added code to check path for uchime and catchall executables

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index dbdee2ad942db51860cb0a7f403662a895def1bf..318409fa8845f91fcaae0765a6f930626299e82d 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -245,6 +245,7 @@ int UnifracUnweightedCommand::execute() {
         T = reader->getTrees();
         tmap = T[0]->getTreeMap();
         map<string, string> nameMap = reader->getNames();
+        map<string, string> unique2Dup = reader->getNameMap();
         delete reader; 
         
                sumFile = outputDir + m->getSimpleName(treefile) + ".uwsummary";
@@ -281,7 +282,7 @@ int UnifracUnweightedCommand::execute() {
                     int thisSize = thisGroupsSeqs.size();
                     
                     if (thisSize >= subsampleSize) {    Groups.push_back(newGroups[i]);        }
-                    else {  m->mothurOut("You have selected a size that is larger than "+newGroups[i]+" number of sequences, removing "+newGroups[i]+".\n"); }
+                    else {   m->mothurOut("You have selected a size that is larger than "+newGroups[i]+" number of sequences, removing "+newGroups[i]+".\n"); }
                 } 
                 m->setGroups(Groups);
             }
@@ -305,7 +306,7 @@ int UnifracUnweightedCommand::execute() {
                for (int i = 0; i < T.size(); i++) {
                        if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
                        
-                       counter = 0;
+            counter = 0;
                        
                        if (random)  {  
                                output = new ColumnFile(outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted", itersString);
@@ -341,18 +342,23 @@ int UnifracUnweightedCommand::execute() {
                        
                        if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0;  }
             
+            int startSubsample = time(NULL);
+            
             //subsample loop
             vector< vector<double> > calcDistsTotals;  //each iter, each groupCombos dists. this will be used to make .dist files
             for (int thisIter = 0; thisIter < subsampleIters; thisIter++) { //subsampleIters=0, if subsample=f.
-                
                 if (m->control_pressed) { break; }
                 
                 //copy to preserve old one - would do this in subsample but memory cleanup becomes messy.
                 TreeMap* newTmap = new TreeMap();
-                newTmap->getCopy(*tmap);
+                //newTmap->getCopy(*tmap);
+                
+                //SubSample sample;
+                //Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
                 
+                //uses method of setting groups to doNotIncludeMe
                 SubSample sample;
-                Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
+                Tree* subSampleTree = sample.getSample(T[i], tmap, newTmap, subsampleSize, unique2Dup);
                 
                 //call new weighted function
                 vector<double> iterData; iterData.resize(numComp,0);
@@ -367,6 +373,7 @@ int UnifracUnweightedCommand::execute() {
                 
                 if((thisIter+1) % 100 == 0){   m->mothurOut(toString(thisIter+1)); m->mothurOutEndLine();              }
             }
+            m->mothurOut("It took " + toString(time(NULL) - startSubsample) + " secs to run the subsampling."); m->mothurOutEndLine();
             
             if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0;  }