added get.repseqs command, started matrix output command

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index ac82da5e558d2965829de82f170b1514c8972c84..43e39f52d6447384133c1c566bfa1fcfe9c7179e 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -27,8 +27,7 @@ TreeGroupCommand::TreeGroupCommand(){
                globaldata = GlobalData::getInstance();
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
-               util = new SharedUtil();
-               
+                       
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
                        if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) { 
@@ -74,7 +73,6 @@ TreeGroupCommand::TreeGroupCommand(){
 TreeGroupCommand::~TreeGroupCommand(){
        delete input;
        delete read;
-       delete util;
 }
 
 //**********************************************************************************************************************
@@ -95,7 +93,7 @@ int TreeGroupCommand::execute(){
                input = globaldata->ginput;
                lookup = input->getSharedRAbundVectors();
                                
-               if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; }
+               if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0; }
                
                numGroups = globaldata->Groups.size();
                groupNames = "";
@@ -136,7 +134,8 @@ int TreeGroupCommand::execute(){
                
                                        //create a new filename
                                        outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
-                                                       
+                                       
+                                                                                               
                                        for (int k = 0; k < lookup.size(); k++) { 
                                                for (int l = k; l < lookup.size(); l++) {
                                                        if (k != l) { //we dont need to similiarity of a groups to itself
@@ -158,7 +157,10 @@ int TreeGroupCommand::execute(){
                                        createTree();
                                }
                        }
-               
+                       
+                       //prevent memory leak
+                       for (int i = 0; i < lookup.size(); i++) {       delete lookup[i];       }
+                       
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();
                        count++;
@@ -256,14 +258,21 @@ void TreeGroupCommand::createTree(){
        }
 }
 /***********************************************************/
-void TreeGroupCommand::printSims() {
+void TreeGroupCommand::printSims(ostream& out) {
        try {
-               cout << "simsMatrix" << endl;
+               
+               //output column headers
+               out << '\t';
+               for (int i = 0; i < lookup.size(); i++) {       out << lookup[i]->getGroup() << '\t';           }
+               out << endl;
+               
+               
                for (int m = 0; m < simMatrix.size(); m++)      {
+                       out << lookup[m]->getGroup() << '\t';
                        for (int n = 0; n < simMatrix.size(); n++)      {
-                               cout << simMatrix[m][n] << '\t'; 
+                               out << simMatrix[m][n] << '\t'; 
                        }
-                       cout << endl;
+                       out << endl;
                }
 
        }