X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=6c04c1255ab94010da7cacfb409d497b4f0354d4;hb=7c08fa69c0b89e7a08341af2aa724f206f182075;hp=fcfd320e0b6be3aa3572b661a579311c9dead5bf;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index fcfd320..6c04c12 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -9,13 +9,61 @@
 
 #include "deconvolutecommand.h"
 
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"fasta", "name","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DeconvoluteCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+DeconvoluteCommand::DeconvoluteCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		vector<string> tempOutNames;
+		outputTypes["fasta"] = tempOutNames;
+		outputTypes["name"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"fasta"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 /**************************************************************************************/
 DeconvoluteCommand::DeconvoluteCommand(string option)  {	
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -33,6 +81,11 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["fasta"] = tempOutNames;
+			outputTypes["name"] = 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 = "";		}
@@ -41,7 +94,7 @@ DeconvoluteCommand::DeconvoluteCommand(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;		}
 				}
@@ -49,7 +102,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
 				it = parameters.find("name");
 				//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["name"] = inputDir + it->second;		}
 				}
@@ -64,7 +117,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
 			//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(inFastaName); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it	
 			}
 			
 			oldNameMapFName = validParameter.validFile(parameters, "name", true);
@@ -99,24 +152,29 @@ void DeconvoluteCommand::help(){
 int DeconvoluteCommand::execute() {	
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 
 		//prepare filenames and open files
-		string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names";
-		string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName);
+		string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
+		string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
 		
 		FastaMap fastamap;
 	
 		if(oldNameMapFName == "")	{	fastamap.readFastaFile(inFastaName);					}
 		else						{	fastamap.readFastaFile(inFastaName, oldNameMapFName);	}
 		
+		if (m->control_pressed) { return 0; }
+		
 		fastamap.printCondensedFasta(outFastaFile);
 		fastamap.printNamesFile(outNameFile);
 		
+		if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(outFastaFile); m->mothurOutEndLine();	
 		m->mothurOut(outNameFile); m->mothurOutEndLine();
+		outputNames.push_back(outFastaFile);  outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile);  outputTypes["name"].push_back(outNameFile); 
 		m->mothurOutEndLine();