int main(int argc, char **argv)
{
/* Variable Declarations */
AjPFile inf = NULL;
AjPFile outf = NULL;
AjPStr line = NULL; /* Line from inf */
AjPStr option = NULL;
AjBool doall = AJFALSE;
AjBool doend = AJFALSE;
AjBool doexcess = AJFALSE;
/* ACD File Processing */
embInit("nospace", argc, argv);
inf = ajAcdGetInfile("infile");
outf = ajAcdGetOutfile("outfile");
option = ajAcdGetListSingle("menu");
if(ajStrMatchC(option, "all"))
doall = ajTrue;
else if(ajStrMatchC(option, "end"))
doend = ajTrue;
else if(ajStrMatchC(option, "excess"))
doexcess = ajTrue;
/* Application logic */
line = ajStrNew();
while(ajReadline(inf,&line))
{
if(doall)
ajStrRemoveWhite(&line);
else if(doend)
ajStrTrimWhiteEnd(&line);
else if(doexcess)
ajStrRemoveWhiteExcess(&line);
ajFmtPrintF(outf, "%S\n", line);
}
/* Memory management and exit */
ajFileClose(&inf);
ajFileClose(&outf);
ajStrDel(&line);
ajStrDel(&option);
embExit();
return 0;
}
AjPPatlistSeq ajPatlistSeqRead (const AjPStr patspec,
const AjPStr patname,
const AjPStr fmt,
AjBool protein, ajuint mismatches)
{
AjPPatlistSeq patlist = NULL;
AjPStr line = NULL;
AjPStr name = NULL;
AjPFilebuff infile = NULL;
AjPRegexp mismreg = NULL;
AjPStr patstr = NULL;
AjPStr pat = NULL;
ajuint mismatch = 0;
ajint ifmt = 0;
ajuint npat = 0;
AjPStr namestr = NULL;
ajStrAssignS(&namestr, patname);
ajStrAssignEmptyC(&namestr, "pattern");
ajStrAssignS(&patstr, patspec);
patlist = ajPatlistSeqNewType(protein);
ifmt = patternSeqFormat(fmt);
ajDebug("ajPatlistSeqRead patspec: '%S' patname: '%S' "
"protein: %B mismatches: %d\n",
patspec, patname, protein, mismatches);
if(ajStrGetCharFirst(patstr) == '@')
{
ajStrCutStart(&patstr, 1);
infile = ajFilebuffNewNameS(patstr);
if(!infile)
{
ajErr("Unable to open pattern file '%S'", patstr);
return NULL;
}
line = ajStrNew();
name = ajStrNew();
if(!ifmt)
{
ajBuffreadLineTrim(infile,&line);
if(ajStrPrefixC(line, ">"))
ifmt = 2;
else
ifmt = 1;
ajFilebuffReset(infile);
}
switch(ifmt)
{
case 1:
while (ajBuffreadLineTrim(infile,&line))
{
npat++;
ajStrAppendS (&pat,line);
ajFmtPrintS(&name, "%S%u", namestr, npat);
ajPatternSeqNewList(patlist,name,pat,mismatches);
ajStrSetClear(&pat);
}
break;
default:
mismreg = ajRegCompC("<mismatch=(\\d+)>");
while (ajBuffreadLineTrim(infile,&line))
{
if (ajStrGetCharFirst(line) == '>')
{
if (ajStrGetLen(name))
{
ajPatternSeqNewList(patlist,name,pat,
mismatch);
ajStrSetClear(&name);
ajStrSetClear(&pat);
mismatch=mismatches;
}
ajStrCutStart(&line,1);
if (ajRegExec(mismreg,line))
{
ajRegSubI(mismreg,1,&name);
ajStrToUint(name,&mismatch);
ajStrTruncateLen(&line,ajRegOffset(mismreg));
ajStrTrimWhiteEnd(&line);
}
ajStrAssignS (&name,line);
ajStrAssignEmptyS(&name, patname);
}
else
ajStrAppendS (&pat,line);
}
ajStrAssignEmptyS(&name, patname);
ajPatternSeqNewList(patlist,name,pat,mismatch);
ajRegFree(&mismreg);
break;
}
ajFilebuffDel(&infile);
}
else
{
ajStrAssignS(&name, namestr);
ajPatternSeqNewList(patlist,name,patstr,mismatches);
}
ajStrDel(&name);
ajStrDel(&line);
ajStrDel(&pat);
ajStrDel(&namestr);
ajStrDel(&patstr);
return patlist;
}
