added normalize.shared command

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 57228ad4c789124126d71781357f4328bfd143a5..608c0a06a93b955c6021dbb565df7b3d98cb13ea 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -52,7 +52,7 @@ VennCommand::VennCommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
 
                        //check for optional parameter and set defaults
@@ -60,7 +60,7 @@ VennCommand::VennCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -73,7 +73,7 @@ VennCommand::VennCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                        
@@ -89,7 +89,7 @@ VennCommand::VennCommand(string option)  {
                                        else { calc = "sharedsobs"; }
                                }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
@@ -128,8 +128,11 @@ VennCommand::VennCommand(string option)  {
                                        }
                                }
                                
-                               venn = new Venn(outputDir);
+                               //if the users entered no valid calculators don't execute command
+                               if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true;  }
+                               else {  venn = new Venn(outputDir);  }
                        }
+                       
                }
 
                
@@ -173,6 +176,7 @@ VennCommand::~VennCommand(){
                delete read;
                delete venn;
                globaldata->sabund = NULL;
+               delete validCalculator;
        }
        
 }
@@ -187,9 +191,6 @@ int VennCommand::execute(){
                string lastLabel;
                vector<string> outputNames;
                
-               //if the users entered no valid calculators don't execute command
-               if (vennCalculators.size() == 0) { return 0; }
-               
                if (format == "sharedfile") {
                        //you have groups
                        read = new ReadOTUFile(globaldata->inputFileName);      
@@ -216,6 +217,14 @@ int VennCommand::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) {
+                                       for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
+                                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+                                       globaldata->Groups.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       return 0;
+                               }
 
                                if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
@@ -228,10 +237,10 @@ int VennCommand::execute(){
                                        }
                                        
                                        vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
-                                       for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); } 
+                                       for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
                                }
                                
-                               if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                               if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = lookup[0]->getLabel();
                                        
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
@@ -246,7 +255,7 @@ int VennCommand::execute(){
                                                for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
                                        }                               
                                        vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
-                                       for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); } 
+                                       for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
                                        
                                        //restore real lastlabel to save below
                                        lookup[0]->setLabel(saveLabel);
@@ -260,6 +269,14 @@ int VennCommand::execute(){
                                lookup = input->getSharedRAbundVectors();
                        }
                        
+                       if (m->control_pressed) {
+                                       for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
+                                       globaldata->Groups.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       return 0;
+                       }
+
+                       
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
                        bool needToRun = false;
@@ -287,7 +304,7 @@ int VennCommand::execute(){
                                                for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
                                        }                               
                                        vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
-                                       for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); } 
+                                       for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                        }
@@ -296,22 +313,36 @@ int VennCommand::execute(){
                        //reset groups parameter
                        globaldata->Groups.clear();  
                        
+                       if (m->control_pressed) {
+                                       for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       return 0;
+                       }
+
+                       
                }else{
                
                        while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+                       
+                               if (m->control_pressed) {
+                                       for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
+                                       delete sabund;
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       return 0;
+                               }
                
                                if(allLines == 1 || labels.count(sabund->getLabel()) == 1){                     
        
                                        m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
                                        vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
-                                       for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); } 
+                                       for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 
                                        
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
                                }
                                
-                               if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                               if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = sabund->getLabel();
                                
                                        delete sabund;
@@ -319,7 +350,7 @@ int VennCommand::execute(){
                                        
                                        m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
                                        vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
-                                       for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); } 
+                                       for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 
                                        
                                        processedLabels.insert(sabund->getLabel());
@@ -335,6 +366,12 @@ int VennCommand::execute(){
                                sabund = input->getSAbundVector();
                        }
                        
+                       if (m->control_pressed) {
+                                       for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       return 0;
+                       }
+                       
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
                        bool needToRun = false;
@@ -355,12 +392,17 @@ int VennCommand::execute(){
                                        
                                m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
                                vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
-                               for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); } 
+                               for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 
                                delete sabund;
                                        
                        }
                        
+                       if (m->control_pressed) {
+                                       for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       return 0;
+                       }
                }
                
                for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }