X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=d179f0d89c54923de0516aceb6bf6aef9fe406c6;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=274240158068655fcbbc501d81e335238966edfa;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 2742401..d179f0d 100644
--- 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);
 	}
 }