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;
--
2.39.5