fixed cluster.split bug

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index a50d147de23d7cbc882be909e4a78870a867d4c3..24c7b548946a0715e49a7d3818142d50032691fc 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -9,6 +9,58 @@
 
 #include "unifracunweightedcommand.h"
 
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"groups","iters","distance","random", "processors","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+UnifracUnweightedCommand::UnifracUnweightedCommand(){  
+       try {
+               globaldata = GlobalData::getInstance();
+               abort = true;
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["unweighted"] = tempOutNames;
+               outputTypes["uwsummary"] = tempOutNames;
+               outputTypes["phylip"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredParameters(){      
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredFiles(){   
+       try {
+               string Array[] =  {"tree","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /***********************************************************/
 UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
        try {
@@ -34,6 +86,12 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["unweighted"] = tempOutNames;
+                       outputTypes["uwsummary"] = tempOutNames;
+                       outputTypes["phylip"] = 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;  }
                        
@@ -77,7 +135,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                                T = globaldata->gTree;
                                tmap = globaldata->gTreemap;
                                sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".uwsummary";
-                               outputNames.push_back(sumFile);
+                               outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
                                m->openOutputFile(sumFile, outSum);
                                
                                util = new SharedUtil();
@@ -104,11 +162,12 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 void UnifracUnweightedCommand::help(){
        try {
                m->mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
-               m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance and random.  No parameters are required.\n");
+               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 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");
                m->mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
                m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
@@ -150,6 +209,7 @@ int UnifracUnweightedCommand::execute() {
                        if (random)  {  
                                output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted", itersString);
                                outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
+                               outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
                        }
                        
                        
@@ -315,7 +375,7 @@ 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);
+               outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
                
                ofstream out;
                m->openOutputFile(phylipFileName, out);