static void infoalign_OutputStr(AjPFile outfile, const AjPStr str, AjBool html,
AjBool after, ajuint minlength)
{
AjPStr marginfmt;
marginfmt = ajStrNewRes(10);
/* ajFmtPrintF doesn't seem to deal with formats like "%-*S" correctly */
ajFmtPrintS(&marginfmt, "%%-%dS", minlength);
if(html)
ajFmtPrintF(outfile, "<td>");
if(html || !after || minlength == NOLIMIT)
ajFmtPrintF(outfile, "%S", str);
else
/*
** Format:
** If this is the last item, don't put spaces or TABs after it.
** Try to fit the name in 'minlength' spaces, else just add a
** TAB after it
*/
ajFmtPrintF(outfile, ajStrGetPtr(marginfmt), str);
if(html)
ajFmtPrintF(outfile, "</td>\n");
else
if(after && ajStrGetLen(str) >= minlength)
ajFmtPrintF(outfile, "\t");
ajStrDel(&marginfmt);
return;
}
AjPStr embPropProt1to3(AjPSeq seq, ajint pad)
{
const char *p;
const char *p3;
AjPStr temp;
ajint i;
temp = ajStrNewRes(ajSeqGetLen(seq)*3 + pad+1);
/* put any required padding spaces at the start */
for(i=0; i<pad; i++)
ajStrAppendC(&temp, " ");
for(p=ajSeqGetSeqC(seq); *p; p++)
{
if(*p == '*')
ajStrAppendC(&temp, "***");
else if(*p == '.')
ajStrAppendC(&temp, "...");
else if(*p == '-')
ajStrAppendC(&temp, "---");
else if(!isalpha((ajint)*p))
ajStrAppendC(&temp, "???");
else
{
p3 = embPropCharToThree(*p);
ajStrAppendK(&temp, *p3);
ajStrAppendK(&temp, *(p3+1));
ajStrAppendK(&temp, *(p3+2));
}
}
return temp;
}
AjPStr ajMatrixfGetCodes(const AjPMatrixf thys)
{
AjPStr ret = NULL;
ajint i;
ajint maxcode;
ret = ajStrNewRes(thys->Size + 1);
maxcode = thys->Size - 1;
for (i=0;i<maxcode;i++)
ajStrAppendK(&ret, ajStrGetCharFirst(thys->Codes[i]));
return ret;
}
AjBool ajReadlineAppend(AjPFile file, AjPStr* Pdest)
{
static AjPStr locbuff = 0;
AjBool ok;
if(!locbuff)
locbuff = ajStrNewRes(512);
ok = ajReadline(file, &locbuff);
if(ok)
ajStrAppendS(Pdest, locbuff);
ajStrDel(&locbuff);
return ok;
}
AjPStr embPropProt1to3Rev(AjPSeq seq, ajint pad)
{
const char *p;
const char *p3;
AjPStr temp;
ajint i=0;
temp = ajStrNewRes(ajSeqGetLen(seq)*3 + pad+1);
for(p=ajSeqGetSeqC(seq); *p; p++)
{
if(*p == '*')
ajStrAppendC(&temp, "***");
else if(*p == '.')
ajStrAppendC(&temp, "...");
else if(*p == '-')
ajStrAppendC(&temp, "---");
else if(!isalpha((ajint)*p))
ajStrAppendC(&temp, "???");
else
{
p3 = embPropCharToThree(*p);
if(i++)
{
ajStrAppendK(&temp, *(p3+2));
ajStrAppendK(&temp, *(p3+1));
ajStrAppendK(&temp, *p3);
}
else
{
if(pad >= 2)
ajStrAppendK(&temp, *(p3+2));
if(pad >= 1)
ajStrAppendK(&temp, *(p3+1));
ajStrAppendK(&temp, *p3);
}
}
}
return temp;
}
AjPStr embPropProtGaps(AjPSeq seq, ajint pad)
{
const char *p;
AjPStr temp;
ajint i;
temp = ajStrNewRes(ajSeqGetLen(seq)*3 + pad+1);
/* put any required padding spaces at the start */
for(i=0; i<pad; i++)
ajStrAppendC(&temp, " ");
for(p=ajSeqGetSeqC(seq); *p; p++)
{
ajStrAppendK(&temp, *p);
ajStrAppendC(&temp, " ");
}
return temp;
}
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;
}
int main(int argc, char **argv)
{
AjPSeqall seq1;
AjPSeqset seq2;
AjPSeq a;
const AjPSeq b;
AjPStr m = 0;
AjPStr n = 0;
AjPFile errorf;
AjBool show = ajFalse;
ajint lena = 0;
ajint lenb = 0;
const char *p;
const char *q;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
ajint *compass = NULL;
float *path = NULL;
float gapopen;
float gapextend;
float score;
ajint begina;
ajint i;
ajuint k;
ajint beginb;
ajint start1 = 0;
ajint start2 = 0;
ajint end1 = 0;
ajint end2 = 0;
ajint width = 0;
AjPTable seq1MatchTable = 0;
