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

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 10579a3b209c3f5b15b1590d44d2ab99f90326b1..3c957a6ce84b5e5a489faaccf18a1dc40f99a02b 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -15,6 +15,56 @@
 #include "readmatrix.hpp"
 #include "inputdata.h"
 
+
+//**********************************************************************************************************************
+vector<string> ClusterSplitCommand::getValidParameters(){      
+       try {
+               string AlignArray[] =  {"fasta","phylip","column","name","cutoff","precision","method","splitmethod","taxonomy","taxlevel","large","showabund","timing","hard","processors","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterSplitCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ClusterSplitCommand::ClusterSplitCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterSplitCommand", "ClusterSplitCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ClusterSplitCommand::getRequiredParameters(){   
+       try {
+               string Array[] =  {"fasta","phylip","column","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterSplitCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ClusterSplitCommand::getRequiredFiles(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterSplitCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
 ClusterSplitCommand::ClusterSplitCommand(string option)  {
@@ -44,6 +94,12 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                                }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       outputTypes["sabund"] = tempOutNames;
+                       
                        globaldata->newRead();
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -292,7 +348,7 @@ int ClusterSplitCommand::execute(){
                SplitMatrix* split;
                if (splitmethod == "distance")                  {       split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod, large);                                                       }
                else if (splitmethod == "classify")             {       split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod, large);                                       }
-               else if (splitmethod == "fasta")                {       split = new SplitMatrix(fastafile, namefile, taxFile, taxLevelCutoff, splitmethod, processors, outputDir);      }
+               else if (splitmethod == "fasta")                {       split = new SplitMatrix(fastafile, namefile, taxFile, taxLevelCutoff, cutoff, splitmethod, processors, outputDir);      }
                else { m->mothurOut("Not a valid splitting method.  Valid splitting algorithms are distance, classify or fasta."); m->mothurOutEndLine(); return 0;             }
                
                split->split();
@@ -696,9 +752,9 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                m->openOutputFile(fileroot+ tag + ".rabund",    outRabund);
                m->openOutputFile(fileroot+ tag + ".list",              outList);
                                
-               outputNames.push_back(fileroot+ tag + ".sabund");
-               outputNames.push_back(fileroot+ tag + ".rabund");
-               outputNames.push_back(fileroot+ tag + ".list");
+               outputNames.push_back(fileroot+ tag + ".sabund");  outputTypes["list"].push_back(fileroot+ tag + ".list");
+               outputNames.push_back(fileroot+ tag + ".rabund");  outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
+               outputNames.push_back(fileroot+ tag + ".list");    outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
                
                map<float, int>::iterator itLabel;