static AjPTable btwisted_getdinucdata(AjPFile inf)
{
AjPStr valstr = NULL;
AjPStr key = NULL;
AjPStr line = NULL;
AjPStrTok token = NULL;
AjPTable table = NULL;
valstr = ajStrNew();
line = ajStrNew();
table = ajTablestrNewCase(20);
while(ajReadlineTrim(inf,&line))
{
if(*ajStrGetPtr(line)=='#')
continue;
token = ajStrTokenNewC(line," \n\t\r");
key = ajStrNew();
ajStrTokenNextParseC(&token," \n\t\r",&key);
valstr = ajStrNew();
ajStrTokenNextParseC(&token," \n\t\r",&valstr);
ajTablePut(table,(void *)key,(void *) valstr);
ajStrTokenDel(&token);
}
ajStrDel(&line);
return table;
}
AjBool embMiscMatchPatternDelimC (const AjPStr str, const AjPStr pattern,
const char* delim)
{
char whiteSpace[] = " \t\n\r"; /* skip whitespace */
AjPStrTok tokens;
AjPStr delimstr = NULL;
AjPStr key = NULL;
AjBool val = ajFalse;
delimstr = ajStrNewC(whiteSpace);
ajStrAppendC(&delimstr, delim);
tokens = ajStrTokenNewS(pattern, delimstr);
while (ajStrTokenNextParse( &tokens, &key))
if (ajStrMatchWildCaseS(str, key))
{
val = ajTrue;
break;
}
ajStrTokenDel( &tokens);
ajStrDel(&key);
ajStrDel(&delimstr);
return val;
}
static ajint cutgextract_readcodons(AjPFile inf, AjBool allrecords,
ajint *count)
{
static int cutidx[] =
{
42,43,46,41,45,44,26,30,31,29,27,28,48,51,47,50,
52,49,55,56,53,54,36,38,35,37, 4, 6, 3, 5,17,18,
16,15,57,59,60,58,24,25,34,33,39,40,20,19,11,12,
10, 9,63,62, 8, 7,14,13,21,23,22,32,61, 1, 0, 2
};
AjPStr line = NULL;
AjPStr value = NULL;
ajint thiscount[64];
AjPStrTok token = NULL;
ajint i;
ajint n = 0;
ajint nstops = 0;
if(!line)
{
line = ajStrNew();
value = ajStrNew();
}
if(!ajReadlineTrim(inf,&line))
ajFatal("Premature end of file");
token = ajStrTokenNewC(line," \n\t\r");
for(i=0;i<CODONS;++i)
{
ajStrTokenNextParseC(&token," \n\t\r",&value);
ajStrToInt(value,&n);
thiscount[cutidx[i]] = n;
if(i>60)
nstops += n;
}
ajStrDel(&line);
ajStrDel(&value);
ajStrTokenDel(&token);
if(!allrecords)
if(nstops > 1)
return -1;
for(i=0;i<CODONS;++i)
{
count[i] += thiscount[i];
}
return nstops;
}
static void remap_NoCutList(AjPFile outfile, const AjPTable hittable,
AjBool html, const AjPStr enzymes, AjBool blunt,
AjBool sticky, ajuint sitelen, AjBool commercial,
AjBool ambiguity, AjBool limit,
const AjPTable retable)
{
/* for iterating over hittable */
PValue value;
void **keyarray = NULL; /* array for table */
void **valarray = NULL; /* array for table */
ajint i;
/* list of enzymes that cut */
AjPList cutlist;
AjIList citer; /* iterator for cutlist */
AjPStr cutname = NULL;
AjBool found;
/* for parsing value->iso string */
AjPStrTok tok;
char tokens[] = " ,";
AjPStr code = NULL;
const char *p;
/* for reading in enzymes names */
AjPFile enzfile = NULL;
AjPStr *ea;
ajint ne; /* number of enzymes */
AjBool isall = ajTrue;
/* list of enzymes that don't cut */
AjPList nocutlist;
AjIList niter; /* iterator for nocutlist */
AjPStr nocutname = NULL;
/* count of rejected enzymes not matching criteria */
ajint rejected_count = 0;
EmbPPatRestrict enz;
/* for renaming preferred isoschizomers */
AjPList newlist;
/*
**
** Make a list of enzymes('cutlist') that hit
** including the isoschizomer names
**
*/
ajDebug("Make a list of all enzymes that cut\n");
cutlist = ajListstrNew();
nocutlist = ajListstrNew();
ajTableToarrayKeysValues(hittable, &keyarray, &valarray);
for(i = 0; keyarray[i]; i++)
{
value = (PValue) valarray[i];
cutname = ajStrNew();
ajStrAssignRef(&cutname, keyarray[i]);
ajListstrPushAppend(cutlist, cutname);
/* Add to cutlist all isoschizomers of enzymes that cut */
ajDebug("Add to cutlist all isoschizomers of enzymes that cut\n");
/* start token to parse isoschizomers names */
tok = ajStrTokenNewC(value->iso, tokens);
while(ajStrTokenNextParseC(&tok, tokens, &code))
{
cutname = ajStrNew();
ajStrAssignS(&cutname, code);
ajListstrPushAppend(cutlist, cutname);
}
ajStrTokenDel(&tok);
}
ajStrDel(&code);
AJFREE(keyarray);
AJFREE(valarray);
