int main(int argc, char **argv) { AjPSeqset seqset; const AjPSeq seq1; const AjPSeq seq2; ajint wordlen; AjPTable seq1MatchTable = NULL; AjPList matchlist ; AjPGraph graph = 0; ajuint i; ajuint j; float total=0; ajuint acceptableticks[]= { 1,10,50,100,200,500,1000,1500,10000,50000, 100000,500000,1000000,5000000 }; ajint numbofticks = 10; ajint gap,tickgap; AjBool boxit = AJTRUE; AjBool dumpfeat = AJFALSE; float xmargin; float ymargin; float k; char ptr[10]; float ticklen; float onefifth; AjPFeattable *tabptr = NULL; AjPFeattabOut seq1out = NULL; AjPStr sajb = NULL; float flen1; float flen2; ajuint tui; embInit("polydot", argc, argv); wordlen = ajAcdGetInt("wordsize"); seqset = ajAcdGetSeqset("sequences"); graph = ajAcdGetGraph("graph"); gap = ajAcdGetInt("gap"); boxit = ajAcdGetBoolean("boxit"); seq1out = ajAcdGetFeatout("outfeat"); dumpfeat = ajAcdGetToggle("dumpfeat"); sajb = ajStrNew(); embWordLength(wordlen); AJCNEW(lines,ajSeqsetGetSize(seqset)); AJCNEW(pts,ajSeqsetGetSize(seqset)); AJCNEW(tabptr,ajSeqsetGetSize(seqset)); for(i=0;i<ajSeqsetGetSize(seqset);i++) { seq1 = ajSeqsetGetseqSeq(seqset, i); total += ajSeqGetLen(seq1); } total +=(float)(gap*(ajSeqsetGetSize(seqset)-1)); xmargin = total*(float)0.15; ymargin = total*(float)0.15; ticklen = xmargin*(float)0.1; onefifth = xmargin*(float)0.2; i = 0; while(acceptableticks[i]*numbofticks < ajSeqsetGetLen(seqset)) i++; if(i<=13) tickgap = acceptableticks[i]; else tickgap = acceptableticks[13]; ajGraphAppendTitleS(graph, ajSeqsetGetUsa(seqset)); ajGraphOpenWin(graph, (float)0.0-xmargin,(total+xmargin)*(float)1.35, (float)0.0-ymargin, total+ymargin); ajGraphicsSetCharscale((float)0.3); for(i=0;i<ajSeqsetGetSize(seqset);i++) { which = i; seq1 = ajSeqsetGetseqSeq(seqset, i); tui = ajSeqGetLen(seq1); flen1 = (float) tui; if(embWordGetTable(&seq1MatchTable, seq1)){ /* get table of words */ for(j=0;j<ajSeqsetGetSize(seqset);j++) { seq2 = ajSeqsetGetseqSeq(seqset, j); tui = ajSeqGetLen(seq2); flen2 = (float) tui; if(boxit) ajGraphicsDrawposRect(xstart,ystart, xstart+flen1, ystart+flen2); matchlist = embWordBuildMatchTable(seq1MatchTable, seq2, ajTrue); if(matchlist) polydot_plotMatches(matchlist); if(i<j && dumpfeat) embWordMatchListConvToFeat(matchlist,&tabptr[i], &tabptr[j],seq1, seq2); if(matchlist) /* free the match structures */ embWordMatchListDelete(&matchlist); if(j==0) { for(k=0.0;k<ajSeqGetLen(seq1);k+=tickgap) { ajGraphicsDrawposLine(xstart+k,ystart,xstart+k, ystart-ticklen); sprintf(ptr,"%d",(ajint)k); ajGraphicsDrawposTextAtmid(xstart+k, ystart-(onefifth), ptr); } ajGraphicsDrawposTextAtmid( xstart+(flen1/(float)2.0), ystart-(3*onefifth), ajStrGetPtr(ajSeqsetGetseqNameS(seqset, i))); } if(i==0) { for(k=0.0;k<ajSeqGetLen(seq2);k+=tickgap) { ajGraphicsDrawposLine(xstart,ystart+k,xstart-ticklen, ystart+k); sprintf(ptr,"%d",(ajint)k); ajGraphicsDrawposTextAtend(xstart-(onefifth), ystart+k, ptr); } ajGraphicsDrawposTextAtlineJustify( xstart-(3*onefifth), ystart+(flen2/(float)2.0), xstart-(3*onefifth),ystart+flen2, ajStrGetPtr(ajSeqsetGetseqNameS(seqset, j)),0.5); } ystart += flen2+(float)gap; } } embWordFreeTable(&seq1MatchTable); seq1MatchTable = NULL; xstart += flen1+(float)gap; ystart = 0.0; } ajGraphicsDrawposTextAtstart(total+onefifth,total-(onefifth), "No. Length Lines Points Sequence"); for(i=0;i<ajSeqsetGetSize(seqset);i++) { seq1 = ajSeqsetGetseqSeq(seqset, i); ajFmtPrintS(&sajb,"%3u %6d %5d %6d %s",i+1, ajSeqGetLen(seq1),lines[i], pts[i],ajSeqGetNameC(seq1)); ajGraphicsDrawposTextAtstart(total+onefifth,total-(onefifth*(i+2)), ajStrGetPtr(sajb)); } if(dumpfeat && seq1out) { for(i=0;i<ajSeqsetGetSize(seqset);i++) { ajFeattableWrite(seq1out, tabptr[i]); ajFeattableDel(&tabptr[i]); } } ajGraphicsClose(); ajGraphxyDel(&graph); ajStrDel(&sajb); AJFREE(lines); AJFREE(pts); AJFREE(tabptr); ajSeqsetDel(&seqset); ajFeattabOutDel(&seq1out);; embExit(); return 0; }
