added checks for ^C to quit command instead of program

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 46a04077b839ec7538f641336b9254961693eb0d..e9373a93cbf81ae6bcd84bdd063e01947994de6e 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -244,6 +244,8 @@ int GetOTURepCommand::execute(){
                        }else{  nameMap = NULL;         }
                        
                        readMatrix->read(nameMap);
+                       
+                       if (m->control_pressed) { delete readMatrix; delete groupMap; return 0; }
 
                        //get matrix
                        if (globaldata->gListVector != NULL) {  delete globaldata->gListVector;  }
@@ -257,11 +259,14 @@ int GetOTURepCommand::execute(){
                        // via the index of a sequence in the distance matrix
                        seqVec = vector<SeqMap>(globaldata->gListVector->size()); 
                        for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) {
+                               if (m->control_pressed) { delete readMatrix; delete groupMap; return 0; }
                                seqVec[currentCell->row][currentCell->column] = currentCell->dist;
                        }
                        
                        delete matrix;
                        delete readMatrix;
+                       
+                       if (m->control_pressed) {  delete groupMap; return 0; }
                }else {
                        //process file and set up indexes
                        if (format == "column") { formatMatrix = new FormatColumnMatrix(distFile); }    
@@ -276,6 +281,8 @@ int GetOTURepCommand::execute(){
                        }else{  nameMap = NULL;         }
                        
                        formatMatrix->read(nameMap);
+                       
+                       if (m->control_pressed) { delete formatMatrix; delete groupMap; return 0; }
 
                        //get matrix
                        if (globaldata->gListVector != NULL) {  delete globaldata->gListVector;  }
@@ -291,8 +298,11 @@ int GetOTURepCommand::execute(){
                        
                        //openfile for getMap to use
                        openInputFile(distFile, inRow);
+                       
+                       if (m->control_pressed) { inRow.close(); remove(distFile.c_str()); delete groupMap; return 0; }
                }
                
+               
                //globaldata->gListVector bin 0 = first name read in distance matrix, globaldata->gListVector bin 1 = second name read in distance matrix
                if (globaldata->gListVector != NULL) {
                        vector<string> names;
@@ -314,6 +324,11 @@ int GetOTURepCommand::execute(){
                
                //read fastafile
                fasta->readFastaFile(fastafile);
+               
+               if (m->control_pressed) { 
+                       if (large) {  inRow.close(); remove(distFile.c_str());  }
+                       delete groupMap; delete fasta; return 0; 
+               }
                                
                //if user gave a namesfile then use it
                if (namefile != "") {   readNamesFile();        }
@@ -332,6 +347,11 @@ int GetOTURepCommand::execute(){
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = labels;
+               
+               if (m->control_pressed) { 
+                       if (large) {  inRow.close(); remove(distFile.c_str());  }
+                       delete groupMap; delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
+               }
        
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -340,6 +360,13 @@ int GetOTURepCommand::execute(){
                                        error = process(list);
                                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
                                        
+                                       if (m->control_pressed) { 
+                                               if (large) {  inRow.close(); remove(distFile.c_str());  }
+                                               if (groupfile != "") {  delete groupMap;  globaldata->gGroupmap = NULL; }
+                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                               delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
+                                       }
+                                       
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
                        }
@@ -353,6 +380,13 @@ int GetOTURepCommand::execute(){
                                        error = process(list);
                                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
                                        
+                                       if (m->control_pressed) { 
+                                               if (large) {  inRow.close(); remove(distFile.c_str());  }
+                                               if (groupfile != "") {  delete groupMap;  globaldata->gGroupmap = NULL; }
+                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                               delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
+                                       }
+                                       
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
                                        
@@ -386,6 +420,13 @@ int GetOTURepCommand::execute(){
                        error = process(list);
                        delete list;
                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
+                       
+                       if (m->control_pressed) { 
+                                       if (large) {  inRow.close(); remove(distFile.c_str());  }
+                                       if (groupfile != "") {  delete groupMap;  globaldata->gGroupmap = NULL; }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
+                       }
                }
                
                //close and remove formatted matrix file
@@ -402,6 +443,8 @@ int GetOTURepCommand::execute(){
                        delete groupMap;  globaldata->gGroupmap = NULL;
                }
                
+               if (m->control_pressed) {  return 0; }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
@@ -501,6 +544,7 @@ string GetOTURepCommand::findRep(int bin, string& group, ListVector* thisList, i
                        SeqMap::iterator it;
                        SeqMap currMap;
                        for (size_t i=0; i < seqIndex.size(); i++) {
+                               if (m->control_pressed) {  return  "control"; }
                        
                                if (!large) {   currMap = seqVec[seqIndex[i]];  }
                                else            {       currMap = getMap(seqIndex[i]);  }
@@ -526,6 +570,7 @@ string GetOTURepCommand::findRep(int bin, string& group, ListVector* thisList, i
                        float min = 10000;
                        int minIndex;
                        for (size_t i=0; i < max_dist.size(); i++) {
+                               if (m->control_pressed) {  return  "control"; }
                                if (max_dist[i] < min) {
                                        min = max_dist[i];
                                        minIndex = i;
@@ -570,8 +615,13 @@ int GetOTURepCommand::process(ListVector* processList) {
                for (int i = 0; i < processList->size(); i++) {
                        string groups;
                        int binsize;
+                       
+                       if (m->control_pressed) { out.close();  newNamesOutput.close(); return 0; }
+                       
                        nameRep = findRep(i, groups, processList, binsize);
                        
+                       if (m->control_pressed) { out.close();  newNamesOutput.close(); return 0; }
+                       
                        //output to new names file
                        newNamesOutput << nameRep << '\t' << processList->get(i) << endl;