changed normalize.shared and sub.sample commands to fix bug in normalize.shared and...

[mothur.git] / normalizesharedcommand.cpp

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 10c7a3068da7bf4ce015e221b6ca042cbd7ffb7d..1066ab7c33b81cbb230e9f8985fa101c65672c7b 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -197,10 +197,6 @@ int NormalizeSharedCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "norm.shared";
-               ofstream out;
-               m->openOutputFile(outputFileName, out);
-               
                input = new InputData(inputfile, format);
                
                //you are reading a sharedfile and you do not want to make relabund
@@ -244,13 +240,12 @@ 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(); m->mothurRemove(outputFileName); return 0; }
+                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear();   return 0; }
                                
                                if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                        
                                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
-                                       normalize(lookup, out);
+                                       normalize(lookup);
                                        
                                        processedLabels.insert(lookup[0]->getLabel());
                                        userLabels.erase(lookup[0]->getLabel());
@@ -262,8 +257,8 @@ int NormalizeSharedCommand::execute(){
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
                                        lookup = input->getSharedRAbundVectors(lastLabel);
                                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
-                                       normalize(lookup, out);
+                                       
+                                       normalize(lookup);
                                        
                                        processedLabels.insert(lookup[0]->getLabel());
                                        userLabels.erase(lookup[0]->getLabel());
@@ -276,13 +271,13 @@ 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(); m->mothurRemove(outputFileName); return 0; }
+                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();  return 0; }
                                
                                //get next line to process
                                lookup = input->getSharedRAbundVectors();                               
                        }
                        
-                       if (m->control_pressed) { outputTypes.clear(); m->Groups.clear();  out.close(); m->mothurRemove(outputFileName);  return 0; }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();   return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -303,8 +298,8 @@ int NormalizeSharedCommand::execute(){
                                lookup = input->getSharedRAbundVectors(lastLabel);
                                
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
-                               normalize(lookup, out);
+                               
+                               normalize(lookup);
                                
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                        }
@@ -348,14 +343,13 @@ 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(); m->mothurRemove(outputFileName); return 0; }
+                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear();  for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } m->Groups.clear();  return 0; }
                                
                                if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){                     
                                        
                                        m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
                                        
-                                       if (!m->printedHeaders) { lookupFloat[0]->printHeaders(out); }
-                                       normalize(lookupFloat, out);
+                                       normalize(lookupFloat);
                                        
                                        processedLabels.insert(lookupFloat[0]->getLabel());
                                        userLabels.erase(lookupFloat[0]->getLabel());
@@ -368,8 +362,8 @@ int NormalizeSharedCommand::execute(){
                                        lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
                                        
                                        m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
-                                       if (!m->printedHeaders) { lookupFloat[0]->printHeaders(out); }
-                                       normalize(lookupFloat, out);
+               
+                                       normalize(lookupFloat);
                                        
                                        processedLabels.insert(lookupFloat[0]->getLabel());
                                        userLabels.erase(lookupFloat[0]->getLabel());
@@ -382,13 +376,13 @@ 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(); m->mothurRemove(outputFileName); return 0; }
+                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();   return 0; }
                                
                                //get next line to process
                                lookupFloat = input->getSharedRAbundFloatVectors();                             
                        }
                        
-                       if (m->control_pressed) { outputTypes.clear(); m->Groups.clear();  out.close(); m->mothurRemove(outputFileName);  return 0; }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();   return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -410,8 +404,7 @@ int NormalizeSharedCommand::execute(){
                                
                                m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
                                
-                               if (!m->printedHeaders) { lookupFloat[0]->printHeaders(out); }
-                               normalize(lookupFloat, out);
+                               normalize(lookupFloat);
                                
                                for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
                        }
@@ -420,13 +413,13 @@ int NormalizeSharedCommand::execute(){
                //reset groups parameter
                m->Groups.clear();  
                delete input;
-               out.close();
                
-               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+               //m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                m->mothurOutEndLine();
                
