change to phylo.diversity to make output = total branch length seen so far for each...

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 0c937f62c83a5a1b1cac914c1a2e01b356dddc03..40b911bb8c844ad252a714383ce93109772209a0 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -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");
@@ -261,15 +262,22 @@ 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());
                        }
@@ -281,12 +289,12 @@ int CollectSharedCommand::execute(){
                                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;
                }