/*
** Read in list of enzymes ('nocutlist') - either all or
** the input enzyme list.
** Exclude those that don't match the selection criteria - count these.
*/
ajDebug("Read in a list of all input enzyme names\n");
ne = 0;
if(!enzymes)
isall = ajTrue;
else
{
/* get input list of enzymes into ea[] */
ne = ajArrCommaList(enzymes, &ea);
if(ajStrMatchCaseC(ea[0], "all"))
isall = ajTrue;
else
{
isall = ajFalse;
for(i=0; i<ne; ++i)
ajStrRemoveWhite(&ea[i]);
}
}
enzfile = ajDatafileNewInNameC(ENZDATA);
/* push all enzyme names without the required criteria onto nocutlist */
enz = embPatRestrictNew();
while(!ajFileIsEof(enzfile))
{
if(!embPatRestrictReadEntry(enz, enzfile))
continue;
/*
** If user entered explicit enzyme list, then check to see if
** this is one of that explicit list
*/
if(!isall)
{
found = AJFALSE;
for(i=0; i<ne; ++i)
if(ajStrMatchCaseS(ea[i], enz->cod))
{
found = AJTRUE;
break;
}
if(!found) /* not in the explicit list */
continue;
ajDebug("RE %S is in the input explicit list of REs\n", enz->cod);
}
/* ignore ncuts==0 as they are unknown */
if(!enz->ncuts)
{
/* number of cut positions */
ajDebug("RE %S has an unknown number of cut positions\n",
enz->cod);
continue;
}
ajDebug("RE %S has a known number of cut sites\n", enz->cod);
if(enz->len < sitelen)
{
/* recognition site length */
ajDebug("RE %S does not have a long enough recognition site\n",
enz->cod);
rejected_count++;
continue;
}
if(!blunt && enz->blunt)
{
/* blunt/sticky */
ajDebug("RE %S is blunt\n", enz->cod);
rejected_count++;
continue;
}
if(!sticky && !enz->blunt)
{
/* blunt/sticky */
ajDebug("RE %S is sticky\n", enz->cod);
rejected_count++;
continue;
}
/* commercially available enzymes have uppercase patterns */
p = ajStrGetPtr(enz->pat);
/*
** The -commercial qualifier is only used if we are searching
** through 'all' of the REBASE database - if we have specified an
** explicit list of enzymes then they are searched for whether or
** not they are commercially available
*/
if((*p >= 'a' && *p <= 'z') && commercial && isall)
{
ajDebug("RE %S is not commercial\n", enz->cod);
rejected_count++;
continue;
}
if(!ambiguity && remap_Ambiguous(enz->pat)) {
ajDebug("RE %S is ambiguous\n", enz->cod);
rejected_count++;
continue;
}
ajDebug("RE %S matches all required criteria\n", enz->cod);
code = ajStrNew();
ajStrAssignS(&code, enz->cod);
ajListstrPushAppend(nocutlist, code);
}
embPatRestrictDel(&enz);
ajFileClose(&enzfile);
for(i=0; i<ne; ++i)
if(ea[i])
ajStrDel(&ea[i]);
if(ne)
AJFREE(ea);
/*
** Change names of enzymes in the non-cutter list
** to that of preferred (prototype)
** enzyme name so that the isoschizomers of cutters
** will be removed from the
** non-cutter list in the next bit.
** Remove duplicate prototype names.
*/
if(limit)
{
newlist = ajListstrNew();
remap_RenamePreferred(nocutlist, retable, newlist);
ajListstrFreeData(&nocutlist);
nocutlist = newlist;
ajListSortUnique(nocutlist, remap_cmpcase, remap_strdel);
}
/*
** Iterate through the list of input enzymes removing those that are in
** the cutlist.
*/
ajDebug("Remove from the nocutlist all enzymes and isoschizomers "
"that cut\n");
