int main(int argc, char **argv)
{
AjPList list = NULL;
AjPSeq seq;
AjPSeq seq2;
AjPStr aa0str = 0;
AjPStr aa1str = 0;
const char *s1;
const char *s2;
char *strret = NULL;
ajuint i;
ajuint j;
ajuint k;
ajint l;
ajint abovethresh;
ajint total;
ajint starti = 0;
ajint startj = 0;
ajint windowsize;
float thresh;
AjPGraph graph = NULL;
AjPGraph xygraph = NULL;
float flen1;
float flen2;
ajuint len1;
ajuint len2;
AjPTime ajtime = NULL;
time_t tim;
AjBool boxit=AJTRUE;
/* Different ticks as they need to be different for x and y due to
length of string being important on x */
ajuint acceptableticksx[]=
{
1,10,50,100,500,1000,1500,10000,
500000,1000000,5000000
};
ajuint acceptableticks[]=
{
1,10,50,100,200,500,1000,2000,5000,10000,15000,
500000,1000000,5000000
};
ajint numbofticks = 10;
float xmargin;
float ymargin;
float ticklen;
float tickgap;
float onefifth;
float k2;
float max;
char ptr[10];
AjPMatrix matrix = NULL;
ajint** sub;
AjPSeqCvt cvt;
AjPStr subt = NULL;
ajint b1;
ajint b2;
ajint e1;
ajint e2;
AjPStr se1;
AjPStr se2;
ajint ithresh;
AjBool stretch;
PPoint ppt = NULL;
float xa[1];
float ya[1];
AjPGraphdata gdata=NULL;
AjPStr tit = NULL;
AjIList iter = NULL;
float x1 = 0.;
float x2 = 0.;
float y1 = 0.;
float y2 = 0.;
ajuint tui;
se1 = ajStrNew();
se2 = ajStrNew();
embInit("dotmatcher", argc, argv);
seq = ajAcdGetSeq("asequence");
seq2 = ajAcdGetSeq("bsequence");
stretch = ajAcdGetToggle("stretch");
graph = ajAcdGetGraph("graph");
xygraph = ajAcdGetGraphxy("xygraph");
windowsize = ajAcdGetInt("windowsize");
ithresh = ajAcdGetInt("threshold");
matrix = ajAcdGetMatrix("matrixfile");
sub = ajMatrixGetMatrix(matrix);
cvt = ajMatrixGetCvt(matrix);
thresh = (float)ithresh;
ajtime = ajTimeNew();
tim = time(0);
ajTimeSetLocal(ajtime, tim);
b1 = ajSeqGetBegin(seq);
b2 = ajSeqGetBegin(seq2);
e1 = ajSeqGetEnd(seq);
e2 = ajSeqGetEnd(seq2);
len1 = ajSeqGetLen(seq);
len2 = ajSeqGetLen(seq2);
tui = ajSeqGetLen(seq);
flen1 = (float) tui;
tui = ajSeqGetLen(seq2);
flen2 = (float) tui;
ajStrAssignSubC(&se1,ajSeqGetSeqC(seq),b1-1,e1-1);
ajStrAssignSubC(&se2,ajSeqGetSeqC(seq2),b2-1,e2-1);
ajSeqAssignSeqS(seq,se1);
ajSeqAssignSeqS(seq2,se2);
s1 = ajStrGetPtr(ajSeqGetSeqS(seq));
s2 = ajStrGetPtr(ajSeqGetSeqS(seq2));
aa0str = ajStrNewRes(1+len1); /* length plus trailing blank */
aa1str = ajStrNewRes(1+len2);
list = ajListNew();
for(i=0;i<len1;i++)
ajStrAppendK(&aa0str,(char)ajSeqcvtGetCodeK(cvt, *s1++));
for(i=0;i<len2;i++)
ajStrAppendK(&aa1str,(char)ajSeqcvtGetCodeK(cvt, *s2++));
max = (float)len1;
if(len2 > max)
max = (float) len2;
xmargin = ymargin = max *(float)0.15;
ticklen = xmargin*(float)0.1;
onefifth = xmargin*(float)0.2;
subt = ajStrNewC((strret=
ajFmtString("(windowsize = %d, threshold = %3.2f %D)",
windowsize,thresh,ajtime)));
if(!stretch)
{
if( ajStrGetLen(ajGraphGetSubtitleS(graph)) <=1)
ajGraphSetSubtitleS(graph,subt);
ajGraphOpenWin(graph, (float)0.0-ymargin,(max*(float)1.35)+ymargin,
