added get.otus and remove.otus commands

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index df73c9389b99b7ba18725d418d62b36184efa398..4ded9c51d399de1bf07950da88e0cb3a19e333d0 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -30,6 +30,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(){
                outputTypes["weighted"] = tempOutNames;
                outputTypes["wsummary"] = tempOutNames;
                outputTypes["phylip"] = tempOutNames;
+               outputTypes["column"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
@@ -90,6 +91,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        outputTypes["weighted"] = tempOutNames;
                        outputTypes["wsummary"] = tempOutNames;
                        outputTypes["phylip"] = tempOutNames;
+                       outputTypes["column"] = tempOutNames;
                        
                        if (globaldata->gTree.size() == 0) {//no trees were read
                                m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true;  }
@@ -112,9 +114,13 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
                        convert(itersString, iters); 
                        
-                       string temp = validParameter.validFile(parameters, "distance", false);                  if (temp == "not found") { temp = "false"; }
-                       phylip = m->isTrue(temp);
-               
+                       string temp = validParameter.validFile(parameters, "distance", false);                  
+                       if (temp == "not found") { phylip = false; outputForm = ""; }
+                       else{
+                               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"; }
+                       }
+                       
                        temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "F"; }
                        random = m->isTrue(temp);
                        
@@ -497,15 +503,23 @@ void UnifracWeightedCommand::createPhylipFile() {
                //for each tree
                for (int i = 0; i < T.size(); i++) { 
                
-                       string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
-                       outputNames.push_back(phylipFileName);
-                       outputTypes["phylip"].push_back(phylipFileName);
+                       string phylipFileName;
+                       if ((outputForm == "lt") || (outputForm == "square")) {
+                               phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.phylip.dist";
+                               outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
+                       }else { //column
+                               phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.column.dist";
+                               outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); 
+                       }
+                       
                        ofstream out;
                        m->openOutputFile(phylipFileName, out);
                        
-                       //output numSeqs
-                       out << globaldata->Groups.size() << endl;
-                       
+                       if ((outputForm == "lt") || (outputForm == "square")) {
+                               //output numSeqs
+                               out << globaldata->Groups.size() << endl;
+                       }
+
                        //make matrix with scores in it
                        vector< vector<float> > dists;  dists.resize(globaldata->Groups.size());
                        for (int i = 0; i < globaldata->Groups.size(); i++) {
@@ -528,11 +542,30 @@ void UnifracWeightedCommand::createPhylipFile() {
                                if (name.length() < 10) { //pad with spaces to make compatible
                                        while (name.length() < 10) {  name += " ";  }
                                }
-                               out << name << '\t';
                                
-                               //output distances
-                               for (int l = 0; l < r; l++) {   out  << dists[r][l] << '\t';  }
-                               out << endl;
+                               if (outputForm == "lt") {
+                                       out << name << '\t';
+                                       
+                                       //output distances
+                                       for (int l = 0; l < r; l++) {   out  << dists[r][l] << '\t';  }
+                                       out << endl;
+                               }else if (outputForm == "square") {
+                                       out << name << '\t';
+                                       
+                                       //output distances
+                                       for (int l = 0; l < globaldata->Groups.size(); l++) {   out  << dists[r][l] << '\t';  }
+                                       out << endl;
+                               }else{
+                                       //output distances
+                                       for (int l = 0; l < r; l++) {   
+                                               string otherName = globaldata->Groups[l];
+                                               if (otherName.length() < 10) { //pad with spaces to make compatible
+                                                       while (otherName.length() < 10) {  otherName += " ";  }
+                                               }
+                                               
+                                               out  << name << '\t' << otherName << dists[r][l] << endl;  
+                                       }
+                               }
                        }
                        out.close();
                }