X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=2312649d1cff739956638ba2ad8788949669f1d5;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=f627aedef1223caf64b4eca8a37f06217315c2b6;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index f627aed..2312649 100644
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "getsharedotucommand.h"
+#include "sharedutilities.h"
 
 //**********************************************************************************************************************
 vector<string> GetSharedOTUCommand::setParameters(){	
@@ -82,6 +83,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(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();
@@ -147,7 +149,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 					m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); 
 					abort = true;
 				}
-			}else {  format = "list"; 	}
+			}else {  format = "list"; 	m->setListFile(listfile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
@@ -158,7 +160,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 					m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); 
 					abort = true;
 				}
-			}
+			}else { m->setGroupFile(groupfile); }
 						
 			if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
 			
@@ -180,7 +182,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 			else { 
 				userGroups = "unique." + groups;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 				
 			}
 			
@@ -189,14 +191,14 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 			else { 
 				userGroups = groups;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 				unique = false;
 			}
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
 			else if (fastafile == "not found") {  fastafile = "";  }	
-				
+			else { m->setFastaFile(fastafile); }
 		}
 
 	}
@@ -219,12 +221,18 @@ int GetSharedOTUCommand::execute(){
 		if (m->control_pressed) { delete groupMap; return 0; }
 		
 		if (Groups.size() == 0) {
-			Groups = groupMap->namesOfGroups;
+			Groups = groupMap->getNamesOfGroups();
 			
 			//make string for outputfile name
 			userGroups = "unique.";
 			for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
 			userGroups = userGroups.substr(0, userGroups.length()-1);
+		}else{
+			//sanity check for group names
+			SharedUtil util;
+			vector<string> namesOfGroups = groupMap->getNamesOfGroups(); 
+			util.setGroups(Groups, namesOfGroups);
+			groupMap->setNamesOfGroups(namesOfGroups);
 		}
 	
 		//put groups in map to find easier
@@ -260,7 +268,7 @@ int GetSharedOTUCommand::execute(){
 			
 			if (m->control_pressed) { 
 				if (lastlist != NULL) {		delete lastlist;	}
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }  outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }  outputTypes.clear();
 				delete groupMap; return 0;
 			}
 			
@@ -319,11 +327,11 @@ int GetSharedOTUCommand::execute(){
 		
 
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		
 		if (lastlist != NULL) {		delete lastlist;	}
 		
-		if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }  delete groupMap; return 0; } 
+		if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }  delete groupMap; return 0; } 
 		
 		//set fasta file as new current fastafile
 		string current = "";
@@ -375,7 +383,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
 				
 		//go through each bin, find out if shared
 		for (int i = 0; i < shared->getNumBins(); i++) {
-			if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
+			if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
 			
 			bool uniqueOTU = true;
 			
@@ -453,7 +461,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
 		outNames.close();
 		
 		if (!wroteSomething) {
-			remove(outputFileNames.c_str());
+			m->mothurRemove(outputFileNames);
 			string outputString = "\t" + toString(num) + " - No otus shared by groups";
 			
 			string groupString = "";