sffinfo command is working

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index d8da50e0d2f559f25657008d046e7ec6951c4552..88be43b9a283b3313eacb6093ffe4f496c6bc452 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -110,6 +110,7 @@ void CollectCommand::help(){
                m->mothurOut("The collect.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
                m->mothurOut("The collect.single command parameters are label, freq, calc and abund.  No parameters are required. \n");
                m->mothurOut("The collect.single command should be in the following format: \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");
                m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
                m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
                m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
@@ -140,7 +141,9 @@ int CollectCommand::execute(){
                else {  inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
        
                for (int p = 0; p < inputFileNames.size(); p++) {
-               
+                       
+                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         }  globaldata->Groups.clear(); return 0; }
+                       
                        if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
                        string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
                        globaldata->inputFileName = inputFileNames[p];
@@ -230,16 +233,40 @@ int CollectCommand::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) {  
+                               for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                               delete input;  globaldata->ginput = NULL;
+                               delete read;
+                               delete order; globaldata->gorder = NULL;
+                               delete validCalculator;
+                               globaldata->Groups.clear();
+                               return 0;
+                       }
+
 
                        while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+                       
+                               if (m->control_pressed) { 
+                                       for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                                       delete input;  globaldata->ginput = NULL;
+                                       delete read;
+                                       delete order; globaldata->gorder = NULL;
+                                       delete validCalculator;
+                                       globaldata->Groups.clear();
+                                       return 0;
+                               }
+
                                
                                if(allLines == 1 || labels.count(order->getLabel()) == 1){
-                                       
+                               
+                                       m->mothurOut(order->getLabel()); m->mothurOutEndLine();
                                        cCurve = new Collect(order, cDisplays);
                                        cCurve->getCurve(freq);
                                        delete cCurve;
                                        
-                                       m->mothurOut(order->getLabel()); m->mothurOutEndLine();
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
                                        
@@ -252,11 +279,12 @@ int CollectCommand::execute(){
                                        delete order;
                                        order = (input->getOrderVector(lastLabel));
                                        
+                                       m->mothurOut(order->getLabel()); m->mothurOutEndLine();
                                        cCurve = new Collect(order, cDisplays);
                                        cCurve->getCurve(freq);
                                        delete cCurve;
                                        
-                                       m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+                                       
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
                                        
@@ -270,6 +298,17 @@ int CollectCommand::execute(){
                                order = (input->getOrderVector());
                        }
                        
+                       
+                       if (m->control_pressed) { 
+                                       for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                                       delete input;  globaldata->ginput = NULL;
+                                       delete read;
+                                       delete validCalculator;
+                                       globaldata->Groups.clear();
+                                       return 0;
+                       }
+                               
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
                        bool needToRun = false;
@@ -293,6 +332,17 @@ int CollectCommand::execute(){
                                cCurve = new Collect(order, cDisplays);
                                cCurve->getCurve(freq);
                                delete cCurve;
+                               
+                               if (m->control_pressed) { 
+                                       for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                                       delete input;  globaldata->ginput = NULL;
+                                       delete read;
+                                       delete order; globaldata->gorder = NULL;
+                                       delete validCalculator;
+                                       globaldata->Groups.clear();
+                                       return 0;
+                               }
                                delete order;
                        }
                        
@@ -304,6 +354,8 @@ int CollectCommand::execute(){
                        delete validCalculator;
                }
                
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } 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();    }