From d87b4c184bc4d7590b1559295a6b8e60c31bcfa3 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 28 Mar 2011 13:40:46 +0000
Subject: [PATCH] non-variants are light grey and insertions are magenta
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15826 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/variant/VCFview.java | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index feedc67e8..5f44cd1a6 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -171,6 +171,7 @@ public class VCFview extends JPanel
private boolean concatSequences = false;
protected static Pattern tabPattern = Pattern.compile("\t");
+ private Color lighterGrey = new Color(220,220,220);
public static String VCFFILE_SUFFIX = ".*\\.[bv]{1}cf(\\.gz)*$";
private static String FILE_SUFFIX = "\\.[bv]{1}cf(\\.gz)*$";
@@ -947,7 +948,7 @@ public class VCFview extends JPanel
}
- private void drawRegion(Graphics g,
+ private void drawRegion(Graphics2D g,
String chr,
int sbeg,
int send,
@@ -1138,7 +1139,7 @@ public class VCFview extends JPanel
}
- private void drawVariantCall(Graphics g, VCFRecord record, int start, int index,
+ private void drawVariantCall(Graphics2D g, VCFRecord record, int start, int index,
float pixPerBase, FeatureVector features, boolean vcf_v4)
{
int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
@@ -1158,7 +1159,7 @@ public class VCFview extends JPanel
else if(record.getAlt().isDeletion(vcf_v4))
g.setColor(Color.gray);
else if(record.getAlt().isInsertion(vcf_v4))
- g.setColor(Color.yellow);
+ g.setColor(Color.magenta);
else if(record.getAlt().length() == 1 && record.getRef().length() == 1)
{
g.setColor(getColourForSNP(record, features, basePosition));
@@ -1225,7 +1226,7 @@ public class VCFview extends JPanel
else if(variant.equals("T"))
return Color.black;
else
- return Color.magenta; // non-variant
+ return lighterGrey; // non-variant
}
/**
--
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