GCC_MODEL_TUNING = "";
GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.24.0\\\"\"",
- "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
+ "VERSION=\"\\\"1.25.0\\\"\"",
+ "RELEASE_DATE=\"\\\"4/30/2012\\\"\"",
);
GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
/************calculate the probablity that each word will be in a specific taxonomy*************/
- string tfileroot = baseTName.substr(0,baseTName.find_last_of(".")+1);
+ string tfileroot = m->getFullPathName(baseTName.substr(0,baseTName.find_last_of(".")+1));
string tempfileroot = m->getRootName(m->getSimpleName(baseName));
string phyloTreeName = tfileroot + "tree.train";
string phyloTreeSumName = tfileroot + "tree.sum";
delete phyloTree;
phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
-
+
//save probabilities
if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
}
int totalSeqs = 0;
if(processors == 1) { totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); }
- else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups); }
+ else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]); }
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
}
/**************************************************************************************************/
-int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups) {
+int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups, string nameFile, string groupFile, string fastaFile) {
try {
processIDS.clear();
// Allocate memory for thread data.
string extension = toString(i) + ".temp";
- uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastafile, namefile, groupfile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end, i);
+ uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end, i);
tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
int printFile(vector<seqPriorityNode>&, string);
int deconvoluteResults(SequenceParser&, string, string, string);
int driverGroups(SequenceParser&, string, string, string, string, int, int, vector<string>);
- int createProcessesGroups(SequenceParser&, string, string, string, string, vector<string>);
+ int createProcessesGroups(SequenceParser&, string, string, string, string, vector<string>, string, string, string);
};
CYGWIN_BUILD ?= no
USECOMPRESSION ?= no
MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"3/16/2012\""
-VERSION = "\"1.24.1\""
+RELEASE_DATE = "\"4/30/2012\""
+VERSION = "\"1.25.0\""
FORTAN_COMPILER = gfortran
FORTRAN_FLAGS =
data = createProcesses(t, namesOfGroupCombos, tmap);
}
#else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
#endif
return data;
}
//check for necessary files
- string taxFileNameTest = refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum";
+ string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
ifstream FileTest(taxFileNameTest.c_str());
if (!FileTest) {
createProcesses(thisTree, namesOfGroupCombos, rScores);
}
#else
- driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
+ driver(thisTree, namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
#endif
if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }