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added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...
[mothur.git] / unifracweightedcommand.cpp
diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index a4a1bc3defc98beb608b38645471e46541a0b10f..d1e883382890081495dac72238cd05b3c5ad644e 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -24,7 +24,7 @@ vector<string> UnifracWeightedCommand::setParameters(){
         CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
         CommandParameter pconsensus("consensus", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pconsensus);
         CommandParameter prandom("random", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prandom);
-               CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(pdistance);
+               CommandParameter pdistance("distance", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(pdistance);
                CommandParameter proot("root", "Boolean", "F", "", "", "", "",false,false); parameters.push_back(proot);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -64,6 +64,30 @@ string UnifracWeightedCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string UnifracWeightedCommand::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 == "weighted")            {   outputFileName =  "weighted";   }
+            else if (type == "wsummary")        {   outputFileName =  "wsummary";   }
+            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, "UnifracWeightedCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 UnifracWeightedCommand::UnifracWeightedCommand(){      
        try {
                abort = true; calledHelp = true; 
@@ -180,6 +204,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        string temp = validParameter.validFile(parameters, "distance", false);                  
                        if (temp == "not found") { phylip = false; outputForm = ""; }
                        else{
+                if (temp=="phylip") { temp = "lt"; }
                                if ((temp == "lt") || (temp == "column") || (temp == "square")) {  phylip = true;  outputForm = temp; }
                                else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
                        }
@@ -237,11 +262,12 @@ int UnifracWeightedCommand::execute() {
         T = reader->getTrees();
         tmap = T[0]->getTreeMap();
         map<string, string> nameMap = reader->getNames();
+        map<string, string> unique2Dup = reader->getNameMap();
         delete reader;
     
         if (m->control_pressed) {  delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; }
                                
-               sumFile = outputDir + m->getSimpleName(treefile) + ".wsummary";
+               sumFile = outputDir + m->getSimpleName(treefile) + getOutputFileNameTag("wsummary");
                m->openOutputFile(sumFile, outSum);
                outputNames.push_back(sumFile);  outputTypes["wsummary"].push_back(sumFile);
                
@@ -305,9 +331,9 @@ int UnifracWeightedCommand::execute() {
             vector<double> randomData; randomData.resize(numComp,0); //weighted score info for random trees. data[0] = weightedscore AB, data[1] = weightedscore AC...
             
             if (random) {  
-                output = new ColumnFile(outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".weighted", itersString);  
-                outputNames.push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".weighted");
-                outputTypes["weighted"].push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".weighted");
+                output = new ColumnFile(outputDir + m->getSimpleName(treefile)  + toString(i+1) + "." + getOutputFileNameTag("weighted"), itersString);  
+                outputNames.push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + "." + getOutputFileNameTag("weighted"));
+                outputTypes["weighted"].push_back(outputDir + m->getSimpleName(treefile)  + toString(i+1) + "." + getOutputFileNameTag("weighted"));
             } 
             
             userData = weighted.getValues(T[i], processors, outputDir); //userData[0] = weightedscore
@@ -336,11 +362,15 @@ int UnifracWeightedCommand::execute() {
                 
                 //copy to preserve old one - would do this in subsample but memory cleanup becomes messy.
                 TreeMap* newTmap = new TreeMap();
-                newTmap->getCopy(*tmap);
+                //newTmap->getCopy(*tmap);
+                
+                //SubSample sample;
+               //Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
                 
+                //uses method of setting groups to doNotIncludeMe
                 SubSample sample;
-                Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
-                   
+                Tree* subSampleTree = sample.getSample(T[i], tmap, newTmap, subsampleSize, unique2Dup);
+
                 //call new weighted function
                 vector<double> iterData; iterData.resize(numComp,0);
                 Weighted thisWeighted(includeRoot);
@@ -456,15 +486,15 @@ int UnifracWeightedCommand::getAverageSTDMatrices(vector< vector<double> >& dist
             }
         }
         
-        string aveFileName = outputDir + m->getSimpleName(treefile)  + toString(treeNum+1) + ".weighted.ave.dist";
-        outputNames.push_back(aveFileName); outputTypes["phylip"].push_back(aveFileName); 
-        
+        string aveFileName = outputDir + m->getSimpleName(treefile)  + toString(treeNum+1) + ".weighted.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) + ".weighted.std.dist";
-       outputNames.push_back(stdFileName); outputTypes["phylip"].push_back(stdFileName); 
-        
+        string stdFileName = outputDir + m->getSimpleName(treefile)  + toString(treeNum+1) + ".weighted.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);
         
@@ -545,7 +575,7 @@ int UnifracWeightedCommand::getConsensusTrees(vector< vector<double> >& dists, i
         Tree* conTree = con.getTree(newTrees);
         
         //create a new filename
-        string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.cons.tre";                          
+        string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.cons." + getOutputFileNameTag("tree");                              
         outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile); 
         ofstream outTree;
         m->openOutputFile(conFile, outTree);
@@ -569,7 +599,7 @@ vector<Tree*> UnifracWeightedCommand::buildTrees(vector< vector<double> >& dists
         vector<Tree*> trees;
         
         //create a new filename
-        string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.all.tre";                                
+        string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.all." + getOutputFileNameTag("tree");                            
         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
         
         ofstream outAll;
@@ -660,7 +690,7 @@ int UnifracWeightedCommand::runRandomCalcs(Tree* thisTree, vector<double> usersS
                 createProcesses(thisTree,  namesOfGroupCombos, rScores);
             }
 #else
-            driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
+            driver(thisTree, namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
 #endif
             
             if (m->control_pressed) { delete tmap;  for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } return 0; }
@@ -880,10 +910,10 @@ void UnifracWeightedCommand::createPhylipFile() {
                
                        string phylipFileName;
                        if ((outputForm == "lt") || (outputForm == "square")) {
-                               phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".weighted.phylip.dist";
+                               phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".weighted.phylip." + getOutputFileNameTag("phylip");
                                outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
                        }else { //column
-                               phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".weighted.column.dist";
+                               phylipFileName = outputDir + m->getSimpleName(treefile)  + toString(i+1) + ".weighted.column." + getOutputFileNameTag("column");
                                outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); 
                        }
                        
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