From 8338fe821bc5e3f3cf15a5bf165eabe103b1ebce Mon Sep 17 00:00:00 2001 From: Sarah Westcott Date: Fri, 27 Apr 2012 11:05:59 -0400 Subject: [PATCH] changes while testing. --- Mothur.xcodeproj/project.pbxproj | 4 ++-- bayesian.cpp | 4 ++-- chimerauchimecommand.cpp | 6 +++--- chimerauchimecommand.h | 2 +- makefile | 4 ++-- parsimony.cpp | 2 +- phylosummary.cpp | 2 +- unifracweightedcommand.cpp | 2 +- 8 files changed, 13 insertions(+), 13 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 1387399..ff18d58 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -2388,8 +2388,8 @@ 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; diff --git a/bayesian.cpp b/bayesian.cpp index 54a123c..1dc3833 100644 --- a/bayesian.cpp +++ b/bayesian.cpp @@ -27,7 +27,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) { 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"; @@ -230,7 +230,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) { delete phyloTree; phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName); - + //save probabilities if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; } } diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp index f238094..026e91b 100644 --- a/chimerauchimecommand.cpp +++ b/chimerauchimecommand.cpp @@ -544,7 +544,7 @@ int ChimeraUchimeCommand::execute(){ 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; } @@ -1473,7 +1473,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename } /**************************************************************************************************/ -int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector groups) { +int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector groups, string nameFile, string groupFile, string fastaFile) { try { processIDS.clear(); @@ -1552,7 +1552,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o // 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); diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h index 499b182..b7da889 100644 --- a/chimerauchimecommand.h +++ b/chimerauchimecommand.h @@ -59,7 +59,7 @@ private: int printFile(vector&, string); int deconvoluteResults(SequenceParser&, string, string, string); int driverGroups(SequenceParser&, string, string, string, string, int, int, vector); - int createProcessesGroups(SequenceParser&, string, string, string, string, vector); + int createProcessesGroups(SequenceParser&, string, string, string, string, vector, string, string, string); }; diff --git a/makefile b/makefile index d8e6dcd..b8d4e2c 100644 --- a/makefile +++ b/makefile @@ -15,8 +15,8 @@ USEREADLINE ?= yes 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 = diff --git a/parsimony.cpp b/parsimony.cpp index bbb929d..3b0f317 100644 --- a/parsimony.cpp +++ b/parsimony.cpp @@ -77,7 +77,7 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) { data = createProcesses(t, namesOfGroupCombos, tmap); } #else - data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size()); + data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap); #endif return data; diff --git a/phylosummary.cpp b/phylosummary.cpp index 7d9fcac..2f56515 100644 --- a/phylosummary.cpp +++ b/phylosummary.cpp @@ -25,7 +25,7 @@ PhyloSummary::PhyloSummary(string refTfile, string groupFile){ } //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) { diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index a4a1bc3..633cb64 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -660,7 +660,7 @@ int UnifracWeightedCommand::runRandomCalcs(Tree* thisTree, vector usersS 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; } -- 2.39.2