X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=degapseqscommand.cpp;h=8687194778d2da8360b3367c3c5ec2bb00108431;hp=f590d8b3baaf67091f59a741a87a23e09c8873b0;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hpb=220dc345e493cddc569521111ce32ac4d965ab7f

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index f590d8b..8687194 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -13,9 +13,9 @@
 //**********************************************************************************************************************
 vector<string> DegapSeqsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+		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);		}
@@ -46,6 +46,21 @@ string DegapSeqsCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string DegapSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],ng.fasta"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "DegapSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -193,11 +208,13 @@ int DegapSeqsCommand::execute(){
 			ofstream outFASTA;
 			string tempOutputDir = outputDir;
 			if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
-			string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+            map<string, string> variables; 
+            variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+			string degapFile = getOutputFileName("fasta", variables);
 			m->openOutputFile(degapFile, outFASTA);
 			
 			while(!inFASTA.eof()){
-				if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
+				if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} return 0; }
 				 
 				Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 				if (currSeq.getName() != "") {
@@ -210,7 +227,7 @@ int DegapSeqsCommand::execute(){
 			
 			outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
 			
-			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; }
+			if (m->control_pressed) {  outputTypes.clear(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} return 0; }
 		}
 		
 		//set fasta file as new current fastafile
@@ -221,7 +238,7 @@ int DegapSeqsCommand::execute(){
 		}
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}	
 		m->mothurOutEndLine();