From 10ff929859f2ae9afd8f6e7361879096e44a919e Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 10 Mar 2011 12:39:23 +0000
Subject: [PATCH] fix for changing window size in coverage plots
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15700 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 75 ++++++-------------
.../components/alignment/CoveragePanel.java | 51 ++++---------
2 files changed, 37 insertions(+), 89 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 30817c4e7..024494706 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -66,6 +66,7 @@ import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
+import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
@@ -223,7 +224,6 @@ public class BamView extends JPanel
int nbasesInView)
{
super();
-
setBackground(Color.white);
this.bamList = bamList;
this.nbasesInView = nbasesInView;
@@ -442,7 +442,7 @@ public class BamView extends JPanel
thisEnd = thisLength;
//System.out.println("READ "+seqNames.get(i)+" "+thisStart+".."+thisEnd);
- iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd, bamIndex, pixPerBase);
+ iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd, bamIndex, pixPerBase, bam);
}
lastLen = len;
}
@@ -450,7 +450,7 @@ public class BamView extends JPanel
else
{
String refName = (String) combo.getSelectedItem();
- iterateOverBam(inputSam, refName, start, end, bamIndex, pixPerBase);
+ iterateOverBam(inputSam, refName, start, end, bamIndex, pixPerBase, bam);
}
//inputSam.close();
@@ -468,7 +468,8 @@ public class BamView extends JPanel
*/
private void iterateOverBam(final SAMFileReader inputSam,
String refName, int start, int end,
- int bamIndex, float pixPerBase)
+ int bamIndex, float pixPerBase,
+ String bam)
{
boolean multipleBAM = false;
if(bamList.size() > 1)
@@ -478,6 +479,8 @@ public class BamView extends JPanel
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
int checkMemAfter = 8000;
int cnt = 0;
+ int seqOffset = getSequenceOffset(refName);
+ int offset = seqOffset- getBaseAtStartOfView();
while ( it.hasNext() )
{
@@ -495,11 +498,14 @@ public class BamView extends JPanel
if(multipleBAM)
samRecord.setAttribute("FL", bamIndex);
- if(isCoverageView(pixPerBase) || isCoverage)
- coverageView.addRecord(samRecord);
+ if(isCoverageView(pixPerBase))
+ coverageView.addRecord(samRecord, offset, bam);
+
+ if(isCoverage)
+ coveragePanel.addRecord(samRecord, offset, bam);
if(isSNPplot)
- snpPanel.addRecord(samRecord);
+ snpPanel.addRecord(samRecord, seqOffset);
if(!isCoverageView(pixPerBase))
readsInView.add(samRecord);
@@ -633,20 +639,20 @@ public class BamView extends JPanel
if(end > seqLength)
end = seqLength;
}
-
-
+
boolean changeToStackView = false;
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
if(laststart != start ||
lastend != end ||
- coverageView.isRedraw())
+ CoveragePanel.isRedraw())
{
- if(isCoverageView(pixPerBase) || isCoverage)
+ if(isCoverageView(pixPerBase))
coverageView.init(this, pixPerBase, start, end);
-
+ if(isCoverage)
+ coveragePanel.init(this, pixPerBase, start, end);
if(isSNPplot)
snpPanel.init(this, pixPerBase, start, end);
-
+
synchronized (this)
{
try
@@ -705,11 +711,7 @@ public class BamView extends JPanel
}
}
}
-
- //System.out.println(start+".."+end+" " +
- // "sequence length = "+getSequenceLength()+
- // " pixPerBase="+pixPerBase);
-
+
laststart = start;
lastend = end;
@@ -728,17 +730,9 @@ public class BamView extends JPanel
else
drawLineView(g2, seqLength, pixPerBase, start, end);
if(isCoverage)
- {
- coveragePanel.setStartAndEnd(start, end);
- coveragePanel.setPixPerBase(pixPerBase);
coveragePanel.repaint();
- }
if(isSNPplot)
- {
- snpPanel.setStartAndEnd(start, end);
- snpPanel.setPixPerBase(pixPerBase);
snpPanel.repaint();
- }
}
if(waitingFrame.isVisible())
@@ -2077,7 +2071,7 @@ public class BamView extends JPanel
jspView = new JScrollPane(this,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
-
+ jspView.setViewportBorder(BorderFactory.createMatteBorder(0, 0, 1, 0, Color.gray));
setDisplay(1, nbasesInView, null);
mainPanel.setLayout(new BorderLayout());
@@ -2103,10 +2097,6 @@ public class BamView extends JPanel
public void adjustmentValueChanged(AdjustmentEvent e)
{
repaint();
- if(coveragePanel != null)
- coveragePanel.repaint();
- if(snpPanel != null)
- snpPanel.repaint();
}
});
bottomPanel.add(scrollBar, BorderLayout.SOUTH);
@@ -2448,7 +2438,7 @@ public class BamView extends JPanel
//
JMenu coverageMenu = new JMenu("Coverage Options");
coverageView.init(this, 0.f, 0, 0);
- coverageView.createMenus(coverageMenu, BamView.this);
+ coverageView.createMenus(coverageMenu);
viewMenu.add(new JSeparator());
viewMenu.add(coverageMenu);
}
@@ -2783,11 +2773,6 @@ public class BamView extends JPanel
return readsInView;
}
- protected Hashtable<String, int[]> getCoveragePlotData()
- {
- return coverageView.getPlotData();
- }
-
protected int getBasesInView()
{
return nbasesInView;
@@ -2876,28 +2861,12 @@ public class BamView extends JPanel
int width = feature_display.getMaxVisibleBases();
setZoomLevel(width);
repaint();
- if(coveragePanel != null && coveragePanel.isVisible())
- {
- coveragePanel.setStartAndEnd(BamView.this.startBase, BamView.this.endBase);
- coveragePanel.setPixPerBase(getPixPerBaseByWidth());
- coveragePanel.repaint();
- }
- if(snpPanel != null && snpPanel.isVisible())
- {
- snpPanel.setStartAndEnd(BamView.this.startBase, BamView.this.endBase);
- snpPanel.setPixPerBase(getPixPerBaseByWidth());
- snpPanel.repaint();
- }
}
else
{
setDisplay(event.getStart(),
event.getStart()+feature_display.getMaxVisibleBases(), event);
repaint();
- if(coveragePanel != null && coveragePanel.isVisible())
- coveragePanel.repaint();
- if(snpPanel != null && snpPanel.isVisible())
- snpPanel.repaint();
}
}
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 9e332d9e3..3a287fcf1 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -57,27 +57,24 @@ import net.sf.samtools.SAMRecord;
private int combinedCoverage[];
private int nBins;
- private boolean redraw = false;
+ private static boolean redraw = false;
private boolean setMaxBases = false;
protected CoveragePanel(final BamView bamView)
{
this();
this.bamView = bamView;
- //initPopupMenu(this, popup);
- createMenus(popup, this);
+ createMenus(popup);
addMouseListener(new PopupListener());
}
protected CoveragePanel()
{
super();
- setBackground(Color.white);
- addMouseListener(new PopupListener());
setMaxBases = true;
}
- protected void createMenus(JComponent menu, final JPanel panel)
+ protected void createMenus(JComponent menu)
{
JMenuItem configure = new JMenuItem("Configure Line(s)...");
configure.addActionListener(new ActionListener()
@@ -100,7 +97,7 @@ import net.sf.samtools.SAMRecord;
public void actionPerformed(ActionEvent e)
{
defineOpts();
- panel.repaint();
+ bamView.repaint();
}
});
menu.add(optMenu);
@@ -113,8 +110,7 @@ import net.sf.samtools.SAMRecord;
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
- List<SAMRecord> readsInView = bamView.getReadsInView();
- if(readsInView == null)
+ if(plots == null)
return;
drawPlot(g2);
drawMax(g2);
@@ -126,7 +122,6 @@ import net.sf.samtools.SAMRecord;
setPixPerBase(pixPerBase);
setStartAndEnd(start, end);
init();
- redraw = false;
}
private void init()
@@ -157,9 +152,7 @@ import net.sf.samtools.SAMRecord;
private void drawPlot(Graphics2D g2)
{
- init();
max = 0;
- plots = bamView.getCoveragePlotData();
Enumeration<String> plotEum = plots.keys();
while(plotEum.hasMoreElements())
{
@@ -169,45 +162,36 @@ import net.sf.samtools.SAMRecord;
if(max < thisPlot[i])
max = thisPlot[i];
}
-
draw(g2, getWidth(), getHeight());
}
- protected void addRecord(SAMRecord thisRead)
+ protected void addRecord(SAMRecord thisRead, int offset, String fileName)
{
- int offset = bamView.getSequenceOffset(thisRead.getReferenceName());
- offset = offset - bamView.getBaseAtStartOfView();
-
- String fileName;
- if(bamView.bamList.size() > 1)
- fileName = bamView.bamList.get((Integer) thisRead.getAttribute("FL"));
- else
- fileName = bamView.bamList.get(0);
int coverage[] = plots.get(fileName);
-
if(coverage == null)
{
coverage = new int[nBins];
for(int k=0; k<coverage.length; k++)
coverage[k] = 0;
plots.put(fileName, coverage);
- }
-
+ }
+
List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
for(int j=0; j<blocks.size(); j++)
{
AlignmentBlock block = blocks.get(j);
+ int refStart = block.getReferenceStart();
for(int k=0; k<block.getLength(); k++)
{
- int pos = block.getReferenceStart() + k + offset;
+ int pos = refStart + k + offset;
int bin = pos/windowSize;
if(bin < 0 || bin > nBins-1)
continue;
-
+
coverage[bin]+=1;
if(coverage[bin] > max)
max = coverage[bin];
-
+
if(includeCombined)
{
combinedCoverage[bin]+=1;
@@ -228,7 +212,7 @@ import net.sf.samtools.SAMRecord;
}
else
lines = getLineAttributes(size);
-
+
Enumeration<String> plotEum = plots.keys();
while(plotEum.hasMoreElements())
{
@@ -242,7 +226,6 @@ import net.sf.samtools.SAMRecord;
index = bamView.bamList.indexOf(fileName);
g2.setColor(lines[index].getLineColour());
-
if(lines[index].getPlotType() == LineAttributes.PLOT_TYPES[0])
{
g2.setStroke(lines[index].getStroke());
@@ -298,7 +281,7 @@ import net.sf.samtools.SAMRecord;
/**
* @return the redraw
*/
- protected boolean isRedraw()
+ protected static boolean isRedraw()
{
if(redraw)
{
@@ -378,9 +361,5 @@ import net.sf.samtools.SAMRecord;
return;
}
}
-
- protected Hashtable<String, int[]> getPlotData()
- {
- return plots;
- }
+
}
\ No newline at end of file
--
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