added pipeline commands which involved change to command factory and command class...

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index e8add90a259bac0da04bf2b8d52be247e9fc1fd1..9f961a9a6658683a3661290757ebe01048002371 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -9,6 +9,56 @@
 
 #include "unifracweightedcommand.h"
 
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::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, "UnifracWeightedCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+UnifracWeightedCommand::UnifracWeightedCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["weighted"] = tempOutNames;
+               outputTypes["wsummary"] = tempOutNames;
+               outputTypes["phylip"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getRequiredParameters(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracWeightedCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getRequiredFiles(){     
+       try {
+               string Array[] =  {"tree","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracWeightedCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /***********************************************************/
 UnifracWeightedCommand::UnifracWeightedCommand(string option) {
        try {
@@ -34,6 +84,12 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["weighted"] = tempOutNames;
+                       outputTypes["wsummary"] = 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.weighted command."); m->mothurOutEndLine(); abort = true;  }
                        
@@ -72,7 +128,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                                tmap = globaldata->gTreemap;
                                sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".wsummary";
                                m->openOutputFile(sumFile, outSum);
-                               outputNames.push_back(sumFile);
+                               outputNames.push_back(sumFile);  outputTypes["wsummary"].push_back(sumFile);
                                
                                util = new SharedUtil();
                                string s; //to make work with setgroups
@@ -138,6 +194,7 @@ int UnifracWeightedCommand::execute() {
                        if (random) {  
                                output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted", itersString);  
                                outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted");
+                               outputTypes["weighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted");
                        } 
 
                        userData = weighted->getValues(T[i], processors, outputDir);  //userData[0] = weightedscore
@@ -438,6 +495,7 @@ void UnifracWeightedCommand::createPhylipFile() {
                
                        string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
                        outputNames.push_back(phylipFileName);
+                       outputTypes["phylip"].push_back(phylipFileName);
                        ofstream out;
                        m->openOutputFile(phylipFileName, out);