double* embIeppKNew(void)
{
double *pK = NULL;
AJCNEW(pK,EMBIEPSIZE);
embIepPkRead(pK); /* read pK's */
return pK;
}
AjBool embIepIepC(const char *s, ajint amino, ajint carboxyl,
ajint sscount, ajint modlysine,
double *pK, double *iep, AjBool termini)
{
ajint *c = NULL;
ajint *op = NULL;
double *K = NULL;
double *pro = NULL;
*iep = 0.0;
AJCNEW(c, EMBIEPSIZE);
AJCNEW(op, EMBIEPSIZE);
AJCNEW(K, EMBIEPSIZE);
AJCNEW(pro, EMBIEPSIZE);
embIepCalcK(K,pK); /* Convert to dissoc consts */
/* Get sequence composition */
embIepCompC(s,amino,carboxyl,sscount, modlysine,c);
if(!termini)
c[EMBIEPAMINO] = c[EMBIEPCARBOXYL] = 0;
*iep = embIepPhConverge(c,K,op,pro);
AJFREE(pro);
AJFREE(K);
AJFREE(op);
AJFREE(c);
if(!*iep)
return ajFalse;
return ajTrue;
}
AjBool ajRegExecallC(AjPRegexp prog, const char* str)
{
int startoffset = 0;
int options = 0;
if(!regDfaWorkspace)
AJCNEW(regDfaWorkspace, regDfaWsCount);
prog->matches = pcre_dfa_exec(prog->pcre, prog->extra,
str, strlen(str),
startoffset, options,
prog->ovector, 3*prog->ovecsize,
regDfaWorkspace, regDfaWsCount);
if(prog->matches >= 0)
{
prog->orig = str;
if(prog->matches == 0)
ajWarn("ajRegExecallC too many substrings");
return ajTrue;
}
if(prog->matches < -1) /* -1 is a simple fail to match */
{ /* others are recursion limits etc. */
ajDebug("ajRegExecallC returned unexpected status '%d'\n",
prog->matches);
prog->orig = str; /* needed for the trace */
ajRegTrace(prog);
}
prog->orig = NULL;
return ajFalse;
}
int main(int argc, char **argv)
{
AjPAlign align;
AjPSeq a;
AjPSeq b;
AjPSeqout seqout;
AjPStr m;
AjPStr n;
AjPStr merged = NULL;
ajuint lena;
ajuint lenb;
const char *p;
const char *q;
ajint start1 = 0;
ajint start2 = 0;
float *path;
ajint *compass;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
float gapopen;
float gapextend;
ajulong maxarr = 1000;
ajulong len; /* arbitrary. realloc'd if needed */
size_t stlen;
float score;
ajint begina;
ajint beginb;
embInit("merger", argc, argv);
a = ajAcdGetSeq("asequence");
b = ajAcdGetSeq("bsequence");
seqout = ajAcdGetSeqout("outseq");
matrix = ajAcdGetMatrixf("datafile");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
align = ajAcdGetAlign("outfile");
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
/*
** make the two sequences lowercase so we can show which one we are
** using in the merge by uppercasing it
*/
ajSeqFmtLower(a);
ajSeqFmtLower(b);
m = ajStrNew();
n = ajStrNew();
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
begina = ajSeqGetBegin(a);
beginb = ajSeqGetBegin(b);
lena = ajSeqGetLen(a);
lenb = ajSeqGetLen(b);
if(lenb > (ULONG_MAX/(ajulong)(lena+1)))
ajFatal("Sequences too big. Try 'supermatcher'");
len = lena*lenb;
if(len>maxarr)
{
ajDebug("merger: resize path, len to %d (%d * $d)\n",
len, lena, lenb);
stlen = (size_t) len;
AJCRESIZE(path,stlen);
AJCRESIZE(compass,stlen);
maxarr=len;
}
p = ajSeqGetSeqC(a);
q = ajSeqGetSeqC(b);
ajStrAssignC(&m,"");
ajStrAssignC(&n,"");
score = embAlignPathCalc(p,q,lena,lenb,gapopen,gapextend,path,sub,cvt,
compass, ajFalse);
/*score = embAlignScoreNWMatrix(path,compass,gapopen,gapextend,
a,b,lena,lenb,sub,cvt,
&start1,&start2);*/
embAlignWalkNWMatrix(path,a,b,&m,&n,lena,lenb, &start1,&start2,gapopen,
gapextend,compass);
/*
** now construct the merged sequence, uppercase the bits of the two
** input sequences which are used in the merger
*/
merger_Merge(align, &merged,p,q,m,n,start1,start2,
ajSeqGetNameC(a),ajSeqGetNameC(b));
embAlignReportGlobal(align, a, b, m, n,
start1, start2, gapopen, gapextend,
score, matrix, begina, beginb);
ajAlignWrite(align);
ajAlignReset(align);
/* write the merged sequence */
ajSeqAssignSeqS(a, merged);
ajSeqoutWriteSeq(seqout, a);
ajSeqoutClose(seqout);
ajSeqoutDel(&seqout);
ajSeqDel(&a);
ajSeqDel(&b);
ajAlignClose(align);
ajAlignDel(&align);
ajStrDel(&merged);
AJFREE(compass);
AJFREE(path);
ajStrDel(&n);
ajStrDel(&m);
embExit();
return 0;
}
static EmbPEntry dbiblast_nextblastentry(PBlastDb db, ajint ifile,
const AjPStr idformat,
AjBool systemsort,
AjPStr const * fields,
ajint * maxFieldLen,
ajuint* maxidlen, ajuint* countfield,
AjPFile elistfile,
AjPFile * alistfile)
{
ajint i;
static ajint lastfile = -1;
static ajint iparser = -1;
static ajint called = 0;
static ajuint tabhdr[TABLESIZE];
static ajint iload = TABLESIZE-1;
static ajint irest = 0;
static ajint ipos = 0;
static ajint jpos = 0;
ajint ir;
ajint j;
static ajint is = 0;
char* token;
static ajint nfields;
ajint ifield;
if(!called)
{
for(i=0; parser[i].Name; i++)
if(ajStrMatchC(idformat, parser[i].Name))
{
iparser = i;
break;
}
if(iparser < 0)
ajFatal("idformat '%S' unknown", idformat);
ajDebug("idformat '%S' Parser %d\n", idformat, iparser);
ajStrSetRes(&id, HDRSIZE);
ajStrSetRes(&acc, HDRSIZE);
ajStrSetRes(&hline, HDRSIZE);
called = 1;
}
if(!fdl)
{
nfields=0;
while(fields[nfields])
nfields++;
if(nfields)
AJCNEW(fdl, nfields);
for(i=0; i < nfields; i++)
fdl[i] = ajListNew();
}
if(lastfile != ifile)
{
lastfile = ifile;
ipos = 1;
/* isize = 0;*/
irest = 0;
iload = TABLESIZE-1;
}
if(!dbiblastEntry || !systemsort)
dbiblastEntry = embDbiEntryNew(nfields);
/* pick up the next entry, parse it and dump it */
if(ipos > db->Size)
return NULL;
if( ipos >= irest)
{
ajDebug("ipos: %d iload: %d irest: %d\n", ipos, iload, irest);
irest = ipos + TABLESIZE - 2;
if(irest > db->Size)
{
iload = db->Size - ipos + 1;
irest = db->Size;
}
jpos=0;
j = dbiblast_loadtable(tabhdr, iload, db, db->TopHdr, ipos-1);
if(!j)
ajDebug("No elements read");
}
j = dbiblast_ncblreadhdr(&hline, db, tabhdr[jpos], tabhdr[jpos+1]);
if(!parser[iparser].Parser(hline, alistfile, systemsort, fields,
maxFieldLen, countfield, &id, fdl))
ajFatal("failed to parse '%S'", hline);
ir = ipos;
if(ajStrGetLen(id) > *maxidlen)
*maxidlen = ajStrGetLen(id);
if(systemsort)
ajFmtPrintF(elistfile, "%S %d %d %d\n", id, ir, is, ifile+1);
else
{
dbiblastEntry->entry = ajCharNewS(id);
dbiblastEntry->rpos = ir;
dbiblastEntry->spos = is;
dbiblastEntry->filenum = ifile+1;
/* field tokens as list, then move to dbiblastEntry->field */
for(ifield=0; ifield < nfields; ifield++)
{
dbiblastEntry->nfield[ifield] = ajListGetLength(fdl[ifield]);
if(dbiblastEntry->nfield[ifield])
{
AJCNEW(dbiblastEntry->field[ifield],
dbiblastEntry->nfield[ifield]);
i = 0;
while(ajListPop(fdl[ifield], (void**) &token))
dbiblastEntry->field[ifield][i++] = token;
}
else
dbiblastEntry->field[ifield] = NULL;
}
}
ipos++;
jpos++;
return dbiblastEntry;
}
int main(int argc, char **argv)
{
AjPList idlist;
AjPList* fieldList = NULL;
AjBool systemsort;
AjBool cleanup;
ajint blastv = 0;
char dbtype = '\0';
ajuint maxindex;
ajuint maxidlen = 0;
ajuint maxlen;
AjPStr version = NULL;
AjPStr seqtype = NULL;
AjPFile elistfile = NULL;
AjPFile* alistfile = NULL;
AjPStr dbname = NULL;
AjPStr release = NULL;
AjPStr datestr = NULL;
AjPStr sortopt = NULL;
void **entryIds = NULL;
AjBool usesrc = AJTRUE;
AjPStr directory;
AjPStr indexdir;
AjPStr filename;
AjPStr exclude;
AjPStr curfilename = NULL;
AjPStr idformat = NULL;
EmbPEntry entry;
PBlastDb db = NULL;
ajuint idCount = 0;
ajuint idDone;
AjPList listTestFiles = NULL;
void ** testFiles = NULL;
ajuint nfiles;
ajuint ifile;
ajuint jfile;
ajuint filesize;
short recsize;
ajuint maxfilelen = 20;
char date[4] =
{
0,0,0,0
};
AjPStr tmpfname = NULL;
AjPStr* fields = NULL;
AjPFile entFile = NULL;
AjPStr* divfiles = NULL;
ajint* maxFieldLen = NULL;
ajuint ifield = 0;
ajuint nfields = 0;
AjPFile logfile = NULL;
ajuint* countField = NULL;
ajuint* fieldTot = NULL;
ajuint idCountFile = 0;
ajuint i = 0;
embInit("dbiblast", argc, argv);
idformat = ajStrNewC("NCBI");
fields = ajAcdGetList("fields");
directory = ajAcdGetDirectoryName("directory");
indexdir = ajAcdGetOutdirName("indexoutdir");
filename = ajAcdGetString("filenames");
exclude = ajAcdGetString("exclude");
dbname = ajAcdGetString("dbname");
release = ajAcdGetString("release");
datestr = ajAcdGetString("date");
systemsort = ajAcdGetBoolean("systemsort");
cleanup = ajAcdGetBoolean("cleanup");
sortopt = ajAcdGetString("sortoptions");
maxindex = ajAcdGetInt("maxindex");
version = ajAcdGetListSingle("blastversion");
seqtype = ajAcdGetListSingle("seqtype");
usesrc = ajAcdGetBoolean("sourcefile");
logfile = ajAcdGetOutfile("outfile");
while(fields[nfields]) /* array ends with a NULL */
nfields++;
if(nfields)
{
AJCNEW(maxFieldLen, nfields);
AJCNEW0(countField, nfields);
AJCNEW0(fieldTot, nfields);
for(ifield=0; ifield < nfields; ifield++)
maxFieldLen[ifield] = (ajint) maxindex * -1;
if(systemsort)
