fixed seq. error align=f issue. added std and ave calcs to mothurout. working on...

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 5f3cffc2b1ab807b279ba3185444dc96a0a3b863..19a2ece3bb4253e6da6199515d9c203d2d656400 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -481,20 +481,29 @@ int UnifracUnweightedCommand::execute() {
 int UnifracUnweightedCommand::getAverageSTDMatrices(vector< vector<double> >& dists, int treeNum) {
        try {
         //we need to find the average distance and standard deviation for each groups distance
-        
         //finds sum
-        vector<double> averages; averages.resize(numComp, 0); 
+        vector<double> averages; //averages.resize(numComp, 0.0);
+        for (int i = 0; i < numComp; i++) { averages.push_back(0.0); }
+        
+        if (m->debug) { m->mothurOut("[DEBUG]: numcomparisons = " + toString(numComp) + ", subsampleIters = " + toString(subsampleIters) + "\n"); }
+        
         for (int thisIter = 0; thisIter < subsampleIters; thisIter++) {
             for (int i = 0; i < dists[thisIter].size(); i++) {  
                 averages[i] += dists[thisIter][i];
             }
         }
         
+        if (m->debug) { m->mothurOut("[DEBUG]: numcomparisons = " + toString(numComp) + ", subsampleIters = " + toString(subsampleIters) + "\n"); }
+        
         //finds average.
-        for (int i = 0; i < averages.size(); i++) {  averages[i] /= (float) subsampleIters; }
+        for (int i = 0; i < averages.size(); i++) {  
+            averages[i] /= (float) subsampleIters; 
+            if (m->debug) { m->mothurOut("[DEBUG]: i = " + toString(i) + ", averages[i] = " + toString(averages[i]) + "\n"); }
+        }
         
         //find standard deviation
-        vector<double> stdDev; stdDev.resize(numComp, 0);
+        vector<double> stdDev; //stdDev.resize(numComp, 0.0);
+        for (int i = 0; i < numComp; i++) { stdDev.push_back(0.0); }
         
         for (int thisIter = 0; thisIter < subsampleIters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
             for (int j = 0; j < dists[thisIter].size(); j++) {
@@ -504,20 +513,28 @@ int UnifracUnweightedCommand::getAverageSTDMatrices(vector< vector<double> >& di
         for (int i = 0; i < stdDev.size(); i++) {  
             stdDev[i] /= (float) subsampleIters; 
             stdDev[i] = sqrt(stdDev[i]);
+            if (m->debug) { m->mothurOut("[DEBUG]: i = " + toString(i) + ", stdDev[i] = " + toString(stdDev[i]) + "\n"); }
         }
         
         //make matrix with scores in it
-        vector< vector<double> > avedists;     avedists.resize(m->getNumGroups());
+        vector< vector<double> > avedists;     //avedists.resize(m->getNumGroups());
         for (int i = 0; i < m->getNumGroups(); i++) {
-            avedists[i].resize(m->getNumGroups(), 0.0);
+            vector<double> temp;
+            for (int j = 0; j < m->getNumGroups(); j++) { temp.push_back(0.0); }
+            avedists.push_back(temp);
         }
         
         //make matrix with scores in it
-        vector< vector<double> > stddists;     stddists.resize(m->getNumGroups());
+        vector< vector<double> > stddists;     //stddists.resize(m->getNumGroups());
         for (int i = 0; i < m->getNumGroups(); i++) {
-            stddists[i].resize(m->getNumGroups(), 0.0);
+            vector<double> temp;
+            for (int j = 0; j < m->getNumGroups(); j++) { temp.push_back(0.0); }
+            //stddists[i].resize(m->getNumGroups(), 0.0);
+            stddists.push_back(temp);
         }
         
+        if (m->debug) { m->mothurOut("[DEBUG]: about to fill matrix.\n"); }
+        
         //flip it so you can print it
         int count = 0;
         for (int r=0; r<m->getNumGroups(); r++) { 
@@ -530,6 +547,8 @@ int UnifracUnweightedCommand::getAverageSTDMatrices(vector< vector<double> >& di
             }
         }
         
+        if (m->debug) { m->mothurOut("[DEBUG]: done filling matrix.\n"); }
+        
         map<string, string> variables; 
                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
         variables["[tag]"] = toString(treeNum+1);