added get.otus and remove.otus commands

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 24c7b548946a0715e49a7d3818142d50032691fc..b80a3abb4bb76bd0a5da3afa5548df0771797e45 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -31,6 +31,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(){
                outputTypes["unweighted"] = tempOutNames;
                outputTypes["uwsummary"] = tempOutNames;
                outputTypes["phylip"] = tempOutNames;
+               outputTypes["column"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
@@ -91,6 +92,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        outputTypes["unweighted"] = tempOutNames;
                        outputTypes["uwsummary"] = 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.unweighted command."); m->mothurOutEndLine(); abort = true;  }
@@ -113,8 +115,12 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(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);
@@ -165,7 +171,7 @@ void UnifracUnweightedCommand::help(){
                m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance, processors and random.  No parameters are required.\n");
                m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group.\n");
                m->mothurOut("The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
-               m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
+               m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false. You may set distance to lt, square or column.\n");
                m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n");
                m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
                m->mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
@@ -374,15 +380,23 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) {
 /***********************************************************/
 void UnifracUnweightedCommand::createPhylipFile(int i) {
        try {
-               string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.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) + ".unweighted.phylip.dist";
+                       outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
+               }else { //column
+                       phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.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++) {
@@ -406,11 +420,30 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
                        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();
        }