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)
{
/* ACD data item variables */
AjPSeqset dataset = NULL;
AjPFile bfile = NULL;
AjPFile plib = NULL;
AjPStr mod = NULL;
ajint nmotifs = 0;
AjBool text = ajFalse;
AjPStr prior = NULL;
float evt = 0.0;
ajint nsites = 0;
ajint minsites = 0;
ajint maxsites = 0;
float wnsites = 0.0;
ajint w = 0;
ajint minw = 0;
ajint maxw = 0;
AjBool nomatrim = ajFalse;
ajint wg = 0;
ajint ws = 0;
AjBool noendgaps = ajFalse;
AjBool revcomp = ajFalse;
AjBool pal = ajFalse;
AjBool nostatus = ajFalse;
ajint maxiter = 0;
float distance = 0.0;
float b = 0.0;
float spfuzz = 0.0;
AjPStr spmap = NULL;
AjPStr cons = NULL;
ajint maxsize = 0;
ajint p = 0;
ajint time = 0;
AjPStr sf = NULL;
ajint heapsize = 64;
AjBool xbranch = ajFalse;
AjBool wbranch = ajFalse;
ajint bfactor = 0;
AjPFile outtext = NULL;
/* Housekeeping variables */
AjPStr cmd = NULL;
AjPStr ssname = NULL;
AjPSeqout outseq = NULL;
AjPStr tmp = NULL;
char option;
/* ACD file processing */
embInitPV("ememetext",argc,argv,"MEME",VERSION);
dataset = ajAcdGetSeqset("dataset");
bfile = ajAcdGetInfile("bfile");
plib = ajAcdGetInfile("plibfile");
mod = ajAcdGetSelectSingle("mod");
nmotifs = ajAcdGetInt("nmotifs");
text = ajAcdGetBoolean("text");
prior = ajAcdGetSelectSingle("prior");
evt = ajAcdGetFloat("evt");
nsites = ajAcdGetInt("nsites");
minsites = ajAcdGetInt("minsites");
maxsites = ajAcdGetInt("maxsites");
wnsites = ajAcdGetFloat("wnsites");
w = ajAcdGetInt("w");
minw = ajAcdGetInt("minw");
maxw = ajAcdGetInt("maxw");
nomatrim = ajAcdGetBoolean("nomatrim");
wg = ajAcdGetInt("wg");
ws = ajAcdGetInt("ws");
noendgaps = ajAcdGetBoolean("noendgaps");
revcomp = ajAcdGetBoolean("revcomp");
pal = ajAcdGetBoolean("pal");
nostatus = ajAcdGetBoolean("nostatus");
maxiter = ajAcdGetInt("maxiter");
distance = ajAcdGetFloat("distance");
b = ajAcdGetFloat("b");
spfuzz = ajAcdGetFloat("spfuzz");
spmap = ajAcdGetSelectSingle("spmap");
cons = ajAcdGetString("cons");
maxsize = ajAcdGetInt("maxsize");
p = ajAcdGetInt("p");
time = ajAcdGetInt("time");
sf = ajAcdGetString("sf");
heapsize = ajAcdGetInt("heapsize");
xbranch = ajAcdGetBoolean("xbranch");
wbranch = ajAcdGetBoolean("wbranch");
bfactor = ajAcdGetInt("bfactor");
outtext = ajAcdGetOutfile("outtext");
outseq = ajAcdGetSeqoutset("outseq");
/* MAIN APPLICATION CODE */
/* 1. Housekeeping */
cmd = ajStrNew();
tmp = ajStrNew();
/* 2. Re-write dataset to a temporary file in a format (fasta) MEME
** can understand.
** Can't just pass the name of dataset to MEME as the name provided
** might be a USA which MEME would not understand.
*/
ssname = ajStrNewS(ajFileGetNameS(outseq->File));
ajSeqoutSetFormatC(outseq, "fasta");
ajSeqoutWriteSet(outseq, dataset);
ajSeqoutClose(outseq);
ajSeqoutDel(&outseq);
/* 3. Build ememe command line */
/* Command line is built in this order:
i. Application name.
ii. Original MEME options (in order they appear in ACD file)
iii.Original MEME options (that don't appear in ACD file)
iv. EMBASSY MEME new qualifiers and parameters.