ajint wordlen = 6;
ajint oldmax = 0;
AjPAlign align = NULL;
embInit("supermatcher", argc, argv);
matrix = ajAcdGetMatrixf("datafile");
seq1 = ajAcdGetSeqall("asequence");
seq2 = ajAcdGetSeqset("bsequence");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
wordlen = ajAcdGetInt("wordlen");
align = ajAcdGetAlign("outfile");
errorf = ajAcdGetOutfile("errorfile");
width = ajAcdGetInt("width"); /* not the same as awidth */
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
embWordLength(wordlen);
ajSeqsetTrim(seq2);
while(ajSeqallNext(seq1,&a))
{
ajSeqTrim(a);
begina = 1 + ajSeqGetOffset(a);
m = ajStrNewRes(1+ajSeqGetLen(a));
lena = ajSeqGetLen(a);
ajDebug("Read '%S'\n", ajSeqGetNameS(a));
if(!embWordGetTable(&seq1MatchTable, a)) /* get table of words */
ajErr("Could not generate table for %s\n",
ajSeqGetNameC(a));
for(k=0;k<ajSeqsetGetSize(seq2);k++)
{
b = ajSeqsetGetseqSeq(seq2, k);
lenb = ajSeqGetLen(b);
beginb = 1 + ajSeqGetOffset(b);
ajDebug("Processing '%S'\n", ajSeqGetNameS(b));
p = ajSeqGetSeqC(a);
q = ajSeqGetSeqC(b);
if(!supermatcher_findstartpoints(seq1MatchTable,b,a,
&start1, &start2,
&end1, &end2))
{
ajFmtPrintF(errorf,
"No wordmatch start points for "
"%s vs %s. No alignment\n",
ajSeqGetNameC(a),ajSeqGetNameC(b));
continue;
}
n=ajStrNewRes(1+ajSeqGetLen(b));
ajStrAssignC(&m,"");
ajStrAssignC(&n,"");
ajDebug("++ %S v %S start:%d %d end:%d %d\n",
ajSeqGetNameS(a), ajSeqGetNameS(b),
start1, start2, end1, end2);
if(end1-start1+1 > oldmax)
{
oldmax = ((end1-start1)+1);
AJRESIZE(path,oldmax*width*sizeof(float));
AJRESIZE(compass,oldmax*width*sizeof(ajint));
ajDebug("++ resize to oldmax: %d\n", oldmax);
}
for(i=0;i<((end1-start1)+1)*width;i++)
path[i] = 0.0;
ajDebug("Calling embAlignPathCalcFast "
"%d..%d [%d/%d] %d..%d [%d/%d]\n",
start1, end1, (end1 - start1 + 1), lena,
start2, end2, (end2 - start2 + 1), lenb);
score = embAlignPathCalcSWFast(&p[start1],&q[start2],
end1-start1+1,end2-start2+1,
0,width,
gapopen,gapextend,
path,sub,cvt,
compass,show);
embAlignWalkSWMatrixFast(path,compass,gapopen,gapextend,a,b,
&m,&n,end1-start1+1,end2-start2+1,
0,width,
&start1,&start2);
if(!ajAlignFormatShowsSequences(align))
{
ajAlignDefineCC(align, ajStrGetPtr(m),
ajStrGetPtr(n), ajSeqGetNameC(a),
ajSeqGetNameC(b));
ajAlignSetScoreR(align, score);
}
else
{
embAlignReportLocal(align, a, b,
m,n,start1,start2,
gapopen, gapextend,
score,matrix, begina, beginb);
}
ajAlignWrite(align);
ajAlignReset(align);
ajStrDel(&n);
}
embWordFreeTable(&seq1MatchTable); /* free table of words */
seq1MatchTable=0;
ajStrDel(&m);
}
if(!ajAlignFormatShowsSequences(align))
{
ajMatrixfDel(&matrix);
}
AJFREE(path);
AJFREE(compass);
ajAlignClose(align);
ajAlignDel(&align);
ajSeqallDel(&seq1);
ajSeqDel(&a);
ajSeqsetDel(&seq2);
ajFileClose(&errorf);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPFile outfile = NULL;
AjBool full = AJFALSE;
AjPStr tmpstr = NULL;
embInit("embossversion", argc, argv);
full = ajAcdGetBoolean("full");
outfile = ajAcdGetOutfile("outfile");
if (!full) {
ajFmtPrintF(outfile,"%s\n", VERSION);
}
else {
tmpstr = ajStrNewRes(128);
