some bug fixes

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 5ad1ee6432bf17220e3b8fd2187734ba4a7a098a..b086dff619d18046dd0d3cbaabf109a2976421b3 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -136,10 +136,11 @@ int SummaryCommand::execute(){
                
                vector<string> outputNames;
                
+               string hadShared = "";
                if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
-               else {  inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
+               else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
                
-               if (m->control_pressed) { return 0; }
+               if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
                
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
@@ -204,7 +205,7 @@ int SummaryCommand::execute(){
                        }
                        
                        //if the users entered no valid calculators don't execute command
-                       if (sumCalculators.size() == 0) { return 0; }
+                       if (sumCalculators.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
                        
                        ofstream outputFileHandle;
                        openOutputFile(fileNameRoot, outputFileHandle);
@@ -231,11 +232,11 @@ int SummaryCommand::execute(){
                        set<string> processedLabels;
                        set<string> userLabels = labels;
                        
-                       if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
+                       if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
                        
                        while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                
-                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
+                               if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
                                
                                if(allLines == 1 || labels.count(sabund->getLabel()) == 1){                     
                                        
@@ -247,7 +248,7 @@ int SummaryCommand::execute(){
                                        for(int i=0;i<sumCalculators.size();i++){
                                                vector<double> data = sumCalculators[i]->getValues(sabund);
                                                
-                                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
+                                               if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 
                                                outputFileHandle << '\t';
                                                sumCalculators[i]->print(outputFileHandle);
@@ -269,7 +270,7 @@ int SummaryCommand::execute(){
                                        for(int i=0;i<sumCalculators.size();i++){
                                                vector<double> data = sumCalculators[i]->getValues(sabund);
                                                
-                                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
+                                               if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
                                                
                                                outputFileHandle << '\t';
                                                sumCalculators[i]->print(outputFileHandle);
@@ -286,7 +287,7 @@ int SummaryCommand::execute(){
                                sabund = input->getSAbundVector();
                        }
                        
-                       if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
+                       if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
 
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -311,7 +312,7 @@ int SummaryCommand::execute(){
                                for(int i=0;i<sumCalculators.size();i++){
                                        vector<double> data = sumCalculators[i]->getValues(sabund);
                                        
-                                       if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
+                                       if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 
                                        outputFileHandle << '\t';
                                        sumCalculators[i]->print(outputFileHandle);
@@ -322,7 +323,7 @@ int SummaryCommand::execute(){
                        
                        outputFileHandle.close();
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
+                       if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
 
                        
                        delete input;  globaldata->ginput = NULL;
@@ -332,6 +333,8 @@ int SummaryCommand::execute(){
                        for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
                }
                
+               if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
+               
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
                
                m->mothurOutEndLine();