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

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index a7f211345697a72c18b6fa0aaa1ac40200c46d94..e6ccc9b70455089d5dffc1c6f512f3e17ca1d76e 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -12,6 +12,54 @@
 //**********************************************************************************************************************
 inline bool comparePriority(seqPNode first, seqPNode second) {  return (first.numIdentical > second.numIdentical); }
 //**********************************************************************************************************************
+vector<string> PreClusterCommand::getValidParameters(){        
+       try {
+               string Array[] =  {"fasta", "name", "diffs", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PreClusterCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+PreClusterCommand::PreClusterCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PreClusterCommand::getRequiredParameters(){     
+       try {
+               string Array[] =  {"fasta"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PreClusterCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PreClusterCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PreClusterCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 
 PreClusterCommand::PreClusterCommand(string option) {
        try {
@@ -36,6 +84,11 @@ PreClusterCommand::PreClusterCommand(string option) {
                                if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["name"] = 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 = "";          }
@@ -189,8 +242,8 @@ int PreClusterCommand::execute(){
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(newFastaFile); m->mothurOutEndLine();      
-               m->mothurOut(newNamesFile); m->mothurOutEndLine();      
+               m->mothurOut(newFastaFile); m->mothurOutEndLine();      outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
+               m->mothurOut(newNamesFile); m->mothurOutEndLine();      outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
                m->mothurOutEndLine();
 
                return 0;