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

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index c4f367a06d3e810afd954800ac637f29dc1818a1..c4751b5481a8c11803f3fd2582bdd013810644ff 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -13,6 +13,55 @@
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"taxonomy","cutoff","label","name","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"taxonomy"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredFiles(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /**********************************************************************************************************************/
 PhylotypeCommand::PhylotypeCommand(string option)  {
        try {
@@ -38,6 +87,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+                       outputTypes["sabund"] = tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -127,8 +182,6 @@ int PhylotypeCommand::execute(){
        
                if (abort == true) { return 0; }
                
-               vector<string> outputNames;
-               
                //reads in taxonomy file and makes all the taxonomies the same length 
                //by appending the last taxon to a given taxonomy as many times as needed to 
                //make it as long as the longest taxonomy in the file 
@@ -164,9 +217,9 @@ int PhylotypeCommand::execute(){
                string outputRabundFile = fileroot + "tx.rabund";
                m->openOutputFile(outputRabundFile, outRabund);
                
-               outputNames.push_back(outputListFile);
-               outputNames.push_back(outputSabundFile);
-               outputNames.push_back(outputRabundFile);
+               outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
+               outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
+               outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
                
                int count = 1;          
                //start at leaves of tree and work towards root, processing the labels the user wants