AJCNEW(alistfile, nfields);
else
{
AJCNEW(fieldList, nfields);
for(ifield=0; ifield < nfields; ifield++)
fieldList[ifield] = ajListNew();
}
}
if(ajStrMatchC(datestr, "00/00/00"))
ajFmtPrintS(&datestr, "%D", ajTimeRefTodayFmt("dbindex"));
ajStrRemoveWhite(&dbname); /* used for temp filenames */
embDbiDateSet(datestr, date);
idlist = ajListNew();
if(ajUtilGetBigendian())
readReverse = ajFalse;
else
readReverse = ajTrue;
ajStrToInt(version, &blastv);
dbtype = ajStrGetCharFirst(seqtype);
ajDebug("reading '%S/%S'\n", directory, filename);
ajDebug("writing '%S/'\n", indexdir);
listTestFiles = embDbiFileListExc(directory, filename, exclude);
ajListSort(listTestFiles, ajStrVcmp);
nfiles = ajListToarray(listTestFiles, &testFiles);
if(!nfiles)
ajDie("No input files in '%S' matched filename '%S'",
directory, filename);
embDbiLogHeader(logfile, dbname, release, datestr,
indexdir, maxindex);
embDbiLogFields(logfile, fields, nfields);
embDbiLogSource(logfile, directory, filename, exclude,
(AjPStr*) testFiles, nfiles);
embDbiLogCmdline(logfile);
AJCNEW0(divfiles, nfiles);
/*
** process each input file, one at a time
*/
jfile = 0;
for(ifile=0; ifile < nfiles; ifile++)
{
curfilename = (AjPStr) testFiles[ifile];
if(!dbiblast_blastopenlib(curfilename,
usesrc, blastv, dbtype, &db))
continue; /* could be the wrong file type with "*.*" */
ajDebug("processing filename '%S' ...\n", curfilename);
ajDebug("processing file '%S' ...\n", db->TFile->Name);
ajStrAssignS(&divfiles[jfile], db->TFile->Name);
ajFilenameTrimPath(&divfiles[jfile]);
if(ajStrGetLen(divfiles[jfile]) >= maxfilelen)
maxfilelen = ajStrGetLen(divfiles[jfile]) + 1;
if(systemsort) /* elistfile for entries, alist for fields */
elistfile = embDbiSortOpen(alistfile, jfile,
dbname, fields, nfields);
idCountFile = 0;
for(i=0;i<nfields;i++)
countField[i] = 0;
while((entry=dbiblast_nextblastentry(db, jfile,
idformat, systemsort,
fields,
maxFieldLen,
&maxidlen, countField,
elistfile, alistfile)))
{
idCountFile++;
if(!systemsort) /* save the entry data in lists */
{
embDbiMemEntry(idlist, fieldList, nfields, entry, jfile);
}
}
idCount += idCountFile;
if(systemsort)
{
embDbiSortClose(&elistfile, alistfile, nfields);
/* lost the entry, so can't free it :-) */
}
embDbiLogFile(logfile, curfilename, idCountFile, fields,
countField, nfields);
dbiblast_dbfree(&db);
jfile++;
}
nfiles = jfile;
/*
** write the division.lkp file
*/
embDbiWriteDivision(indexdir, dbname, release, date,
maxfilelen, nfiles, divfiles, NULL);
/*
** Write the entryname.idx index
*/
ajStrAssignC(&tmpfname, "entrynam.idx");
entFile = ajFileNewOutNamePathS(tmpfname, indexdir);
recsize = maxidlen+10;
filesize = 300 + (idCount*(ajint)recsize);
embDbiHeader(entFile, filesize, idCount, recsize, dbname, release, date);
if(systemsort)
idDone = embDbiSortWriteEntry(entFile, maxidlen,
dbname, nfiles, cleanup, sortopt);
else /* save entries in entryIds array */
{
idDone = embDbiMemWriteEntry(entFile, maxidlen,
idlist, &entryIds);
if(idDone != idCount)
ajFatal("Duplicates not allowed for in-memory processing");
}
embDbiHeaderSize(entFile, 300+(idDone*(ajint)recsize), idDone);
ajFileClose(&entFile);
/*
** Write the fields index files
*/
for(ifield=0; ifield < nfields; ifield++)
{
if(maxindex)
maxlen = maxindex;
else
{
if(maxFieldLen[ifield] >= 0)
maxlen = maxFieldLen[ifield];
else
maxlen = - maxFieldLen[ifield];
}
if(systemsort)
fieldTot[ifield] = embDbiSortWriteFields(dbname, release,
date, indexdir,
fields[ifield], maxlen,
nfiles, idCount,
cleanup, sortopt);
else
fieldTot[ifield] = embDbiMemWriteFields(dbname, release,
date, indexdir,
fields[ifield], maxlen,
fieldList[ifield],
entryIds);
}
embDbiLogFinal(logfile,maxindex, maxFieldLen, fields, fieldTot,
nfields, nfiles, idDone, idCount);
if(systemsort)
embDbiRmEntryFile(dbname, cleanup);
ajListMap(idlist, embDbiEntryDelMap, NULL);
ajListFree(&idlist);
AJFREE(entryIds);
ajStrDelarray(&fields);
for(i=0;i<nfields;i++)
{
if(systemsort)
{
ajFileClose(&alistfile[i]);
}
else
{
ajListMap(fieldList[i], embDbiFieldDelMap, NULL);
ajListFree(&fieldList[i]);
}
}
AJFREE(alistfile);
AJFREE(fieldList);
ajStrDel(&version);
ajStrDel(&seqtype);
ajFileClose(&elistfile);
for(i=0;i<nfiles;i++)
{
ajStrDel(&divfiles[i]);
}
AJFREE(countField);
AJFREE(fieldTot);
ajStrDel(&dbname);
ajStrDel(&release);
ajStrDel(&datestr);
ajStrDel(&sortopt);
ajStrDel(&directory);
ajStrDel(&indexdir);
ajStrDel(&filename);
ajStrDel(&exclude);
ajStrDel(&idformat);
ajStrDel(&tmpfname);
AJFREE(maxFieldLen);
ajFileClose(&logfile);
ajListstrFreeData(&listTestFiles);
ajStrDel(&t);
ajStrDel(&id);
ajStrDel(&acc);
ajStrDel(&hline);
ajStrDel(&tmpdes);
ajStrDel(&tmpfd);
ajStrDel(&tmpgi);
ajStrDel(&tmpdb);
ajStrDel(&tmpac);
ajStrDel(&tmpsv);
ajRegFree(&wrdexp);
embDbiEntryDel(&dbiblastEntry);
if(fdl)
{
for(i=0; i < nfields; i++)
ajListFree(&fdl[i]);
AJFREE(fdl);
}
for(i=0;i<nfiles;i++)
{
ajStrDel(&divfiles[i]);
}
AJFREE(divfiles);
AJFREE(testFiles);
embExit();
return 0;
}
int main(int argc, char **argv)
{
ajint i;
ajint numseq;
ajint j = 0;
ajint numres;
ajint count;
ajint k;
ajint kmax;
float defheight;
float currentscale;
AjPStr shade = NULL;
AjPFloat pair = NULL;
AjPGraph graph = NULL;
AjPMatrix cmpmatrix = NULL;
AjPSeqCvt cvt = NULL;
AjPStr matcodes = NULL;
AjBool consensus;
AjBool colourbyconsensus;
AjBool colourbyresidues;
AjBool colourbyshade = AJFALSE;
AjBool boxit;
AjBool boxcol;
AjBool portrait;
AjBool collision;
ajint identity;
AjBool listoptions;
ajint alternative;
AjPStr altstr = NULL;
AjPStr sidentity = NULL;
AjPStr ssimilarity = NULL;
AjPStr sother = NULL;
AjPStr sboxcolval = NULL;
AjPStr options = NULL;
/* ajint showscore = 0; */
ajint iboxcolval = 0;
ajint cidentity = RED;
ajint csimilarity = GREEN;
ajint cother = BLACK;
float fxp;
float fyp;
float yincr;
float y;
ajint ixlen;
ajint iylen;
ajint ixoff;
ajint iyoff;
char res[2] = " ";
float *score = 0;
float scoremax = 0;
float *identical = NULL;
ajint identicalmaxindex;
float *matching = NULL;
ajint matchingmaxindex;
float *colcheck = NULL;
ajint **matrix;
ajint m1 = 0;
ajint m2 = 0;
ajint ms = 0;
ajint highindex = 0;
ajint myindex;
ajint *previous = 0;
AjBool iscons = ajFalse;
ajint currentstate = 0;
ajint oldfg = 0;
float fold = 0.0;
ajint *colmat = 0;
ajint *shadecolour = 0;
/* float identthresh = 1.5; */
/* float simthresh = 1.0; */
/* float relthresh = 0.5; */
float part = 0.0;
const char *cptr;
ajint resbreak;
float fplural;
float ystart;
float xmin;
float xmax;
float xmid;
AjPTime ajtime;
ajint gapcount = 0;
ajint countforgap = 0;
ajint boxindex;
float max;
ajint matsize;
ajint seqperpage = 0;
ajint startseq;
ajint endseq;
ajint newILend = 0;
ajint newILstart;
void *freeptr;
ajint itmp;
embInit("prettyplot", argc, argv);
seqset = ajAcdGetSeqset("sequences");
numres = ajAcdGetInt("residuesperline");
resbreak = ajAcdGetInt("resbreak");
ajSeqsetFill(seqset); /* Pads sequence set with gap characters */
numseq = ajSeqsetGetSize(seqset);
graph = ajAcdGetGraph("graph");
colourbyconsensus = ajAcdGetBoolean("ccolours");
colourbyresidues = ajAcdGetBoolean("docolour");
shade = ajAcdGetString("shade");
pair = ajAcdGetArray("pair");
identity = ajAcdGetInt("identity");
boxit = ajAcdGetBoolean("box");
ajtime = ajTimeNewTodayFmt("daytime");
ajSeqsetTrim(seqset);
/* offset = ajSeqsetGetOffset(seqset); Unused */
ajGraphAppendTitleS(graph, ajSeqsetGetUsa(seqset));
if(boxit)
{
AJCNEW(seqboxptr, numseq);
for(i=0;i<numseq;i++)
AJCNEW(seqboxptr[i], ajSeqsetGetLen(seqset));
}
boxcol = ajAcdGetBoolean("boxcol");
sboxcolval = ajAcdGetString("boxuse");
if(boxcol)
{
iboxcolval = ajGraphicsCheckColourS(sboxcolval);
if(iboxcolval == -1)
iboxcolval = GREY;
}
consensus = ajAcdGetBoolean("consensus");
if(consensus)
{
AJCNEW(constr, ajSeqsetGetLen(seqset)+1);
constr[0] = '\0';
}
shownames = ajAcdGetBoolean("name");
shownumbers = ajAcdGetBoolean("number");
charlen = ajAcdGetInt("maxnamelen");
fplural = ajAcdGetFloat("plurality");
portrait = ajAcdGetBoolean("portrait");
collision = ajAcdGetBoolean("collision");
listoptions = ajAcdGetBoolean("listoptions");
altstr = ajAcdGetListSingle("alternative");
cmpmatrix = ajAcdGetMatrix("matrixfile");
ajStrToInt(altstr, &alternative);
matrix = ajMatrixGetMatrix(cmpmatrix);
cvt = ajMatrixGetCvt(cmpmatrix);
matsize = ajMatrixGetSize(cmpmatrix);
AJCNEW(identical,matsize);
AJCNEW(matching,matsize);
AJCNEW(colcheck,matsize);
numgaps = numres/resbreak;
numgaps--;
if(portrait)
{
ajGraphicsSetPortrait(1);
ystart = (float) 75.0;
}
else
ystart = (float) 75.0;
