added checks for ^C to quit command instead of program

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 078f411d669426daed4dcc1f09f65810644350ad..390f47f9fac6f255ce6e30fec4c7b2264e25cdad 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -193,10 +193,14 @@ int MatrixOutputCommand::execute(){
                if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0;}
                
                numGroups = lookup.size();
+               
+               if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); return 0;  }
                                
                //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) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+               
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                process(lookup);
@@ -228,6 +232,8 @@ int MatrixOutputCommand::execute(){
                        lookup = input->getSharedRAbundVectors();
                }
                
+               if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+
                //output error messages about any remaining user labels
                set<string>::iterator it;
                bool needToRun = false;
@@ -241,6 +247,8 @@ int MatrixOutputCommand::execute(){
                        }
                }
                
+               if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+
                //run last label if you need to
                if (needToRun == true)  {
                        for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {  delete lookup[i]; }  } 
@@ -251,7 +259,8 @@ int MatrixOutputCommand::execute(){
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                }
                
-                               
+               if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+               
                //reset groups parameter
                globaldata->Groups.clear();  
                
@@ -301,7 +310,7 @@ void MatrixOutputCommand::printSims(ostream& out) {
        }
 }
 /***********************************************************/
-void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
+int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
        try {
        
                                EstOutput data;
@@ -313,9 +322,9 @@ void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                                        //initialize simMatrix
                                        simMatrix.clear();
                                        simMatrix.resize(numGroups);
-                                       for (int m = 0; m < simMatrix.size(); m++)      {
+                                       for (int p = 0; p < simMatrix.size(); p++)      {
                                                for (int j = 0; j < simMatrix.size(); j++)      {
-                                                       simMatrix[m].push_back(0.0);
+                                                       simMatrix[p].push_back(0.0);
                                                }
                                        }
                                
@@ -324,6 +333,8 @@ void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                                                        if (k != l) { //we dont need to similiarity of a groups to itself
                                                                //get estimated similarity between 2 groups
                                                                
+                                                               if (m->control_pressed) { return 0; }
+                                                               
                                                                subset.clear(); //clear out old pair of sharedrabunds
                                                                //add new pair of sharedrabunds
                                                                subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
@@ -345,7 +356,7 @@ void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                                        
                                }
 
-       
+                               return 0;
                
        }
        catch(exception& e) {