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; }
int main(int argc, char *argv[]) { char *string; char *structure=NULL; char *cstruc=NULL; char *ns_bases=NULL; char *c; int n_seq; int i; int length; int sym; int endgaps = 0; int mis = 0; double min_en; double real_en; double sfact = 1.07; int pf = 0; int istty; char *AS[MAX_NUM_NAMES]; /* aligned sequences */ char *names[MAX_NUM_NAMES]; /* sequence names */ AjPSeqset seq = NULL; AjPFile confile = NULL; AjPFile alifile = NULL; AjPFile paramfile = NULL; AjPFile outf = NULL; AjPFile essfile = NULL; AjPFile dotfile = NULL; AjPStr constring = NULL; float eT = 0.; AjBool eGU; AjBool eclose; AjBool lonely; AjPStr ensbases = NULL; AjBool etloop; AjPStr eenergy = NULL; char ewt = '\0'; float escale = 0.; AjPStr edangles = NULL; char edangle = '\0'; ajint len; AjPSeq tseq = NULL; AjPStr tname = NULL; int circ = 0; int doAlnPS = 0; int doColor = 0; embInitPV("vrnaalifoldpf",argc,argv,"VIENNA",VERSION); constring = ajStrNew(); seq = ajAcdGetSeqset("sequence"); confile = ajAcdGetInfile("constraintfile"); paramfile = ajAcdGetInfile("paramfile"); eT = ajAcdGetFloat("temperature"); eGU = ajAcdGetBoolean("gu"); eclose = ajAcdGetBoolean("closegu"); lonely = ajAcdGetBoolean("lp"); ensbases = ajAcdGetString("nsbases"); etloop = ajAcdGetBoolean("tetraloop"); eenergy = ajAcdGetListSingle("energy"); escale = ajAcdGetFloat("scale"); edangles = ajAcdGetListSingle("dangles"); mis = !!ajAcdGetBoolean("most"); endgaps = !!ajAcdGetBoolean("endgaps"); nc_fact = (double) ajAcdGetFloat("nspenalty"); cv_fact = (double) ajAcdGetFloat("covariance"); outf = ajAcdGetOutfile("outfile"); essfile = ajAcdGetOutfile("ssoutfile"); alifile = ajAcdGetOutfile("alignoutfile"); circ = !!ajAcdGetBoolean("circular"); doColor = !!ajAcdGetBoolean("colour"); dotfile = ajAcdGetOutfile("dotoutfile"); do_backtrack = 1; pf = 1; string = NULL; istty = 0; dangles = 2; temperature = (double) eT; noGU = (eGU) ? 0 : 1; no_closingGU = (eclose) ? 0 : 1; noLonelyPairs = (lonely) ? 0 : 1; ns_bases = (ajStrGetLen(ensbases)) ? MAJSTRGETPTR(ensbases) : NULL; tetra_loop = !!etloop; ewt = *ajStrGetPtr(eenergy); if(ewt == '0') energy_set = 0; else if(ewt == '1') energy_set = 1; else if(ewt == '2') energy_set = 2; sfact = (double) escale; edangle = *ajStrGetPtr(edangles); if(edangle == '0') dangles = 0; else if(edangle == '1') dangles = 1; else if(edangle == '2') dangles = 2; else if(edangle == '3') dangles = 3; if(paramfile) read_parameter_file(paramfile); if (ns_bases != NULL) { nonstandards = space(33); c=ns_bases; i=sym=0; if (*c=='-') { sym=1; c++; } while (*c!='\0') { if (*c!=',') { nonstandards[i++]=*c++; nonstandards[i++]=*c; if ((sym)&&(*c!