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 274240158068655fcbbc501d81e335238966edfa..d179f0d89c54923de0516aceb6bf6aef9fe406c6 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -10,10 +10,56 @@
 #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){
+ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
        try {
                abort = false;
                
@@ -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 = "";          }
@@ -44,7 +94,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
                                it = parameters.find("fasta");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
                                }
@@ -53,18 +103,18 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
                        //check for required parameters
                        fasta = validParameter.validFile(parameters, "fasta", true);
                        if (fasta == "not open") { abort = true; }
-                       else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true;  }     
+                       else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }       
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(fasta); //if user entered a file with a path then preserve it      
+                               outputDir += m->hasPath(fasta); //if user entered a file with a path then preserve it   
                        }
 
                }
        }
        catch(exception& e) {
-               errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+               m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
                exit(1);
        }
 }
@@ -72,13 +122,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
 
 void ReverseSeqsCommand::help(){
        try {
-               mothurOut("The reverse.seqs command reads a fastafile and ....\n");
-               mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
-               mothurOut("The reverse.seqs command should be in the following format: \n");
-               mothurOut("reverse.seqs(fasta=yourFastaFile) \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");   
        }
        catch(exception& e) {
-               errorOut(e, "ReverseSeqsCommand", "help");
+               m->errorOut(e, "ReverseSeqsCommand", "help");
                exit(1);
        }
 }
@@ -96,14 +146,16 @@ int ReverseSeqsCommand::execute(){
                if (abort == true) { return 0; }
                
                ifstream inFASTA;
-               openInputFile(fasta, inFASTA);
+               m->openInputFile(fasta, inFASTA);
                
                ofstream outFASTA;
-               string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
-               openOutputFile(reverseFile, outFASTA);
+               string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta);
+               m->openOutputFile(reverseFile, outFASTA);
                
                while(!inFASTA.eof()){
-                       Sequence currSeq(inFASTA);  gobble(inFASTA);
+                       if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(reverseFile.c_str()); return 0; }
+                        
+                       Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                        if (currSeq.getName() != "") {
                                currSeq.reverseComplement();
                                currSeq.printSequence(outFASTA);
@@ -112,11 +164,19 @@ int ReverseSeqsCommand::execute(){
                inFASTA.close();
                outFASTA.close();
                
+               if (m->control_pressed) {  remove(reverseFile.c_str()); return 0; }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(reverseFile); m->mothurOutEndLine();       outputNames.push_back(reverseFile); outputTypes["fasta"].push_back(reverseFile);
+               m->mothurOutEndLine();
+
+               
                return 0;
                
        }
        catch(exception& e) {
-               errorOut(e, "ReverseSeqsCommand", "execute");
+               m->errorOut(e, "ReverseSeqsCommand", "execute");
                exit(1);
        }
 }