X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=02d8413675bade0cf79f8781987cc45078b74db2;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=02461365b505bdea22cc977594fc1341ca7bac46;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 0246136..02d8413 100644
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -46,8 +46,8 @@ string GetSharedOTUCommand::getHelpString(){
 		helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
 		helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
 		helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
-		helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
-		helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+		helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+		helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
 		helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
 		helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
 		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
@@ -182,7 +182,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 			else { 
 				userGroups = "unique." + groups;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 				
 			}
 			
@@ -191,7 +191,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 			else { 
 				userGroups = groups;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 				unique = false;
 			}
 			
@@ -221,7 +221,7 @@ 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.";
@@ -230,7 +230,9 @@ int GetSharedOTUCommand::execute(){
 		}else{
 			//sanity check for group names
 			SharedUtil util;
-			util.setGroups(Groups, groupMap->namesOfGroups);
+			vector<string> namesOfGroups = groupMap->getNamesOfGroups(); 
+			util.setGroups(Groups, namesOfGroups);
+			groupMap->setNamesOfGroups(namesOfGroups);
 		}
 	
 		//put groups in map to find easier
@@ -325,7 +327,7 @@ int GetSharedOTUCommand::execute(){
 		
 
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		
 		if (lastlist != NULL) {		delete lastlist;	}