static void jaspscan_GetFileList(const AjPStr dir, const AjPStr jaspdir,
const char *wild, AjPList list)
{
AjPList tlist = NULL;
AjPStr jdir = NULL;
AjPStr wstr = NULL;
AjPStr str = NULL;
tlist = ajListNew();
jdir = ajStrNew();
wstr = ajStrNew();
ajFmtPrintS(&jdir,"%S%S",dir,jaspdir);
if(!ajDirnameFixExists(&jdir))
ajFatal("EMBOSS_DATA undefined or 'jaspextract' needs to be run");
ajFmtPrintS(&wstr,"%s%s",wild,J_EXT);
ajFilelistAddPathWild(tlist,jdir,wstr);
if(!ajListGetLength(tlist))
ajWarn("Matrix file(s) %S not found",wstr);
while(ajListPop(tlist,(void **)&str))
ajListPushAppend(list,(void *)str);
ajStrDel(&wstr);
ajStrDel(&jdir);
ajListFree(&tlist);
return;
}
static void jaspextract_writematrixfile(const AjPTable mtable,
const AjPStr directory)
{
AjPStr wild = NULL;
AjPList flist = NULL;
AjPStr key = NULL;
AjPStr fname = NULL;
AjPStr dest = NULL;
const AjPStr value = NULL;
AjPFile outf = NULL;
const char *p = NULL;
char *q = NULL;
wild = ajStrNewC("*.pfm");
flist = ajListNew();
key = ajStrNew();
dest = ajStrNew();
ajFmtPrintS(&dest,"%S%c%s",directory,SLASH_CHAR,MATRIXFILE);
outf = ajFileNewOutNameS(dest);
if(!outf)
ajFatal("Cannot open output file %S",dest);
ajFilelistAddPathWild(flist, directory, wild);
while(ajListPop(flist,(void**)&fname))
{
ajFilenameTrimPath(&fname);
p = ajStrGetPtr(fname);
q = strrchr(p,(int)'.');
ajStrAssignSubC(&key,p,0,q-p-1);
value = ajTableFetchS(mtable, key);
if(value)
ajFmtPrintF(outf,"%S",value);
ajStrDel(&fname);
}
ajFileClose(&outf);
ajStrDel(&wild);
ajStrDel(&dest);
ajStrDel(&key);
ajListFree(&flist);
return;
}
static void jaspextract_copyfiles(AjPStr directory)
{
AjPStr matrixfile = NULL;
AjPList flist = NULL;
AjPStr wild = NULL;
AjPStr entry = NULL;
AjPStr bname = NULL;
AjPStr line = NULL;
AjPStr dest = NULL;
const AjPStr datadir = NULL;
ajuint preflen = 0;
ajuint i = 0;
const char *p = NULL;
AjPFile inf = NULL;
AjPFile outf = NULL;
matrixfile = ajStrNew();
flist = ajListNew();
wild = ajStrNewC("*.pfm");
bname = ajStrNew();
line = ajStrNew();
dest = ajStrNew();
datadir = ajDatafileValuePath();
if(!datadir)
ajFatal("jaspextract: Cannot determine the EMBOSS data directory");
ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE);
if(!ajFilenameExistsRead(matrixfile))
ajFatal("jaspextract: Directory (%S) doesn't appear to be a JASPAR "
"one\nNo matrix_list.txt file found",directory);
ajFilelistAddPathWild(flist, directory, wild);
while(ajListPop(flist,(void **)&entry))
{
ajStrAssignS(&bname,entry);
ajFilenameTrimPath(&bname);
i = 0;
while(Jprefix[i].Prefix)
{
if(!ajStrPrefixC(bname,Jprefix[i].Prefix))
{
++i;
continue;
}
preflen = strlen(Jprefix[i].Prefix);
p = ajStrGetPtr(bname);
if(p[preflen]>='0' && p[preflen]<='9')
break;
++i;
}
if(!Jprefix[i].Prefix)
{
ajStrDel(&entry);
continue;
}
ajFmtPrintS(&dest,"%S%s%c%S",datadir,Jprefix[i].Directory,SLASH_CHAR,
bname);
outf = ajFileNewOutNameS(dest);
if(!outf)
ajFatal("Cannot open output file %S",dest);
/* Avoid UNIX copy for portability */
inf = ajFileNewInNameS(entry);
if(!inf)
ajFatal("Cannot open input file: %S",entry);
while(ajReadlineTrim(inf,&line))
ajFmtPrintF(outf,"%S\n",line);
ajFileClose(&inf);
ajFileClose(&outf);
ajStrDel(&entry);
}
ajListFree(&flist);
ajStrDel(&wild);
ajStrDel(&dest);
ajStrDel(&line);
ajStrDel(&bname);
ajStrDel(&matrixfile);
return;
}
