added checks for ^C to quit command instead of program

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index bf0b82b3973edce4353325d3364010bdadd20c54..6d5acb2386ad0ccd836ee41d2d8f5b24c5e4048e 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -164,6 +164,8 @@ int MGClusterCommand::execute(){
                list = new ListVector(nameMap->getListVector());
                RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
                
+               if (m->control_pressed) { delete nameMap; delete read; delete list; delete rabund; return 0; }
+               
                start = time(NULL);
                oldList = *list;
                
@@ -176,6 +178,12 @@ int MGClusterCommand::execute(){
                openOutputFile(fileroot+ tag + ".rabund",  rabundFile);
                openOutputFile(fileroot+ tag + ".sabund",  sabundFile);
                
+               if (m->control_pressed) { 
+                       delete nameMap; delete read; delete list; delete rabund; 
+                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                       return 0; 
+               }
+               
                if (!hclusterWanted) {
                        //get distmatrix and overlap
                        SparseMatrix* distMatrix = read->getDistMatrix();
@@ -188,10 +196,23 @@ int MGClusterCommand::execute(){
                        else if(method == "average"){   cluster = new AverageLinkage(rabund, list, distMatrix, cutoff, method); }
                        cluster->setMapWanted(true);
                        
+                       if (m->control_pressed) { 
+                               delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+                               listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               return 0; 
+                       }
+                       
                        //cluster using cluster classes
                        while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
                                
                                cluster->update(cutoff);
+                               
+                               if (m->control_pressed) { 
+                                       delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                       return 0; 
+                               }
+                               
                                float dist = distMatrix->getSmallDist();
                                float rndDist = roundDist(dist, precision);
                                
@@ -203,6 +224,13 @@ int MGClusterCommand::execute(){
                                        if (merge) {
                                                map<string, int> seq2Bin = cluster->getSeqtoBin();
                                                ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+                                               
+                                               if (m->control_pressed) { 
+                                                       delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       return 0; 
+                                               }
+                                               
                                                temp->setLabel(toString(rndPreviousDist,  precisionLength-1));
                                                printData(temp);
                                                delete temp;
@@ -225,6 +253,13 @@ int MGClusterCommand::execute(){
                                if (merge) {
                                        map<string, int> seq2Bin = cluster->getSeqtoBin();
                                        ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+                                       
+                                       if (m->control_pressed) { 
+                                                       delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       return 0; 
+                                       }
+                                       
                                        temp->setLabel(toString(rndPreviousDist,  precisionLength-1));
                                        printData(temp);
                                        delete temp;
@@ -247,6 +282,12 @@ int MGClusterCommand::execute(){
                
                        //sort the distance and overlap files
                        sortHclusterFiles(distFile, overlapFile);
+                       
+                       if (m->control_pressed) { 
+                               delete nameMap;  delete list; delete rabund; 
+                               listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               return 0; 
+                       }
                
                        //create cluster
                        hcluster = new HCluster(rabund, list, method, distFile, nameMap, cutoff);
@@ -255,16 +296,38 @@ int MGClusterCommand::execute(){
                        vector<seqDist> seqs; seqs.resize(1); // to start loop
                        //ifstream inHcluster;
                        //openInputFile(distFile, inHcluster);
+                       
+                       if (m->control_pressed) { 
+                               delete nameMap;  delete list; delete rabund; delete hcluster;
+                               listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               return 0; 
+                       }
 
                        while (seqs.size() != 0){
                
                                seqs = hcluster->getSeqs();
                                
+                               if (m->control_pressed) { 
+                                       delete nameMap;  delete list; delete rabund; delete hcluster;
+                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                       remove(distFile.c_str());
+                                       remove(overlapFile.c_str());
+                                       return 0; 
+                               }
+                               
                                for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
                                        
                                        if (seqs[i].seq1 != seqs[i].seq2) {
                
                                                hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+                                               
+                                               if (m->control_pressed) { 
+                                                       delete nameMap;  delete list; delete rabund; delete hcluster;
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       remove(distFile.c_str());
+                                                       remove(overlapFile.c_str());
+                                                       return 0; 
+                                               }
        
                                                float rndDist = roundDist(seqs[i].dist, precision);
                                                                                                
@@ -276,6 +339,15 @@ int MGClusterCommand::execute(){
                                                        if (merge) {
                                                                map<string, int> seq2Bin = hcluster->getSeqtoBin();
                                                                ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+                                                               
+                                                               if (m->control_pressed) { 
+                                                                       delete nameMap;  delete list; delete rabund; delete hcluster; delete temp;
+                                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                                       remove(distFile.c_str());
+                                                                       remove(overlapFile.c_str());
+                                                                       return 0; 
+                                                               }
+
                                                                temp->setLabel(toString(rndPreviousDist,  precisionLength-1));
                                                                printData(temp);
                                                                delete temp;
@@ -301,6 +373,15 @@ int MGClusterCommand::execute(){
                                if (merge) {
                                        map<string, int> seq2Bin = hcluster->getSeqtoBin();
                                        ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+                                       
+                                       if (m->control_pressed) { 
+                                                       delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       remove(distFile.c_str());
+                                                       remove(overlapFile.c_str());
+                                                       return 0; 
+                                       }
+                                       
                                        temp->setLabel(toString(rndPreviousDist,  precisionLength-1));
                                        printData(temp);
                                        delete temp;
@@ -324,6 +405,14 @@ int MGClusterCommand::execute(){
                globaldata->setListFile(fileroot+ tag + ".list");
                globaldata->setFormat("list");
                
+               if (m->control_pressed) { 
+                       delete nameMap; 
+                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                       globaldata->setListFile("");
+                       globaldata->setFormat("");
+                       return 0; 
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine();   
@@ -373,6 +462,10 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
                }else { if (overlapMatrix.size() == 0)  {  done = true;  } } 
                
                while (!done) {
+                       if (m->control_pressed) { 
+                               if (hclusterWanted) {   inOverlap.close();  }           
+                               return newList;
+                       }
                        
                        //get next overlap
                        seqDist overlapNode;