ajStrAssignS(&tmpstr, ajNamValuePackage());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "PackageName: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueVersion());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "LibraryVersion: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueSystem());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "System: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueInstalldir());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "InstallDirectory: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueRootdir());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "RootDirectory: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueBasedir());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "BaseDirectory: %S\n", tmpstr);
if (!ajNamGetValueC("acdroot", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_AcdRoot: %S\n", tmpstr);
if (!ajNamGetValueC("data", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Data: %S\n", tmpstr);
if (!ajNamGetValueC("filter", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Filter: %S\n", tmpstr);
if (!ajNamGetValueC("format", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Format: %S\n", tmpstr);
if (!ajNamGetValueC("graphics", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Graphics: %S\n", tmpstr);
if (!ajNamGetValueC("httpversion", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_HttpVersion: %S\n", tmpstr);
if (!ajNamGetValueC("language", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Language: %S\n", tmpstr);
if (!ajNamGetValueC("options", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Options: %S\n", tmpstr);
if (!ajNamGetValueC("outdirectory", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_OutDirectory: %S\n", tmpstr);
if (!ajNamGetValueC("outfeatformat", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_OutFeatFormat: %S\n", tmpstr);
if (!ajNamGetValueC("outformat", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_OutFormat: %S\n", tmpstr);
if (!ajNamGetValueC("proxy", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Proxy: %S\n", tmpstr);
if (!ajNamGetValueC("stdout", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Stdout: %S\n", tmpstr);
if (!ajNamGetValueC("warnrange", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_WarnRange: %S\n", tmpstr);
}
ajFileClose(&outfile);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/*
** All pointers set to NULL for safety.
** Variables names and initialisation values aligned for clarity.
*/
AjBool boo = ajFalse;
ajint n1 = 0;
ajint n2 = 0;
ajlong l1 = 0; /* long int */
float f1 = 0.0;
double d1 = 0.0; /* there is no long double */
size_t size = 100; /* Reserved memory size. Could be any value you know in advance. */
embInit("demostringnew", argc, argv);
demostringnew_msg("/* Starting string values */");
/* Functions with the prefix ajStr are for manipulating EMBOSS strings.
Functions with the prefix ajChar are for manipulating C-type (char*) string
See filesection and datasection sections in ajstr.c */
/*
** String constructor functions
** See "@section constructors" in ajstr.c
*/
/* Construct a new string with no starting value or reserved size.
There is no equivlent function for C-type (char*) strings */
str0 = ajStrNew ();
/* Construct a new string with a reserved size but no starting value */
txt1 = ajCharNewRes(size);
str1 = ajStrNewRes (size);
/* Construct a new C-type (char*) string with a starting value ... */
txt2 = ajCharNewC ("Starting value"); /* ... copied from a C-type (char*) string */
str2 = ajStrNewC (txt2); /* ... copied from a C-type (char*) string */
txt3 = ajCharNewS (str2); /* ... copied from a string */
str3 = ajStrNewS (str2); /* ... copied from a string */
/* Construct a new string with a reserved size and starting value ... */
