From a6bc0eea3c5c17e824d9922ec742bc30814f70a0 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 30 Jun 2010 13:51:08 +0000
Subject: [PATCH] fix for zoomed in nucleotide view showing reads with gaps
joined by lines
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14129 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 48 ++++++++++++++-----
1 file changed, 35 insertions(+), 13 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 9b579072a..82a69a680 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -878,8 +878,10 @@ public class BamView extends JPanel
g2.drawString(readSeq.substring(readPos, readPos+1),
refPos*ALIGNMENT_PIX_PER_BASE, ypos);
+
+
}
-
+
// look for insertions
if(markInsertions.isSelected() && i < blocks.size()-1)
{
@@ -905,24 +907,44 @@ public class BamView extends JPanel
g2.setColor(col);
}
}
+
+ // highlight
+ if(highlightSAMRecord != null &&
+ highlightSAMRecord.getReadName().equals(samRecord.getReadName()))
+ {
+ refPos = block.getReferenceStart() + offset - refSeqStart;
+ int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
+ int width = block.getLength()*ALIGNMENT_PIX_PER_BASE;
+ Color col1 = g2.getColor();
+ g2.setColor(Color.red);
+ g2.drawRect(xstart, ypos-BASE_HEIGHT, width, BASE_HEIGHT);
+ if(i < blocks.size()-1)
+ {
+ int nextStart =
+ (blocks.get(i+1).getReferenceStart() + offset - refSeqStart)*ALIGNMENT_PIX_PER_BASE;
+ g2.drawLine(xstart+width, ypos-(BASE_HEIGHT/2), nextStart, ypos-(BASE_HEIGHT/2));
+ }
+
+ g2.setColor(col1);
+ }
+ else if(i < blocks.size()-1)
+ {
+ refPos = block.getReferenceStart() + offset - refSeqStart;
+ int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
+ int width = block.getLength()*ALIGNMENT_PIX_PER_BASE;
+ int nextStart =
+ (blocks.get(i+1).getReferenceStart() + offset - refSeqStart)*ALIGNMENT_PIX_PER_BASE;
+ g2.drawLine(xstart+width, ypos-(BASE_HEIGHT/2), nextStart, ypos-(BASE_HEIGHT/2));
+ }
}
- // highlight
- if(highlightSAMRecord != null &&
- highlightSAMRecord.getReadName().equals(samRecord.getReadName()) &&
- blocks.size() > 0)
- {
- refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
- int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
- int width = len*ALIGNMENT_PIX_PER_BASE;
- g2.setColor(Color.red);
- g2.drawRect(xstart, ypos-BASE_HEIGHT, width, BASE_HEIGHT);
- }
-
if(lastMousePoint != null && blocks.size() > 0)
{
refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
+
+ refPos = blocks.get(blocks.size()-1).getReferenceStart()+
+ blocks.get(blocks.size()-1).getLength()+offset-refSeqStart;
int xend = (refPos+len)*ALIGNMENT_PIX_PER_BASE;
if(lastMousePoint.getY() > ypos-11 && lastMousePoint.getY() < ypos)
--
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