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

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 296c95410df58f1aeabfbd5b3195b327a18fe170..d179f0d89c54923de0516aceb6bf6aef9fe406c6 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -10,7 +10,53 @@
 #include "reversecommand.h"
 #include "sequence.hpp"
 
-
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getValidParameters(){       
+       try {
+               string Array[] =  {"fasta", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReverseSeqsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ReverseSeqsCommand::ReverseSeqsCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getRequiredParameters(){    
+       try {
+               string Array[] =  {"fasta"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getRequiredFiles(){ 
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
 
 ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
@@ -36,6 +82,10 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = 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 = "";          }
@@ -72,7 +122,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
 
 void ReverseSeqsCommand::help(){
        try {
-               m->mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+               m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n");
                m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
                m->mothurOut("The reverse.seqs command should be in the following format: \n");
                m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");   
@@ -118,7 +168,7 @@ int ReverseSeqsCommand::execute(){
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(reverseFile); m->mothurOutEndLine();       
+               m->mothurOut(reverseFile); m->mothurOutEndLine();       outputNames.push_back(reverseFile); outputTypes["fasta"].push_back(reverseFile);
                m->mothurOutEndLine();