X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;h=7fd2803a4ec6c5e578d7b180a9e08fda1af33385;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=290d5dc0996a62783ab3365513f7441b1aafd717;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 290d5dc..7fd2803 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -25,7 +25,7 @@ vector<string> DegapSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 	}
@@ -60,10 +60,10 @@ vector<string> DegapSeqsCommand::getRequiredFiles(){
 //***************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(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
@@ -112,7 +112,9 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 						if (m->getDefaultPath() != "") { //default path is set
 							string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							fastaFileNames[i] = tryPath;
 						}
 					}
@@ -122,7 +124,9 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 						if (m->getOutputDir() != "") { //default path is set
 							string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							fastaFileNames[i] = tryPath;
 						}
 					}
@@ -184,7 +188,7 @@ DegapSeqsCommand::~DegapSeqsCommand(){	/*	do nothing	*/	}
 int DegapSeqsCommand::execute(){
 	try{
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		for (int s = 0; s < fastaFileNames.size(); s++) {
 				
@@ -215,6 +219,13 @@ int DegapSeqsCommand::execute(){
 			if (m->control_pressed) {  outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} 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); }
+		}
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}