X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removerarecommand.cpp;h=24b616560de3bed794d423f4cb7a3544f0d48f5f;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=cd0b602113f496af4a1db27850e882ae04d29077;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index cd0b602..24b6165 100644
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -160,23 +160,28 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
 			//check for file parameters
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
-			else if (listfile == "not found") {  listfile = "";  }	
+			else if (listfile == "not found") {  listfile = "";  }
+			else { m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
 			if (sabundfile == "not open") { abort = true; }
 			else if (sabundfile == "not found") {  sabundfile = "";  }	
+			else { m->setSabundFile(sabundfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { abort = true; }
 			else if (rabundfile == "not found") {  rabundfile = "";  }				
+			else { m->setRabundFile(rabundfile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { groupfile = ""; abort = true; }
 			else if (groupfile == "not found") {  groupfile = "";  }	
+			else { m->setGroupFile(groupfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = "";  abort = true; }
 			else if (sharedfile == "not found") {  sharedfile = "";  }
+			else { m->setSharedFile(sharedfile); }
 			
 			if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
 				//is there are current file available for any of these?
@@ -215,7 +220,7 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "nseqs", false);	 
 			if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
-			else { convert(temp, nseqs); }
+			else { m->mothurConvert(temp, nseqs); }
 			
 			temp = validParameter.validFile(parameters, "bygroup", false);	 if (temp == "not found") { temp = "f"; }
 			byGroup = m->isTrue(temp);
@@ -246,7 +251,7 @@ int RemoveRareCommand::execute(){
 		if (listfile != "")			{		processList();		}
 		if (sharedfile != "")		{		processShared();	}
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 			
 		if (outputNames.size() != 0) {
 			m->mothurOutEndLine();
@@ -348,7 +353,8 @@ int RemoveRareCommand::processList(){
 		if (groupfile != "") { 
 			groupMap = new GroupMap(groupfile); groupMap->readMap(); 
 			SharedUtil util;
-			util.setGroups(Groups, groupMap->namesOfGroups);
+			vector<string> namesGroups = groupMap->getNamesOfGroups();
+			util.setGroups(Groups, namesGroups);
 			m->openOutputFile(outputGroupFileName, outGroup);
 		}
 		
@@ -360,7 +366,7 @@ int RemoveRareCommand::processList(){
 			
 			//for each bin
 			for (int i = 0; i < list->getNumBins(); i++) {
-				if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); remove(outputGroupFileName.c_str()); } out.close();  remove(outputFileName.c_str());  return 0; }
+				if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close();  m->mothurRemove(outputFileName);  return 0; }
 				
 				//parse out names that are in accnos file
 				string binnames = list->get(i);
@@ -619,7 +625,7 @@ int RemoveRareCommand::processRabund(){
 //**********************************************************************************************************************
 int RemoveRareCommand::processShared(){
 	try {
-		m->Groups = Groups;
+		m->setGroups(Groups);
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
@@ -646,6 +652,7 @@ int RemoveRareCommand::processShared(){
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
 				
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				processLookup(lookup, out);
 			}
 			
@@ -659,6 +666,7 @@ int RemoveRareCommand::processShared(){
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
 				
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				processLookup(lookup, out);			
 				
 				//restore real lastlabel to save below
@@ -693,6 +701,7 @@ int RemoveRareCommand::processShared(){
 			
 			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 			
+			if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 			processLookup(lookup, out);	
 			
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }