From 219104a887d4725af80487729f4c34a030fe4358 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Thu, 6 Aug 2009 15:14:39 +0000
Subject: [PATCH] bugs fixes while testing for 1.5 release

---
 readtreecommand.cpp |  1 +
 treemap.cpp         | 21 +++++++++++++++++++++
 treemap.h           |  1 +
 3 files changed, 23 insertions(+)

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 2a3c5d0..0f07ac2 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -119,6 +119,7 @@ int ReadTreeCommand::execute(){
 				//then you did not find it so report it 
 				if (count == globaldata->Treenames.size()) { 
 					mothurOut(treeMap->namesOfSeqs[i] + " is in your namefile and not in your tree. It will be disregarded."); mothurOutEndLine();
+					treeMap->removeSeq(treeMap->namesOfSeqs[i]);
 				}
 			}
 		}
diff --git a/treemap.cpp b/treemap.cpp
index 044e87c..e472570 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -44,6 +44,27 @@ void TreeMap::readMap() {
 		fileHandle.close();
 }
 /************************************************************/
+void TreeMap::removeSeq(string seqName) {
+	
+	//erase name from namesOfSeqs
+	for (int i = 0; i < namesOfSeqs.size(); i++) {
+		if (namesOfSeqs[i] == seqName)  {
+			namesOfSeqs.erase (namesOfSeqs.begin()+i);
+			break;
+		}
+	}
+	
+	//decrement sequences in this group
+	string group = treemap[seqName].groupname;
+	seqsPerGroup[group]--;
+	
+	//remove seq from treemap
+	it = treemap.find(seqName);
+	treemap.erase(it);
+	
+
+}
+/************************************************************/
 
 int TreeMap::getNumGroups() {
 			
diff --git a/treemap.h b/treemap.h
index 8f744c8..0824ebf 100644
--- a/treemap.h
+++ b/treemap.h
@@ -34,6 +34,7 @@ public:
 	void setIndex(string, int);  //sequencename, index
 	int getIndex(string);		//returns vector index of sequence
 	bool isValidGroup(string);  //return true if string is a valid group
+	void removeSeq(string);  //removes a sequence, this is to accomadate trees that do not contain all the seqs in your groupfile
 	string getGroup(string);
 	vector<string> namesOfGroups;
 	vector<string> namesOfSeqs;
-- 
2.39.2