txt4 = ajCharNewResC("Starting value, reserved size", size); /* ... copied from a C-type (char*) string)*/
str4 = ajStrNewResC (txt4, size); /* ... copied from a C-type (char*) string */
/* or str4 = ajStrNewResLenC(txt4, size, strlen(txt4)); to specify string length */
txt5 = ajCharNewResS(str4, size); /* ... copied from a string */
str5 = ajStrNewResS (str4, size); /* ... copied from a string */
demostringnew_msg("/* After string constructor functions */");
/*
** String destructor functions
** See "@section destructors" in ajstr.c)
*/
/* Destruct a string */
ajCharDel(&txt1);
ajCharDel(&txt2);
ajCharDel(&txt3);
ajCharDel(&txt4);
ajCharDel(&txt5);
ajStrDel (&str0);
ajStrDel (&str1);
ajStrDel (&str3);
ajStrDel (&str5);
/* str2 & str4 still in memory */
demostringnew_msg("/* After string destructor functions */");
/*
** String (de)referencing functions
** See "@section destructors" in ajstr.c)
*/
str0 = ajStrNewRef(str2);
/* or ajStrAssignRef(&str0, str2); */
demostringnew_msg("/* After string reference */");
ajStrDelStatic(&str0);
demostringnew_msg("/* After string dereference */");
/*
** String assignment functions
** See "@section assignment" in ajstr.c)
*/
/* Still only str2 & str4 in memory */
/* Assign a string value using ... */
ajStrAssignC(&str1, "Assigned value"); /* ... a C-type (char*) string */
/* or ajStrAssignLenC(&str1, "Assigned value", strlen("Assigned value")); to specify string length. */
ajStrAssignS(&str3, str1); /* ... a string */
ajStrAssignK(&str5, 'A'); /* ... a character */
demostringnew_msg("/* After string assignment 1 */");
ajStrAssignSubC(&str1, "Assigned value", 0, 11);
ajStrAssignSubS(&str3, str1, 0, 9);
demostringnew_msg("/* After string assignment 2 */");
/* The assignment functions allocate memory if necessary so str1, str3 and str5 will be created for you. It's bad practice to use this mechanism however because it's not obvious the string has been allocated (and needs freeing). Much cleaner to call the construct (ajStrNew) explicitly. */
/* Assign a string with a reserved size and value using ... */
ajStrAssignResC(&str1, size, "Assigned value, reserved size"); /* ... a C-type (char*) string */
ajStrAssignResS(&str3, size, str1); /* ... a string */
demostringnew_msg("/* After string assignment 3 */");
/* Assign a string value only if the string is empty using ... */
str0 = ajStrNew();
ajStrAssignEmptyC(&str0, "New value if string was empty"); /* ... a C-type (char*) string */
ajStrAssignEmptyS(&str1, str0); /* ... a string */
demostringnew_msg("/* After string assignment 4 */");
/* Now str0-5 in memory. The above code is for illustrative purposes: it's much cleaner to put all the constructors / destructors at the top / bottom of the code where possible. */
/* Assign all strings intuitive values */
txt0 = ajCharNewResC("TEXT 0", 100);
txt1 = ajCharNewResC("TEXT 1", 100);
txt2 = ajCharNewResC("Text 2", 100);
txt3 = ajCharNewResC("Text 3", 100);
txt4 = ajCharNewResC("Text 4", 100);
txt5 = ajCharNewResC("Text 5", 100);
ajStrAssignC(&str0, "STRING 0");
ajStrAssignC(&str1, "STRING 1");
ajStrAssignC(&str2, "String 2");
ajStrAssignC(&str3, "String 3");
ajStrAssignC(&str4, "String 4 WITHSOMETEXTINABLOCK");
ajStrAssignC(&str5, "String 5 WITHSOMETEXTINABLOCK");
demostringnew_msg("/* After string assignment 5 */");
/*
** String formatting functions
** See "@section formatting" in ajstr.c
*/
ajCharFmtLower(txt0);
ajCharFmtLower(txt1);
ajStrFmtLower(&str0);