(float)0.0-xmargin,(float)max+xmargin);
ajGraphicsDrawposTextAtmid(flen1*(float)0.5,
(float)0.0-(xmargin/(float)2.0),
ajGraphGetXlabelC(graph));
ajGraphicsDrawposTextAtlineJustify((float)0.0-(xmargin*(float)0.75),
flen2*(float)0.5,
(float)0.0-(xmargin*(float)0.75),flen1,
ajGraphGetYlabelC(graph),0.5);
ajGraphicsSetCharscale(0.5);
}
s1= ajStrGetPtr(aa0str);
s2 = ajStrGetPtr(aa1str);
for(j=0; (ajint)j < (ajint)len2-windowsize;j++)
{
i =0;
total = 0;
abovethresh =0;
k = j;
for(l=0;l<windowsize;l++)
total = total + sub[(ajint)s1[i++]][(ajint)s2[k++]];
if(total >= thresh)
{
abovethresh=1;
starti = i-windowsize;
startj = k-windowsize;
}
while(i < len1 && k < len2)
{
total = total - sub[(ajint)s1[i-windowsize]]
[(ajint)s2[k-windowsize]];
total = total + sub[(ajint)s1[i]][(ajint)s2[k]];
if(abovethresh)
{
if(total < thresh)
{
abovethresh = 0;
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)i-1,(float)k-1,stretch);
}
}
else if(total >= thresh)
{
starti = i-windowsize;
startj = k-windowsize;
abovethresh= 1;
}
i++;
k++;
}
if(abovethresh)
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)i-1,(float)k-1,
stretch);
}
for(i=0; (ajint)i < (ajint)len1-windowsize;i++)
{
j = 0;
total = 0;
abovethresh =0;
k = i;
for(l=0;l<windowsize;l++)
total = total + sub[(ajint)s1[k++]][(ajint)s2[j++]];
if(total >= thresh)
{
abovethresh=1;
starti = k-windowsize;
startj = j-windowsize;
}
while(k < len1 && j < len2)
{
total = total - sub[(ajint)s1[k-windowsize]]
[(ajint)s2[j-windowsize]];
total = total + sub[(ajint)s1[k]][(ajint)s2[j]];
if(abovethresh)
{
if(total < thresh)
{
abovethresh = 0;
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)k-1,(float)j-1,stretch);
}
}
else if(total >= thresh)
{
starti = k-windowsize;
startj = j-windowsize;
abovethresh= 1;
}
j++;
k++;
}
if(abovethresh)
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)k-1,(float)j-1,
stretch);
}
if(boxit && !stretch)
{
ajGraphicsDrawposRect(0.0,0.0,flen1, flen2);
i=0;
while(acceptableticksx[i]*numbofticks < len1)
i++;
if(i<=13)
tickgap = (float)acceptableticksx[i];
else
tickgap = (float)acceptableticksx[10];
ticklen = xmargin*(float)0.1;
onefifth = xmargin*(float)0.2;
if(len2/len1 > 10 )
{
/* if a lot smaller then just label start and end */
ajGraphicsDrawposLine((float)0.0,(float)0.0,(float)0.0,(float)0.0-ticklen);
sprintf(ptr,"%d",b1-1);
ajGraphicsDrawposTextAtmid((float)0.0,(float)0.0-(onefifth),ptr);
ajGraphicsDrawposLine(flen1,(float)0.0,
flen1,(float)0.0-ticklen);
sprintf(ptr,"%d",len1+b1-1);
ajGraphicsDrawposTextAtmid(flen1,(float)0.0-(onefifth),ptr);
}
else
for(k2=0.0;k2<len1;k2+=tickgap)
{
ajGraphicsDrawposLine(k2,(float)0.0,k2,(float)0.0-ticklen);
sprintf(ptr,"%d",(ajint)k2+b1-1);
ajGraphicsDrawposTextAtmid(k2,(float)0.0-(onefifth),ptr);
}
i = 0;
while(acceptableticks[i]*numbofticks < len2)
i++;
tickgap = (float)acceptableticks[i];
ticklen = ymargin*(float)0.01;
onefifth = ymargin*(float)0.02;
if(len1/len2 > 10 )
{
/* if a lot smaller then just label start and end */
