paralellized phylo.diversity

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 0c937f62c83a5a1b1cac914c1a2e01b356dddc03..c0b8248e58981473b1f7bf70709863c36c68992b 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -79,7 +79,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -94,12 +94,12 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                        }
                        globaldata->Groups = Groups;
                        
@@ -108,12 +108,12 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        convert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "false"; }
-                       all = isTrue(temp);
+                       all = m->isTrue(temp);
                                                
                        if (abort == false) {
                                
-                               if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
-                               string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+                               if (outputDir == "") { outputDir += m->hasPath(globaldata->inputFileName); }
+                               string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
                                format = globaldata->getFormat();
                                int i;
                                
@@ -208,6 +208,7 @@ void CollectSharedCommand::help(){
                m->mothurOut("Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
                m->mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
                m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+               m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
                validCalculator->printCalc("shared", cout);
                m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
                m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
@@ -261,32 +262,39 @@ int CollectSharedCommand::execute(){
                util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
                while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+                       if (m->control_pressed) { 
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  
+                                       for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
+                                       delete order; 
+                                       globaldata->Groups.clear();
+                                       return 0;
+                       }
 
                        if(allLines == 1 || labels.count(order->getLabel()) == 1){
-                               
+                       
+                               m->mothurOut(order->getLabel()); m->mothurOutEndLine();
                                //create collectors curve
                                cCurve = new Collect(order, cDisplays);
                                cCurve->getSharedCurve(freq);
                                delete cCurve;
                        
-                               m->mothurOut(order->getLabel()); m->mothurOutEndLine();
                                processedLabels.insert(order->getLabel());
                                userLabels.erase(order->getLabel());
                        }
                        
                        //you have a label the user want that is smaller than this label and the last label has not already been processed
-                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = order->getLabel();
                                
                                delete order;
                                order = input->getSharedOrderVector(lastLabel);
                                
+                               m->mothurOut(order->getLabel()); m->mothurOutEndLine();
                                //create collectors curve
                                cCurve = new Collect(order, cDisplays);
                                cCurve->getSharedCurve(freq);
                                delete cCurve;
-                       
-                               m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+                               
                                processedLabels.insert(order->getLabel());
                                userLabels.erase(order->getLabel());
                                
@@ -302,6 +310,13 @@ int CollectSharedCommand::execute(){
                        order = input->getSharedOrderVector();
                }
                
+               if (m->control_pressed) { 
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  
+                                       for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
+                                       globaldata->Groups.clear();
+                                       return 0;
+               }
+               
                //output error messages about any remaining user labels
                set<string>::iterator it;
                bool needToRun = false;
@@ -319,12 +334,20 @@ int CollectSharedCommand::execute(){
                if (needToRun == true)  {
                        if (order != NULL) {  delete order;  }
                        order = input->getSharedOrderVector(lastLabel);
-
+                       
+                       m->mothurOut(order->getLabel()); m->mothurOutEndLine();
                        cCurve = new Collect(order, cDisplays);
                        cCurve->getSharedCurve(freq);
                        delete cCurve;
                        
-                       m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+                       if (m->control_pressed) { 
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  
+                               for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
+                               delete order; 
+                               globaldata->Groups.clear();
+                               return 0;
+                       }
+
                        delete order;
                }