From d8c8bbc9d83e5fa6a5cd3438748c74b6aaacea88 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 29 Mar 2011 10:00:50 +0000
Subject: [PATCH] make non-variant translucent
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15836 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/components/variant/VCFview.java | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 5f44cd1a6..270ef9598 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -166,12 +166,14 @@ public class VCFview extends JPanel
private int colourScheme = 0;
private Color colMap[] = makeColours(Color.RED, 255);
+ private Color lighterGrey = new Color(220,220,220);
+ private Composite composite;
+ private Composite originalComposite;
Hashtable<String, Integer> offsetLengths = null;
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)*$";
private static String FILE_SUFFIX = "\\.[bv]{1}cf(\\.gz)*$";
@@ -1143,7 +1145,6 @@ public class VCFview extends JPanel
float pixPerBase, FeatureVector features, boolean vcf_v4)
{
int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
-
if( !showVariant(record, features, basePosition, vcf_v4) )
return;
@@ -1165,7 +1166,13 @@ public class VCFview extends JPanel
g.setColor(getColourForSNP(record, features, basePosition));
if(record.getAlt().isNonVariant())
{
- g.drawLine(pos[0], pos[1]-2, pos[0], pos[1]-LINE_HEIGHT+4);
+ if(originalComposite == null)
+ originalComposite = g.getComposite();
+ if(composite == null)
+ composite = makeComposite(0.1f);
+ g.setComposite(composite);
+ g.drawLine(pos[0], pos[1], pos[0], pos[1]-LINE_HEIGHT+6);
+ g.setComposite(originalComposite);
return;
}
}
--
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