                //set shared file as new current sharedfile
@@ -445,9 +438,17 @@ int NormalizeSharedCommand::execute(){
 }
 //**********************************************************************************************************************
 
-int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
+int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp){
        try {
+               //save mothurOut's binLabels to restore for next label
+               vector<string> saveBinLabels = m->currentBinLabels;
+               
                if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
+               
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+               ofstream out;
+               m->openOutputFile(outputFileName, out);
+               outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
                                
                if (method == "totalgroup") { 
                        
@@ -459,7 +460,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
                                                
                                        for (int i = 0; i < thisLookUp.size(); i++) {
                                                        
-                                               if (m->control_pressed) { return 0; }
+                                               if (m->control_pressed) { out.close(); return 0; }
                                                        
                                                int abund = thisLookUp[i]->getAbundance(j);
                                                        
@@ -477,7 +478,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
                        
                        for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
                                
-                               if (m->control_pressed) { return 0; }
+                               if (m->control_pressed) { out.close(); return 0; }
                                
                                //calc mean
                                float mean = 0.0;
@@ -508,12 +509,18 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
                                
                                                
                eliminateZeroOTUS(thisLookUp);
+               
+               thisLookUp[0]->printHeaders(out); 
                 
                for (int i = 0; i < thisLookUp.size(); i++) {
                        out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t';
                        thisLookUp[i]->print(out);
                }
                
+               out.close();
+               
+               m->currentBinLabels = saveBinLabels;
+               
                return 0;
        }
        catch(exception& e) {
@@ -523,8 +530,18 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
 }
 //**********************************************************************************************************************
 
-int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLookUp, ofstream& out){
+int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLookUp){
        try {
+               
+               //save mothurOut's binLabels to restore for next label
+               vector<string> saveBinLabels = m->currentBinLabels;
+               
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+               ofstream out;
+               m->openOutputFile(outputFileName, out);
+               outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+               
+               
                if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
                
                if (method == "totalgroup") { 
@@ -537,7 +554,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
                                
                                for (int i = 0; i < thisLookUp.size(); i++) {
                                        
-                                       if (m->control_pressed) { return 0; }
+                                       if (m->control_pressed) { out.close(); return 0; }
                                        
                                        float abund = thisLookUp[i]->getAbundance(j);
                                        
@@ -551,7 +568,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
                }else if (method == "zscore") {
                        for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
                                
-                               if (m->control_pressed) { return 0; }
+                               if (m->control_pressed) { out.close(); return 0; }
                                
                                //calc mean
                                float mean = 0.0;
@@ -579,11 +596,17 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
                
                eliminateZeroOTUS(thisLookUp);
                
+               thisLookUp[0]->printHeaders(out); 
+               
                for (int i = 0; i < thisLookUp.size(); i++) {
                        out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t';
                        thisLookUp[i]->print(out);
                }
                
+               out.close();
+               
+               m->currentBinLabels = saveBinLabels;
+               
                return 0;
        }
        catch(exception& e) {
@@ -604,6 +627,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thisl
                }
                
                //for each bin
+               vector<string> newBinLabels;
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                
@@ -618,12 +642,18 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thisl
                                for (int j = 0; j < thislookup.size(); j++) {
                                        newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
                                }
+                               //if there is a bin label use it otherwise make one
+                               string binLabel = "Otu" + (i+1);
+                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               
+                               newBinLabels.push_back(binLabel);
                        }
                }
 
                for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 
                thislookup = newLookup;
+               m->currentBinLabels = newBinLabels;
                
                return 0;
  
@@ -646,6 +676,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                }
                
                //for each bin
+               vector<string> newBinLabels;
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                        
@@ -660,12 +691,18 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                                for (int j = 0; j < thislookup.size(); j++) {
                                        newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
                                }
+                               //if there is a bin label use it otherwise make one
+                               string binLabel = "Otu" + (i+1);
+                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               
+                               newBinLabels.push_back(binLabel);
                        }
                }
                
                for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
                
                thislookup = newLookup;
+               m->currentBinLabels = newBinLabels;
                
                return 0;