X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=62daa612d52a04fa72b85c1c621b89b539d14ab0;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=b3fa7ddd397e973b7ac3895acfb8c0ebf0505f1f;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index b3fa7dd..62daa61 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 = "";		}
@@ -99,7 +152,7 @@ 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 + m->getRootName(m->getSimpleName(inFastaName)) + "names";
@@ -115,15 +168,26 @@ int DeconvoluteCommand::execute() {
 		fastamap.printCondensedFasta(outFastaFile);
 		fastamap.printNamesFile(outNameFile);
 		
-		if (m->control_pressed) { remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+		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();
 
-
+		//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("name");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+		}
 		
 		return 0;
 	}