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

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 2f6f810e0add659c6c661cef7e383fd36b2f8ad2..4967f245fb11c2ff37195a83baf39d29667fc582 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -95,6 +95,27 @@ string GetOTURepCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string GetOTURepCommand::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 == "fasta")            {   outputFileName =  "rep.fasta";   }
+            else if (type == "name")        {   outputFileName =  "rep.names";   }
+            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, "GetOTURepCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetOTURepCommand::GetOTURepCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -297,10 +318,10 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        if ((weighted) && (namefile == "")) { m->mothurOut("You cannot set weighted to true unless you provide a namesfile."); m->mothurOutEndLine(); abort = true; }
                        
                        temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
                }
        }
@@ -338,16 +359,19 @@ int GetOTURepCommand::execute(){
 
                        list = readMatrix->getListVector();
 
-                       SparseMatrix* matrix = readMatrix->getMatrix();
+                       SparseDistanceMatrix* matrix = readMatrix->getDMatrix();
                        
                        // Create a data structure to quickly access the distance information.
                        // It consists of a vector of distance maps, where each map contains
                        // all distances of a certain sequence. Vector and maps are accessed
                        // via the index of a sequence in the distance matrix
                        seqVec = vector<SeqMap>(list->size()); 
-                       for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) {
-                               if (m->control_pressed) { delete readMatrix; return 0; }
-                               seqVec[currentCell->row][currentCell->column] = currentCell->dist;
+            for (int i = 0; i < matrix->seqVec.size(); i++) {
+                for (int j = 0; j < matrix->seqVec[i].size(); j++) {
+                    if (m->control_pressed) { delete readMatrix; return 0; }
+                    //already added everyone else in row
+                    if (i < matrix->seqVec[i][j].index) {  seqVec[i][matrix->seqVec[i][j].index] = matrix->seqVec[i][j].dist;  }
+                }
                        }
                        //add dummy map for unweighted calc
                        SeqMap dummy;
@@ -771,7 +795,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                map<string, ofstream*> filehandles;
                
                if (Groups.size() == 0) { //you don't want to use groups
-                       outputNamesFile  = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
+                       outputNamesFile  = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + getOutputFileNameTag("name");
                        m->openOutputFile(outputNamesFile, newNamesOutput);
                        outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); 
                        outputNameFiles[outputNamesFile] = processList->getLabel();
@@ -780,7 +804,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                        for (int i=0; i<Groups.size(); i++) {
                                temp = new ofstream;
                                filehandles[Groups[i]] = temp;
-                               outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
+                               outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + "." + getOutputFileNameTag("name");
                                
                                m->openOutputFile(outputNamesFile, *(temp));
                                outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile);
@@ -868,7 +892,7 @@ int GetOTURepCommand::processFastaNames(string filename, string label) {
 
                //create output file
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + ".rep.fasta";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("fasta");
                m->openOutputFile(outputFileName, out);
                vector<repStruct> reps;
                outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);