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

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index b2810741ae7b2b6591a7f0aa8e3b52b143dcfe3d..fc2d9a7faf24c7cfa433482e6897ac7b224844a6 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -11,7 +11,54 @@
 #include "sequence.hpp"
 
 //**********************************************************************************************************************
-
+vector<string> ChopSeqsCommand::getValidParameters(){  
+       try {
+               string AlignArray[] =  {"fasta","numbases","countgaps","keep","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ChopSeqsCommand::ChopSeqsCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChopSeqsCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"fasta","numbases"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChopSeqsCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChopSeqsCommand::ChopSeqsCommand(string option)  {
        try {
                abort = false;
@@ -35,6 +82,11 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["accnos"] = 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 = "";          }
@@ -118,7 +170,7 @@ int ChopSeqsCommand::execute(){
                        
                        Sequence seq(in);
                        
-                       if (m->control_pressed) { in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
+                       if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
                        
                        if (seq.getName() != "") {
                                string newSeqString = getChopped(seq);
@@ -138,9 +190,9 @@ int ChopSeqsCommand::execute(){
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
                
-               if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine();  }
+               if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
                else {  remove(outputFileNameAccnos.c_str());  }
                
                m->mothurOutEndLine();