From 4a4042674ccdd35234e998581ba6b4dfffa153e2 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 11 Sep 2012 14:36:59 +0100
Subject: [PATCH] define SNP arraylist as List
---
.../artemis/components/alignment/BamView.java | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 0e2c3afd6..7cbc78924 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1313,7 +1313,7 @@ public class BamView extends JPanel
BamViewRecord bamViewNextRecord = null;
SAMRecord samNextRecord = null;
- ArrayList<Integer> snps = getSNPs(samRecord);
+ List<Integer> snps = getSNPs(samRecord);
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
@@ -1451,7 +1451,7 @@ public class BamView extends JPanel
int recordStart = samRecord.getAlignmentStart()+offset;
int recordEnd = samRecord.getAlignmentEnd()+offset;
- ArrayList<Integer> snps = getSNPs(samRecord);
+ List<Integer> snps = getSNPs(samRecord);
if(colourByCoverageColour.isSelected() ||
lstStart != recordStart || lstEnd != recordEnd || snps != null)
@@ -1554,7 +1554,7 @@ public class BamView extends JPanel
final int offset = getSequenceOffset(samRecord.getReferenceName());
final int recordStart = samRecord.getAlignmentStart()+offset;
final int recordEnd = samRecord.getAlignmentEnd()+offset;
- ArrayList<Integer> snps = getSNPs(samRecord);
+ List<Integer> snps = getSNPs(samRecord);
if(colourByCoverageColour.isSelected() ||
lstStart != recordStart || lstEnd != recordEnd || snps != null)
@@ -1832,7 +1832,7 @@ public class BamView extends JPanel
* @param stroke
*/
private void drawLoneRead(Graphics2D g2, BamViewRecord bamViewRecord, int ypos,
- float pixPerBase, int baseAtStartOfView, int scaleHeight, ArrayList<Integer> snps)
+ float pixPerBase, int baseAtStartOfView, int scaleHeight, List<Integer> snps)
{
SAMRecord samRecord = bamViewRecord.sam;
boolean offTheTop = false;
@@ -1994,7 +1994,7 @@ public class BamView extends JPanel
final float pixPerBase,
final int ypos,
final int baseAtStartOfView,
- final ArrayList<Integer> snps)
+ final List<Integer> snps)
{
SAMRecord thisRead = bamViewRecord.sam;
int offset = getSequenceOffset(thisRead.getReferenceName());
@@ -2163,7 +2163,7 @@ public class BamView extends JPanel
* @param pixPerBase
* @param ypos
*/
- private void showSNPsOnReads(final ArrayList<Integer> snps,
+ private void showSNPsOnReads(final List<Integer> snps,
final Graphics2D g2,
float pixPerBase, int ypos)
{
@@ -2178,7 +2178,7 @@ public class BamView extends JPanel
* Get the SNP positions
* @param samRecord
*/
- private ArrayList<Integer> getSNPs(final SAMRecord samRecord)
+ private List<Integer> getSNPs(final SAMRecord samRecord)
{
if(!isSNPs) // return null if not displaying SNPs
return null;
--
GitLab