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;
}
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;
}