ajGraphicsDrawposLine((float)0.0,(float)0.0,(float)0.0-ticklen,(float)0.0);
sprintf(ptr,"%d",b2-1);
ajGraphicsDrawposTextAtend((float)0.0-(onefifth),(float)0.0,ptr);
ajGraphicsDrawposLine((float)0.0,flen2,(float)0.0-ticklen,
flen2);
sprintf(ptr,"%d",len2+b2-1);
ajGraphicsDrawposTextAtend((float)0.0-(onefifth),flen2,ptr);
}
else
for(k2=0.0;k2<len2;k2+=tickgap)
{
ajGraphicsDrawposLine((float)0.0,k2,(float)0.0-ticklen,k2);
sprintf(ptr,"%d",(ajint)k2+b2-1);
ajGraphicsDrawposTextAtend((float)0.0-(onefifth),k2,ptr);
}
}
if(!stretch)
ajGraphicsClose();
else /* the xy graph for -stretch */
{
tit = ajStrNew();
ajFmtPrintS(&tit,"%S",ajGraphGetTitleS(xygraph));
gdata = ajGraphdataNewI(1);
xa[0] = (float)b1;
ya[0] = (float)b2;
ajGraphSetTitleC(xygraph,ajStrGetPtr(tit));
ajGraphSetXlabelC(xygraph,ajSeqGetNameC(seq));
ajGraphSetYlabelC(xygraph,ajSeqGetNameC(seq2));
ajGraphdataSetTypeC(gdata,"2D Plot Float");
ajGraphdataSetTitleS(gdata,subt);
ajGraphdataSetMinmax(gdata,(float)b1,(float)e1,(float)b2,
(float)e2);
ajGraphdataSetTruescale(gdata,(float)b1,(float)e1,(float)b2,
(float)e2);
ajGraphxySetXstartF(xygraph,(float)b1);
ajGraphxySetXendF(xygraph,(float)e1);
ajGraphxySetYstartF(xygraph,(float)b2);
ajGraphxySetYendF(xygraph,(float)e2);
ajGraphxySetXrangeII(xygraph,b1,e1);
ajGraphxySetYrangeII(xygraph,b2,e2);
if(list)
{
iter = ajListIterNewread(list);
while((ppt = ajListIterGet(iter)))
{
x1 = ppt->x1+b1-1;
y1 = ppt->y1+b2-1;
x2 = ppt->x2+b1-1;
y2 = ppt->y2+b2-1;
ajGraphAddLine(xygraph,x1,y1,x2,y2,0);
AJFREE(ppt);
}
ajListIterDel(&iter);
}
ajGraphdataAddXY(gdata,xa,ya);
ajGraphDataReplace(xygraph,gdata);
ajGraphxyDisplay(xygraph,ajFalse);
ajGraphicsClose();
ajStrDel(&tit);
}
ajListFree(&list);
ajSeqDel(&seq);
ajSeqDel(&seq2);
ajGraphxyDel(&graph);
ajGraphxyDel(&xygraph);
ajMatrixDel(&matrix);
ajTimeDel(&ajtime);
/* deallocate memory */
ajStrDel(&aa0str);
ajStrDel(&aa1str);
ajStrDel(&se1);
ajStrDel(&se2);
ajStrDel(&subt);
AJFREE(strret); /* created withing ajFmtString */
embExit();
return 0;
}
static void infoalign_Compare(const AjPSeq ref, const AjPSeq seq,
ajint * const *sub,
const AjPSeqCvt cvt, ajint *seqlength,
ajint *alignlength, ajint *gaps,
ajint *gapcount, ajint *idcount,
ajint *simcount, ajint *difcount,
float *change)
{
ajint i;
ajint lenseq;
ajint lenref;
const char *s;
const char *r;
AjBool inGap = ajFalse; /* true if in a gap in 'seq' */
ajint begin;
ajint end;
lenseq = ajSeqGetLen(seq);
lenref = ajSeqGetLen(ref);
s = ajSeqGetSeqC(seq);
r = ajSeqGetSeqC(ref);
/* initialise counts */
*seqlength = 0;
*alignlength = 0;
*gaps = 0;
*gapcount = 0;
*idcount = 0;
*simcount = 0;
*difcount = 0;
*change = 0.0;
/* ignore gaps at the ends of the sequence */
for(begin = 0; s[begin] == '-'; begin++);
for(end = lenseq-1; s[end] == '-'; end--);
for(i=begin; i<=end; i++)
{
/* count gaps and their length */
if(s[i] == '-')
{
if(!inGap)
{
inGap = ajTrue;
(*gaps)++;
}
(*gapcount)++;
}
else
{
inGap = ajFalse;