ajStrFmtLowerSub(&str1, 0, 2);
ajCharFmtUpper(txt2);
ajCharFmtUpper(txt3);
ajStrFmtUpper(&str2);
ajStrFmtUpperSub(&str3, 0, 2);
demostringnew_msg("/* After string formatting 1 */");
ajStrFmtTitle(&str0);
ajStrFmtQuote(&str1);
ajStrFmtBlock(&str4, 3);
demostringnew_msg("/* After string formatting 2 */");
/* See also ajStrFmtWrap, ajStrFmtWrapLeft
... these need checking. */
/*
** String conversion functions
** See "@section datatype to string conversion" in ajstr.c
*/
n1 = n2 = l1 = 1;
f1 = d1 = 0.5;
ajStrFromBool( &str0, boo);
ajStrFromInt(&str1, n1);
ajStrFromLong(&str2, l1);
ajStrFromFloat(&str3, f1, 5);
ajStrFromDouble(&str4, d1, 5);
ajStrFromDoubleExp(&str5, d1, 5);
demostringnew_msg("/* After datatype to string conversion */");
/*
** String conversion functions
** See "@section string to datatype conversion" in ajstr.c
*/
ajStrToBool(str0, &boo);
ajStrToInt(str1, &n1);
ajStrToLong(str2, &l1);
ajStrToDouble(str4, &d1);
ajUser("/* After string to datatype conversion */\n"
"boo (from str0): %B\nn1 (from str1): %d\nl1 (from str2): %d",
boo, n1, l1);
ajFmtPrint("f1 (from str3): %f\nd1 (from str4): %f\n", f1, d1);
/* Check ajUser ... doesn't support %f */
/* See also ajStrToHex */
/* Assign all strings new values */
strcpy(txt0, "Text String");
strcpy(txt1, "TEXT STRING");
strcpy(txt2, "Text*");
strcpy(txt3, "Text");
strcpy(txt4, "Text String 4");
strcpy(txt5, "Text String 5");
ajStrAssignC(&str0, "String");
ajStrAssignC(&str1, "STRING");
ajStrAssignC(&str2, "String*");
ajStrAssignC(&str3, "*String");
ajStrAssignC(&str4, "String 4");
ajStrAssignC(&str5, "String 5");
demostringnew_msg("/* After resetting strings */");
/*
** String comparison functions
** See "@section comparison" in ajstr.c
*/
ajUserDumpC("/* String comparison functions */");
boo = ajCharMatchC(txt0, txt1);
ajUser("ajCharMatchC(txt0 txt1); == %B", boo);
boo = ajCharMatchCaseC(txt0, txt1);
ajUser("ajCharMatchCaseC(txt0 txt1); == %B", boo);
boo = ajCharMatchC(txt0, txt2);
ajUser("ajCharMatchC(txt0,txt2); == %B", boo);
boo = ajCharMatchWildC(txt0, txt2);
ajUser("ajCharMatchWildC(txt0,txt2); == %B", boo);
boo = ajCharMatchWildS(txt0, str2);
ajUser("ajCharMatchWildS(txt0,str2); == %B", boo);
/* See also ajCharMatchWildNextC, ajCharMatchWildWordC
... these need checking & documentation updated. */
boo = ajCharPrefixC(txt0, txt3);
ajUser("ajCharPrefixC(txt0, txt3); == %B", boo);
boo = ajCharPrefixS(txt0, str0);
ajUser("ajCharPrefixS(txt0, str0); == %B", boo);
boo = ajCharPrefixCaseC(txt5, txt1);
ajUser("ajCharPrefixCaseC(txt5, txt1); == %B", boo);
boo = ajCharPrefixCaseC(txt1, txt5);
ajUser("ajCharPrefixCaseC(txt1, txt5); == %B", boo);
boo = ajCharPrefixCaseS(txt0, str0);
ajUser("ajCharPrefixCaseS(txt0, str0); == %B", boo);
boo = ajCharSuffixC(txt0, txt3);
ajUser("ajCharSuffixC(txt0, txt3); === %B", boo);
boo = ajCharSuffixS(txt0, str0);
ajUser("ajCharSuffixS(txt0, str0); == %B", boo);
/* See also ajCharSuffixCaseC, ajCharSuffixCaseC, ajCharSuffixCaseS, ajCharSuffixCaseS
... these need checking. */
boo = ajStrMatchC (str0, txt0);
ajUser("ajStrMatchC (str0, txt0); == %B", boo);
boo = ajStrMatchS(str0, str1);
ajUser("ajStrMatchS(str0, str1); == %B", boo);
boo = ajStrMatchCaseC(str0, txt0);
ajUser("ajStrMatchCaseC(str0, txt0); == %B", boo);
boo = ajStrMatchCaseS(str0, str0);
ajUser("ajStrMatchCaseS(str0, str0); == %B", boo);
/*
ajUser("== %B", boo);
boo = ajStrMatchWildC(str2, const char* text);
