fixed multiple bugs for 1.4 release

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 46055c0f6f9f428db22e258b9f4a28c060ac774f..d1d1be0bf4f21879e20429bc5e292273f1cda59a 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -42,7 +42,6 @@ SummarySharedCommand::SummarySharedCommand(){
                openOutputFile(outputFileName, outputFileHandle);
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
-               util = new SharedUtil();
                mult = false;
                
                int i;
@@ -111,7 +110,6 @@ SummarySharedCommand::SummarySharedCommand(){
 SummarySharedCommand::~SummarySharedCommand(){
        delete input;
        delete read;
-       delete util;
 }
 
 //**********************************************************************************************************************
@@ -119,7 +117,7 @@ SummarySharedCommand::~SummarySharedCommand(){
 int SummarySharedCommand::execute(){
        try {
                int count = 1;  
-               
+       
                //if the users entered no valid calculators don't execute command
                if (sumCalculators.size() == 0) { return 0; }
                //check if any calcs can do multiples
@@ -129,14 +127,12 @@ int SummarySharedCommand::execute(){
                        }
                }
                
+               //read first line
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
                        
                input = globaldata->ginput;
-               order = input->getSharedOrderVector();
-                               
-               //set users groups
-               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
+               lookup = input->getSharedRAbundVectors();
                
                //output estimator names as column headers
                outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
@@ -146,7 +142,7 @@ int SummarySharedCommand::execute(){
                outputFileHandle << endl;
                
                //create file and put column headers for multiple groups file
-               if (mult = true) {
+               if (mult == true) {
                        outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
                        openOutputFile(outAllFileName, outAll);
                        
@@ -159,17 +155,27 @@ int SummarySharedCommand::execute(){
                        outAll << endl;
                }
                
-               while(order != NULL){
+               if (lookup.size() < 2) { 
+                       cout << "I cannot run the command without at least 2 valid groups."; 
+                       for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+                       
+                       //close files and clean up
+                       outputFileHandle.close();  remove(outputFileName.c_str());
+                       if (mult == true) {  outAll.close();  remove(outAllFileName.c_str());  }
+                       return 0;
+               }
+                                       
+               
+               while(lookup[0] != NULL){
                
-                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
+                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){                   
        
-                               cout << order->getLabel() << '\t' << count << endl;
-                               util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.  //fills group vectors from order vector.
+                               cout << lookup[0]->getLabel() << '\t' << count << endl;
                                
                                //loop through calculators and add to file all for all calcs that can do mutiple groups
-                               if (mult = true) {
+                               if (mult == true) {
                                        //output label
-                                       outAll << order->getLabel() << '\t';
+                                       outAll << lookup[0]->getLabel() << '\t';
                                        
                                        //output groups names
                                        string outNames = "";
@@ -188,13 +194,13 @@ int SummarySharedCommand::execute(){
                                        }
                                        outAll << endl;
                                }
-
+       
                                int n = 1; 
                                vector<SharedRAbundVector*> subset;
                                for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
                                        for (int l = n; l < lookup.size(); l++) {
                                                
-                                               outputFileHandle << order->getLabel() << '\t';
+                                               outputFileHandle << lookup[0]->getLabel() << '\t';
                                                
                                                subset.clear(); //clear out old pair of sharedrabunds
                                                //add new pair of sharedrabunds
@@ -208,6 +214,7 @@ int SummarySharedCommand::execute(){
                                                }
                                                
                                                for(int i=0;i<sumCalculators.size();i++) {
+
                                                        sumCalculators[i]->getValues(subset); //saves the calculator outputs
                                                        outputFileHandle << '\t';
                                                        sumCalculators[i]->print(outputFileHandle);
@@ -218,13 +225,20 @@ int SummarySharedCommand::execute(){
                                }
                        }
                
+                       //prevent memory leak
+                       for (int i = 0; i < lookup.size(); i++) {       delete lookup[i];       }
+                               
                        //get next line to process
-                       order = input->getSharedOrderVector();
+                       lookup = input->getSharedRAbundVectors();
                        count++;
                }
                
                //reset groups parameter
                globaldata->Groups.clear();  globaldata->setGroups("");
+               
+               //close files
+               outputFileHandle.close();
+               if (mult == true) {  outAll.close();  }
 
                return 0;
        }