/*
** This steps down both lists at the same time, comparing names and
** iterating to the next name in whichever list whose name compares
** alphabetically before the other. Where a match is found, the
** nocutlist item is deleted.
*/
ajListSort(nocutlist, remap_cmpcase);
ajListSort(cutlist, remap_cmpcase);
citer = ajListIterNewread(cutlist);
niter = ajListIterNew(nocutlist);
/*
while((cutname = (AjPStr)ajListIterGet(citer)) != NULL)
ajDebug("dbg cutname = %S\n", cutname);
*/
nocutname = (AjPStr)ajListIterGet(niter);
cutname = (AjPStr)ajListIterGet(citer);
ajDebug("initial cutname, nocutname: '%S' '%S'\n", cutname, nocutname);
while(nocutname != NULL && cutname != NULL)
{
i = ajStrCmpCaseS(cutname, nocutname);
ajDebug("compare cutname, nocutname: %S %S ", cutname, nocutname);
ajDebug("ajStrCmpCase=%d\n", i);
if(i == 0)
{
/* match - so remove from nocutlist */
ajDebug("ajListstrRemove %S\n", nocutname);
ajListstrIterRemove(niter);
nocutname = (AjPStr)ajListIterGet(niter);
/*
** Don't increment the cutname list pointer here
** - there may be more than one entry in the nocutname
** list with the same name because we have converted
** isoschizomers to their preferred name
*/
/* cutname = (AjPStr)ajListIterGet(citer); */
}
else if(i == -1)
/* cutlist name sorts before nocutlist name */
cutname = (AjPStr)ajListIterGet(citer);
else if(i == 1)
/* nocutlist name sorts before cutlist name */
nocutname = (AjPStr)ajListIterGet(niter);
}
ajListIterDel(&citer);
ajListIterDel(&niter);
ajListstrFreeData(&cutlist);
/* Print the resulting list of those that do not cut*/
ajDebug("Print out the list\n");
/* print the title */
if(html)
ajFmtPrintF(outfile, "<H2>");
ajFmtPrintF(outfile, "\n\n# Enzymes that do not cut\n\n");
if(html)
ajFmtPrintF(outfile, "</H2>\n");
if(html)
ajFmtPrintF(outfile, "<PRE>");
/* ajListSort(nocutlist, ajStrVcmp);*/
niter = ajListIterNewread(nocutlist);
i = 0;
while((nocutname = (AjPStr)ajListIterGet(niter)) != NULL)
{
ajFmtPrintF(outfile, "%-10S", nocutname);
/* new line after every 7 names printed */
if(i++ == 7)
{
ajFmtPrintF(outfile, "\n");
i = 0;
}
}
ajListIterDel(&niter);
/* end the output */
ajFmtPrintF(outfile, "\n");
if(html) {ajFmtPrintF(outfile, "</PRE>\n");}
/*
** Print the count of rejected enzymes
** N.B. This is the count of ALL rejected enzymes including all
** isoschizomers
*/
if(html)
ajFmtPrintF(outfile, "<H2>");
ajFmtPrintF(outfile,
"\n\n# No. of cutting enzymes which do not match the\n"
"# SITELEN, BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria\n\n");
if(html)
ajFmtPrintF(outfile, "</H2>\n");
ajFmtPrintF(outfile, "%d\n", rejected_count);
ajDebug("Tidy up\n");
ajListstrFreeData(&nocutlist);
ajListstrFreeData(&cutlist);
return;
}
static void remap_RestrictPreferred(const AjPList l, const AjPTable t)
{
AjIList iter = NULL;
EmbPMatMatch m = NULL;
const AjPStr value = NULL;
AjPStr newiso = NULL;
AjBool found; /* name found in isoschizomer list */
/* for parsing value->iso string */
AjPStrTok tok = NULL;
char tokens[] = " ,";
AjPStr code = NULL;
iter = ajListIterNewread(l);
while((m = (EmbPMatMatch)ajListIterGet(iter)))
{
found = ajFalse;
/* get prototype name */
value = ajTableFetchS(t, m->cod);
if(value)
{
ajStrAssignC(&newiso, "");
/* parse isoschizomer names from m->iso */
ajStrTokenDel(&tok);
tok = ajStrTokenNewC(m->iso, tokens);
while(ajStrTokenNextParseC(&tok, tokens, &code))
{
if(ajStrGetLen(newiso) > 0)
ajStrAppendC(&newiso, ",");
/* found the prototype name? */
if(!ajStrCmpCaseS(code, value))
{
ajStrAppendS(&newiso, m->cod);
found = ajTrue;
}
else
ajStrAppendS(&newiso, code);
}
ajStrTokenDel(&tok);
/* if the name was not replaced, then add it in now */
if(!found)
{
if(ajStrGetLen(newiso) > 0)
ajStrAppendC(&newiso, ",");
ajStrAppendS(&newiso, m->cod);
}
ajDebug("RE: %S -> %S iso=%S newiso=%S\n", m->cod, value,
m->iso, newiso);
/* replace the old iso string with the new one */
ajStrAssignS(&m->iso, newiso);
/* rename the enzyme to the prototype name */
ajStrAssignS(&m->cod, value);
}
}
ajListIterDel(&iter);
ajStrDel(&newiso);
ajStrDel(&code);
ajStrTokenDel(&tok);
return;
}
static AjBool extractfeat_MatchFeature(const AjPFeature gf,
const AjPStr source,
const AjPStr type, ajint sense,
AjBool testscore, float minscore,
float maxscore, const AjPStr tag,
const AjPStr value, AjBool *tagsmatch)
{
AjPStrTok tokens = NULL;
AjPStr key = NULL;
AjBool val = ajFalse;
/*
** is this a child of a join() ?
** if it is a child, then we use the previous result of MatchPatternTags
*/
if(!ajFeatIsMultiple(gf) || !ajFeatIsChild(gf))
*tagsmatch = extractfeat_MatchPatternTags(gf, tag, value);
