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

[mothur.git] / normalizesharedcommand.cpp

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index a4bdd47099c350e77cfe238bcf34e254d1db9341..10c7a3068da7bf4ce015e221b6ca042cbd7ffb7d 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -244,7 +244,7 @@ int NormalizeSharedCommand::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();   out.close(); remove(outputFileName.c_str()); return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear();   out.close(); m->mothurRemove(outputFileName); return 0; }
                                
                                if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                        
@@ -276,13 +276,13 @@ int NormalizeSharedCommand::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();  out.close(); remove(outputFileName.c_str()); return 0; }
+                               if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear();  out.close(); m->mothurRemove(outputFileName); return 0; }
                                
                                //get next line to process
                                lookup = input->getSharedRAbundVectors();                               
                        }
                        
-                       if (m->control_pressed) { outputTypes.clear(); m->Groups.clear();  out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); m->Groups.clear();  out.close(); m->mothurRemove(outputFileName);  return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -348,7 +348,7 @@ int NormalizeSharedCommand::execute(){
                        //as long as you are not at the end of the file or done wih the lines you want
                        while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                
-                               if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } m->Groups.clear();   out.close(); remove(outputFileName.c_str()); return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } m->Groups.clear();   out.close(); m->mothurRemove(outputFileName); return 0; }
                                
                                if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){                     
                                        
@@ -382,13 +382,13 @@ int NormalizeSharedCommand::execute(){
                                //prevent memory leak
                                for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
                                
-                               if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear();  out.close(); remove(outputFileName.c_str()); return 0; }
+                               if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear();  out.close(); m->mothurRemove(outputFileName); return 0; }
                                
                                //get next line to process
                                lookupFloat = input->getSharedRAbundFloatVectors();                             
                        }
                        
-                       if (m->control_pressed) { outputTypes.clear(); m->Groups.clear();  out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); m->Groups.clear();  out.close(); m->mothurRemove(outputFileName);  return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -422,7 +422,7 @@ int NormalizeSharedCommand::execute(){
                delete input;
                out.close();
                
-               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
+               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -450,6 +450,10 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
                if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
                                
                if (method == "totalgroup") { 
+                       
+                       //save numSeqs since they will change as the data is normalized
+                       vector<int> sizes;
+                       for (int i = 0; i < thisLookUp.size(); i++) {  sizes.push_back(thisLookUp[i]->getNumSeqs()); }
                                        
                        for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
                                                
@@ -459,7 +463,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
                                                        
                                                int abund = thisLookUp[i]->getAbundance(j);
                                                        
-                                               float relabund = abund / (float) thisLookUp[i]->getNumSeqs();
+                                               float relabund = abund / (float) sizes[i];
                                                float newNorm = relabund * norm;
                                                
                                                //round to nearest int
@@ -525,6 +529,10 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
                
                if (method == "totalgroup") { 
                        
+                       //save numSeqs since they will change as the data is normalized
+                       vector<float> sizes;
+                       for (int i = 0; i < thisLookUp.size(); i++) {  sizes.push_back(thisLookUp[i]->getNumSeqs()); }
+                       
                        for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
                                
                                for (int i = 0; i < thisLookUp.size(); i++) {
@@ -533,7 +541,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
                                        
                                        float abund = thisLookUp[i]->getAbundance(j);
                                        
-                                       float relabund = abund / (float) thisLookUp[i]->getNumSeqs();
+                                       float relabund = abund / (float) sizes[i];
                                        float newNorm = relabund * norm;
                                        
                                        thisLookUp[i]->set(j, newNorm, thisLookUp[i]->getGroup());