ajStrMatchWildS (const AjPStr thys, const AjPStr wild);
ajStrMatchWildWordC (const AjPStr str, const char* text);
ajStrMatchWildWordS (const AjPStr str, const AjPStr text);
ajStrPrefixC(const AjPStr str, const char* txt2);
ajStrPrefixS(const AjPStr str, const AjPStr str2);
ajStrPrefixCaseC (const AjPStr str, const char* pref);
ajStrPrefixCaseS (const AjPStr str, const AjPStr pref);
ajStrSuffixC (const AjPStr thys, const char* suff);
ajStrSuffixS (const AjPStr thys, const AjPStr suff);
*/
/**************************************************************************/
/* String substitution functions (See "@section substitution" in ajstr.c) */
/**************************************************************************/
/*
AjBool ajStrExchangeCC(AjPStr* Pstr, const char* txt, const char* txtnew);
AjBool ajStrExchangeCS(AjPStr* Pstr, const char* txt,
const AjPStr strnew);
AjBool ajStrExchangeKK(AjPStr* Pstr, char chr, char chrnew);
AjBool ajStrExchangeSC(AjPStr* Pstr, const AjPStr str,
const char* txtnew);
AjBool ajStrExchangeSS(AjPStr* Pstr, const AjPStr str,
const AjPStr strnew);
AjBool ajStrExchangeSetCC(AjPStr* Pstr, const char* oldc,
const char* newc);
AjBool ajStrExchangeSetSS(AjPStr* Pstr, const AjPStr str,
const AjPStr strnew);
AjBool ajStrRandom(AjPStr *s);
AjBool ajStrReverse(AjPStr* Pstr);
*/
embExit();
return 0;
}
static AjBool assemoutWriteSamAlignment(AjPFile outf, const AjPAssemRead r,
AjPAssemContig const * contigs,
ajint ncontigs)
{
AjPAssemTag t = NULL;
AjIList l = NULL;
AjPStr qualstr = NULL;
AjPStr tmp = NULL;
ajint POS = 0;
AjPStr CIGAR = NULL;
const char* RNEXT = NULL;
AjPStr SEQ = NULL;
AjPStr QUAL = NULL;
AjPStr SEQunpadded = NULL;
AjPStr QUALunpadded = NULL;
AjPStr consensus = NULL;
AjBool rc= ajFalse;
AjBool ret = ajTrue;
const char* refseq = NULL;
const AjPAssemContig contig = NULL;
ajuint k = 0;
if(r->Reference>=ncontigs)
ajDie("assemoutWriteSamAlignment: reference sequence number"
" '%d' is larger than or equal to known number of reference"
" sequences '%d'. Problem while processing read '%S'.",
r->Reference,
ncontigs,
r->Name);
contig = (r->Reference==-1 ? NULL : contigs[r->Reference]);
ajStrAssignRef(&SEQ, r->Seq);
consensus = contig==NULL? NULL : contig->Consensus;
if (r->Rnext==-1)
RNEXT= "*";
else if(r->Rnext==r->Reference)
RNEXT = "=";
else
RNEXT = ajStrGetPtr(contigs[r->Rnext]->Name);
if (r->Flag & BAM_FREVERSE)
{
rc = ajTrue;
qualstr = ajStrNewS(r->SeqQ);
if(!r->Reversed)
{
ajStrReverse(&qualstr);
ajSeqstrReverse(&SEQ);
}
QUAL = qualstr;
POS = r->y1;
ajStrAssignSubS(&tmp, SEQ,
ajStrGetLen(r->Seq) - r->y2,
ajStrGetLen(r->Seq) - r->x2
);
}
else
{
rc= ajFalse;
POS = r->x1;
QUAL = r->SeqQ;
ajStrAssignSubS(&tmp, SEQ,
r->x2-1,
r->y2-1
);
}
if(r->Cigar==NULL && consensus)
{
refseq = ajStrGetPtr(consensus) + (rc ? r->y1-1 : r->x1-1);
CIGAR = assemoutMakeCigar(refseq, ajStrGetPtr(tmp));
SEQunpadded = ajStrNewRes(ajStrGetLen(SEQ));
QUALunpadded = ajStrNewRes(ajStrGetLen(SEQ));
for(k=0; k< ajStrGetLen(SEQ); k++)
{
if (ajStrGetCharPos(SEQ, k) == '*')
continue;
ajStrAppendK(&SEQunpadded, ajStrGetCharPos(SEQ, k));
ajStrAppendK(&QUALunpadded, ajStrGetCharPos(QUAL, k));
}
ajDebug("cigar: %S\n", CIGAR);
ajStrAssignS(&tmp, CIGAR);
if(rc)
{
if(r->y2 < (ajint)ajStrGetLen(SEQ))
ajFmtPrintS(&CIGAR, "%dS%S",
ajStrGetLen(SEQ) - r->y2, tmp);
if(r->x2 > 1)
ajFmtPrintAppS(&CIGAR, "%dS", r->x2 - 1);
}
else
{
if(r->x2 > 1)
ajFmtPrintS(&CIGAR, "%dS%S", r->x2 - 1, tmp);
if(r->y2 < (ajint)ajStrGetLen(SEQ))