/* ignore remote IDs */
/*
** No - don't reject remote IDs here. We want to include all features
** in this routine so that we can reject a whole join later on if any one
** member of the join is remote.
** if(!ajFeatIsLocal(gf))
** return ajFalse;
*/
/* check source, type, sense, score, tags, values */
/* Special values indication that we match anything:
** for strings, '*'
** for sense, 0
** for score, maxscore <= minscore
*/
ajDebug("extractfeat_MatchFeature\n");
ajDebug("embMiscMatchPatternDelim(ajFeatGetSource(gf), source) %B\n",
embMiscMatchPatternDelimC(ajFeatGetSource(gf), source, ",;|"));
ajDebug("ajFeatTypeMatchS(gf, type) %B\n",
ajFeatTypeMatchWildS(gf, type));
ajDebug("ajFeatGetStrand(gf) '%x' sense %d\n", ajFeatGetStrand(gf), sense);
ajDebug("testscore: %B ajFeatGetScore(gf): %f minscore:%f maxscore:%f\n",
testscore, ajFeatGetScore(gf), minscore, maxscore);
if(!embMiscMatchPatternDelimC(ajFeatGetSource(gf), source, ",;|"))
return ajFalse;
if(ajStrGetLen(type))
{
val = ajFalse;
tokens = ajStrTokenNewC(type, " \t\n\r,;|");
while (ajStrTokenNextParse( &tokens, &key))
{
if (ajFeatTypeMatchWildS(gf, key))
{
val = ajTrue;
break;
}
}
ajStrTokenDel( &tokens);
ajStrDel(&key);
if(!val)
return ajFalse;
}
if(ajFeatGetStrand(gf) == '+' && sense == -1)
return ajFalse;
if(ajFeatGetStrand(gf) == '-' && sense == +1)
return ajFalse;
if(testscore && ajFeatGetScore(gf) < minscore)
return ajFalse;
if(testscore && ajFeatGetScore(gf) > maxscore)
return ajFalse;
if(!*tagsmatch)
return ajFalse;
ajDebug("All tests passed, return ajTrue\n");
/*ajUser("All tests passed, return ajTrue");*/
return ajTrue;
}
static void primersearch_read_primers(AjPList *primerList, AjPFile primerFile,
ajint mmp)
{
AjPStr rdline = NULL;
AjPStrTok handle = NULL;
ajint nprimers = 0;
Primer primdata = NULL;
while (ajReadlineTrim(primerFile, &rdline))
{
primdata = NULL;
if (ajStrGetCharFirst(rdline) == '#')
continue;
if (ajStrSuffixC(rdline, ".."))
continue;
AJNEW(primdata);
primdata->Name = NULL;
primersearch_initialise_pguts(&primdata->forward);
primersearch_initialise_pguts(&primdata->reverse);
primdata->hitlist = ajListNew();
handle = ajStrTokenNewC(rdline, " \t");
ajStrTokenNextParse(&handle, &primdata->Name);
ajStrTokenNextParse(&handle, &primdata->forward->patstr);
ajStrFmtUpper(&primdata->forward->patstr);
ajStrTokenNextParse(&handle, &primdata->reverse->patstr);
ajStrFmtUpper(&primdata->reverse->patstr);
ajStrTokenDel(&handle);
/* copy patterns for Henry Spencer code */
ajStrAssignC(&primdata->forward->origpat,
ajStrGetPtr(primdata->forward->patstr));
ajStrAssignC(&primdata->reverse->origpat,
ajStrGetPtr(primdata->reverse->patstr));
/* set the mismatch level */
primdata->forward->mm = (ajint)
(ajStrGetLen(primdata->forward->patstr)*mmp)/100;
primdata->reverse->mm = (ajint)
(ajStrGetLen(primdata->reverse->patstr)*mmp)/100;
if(primersearch_classify_and_compile(&primdata))
{
ajListPushAppend(*primerList, primdata);
nprimers++;
}
else /* there was something funny about the primer sequences */
{
ajUser("Cannot use %s\n", ajStrGetPtr(primdata->Name));
primersearch_free_pguts(&primdata->forward);
primersearch_free_pguts(&primdata->reverse);
ajStrDel(&primdata->Name);
ajListFree(&primdata->hitlist);
ajListFree(&primdata->hitlist);
AJFREE(primdata);
}
}
ajStrDel(&rdline);
return;
}
static void eprimer3_report(AjPFile outfile, const AjPStr output,
ajint numreturn, ajint begin)
{
AjPStr line = NULL;
AjPStrTok linetokenhandle;
char eol[] = "\n\r";
AjPStrTok keytokenhandle;
char equals[] = "=";
AjPStr key = NULL;
AjPStr value = NULL;
AjBool gotsequenceid = AJFALSE;
AjPTable table;
linetokenhandle = ajStrTokenNewC(output, eol);
/* get next line of relevant results */
while(ajStrTokenNextParseC(&linetokenhandle, eol, &line))
{
if(!gotsequenceid)
{
/*
** Att the start of another sequence's results?
** Start storing the results in the table.
*/
if(ajStrCmpLenC(line, "PRIMER_SEQUENCE_ID=", 19) == 0)
{
gotsequenceid = AJTRUE;
table = ajTablestrNew(TABLEGUESS);
}
else
continue;
}
else
{
/*
** At the end of this sequence? - marked by a '=' in the primer3
** output - then output the results.
*/
if(ajStrCmpC(line, "=") == 0)
{
gotsequenceid = AJFALSE;
eprimer3_output_report(outfile, table, numreturn, begin);
ajTablestrFree(&table);
continue;
}
}
/*
** store key and value in table and parse values
** when have all of the sequence
** results in the table because the LEFT, RIGHT
** and INTERNAL results for each
** resulting primer are interleaved
*/
keytokenhandle = ajStrTokenNewC(line, equals);
key = ajStrNew();
ajStrTokenNextParse(&keytokenhandle, &key);
value = ajStrNew();
ajStrTokenNextParse(&keytokenhandle, &value);
ajDebug("key=%S\tvalue=%S\n", key, value);
ajTablePut(table,(void *)key, (void *)value);
ajStrTokenDel(&keytokenhandle);
}
ajStrDel(&line);
ajStrTokenDel(&linetokenhandle);
ajTablestrFree(&table);
return;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPFile primfile;
AjPStr rdline = NULL;
Primer primdata;
AjPStrTok handle = NULL;
AjPList primList = NULL;
embInit("stssearch", argc, argv);
primfile = ajAcdGetInfile("infile");
out = ajAcdGetOutfile("outfile");
seqall = ajAcdGetSeqall("seqall");
while(ajReadlineTrim(primfile, &rdline))
{
if(ajStrGetCharFirst(rdline) == '#')
continue;
if(ajStrSuffixC(rdline, ".."))
