added SequenceCountParser class to parse the count table by group. added count parame...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index c26199d673088b5b64872b672ab8e64ca780e616..6633e5160559297c23a542c373ed1b1cc9a3ccdc 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -70,6 +70,26 @@ string TreeGroupCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string TreeGroupCommand::getOutputFileNameTag(string type, string inputName=""){       
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "tree")            {   outputFileName =  "tre";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TreeGroupCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 TreeGroupCommand::TreeGroupCommand(){  
        try {
                abort = true; calledHelp = true;
@@ -266,7 +286,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 TreeGroupCommand::~TreeGroupCommand(){
        if (abort == false) {
                if (format == "sharedfile") {  delete input; }
-               else { delete readMatrix;  delete matrix; delete list; }
+               else { delete list; }
                delete tmap;  
        }
        
@@ -398,7 +418,8 @@ int TreeGroupCommand::execute(){
                }else{
                        //read in dist file
                        filename = inputfile;
-               
+            
+            ReadMatrix* readMatrix;
                        if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }        
                        else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
                                
@@ -414,7 +435,7 @@ int TreeGroupCommand::execute(){
        
                        readMatrix->read(nameMap);
                        list = readMatrix->getListVector();
-                       matrix = readMatrix->getMatrix();
+                       SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
 
                        //make treemap
                        tmap = new TreeMap();
@@ -437,12 +458,14 @@ int TreeGroupCommand::execute(){
                        
                        if (m->control_pressed) { return 0; }
                        
-                       vector< vector<double> > matrix = makeSimsDist();
+                       vector< vector<double> > matrix = makeSimsDist(dMatrix);
+            delete readMatrix;
+            delete dMatrix;
                        
                        if (m->control_pressed) { return 0; }
 
                        //create a new filename
-                       string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "tre";    
+                       string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("tree");     
                        outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
                                
                        Tree* newTree = createTree(matrix);
@@ -534,7 +557,7 @@ void TreeGroupCommand::printSims(ostream& out, vector< vector<double> >& simMatr
        }
 }
 /***********************************************************/
-vector< vector<double> > TreeGroupCommand::makeSimsDist() {
+vector< vector<double> > TreeGroupCommand::makeSimsDist(SparseDistanceMatrix* matrix) {
        try {
                numGroups = list->size();
                
@@ -549,13 +572,17 @@ vector< vector<double> > TreeGroupCommand::makeSimsDist() {
                
                //go through sparse matrix and fill sims
                //go through each cell in the sparsematrix
-               for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
-                       //similairity = -(distance-1)
-                       simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);   
-                       simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);   
-                       
-                       if (m->control_pressed) { return simMatrix; }
+        for (int i = 0; i < matrix->seqVec.size(); i++) {
+            for (int j = 0; j < matrix->seqVec[i].size(); j++) {
+                
+                //already checked everyone else in row
+                if (i < matrix->seqVec[i][j].index) {   
+                    simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0);      
+                    simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].dist -1.0);      
                        
+                    if (m->control_pressed) { return simMatrix; }
+                }
+            }
                }
 
                return simMatrix;
@@ -896,7 +923,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 }
                 
                 //create a new filename
-                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave.tre";                            
+                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave." + getOutputFileNameTag("tree");                                
                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
                 
                 //creates tree from similarity matrix and write out file
@@ -909,7 +936,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 if (m->control_pressed) { break; }
                 
                 //create a new filename
-                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all.tre";                            
+                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all." + getOutputFileNameTag("tree");                                
                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
                 
                 ofstream outAll;
@@ -950,7 +977,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 Tree* conTree = consensus.getTree(trees);
                 
                 //create a new filename
-                string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons.tre";                              
+                string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons." + getOutputFileNameTag("tree");                          
                 outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile); 
                 ofstream outTree;
                 m->openOutputFile(conFile, outTree);
@@ -978,7 +1005,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 }
                 
                 //create a new filename
-                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";                                
+                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag("tree");                            
                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
                 
                 //creates tree from similarity matrix and write out file