X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=c9908fbc715f33eb33f75ff2005d51c9347678ff;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=e0943cf0cb52f2c2ba3faf7fe8a5e2add7281597;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index e0943cf..c9908fb 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -79,6 +79,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(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();
@@ -165,14 +166,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 			accnosfile = validParameter.validFile(parameters, "accnos", true);
 			if (accnosfile == "not open") { abort = true; }
 			else if (accnosfile == "not found") {  accnosfile = ""; }	
+			else { m->setAccnosFile(accnosfile); }
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
 			else if (fastafile == "not found") {  fastafile = "";  }	
+			else { m->setFastaFile(fastafile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }
 			else if (namefile == "not found") {  namefile = "";  }	
+			else { m->setNameFile(namefile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
@@ -181,15 +185,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 				groupfile = m->getGroupFile(); 
 				if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setGroupFile(groupfile); }	
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
 			else if (listfile == "not found") {  listfile = "";  }
+			else { m->setListFile(listfile); }
 			
 			taxfile = validParameter.validFile(parameters, "taxonomy", true);
 			if (taxfile == "not open") { abort = true; }
 			else if (taxfile == "not found") {  taxfile = "";  }
+			else { m->setTaxonomyFile(taxfile); }
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
@@ -239,10 +245,10 @@ int RemoveGroupsCommand::execute(){
 		if (listfile != "")			{		readList();		}
 		if (taxfile != "")			{		readTax();		}
 		
-		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; }
 		
 		m->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
-		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i])) + " sequences."); m->mothurOutEndLine();	}
+		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine();	}
 		m->mothurOutEndLine();
 		
 		if (outputNames.size() != 0) {
@@ -305,7 +311,7 @@ int RemoveGroupsCommand::readFasta(){
 		bool wroteSomething = false;
 		
 		while(!in.eof()){
-			if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
@@ -360,7 +366,7 @@ int RemoveGroupsCommand::readList(){
 			
 			//for each bin
 			for (int i = 0; i < list.getNumBins(); i++) {
-				if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+				if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 				
 				//parse out names that are in accnos file
 				string binnames = list.get(i);
@@ -423,7 +429,7 @@ int RemoveGroupsCommand::readName(){
 		bool wroteSomething = false;
 		
 		while(!in.eof()){
-			if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
 			in >> firstCol;		m->gobble(in);		
 			in >> secondCol;			
@@ -499,7 +505,7 @@ int RemoveGroupsCommand::readGroup(){
 		bool wroteSomething = false;
 		
 		while(!in.eof()){
-			if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
 			in >> name;				//read from first column
 			in >> group;			//read from second column
@@ -541,7 +547,7 @@ int RemoveGroupsCommand::readTax(){
 		bool wroteSomething = false;
 		
 		while(!in.eof()){
-			if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
 			in >> name;				//read from first column
 			in >> tax;			//read from second column