From 577afa99ff4e5f02e564bc0c981901de6bd711ce Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 2 Mar 2011 16:32:21 +0000
Subject: [PATCH] change zoom out so it switches to a coverage plot
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15638 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../alignment/AbstractGraphPanel.java | 5 +-
.../artemis/components/alignment/BamView.java | 274 ++++++++++-----
.../components/alignment/CoveragePanel.java | 330 ++++++++++++------
.../components/alignment/SnpPanel.java | 2 +-
4 files changed, 418 insertions(+), 193 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java b/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
index d06e68d6e..17d9d1e01 100644
--- a/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
@@ -31,6 +31,7 @@ import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import javax.swing.JCheckBox;
+import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
@@ -49,7 +50,7 @@ public class AbstractGraphPanel extends JPanel
protected int userWinSize = 1;
protected JPopupMenu popup = new JPopupMenu();
- public void initPopupMenu(final JPanel graphPanel)
+ public void initPopupMenu(final JPanel graphPanel, JComponent menu)
{
final JMenuItem setScale = new JMenuItem("Set the Window Size...");
setScale.addActionListener(new ActionListener()
@@ -97,7 +98,7 @@ public class AbstractGraphPanel extends JPanel
graphPanel.repaint();
}
});
- popup.add(setScale);
+ menu.add(setScale);
addMouseListener(new PopupListener());
}
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 630b0298d..3a66ed5bd 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -148,9 +148,7 @@ public class BamView extends JPanel
private boolean isOrientation = false;
private boolean isSingle = false;
private boolean isSNPs = false;
- private boolean isStackView = true;
- private boolean isPairedStackView = false;
- private boolean isStrandStackView = false;
+
private boolean isCoverage = false;
private boolean isSNPplot = false;
@@ -175,18 +173,29 @@ public class BamView extends JPanel
private JMenu bamFilesMenu = new JMenu("BAM files");
private JCheckBoxMenuItem logMenuItem = new JCheckBoxMenuItem("Use Log Scale", logScale);
- private JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View", isStackView);
+
+ private JCheckBoxMenuItem cbStackView = new JCheckBoxMenuItem("Stack", true);
+ private JCheckBoxMenuItem cbPairedStackView = new JCheckBoxMenuItem("Paired Stack");
+ private JCheckBoxMenuItem cbStrandStackView = new JCheckBoxMenuItem("Strand Stack");
+ private JCheckBoxMenuItem cbIsizeStackView = new JCheckBoxMenuItem("Inferred Size", false);
+ private JCheckBoxMenuItem cbCoverageView = new JCheckBoxMenuItem("Coverage", false);
+ private JCheckBoxMenuItem cbLastSelected;
+
+ private ButtonGroup buttonGroup = new ButtonGroup();
+
private JCheckBoxMenuItem colourByCoverageColour = new JCheckBoxMenuItem("Coverage Plot Colours");
private JCheckBoxMenuItem baseQualityColour = new JCheckBoxMenuItem("Base Quality");
private JCheckBoxMenuItem markInsertions = new JCheckBoxMenuItem("Mark Insertions", true);
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
+ private CoveragePanel coverageView = new CoveragePanel();
+
/** Used to colour the frames. */
- private Color lightGrey = new Color(200, 200, 200);
- private Color darkGreen = new Color(0, 150, 0);
- private Color darkOrange = new Color(255,140,0);
- private Color deepPink = new Color(139,10,80);
+ private static Color LIGHT_GREY = new Color(200, 200, 200);
+ private static Color DARK_GREEN = new Color(0, 150, 0);
+ private static Color DARK_ORANGE = new Color(255,140,0);
+ private static Color DEEP_PINK = new Color(139,10,80);
private Point lastMousePoint = null;
private SAMRecord mouseOverSAMRecord = null;
@@ -195,6 +204,7 @@ public class BamView extends JPanel
// record of where a mouse drag starts
private int dragStart = -1;
+ private static int MAX_BASES = 26000;
private int maxHeight = 800;
private boolean concatSequences = false;
@@ -270,6 +280,12 @@ public class BamView extends JPanel
MultiLineToolTipUI.initialize();
setToolTipText("");
+
+ buttonGroup.add(cbStackView);
+ buttonGroup.add(cbPairedStackView);
+ buttonGroup.add(cbStrandStackView);
+ buttonGroup.add(cbIsizeStackView);
+ buttonGroup.add(cbCoverageView);
}
public String getToolTipText()
@@ -392,7 +408,7 @@ public class BamView extends JPanel
* Read a SAM or BAM file.
