X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=b3fa7ddd397e973b7ac3895acfb8c0ebf0505f1f;hb=7bf581f8c46b08eb3bb40715dac94695edee4a67;hp=fcfd320e0b6be3aa3572b661a579311c9dead5bf;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index fcfd320..b3fa7dd 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -41,7 +41,7 @@ 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 +49,7 @@ 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 +64,7 @@ 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);
@@ -102,17 +102,21 @@ int DeconvoluteCommand::execute() {
 		if (abort == true) { return 0; }
 
 		//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) { remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(outFastaFile); m->mothurOutEndLine();