changes while testing.

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1387399e7be27dcf0f80316478c2519fb5d5daf3..ff18d5890cef43d65aabd4f444cef07b6bf2b0fe 100644 (file)
--- 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 54a123c5a7835d7c1a2c48d36fe3ec7070462027..1dc38337aef1bcc3b695ff56e86061cdab58c13d 100644 (file)
--- 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 f238094c9563587be29064a8f3fdbce54314c0f9..026e91b01f188ce180c3b645de8451138efe0e02 100644 (file)
--- 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<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();
@@ -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 499b18298dfffc66657f62fd00d48d7c3846bb15..b7da889701f3ac2bc7883cf5c39356550eb2e25d 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -59,7 +59,7 @@ private:
        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);
 
 
 };

diff --git a/makefile b/makefile
index d8e6dcd603913805b0355d3f69173f25cf7803b2..b8d4e2c3e30844c436e44015696ec04d5c4264d8 100644 (file)
--- 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 bbb929d78d9aa6550c587c77eccec294cbe3c715..3b0f31759c0563031874aa16cb0d3d515a65653b 100644 (file)
--- 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 7d9fcac2558da8f50653a11ddafd997b58c1c286..2f565150aabeec35cc8a3c03a459d8b85090550b 100644 (file)
--- 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 a4a1bc3defc98beb608b38645471e46541a0b10f..633cb643a213044e4f7e92c108ad012690deff09 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -660,7 +660,7 @@ int UnifracWeightedCommand::runRandomCalcs(Tree* thisTree, vector<double> 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; }