added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 318409fa8845f91fcaae0765a6f930626299e82d..0650ea0e8e42e564213d285183e48594f54fc722 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -63,6 +63,31 @@ string UnifracUnweightedCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string UnifracUnweightedCommand::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 == "unweighted")            {   outputFileName =  "unweighted";   }
+            else if (type == "uwsummary")        {   outputFileName =  "uwsummary";   }
+            else if (type == "phylip")           {   outputFileName =  "dist";   }
+            else if (type == "column")           {   outputFileName =  "dist";   }
+            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, "UnifracUnweightedCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 UnifracUnweightedCommand::UnifracUnweightedCommand(){  
        try {
@@ -248,7 +273,7 @@ int UnifracUnweightedCommand::execute() {
         map<string, string> unique2Dup = reader->getNameMap();
         delete reader; 
         
-               sumFile = outputDir + m->getSimpleName(treefile) + ".uwsummary";
+               sumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("uwsummary");
                outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
                m->openOutputFile(sumFile, outSum);
                
@@ -309,9 +334,9 @@ int UnifracUnweightedCommand::execute() {
             counter = 0;
                        
                        if (random)  {  
-                               output = new ColumnFile(outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted", itersString);
-                               outputNames.push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted");
-                               outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted");
+                               output = new ColumnFile(outputDir + m->getSimpleName(treefile)  + toString(i+1) + "." + getOutputFileNameTag("unweighted"), itersString);
+                               outputNames.push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + "." + getOutputFileNameTag("unweighted"));
+                               outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + "." + getOutputFileNameTag("unweighted"));
                        }
                        
                        
@@ -480,15 +505,15 @@ int UnifracUnweightedCommand::getAverageSTDMatrices(vector< vector<double> >& di
             }
         }
         
-        string aveFileName = outputDir + m->getSimpleName(treefile)  + toString(treeNum+1) + ".unweighted.ave.dist";
-        outputNames.push_back(aveFileName); outputTypes["phylip"].push_back(aveFileName); 
-        
+        string aveFileName = outputDir + m->getSimpleName(treefile)  + toString(treeNum+1) + ".unweighted.ave." + getOutputFileNameTag("phylip");
+        if (outputForm != "column") { outputNames.push_back(aveFileName); outputTypes["phylip"].push_back(aveFileName);  }
+        else { outputNames.push_back(aveFileName); outputTypes["column"].push_back(aveFileName);  }
         ofstream out;
         m->openOutputFile(aveFileName, out);
         
-        string stdFileName = outputDir + m->getSimpleName(treefile)  + toString(treeNum+1) + ".unweighted.std.dist";
-        outputNames.push_back(stdFileName); outputTypes["phylip"].push_back(stdFileName); 
-        
+        string stdFileName = outputDir + m->getSimpleName(treefile)  + toString(treeNum+1) + ".unweighted.std." + getOutputFileNameTag("phylip");
+        if (outputForm != "column") { outputNames.push_back(stdFileName); outputTypes["phylip"].push_back(stdFileName); }
+        else { outputNames.push_back(stdFileName); outputTypes["column"].push_back(stdFileName); }
         ofstream outStd;
         m->openOutputFile(stdFileName, outStd);
         
@@ -569,7 +594,7 @@ int UnifracUnweightedCommand::getConsensusTrees(vector< vector<double> >& dists,
         Tree* conTree = con.getTree(newTrees);
         
         //create a new filename
-        string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.cons.tre";                                
+        string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.cons." + getOutputFileNameTag("tree");                            
         outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile); 
         ofstream outTree;
         m->openOutputFile(conFile, outTree);
@@ -593,7 +618,7 @@ vector<Tree*> UnifracUnweightedCommand::buildTrees(vector< vector<double> >& dis
         vector<Tree*> trees;
         
         //create a new filename
-        string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.all.tre";                              
+        string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.all." + getOutputFileNameTag("tree");                          
         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
         
         ofstream outAll;
@@ -761,10 +786,10 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
        try {
                string phylipFileName;
                if ((outputForm == "lt") || (outputForm == "square")) {
-                       phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted.phylip.dist";
+                       phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted.phylip." + getOutputFileNameTag("phylip");
                        outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
                }else { //column
-                       phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted.column.dist";
+                       phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".unweighted.column." + getOutputFileNameTag("column");
                        outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); 
                }