continue;
AJNEW(primdata);
primdata->Name = NULL;
primdata->Oligoa = NULL;
primdata->Oligob = NULL;
handle = ajStrTokenNewC(rdline, " \t");
ajStrTokenNextParse(&handle, &primdata->Name);
if(!(nprimers % 1000))
ajDebug("Name [%d]: '%S'\n", nprimers, primdata->Name);
ajStrTokenNextParse(&handle, &primdata->Oligoa);
ajStrFmtUpper(&primdata->Oligoa);
primdata->Prima = ajRegComp(primdata->Oligoa);
ajStrTokenNextParse(&handle, &primdata->Oligob);
ajStrFmtUpper(&primdata->Oligob);
primdata->Primb = ajRegComp(primdata->Oligob);
ajStrTokenDel(&handle);
if(!nprimers)
primList = ajListNew();
ajListPushAppend(primList, primdata);
nprimers++;
}
if(!nprimers)
ajFatal("No primers read\n");
ajDebug("%d primers read\n", nprimers);
while(ajSeqallNext(seqall, &seq))
{
ajSeqFmtUpper(seq);
ajStrAssignS(&seqstr, ajSeqGetSeqS(seq));
ajStrAssignS(&revstr, ajSeqGetSeqS(seq));
ajSeqstrReverse(&revstr);
ajDebug("Testing: %s\n", ajSeqGetNameC(seq));
ntests = 0;
ajListMap(primList, stssearch_primTest, NULL);
}
ajFileClose(&out);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajFileClose(&out);
ajStrDel(&revstr);
ajStrDel(&seqstr);
ajFileClose(&primfile);
ajListMap(primList, stssearch_primDel, NULL);
ajListFree(&primList);
ajStrDel(&rdline);
embExit();
return 0;
}
static AjBool resourceoutWriteWebpage(AjPFile outf, const AjPResource resource)
{
AjPResquery tmpqry = NULL;
AjPResterm resterm = NULL;
AjPStr snstr = NULL;
AjPStr tmpstr = NULL;
AjPStr tmpurl = NULL;
AjPStr tmpid = NULL;
AjPStr tmpname = NULL;
AjPStr tmpqid = NULL;
AjPStr tmpqname = NULL;
AjPStr tmpqterm = NULL;
AjIList iter = NULL;
AjIList iterq = NULL;
ajuint i = 0;
AjPStrTok handle = NULL;
AjPStrTok namehandle = NULL;
AjPStrTok termhandle = NULL;
const char* biourl = "http://bioportal.bioontology.org/ontologies/45846";
if(!outf)
return ajFalse;
ajFmtPrintF(outf,
"<!DOCTYPE HTML PUBLIC "
"\"-//W3C//DTD HTML 4.01 Transitional//EN\">\n");
ajFmtPrintF(outf,
"<html>\n");
ajFmtPrintF(outf,
"<head>\n");
ajFmtPrintF(outf,
"<meta http-equiv=\"Content-Type\" "
"content=\"text/html;charset=UTF-8\" />\n");
ajFmtPrintF(outf,
"<title>Bioinformatics Data Resource Catalogue</title>\n");
ajFmtPrintF(outf,
"</head>\n\n\n");
ajFmtPrintF(outf,
"<body bgcolor=\"#ffffff\">\n");
ajFmtPrintF(outf,
"<!-- ID -->\n");
if(ajStrGetLen(resource->Url))
ajFmtPrintF(outf,
"<center><h1><a href=\"%S\">%S</a></h1></center>\n",
resource->Url, resource->Id);
else
ajFmtPrintF(outf,
"<center><h1>%S</h1></center>\n",
resource->Id);
ajFmtPrintF(outf,
"<!-- Name -->\n");
ajFmtPrintF(outf,
"<center><h2>%S</h2> </center>\n",
resource->Name);
ajFmtPrintF(outf,
"<!-- Desc -->\n");
ajFmtPrintF(outf,
"<p><i>%S</i></p>\n",
resource->Desc);
ajFmtPrintF(outf,
"<table>\n");
ajFmtPrintF(outf,
"<!-- ID -->\n");
ajFmtPrintF(outf,
" <tr align=\"left\"><th>ID</th><td>%S</td></tr>\n",
resource->Id);
ajFmtPrintF(outf,
"<!-- IDalt or omit -->\n");
if(ajListGetLength(resource->Idalt))
{
ajFmtPrintF(outf,
" <tr align=\"left\"><th>IDalt</th><td>");
i = 0;
iter = ajListIterNew(resource->Idalt);
while((tmpstr = ajListstrIterGet(iter)))
{
if(i++)
ajFmtPrintF(outf, ", ");
ajFmtPrintF(outf, "%S", tmpstr);
}
ajListIterDel(&iter);
ajFmtPrintF(outf,
"</td></tr>\n");
}
if(ajStrGetLen(resource->Acc))
{
ajFmtPrintF(outf,
"<!-- ACC or omit -->\n");
ajFmtPrintF(outf,
" <tr align=\"left\"><th>Acc</th><td>%S</td></tr>\n",