*/
ajStrAssignS(&cmd, ajAcdGetpathC("meme"));
ajFmtPrintAppS(&cmd, " %S", ssname);
if(bfile)
ajFmtPrintAppS(&cmd, " -bfile %s ", ajFileGetNameC(bfile));
if(plib)
ajFmtPrintAppS(&cmd, " -plib %s ", ajFileGetNameC(plib));
option = ajStrGetCharFirst(mod);
if(option == 'o')
ajStrAppendC(&cmd, " -mod oops ");
else if(option == 'z')
ajStrAppendC(&cmd, " -mod zoops ");
else if(option == 'a')
ajStrAppendC(&cmd, " -mod anr ");
if(nmotifs != 1)
ajFmtPrintAppS(&cmd, " -nmotifs %d ", nmotifs);
if(text)
ajFmtPrintAppS(&cmd, " -text ");
ajFmtPrintAppS(&cmd, " -prior %S ", prior);
if(evt != -1)
ajFmtPrintAppS(&cmd, " -evt %f ", evt);
if(nsites != -1)
ajFmtPrintAppS(&cmd, " -nsites %d ", nsites);
else
{
if(minsites != -1)
ajFmtPrintAppS(&cmd, " -minsites %d ", minsites);
if(maxsites != -1)
ajFmtPrintAppS(&cmd, " -maxsites %d ", maxsites);
}
if(wnsites < 0.7999 || wnsites > .8001)
ajFmtPrintAppS(&cmd, " -wnsites %f ", wnsites);
if(w != -1)
ajFmtPrintAppS(&cmd, " -w %d ", w);
if(minw != 8)
ajFmtPrintAppS(&cmd, " -minw %d ", minw);
if(maxw != 50)
ajFmtPrintAppS(&cmd, " -maxw %d ", maxw);
if(nomatrim)
ajFmtPrintAppS(&cmd, " -nomatrim ");
if(wg != 11)
ajFmtPrintAppS(&cmd, " -wg %d ", wg);
if(ws != 1)
ajFmtPrintAppS(&cmd, " -ws %d ", ws);
if(noendgaps)
ajFmtPrintAppS(&cmd, " -noendgaps ");
if(revcomp)
ajFmtPrintAppS(&cmd, " -revcomp ");
if(pal && ajSeqsetIsNuc(dataset))
ajFmtPrintAppS(&cmd, " -pal ");
if(nostatus)
ajFmtPrintAppS(&cmd, " -nostatus ");
if(maxiter != 50)
ajFmtPrintAppS(&cmd, " -maxiter %d ", maxiter);
if(distance < 0.00099 || distance > 0.00101)
ajFmtPrintAppS(&cmd, " -distance %f ", distance);
if(b != -1)
ajFmtPrintAppS(&cmd, " -b %f ", b);
if(spfuzz != -1)
ajFmtPrintAppS(&cmd, " -spfuzz %f ", spfuzz);
if(!ajStrMatchC(spmap,"default"))
ajFmtPrintAppS(&cmd, " -spmap %S ", spmap);
if(MAJSTRGETLEN(cons))
ajFmtPrintAppS(&cmd, "-cons %S", cons);
if(maxsize != -1)
ajFmtPrintAppS(&cmd, " -maxsize %d ", maxsize);
if(p > 0)
ajFmtPrintAppS(&cmd, " -p %d ", p);
if(time > 0)
ajFmtPrintAppS(&cmd, " -time %d ", time);
if(MAJSTRGETLEN(sf))
ajFmtPrintAppS(&cmd, " -sf %S", sf);
if(heapsize != 64)
ajFmtPrintAppS(&cmd, " -heapsize %d ", heapsize);
if(xbranch)
ajFmtPrintAppS(&cmd, " -x_branch");
if(wbranch)
ajFmtPrintAppS(&cmd, " -w_branch");
if(bfactor != 3)
ajFmtPrintAppS(&cmd, " -bfactor %d ", bfactor);
if(ajSeqsetIsProt(dataset))
ajFmtPrintAppS(&cmd, "-protein ");
else
ajFmtPrintAppS(&cmd, "-dna ");
ajFmtPrintAppS(&cmd, " -text");
ajFmtPrintAppS(&cmd, " > %S ", ajFileGetNameS(outtext));
/* 4. Close files from ACD before calling meme */
ajFileClose(&bfile);
ajFileClose(&plib);
/* 5. Call meme */
/* ajFmtPrint("\n%S\n", cmd); */