=*(c-1))) { nonstandards[i++]=*c; nonstandards[i++]=*(c-1); } } c++; } } if(alifile) doAlnPS = 1; if(confile) vienna_GetConstraints(confile,&constring); n_seq = ajSeqsetGetSize(seq); if(n_seq > MAX_NUM_NAMES - 1) ajFatal("[e]RNAalifold is restricted to %d sequences\n", MAX_NUM_NAMES - 1); if (n_seq==0) ajFatal("No sequences found"); for(i=0;i<n_seq;++i) { tseq = (AjPSeq) ajSeqsetGetseqSeq(seq,i); ajSeqGapStandard(tseq, '-'); tname = (AjPStr) ajSeqsetGetseqNameS(seq,i); len = ajSeqGetLen(tseq); AS[i] = (char *) space(len+1); names[i] = (char *) space(ajStrGetLen(tname)+1); strcpy(AS[i],ajSeqGetSeqC(tseq)); strcpy(names[i],ajStrGetPtr(tname)); } AS[n_seq] = NULL; names[n_seq] = NULL; if (endgaps) for (i=0; i<n_seq; i++) mark_endgaps(AS[i], '~'); length = (int) strlen(AS[0]); structure = (char *) space((unsigned) length+1); if(confile) { fold_constrained = 1; strcpy(structure,ajStrGetPtr(constring)); } if (circ && noLonelyPairs) ajWarn( "warning, depending on the origin of the circular sequence, " "some structures may be missed when using -noLP\n" "Try rotating your sequence a few times\n"); if (circ) min_en = circalifold((const char **)AS, structure); else min_en = alifold(AS, structure); { int i; double s=0; extern int eos_debug; eos_debug=-1; /* shut off warnings about nonstandard pairs */ for (i=0; AS[i]!=NULL; i++) if (circ) s += energy_of_circ_struct(AS[i], structure); else s += energy_of_struct(AS[i], structure); real_en = s/i; } string = (mis) ? consens_mis((const char **) AS) : consensus((const char **) AS); ajFmtPrintF(outf,"%s\n%s", string, structure); ajFmtPrintF(outf," (%6.2f = %6.2f + %6.2f) \n", min_en, real_en, min_en-real_en ); if (length<=2500) { char **A; A = annote(structure, (const char**) AS); if (doColor) (void) PS_rna_plot_a(string, structure, essfile, A[0], A[1]); else (void) PS_rna_plot_a(string, structure, essfile, NULL, A[1]); free(A[0]); free(A[1]);free(A); } else ajWarn("INFO: structure too long, not doing xy_plot\n"); if (doAlnPS) PS_color_aln(structure, alifile, AS, names); { /* free mfe arrays but preserve base_pair for PS_dot_plot */ struct bond *bp; bp = base_pair; base_pair = space(16); free_alifold_arrays(); /* free's base_pair */ free_alipf_arrays(); base_pair = bp; } if (pf) { double energy, kT; pair_info *pi; char * mfe_struc; mfe_struc = strdup(structure); kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */ pf_scale = exp(-(sfact*min_en)/kT/length); if (length>2000) ajWarn("scaling factor %f\n", pf_scale); /* init_alipf_fold(length); */ if (confile) strncpy(structure, ajStrGetPtr(constring), length+1); energy = (circ) ? alipf_circ_fold(AS, structure, &pi) : alipf_fold(AS, structure, &pi); if (do_backtrack) { ajFmtPrintF(outf,"%s", structure); ajFmtPrintF(outf," [%6.2f]\n", energy); } if ((istty)||(!do_backtrack)) ajFmtPrintF(outf," free energy of ensemble = %6.2f kcal/mol\n", energy); ajFmtPrintF(outf," frequency of mfe structure in ensemble %g\n", exp((energy-min_en)/kT)); if (do_backtrack) { FILE *aliout; cpair *cp; short *ptable; int k; ptable = make_pair_table(mfe_struc); ajFmtPrintF(outf,"\n# Alignment section\n\n"); aliout = ajFileGetFileptr(outf); fprintf(aliout, "%d sequences; length of alignment %d\n", n_seq, length); fprintf(aliout, "alifold output\n"); for (k=0; pi[k].i>0; k++) { pi[k].comp = (ptable[pi[k].i] == pi[k].j) ? 1:0; print_pi(pi[k], aliout); } fprintf(aliout, "%s\n", structure); free(ptable); cp = make_color_pinfo(pi); (void) PS_color_dot_plot(string, cp, dotfile); free(cp); free(mfe_struc); free(pi); } } if (cstruc!=NULL) free(cstruc); free(base_pair); (void) fflush(stdout); free(string); free(structure); for (i=0; AS[i]; i++) { free(AS[i]); free(names[i]); } ajSeqsetDel(&seq); ajStrDel(&constring); ajStrDel(&eenergy); ajStrDel(&edangles); ajStrDel(&ensbases); ajFileClose(&confile); ajFileClose(¶mfile); ajFileClose(&outf); ajFileClose(&essfile); ajFileClose(&alifile); ajFileClose(&dotfile); embExit(); return 0; }