X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=2f99aa6091452933f6796f21aa043449bfce1dd4;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=17e29d9528c1122f73a2f81a32c1998dded037cf;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 17e29d9..2f99aa6 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -38,7 +38,7 @@ string OtuHierarchyCommand::getHelpString(){
 		helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
 		helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
 		helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -67,6 +67,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 		
 		//allow user to run help
 		if(option == "help") {  help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -109,6 +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"){	
@@ -184,7 +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);
 			
@@ -217,7 +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();