From b1d143351bcd1b3b4a06ec525c386f161579ee32 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Tue, 21 Jun 2011 16:07:40 +0000
Subject: [PATCH] added cutoff change to mgcluster
---
mgclustercommand.cpp | 16 +++++++++++++++-
1 file changed, 15 insertions(+), 1 deletion(-)
diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index fd26717..b982b8d 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -235,6 +235,8 @@ int MGClusterCommand::execute(){
return 0;
}
+ double saveCutoff = cutoff;
+
if (!hclusterWanted) {
//get distmatrix and overlap
SparseMatrix* distMatrix = read->getDistMatrix();
@@ -373,6 +375,11 @@ int MGClusterCommand::execute(){
seqs = hcluster->getSeqs();
+ //to account for cutoff change in average neighbor
+ if (seqs.size() != 0) {
+ if (seqs[0].dist > cutoff) { break; }
+ }
+
if (m->control_pressed) {
delete nameMap; delete list; delete rabund; delete hcluster;
listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
@@ -386,7 +393,7 @@ int MGClusterCommand::execute(){
if (seqs[i].seq1 != seqs[i].seq2) {
- hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+ cutoff = hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
if (m->control_pressed) {
delete nameMap; delete list; delete rabund; delete hcluster;
@@ -491,6 +498,13 @@ int MGClusterCommand::execute(){
m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
m->mothurOutEndLine();
+ if (saveCutoff != cutoff) {
+ if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
+ else { saveCutoff = m->roundDist(saveCutoff, precision); }
+
+ m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
+ }
+
//set list file as new current listfile
string current = "";
itTypes = outputTypes.find("list");
--
2.39.5