/*
** count identity, similarity, differences
** Past the end of the reference sequence ?
*/
if(i >= lenref)
(*difcount)++;
else
{
/* identity */
if((toupper((int)r[i]) == toupper((int)s[i])))
(*idcount)++;
/* similarity */
else if(sub[ajSeqcvtGetCodeK(cvt, r[i])][ajSeqcvtGetCodeK(cvt, s[i])] > 0)
(*simcount)++;
/* difference */
else
(*difcount)++;
}
}
}
*seqlength = *idcount + *simcount + *difcount;
*alignlength = end-begin+1;
*change = (float)(*alignlength - *idcount)*(float)100.0/
(float)(*alignlength);
return;
}
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;
}
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;
}
void embConsCalc(const AjPSeqset seqset,const AjPMatrix cmpmatrix,
ajint nseqs, ajint mlen,float fplural,float setcase,
ajint identity, AjBool gaps, AjPStr *cons)
{
ajint i;
ajint j;
ajint k;
ajint **matrix;
ajint m1 = 0;
ajint m2 = 0;
ajint highindex;
ajint matsize;
ajint matchingmaxindex;
ajint identicalmaxindex;
float max;
float contri = 0;
float contrj = 0;
float *identical;
float *matching;
AjPSeqCvt cvt = 0;
AjPFloat score = NULL;
const char **seqcharptr;
char res;
char nocon = '-';
void *freeptr;
matrix = ajMatrixGetMatrix(cmpmatrix);
cvt = ajMatrixGetCvt(cmpmatrix); /* return conversion table */
matsize = ajMatrixGetSize(cmpmatrix);
AJCNEW(seqcharptr,nseqs);
AJCNEW(identical,matsize);
AJCNEW(matching,matsize);
score = ajFloatNew();
if(ajSeqsetIsNuc(seqset)) /* set non-consensus character */
nocon = 'N';
else if ( ajSeqsetIsProt(seqset))
nocon = 'X';
for(i=0;i<nseqs;i++) /* get sequence as string */
seqcharptr[i] = ajSeqsetGetseqSeqC(seqset, i);
for(k=0; k< mlen; k++)
{
res = nocon;
for(i=0;i<matsize;i++) /* reset id's and +ve matches */
{
identical[i] = 0.0;
matching[i] = 0.0;
}
for(i=0;i<nseqs;i++)
ajFloatPut(&score,i,0.);
for(i=0;i<nseqs;i++) /* generate score for columns */
{
m1 = ajSeqcvtGetCodeK(cvt,seqcharptr[i][k]);
if(m1 || gaps)
identical[m1] += ajSeqsetGetseqWeight(seqset,i);
for(j=i+1;j<nseqs;j++)
{
m2 = ajSeqcvtGetCodeK(cvt,seqcharptr[j][k]);
if(m1 && m2)
{
contri = (float)matrix[m1][m2]*
ajSeqsetGetseqWeight(seqset,j)
+ajFloatGet(score,i);
contrj = (float)matrix[m1][m2]*
ajSeqsetGetseqWeight(seqset,i)
+ajFloatGet(score,j);
ajFloatPut(&score,i,contri);
ajFloatPut(&score,j,contrj);
}
}
}
highindex = -1;
max = -(float)INT_MAX;
for(i=0;i<nseqs;i++)
if( ajFloatGet(score,i) > max ||
(ajFloatGet(score,i) == max &&
seqcharptr[highindex][k] == '-') )
{
highindex = i;
max = ajFloatGet(score,i);
}
for(i=0;i<nseqs;i++) /* find +ve matches in the column */
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(!matching[m1])
for(j=0;j<nseqs;j++)
{
/*
// if( i != j)
// {
// m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]);
// if(m1 && m2 && matrix[m1][m2] > 0)
// matching[m1] += ajSeqsetGetseqWeight(seqset, j);
// }
*/
m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]);
if(m1 && m2 && matrix[m1][m2] > 0)
matching[m1] += ajSeqsetGetseqWeight(seqset, j);
if(gaps && !m1 && !m2)
matching[m1] += ajSeqsetGetseqWeight(seqset, j);
}
}
matchingmaxindex = 0; /* get max matching and identical */
identicalmaxindex = 0;
for(i=0;i<nseqs;i++)
{
m1 = ajSeqcvtGetCodeK(cvt,seqcharptr[i][k]);
if(identical[m1] > identical[identicalmaxindex])
identicalmaxindex = m1;
}
for(i=0;i<nseqs;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;
}
/* plurality check */
m1 = ajSeqcvtGetCodeK(cvt,seqcharptr[highindex][k]);
/* if(matching[m1] >= fplural
&& seqcharptr[highindex][k] != '-')
res = seqcharptr[highindex][k];*/
if(matching[m1] >= fplural)
res = seqcharptr[highindex][k];
if(matching[m1]<= setcase)
res = tolower((int)res);
if(identity) /* if just looking for id's */
{
j = 0;
for(i=0;i<nseqs;i++)
if(matchingmaxindex == ajSeqcvtGetCodeK(cvt,seqcharptr[i][k]))
j++;
if(j<identity)
res = nocon;
}
ajStrAppendK(cons,res);
}
freeptr = (void *) seqcharptr;
AJFREE(freeptr);
AJFREE(matching);
AJFREE(identical);
ajFloatDel(&score);
return;
}