/* pair is an array of three non-negative floats */
/* identthresh = ajFloatGet(pair,0); Unused */
/* simthresh = ajFloatGet(pair,1); Unused */
/* relthresh = ajFloatGet(pair,2); Unused */
/*
** shade is a formatted 4-character string. Characters BLPW only.
** controlled by a pattern in ACD.
*/
if(ajStrGetLen(shade))
{
AJCNEW(shadecolour,4);
cptr = ajStrGetPtr(shade);
for(i=0;i<4;i++){
if(cptr[i]== 'B' || cptr[i]== 'b')
shadecolour[i] = BLACK;
else if(cptr[i]== 'L' || cptr[i]== 'l')
shadecolour[i] = BROWN;
else if(cptr[i]== 'P' || cptr[i]== 'p')
shadecolour[i] = WHEAT;
else if(cptr[i]== 'W' || cptr[i]== 'w')
shadecolour[i] = WHITE;
}
colourbyconsensus = colourbyresidues = ajFalse;
colourbyshade = ajTrue;
}
/*
** we can colour by consensus or residue but not both
** if we have to choose, use the consensus
*/
if(colourbyconsensus && colourbyresidues)
colourbyconsensus = AJFALSE;
sidentity = ajAcdGetString("cidentity");
ssimilarity = ajAcdGetString("csimilarity");
sother = ajAcdGetString("cother");
if(colourbyconsensus)
{
cidentity = ajGraphicsCheckColourS(sidentity);
if(cidentity == -1)
cidentity = RED;
csimilarity = ajGraphicsCheckColourS(ssimilarity);
if(csimilarity == -1)
csimilarity = GREEN;
cother = ajGraphicsCheckColourS(sother);
if(cother == -1)
cother = BLACK;
}
else if(colourbyresidues)
{
matcodes = ajMatrixGetCodes(cmpmatrix);
if(ajSeqsetIsProt(seqset))
colmat = ajGraphicsBasecolourNewProt(matcodes);
else
colmat = ajGraphicsBasecolourNewNuc(matcodes);
}
/* output the options used as the subtitle for the bottom of the graph */
if(listoptions)
{
ajStrAssignC(&options,"");
ajFmtPrintAppS(&options,"-plurality %.1f",fplural);
if(collision)
ajStrAppendC(&options," -collision");
else
ajStrAppendC(&options," -nocollision");
if(boxit)
ajStrAppendC(&options," -box");
else
ajStrAppendC(&options," -nobox");
if(boxcol)
ajStrAppendC(&options," -boxcol");
else
ajStrAppendC(&options," -noboxcol");
if(colourbyconsensus)
ajStrAppendC(&options," -colbyconsensus");
else if(colourbyresidues)
ajStrAppendC(&options," -colbyresidues");
else if(colourbyshade)
ajStrAppendC(&options," -colbyshade");
else
ajStrAppendC(&options," -nocolour");
if(alternative==2)
ajStrAppendC(&options," -alt 2");
else if(alternative==1)
ajStrAppendC(&options," -alt 1");
else if(alternative==3)
ajStrAppendC(&options," -alt 3");
}
AJCNEW(seqcolptr, numseq);
for(i=0;i<numseq;i++)
AJCNEW(seqcolptr[i], ajSeqsetGetLen(seqset));
AJCNEW(seqcharptr, numseq);
AJCNEW(seqnames, numseq);
AJCNEW(score, numseq);
AJCNEW(previous, numseq);
AJCNEW(seqcount, numseq);
for(i=0;i<numseq;i++)
{
ajSeqsetFmtUpper(seqset);
seqcharptr[i] = ajSeqsetGetseqSeqC(seqset, i);
seqnames[i] = 0;
ajStrAppendS(&seqnames[i],ajSeqsetGetseqNameS(seqset, i));
ajStrTruncateLen(&seqnames[i],charlen);
previous[i] = 0;
seqcount[i] = 0;
}
/*
** user will pass the number of residues to fit a page
** therefore we now need to calculate the size of the chars
** based on this and get the new char width.
** 'charlen' maximum characters for the name (truncated above)
*/
ajGraphicsGetCharsize(&defheight,¤tscale);
xmin = -charlen - (float)2.0;
xmax = (float)numres+(float)11.0+(float)(numres/resbreak);
xmid = (xmax + xmin)/(float)2.0;
ajGraphOpenWin(graph, xmin, xmax,
(float)0.0, ystart+(float)1.0);
ajGraphGetParamsPage(graph, &fxp,&fyp,&ixlen,&iylen,&ixoff,&iyoff);
if(portrait)
{
itmp = ixlen;
ixlen = iylen;
iylen = itmp;
}
ajGraphicsGetCharsize(&defheight,¤tscale);
ajGraphicsSetCharscale(((float)ixlen/((float)(numres+charlen+1)*
(currentscale * (float) 1.5)))/
currentscale);
/* ajGraphicsSetCharscale(((float)ixlen/((float)(numres+charlen)*
(currentscale+(float)1.0)))/
currentscale); */
ajGraphicsGetCharsize(&defheight,¤tscale);
yincr = (currentscale + (float)3.0)*(float)0.3;
/*
** If we have titles (now the standard graph title and subtitle and footer)
** leave 7 rows of space for them
*/
y=ystart-(float)7.0;
if(ajStrGetLen(options))
{
fold = ajGraphicsSetCharscale(1.0);
ajGraphicsDrawposTextAtmid(xmid,2.0,
ajStrGetPtr(options));
ajGraphicsSetCharscale(fold);
}
/* if sequences per page not set then calculate it */
if(!seqperpage)
{
seqperpage = prettyplot_calcseqperpage(yincr,y,consensus);
if(seqperpage>numseq)
seqperpage=numseq;
}
count = 0;
/*
** for boxes we need to set a foreground colour for the box lines
** and save the current foreground colour
*/
if(boxit && boxcol)
oldfg = ajGraphicsSetFgcolour(iboxcolval);
/*
** step through each residue position
*/
kmax = ajSeqsetGetLen(seqset) - 1;
for(k=0; k<= kmax; k++)
{
/* reset column score array */
for(i=0;i<numseq;i++)
score[i] = 0.0;
/* reset matrix character testing arrays */
for(i=0;i<matsize;i++)
{
identical[i] = 0.0;
matching[i] = 0.0;
colcheck[i] = 0.0;
}
/* generate a score for this residue in each sequence */
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
for(j=0;j<numseq;j++)
{
m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]);
if(m1 && m2)
score[i] += (float)matrix[m1][m2]*
ajSeqsetGetseqWeight(seqset, j);
}
if(m1)
identical[m1] += ajSeqsetGetseqWeight(seqset, i);
}
/* find the highest score */
highindex = -1;
scoremax = INT_MIN;
/*ajDebug("Scores at position %d:\n", k);*/
for(i=0;i<numseq;i++)
{
/*ajDebug(" seq %d: '%c' %f\n",i,seqcharptr[i][k],score[i]);*/
if(score[i] > scoremax)
{
scoremax = score[i];
highindex = i;
}
}
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(!matching[m1])
{
for(j=0;j<numseq;j++)
{
m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]);
if(m1 && m2 && matrix[m1][m2] > 0)
matching[m1] += ajSeqsetGetseqWeight(seqset, j);
}
}
}
/* find highs for matching and identical */
matchingmaxindex = 0;
identicalmaxindex = 0;
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(identical[m1] > identical[identicalmaxindex])
identicalmaxindex = m1;
}
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(matching[m1] > matching[matchingmaxindex])
matchingmaxindex = m1;
else if(matching[m1] == matching[matchingmaxindex])
{
if(identical[m1] > identical[matchingmaxindex])
matchingmaxindex= m1;
}
}
iscons = ajFalse;
boxindex = -1;
max = -3;
ajDebug("k:%2d highindex:%2d matching:%4.2f\n",
k, highindex,
matching[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])]);
if(highindex != -1 &&
matching[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])] >= fplural)
{
iscons = ajTrue;
boxindex = highindex;
}
else
{
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(matching[m1] > max)
{
max = matching[m1];
highindex = i;
}
else if(matching[m1] == max)
{
if(identical[m1] >
identical[ajSeqcvtGetCodeK(cvt,
seqcharptr[highindex][k])] )
{
max = matching[m1];
highindex = i;
}
}
}
if(matching[ajSeqcvtGetCodeK(cvt,
seqcharptr[highindex][k])] >= fplural)
{
iscons = ajTrue;
boxindex = highindex;
}
}
if(iscons)
{
if(!collision)
{
/* check for collisions */
if(alternative == 1)
{
/* check to see if this is unique for collisions */
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(identical[m1] >= identical[identicalmaxindex] &&
m1 != identicalmaxindex)
iscons = ajFalse;
}
/*ajDebug("after (alt=1) iscons: %B",iscons);*/
}
else if(alternative == 2)
{
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if((matching[m1] >= matching[matchingmaxindex] &&
m1 != matchingmaxindex &&
matrix[m1][matchingmaxindex] < 0.1)||
(identical[m1] >= identical[matchingmaxindex]
&& m1 != matchingmaxindex))
iscons = ajFalse;
}
}
else if(alternative == 3)
{
/*
** to do this check one is NOT in consensus to see if
** another score of fplural has been found
*/
ms = ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k]);
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(ms != m1 && colcheck[m1] == 0.0)
/* NOT in the current consensus */
for(j=0;j<numseq;j++)
{
m2 = ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]);
if( matrix[ms][m2] < 0.1)
{
/* NOT in the current consensus */
if( matrix[m1][m2] > 0.1)
colcheck[m1] +=
ajSeqsetGetseqWeight(seqset,
j);
}
}
}
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
/* if any other matches then we have a collision */
if(colcheck[m1] >= fplural)
iscons = ajFalse;
}
/*ajDebug("after alt=2 iscons: %B", iscons);*/
}
else
{
