From c4265973b98fb1c25891cf1cf5684dc213d589ae Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 29 Oct 2012 15:46:36 +0000
Subject: [PATCH] add heatmap options
---
.../artemis/components/alignment/BamView.java | 15 ++++++--
.../components/alignment/CoveragePanel.java | 5 +++
.../components/alignment/GroupBamFrame.java | 37 +++++++++++++++----
3 files changed, 45 insertions(+), 12 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index d77f92a96..34199b863 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -216,6 +216,7 @@ public class BamView extends JPanel
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
+ private GroupBamFrame groupsFrame = new GroupBamFrame(this, bamFilesMenu);
private CoveragePanel coverageView = new CoveragePanel();
protected static String BAM_SUFFIX = ".*\\.(bam|cram)$";
@@ -2413,9 +2414,8 @@ public class BamView extends JPanel
});
bamFilesMenu.setFont(addBam.getFont());
-
+
final JMenuItem groupBams = new JMenuItem("Group BAMs ...");
- final GroupBamFrame groupsFrame = new GroupBamFrame(this, bamFilesMenu);
groupBams.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
@@ -3688,7 +3688,7 @@ public class BamView extends JPanel
if(coverageMenu == null)
{
coverageMenu = new JMenu("Coverage HeatMap");
- final JCheckBoxMenuItem coverageGrid = new JCheckBoxMenuItem("Heatmap grid", false);
+ final JCheckBoxMenuItem coverageGrid = new JCheckBoxMenuItem("Show heatmap grid", false);
coverageGrid.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -3701,9 +3701,16 @@ public class BamView extends JPanel
createGroup = new JMenuItem("Create group from selected BAMs");
createGroup.addActionListener(new ActionListener()
{
+ private int n = 1;
public void actionPerformed(ActionEvent e)
{
-
+ String groupName = "group_"+n;
+ groupsFrame.addGroup(groupName);
+ final List<String> selected = coverageView.getSelected();
+ for(String sel: selected)
+ groupsFrame.addToGroup((new File(sel)).getName(), groupName);
+ groupsFrame.updateAndDisplay();
+ n++;
}
});
coverageMenu.add(createGroup);
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 1f3c6e0a4..4810c54fb 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -624,6 +624,11 @@ import net.sf.samtools.SAMRecord;
{
return (selected.size() > 0);
}
+
+ protected List<String> getSelected()
+ {
+ return selected;
+ }
class HeatMapLn
{
diff --git a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
index 148a80d90..ee720fca2 100644
--- a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
+++ b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
@@ -66,7 +66,7 @@ class GroupBamFrame extends JFrame
newGroup.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
{
- addGroup(bamView, bamFilesMenu, newGroup, jsp);
+ addGroup(newGroup.getText().trim());
}
});
newGroup.addFocusListener(new java.awt.event.FocusAdapter() {
@@ -92,7 +92,7 @@ class GroupBamFrame extends JFrame
JOptionPane.INFORMATION_MESSAGE);
return;
}
- addGroup(bamView, bamFilesMenu, newGroup, jsp);
+ addGroup(newGroup.getText().trim());
}
});
xBox.add(Box.createHorizontalGlue());
@@ -148,18 +148,16 @@ class GroupBamFrame extends JFrame
setVisible(true);
}
- private void addGroup(final BamView bamView, final JMenu bamFilesMenu,
- final JTextField newGroup, final JScrollPane jsp)
+ protected void addGroup(final String newGroup)
{
final String tmpGroups[] = new String[groups.length+1];
- for(int i=0; i<groups.length; i++)
- tmpGroups[i] = groups[i];
- tmpGroups[tmpGroups.length-1] = newGroup.getText().trim();
+ System.arraycopy(groups, 0, tmpGroups, 0, groups.length);
+ tmpGroups[tmpGroups.length-1] = newGroup;
groups = tmpGroups;
updateGroupPanel();
updateBamPanel();
- jsp.validate();
+ validate();
}
private void updateBamPanel()
@@ -203,6 +201,29 @@ class GroupBamFrame extends JFrame
}
}
+ /**
+ * Add a BAM to a specified group
+ * @param bam
+ * @param group
+ */
+ protected void addToGroup(String bam, String group)
+ {
+ final Component cs[] = bamFilesMenu.getMenuComponents();
+ for(Component cp : cs)
+ {
+ if(cp instanceof JCheckBoxMenuItem)
+ {
+ final JCheckBoxMenuItem cbBam = (JCheckBoxMenuItem) cp;
+ final String thisBam = cbBam.getText();
+ if(bam.equals(thisBam))
+ {
+ bamGroupMap.get(cbBam).setSelectedItem(group);
+ return;
+ }
+ }
+ }
+ }
+
/**
* For a give BAM file return the group it belongs to.
* @param bamName
--
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