adding mothurout.h and .cpp to repo

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index b44ce4b15d8f4121db33d12285616da1c8fde8f7..6b76918044201a7438413c0f695f83c141d5638f 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -223,7 +223,8 @@ int BootSharedCommand::execute(){
                        if(allLines == 1 || labels.count(order->getLabel()) == 1){                      
                                
                                m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                               process(order);
+                               int error = process(order);
+                               if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); return 0;        } 
                                
                                processedLabels.insert(order->getLabel());
                                userLabels.erase(order->getLabel());
@@ -236,7 +237,8 @@ int BootSharedCommand::execute(){
                                delete order;
                                order = input->getSharedOrderVector(lastLabel);                                                                                                 
                                m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                               process(order);
+                               int error = process(order);
+                               if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); return 0;        } 
 
                                processedLabels.insert(order->getLabel());
                                userLabels.erase(order->getLabel());
@@ -271,7 +273,9 @@ int BootSharedCommand::execute(){
                                if (order != NULL) {    delete order;   }
                                order = input->getSharedOrderVector(lastLabel);                                                                                                 
                                m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                               process(order);
+                               int error = process(order);
+                               if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); return 0;        } 
+                               
                                delete order;
 
                }
@@ -294,13 +298,15 @@ int BootSharedCommand::execute(){
 }
 //**********************************************************************************************************************
 
-void BootSharedCommand::createTree(ostream* out, Tree* t){
+int BootSharedCommand::createTree(ostream* out, Tree* t){
        try {
                
                //do merges and create tree structure by setting parents and children
                //there are numGroups - 1 merges to do
                for (int i = 0; i < (numGroups - 1); i++) {
                
+                       if (m->control_pressed) {  return 1; }
+               
                        float largest = -1000.0;
                        int row, column;
                        //find largest value in sims matrix by searching lower triangle
@@ -357,6 +363,8 @@ void BootSharedCommand::createTree(ostream* out, Tree* t){
        
                //print newick file
                t->print(*out);
+               
+               return 0;
        
        }
        catch(exception& e) {
@@ -382,7 +390,7 @@ void BootSharedCommand::printSims() {
        }
 }
 /***********************************************************/
-void BootSharedCommand::process(SharedOrderVector* order) {
+int BootSharedCommand::process(SharedOrderVector* order) {
        try{
                                EstOutput data;
                                vector<SharedRAbundVector*> subset;
@@ -400,18 +408,22 @@ void BootSharedCommand::process(SharedOrderVector* order) {
                                //create a file for each calculator with the 1000 trees in it.
                                for (int p = 0; p < iters; p++) {
                                        
+                                       if (m->control_pressed) {  return 1; }
+                                       
                                        util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order);  //fills group vectors from order vector.
 
                                
                                        //for each calculator                                                                                           
                                        for(int i = 0 ; i < treeCalculators.size(); i++) {
-                                       
+                                               
+                                               if (m->control_pressed) {  return 1; }
+                                               
                                                //initialize simMatrix
                                                simMatrix.clear();
                                                simMatrix.resize(numGroups);
-                                               for (int m = 0; m < simMatrix.size(); m++)      {
+                                               for (int o = 0; o < simMatrix.size(); o++)      {
                                                        for (int j = 0; j < simMatrix.size(); j++)      {
-                                                               simMatrix[m].push_back(0.0);
+                                                               simMatrix[o].push_back(0.0);
                                                        }
                                                }
                                
@@ -437,6 +449,8 @@ void BootSharedCommand::process(SharedOrderVector* order) {
                                                
                                                tempTree = new Tree();
                                                
+                                               if (m->control_pressed) {   delete tempTree; return 1; }
+                                               
                                                //creates tree from similarity matrix and write out file
                                                createTree(out[i], tempTree);
                                                
@@ -456,6 +470,8 @@ void BootSharedCommand::process(SharedOrderVector* order) {
                                        
                                        m->mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); m->mothurOutEndLine();
                                        
+                                       if (m->control_pressed) {  return 1; }
+                                       
                                        //set global data to calc trees
                                        globaldata->gTree = trees[k];
                                        
@@ -477,6 +493,8 @@ void BootSharedCommand::process(SharedOrderVector* order) {
                                        
                                //close ostream for each calc
                                for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
+                               
+                               return 0;
        
        }
        catch(exception& e) {