diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 4db318a0869c2005c9b0b715237b3478ba23cfa2..31931887598a7fc0973a2535070b70a13ab5013e 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -53,6 +53,8 @@ import java.awt.event.MouseMotionListener;
import java.awt.event.WindowEvent;
import java.awt.event.WindowFocusListener;
import java.io.File;
+import java.lang.management.ManagementFactory;
+import java.lang.management.MemoryMXBean;
import java.util.Collections;
import java.util.Enumeration;
import java.util.Hashtable;
@@ -75,6 +77,7 @@ import javax.swing.JPopupMenu;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
+import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.UIManager;
import javax.swing.border.Border;
@@ -100,6 +103,7 @@ import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.EntryFileDialog;
import uk.ac.sanger.artemis.components.FeatureDisplay;
import uk.ac.sanger.artemis.components.MessageDialog;
+import uk.ac.sanger.artemis.components.Utilities;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.Range;
@@ -148,6 +152,7 @@ public class BamView extends JPanel
private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
private boolean showBaseAlignment = false;
+ private JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View");
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
@@ -170,8 +175,8 @@ public class BamView extends JPanel
private int BASE_HEIGHT;
private JPopupMenu popup;
+ private PopupMessageFrame popFrame = new PopupMessageFrame();
-
public BamView(String bam,
String reference,
int nbasesInView)
@@ -194,7 +199,16 @@ public class BamView extends JPanel
}
}
- readHeaderPicard();
+ try
+ {
+ readHeaderPicard();
+ }
+ catch(java.lang.UnsupportedClassVersionError err)
+ {
+ JOptionPane.showMessageDialog(null,
+ "This requires Java 1.6 or higher.",
+ "Check Java Version", JOptionPane.WARNING_MESSAGE);
+ }
// set font size
//setFont(getFont().deriveFont(12.f));
@@ -338,7 +352,7 @@ public class BamView extends JPanel
File indexFile = new File(bam+".bai");
final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
inputSam.setValidationStringency(ValidationStringency.SILENT);
-
+
if(readsInView == null)
readsInView = new Vector<SAMRecord>();
else
@@ -367,6 +381,7 @@ public class BamView extends JPanel
thisEnd = thisLength;
//System.out.println("READ "+seqNames.get(i)+" "+thisStart+".."+thisEnd);
+
iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd);
}
lastLen = len;
@@ -392,14 +407,29 @@ public class BamView extends JPanel
*/
private void iterateOverBam(final SAMFileReader inputSam,
String refName, int start, int end)
- {
+ {
CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
+ MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
+
while ( it.hasNext() )
{
try
{
SAMRecord samRecord = it.next();
readsInView.add(samRecord);
+
+ float heapNow =
+ (float)((float)memory.getHeapMemoryUsage().getUsed()/(float)memory.getHeapMemoryUsage().getMax());
+ if(heapNow > 0.97)
+ {
+ popFrame.show("Memory Limit",
+ "Over 97 % of the maximum memory limit ("+
+ (memory.getHeapMemoryUsage().getMax()/1000000.f)+" Mb).\n"+
+ "Zoom in or consider increasing the memory for this application.",
+ BamView.this.getLocationOnScreen().y,
+ 20000);
+ break;
+ }
}
catch(Exception e)
{
@@ -479,14 +509,35 @@ public class BamView extends JPanel
// "sequence length = "+getSequenceLength()+
// " pixPerBase="+pixPerBase);
-
+ boolean changeToStackView = false;
+ MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
if(laststart != start ||
lastend != end)
{
setCursor(cbusy);
try
{
+ float heapFractionUsedBefore = (float)((float)memory.getHeapMemoryUsage().getUsed()/(float)memory.getHeapMemoryUsage().getMax());
+ //System.out.println("Heap memory used before "+heapFractionUsedBefore+"\n");
+
readFromBamPicard(start, end);
+
+ float heapFractionUsedAfter =
+ (float)((float)memory.getHeapMemoryUsage().getUsed()/
+ (float)memory.getHeapMemoryUsage().getMax());
+
+ //System.out.println("Heap Max : "+memory.getHeapMemoryUsage().getMax());
+ //System.out.println("Heap Used : "+memory.getHeapMemoryUsage().getUsed());
+ //System.out.println("Heap memory used "+heapFractionUsedAfter);
+
+ if((heapFractionUsedAfter-heapFractionUsedBefore) > 0.06 && !isStackView &&
+ heapFractionUsedAfter > 0.8)
+ {
+ checkBoxStackView.setSelected(true);
+ isStackView = true;
+ changeToStackView = true;
+ }
+
if((!isStackView && !isStrandStackView) || pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
Collections.sort(readsInView, new SAMRecordComparator());
@@ -495,6 +546,7 @@ public class BamView extends JPanel
catch(OutOfMemoryError ome)
{
JOptionPane.showMessageDialog(this, "Out of Memory");
+ readsInView.clear();
return;
}
}
@@ -520,6 +572,18 @@ public class BamView extends JPanel
coveragePanel.repaint();
}
}
+
+ if(changeToStackView)
+ {
+ popFrame.show("Stack View",
+ "Note :: Changed to the stack view to save memory.\n"+
+ "Currently this is using "+
+ (memory.getHeapMemoryUsage().getUsed()/1000000.f)+" Mb "+
+ "and the maximum\nmemory limit is "+
+ (memory.getHeapMemoryUsage().getMax()/1000000.f)+" Mb.",
+ BamView.this.getLocationOnScreen().y,
+ 20000);
+ }
}
@@ -1628,7 +1692,6 @@ public class BamView extends JPanel
view.add(checkBoxSNPs);
view.add(new JSeparator());
- final JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View");
final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
final JCheckBoxMenuItem checkBoxStrandStackView = new JCheckBoxMenuItem("Strand Stack View");
@@ -2143,6 +2206,58 @@ public class BamView extends JPanel
SAMRecord sam2;
}
+ class PopupMessageFrame extends JFrame
+ {
+ private static final long serialVersionUID = 1L;
+ private JTextArea textArea = new JTextArea();
+ PopupMessageFrame()
+ {
+ getRootPane().putClientProperty("Window.alpha", new Float(0.8f));
+ textArea.setWrapStyleWord(true);
+ textArea.setEditable(false);
+ getContentPane().add(textArea);
+ }
+
+ protected void show(String title, String msg, int ypos, long aliveTime)
+ {
+ setTitle(title);
+ textArea.setText(msg);
+ pack();
+ Utilities.centreJustifyFrame(this, ypos);
+ setVisible(true);
+ requestFocus();
+
+ HideFrameThread thread = new HideFrameThread(this, aliveTime);
+ thread.start();
+ }
+ }
+
+ class HideFrameThread extends Thread
+ {
+ private long aliveTime;
+ private JFrame f;
+
+ public HideFrameThread(JFrame f, long aliveTime)
+ {
+ this.f = f;
+ this.aliveTime = aliveTime;
+ }
+
+ public void run()
+ {
+ try
+ {
+ Thread.sleep(aliveTime);
+ }
+ catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ f.setVisible(false);
+ }
+ }
+
+
public static void main(String[] args)
{
String bam = args[0];