added checks for ^C to quit command instead of program

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 6ce5ee9dfcb29dfd495bb7dc5f83aec8681eb3d6..c4e58c28b3a7c56892981c7e221b738daa610ccd 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -223,6 +223,7 @@ void TreeGroupCommand::help(){
 //**********************************************************************************************************************
 
 TreeGroupCommand::~TreeGroupCommand(){
+       globaldata->Groups.clear();  
        if (abort == false) {
                
                if (format == "sharedfile") { delete read;  delete input; globaldata->ginput = NULL; }
@@ -257,8 +258,23 @@ int TreeGroupCommand::execute(){
                        //used in tree constructor 
                        globaldata->runParse = false;
                        
+                       //clear globaldatas old tree names if any
+                       globaldata->Treenames.clear();
+               
+                       //fills globaldatas tree names
+                       globaldata->Treenames = globaldata->Groups;
+               
+                       //create treemap class from groupmap for tree class to use
+                       tmap = new TreeMap();
+                       tmap->makeSim(globaldata->gGroupmap);
+                       globaldata->gTreemap = tmap;
+                       
+                       if (m->control_pressed) { return 0; }
+                       
                        //create tree file
                        makeSimsShared();
+                       
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
                }else{
                        //read in dist file
                        filename = globaldata->inputFileName;
@@ -282,6 +298,9 @@ int TreeGroupCommand::execute(){
 
                        //make treemap
                        tmap = new TreeMap();
+                       
+                       if (m->control_pressed) { return 0; }
+                       
                        tmap->makeSim(list);
                        globaldata->gTreemap = tmap;
                        
@@ -296,14 +315,22 @@ int TreeGroupCommand::execute(){
                        //used in tree constructor 
                        globaldata->runParse = false;
                        
+                       if (m->control_pressed) { return 0; }
+                       
                        makeSimsDist();
+                       
+                       if (m->control_pressed) { return 0; }
 
                        //create a new filename
                        outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "tre"; 
                        outputNames.push_back(outputFile);
                                
                        createTree();
+                       
+                       if (m->control_pressed) { return 0; }
+
                        m->mothurOut("Tree complete. "); m->mothurOutEndLine();
+                       
                }
                                
                //reset groups parameter
@@ -323,7 +350,7 @@ int TreeGroupCommand::execute(){
 }
 //**********************************************************************************************************************
 
-void TreeGroupCommand::createTree(){
+int TreeGroupCommand::createTree(){
        try {
                //create tree
                t = new Tree();
@@ -332,7 +359,9 @@ void TreeGroupCommand::createTree(){
                //there are numGroups - 1 merges to do
                for (int i = 0; i < (numGroups - 1); i++) {
                        float largest = -1000.0;
-
+                       
+                       if (m->control_pressed) { delete t; return 1; }
+                       
                        int row, column;
                        //find largest value in sims matrix by searching lower triangle
                        for (int j = 1; j < simMatrix.size(); j++) {
@@ -386,11 +415,17 @@ void TreeGroupCommand::createTree(){
                //assemble tree
                t->assembleTree();
                
+               if (m->control_pressed) { delete t; return 1; }
+               
                //print newick file
                t->createNewickFile(outputFile);
                
                //delete tree
                delete t;
+               
+               if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
+               
+               return 0;
        
        }
        catch(exception& e) {
@@ -423,7 +458,7 @@ void TreeGroupCommand::printSims(ostream& out) {
        }
 }
 /***********************************************************/
-void TreeGroupCommand::makeSimsDist() {
+int TreeGroupCommand::makeSimsDist() {
        try {
                numGroups = list->size();
                
@@ -434,9 +469,9 @@ void TreeGroupCommand::makeSimsDist() {
                //initialize simMatrix
                simMatrix.clear();
                simMatrix.resize(numGroups);
-               for (int m = 0; m < simMatrix.size(); m++)      {
+               for (int k = 0; k < simMatrix.size(); k++)      {
                        for (int j = 0; j < simMatrix.size(); j++)      {
-                               simMatrix[m].push_back(0.0);
+                               simMatrix[k].push_back(0.0);
                        }
                }
                
@@ -445,10 +480,13 @@ void TreeGroupCommand::makeSimsDist() {
                for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
                        //similairity = -(distance-1)
                        simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);   
-                       simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);                           
+                       simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);   
+                       
+                       if (m->control_pressed) { return 1; }
+                       
                }
 
-
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
@@ -457,25 +495,14 @@ void TreeGroupCommand::makeSimsDist() {
 }
 
 /***********************************************************/
-void TreeGroupCommand::makeSimsShared() {
+int TreeGroupCommand::makeSimsShared() {
        try {
-       
-               //clear globaldatas old tree names if any
-               globaldata->Treenames.clear();
-               
-               //fills globaldatas tree names
-               globaldata->Treenames = globaldata->Groups;
-               
-               //create treemap class from groupmap for tree class to use
-               tmap = new TreeMap();
-               tmap->makeSim(globaldata->gGroupmap);
-               globaldata->gTreemap = tmap;
-               
                set<string> processedLabels;
                set<string> userLabels = labels;
                
                //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 < lookup.size(); i++) {  delete lookup[i];  } for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; } return 1; }
                
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
@@ -508,6 +535,8 @@ void TreeGroupCommand::makeSimsShared() {
                        lookup = input->getSharedRAbundVectors();
                }
                
+               if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; } return 1; }
+
                //output error messages about any remaining user labels
                set<string>::iterator it;
                bool needToRun = false;
@@ -532,6 +561,8 @@ void TreeGroupCommand::makeSimsShared() {
                }
                
                for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
+               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
@@ -540,7 +571,7 @@ void TreeGroupCommand::makeSimsShared() {
 }
 
 /***********************************************************/
-void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
+int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
        try{
                                EstOutput data;
                                vector<SharedRAbundVector*> subset;
@@ -551,9 +582,9 @@ void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                        //initialize simMatrix
                                        simMatrix.clear();
                                        simMatrix.resize(numGroups);
-                                       for (int m = 0; m < simMatrix.size(); m++)      {
+                                       for (int k = 0; k < simMatrix.size(); k++)      {
                                                for (int j = 0; j < simMatrix.size(); j++)      {
-                                                       simMatrix[m].push_back(0.0);
+                                                       simMatrix[k].push_back(0.0);
                                                }
                                        }
                
@@ -575,16 +606,24 @@ void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                                                subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
                                                                
                                                                data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
+                                                               
+                                                               if (m->control_pressed) { return 1; }
+                                                               
                                                                //save values in similarity matrix
                                                                simMatrix[k][l] = data[0];
                                                                simMatrix[l][k] = data[0];
                                                        }
                                                }
                                        }
-                               
+                                       
+                                       if (m->control_pressed) { return 1; }
                                        //creates tree from similarity matrix and write out file
                                        createTree();
+                                       
+                                       if (m->control_pressed) { return 1; }
                                }
+                               
+                               return 0;
 
        }
        catch(exception& e) {