system(ajStrGetPtr(cmd));
/* 6. Exit cleanly */
ajSeqsetDel(&dataset);
ajStrDel(&cons);
ajStrDel(&sf);
ajStrDel(&mod);
ajStrDel(&prior);
ajStrDel(&spmap);
ajStrDel(&cmd);
ajStrDel(&ssname);
ajStrDel(&tmp);
ajFileClose(&bfile);
ajFileClose(&plib);
ajFileClose(&outtext);
ajSeqoutDel(&outseq);
embExit();
return 0;
}
void emboss_copy(AjPSeqset seqset, char ***retseqs, AINFO *info)
{
ajint n;
ajint maxlen;
ajint len;
char **seqs;
const AjPSeq seq = NULL;
ajint i=0;
const AjPStr fmt=NULL;
const char *p=NULL;
char c='\0';
/*
char *q=NULL;
AjPSelexseq sqdata=NULL;
AjPSelexdata sdata=NULL;
*/
ajint cnt=0;
info->name = NULL;
info->rf=NULL;
info->cs=NULL;
info->desc=NULL;
info->acc=NULL;
info->au=NULL;
info->flags=0;
AjPStr tmpstr = NULL;
ajSeqsetFill(seqset);
fmt = ajSeqsetGetFormat(seqset);
n = ajSeqsetGetSize(seqset);
ajSeqsetFmtUpper(seqset);
maxlen = ajSeqsetGetLen(seqset);
/* First allocate and copy sequences */
AJCNEW0(seqs,n);
for(i=0; i<n; ++i)
{
seqs[i] = ajCharNewRes(maxlen+1);
strcpy(seqs[i],ajSeqGetSeqC(ajSeqsetGetseqSeq(seqset,i)));
}
info->sqinfo = (SQINFO *) calloc (sizeof(SQINFO), n);
for(i=0; i<n; ++i)
{
info->sqinfo[i].flags = 0;
strcpy(info->sqinfo[i].name,"");
strcpy(info->sqinfo[i].id,"");
strcpy(info->sqinfo[i].acc,"");
strcpy(info->sqinfo[i].desc,"");
info->sqinfo[i].len = 0;
info->sqinfo[i].start = 0;
info->sqinfo[i].stop = 0;
info->sqinfo[i].olen = 0;
info->sqinfo[i].type = 0;
info->sqinfo[i].ss = NULL;
info->sqinfo[i].sa =NULL;
}
AJCNEW0(info->wgt,n);
for(i=0; i<n; ++i)
{
info->sqinfo[i].flags = 0;
info->wgt[i] = ajSeqsetGetseqWeight(seqset,i);
}
info->nseq = n;
info->alen = maxlen;
for(i=0; i<n; ++i)
{
seq = ajSeqsetGetseqSeq(seqset,i);
if((len=ajStrGetLen(ajSeqGetNameS(seq))))
{
if(len>= SQINFO_NAMELEN)
len = SQINFO_NAMELEN - 1;
ajStrAssignSubS(&tmpstr, ajSeqGetNameS(seq), 0, len);
strcpy(info->sqinfo[i].id,ajStrGetPtr(tmpstr));
info->sqinfo[i].flags |= SQINFO_ID;
strcpy(info->sqinfo[i].name,ajStrGetPtr(tmpstr));
info->sqinfo[i].flags |= SQINFO_NAME;
}
if((len=ajStrGetLen(ajSeqGetAccS(seq))))
{
if(len>= SQINFO_NAMELEN)
len = SQINFO_NAMELEN - 1;
ajStrAssignSubS(&tmpstr, ajSeqGetAccS(seq), 0, len);
strcpy(info->sqinfo[i].acc,ajStrGetPtr(tmpstr));
info->sqinfo[i].flags |= SQINFO_ACC;
}
}
seq = ajSeqsetGetseqSeq(seqset,0);
info->cs = ajCharNewS(ajSeqGetSeqS(seq));
info->name = ajCharNewS(ajSeqGetNameS(seq));
info->acc = ajCharNewS(ajSeqGetAccS(seq));
info->desc = ajCharNewS(ajSeqGetDescS(seq));
info->rf = ajCharNewS(ajSeqGetSeqS(seq));
/*
info->rf = ajCharNewS(seq);
len = ajStrGetLen(seq->Selexdata->name);
info->name = ajCharNewRes(len+1);
strcpy(info->name,ajStrGetPtr(seq->Selexdata->name));