ajFmtPrintAppS(&CIGAR, "%dS",
ajStrGetLen(SEQ) - r->y2);
}
ajStrDel(&tmp);
}
else if(r->Cigar==NULL)
{
ajErr("both CIGAR string and consensus sequence not available");
ret = ajFalse;
ajStrAssignK(&CIGAR, '*');
}
else if(!ajStrGetLen(r->Cigar))
ajStrAssignK(&CIGAR, '*');
else if(ajStrGetLen(r->Cigar))
{
if(!ajStrGetLen(SEQ))
ajStrAssignK(&SEQ, '*');
if(!ajStrGetLen(QUAL))
ajStrAssignK(&QUAL, '*');
}
ajStrDel(&tmp);
ajFmtPrintF(outf, "%S\t%d\t%s\t%d\t%d\t%S\t%s\t%Ld\t%d\t%S\t%S",
r->Name,
r->Flag,
(contig==NULL ? "*" : ajStrGetPtr(contig->Name)),
POS,
r->MapQ,
(CIGAR ? CIGAR : r->Cigar),
RNEXT,
r->Pnext,
r->Tlen,
(r->Cigar ? SEQ : SEQunpadded),
(r->Cigar ? QUAL : QUALunpadded));
l = ajListIterNewread(r->Tags);
while (!ajListIterDone(l))
{
t = ajListIterGet(l);
/* TODO: array type, 'B' */
/* In SAM, all single integer types are mapped to int32_t [SAM spec] */
ajFmtPrintF(outf, "\t%S:%c:",
t->Name,
(t->type == 'c' || t->type == 'C' ||
t->type == 's' || t->type == 'S'
|| t->type == 'I') ? 'i' : t->type
);
if(t->x1 || t->y1)
ajFmtPrintF(outf, " %u %u", t->x1, t->y1);
if(t->Comment && ajStrGetLen(t->Comment)>0)
ajFmtPrintF(outf, "%S", t->Comment);
}
ajListIterDel(&l);
ajFmtPrintF(outf, "\n");
if(qualstr)
ajStrDel(&qualstr);
ajStrDel(&SEQ);
ajStrDel(&CIGAR);
ajStrDel(&SEQunpadded);
ajStrDel(&QUALunpadded);
return ret;
}
int main(int argc, char **argv)
{
AjPSeqall queryseqs;
AjPSeqset targetseqs;
AjPSeq queryseq;
const AjPSeq targetseq;
AjPStr queryaln = 0;
AjPStr targetaln = 0;
AjPFile errorf;
AjBool show = ajFalse;
const char *queryseqc;
const char *targetseqc;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
ajint *compass = NULL;
float *path = NULL;
float gapopen;
float gapextend;
float score;
float minscore;
ajuint j, k;
ajint querystart = 0;
ajint targetstart = 0;
ajint queryend = 0;
ajint targetend = 0;
ajint width = 0;
AjPTable kmers = 0;
ajint wordlen = 6;
ajint oldmax = 0;
ajint newmax = 0;
ajuint ntargetseqs;
ajuint nkmers;
AjPAlign align = NULL;
EmbPWordMatch maxmatch; /* match with maximum score */
/* Cursors for the current sequence being scanned,
** i.e., until which location it was scanned.
** Separate cursor/location entries for each sequence in the seqset.
*/
ajuint* lastlocation;
EmbPWordRK* wordsw = NULL;
AjPList* matchlist = NULL;
embInit("supermatcher", argc, argv);
matrix = ajAcdGetMatrixf("datafile");
queryseqs = ajAcdGetSeqall("asequence");
targetseqs= ajAcdGetSeqset("bsequence");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
wordlen = ajAcdGetInt("wordlen");
align = ajAcdGetAlign("outfile");
errorf = ajAcdGetOutfile("errorfile");
width = ajAcdGetInt("width"); /* width for banded Smith-Waterman */
minscore = ajAcdGetFloat("minscore");
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
embWordLength(wordlen);
/* seqset sequence is the reference sequence for SAM format */
ajAlignSetRefSeqIndx(align, 1);
ajSeqsetTrim(targetseqs);
ntargetseqs = ajSeqsetGetSize(targetseqs);
AJCNEW0(matchlist, ntargetseqs);
/* get tables of words */
for(k=0;k<ntargetseqs;k++)
{
targetseq = ajSeqsetGetseqSeq(targetseqs, k);
embWordGetTable(&kmers, targetseq);
ajDebug("Number of distinct kmers found so far: %d\n",
ajTableGetLength(kmers));
}
AJCNEW0(lastlocation, ntargetseqs);
if(ajTableGetLength(kmers)<1)
ajErr("no kmers found");
nkmers = embWordRabinKarpInit(kmers, &wordsw, wordlen, targetseqs);
while(ajSeqallNext(queryseqs,&queryseq))
{
ajSeqTrim(queryseq);