resource->Acc);
}
if(ajStrGetLen(resource->Url))
ajFmtPrintF(outf,
" <tr align=\"left\"><th>Home</th><td>"
"<a href=\"%S\">%S</a></td></tr>\n",
resource->Url, resource->Url);
if(ajListGetLength(resource->Edamtpc))
{
ajFmtPrintF(outf,
"<!-- EDAMtpc -->\n");
iter = ajListIterNew(resource->Edamtpc);
while((resterm = ajListIterGet(iter)))
{
ajStrAssignS(&tmpid, resterm->Id);
ajStrCutBraces(&tmpid);
ajStrFmtPercentEncodeC(&tmpid, " /()");
ajFmtPrintF(outf,
" <tr align=\"left\"><th>EDAM topic</th><td>"
"<a href=\"%s?p=terms&conceptid=EDAM%%3A%S\">%S</a>"
"</td></tr>\n",
biourl, tmpid, resterm->Name);
}
ajListIterDel(&iter);
}
ajFmtPrintF(outf,
"<!-- Cat or omit -->\n");
if(ajListGetLength(resource->Cat))
{
iter = ajListIterNew(resource->Cat);
while((tmpstr = ajListstrIterGet(iter)))
ajFmtPrintF(outf,
" <tr align=\"left\"><th>Category</th>"
"<td>%S</td></tr>\n",
tmpstr);
ajListIterDel(&iter);
}
ajFmtPrintF(outf,
"<!-- Taxon (comma-separated list) -->\n");
ajFmtPrintF(outf,
" <tr align=\"left\"><th>Taxon</th><td>");
i = 0;
iter = ajListIterNew(resource->Taxon);
while((resterm = ajListIterGet(iter)))
{
if(i++)
ajFmtPrintF(outf, ", ");
ajFmtPrintF(outf,
"<a href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/"
"wwwtax.cgi?id=%S\">%S</a>",
resterm->Id, resterm->Name);
}
ajListIterDel(&iter);
ajFmtPrintF(outf,
"</td></tr>\n");
ajFmtPrintF(outf,
"<!-- URLlink or omit -->\n");
if(ajStrGetLen(resource->Urllink))
ajFmtPrintF(outf,
"<tr align=\"left\"><th>Linking</th><td>"
"<a href=\"%S\">%S</a></td></tr>\n",
resource->Urllink, resource->Urllink);
ajFmtPrintF(outf,
"<!-- URLrest or omit -->\n");
if(ajStrGetLen(resource->Urlrest))
ajFmtPrintF(outf,
"<tr align=\"left\"><th>REST</th><td>"
"<a href=\"%S\">%S</a></td></tr>\n",
resource->Urlrest, resource->Urlrest);
ajFmtPrintF(outf,
"<!-- URLsoap or omit -->\n");
if(ajStrGetLen(resource->Urlsoap))
ajFmtPrintF(outf,
"<tr align=\"left\"><th>SOAP</th><td>"
"<a href=\"%S\">%S</a></td></tr>\n",
resource->Urlsoap, resource->Urlsoap);
ajFmtPrintF(outf,
"<!-- Xref - omit ! -->\n");
ajFmtPrintF(outf,
"</table>\n");
ajFmtPrintF(outf,
"<!-- Query or omit, free-text comments given in {} --> \n");
if(ajListGetLength(resource->Query))
{
ajFmtPrintF(outf,
"<h3>Available data</h3>\n");
ajFmtPrintF(outf,
"<table>\n");
ajFmtPrintF(outf,
" <thead>\n");
ajFmtPrintF(outf,
" <tr align=\"left\">\n");
ajFmtPrintF(outf,
" <th>Data</th>\n");
ajFmtPrintF(outf,
" <th>Format</th>\n");
ajFmtPrintF(outf,
" <th>Query</th>\n");
ajFmtPrintF(outf,
" <th>Link</th>\n");
ajFmtPrintF(outf,
" </tr>\n");
ajFmtPrintF(outf,
" </thead>\n");
ajFmtPrintF(outf,
" <tbody>\n");
iter = ajListIterNew(resource->Query);
while((tmpqry = ajListIterGet(iter)))
{
ajStrAssignS(&tmpname, tmpqry->Datatype);
ajStrCutBraces(&tmpname);
ajStrFmtPercentEncodeC(&tmpname, " /()");
ajFmtPrintF(outf,
" <tr>\n");
ajFmtPrintF(outf,
" <td>"
"<a href=\"%s?"
"p=terms&conceptid=EDAM%%3A%S\">%S</a></td>\n",
biourl, tmpname, tmpqry->Datatype);
ajStrAssignS(&tmpname, tmpqry->Format);
ajStrCutBraces(&tmpname);
ajStrFmtPercentEncodeC(&tmpname, " /()");
ajFmtPrintF(outf,
" <td>"
"<a href=\"%s?"
"p=terms&conceptid=EDAM%%3A%S\">%S</a></td>\n",
biourl, tmpname, tmpqry->Format);
ajStrAssignS(&tmpname, tmpqry->Term);
ajStrCutBraces(&tmpname);
ajStrFmtPercentEncodeC(&tmpname, " /()");
ajFmtPrintF(outf,
" <td>"
"<a href=\"%s?"
