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

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 6e9e7b1525301a59c825c283a4de3607f338a25e..6198f139ccb117b157dea30fb31a5ef2330e1aae 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -9,6 +9,55 @@
 
 #include "phylodiversitycommand.h"
 
+//**********************************************************************************************************************
+vector<string> PhyloDiversityCommand::getValidParameters(){    
+       try {
+               string Array[] =  {"freq","rarefy","iters","groups","processors","summary","collect","scale","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloDiversityCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+PhyloDiversityCommand::PhyloDiversityCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["phylodiv"] = tempOutNames;
+               outputTypes["rarefy"] = tempOutNames;
+               outputTypes["summary"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloDiversityCommand", "PhyloDiversityCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PhyloDiversityCommand::getRequiredParameters(){ 
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloDiversityCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PhyloDiversityCommand::getRequiredFiles(){      
+       try {
+               string Array[] =  {"tree","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloDiversityCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
        try {
@@ -33,6 +82,12 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["phylodiv"] = tempOutNames;
+                       outputTypes["rarefy"] = tempOutNames;
+                       outputTypes["summary"] = tempOutNames;
+                       
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(globaldata->getTreeFile());              }
                        
@@ -132,9 +187,9 @@ int PhyloDiversityCommand::execute(){
                        string outRareFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv.rarefaction";
                        string outCollectFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv";
                        
-                       if (summary)    { m->openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile);                             }
-                       if (rarefy)             { m->openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile);                          }
-                       if (collect)    { m->openOutputFile(outCollectFile, outCollect); outputNames.push_back(outCollectFile); }
+                       if (summary)    { m->openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile);             outputTypes["summary"].push_back(outSumFile);                   }
+                       if (rarefy)             { m->openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile);  outputTypes["rarefy"].push_back(outRareFile);                   }
+                       if (collect)    { m->openOutputFile(outCollectFile, outCollect); outputNames.push_back(outCollectFile);  outputTypes["phylodiv"].push_back(outCollectFile);  }
                        
                        int numLeafNodes = trees[i]->getNumLeaves();