X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=9cba70b9d2772edba281cd5f03459d1fdc32a966;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=7f4fbbab1096101aa8f09931e4c9ac40e04052b1;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;p=mothur.git

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 7f4fbba..9cba70b 100644
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -11,50 +11,48 @@
 #include "sequence.hpp"
 
 //**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getValidParameters(){	
+vector<string> ParseFastaQCommand::setParameters(){	
 	try {
-		string Array[] =  {"fastq", "outputdir","inputdir"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
 		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ParseFastaQCommand", "getValidParameters");
+		m->errorOut(e, "ParseFastaQCommand", "setParameters");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-ParseFastaQCommand::ParseFastaQCommand(){	
+string ParseFastaQCommand::getHelpString(){	
 	try {
-		abort = true; calledHelp = true; 
-		vector<string> tempOutNames;
-		outputTypes["fasta"] = tempOutNames;
-		outputTypes["qual"] = tempOutNames;
+		string helpString = "";
+		helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
+		helpString += "The fastq.info command parameter is fastq, and it is required.\n";
+		helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+		helpString += "Example fastq.info(fastaq=test.fastaq).\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
+		return helpString;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+		m->errorOut(e, "ParseFastaQCommand", "getHelpString");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getRequiredParameters(){	
-	try {
-		string Array[] =  {"fastq"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ParseFastaQCommand", "getRequiredParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getRequiredFiles(){	
+ParseFastaQCommand::ParseFastaQCommand(){	
 	try {
-		vector<string> myArray;
-		return myArray;
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["fasta"] = tempOutNames;
+		outputTypes["qfile"] = tempOutNames;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ParseFastaQCommand", "getRequiredFiles");
+		m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
 		exit(1);
 	}
 }
@@ -64,11 +62,10 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 		abort = false; calledHelp = false;   
 		
 		if(option == "help") {	help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
-			//valid paramters for this command
-			string Array[] =  {"fastq", "outputdir", "inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -84,7 +81,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 			//initialize outputTypes
 			vector<string> tempOutNames;
 			outputTypes["fasta"] = tempOutNames;
-			outputTypes["qual"] = tempOutNames;
+			outputTypes["qfile"] = 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);		
@@ -117,26 +114,6 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 }
 //**********************************************************************************************************************
 
-void ParseFastaQCommand::help(){
-	try {
-		m->mothurOut("The fastq.info command reads a fastq file and creates a fasta and quality file.\n");
-		m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n");
-		m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n");
-		m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n");
-		m->mothurOut("Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n");
-		m->mothurOutEndLine();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ParseFastaQCommand", "help");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-
-ParseFastaQCommand::~ParseFastaQCommand()	{	/*	do nothing	*/	}
-
-//**********************************************************************************************************************
-
 int ParseFastaQCommand::execute(){
 	try {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
@@ -146,7 +123,7 @@ int ParseFastaQCommand::execute(){
 		string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
 		ofstream outFasta, outQual;
 		m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);
-		m->openOutputFile(qualFile, outQual);	outputNames.push_back(qualFile);  outputTypes["qual"].push_back(qualFile);
+		m->openOutputFile(qualFile, outQual);	outputNames.push_back(qualFile);  outputTypes["qfile"].push_back(qualFile);
 		
 		ifstream in;
 		m->openInputFile(fastaQFile, in);
@@ -192,7 +169,19 @@ int ParseFastaQCommand::execute(){
 		outFasta.close();
 		outQual.close();
 		
-		if (m->control_pressed) { outputTypes.clear(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
+		
+		//set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("fasta");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+		}
+		
+		itTypes = outputTypes.find("qfile");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+		}		
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();