"p=terms&conceptid=EDAM%%3A%S\">%S</a></td>\n",
biourl, tmpname, tmpqry->Term);
ajFmtPrintF(outf,
" <td>%S</td>\n",
tmpqry->Url);
ajFmtPrintF(outf,
" </tr>\n\n");
}
ajListIterDel(&iter);
ajFmtPrintF(outf,
" </tbody>\n");
ajFmtPrintF(outf,
"</table>\n");
}
ajFmtPrintF(outf,
"<!-- Example or omit -->\n");
if(ajListGetLength(resource->Example))
{
ajFmtPrintF(outf,
"<h3>Example queries</h3>\n");
ajFmtPrintF(outf,
"<table>\n");
ajFmtPrintF(outf,
" <thead>\n");
ajFmtPrintF(outf,
" <tr align=\"left\">\n");
ajFmtPrintF(outf,
" <th>Data</th>\n");
ajFmtPrintF(outf,
" <th>Format</th>\n");
ajFmtPrintF(outf,
" <th>Query</th>\n");
ajFmtPrintF(outf,
" <th>Example</th>\n");
ajFmtPrintF(outf,
" </tr>\n");
ajFmtPrintF(outf,
" </thead>\n");
ajFmtPrintF(outf,
" <tbody>\n");
iter = ajListIterNew(resource->Example);
while((tmpstr = ajListstrIterGet(iter)))
{
ajStrTokenAssignC(&handle, tmpstr, "|");
ajStrTokenNextParse(handle, &tmpid);
ajStrRemoveWhiteExcess(&tmpid);
ajStrTokenNextParse(handle, &tmpname);
ajStrRemoveWhiteExcess(&tmpname);
iterq = ajListIterNew(resource->Query);
while((tmpqry = ajListIterGet(iterq)))
{
if(!ajStrMatchS(tmpid, tmpqry->Term))
continue;
ajStrAssignS(&tmpqid, tmpqry->Datatype);
ajStrCutBraces(&tmpqid);
ajStrFmtPercentEncodeC(&tmpqid, " /()");
ajFmtPrintF(outf,
" <tr>\n");
ajFmtPrintF(outf,
" <td>"
"<a href=\"%s?"
"p=terms&conceptid=EDAM%%3A%S\">%S</a></td>\n",
biourl, tmpqid, tmpqry->Datatype); /* datatype */
ajStrAssignS(&tmpqid, tmpqry->Format);
ajStrCutBraces(&tmpqid);
ajStrFmtPercentEncodeC(&tmpqid, " /()");
ajFmtPrintF(outf,
" <td>"
"<a href=\"%s?"
"p=terms&conceptid=EDAM%%3A%S\">%S</a></td>\n",
biourl, tmpqid, tmpqry->Format); /* format */
ajStrAssignS(&tmpurl, tmpqry->Url);
ajStrAssignS(&tmpqid, tmpqry->Term);
ajStrCutBraces(&tmpqid);
ajStrFmtPercentEncodeC(&tmpqid, " /()");
i = 0;
ajStrTokenAssignC(&handle, tmpid, ";");
ajStrTokenAssignC(&namehandle, tmpname, ";");
ajStrTokenAssignC(&termhandle, tmpqry->Term, ";");
ajFmtPrintF(outf,
" <td>");
while(ajStrTokenNextParse(handle, &tmpqid))
{
ajStrTokenNextParse(namehandle, &tmpqname);
ajStrTokenNextParse(termhandle, &tmpqterm);
if(i)
ajFmtPrintF(outf,
"; ");
ajStrRemoveWhiteExcess(&tmpqid);
ajStrCutBraces(&tmpqid);
ajFmtPrintF(outf,
"<a href=\"%s?"
"p=terms&conceptid=EDAM%%3A%S\">%S</a>",
biourl, tmpqid, tmpqterm); /* id term */
ajFmtPrintS(&snstr, "%%s%u", (i+1));
ajStrExchangeSS(&tmpurl, snstr, tmpqname);
i++;
}
ajFmtPrintF(outf,
"</td>\n");
ajFmtPrintS(&snstr, "%%s");
ajStrExchangeSS(&tmpurl, snstr, tmpname);
ajFmtPrintF(outf,
" <td><a href=\"%S\">%S</a></td>\n",
tmpurl, tmpname); /* url, exampleid */
ajFmtPrintF(outf,
" </tr>\n");
}
ajListIterDel(&iterq);
}
ajListIterDel(&iter);
ajFmtPrintF(outf,
" </tbody>\n");
ajFmtPrintF(outf,
"</table>\n");
}
ajFmtPrintF(outf, "\n\n</body></html>\n");
ajStrDel(&tmpid);
ajStrDel(&tmpname);
ajStrDel(&tmpurl);
ajStrDel(&tmpqid);
ajStrDel(&tmpqname);
ajStrDel(&tmpqterm);
ajStrDel(&snstr);
ajStrTokenDel(&handle);
ajStrTokenDel(&namehandle);
ajStrTokenDel(&termhandle);
return ajTrue;
}
static char* cutgextract_next(AjPFile inf, const AjPStr wildspecies,
AjPStr* pspecies, AjPStr* pdoc)
{
AjPStrTok handle = NULL;
AjPStr token = NULL;
ajint i;
ajint len;
char *p = NULL;
char c;
AjBool done = ajFalse;
if(!cutgextractLine)
cutgextractLine = ajStrNew();
if(!cutgextractOrg)
cutgextractOrg = ajStrNew();
ajStrAssignC(&cutgextractLine,"");
ajStrAssignC(pdoc,"");
while (!done)
{
while(ajStrGetCharFirst(cutgextractLine) != '>')
if(!ajReadlineTrim(inf,&cutgextractLine))
return NULL;
handle = ajStrTokenNewC(cutgextractLine,"\\\n\t\r");
for(i=0;i<7;++i) {
ajStrTokenNextParseC(&handle,"\\\n\t\r",&token);