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if((matching[m1] >= matching[matchingmaxindex] &&
m1 != matchingmaxindex &&
matrix[m1][matchingmaxindex] < 0.1))
iscons = ajFalse;
if(identical[m1] >= identical[matchingmaxindex] &&
m1 != matchingmaxindex &&
matrix[m1][matchingmaxindex] > 0.1)
iscons = ajFalse;
}
if(!iscons)
{ /* matches failed try identicals */
if(identical[identicalmaxindex] >= fplural)
{
iscons = ajTrue;
/*
** if nothing has an equal or higher match that
** does not match highest then false
*/
for(i=0;i<numseq;i++)
{
m1 = ajSeqcvtGetCodeK(cvt, seqcharptr[i][k]);
if(identical[m1] >=
identical[identicalmaxindex] &&
m1 != identicalmaxindex)
iscons = ajFalse;
else if(matching[m1] >=
matching[identicalmaxindex] &&
matrix[m1][matchingmaxindex] <= 0.0)
iscons = ajFalse;
else if(m1 == identicalmaxindex)
j = i;
}
if(iscons)
highindex = j;
}
}
}
}
if(identity)
{
j = 0;
for(i=0;i<numseq;i++)
if(seqcharptr[highindex][k] == seqcharptr[i][k])
j++;
if(j<identity)
iscons = ajFalse;
}
}
/*
** Done a full line of residues
** Boxes have been defined up to this point
*/
if(count >= numres )
{
/* check y position for next set */
y=y-(yincr*((float)numseq+(float)2.0+((float)consensus*(float)2)));
if(y<yincr*((float)numseq+(float)2.0+((float)consensus*(float)2)))
{
/* full page - print it */
y=ystart-(float)6.0;
startseq = 0;
endseq = seqperpage;
newILstart = newILend;
newILend = k;
while(startseq < numseq)
{
/* AJB */
/*if(startseq != 0)
ajGraphNewpage(graph, AJFALSE);*/
/*ajDebug("Inner loop: startseq: %d numseq: %d endseq: %d\n",
startseq, numseq, endseq);*/
if(endseq>numseq)
endseq=numseq;
prettyplot_fillinboxes(numseq,ajSeqsetGetLen(seqset),
startseq,endseq,
newILstart,newILend,
numres,resbreak,
boxit,boxcol,consensus,
ystart,yincr,cvt);
startseq = endseq;
endseq += seqperpage;
ajGraphNewpage(graph, AJFALSE);
}
}
count = 0;
gapcount = 0;
}
count++;
countforgap++;
for(j=0;j<numseq;j++)
{
/* START OF BOXES */
if(boxit)
{
seqboxptr[j][k] = 0;
if(boxindex!=-1)
{
myindex = boxindex;
if(matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])]
[ajSeqcvtGetCodeK(cvt, seqcharptr[myindex][k])] > 0)
part = 1.0;
else
{
if(identical[ajSeqcvtGetCodeK(cvt,
seqcharptr[j][k])] >=
fplural)
part = 1.0;
else
part = 0.0;
}
if(previous[j] != part)
/* draw vertical line */
seqboxptr[j][k] |= BOXLEF;
if(j==0)
{
/* special case for horizontal line */
if(part)
{
currentstate = 1;
/* draw hori line */
seqboxptr[j][k] |= BOXTOP;
}
else
currentstate = 0;
}
else
{
/* j != 0 Normal case for horizontal line */
if(part != currentstate)
{
/*draw hori line */
seqboxptr[j][k] |= BOXTOP;
currentstate = (ajint) part;
}
}
if(j== numseq-1 && currentstate)
/* draw horiline at bottom */
seqboxptr[j][k] |= BOXBOT;
previous[j] = (ajint) part;
}
else
{
part = 0;
if(previous[j])
{
/* draw vertical line */
seqboxptr[j][k] |= BOXLEF;
}
previous[j] = 0;
}
if(count == numres || k == kmax || countforgap >= resbreak )
{ /* last one on the row or a break*/
if(previous[j])
{
/* draw vertical line */
seqboxptr[j][k] |= BOXRIG;
}
previous[j] = 0;
}
} /* end box */
if(boxit && boxcol)
if(boxindex != -1)
{
myindex = boxindex;
if(matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])]
[ajSeqcvtGetCodeK(cvt, seqcharptr[myindex][k])] > 0
|| identical[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])] >=
fplural )
seqboxptr[j][k] |= BOXCOLOURED;
}
/* END OF BOXES */
if(ajSeqcvtGetCodeK(cvt, seqcharptr[j][k]))
res[0] = seqcharptr[j][k];
else
res[0] = '-';
if(colourbyconsensus)
{
part = (float) matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])]
[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])];
if(iscons && seqcharptr[highindex][k] == seqcharptr[j][k])
seqcolptr[j][k] = cidentity;
else if(part > 0.0)
seqcolptr[j][k] = csimilarity;
else
seqcolptr[j][k] = cother;
}
else if(colourbyresidues)
seqcolptr[j][k] = colmat[ajSeqcvtGetCodeK(cvt,
seqcharptr[j][k])];
else if(iscons && colourbyshade)
{
part = (float) matrix[ajSeqcvtGetCodeK(cvt, seqcharptr[j][k])]
[ajSeqcvtGetCodeK(cvt, seqcharptr[highindex][k])];
if(part >= 1.5)
seqcolptr[j][k] = shadecolour[0];
else if(part >= 1.0)
seqcolptr[j][k] = shadecolour[1];
else if(part >= 0.5)
seqcolptr[j][k] = shadecolour[2];
else
seqcolptr[j][k] = shadecolour[3];
}
else if(colourbyshade)
seqcolptr[j][k] = shadecolour[3];
else
seqcolptr[j][k] = BLACK;
}
if(consensus)
{
if(iscons)
res[0] = seqcharptr[highindex][k];
else
res[0] = '-';
strcat(constr,res);
}
if(countforgap >= resbreak)
{
gapcount++;
countforgap=0;
}
}
startseq = 0;
endseq=seqperpage;
newILstart = newILend;
newILend = k;
while(startseq < numseq)
{
if(startseq)
ajGraphNewpage(graph, AJFALSE);
/*ajDebug("Final loop: startseq: %d numseq: %d endseq: %d\n",
startseq, numseq, endseq);*/
if(endseq>numseq)
endseq = numseq;
prettyplot_fillinboxes(numseq,ajSeqsetGetLen(seqset),
startseq,endseq,
newILstart,newILend,
numres,resbreak,
boxit,boxcol,consensus,
ystart,yincr,cvt);
startseq = endseq;
endseq += seqperpage;
}
ajGraphicsGetCharsize(&defheight,¤tscale);
if(boxit && boxcol)
oldfg = ajGraphicsSetFgcolour(oldfg);
ajGraphicsCloseWin();
ajGraphxyDel(&graph);
ajStrDel(&sidentity);
ajStrDel(&ssimilarity);
ajStrDel(&sother);
ajStrDel(&options);
ajStrDel(&altstr);
ajStrDel(&matcodes);
for(i=0;i<numseq;i++)
{
ajStrDel(&seqnames[i]);
AJFREE(seqcolptr[i]);
if(seqboxptr)
AJFREE(seqboxptr[i]);
}
AJFREE(seqcolptr);
AJFREE(seqboxptr);
AJFREE(seqnames);
AJFREE(score);
AJFREE(previous);
AJFREE(seqcount);
AJFREE(colmat);
AJFREE(shadecolour);
freeptr = (void *) seqcharptr;
AJFREE(freeptr);
AJFREE(identical);
AJFREE(matching);
AJFREE(colcheck);
ajSeqsetDel(&seqset);
ajMatrixDel(&cmpmatrix);
ajStrDel(&shade);
ajStrDel(&sboxcolval);
ajStrDel(&sidentity);
ajStrDel(&ssimilarity);
ajStrDel(&sother);
ajFloatDel(&pair);
ajTimeDel(&ajtime);
AJFREE(constr);
embExit();
return 0;
}
/* @funcstatic newcoils_pred_coils ********************************************
**
** Undocumented
**
** @param [u] outf [AjPFile] Undocumented
** @param [r] seq [const char*] Undocumented
** @param [r] ident [const char*] Undocumented
** @param [r] str [const AjPStr] Undocumented
** @param [r] h [const struct hept_pref *] Undocumented
** @param [r] win [ajint] Undocumented
** @param [r] which [ajint] Undocumented
** @param [r] weighted [ajint] Undocumented
** @param [r] mode [ajint] Undocumented
** @param [r] min_P [float] Undocumented
** @param [w] t [ajint*] Undocumented
** @param [w] tc [ajint*] Undocumented
** @param [r] min_seg [ajint] Undocumented
** @return [void]
******************************************************************************/
static void newcoils_pred_coils(AjPFile outf, const char *seq,
const char *ident, const AjPStr str,
const struct hept_pref *h,
ajint win, ajint which,
ajint weighted,ajint mode,
float min_P, ajint *t,
ajint *tc, ajint min_seg)
{
ajint i;
ajint j;
ajint coillen = 0;
ajint len;
ajint pos;
ajint aa_pt;
ajint total_coil_segments;
ajint are_there_coils;
float actual_win;
float this_score;
float Gg;
float Gcc;
float power;
float t1;
float t2;
float t3;
float t4;
float *score;
float *P;
char *hept_seq;
len = strlen(seq);
AJCNEW(score,len);
AJCNEW(P,len);
AJCNEW(hept_seq,len);
/* printf("Sequence is %s length is %d\n",seq,len); */
for(i=0; i<len; ++i)
{
P[i] = 0.0;
score[i] = 0.0;
hept_seq[i] = 'x';
}
for(i=0; i<(len-win+1); ++i)
{
this_score = 1.0;
actual_win = 0.0;
for(j=0; ((j<win) && ((i+j)<len)); ++j)
{
aa_pt = (int)(seq[i+j]-'A');
if((aa_pt>=0) && (aa_pt<26) && (NCAAs[aa_pt]!='_'))
{
pos = j%NCHEPTAD; /* Position in the heptad? pos modulus 7 */
if(weighted && (pos==0 || pos==3))
power = 2.5;
else
power = 1.0;
actual_win += power;
if(h->m[aa_pt][pos]!=-1)
this_score *= pow(h->m[aa_pt][pos],power);
else
this_score *= pow(h->smallest,power);
}
}
if(actual_win>0)
this_score = pow(this_score,(1/(float)actual_win));
else
this_score = 0;
for(j=0; ((j<win) && ((i+j)<len)); ++j)
{
aa_pt = (int)(seq[i+j]-'A');
if((aa_pt>=0) && (aa_pt<26) && (NCAAs[aa_pt]!='_'))
{
pos = j%NCHEPTAD; /* Position in the heptad? pos modulus 7 */
if(this_score>score[i+j])
{
score[i+j] = this_score;
hept_seq[i+j] = 'a'+pos;
}
}
}
}
if(mode==1)
ajFmtPrintF(outf,">%s %S\n",ident,str);
are_there_coils = 0;
