From 201a68f9aaed8c5bbd563cc80c42e5225c878778 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 12 Oct 2009 10:14:50 +0000
Subject: [PATCH] changes to memory monitoring
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@12044 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 65 +++++++++++++++----
1 file changed, 52 insertions(+), 13 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 319318875..8a0ed8a88 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -176,7 +176,9 @@ public class BamView extends JPanel
private JPopupMenu popup;
private PopupMessageFrame popFrame = new PopupMessageFrame();
-
+ public static org.apache.log4j.Logger logger4j =
+ org.apache.log4j.Logger.getLogger(BamView.class);
+
public BamView(String bam,
String reference,
int nbasesInView)
@@ -410,25 +412,35 @@ public class BamView extends JPanel
{
CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
-
+ int checkMemAfter = 8000;
+ int cnt = 0;
+
while ( it.hasNext() )
{
try
{
+ cnt++;
SAMRecord samRecord = it.next();
readsInView.add(samRecord);
- float heapNow =
- (float)((float)memory.getHeapMemoryUsage().getUsed()/(float)memory.getHeapMemoryUsage().getMax());
- if(heapNow > 0.97)
+ if(cnt > checkMemAfter)
{
- popFrame.show("Memory Limit",
- "Over 97 % of the maximum memory limit ("+
+ cnt = 0;
+ float heapFraction =
+ (float)((float)memory.getHeapMemoryUsage().getUsed()/
+ (float)memory.getHeapMemoryUsage().getMax());
+ logger4j.debug("Heap memory usage (used/max): "+heapFraction);
+
+ if(heapFraction > 0.97)
+ {
+ popFrame.show("Data Read Incomplete",
+ "Over 97 % of the maximum memory\nlimit ("+
(memory.getHeapMemoryUsage().getMax()/1000000.f)+" Mb).\n"+
- "Zoom in or consider increasing the memory for this application.",
- BamView.this.getLocationOnScreen().y,
+ "Zoom in or consider increasing the\nmemory for this application.",
+ mainPanel.getLocationOnScreen().y,
20000);
- break;
+ break;
+ }
}
}
catch(Exception e)
@@ -581,7 +593,7 @@ public class BamView extends JPanel
(memory.getHeapMemoryUsage().getUsed()/1000000.f)+" Mb "+
"and the maximum\nmemory limit is "+
(memory.getHeapMemoryUsage().getMax()/1000000.f)+" Mb.",
- BamView.this.getLocationOnScreen().y,
+ mainPanel.getLocationOnScreen().y,
20000);
}
}
@@ -1692,9 +1704,34 @@ public class BamView extends JPanel
view.add(checkBoxSNPs);
view.add(new JSeparator());
+ ButtonGroup group = new ButtonGroup();
final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
final JCheckBoxMenuItem checkBoxStrandStackView = new JCheckBoxMenuItem("Strand Stack View");
-
+ final JCheckBoxMenuItem checkIsizeStackView = new JCheckBoxMenuItem("Inferred Size View", true);
+ group.add(checkBoxStackView);
+ group.add(checkBoxPairedStackView);
+ group.add(checkBoxStrandStackView);
+ group.add(checkIsizeStackView);
+
+ checkIsizeStackView.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ laststart = -1;
+ lastend = -1;
+
+ if(checkIsizeStackView.isSelected())
+ {
+ isStackView = false;
+ isPairedStackView = false;
+ isStrandStackView = false;
+ }
+ repaint();
+ }
+ });
+ view.add(checkIsizeStackView);
+
+
checkBoxStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -2215,6 +2252,7 @@ public class BamView extends JPanel
getRootPane().putClientProperty("Window.alpha", new Float(0.8f));
textArea.setWrapStyleWord(true);
textArea.setEditable(false);
+ setUndecorated(true);
getContentPane().add(textArea);
}
@@ -2223,7 +2261,8 @@ public class BamView extends JPanel
setTitle(title);
textArea.setText(msg);
pack();
- Utilities.centreJustifyFrame(this, ypos);
+ //PopupMessageFrame.this.setLocationRelativeTo(BamView.this);
+ Utilities.centreJustifyFrame(this, Math.abs(ypos));
setVisible(true);
requestFocus();
--
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