if(i==5)
{
ajStrAssignC(&cutgextractOrg,"E");
ajStrAppendS(&cutgextractOrg, token);
ajStrAssignS(pspecies, token);
if(ajStrMatchWildS(token,wildspecies))
{
done = ajTrue;
}
}
switch(i)
{
case 0:
ajStrAppendC(pdoc, "#ID ");
ajStrAppendS(pdoc, token);
ajStrAppendC(pdoc, "\n");
break;
case 1:
ajStrAppendC(pdoc, "#AC ");
ajStrAppendS(pdoc, token);
ajStrAppendC(pdoc, "\n");
break;
case 2:
ajStrAppendC(pdoc, "#FT ");
ajStrAppendS(pdoc, token);
ajStrAppendC(pdoc, "\n");
break;
case 3:
ajStrAppendC(pdoc, "#FL ");
ajStrAppendS(pdoc, token);
ajStrAppendC(pdoc, "\n");
break;
case 4:
ajStrAppendC(pdoc, "#PI ");
ajStrAppendS(pdoc, token);
ajStrAppendC(pdoc, "\n");
ajStrAssignS(&cutgextractSavepid, token);
break;
case 5:
ajStrAppendC(pdoc, "#OS ");
ajStrAppendS(pdoc, token);
ajStrAppendC(pdoc, "\n");
break;
case 6:
ajStrAppendC(pdoc, "#DE ");
ajStrAppendS(pdoc, token);
ajStrAppendC(pdoc, "\n");
break;
default:
break;
}
}
ajStrTokenDel(&handle);
ajStrDel(&token);
if(!done)
if(!ajReadlineTrim(inf,&cutgextractLine))
return NULL;
}
len = ajStrGetLen(cutgextractOrg);
p = ajStrGetuniquePtr(&cutgextractOrg);
for(i=0;i<len;++i)
{
c = p[i];
if(c=='/' || c==' ' || c=='.' || c=='\'')
p[i]='_';
}
if(p[strlen(p)-1]=='_')
p[strlen(p)-1]='\0';
ajStrDel(&token);
ajStrTokenDel(&handle);
return p;
}
int main(int argc, char **argv)
{
/* Variable declarations */
AjPStr query;
AjPOutfile outfile = NULL;
AjPResource resource = NULL;
AjPResourcein resourcein = NULL;
AjPOboin oboin = NULL;
AjPObo obo = NULL;
AjPStr oboqry = NULL;
AjPStr resourceqry = NULL;
AjPStr qrystr = NULL;
AjPTable obotable = NULL;
AjPTable foundtable = NULL;
AjBool subclasses = ajFalse;
AjPStrTok handle = NULL;
AjPList obolist = NULL;
AjPObo obotest = NULL;
ajuint i;
ajuint imax = 3;
const char* fields[] = {"id", "acc", "nam", "des"};
/* ACD processing */
embInit("drfindid", argc, argv);
query = ajAcdGetString("query");
outfile = ajAcdGetOutresource("outfile");
/* sensitive = ajAcdGetBoolean("sensitive"); */
subclasses = ajAcdGetBoolean("subclasses");
resourcein = ajResourceinNew();
resource = ajResourceNew();
oboin = ajOboinNew();
obo = ajOboNew();
obolist = ajListNew();
obotable = ajTablestrNew(600);
foundtable = ajTablestrNew(600);
handle = ajStrTokenNewC(query, ",");
while(ajStrTokenNextParse(&handle, &qrystr))
{
for(i=0; i<imax; i++)
{
ajFmtPrintS(&oboqry, "edam-%s:%S", fields[i], qrystr);
ajOboinQryS(oboin, oboqry);
while(ajOboinRead(oboin, obo))
{
ajListPushAppend(obolist, ajOboNewObo(obo));
if(subclasses)
ajOboGetTree(obo, obolist);
ajDebug("%S '%S' %u\n",
qrystr, obo->Id, ajListGetLength(obolist));
while(ajListGetLength(obolist))
{
ajListPop(obolist, (void**) &obotest);
if(!ajTableMatchS(obotable, obotest->Id))
{
ajDebug("edam %s '%S' namespace '%S' name '%S'\n",
fields[i], obotest->Id, obotest->Namespace,
obotest->Name);
ajTablePut(obotable, ajStrNewS(obotest->Id),
(void *) 1);
ajFmtPrintS(&resourceqry, "drcat-eid:%S",
ajOboGetId(obotest));
ajResourceinQryS(resourcein, resourceqry);
while(ajResourceinRead(resourcein, resource))
{
if(!ajTableMatchS(foundtable, resource->Id))
{
ajDebug("drcat id '%S' category '%S'\n",
resource->Id, resource->Cat);
ajResourceoutWrite(outfile, resource);
ajTablePut(foundtable, ajStrNewS(resource->Id),
(void *) 1);
}
}
}
ajOboDel(&obotest);
}
}
}
}
/* Memory clean-up and exit */
ajOboDel(&obo);
ajOboinDel(&oboin);
ajResourceDel(&resource);
ajResourceinDel(&resourcein);
ajListFree(&obolist);
ajStrTokenDel(&handle);
ajStrDel(&qrystr);
ajStrDel(&query);
ajStrDel(&oboqry);
ajStrDel(&resourceqry);
ajTablestrFreeKey(&obotable);
ajTablestrFreeKey(&foundtable);
ajOutfileClose(&outfile);
embExit();
return 0;
}