len = ajStrGetLen(seq->Selexdata->de);
info->desc = ajCharNewRes(len+1);
sdata = seq->Selexdata;
strcpy(info->desc,ajStrGetPtr(sdata->de));
len = ajStrGetLen(sdata->ac);
info->acc = ajCharNewRes(len+1);
strcpy(info->acc,ajStrGetPtr(sdata->ac));
len = ajStrGetLen(sdata->au);
info->au = ajCharNewRes(len+1);
strcpy(info->au,ajStrGetPtr(sdata->au));
if(sdata->tc[0] || sdata->tc[1])
{
info->flags |= AINFO_TC;
info->tc1 = sdata->tc[0];
info->tc2 = sdata->tc[1];
}
if(sdata->nc[0] || sdata->nc[1])
{
info->flags |= AINFO_NC;
info->nc1 = sdata->nc[0];
info->nc2 = sdata->nc[1];
}
if(sdata->ga[0] || sdata->ga[1])
{
info->flags |= AINFO_GA;
info->ga1 = sdata->ga[0];
info->ga2 = sdata->ga[1];
}
for(i=0;i<n;++i)
{
seq = ajSeqsetGetseqSeq(seqset,i);
sqdata = seq->Selexdata->sq;
if((len=ajStrGetLen(sqdata->name)))
{
if(len<64)
strcpy(info->sqinfo[i].name,ajStrGetPtr(sqdata->name));
else
strncpy(info->sqinfo[i].name,ajStrGetPtr(sqdata->name),63);
info->sqinfo[i].name[63]='\0';
info->sqinfo[i].flags |= SQINFO_NAME;
}
/ *
if((len=ajStrGetLen(sqdata->id)))
{
if(len<64)
strcpy(info->sqinfo[i].id,ajStrGetPtr(sqdata->id));
else
strncpy(info->sqinfo[i]->id,ajStrGetPtr(sqdata->id),63);
info->sqinfo[i].id[63]='\0';
info->sqinfo[i].flags |= SQINFO_ID;
}
* /
strcpy(info->sqinfo[i].id,info->sqinfo[i].name);
info->sqinfo[i].flags |= SQINFO_ID;
if((len=ajStrGetLen(sqdata->ac)))
{
if(len<64)
strcpy(info->sqinfo[i].acc,ajStrGetPtr(sqdata->ac));
else
strncpy(info->sqinfo[i].acc,ajStrGetPtr(sqdata->ac),63);
info->sqinfo[i].acc[63]='\0';
info->sqinfo[i].flags |= SQINFO_ACC;
}
if((len=ajStrGetLen(sqdata->de)))
{
if(len<127)
strcpy(info->sqinfo[i].desc,ajStrGetPtr(sqdata->de));
else
strncpy(info->sqinfo[i].desc,ajStrGetPtr(sqdata->de),127);
info->sqinfo[i].desc[127]='\0';
info->sqinfo[i].flags |= SQINFO_DESC;
}
if(sqdata->start || sqdata->stop || sqdata ->len)
{
info->sqinfo[i].start = sqdata->start;
info->sqinfo[i].stop = sqdata->stop;
info->sqinfo[i].olen = sqdata->len;
info->sqinfo[i].flags |= SQINFO_START;
info->sqinfo[i].flags |= SQINFO_STOP;
info->sqinfo[i].flags |= SQINFO_OLEN;
}
if(ajStrGetLen(seq->Selexdata->ss))
{
info->sqinfo[i].ss = ajCharNewRes(maxlen+1);
p = ajStrGetPtr(seq->Selexdata->ss);
q = info->sqinfo[i].ss;
while((c==*p))
{
if(c=='.' || c==' ' || c=='_' || c=='-')
*q++ = c;
++p;
}
*q = '\0';
info->sqinfo[i].flags |= SQINFO_SS;
}
}
}
/ *
}
*/
for(i=0; i<n; ++i)
{
info->sqinfo[i].type = kOtherSeq;
if(ajSeqsetIsDna(seqset))
info->sqinfo[i].type = kDNA;
if(ajSeqsetIsRna(seqset))
info->sqinfo[i].type = kRNA;
if(ajSeqsetIsProt(seqset))
info->sqinfo[i].type = kAmino;
info->sqinfo[i].flags |= SQINFO_TYPE;
seq = ajSeqsetGetseqSeq(seqset,i);
