { myindex = boxindex; if(matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])] [ajSeqcvtGetCodeK(cvt, seqcharptr[myindex][k])] > 0 || identical[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])] >= fplural ) seqboxptr[j][k] |= BOXCOLOURED; } /* END OF BOXES */ if(ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])) res[0] = seqcharptr[j][k]; else res[0] = '-'; if(colourbyconsensus) { part = (float) matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])] [ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])]; if(iscons && seqcharptr[highindex][k] == seqcharptr[j][k]) seqcolptr[j][k] = cidentity; else if(part > 0.0) seqcolptr[j][k] = csimilarity; else seqcolptr[j][k] = cother; } else if(colourbyresidues) seqcolptr[j][k] = colmat[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])]; else if(iscons && colourbyshade) { part = (float) matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])] [ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])]; if(part >= 1.5) seqcolptr[j][k] = shadecolour[0]; else if(part >= 1.0) seqcolptr[j][k] = shadecolour[1]; else if(part >= 0.5) seqcolptr[j][k] = shadecolour[2]; else seqcolptr[j][k] = shadecolour[3]; } else if(colourbyshade) seqcolptr[j][k] = shadecolour[3]; else seqcolptr[j][k] = BLACK; } if(consensus) { if(iscons) res[0] = seqcharptr[highindex][k]; else res[0] = '-'; strcat(constr,res); } if(countforgap >= resbreak) { gapcount++; countforgap=0; } } startseq = 0; endseq=seqperpage; newILstart = newILend; newILend = k; while(startseq < numseq) { if(startseq) ajGraphNewpage(graph, AJFALSE); /*ajDebug("Final loop: startseq: %d numseq: %d endseq: %d\n", startseq, numseq, endseq);*/ if(endseq>numseq) endseq = numseq; prettyplot_fillinboxes(numseq,ajSeqsetGetLen(seqset), startseq,endseq, newILstart,newILend, numres,resbreak, boxit,boxcol,consensus, ystart,yincr,cvt); startseq = endseq; endseq += seqperpage; } ajGraphicsGetCharsize(&defheight,¤tscale); if(boxit && boxcol) oldfg = ajGraphicsSetFgcolour(oldfg); ajGraphicsCloseWin(); ajGraphxyDel(&graph); ajStrDel(&sidentity); ajStrDel(&ssimilarity); ajStrDel(&sother); ajStrDel(&options); ajStrDel(&altstr); ajStrDel(&matcodes); for(i=0;i<numseq;i++) { ajStrDel(&seqnames[i]); AJFREE(seqcolptr[i]); if(seqboxptr) AJFREE(seqboxptr[i]); } AJFREE(seqcolptr); AJFREE(seqboxptr); AJFREE(seqnames); AJFREE(score); AJFREE(previous); AJFREE(seqcount); AJFREE(colmat); AJFREE(shadecolour); freeptr = (void *) seqcharptr; AJFREE(freeptr); AJFREE(identical); AJFREE(matching); AJFREE(colcheck); ajSeqsetDel(&seqset); ajMatrixDel(&cmpmatrix); ajStrDel(&shade); ajStrDel(&sboxcolval); ajStrDel(&sidentity); ajStrDel(&ssimilarity); ajStrDel(&sother); ajFloatDel(&pair); ajTimeDel(&ajtime); AJFREE(constr); embExit(); return 0; }