From 374f5eb57739cb15a9aa8bf39cfbe58b3cb80931 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 23 Sep 2009 15:37:45 +0000
Subject: [PATCH] colour reads in stack view based on if they are unique and if
the have a mapped paired read
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11885 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/JamView.java | 76 +++++++++++--------
1 file changed, 44 insertions(+), 32 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index 0b07938ba..a167abadf 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -139,7 +139,9 @@ public class JamView extends JPanel
private boolean showBaseAlignment = false;
/** Used to colour the frames. */
- private Color light_grey = new Color(200, 200, 200);
+ private Color lightGrey = new Color(200, 200, 200);
+ private Color darkGreen = new Color(0, 150, 0);
+
private int ALIGNMENT_PIX_PER_BASE;
private JPopupMenu popup;
@@ -448,8 +450,7 @@ public class JamView extends JPanel
ruler.repaint();
int ypos = 0;
-
-
+
String refSeq = null;
int refSeqStart = start;
if(bases != null)
@@ -469,7 +470,7 @@ public class JamView extends JPanel
bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
int xpos = (refSeqStart-1)*ALIGNMENT_PIX_PER_BASE;
- g2.setColor(light_grey);
+ g2.setColor(lightGrey);
g2.fillRect(xpos, ypos-11,
jspView.getViewport().getWidth()+(ALIGNMENT_PIX_PER_BASE*2), 11);
drawSelectionRange(g2, pixPerBase, start, end);
@@ -660,7 +661,20 @@ public class JamView extends JPanel
drawYScale(g2, start, pixPerBase);
}
-
+ /**
+ * Draw the reads as lines in vertical stacks. The reads are colour
+ * coded as follows:
+ *
+ * blue - reads are unique and are paired with a mapped mate
+ * black - reads are unique and are not paired or have an unmapped mate
+ * green - reads are non-unique
+ *
+ * @param g2
+ * @param seqLength
+ * @param pixPerBase
+ * @param start
+ * @param end
+ */
private void drawStackView(Graphics2D g2,
int seqLength,
float pixPerBase,
@@ -683,43 +697,41 @@ public class JamView extends JPanel
scaleHeight = 0;
int ypos = (getHeight() - scaleHeight);
- int lastEnd = 0;
+ int maxEnd = 0;
+ int lstStart = 0;
+ int lstEnd = 0;
g2.setColor(Color.blue);
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
-
- int recordStart;
- int recordEnd;
- if(samRecord.getAlignmentEnd() > samRecord.getAlignmentStart())
- {
- recordStart = samRecord.getAlignmentStart();
- recordEnd = samRecord.getAlignmentEnd();
- }
- else
- {
- recordStart = samRecord.getAlignmentEnd();
- recordEnd = samRecord.getAlignmentStart();
- }
+
+ int recordStart = samRecord.getAlignmentStart();;
+ int recordEnd = samRecord.getAlignmentEnd();
- if(lastEnd < recordStart)
- {
- ypos = (getHeight() - scaleHeight)-2;
- lastEnd = recordEnd;
+ if(lstStart != recordStart || lstEnd != recordEnd)
+ {
+ if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
+ samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
+ g2.setColor(Color.black);
+ else
+ g2.setColor(Color.blue);
+
+ if(maxEnd < recordStart)
+ {
+ ypos = (getHeight() - scaleHeight)-2;
+ maxEnd = recordEnd+2;
+ }
+ else
+ ypos = ypos-2;
}
else
- ypos = ypos-2;
+ g2.setColor(darkGreen);
- drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+ lstStart = recordStart;
+ lstEnd = recordEnd;
- if(ypos > getHeight())
- {
- Dimension d = getPreferredSize();
- d.setSize(getPreferredSize().getWidth(), ypos);
- setPreferredSize(d);
- revalidate();
- }
+ drawRead(g2, samRecord, pixPerBase, stroke, ypos);
}
}
--
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