total_coil_segments = 0;
for(i=0; i<len; ++i)
{
/* Calculate P */
t1 = 1/(h->f[which].sd_cc);
t2 = (score[i]-(h->f[which].m_cc))/h->f[which].sd_cc;
t3 = fabs(t2);
t4 = pow(t3,2);
t4 = t3*t3;
Gcc = t1 * exp(-0.5*t4);
t1 = 1/(h->f[which].sd_g);
t2 = (score[i]-(h->f[which].m_g))/h->f[which].sd_g;
t3 = fabs(t2);
t4 = pow(t3,2);
t4 = t3 * t3;
Gg = t1 * exp(-0.5*t4);
P[i] = Gcc/(h->f[which].sc*Gg+Gcc);
if(P[i] >= min_P)
{
++coillen;
are_there_coils = 1;
if((i==0) || (P[i-1]<min_P))
total_coil_segments++;
(*tc)++;
}
(*t)++;
if(mode==1)
{
if(P[i] >= min_P)
ajFmtPrintF(outf,"x");
else
ajFmtPrintF(outf,"%c",seq[i]);
if(((i+1)%60)==0)
ajFmtPrintF(outf,"\n");
}
else if(mode == 0)
ajFmtPrintF(outf,"%4d %c %c %7.3f %7.3f (%-7.3f %7.3f)\n",i+1,
seq[i],hept_seq[i],score[i],P[i],Gcc,Gg);
}
if(mode==1)
ajFmtPrintF(outf,"\n");
if((mode==2) && (are_there_coils==1) && (total_coil_segments >= min_seg))
{
if(total_coil_segments==1)
ajFmtPrintF(outf,"Pred %4d coil segment length:%d : %s %S\n",
total_coil_segments,coillen,ident,str);
else
ajFmtPrintF(outf,"Pred %4d coil segments Total length:%d: %s %S\n",
total_coil_segments,coillen,ident,str);
}
AJFREE(P);
AJFREE(score);
AJFREE(hept_seq);
return;
}
static AjBool ssematch_NWScore(AjPScop temp_scop,
AjPSeq pseq,
ajint mode,
AjPMatrixf matrix,
float gapopen,
float gapextend)
{
ajint start1 =0; /* Start of seq 1, passed as arg but not used.*/
ajint start2 =0; /* Start of seq 2, passed as arg but not used.*/
ajint maxarr =300; /* Initial size for matrix. */
ajint len;
ajint *compass;
const char *p; /* Query sequence. */
const char *q; /* Subject sequence from scop object. */
float **sub;
float id =0.; /* Passed as arg but not used here. */
float sim =0.;
float idx =0.; /* Passed as arg but not used here. */
float simx =0.; /* Passed as arg but not used here. */
float *path;
AjPStr pstr = NULL; /* m walk alignment for first sequence
Passed as arg but not used here. */
AjPStr qstr = NULL; /* n walk alignment for second sequence
Passed as arg but not used here. */
AjPSeq qseq = NULL; /* Subject sequence. */
ajint lenp; /* Length of query sequence. */
ajint lenq; /* Length of subject sequence. */
AjPSeqCvt cvt = 0;
AjBool show = ajFalse; /*Passed as arg but not used here. */
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
pstr = ajStrNew();
qstr = ajStrNew();
gapopen = ajRoundFloat(gapopen,8);
gapextend = ajRoundFloat(gapextend,8);
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
/* Extract subject sequence from scop object, convert to 3 letter code. */
if (mode == 0)
qseq = ssematch_convertbases(temp_scop->Sse);
else if (mode == 1)
qseq = ssematch_convertbases(temp_scop->Sss);
lenp = ajSeqGetLen(pseq); /* Length of query sequence. */
lenq = ajSeqGetLen(qseq); /* Length of subject sequence. */
/* Start of main application loop */
/* Intitialise variables for use by alignment functions*/
len = (lenp * lenq);
if(len>maxarr)
{
AJCRESIZE(path,len);
AJCRESIZE(compass,len);
maxarr=len;
}
p = ajSeqGetSeqC(pseq);
q = ajSeqGetSeqC(qseq);
ajStrAssignC(&pstr,"");
ajStrAssignC(&qstr,"");
/* Check that no sequence length is 0. */
if((lenp == 0)||(lenq == 0))
{
AJFREE(compass);
AJFREE(path);
ajStrDel(&pstr);
ajStrDel(&qstr);
}
/* Call alignment functions. */
embAlignPathCalc(p,q,lenp,lenq, gapopen,
gapextend,path,sub,cvt,compass,show);
/*embAlignScoreNWMatrix(path,compass,gapopen,gapextend,
pseq, qseq,
lenp,lenq,sub,cvt,
&start1,&start2);*/
embAlignWalkNWMatrix(path,pseq,qseq,&pstr,&qstr,
lenp,lenq,&start1,&start2,
gapopen,gapextend,compass);
embAlignCalcSimilarity(pstr,qstr,sub,cvt,lenp,
lenq,&id,&sim,&idx, &simx);
/* Assign score. */
temp_scop->Score = sim;
/* Tidy up */
AJFREE(compass);
AJFREE(path);
ajStrDel(&pstr);
ajStrDel(&qstr);
ajSeqDel(&qseq);
/* Bye Bye */
return ajTrue;
}
EmbPMatPrints embMatProtReadInt(AjPFile fp)
{
EmbPMatPrints ret;
AjPStr line;
ajint i;
ajuint j;
ajuint m;
const char *p;
line = ajStrNewC("#");
p = ajStrGetPtr(line);
while(!*p || *p=='#' || *p=='!' || *p=='\n')
{
if(!ajReadlineTrim(fp,&line))
{
ajStrDel(&line);
return NULL;
}
p = ajStrGetPtr(line);
}
ajDebug("embMatProtReadint starting\n");
ajDebug ("Line: %S\n", line);
AJNEW0 (ret);
ret->cod = ajStrNew();
ajStrAssignS(&ret->cod,line);
ajReadlineTrim(fp,&line);
ret->acc = ajStrNew();
ajStrAssignS(&ret->acc,line);
ajReadlineTrim(fp,&line);
ajStrToUint(line,&ret->n);
ajReadlineTrim(fp,&line);
ret->tit = ajStrNew();
ajStrAssignS(&ret->tit,line);
ajDebug ("Lineb: %S\n", line);
AJCNEW(ret->len, ret->n);
AJCNEW(ret->max, ret->n);
AJCNEW(ret->thresh, ret->n);
AJCNEW(ret->matrix, ret->n);
for(m=0;m<ret->n;++m)
{
ajReadlineTrim(fp,&line);
ajStrToUint(line,&ret->len[m]);
ajReadlineTrim(fp,&line);
ajStrToUint(line,&ret->thresh[m]);
ajReadlineTrim(fp,&line);
ajStrToUint(line,&ret->max[m]);
ajDebug ("m: %d/%d len:%d thresh:%d max:%d\n",
m, ret->n, ret->len[m], ret->thresh[m], ret->max[m]);
for(i=0;i<26;++i)
{
AJCNEW0(ret->matrix[m][i], ret->len[m]);
ajReadlineTrim(fp,&line);
ajDebug ("Linec [%d][%d]: %S\n", m, i, line);
p = ajStrGetPtr(line);
for(j=0;j<ret->len[m];++j)
{
if(!j)
p = ajSysFuncStrtok(p," ");
else
p = ajSysFuncStrtok(NULL," ");
sscanf(p,"%u",&ret->matrix[m][i][j]);
}
}
}
ajReadlineTrim(fp,&line);
ajDebug ("Linec: %S\n", line);
ajStrDel(&line);
return ret;
}
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;
}
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;
}
void embPropCalcFragments(const char *s, ajint n,
AjPList *l, AjPList *pa,
AjBool unfavoured, AjBool overlap,
AjBool allpartials, ajint *ncomp, ajint *npart,
AjPStr *rname, AjBool nterm, AjBool cterm,
AjBool dorag, EmbPPropMolwt const *mwdata,
AjBool mono)
{
static const char *PROPENZReagent[]=
{
"Trypsin","Lys-C","Arg-C","Asp-N","V8-bicarb","V8-phosph",
"Chymotrypsin","CNBr"
};
static const char *PROPENZSite[]=
{
"KR","K","R","D","E","DE","FYWLM","M"
};
static const char *PROPENZAminoCarboxyl[]=
{
"CC","C","C","N","C","CC","CCCCC","C"
};
static const char *PROPENZUnfavoured[]=
{
"KRIFLP","P","P","","KREP","P","P",""
};
ajint i;
ajint j;
ajint lim;
ajint len;
AjPList t;
EmbPPropFrag fr;
ajint *begsa = NULL;
ajint *endsa = NULL;
double molwt;
double *molwtsa = NULL;
AjBool *afrag = NULL;
ajint mark;
ajint bwp;
ajint ewp;
ajint *ival;
ajint defcnt;
ajint it;
ajint st = 0;
ajint mt = 0;
ajint et = 0;
ajStrAssignC(rname,PROPENZReagent[n]);
defcnt = 0;
len = (ajint) strlen(s);
t = ajListNew(); /* Temporary list */
/* First get all potential cut points */
for(i=0;i<len;++i)
{
if(!strchr(PROPENZSite[n],s[i]))
continue;
if(len==i+1)
continue;
if(strchr(PROPENZUnfavoured[n],s[i+1])
&& !unfavoured)
continue;
AJNEW0(ival);
*ival = i;
ajListPushAppend(t,(void *)ival);
++defcnt;
}
if(defcnt)
{
AJCNEW(begsa,(defcnt+1));
AJCNEW(endsa,(defcnt+1));
AJCNEW(molwtsa,(defcnt+1));
AJCNEW(afrag,(defcnt+1));
}
for(i=0;i<defcnt;++i) /* Pop them into a temporary array */
{
ajListPop(t,(void **)&ival);
endsa[i] = *ival;
AJFREE(ival);
}
mark = 0;
for(i=0;i<defcnt;++i) /* Work out true starts, ends and molwts */
{
bwp = mark;
ewp = endsa[i];
if(strchr(PROPENZAminoCarboxyl[n],'N'))
--ewp;
molwt=embPropCalcMolwt(s,bwp,ewp,mwdata,mono);
if(n==PROPENZCNBR)
molwt -= (17.045 + 31.095);
begsa[i] = mark;
endsa[i] = ewp;
molwtsa[i] = molwt;
afrag[i] = ajFalse;
mark = ewp+1;
}
if(defcnt) /* Special treatment for last fragment */
{
molwt = embPropCalcMolwt(s,mark,len-1,mwdata,mono);
if(n==PROPENZCNBR)
molwt -= (17.045 + 31.095);
begsa[i] = mark;
endsa[i] = len-1;
molwtsa[i] = molwt;
afrag[i] = ajFalse;
++defcnt;
}
/* Push the hits */
for(i=0;i<defcnt;++i)
{
if(dorag)
{
st = begsa[i];
et = endsa[i];
for(it=st+RAG_MINPEPLEN-1; it < et; ++it)
{
AJNEW0(fr);
fr->start = st;
fr->end = it;
fr->molwt = embPropCalcMolwt(s,st,it,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
AJNEW0(fr);
fr->start = begsa[i];
fr->end = endsa[i];
fr->molwt = molwtsa[i];
fr->isfrag = afrag[i];
ajListPush(*l,(void *) fr);
if(dorag && nterm)
for(it=st+1; it < et-RAG_MINPEPLEN+2; ++it)
{
AJNEW0(fr);
fr->start = it;
fr->end = et;
fr->molwt = embPropCalcMolwt(s,it,et,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
if(!dorag)
ajListSort(*l, &propFragCompare);
*ncomp = defcnt;
