From 7b75a006b6753240f248a1ef326de20f464ed55a Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Thu, 21 May 2009 18:42:57 +0000
Subject: [PATCH] fixed bugs

---
 globaldata.cpp      | 2 +-
 sharedutilities.cpp | 1 +
 validcommands.cpp   | 1 -
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/globaldata.cpp b/globaldata.cpp
index 4005f40..0078d69 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -28,7 +28,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			gGroupmap = NULL;
 			gTree.clear();
 			Treenames.clear();
-			labels.clear(); lines.clear(); groups.clear();
+			labels.clear(); lines.clear(); Groups.clear();
 			allLines = 1;
 		}
 		
diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index fd0595d..5776b36 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -111,6 +111,7 @@ void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<S
 //need to have mode because different commands require different number of valid groups
 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
 	try {
+//cout << "groups size" << userGroups.size() << endl;
 		if (userGroups.size() != 0) {
 			if (userGroups[0] != "all") {
 				//check that groups are valid
diff --git a/validcommands.cpp b/validcommands.cpp
index 7f7acc2..230d800 100644
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -17,7 +17,6 @@ ValidCommands::ValidCommands() {
 		commands["read.dist"]			= "read.dist"; 
 		commands["read.otu"]			= "read.otu";
 		commands["read.tree"]			= "read.tree"; 
-		commands["read.seqs"]           = "read.seqs";
 		commands["bin.seqs"]			= "bin.seqs"; 
 		commands["get.oturep"]			= "get.oturep";
 		commands["cluster"]				= "cluster"; 
-- 
2.39.5