queryaln = ajStrNewRes(1+ajSeqGetLen(queryseq));
ajDebug("Read '%S'\n", ajSeqGetNameS(queryseq));
for(k=0;k<ntargetseqs;k++)
{
lastlocation[k]=0;
matchlist[k] = ajListstrNew();
}
embWordRabinKarpSearch(ajSeqGetSeqS(queryseq), targetseqs,
(const EmbPWordRK*)wordsw, wordlen, nkmers,
matchlist, lastlocation, ajFalse);
for(k=0;k<ajSeqsetGetSize(targetseqs);k++)
{
targetseq = ajSeqsetGetseqSeq(targetseqs, k);
ajDebug("Processing '%S'\n", ajSeqGetNameS(targetseq));
if(ajListGetLength(matchlist[k])==0)
{
ajFmtPrintF(errorf,
"No wordmatch start points for "
"%s vs %s. No alignment\n",
ajSeqGetNameC(queryseq),ajSeqGetNameC(targetseq));
embWordMatchListDelete(&matchlist[k]);
continue;
}
/* only the maximum match is used as seed
* (if there is more than one location with the maximum match
* only the first one is used)
* TODO: we should add a new option to make above limit optional
*/
maxmatch = embWordMatchFirstMax(matchlist[k]);
supermatcher_findendpoints(maxmatch,targetseq, queryseq,
&targetstart, &querystart,
&targetend, &queryend);
targetaln=ajStrNewRes(1+ajSeqGetLen(targetseq));
queryseqc = ajSeqGetSeqC(queryseq);
targetseqc = ajSeqGetSeqC(targetseq);
ajStrAssignC(&queryaln,"");
ajStrAssignC(&targetaln,"");
ajDebug("++ %S v %S start:%d %d end:%d %d\n",
ajSeqGetNameS(targetseq), ajSeqGetNameS(queryseq),
targetstart, querystart, targetend, queryend);
newmax = (targetend-targetstart+2)*width;
if(newmax > oldmax)
{
AJCRESIZE0(path,oldmax,newmax);
AJCRESIZE0(compass,oldmax,newmax);
oldmax=newmax;
ajDebug("++ memory re/allocation for path/compass arrays"
" to size: %d\n", newmax);
}
else
{
AJCSET0(path,newmax);
AJCSET0(compass,newmax);
}
ajDebug("Calling embAlignPathCalcSWFast "
"%d..%d [%d/%d] %d..%d [%d/%d] width:%d\n",
querystart, queryend, (queryend - querystart + 1),
ajSeqGetLen(queryseq),
targetstart, targetend, (targetend - targetstart + 1),
ajSeqGetLen(targetseq),
width);
score = embAlignPathCalcSWFast(&targetseqc[targetstart],
&queryseqc[querystart],
targetend-targetstart+1,
queryend-querystart+1,
0,width,
gapopen,gapextend,
path,sub,cvt,
compass,show);
if(score>minscore)
{
embAlignWalkSWMatrixFast(path,compass,gapopen,gapextend,
targetseq,queryseq,
&targetaln,&queryaln,
targetend-targetstart+1,
queryend-querystart+1,
0,width,
&targetstart,&querystart);
if(!ajAlignFormatShowsSequences(align))
{
ajAlignDefineCC(align, ajStrGetPtr(targetaln),
ajStrGetPtr(queryaln),
ajSeqGetNameC(targetseq),
ajSeqGetNameC(queryseq));
ajAlignSetScoreR(align, score);
}
else
{
ajDebug(" queryaln:%S \ntargetaln:%S\n",
queryaln,targetaln);
embAlignReportLocal(align,
queryseq, targetseq,
queryaln, targetaln,
querystart, targetstart,
gapopen, gapextend,
score, matrix,
1 + ajSeqGetOffset(queryseq),
1 + ajSeqGetOffset(targetseq)
);
}
ajAlignWrite(align);
ajAlignReset(align);
}
ajStrDel(&targetaln);
embWordMatchListDelete(&matchlist[k]);
}
ajStrDel(&queryaln);
}
for(k=0;k<nkmers;k++)
{
AJFREE(wordsw[k]->seqindxs);
AJFREE(wordsw[k]->nSeqMatches);
for(j=0;j<wordsw[k]->nseqs;j++)
AJFREE(wordsw[k]->locs[j]);
AJFREE(wordsw[k]->nnseqlocs);
AJFREE(wordsw[k]->locs);
AJFREE(wordsw[k]);
}
embWordFreeTable(&kmers);
if(!ajAlignFormatShowsSequences(align))
ajMatrixfDel(&matrix);
AJFREE(path);
AJFREE(compass);
AJFREE(kmers);
AJFREE(wordsw);
AJFREE(matchlist);
AJFREE(lastlocation);
ajAlignClose(align);
ajAlignDel(&align);
ajSeqallDel(&queryseqs);
ajSeqDel(&queryseq);
ajSeqsetDel(&targetseqs);
ajFileClose(&errorf);
embExit();
return 0;
}
