X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=2f99aa6091452933f6796f21aa043449bfce1dd4;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=cc5703223c7db32f31a2bf6db21d256145100f06;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index cc57032..2f99aa6 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -110,6 +110,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 					abort = true;
 				}
 			}else if (listFile == "not open") { abort = true; }	
+			else { m->setListFile(listFile); }
 			
 			//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"){	
@@ -185,7 +186,7 @@ int OtuHierarchyCommand::execute(){
 		//go through each bin in "big" otu and output the bins in "little" otu which created it
 		for (int i = 0; i < lists[1].getNumBins(); i++) {
 		
-			if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
 			
 			string names = lists[1].get(i);
 			
@@ -218,7 +219,7 @@ int OtuHierarchyCommand::execute(){
 		
 		out.close();
 		
-		if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();