/* Now deal with overlaps */
*npart = 0;
lim = defcnt -1;
if(overlap && !allpartials)
{
for(i=0;i<lim;++i)
{
if(dorag)
{
st = begsa[i];
mt = endsa[i];
et = endsa[i+1];
if(cterm)
for(it=mt+1; it < et; ++it)
{
AJNEW0(fr);
fr->start = st;
fr->end = it;
fr->molwt = embPropCalcMolwt(s,st,it,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
AJNEW0(fr);
fr->isfrag = ajTrue;
fr->molwt = embPropCalcMolwt(s,begsa[i],endsa[i+1],mwdata,mono);
if(n==PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->start = begsa[i];
fr->end = endsa[i+1];
ajListPush(*pa,(void *)fr);
++(*npart);
if(dorag && nterm)
for(it=st+1; it<mt; ++it)
{
AJNEW0(fr);
fr->start = it;
fr->end = et;
fr->molwt = embPropCalcMolwt(s,it,et,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
if(*npart) /* Remove complete sequence */
{
--(*npart);
ajListPop(*pa,(void **)&fr);
}
if(!dorag)
ajListSort(*pa, &propFragCompare);
}
if(allpartials)
{
lim = defcnt;
for(i=0;i<lim;++i)
for(j=i+1;j<lim;++j)
{
AJNEW0(fr);
fr->isfrag = ajTrue;
fr->molwt = embPropCalcMolwt(s,begsa[i],endsa[j],mwdata,mono);
if(n==PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->start = begsa[i];
fr->end = endsa[j];
ajListPush(*pa,(void *)fr);
++(*npart);
}
if(*npart) /* Remove complete sequence */
{
--(*npart);
ajListPop(*pa,(void **)&fr);
}
if(!dorag)
ajListSort(*pa, &propFragCompare);
}
if(defcnt)
{
AJFREE(molwtsa);
AJFREE(endsa);
AJFREE(begsa);
AJFREE(afrag);
}
ajListFree(&t);
return;
}
/* @funcstatic newcoils_read_matrix *******************************************
**
** Reads the matrix and stores in a hept_pref structure
**
** @param [u] inf [AjPFile] matrix input file
** @return [struct hept_pref*] Matrix data for heptad preference
******************************************************************************/
static struct hept_pref* newcoils_read_matrix(AjPFile inf)
{
ajint i;
ajint j;
ajint pt;
ajint aa_len;
ajint win;
float m_g;
float sd_g;
float m_cc;
float sd_cc;
float sc;
float hept[NCHEPTAD];
AjPStr buff;
const char *pbuff;
struct hept_pref *h;
buff = ajStrNew();
aa_len = strlen(NCAAs);
AJNEW(h);
AJCNEW(h->m,aa_len);
for(i=0; i<aa_len; ++i)
{
AJCNEW(h->m[i],NCHEPTAD);
for(j=0; j<NCHEPTAD; ++j)
h->m[i][j] = -1;
}
AJNEW(h->f);
h->n = 0;
h->smallest = 1.0;
while(ajReadlineTrim(inf,&buff))
{
pbuff = ajStrGetPtr(buff);
if(*pbuff != '%')
{
if((strncmp(pbuff,"uw ",3)==0) || (strncmp(pbuff,"w ",2)==0))
{
i = h->n;
if(strncmp(pbuff,"uw ",3)==0)
h->f[i].w = 0;
else
h->f[i].w = 1;
ajFmtScanS(buff,"%*s %d %f %f %f %f %f",&win,&m_cc,
&sd_cc,&m_g,&sd_g,&sc);
h->f[i].win = win;
h->f[i].m_cc = (float)m_cc;
h->f[i].sd_cc = (float)sd_cc;
h->f[i].m_g = (float)m_g;
h->f[i].sd_g = (float)sd_g;
h->f[i].sc = (float)sc;
h->n++;
AJCRESIZE(h->f,(h->n)+1);
if((h->n)>=9)
ajFatal("Too many window parms in matrix file\n");
}
else if(*pbuff>='A' && *pbuff<='Z')
{
/* AA data */
pt = (int)(pbuff[0]-'A');
if(h->m[pt][0]==-1)
{
ajFmtScanS(buff,"%*s%f%f%f%f%f%f%f",&hept[0],
&hept[1],&hept[2],&hept[3],&hept[4],
&hept[5],&hept[6]);
for(i=0; i<NCHEPTAD; ++i)
{
h->m[pt][i] = (float)hept[i];
if(h->m[pt][i]>0)
{
if(h->m[pt][i]<h->smallest)
h->smallest = h->m[pt][i];
}
else
h->m[pt][i]=-1; /* Don't permit zero values */
}
}
else
ajWarn("multiple entries for AA %c in matrix file\n",
*pbuff);
}
else
{
ajWarn("strange characters in matrix file\n");
ajWarn("Ignoring line: %S\n",buff);
}
}
}
ajStrDel(&buff);
return h;
}
int main(int argc, char **argv)
{
AjPAlign align;
AjPSeqall seqall;
AjPSeq a;
AjPSeq b;
AjPStr alga;
AjPStr algb;
AjPStr ss;
ajuint lena;
ajuint lenb;
const char *p;
const char *q;
ajint start1 = 0;
ajint start2 = 0;
float *path;
ajint *compass;
float* ix;
float* iy;
float* m;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
float gapopen;
float gapextend;
float endgapopen;
float endgapextend;
ajulong maxarr = 1000; /* arbitrary. realloc'd if needed */
ajulong len;
float score;
AjBool dobrief = ajTrue;
AjBool endweight = ajFalse; /* whether end gap penalties should be applied */
float id = 0.;
float sim = 0.;
float idx = 0.;
float simx = 0.;
AjPStr tmpstr = NULL;
size_t stlen;
embInit("needle", argc, argv);
matrix = ajAcdGetMatrixf("datafile");
a = ajAcdGetSeq("asequence");
ajSeqTrim(a);
seqall = ajAcdGetSeqall("bsequence");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
endgapopen = ajAcdGetFloat("endopen");
endgapextend = ajAcdGetFloat("endextend");
dobrief = ajAcdGetBoolean("brief");
endweight = ajAcdGetBoolean("endweight");
align = ajAcdGetAlign("outfile");
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
AJCNEW(m, maxarr);
AJCNEW(ix, maxarr);
AJCNEW(iy, maxarr);
alga = ajStrNew();
algb = ajStrNew();
ss = ajStrNew();
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
lena = ajSeqGetLen(a);
while(ajSeqallNext(seqall,&b))
{
ajSeqTrim(b);
lenb = ajSeqGetLen(b);
if(lenb > (ULONG_MAX/(ajulong)(lena+1)))
ajFatal("Sequences too big. Try 'stretcher' or 'supermatcher'");
len = lena*lenb;
if(len>maxarr)
{
stlen = (size_t) len;
AJCRESIZETRY(path,stlen);
if(!path)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(compass,stlen);
if(!compass)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(m,stlen);
if(!m)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(ix,stlen);
if(!ix)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(iy,stlen);
if(!iy)
ajDie("Sequences too big. Try 'stretcher'");
maxarr=len;
}
p = ajSeqGetSeqC(a);
q = ajSeqGetSeqC(b);
ajStrAssignC(&alga,"");
ajStrAssignC(&algb,"");
score = embAlignPathCalcWithEndGapPenalties(p, q, lena, lenb,
gapopen, gapextend, endgapopen, endgapextend,
&start1, &start2, path, sub, cvt,
m, ix, iy, compass, ajTrue, endweight);
embAlignWalkNWMatrixUsingCompass(p, q, &alga, &algb,
lena, lenb, &start1, &start2,
compass);
embAlignReportGlobal(align, a, b, alga, algb,
start1, start2,
gapopen, gapextend,
score, matrix,
ajSeqGetOffset(a), ajSeqGetOffset(b));
if(!dobrief)
{
embAlignCalcSimilarity(alga,algb,sub,cvt,lena,lenb,&id,&sim,&idx,
&simx);
ajFmtPrintS(&tmpstr,"Longest_Identity = %5.2f%%\n",
id);
ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n",
sim);
ajFmtPrintAppS(&tmpstr,"Shortest_Identity = %5.2f%%\n",
idx);
ajFmtPrintAppS(&tmpstr,"Shortest_Similarity = %5.2f%%",
simx);
ajAlignSetSubHeaderApp(align, tmpstr);
}
ajAlignWrite(align);
ajAlignReset(align);
}
ajAlignClose(align);
ajAlignDel(&align);
ajSeqallDel(&seqall);
ajSeqDel(&a);
ajSeqDel(&b);
AJFREE(compass);
AJFREE(path);
AJFREE(ix);
AJFREE(iy);
AJFREE(m);
ajStrDel(&alga);
ajStrDel(&algb);
ajStrDel(&ss);
ajStrDel(&tmpstr);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPList idlist;
AjPList* fieldList = NULL;
AjBool systemsort;
AjBool cleanup;
ajuint maxindex;
ajuint maxidlen = 0;
ajuint maxlen;
AjPFile elistfile = NULL;
AjPFile* alistfile = NULL;
AjPStr dbname = NULL;
AjPStr release = NULL;
AjPStr datestr = NULL;
AjPStr sortopt = NULL;
void **entryIds = NULL;
AjPStr directory;
AjPStr indexdir;
AjPStr filename;
AjPStr exclude;
AjPStr curfilename = NULL;
AjPFile libr=NULL;
AjPStr idformat = NULL;
EmbPEntry entry;
ajuint idtype = 0;
ajuint idCount = 0;
ajuint idDone;
AjPList listInputFiles = NULL;
void ** inputFiles = NULL;
ajuint nfiles;
ajuint ifile;
ajuint filesize;
short recsize;
ajuint maxfilelen = 20;
char date[4] =
{
0,0,0,0
};
AjPStr tmpfname = NULL;
AjPStr* fields = NULL;
AjPFile entFile = NULL;
AjPStr* divfiles = NULL;
AjPRegexp regIdExp = NULL;
ajint* maxFieldLen = NULL;
ajuint ifield = 0;
ajuint nfields = 0;
AjPFile logfile = NULL;
ajuint* countField = NULL;
ajuint* fieldTot = NULL;
ajuint idCountFile = 0;
ajuint i;
embInit("dbifasta", argc, argv);
idformat = ajAcdGetListSingle("idformat");
fields = ajAcdGetList("fields");
directory = ajAcdGetDirectoryName("directory");
indexdir = ajAcdGetOutdirName("indexoutdir");
filename = ajAcdGetString("filenames");
exclude = ajAcdGetString("exclude");
dbname = ajAcdGetString("dbname");
release = ajAcdGetString("release");
datestr = ajAcdGetString("date");
systemsort = ajAcdGetBoolean("systemsort");
cleanup = ajAcdGetBoolean("cleanup");
sortopt = ajAcdGetString("sortoptions");
maxindex = ajAcdGetInt("maxindex");
logfile = ajAcdGetOutfile("outfile");
while(fields[nfields]) /* array ends with a NULL */
