From 4574a3aae556ae70c514d5deb9dc93b48b0fc28b Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 10 Apr 2012 14:45:57 +0100
Subject: [PATCH] use ReadCountDialog
---
.../artemis/components/alignment/BamView.java | 16 ++++++++++++----
.../components/alignment/MappedReads.java | 2 +-
2 files changed, 13 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index b489c8b09..6f11ad392 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -2181,7 +2181,12 @@ public class BamView extends JPanel
Box yBox = Box.createVerticalBox();
yBox.add(overlap);
yBox.add(spliced);
- JOptionPane.showMessageDialog(null, yBox, "Read Count Option", JOptionPane.INFORMATION_MESSAGE);
+
+ final ReadCountDialog opts = new ReadCountDialog(new JFrame(),
+ "Read Count Options", feature_display, yBox);
+ if(opts.getStatus() == -1)
+ return;
+ //JOptionPane.showMessageDialog(null, yBox, "Read Count Option", JOptionPane.INFORMATION_MESSAGE);
new MappedReads(features, (String)combo.getSelectedItem(), samFileReaderHash, bamList,
seqNames, offsetLengths, concatSequences, seqLengths,
@@ -2211,9 +2216,12 @@ public class BamView extends JPanel
if(seqLengths.size() > 1)
yBox.add(allRefSeqs);
-
- JOptionPane.showMessageDialog(null, yBox, "Read Count Option", JOptionPane.INFORMATION_MESSAGE);
-
+
+ final ReadCountDialog opts = new ReadCountDialog(new JFrame(),
+ "RPKM Options", feature_display, yBox);
+ if(opts.getStatus() == -1)
+ return;
+
int seqlen = 0;
if(feature_display != null)
seqlen = feature_display.getSequenceLength();
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index 4ff56d521..577a64d9d 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -220,7 +220,7 @@ public class MappedReads
sampleCounts.add(cnt);
}
- featureReadCount.put(f.getSystematicName(), sampleCounts);
+ featureReadCount.put(ReadCountDialog.getFeatureName(f), sampleCounts);
}
return null;
}
--
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