p = ajSeqGetSeqC(seq);
cnt = 0;
while((c=*p))
{
if(!(c=='.' || c==' ' || c=='_' || c=='-' || c=='~'))
++cnt;
++p;
}
info->sqinfo[i].len = cnt;
info->sqinfo[i].flags |= SQINFO_LEN;
}
*retseqs = seqs;
ajStrDel(&tmpstr);
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;
}
int main(int argc, char **argv)
{
AjPStr cl = NULL;
AjPSeqset seqset = NULL;
AjPSeqout seqout = NULL;
AjPStr stmp = NULL;
AjPStr email = NULL;
AjPStr fmt = NULL;
AjPStr trtab = NULL;
const AjPStr ofn = NULL;
AjPStr *applist = NULL;
AjBool crc = ajFalse;
AjBool alt = ajFalse;
AjBool iprlook = ajFalse;
AjBool goterms = ajFalse;
ajint trlen = 0;
ajuint i = 0;
ajuint lcnt = 0;
AjPStr fn = NULL;
AjPFile outf = NULL;
embInitPV("eiprscan", argc, argv, "IPRSCAN", VERSION);
seqset = ajAcdGetSeqset("sequence");
email = ajAcdGetString("email");
crc = ajAcdGetBoolean("crc");
applist = ajAcdGetList("appl");
fmt = ajAcdGetListSingle("format");
trtab = ajAcdGetListSingle("trtable");
trlen = ajAcdGetInt("trlen");
alt = ajAcdGetBoolean("altjobs");
iprlook = ajAcdGetBoolean("iprlookup");
goterms = ajAcdGetBoolean("goterms");
outf = ajAcdGetOutfile("outfile");
stmp = ajStrNew();
cl = ajStrNewC("iprscan -cli");
fn = ajStrNew();
ajFilenameSetTempname(&fn);
seqout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(seqout, fn))
ajFatal("Cannot open temporary file %S",fn);
ajSeqoutSetFormatC(seqout, "fasta");
ajSeqoutWriteSet(seqout,seqset);
ajSeqoutClose(seqout);
ajFmtPrintS(&stmp," -i %S",fn);
ajStrAppendS(&cl,stmp);
if(!ajSeqsetIsProt(seqset))
ajStrAppendC(&cl," -seqtype n");
if(!crc)
ajStrAppendC(&cl," -nocrc");
if(ajStrGetLen(email))
{
ajFmtPrintS(&stmp," -email %S",email);
ajStrAppendS(&cl,stmp);
}
i = 0;
lcnt = 0;
while(applist[i])
{
++lcnt;
++i;
}
i = 0;
while(applist[i])
{
if(ajStrMatchC(applist[i],"all"))
{
if(lcnt != 1)
ajFatal("Cannot specify 'all' with multiple "
"applications");
++i;
continue;
}
ajFmtPrintS(&stmp," -appl %S",applist[i]);
ajStrAppendS(&cl,stmp);
++i;
}
ajFmtPrintS(&stmp," -format %S",fmt);
ajStrAppendS(&cl,stmp);
ajFmtPrintS(&stmp," -trtable %S",trtab);
ajStrAppendS(&cl,stmp);
ajFmtPrintS(&stmp," -trlen %d",trlen);
ajStrAppendS(&cl,stmp);
if(alt)
ajStrAppendC(&cl," -altjobs");
if(iprlook)
ajStrAppendC(&cl," -iprlookup");
if(goterms)
ajStrAppendC(&cl," -goterms");
ofn = ajFileGetNameS(outf);
ajFmtPrintS(&stmp," -o %S",ofn);
ajFileClose(&outf);
ajStrAppendS(&cl,stmp);
#if 0
ajFmtPrint("%S\n",cl);
#endif
#if 1
system(ajStrGetPtr(cl));
#endif
ajSysFileUnlink(fn);
ajStrDel(&cl);
ajStrDel(&fn);
ajStrDel(&stmp);
ajStrDel(&email);
ajStrDel(&fmt);
ajStrDel(&trtab);
ajStrDelarray(&applist);
ajSeqoutDel(&seqout);
ajSeqsetDel(&seqset);
embExit();
return 0;
}