nfields++;
if(nfields)
{
AJCNEW(maxFieldLen, nfields);
AJCNEW0(countField, nfields);
AJCNEW0(fieldTot, nfields);
for(ifield=0; ifield < nfields; ifield++)
maxFieldLen[ifield] = (ajint)maxindex * -1;
if(systemsort)
AJCNEW(alistfile, nfields);
else
{
AJCNEW(fieldList, nfields);
for(ifield=0; ifield < nfields; ifield++)
fieldList[ifield] = ajListNew();
}
}
if(ajStrMatchC(datestr, "00/00/00"))
ajFmtPrintS(&datestr, "%D", ajTimeRefTodayFmt("dbindex"));
ajStrRemoveWhite(&dbname); /* used for temp filenames */
embDbiDateSet(datestr, date);
idlist = ajListNew();
regIdExp = dbifasta_getExpr(idformat, &idtype);
ajDebug("reading '%S/%S'\n", directory, filename);
ajDebug("writing '%S/'\n", indexdir);
listInputFiles = embDbiFileListExc(directory, filename, exclude);
ajListSort(listInputFiles, &ajStrVcmp);
nfiles = (ajuint) ajListToarray(listInputFiles, &inputFiles);
if(!nfiles)
ajDie("No input files in '%S' matched filename '%S'",
directory, filename);
embDbiLogHeader(logfile, dbname, release, datestr,
indexdir, maxindex);
embDbiLogFields(logfile, fields, nfields);
embDbiLogSource(logfile, directory, filename, exclude,
(AjPStr*) inputFiles, nfiles);
embDbiLogCmdline(logfile);
AJCNEW0(divfiles, nfiles);
/*
** process each input file, one at a time
*/
for(ifile=0; ifile < nfiles; ifile++)
{
ajStrAssignS(&curfilename,(AjPStr) inputFiles[ifile]);
embDbiFlatOpenlib(curfilename, &libr);
ajFilenameTrimPath(&curfilename);
if(ajStrGetLen(curfilename) >= maxfilelen)
maxfilelen = ajStrGetLen(curfilename) + 1;
ajDebug("processing filename '%S' ...\n", curfilename);
ajDebug("processing file '%F' ...\n", libr);
ajStrAssignS(&divfiles[ifile], curfilename);
if(systemsort) /* elistfile for entries, alist for fields */
elistfile = embDbiSortOpen(alistfile, ifile,
dbname, fields, nfields);
idCountFile = 0;
for(i=0;i<nfields;i++)
countField[i] = 0;
while((entry=dbifasta_NextFlatEntry(libr, ifile,
regIdExp, idtype,
systemsort, fields,
maxFieldLen, &maxidlen,
countField, elistfile,
alistfile)))
{
idCountFile++;
if(!systemsort) /* save the entry data in lists */
embDbiMemEntry(idlist, fieldList, nfields,
entry, ifile);
entry = NULL;
}
idCount += idCountFile;
if(systemsort)
{
embDbiSortClose(&elistfile, alistfile, nfields);
AJFREE(entry);
}
else
{
embDbiEntryDel(&dbifastaGEntry);
}
embDbiLogFile(logfile, curfilename, idCountFile, fields,
countField, nfields);
}
/* write the division.lkp file */
embDbiWriteDivision(indexdir, dbname, release, date,
maxfilelen, nfiles, divfiles, NULL);
/* Write the entryname.idx index */
ajStrAssignC(&tmpfname, "entrynam.idx");
entFile = ajFileNewOutNamePathS(tmpfname, indexdir);
recsize = maxidlen+10;
filesize = 300 + (idCount*(ajint)recsize);
embDbiHeader(entFile, filesize, idCount, recsize, dbname, release, date);
if(systemsort)
idDone = embDbiSortWriteEntry(entFile, maxidlen,
dbname, nfiles, cleanup, sortopt);
else /* save entries in entryIds array */
{
idDone = embDbiMemWriteEntry(entFile, maxidlen,
idlist, &entryIds);
if(idDone != idCount)
ajFatal("Duplicates not allowed for in-memory processing");
}
embDbiHeaderSize(entFile, 300+(idDone*(ajint)recsize), idDone);
ajFileClose(&entFile);
/* Write the fields index files */
for(ifield=0; ifield < nfields; ifield++)
{
if(maxindex)
maxlen = maxindex;
else
{
if(maxFieldLen[ifield] >= 0)
maxlen = maxFieldLen[ifield];
else
maxlen = - maxFieldLen[ifield];
}
if(systemsort)
fieldTot[ifield] = embDbiSortWriteFields(dbname, release,
date, indexdir,
fields[ifield], maxlen,
nfiles, idCount,
cleanup, sortopt);
else
fieldTot[ifield] = embDbiMemWriteFields(dbname, release,
date, indexdir,
fields[ifield], maxlen,
fieldList[ifield],
entryIds);
}
embDbiLogFinal(logfile,maxindex, maxFieldLen, fields, fieldTot,
nfields, nfiles, idDone, idCount);
if(systemsort)
embDbiRmEntryFile(dbname, cleanup);
ajStrDel(&idformat);
ajStrDelarray(&fields);
ajStrDel(&filename);
ajStrDel(&exclude);
ajStrDel(&dbname);
ajStrDel(&release);
ajStrDel(&datestr);
ajStrDel(&sortopt);
ajStrDel(&directory);
ajStrDel(&indexdir);
ajStrDel(&tmpfname);
ajFileClose(&libr);
ajFileClose(&logfile);
for(i=0;i<nfields;i++)
{
if(systemsort)
{
ajFileClose(&alistfile[i]);
}
else
{
ajListMap(fieldList[i], &embDbiFieldDelMap, NULL);
ajListFree(&fieldList[i]);
}
}
AJFREE(alistfile);
AJFREE(fieldList);
AJFREE(maxFieldLen);
AJFREE(countField);
AJFREE(fieldTot);
for(i=0;i<nfiles;i++)
{
ajStrDel(&divfiles[i]);
}
AJFREE(divfiles);
AJFREE(inputFiles);
embDbiEntryDel(&dbifastaGEntry);
ajStrDel(&dbifastaGRline);
ajStrDel(&dbifastaGTmpId);
if(dbifastaGFdl)
{
for(i=0; i < nfields; i++)
ajListFree(&dbifastaGFdl[i]);
AJFREE(dbifastaGFdl);
}
ajListMap(idlist, &embDbiEntryDelMap, NULL);
ajListFree(&idlist);
ajListstrFreeData(&listInputFiles);
AJFREE(entryIds);
ajRegFree(&dbifastaGIdexp);
ajRegFree(&dbifastaGWrdexp);
ajRegFree(®IdExp);
ajStrDel(&dbifastaGTmpAc);
ajStrDel(&dbifastaGTmpSv);
ajStrDel(&dbifastaGTmpGi);
ajStrDel(&dbifastaGTmpDb);
ajStrDel(&dbifastaGTmpDes);
ajStrDel(&dbifastaGTmpFd);
ajStrDel(&curfilename);
embExit();
return 0;
}
static EmbPEntry dbifasta_NextFlatEntry(AjPFile libr, ajint ifile,
AjPRegexp idexp,
ajuint type, AjBool systemsort,
AjPStr const * fields,
ajint* maxFieldLen,
ajuint* maxidlen, ajuint* countfield,
AjPFile elistfile, AjPFile* alistfile)
{
ajint ir;
ajint is = 0;
char* token;
ajint i;
static ajint nfields;
ajint ifield;
if(!dbifastaGFdl)
{
nfields = 0;
while(fields[nfields])
nfields++;
if(nfields)
AJCNEW(dbifastaGFdl, nfields);
for(i=0; i < nfields; i++)
{
dbifastaGFdl[i] = ajListNew();
}
}
if(!dbifastaGEntry || !systemsort)
dbifastaGEntry = embDbiEntryNew(nfields);
if(!dbifasta_ParseFasta(libr, &ir, maxFieldLen,
countfield, idexp, type,
alistfile, systemsort, fields))
return NULL;
/* id to dbifastaGEntry->entry */
if(ajStrGetLen(dbifastaGTmpId) > *maxidlen)
*maxidlen = ajStrGetLen(dbifastaGTmpId);
if(systemsort)
ajFmtPrintF(elistfile, "%S %d %d %d\n",
dbifastaGTmpId, ir, is, ifile+1);
else
{
dbifastaGEntry->entry = ajCharNewS(dbifastaGTmpId);
dbifastaGEntry->rpos = ir;
dbifastaGEntry->spos = is;
dbifastaGEntry->filenum = ifile+1;
/* field tokens as list, then move to ret->field */
for(ifield=0; ifield < nfields; ifield++)
{
dbifastaGEntry->nfield[ifield] =
(ajuint) ajListGetLength(dbifastaGFdl[ifield]);
if(dbifastaGEntry->nfield[ifield])
{
AJCNEW(dbifastaGEntry->field[ifield],
dbifastaGEntry->nfield[ifield]);
i = 0;
while(ajListPop(dbifastaGFdl[ifield], (void**) &token))
dbifastaGEntry->field[ifield][i++] = token;
}
else
dbifastaGEntry->field[ifield] = NULL;
}
}
return dbifastaGEntry;
}
int main(int argc, char **argv)
{
AjPFile infile = NULL;
AjPFile outfile = NULL;
AjPStr line;
AjPGraph graphLB = NULL;
AjPGraphdata xygraph = NULL;
AjPGraphdata xygraph2 = NULL;
AjBool doplot;
ajint N=0;
float *xdata = NULL;
float *ydata = NULL;
float *V = NULL;
float *S = NULL;
float a;
float b;
float upperXlimit;
float upperYlimit;
float A;
float B;
float C;
float D;
float xmin;
float xmax;
float ymin;
float ymax;
float xmin2;
float xmax2;
float ymin2;
float ymax2;
float Vmax;
float Km;
float cutx;
float cuty;
float amin = 0.;
float amax = 0.;
float bmin = 0.;
float bmax = 0.;
embInit("findkm", argc, argv);
infile = ajAcdGetInfile("infile");
outfile = ajAcdGetOutfile ("outfile");
doplot = ajAcdGetBoolean("plot");
graphLB = ajAcdGetGraphxy("graphLB");
line = ajStrNew();
/* Determine N by reading infile */
while(ajReadlineTrim(infile, &line))
if(ajStrGetLen(line) >0)
N++;
/* only allocate memory to the arrays */
AJCNEW(xdata, N);
AJCNEW(ydata, N);
AJCNEW(S, N);
AJCNEW(V, N);
ajFileSeek(infile, 0L, 0);
N=0;
while(ajReadlineTrim(infile, &line))
{
if(ajStrGetLen(line) > 0)
{
sscanf(ajStrGetPtr(line),"%f %f",&S[N],&V[N]);
if(S[N] > 0.0 && V[N] > 0.0)
{
xdata[N] = S[N];
ydata[N] = S[N]/V[N];
N++;
}
}
}
/* find the max and min values for the graph parameters*/
xmin = (float)0.5*findkm_findmin(xdata, N);
xmax = (float)1.5*findkm_findmax(xdata, N);
ymin = (float)0.5*findkm_findmin(ydata, N);
ymax = (float)1.5*findkm_findmax(ydata, N);
xmin2 = (float)0.5*findkm_findmin(S, N);
xmax2 = (float)1.5*findkm_findmax(S, N);
ymin2 = (float)0.5*findkm_findmin(V, N);
ymax2 = (float)1.5*findkm_findmax(V, N);
