rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 0704f55896e835f331eda28446012e62c790904e..2a55ff08178cb0a7da3d99aff4b157017bb3d27e 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -10,6 +10,7 @@
 #include "metastatscommand.h"
 #include "metastats.h"
 #include "sharedutilities.h"
+#include "mothurmetastats.h"
 
 //**********************************************************************************************************************
 vector<string> MetaStatsCommand::setParameters(){      
@@ -249,7 +250,7 @@ int MetaStatsCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]); } return 0; }
        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
@@ -280,13 +281,13 @@ int MetaStatsCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear(); delete input;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear(); delete input;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
 
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();                               
                }
                
-               if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); }  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); }  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -318,7 +319,7 @@ int MetaStatsCommand::execute(){
                delete input; 
                delete designMap;
                
-               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); } return 0;}
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -404,6 +405,8 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                        double** data;
                        data = new double*[thisLookUp[0]->getNumBins()];
                        
+                       vector< vector<double> > data2; data2.resize(thisLookUp[0]->getNumBins());
+                       
                        vector<SharedRAbundVector*> subset;
                        int setACount = 0;
                        int setBCount = 0;
@@ -428,14 +431,21 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                                //fill data
                                for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
                                        data[j] = new double[subset.size()];
+                                       data2[j].resize(subset.size(), 0.0);
                                        for (int i = 0; i < subset.size(); i++) {
                                                data[j][i] = (subset[i]->getAbundance(j));
+                                               data2[j][i] = (subset[i]->getAbundance(j));
                                        }
                                }
                                
                                m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine(); 
                                metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
                                
+                               m->mothurOutEndLine();
+                               MothurMetastats mothurMeta(threshold, iters);
+                               mothurMeta.runMetastats(outputFileName+".myVersion" , data2, setACount);
+                               m->mothurOutEndLine();
+                               
                                m->mothurOutEndLine(); 
                        }