working on mgcluster count file change

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 2542431f111f85b5bc344d93388662364045a509..888f50202e3443855a99d82d71b126cf715ee380 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;
@@ -442,7 +462,7 @@ int TreeGroupCommand::execute(){
                        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);
@@ -570,13 +590,6 @@ vector< vector<double> > TreeGroupCommand::makeSimsDist() {
 int TreeGroupCommand::makeSimsShared() {
        try {
         
-        numGroups = lookup.size();
-               lines.resize(processors);
-               for (int i = 0; i < processors; i++) {
-                       lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
-                       lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
-               }       
-        
         if (subsample) { 
             if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
                 subsampleSize = lookup[0]->getNumSeqs();
@@ -601,8 +614,17 @@ int TreeGroupCommand::makeSimsShared() {
                 lookup = temp;
                 m->setGroups(Groups);
             }
+            
+            if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
         }
         
+        numGroups = lookup.size();
+               lines.resize(processors);
+               for (int i = 0; i < processors; i++) {
+                       lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
+                       lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
+               }       
+        
                set<string> processedLabels;
                set<string> userLabels = labels;
                
@@ -894,7 +916,7 @@ 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
@@ -907,7 +929,7 @@ 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;
@@ -948,7 +970,7 @@ 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);
@@ -976,7 +998,7 @@ 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