From 559076e09effc6d1c2112baa16acb846c00a7ff0 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 15 Mar 2011 11:25:41 +0000
Subject: [PATCH] optimise writing region
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15719 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/components/variant/IOUtils.java | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 7a6ee7e04..1de636c8f 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -188,7 +188,6 @@ class IOUtils
AbstractVCFReader vcfReaders[] = vcfView.getVcfReaders();
MarkerRange marker = selection.getMarkerRange();
Range range = marker.getRawRange();
- FeatureVector features = entryGroup.getAllFeatures();
FileWriter writer = null;
String fastaFiles = "";
@@ -217,12 +216,12 @@ class IOUtils
Bases bases = entryGroup.getBases();
// reference
writeOrViewRange(null, sbeg, send, writer, buffSeq,
- marker, bases, name, features, vcfView);
+ marker, bases, name, vcfView, entryGroup);
// vcf sequences
for (int i = 0; i < vcfReaders.length; i++)
writeOrViewRange(vcfReaders[i], sbeg, send, writer, buffSeq,
- marker, bases, name, features, vcfView);
+ marker, bases, name, vcfView, entryGroup);
if(writer != null)
writer.close();
@@ -389,8 +388,8 @@ class IOUtils
FileWriter writer, StringBuffer buffSeq,
MarkerRange marker, Bases bases,
String name,
- FeatureVector features,
- VCFview vcfView) throws IOException, OutOfRangeException
+ VCFview vcfView,
+ final EntryGroup entryGroup) throws IOException, OutOfRangeException
{
int direction = ( marker.isForwardMarker() ? Bases.FORWARD : Bases.REVERSE);
int length = send-sbeg+1;
@@ -415,12 +414,12 @@ class IOUtils
MarkerRange m = new MarkerRange(marker.getStrand(), sbegc, sendc);
basesStr = bases.getSubSequence(m.getRange(), direction);
-
+ FeatureVector features = entryGroup.getFeaturesInRange(m.getRange());
//System.out.println((reader == null ? "" : reader.getName())+" "+sbegc+".."+sendc);
if(reader != null)
basesStr = getAllBasesInRegion(reader, sbegc, sendc, basesStr,
features, vcfView, marker.isForwardMarker());
-
+
linePos = writeOrView(writer, header, basesStr, buffSeq, linePos);
header = null;
}
--
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