X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=888f50202e3443855a99d82d71b126cf715ee380;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=3eeeae292e674dbc7823522ce8e35d8d531ab70e;hpb=f55cf350ca6643f8eb070d8336e1957699a3f109;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 3eeeae2..888f502 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -27,7 +27,7 @@ vector<string> TreeGroupCommand::setParameters(){
 		CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
 		
         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-        CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
+//CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 		
@@ -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