/*
** In case the casted ints turn out to be same number on the axis,
** make the max number larger than the min so graph can be seen.
*/
if((ajint)xmax == (ajint)xmin)
++xmax;
if((ajint)ymax == (ajint)ymin)
++ymax;
if((ajint)xmax2 == (ajint)xmin2)
++xmax2;
if((ajint)ymax2 == (ajint)ymin2)
++ymax2;
/*
** Gaussian Elimination for Best-fit curve plotting and
** calculating Km and Vmax
*/
A = findkm_summation(xdata, N);
B = findkm_summation(ydata, N);
C = findkm_multisum(xdata, ydata, N);
D = findkm_multisum(xdata, xdata, N);
/*
** To find the best fit line, Least Squares Fit: y =ax +b;
** Two Simultaneous equations, REARRANGE FOR b
**
** findkm_summation(ydata, N) - findkm_summation(xdata,N)*a - N*b =0;
** b = (findkm_summation(ydata,N) - findkm_summation(xdata,N)*a) / N;
** b = (B - A*a)/ N;
**
** C - D*a - A*((B - A*a)/ N) =0;
** C - D*a - A*B/N + A*A*a/N =0;
** C - A*B/N = D*a - A*A*a/N;
*/
/* REARRANGE FOR a */
a = (N*C - A*B)/ (N*D - A*A);
b = (B - A*a)/ N;
/*
** Equation of Line - Lineweaver burk eqn
** 1/V = (Km/Vmax)*(1/S) + 1/Vmax;
*/
Vmax = 1/a;
Km = b/a;
cutx = -1/Km;
cuty = Km/Vmax;
/* set limits for last point on graph */
upperXlimit = findkm_findmax(xdata,N)+3;
upperYlimit = (upperXlimit)*a + b;
ajFmtPrintF(outfile, "---Hanes Woolf Plot Calculations---\n");
ajFmtPrintF(outfile, "Slope of best fit line is a = %.2f\n", a);
ajFmtPrintF(outfile,"Coefficient in Eqn of line y = ma +b is b "
"= %.2f\n", b);
ajFmtPrintF(outfile, "Where line cuts x axis = (%.2f, 0)\n", cutx);
ajFmtPrintF(outfile, "Where line cuts y axis = (0, %.2f)\n", cuty);
ajFmtPrintF(outfile, "Limit-point of graph for plot = (%.2f, %.2f)\n\n",
upperXlimit, upperYlimit);
ajFmtPrintF(outfile, "Vmax = %.2f, Km = %f\n",Vmax, Km);
/* draw graphs */
if(doplot)
{
xygraph = ajGraphdataNewI(N);
ajGraphdataAddXY(xygraph, S, V);
ajGraphDataAdd(graphLB, xygraph);
ajGraphdataSetTitleC(xygraph, "Michaelis Menten Plot");
ajGraphdataSetXlabelC(xygraph, "[S]");
ajGraphdataSetYlabelC(xygraph, "V");
ajGraphxySetXstartF(graphLB, 0.0);
ajGraphxySetXendF(graphLB, xmax2);
ajGraphxySetYstartF(graphLB, 0.0);
ajGraphxySetYendF(graphLB, ymax2);
ajGraphxySetXrangeII(graphLB, (ajint)0.0, (ajint)xmax2);
ajGraphxySetYrangeII(graphLB, (ajint)0.0, (ajint)ymax2);
ajGraphdataAddposLine(xygraph, 0.0, 0.0, S[0], V[0], (ajint)BLACK);
ajGraphxyShowPointsCircle(graphLB, ajTrue);
ajGraphdataSetMinmax(xygraph,0.0,xmax2,0.0,ymax2);
ajGraphicsCalcRange(S,N,&amin,&amax);
ajGraphicsCalcRange(V,N,&bmin,&bmax);
ajGraphdataSetTruescale(xygraph,amin,amax,bmin,bmax);
ajGraphdataSetTypeC(xygraph,"2D Plot Float");
xygraph2 = ajGraphdataNewI(N);
ajGraphdataAddXY(xygraph2, xdata, ydata);
ajGraphDataAdd(graphLB, xygraph2);
ajGraphdataSetTitleC(xygraph2, "Hanes Woolf Plot");
ajGraphdataSetXlabelC(xygraph2, "[S]");
ajGraphdataSetYlabelC(xygraph2, "[S]/V");
ajGraphxySetXstartF(graphLB, cutx);
ajGraphxySetXendF(graphLB, upperXlimit);
ajGraphxySetYstartF(graphLB, 0.0);
ajGraphxySetYendF(graphLB, upperYlimit);
ajGraphxySetXrangeII(graphLB, (ajint)cutx, (ajint)upperXlimit);
ajGraphxySetYrangeII(graphLB, (ajint)0.0, (ajint)upperYlimit);
ajGraphxyShowPointsCircle(graphLB, ajTrue);
ajGraphdataSetMinmax(xygraph2, cutx,upperXlimit,0.0,upperYlimit);
ajGraphicsCalcRange(xdata,N,&amin,&amax);
ajGraphicsCalcRange(ydata,N,&bmin,&bmax);
ajGraphdataSetTruescale(xygraph2,amin,amax,bmin,bmax);
ajGraphdataSetTypeC(xygraph2,"2D Plot");
ajGraphSetTitleC(graphLB,"FindKm");
ajGraphxySetflagOverlay(graphLB,ajFalse);
ajGraphxyDisplay(graphLB, ajTrue);
}
AJFREE(xdata);
AJFREE(ydata);
AJFREE(S);
AJFREE(V);
ajFileClose(&infile);
ajFileClose(&outfile);
ajGraphxyDel(&graphLB);
ajStrDel(&line);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq seq = NULL;
AjPFile inf = NULL;
AjPStr strand = NULL;
AjPStr substr = NULL;
AjPStr name = NULL;
AjPStr mname = NULL;
AjPStr tname = NULL;
AjPStr pname = NULL;
AjPStr line = NULL;
AjPStr cons = NULL;
AjPStr m = NULL;
AjPStr n = NULL;
AjPAlign align= NULL; /* JISON, replaces AjPOutfile outf */
ajint type;
ajint begin;
ajint end;
ajulong len;
ajint i;
ajint j;
float **fmatrix=NULL;
ajint mlen;
float maxfs;
ajint thresh;
float gapopen;
float gapextend;
float opencoeff;
float extendcoeff;
const char *p;
ajulong maxarr = 1000;
ajulong alen;
float *path;
ajint *compass;
size_t stlen;
embInit("prophet", argc, argv);
seqall = ajAcdGetSeqall("sequence");
inf = ajAcdGetInfile("infile");
opencoeff = ajAcdGetFloat("gapopen");
extendcoeff = ajAcdGetFloat("gapextend");
align = ajAcdGetAlign("outfile"); /*JISON replacing outfile */
opencoeff = ajRoundFloat(opencoeff, 8);
extendcoeff = ajRoundFloat(extendcoeff, 8);
substr = ajStrNew();
name = ajStrNew();
mname = ajStrNew();
tname = ajStrNew();
line = ajStrNew();
m = ajStrNewC("");
n = ajStrNewC("");
type = prophet_getType(inf,&tname);
if(!type)
ajFatal("Unrecognised profile/matrix file format");
prophet_read_profile(inf,&pname,&mname,&mlen,&gapopen,&gapextend,&thresh,
&maxfs, &cons);
ajAlignSetMatrixName(align, mname);
AJCNEW(fmatrix, mlen);
for(i=0;i<mlen;++i)
{
AJCNEW(fmatrix[i], AZ);
if(!ajReadlineTrim(inf,&line))
ajFatal("Missing matrix line");
p = ajStrGetPtr(line);
p = ajSysFuncStrtok(p," \t");
for(j=0;j<AZ;++j)
{
sscanf(p,"%f",&fmatrix[i][j]);
p = ajSysFuncStrtok(NULL," \t");
}
}
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
while(ajSeqallNext(seqall, &seq))
{
begin = ajSeqallGetseqBegin(seqall);
end = ajSeqallGetseqEnd(seqall);
ajStrAssignC(&name,ajSeqGetNameC(seq));
strand = ajSeqGetSeqCopyS(seq);
ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1);
len = ajStrGetLen(substr);
if(len > (ULONG_MAX/(ajulong)(mlen+1)))
ajFatal("Sequences too big. Try 'supermatcher'");
alen = len*mlen;
if(alen>maxarr)
{
stlen = (size_t) alen;
AJCRESIZE(path,stlen);
AJCRESIZE(compass,stlen);
maxarr=alen;
}
ajStrAssignC(&m,"");
ajStrAssignC(&n,"");
/* JISON used to be
prophet_scan_profile(substr,pname,name,mlen,fmatrix,
outf,cons,opencoeff,
extendcoeff,path,compass,&m,&n,len); */
/* JISON new call and reset align */
prophet_scan_profile(substr,name,pname,mlen,fmatrix,
align,cons,opencoeff,
extendcoeff,path,compass,&m,&n,(ajint)len);
ajAlignReset(align);
ajStrDel(&strand);
}
for(i=0;i<mlen;++i)
AJFREE (fmatrix[i]);
AJFREE (fmatrix);
AJFREE(path);
AJFREE(compass);
ajStrDel(&line);
ajStrDel(&cons);
ajStrDel(&name);
ajStrDel(&pname);
ajStrDel(&mname);
ajStrDel(&tname);
ajStrDel(&substr);
ajStrDel(&m);
ajStrDel(&n);
ajSeqDel(&seq);
ajFileClose(&inf);
ajAlignClose(align);
ajAlignDel(&align);
ajSeqallDel(&seqall);
embExit();
return 0;
}