From 2e4218d4b304e7c85f0a3e802c76cb8fb157e49b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 9 Mar 2011 12:21:17 +0000
Subject: [PATCH] space reads out more when orientation is displayed
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15688 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 23 +++++++++++++------
1 file changed, 16 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index f14862120..30817c4e7 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1187,6 +1187,9 @@ public class BamView extends JPanel
scaleHeight = 0;
int ypos = (getHeight() - scaleHeight);
+ int ydiff = 2;
+ if(isOrientation)
+ ydiff= 4;
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
@@ -1215,11 +1218,11 @@ public class BamView extends JPanel
if(maxEnd < recordStart)
{
- ypos = (getHeight() - scaleHeight)-2;
+ ypos = (getHeight() - scaleHeight)-ydiff;
maxEnd = recordEnd+2;
}
else
- ypos = ypos-2;
+ ypos = ypos-ydiff;
}
else
g2.setColor(DARK_GREEN);
@@ -1263,11 +1266,14 @@ public class BamView extends JPanel
drawScale(g2, start, end, pixPerBase, ((getHeight()+scaleHeight)/2));
int ymid = (getHeight()/ 2);
+ int ydiff = 2;
+ if(isOrientation)
+ ydiff= 4;
// positive strand
- drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -2, pixPerBase, stroke);
+ drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -ydiff, pixPerBase, stroke);
// negative strand
- drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), 2, pixPerBase, stroke);
+ drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), ydiff, pixPerBase, stroke);
}
private void drawStrand(Graphics2D g2,
@@ -1402,7 +1408,10 @@ public class BamView extends JPanel
else
scaleHeight = 0;
- int ypos = getHeight() - scaleHeight - 3;
+ int ydiff = 3;
+ if(isOrientation)
+ ydiff= 5;
+ int ypos = getHeight() - scaleHeight - ydiff;
int lastEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
@@ -1413,7 +1422,7 @@ public class BamView extends JPanel
if(pr.sam1.getAlignmentStart() > lastEnd)
{
- ypos = getHeight() - scaleHeight - 3;
+ ypos = getHeight() - scaleHeight - ydiff;
if(pr.sam2 != null)
{
@@ -1423,7 +1432,7 @@ public class BamView extends JPanel
lastEnd = pr.sam1.getAlignmentEnd();
}
else
- ypos = ypos - 3;
+ ypos = ypos - ydiff;
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
--
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