* @throws IOException
*/
- private void readFromBamPicard(int start, int end, int bamIndex)
+ private void readFromBamPicard(int start, int end, int bamIndex, float pixPerBase)
throws IOException
{
// Open the input file. Automatically detects whether input is SAM or BAM
@@ -426,7 +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);
+ iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd, bamIndex, pixPerBase);
}
lastLen = len;
}
@@ -434,7 +450,7 @@ public class BamView extends JPanel
else
{
String refName = (String) combo.getSelectedItem();
- iterateOverBam(inputSam, refName, start, end, bamIndex);
+ iterateOverBam(inputSam, refName, start, end, bamIndex, pixPerBase);
}
//inputSam.close();
@@ -452,7 +468,7 @@ public class BamView extends JPanel
*/
private void iterateOverBam(final SAMFileReader inputSam,
String refName, int start, int end,
- int bamIndex)
+ int bamIndex, float pixPerBase)
{
boolean multipleBAM = false;
if(bamList.size() > 1)
@@ -478,7 +494,12 @@ public class BamView extends JPanel
{
if(multipleBAM)
samRecord.setAttribute("FL", bamIndex);
- readsInView.add(samRecord);
+
+ if(isCoverageView(pixPerBase) || isCoverage)
+ coverageView.addRecord(samRecord);
+
+ if(!isCoverageView(pixPerBase))
+ readsInView.add(samRecord);
}
}
@@ -610,11 +631,18 @@ public class BamView extends JPanel
end = seqLength;
}
+
boolean changeToStackView = false;
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
if(laststart != start ||
- lastend != end)
+ lastend != end ||
+ coverageView.isRedraw())
{
+ if(isCoverageView(pixPerBase) || isCoverage)
+ {
+ coverageView.init(this, pixPerBase, start, end);
+ }
+
synchronized (this)
{
try
@@ -626,11 +654,11 @@ public class BamView extends JPanel
readsInView = new Vector<SAMRecord>();
else
readsInView.clear();
-
+
for(int i=0; i<bamList.size(); i++)
{
if(!hideBamList.contains(i))
- readFromBamPicard(start, end, i);
+ readFromBamPicard(start, end, i, pixPerBase);
}
float heapFractionUsedAfter = (float) ((float) memory.getHeapMemoryUsage().getUsed() /
(float) memory.getHeapMemoryUsage().getMax());
@@ -640,19 +668,17 @@ public class BamView extends JPanel
// System.out.println("Heap memory used "+heapFractionUsedAfter);
if ((heapFractionUsedAfter - heapFractionUsedBefore) > 0.06
- && !isStackView && heapFractionUsedAfter > 0.8)
+ && !isStackView() && heapFractionUsedAfter > 0.8)
{
- checkBoxStackView.setSelected(true);
- isStackView = true;
+ cbStackView.setSelected(true);
changeToStackView = true;
}
- if ((!isStackView && !isStrandStackView)
- || pixPerBase * 1.08f >= ALIGNMENT_PIX_PER_BASE)
+ if((!isStackView() && !isStrandStackView()) || isBaseAlignmentView(pixPerBase))
{
Collections.sort(readsInView, new SAMRecordComparator());
}
- else if( (isStackView || isStrandStackView) &&
+ else if( (isStackView() || isStrandStackView()) &&
bamList.size() > 1)
{
// merge multiple BAM files
@@ -679,18 +705,26 @@ public class BamView extends JPanel
//System.out.println(start+".."+end+" " +
// "sequence length = "+getSequenceLength()+
// " pixPerBase="+pixPerBase);
-
+
laststart = start;
lastend = end;
- if(showBaseAlignment)
+
+ if(showBaseAlignment)
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
{
- if(isStackView)
+ if(isCoverageView(pixPerBase))
+ {
+ int hgt = jspView.getVisibleRect().height;
+ g2.translate(0, getHeight()-hgt);
+ coverageView.draw(g2, getWidth(), hgt);
+ coverageView.drawMax(g2);
+ }
+ else if(isStackView())
drawStackView(g2, seqLength, pixPerBase, start, end);
- else if(isPairedStackView)
+ else if(isPairedStackView())
drawPairedStackView(g2, seqLength, pixPerBase, start, end);
- else if(isStrandStackView)
+ else if(isStrandStackView())
drawStrandStackView(g2, seqLength, pixPerBase, start, end);
else
drawLineView(g2, seqLength, pixPerBase, start, end);
@@ -778,7 +812,7 @@ public class BamView extends JPanel
refSeq =
bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
- g2.setColor(lightGrey);
+ g2.setColor(LIGHT_GREY);
g2.fillRect(0, ypos-11, mainPanel.getWidth(), 11);
drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);
g2.setColor(Color.black);
@@ -925,7 +959,7 @@ public class BamView extends JPanel
if(insertions == null)
insertions = new Hashtable<Integer, String>();
- g2.setColor(deepPink);
+ g2.setColor(DEEP_PINK);
int xscreen = (refPos+1)*ALIGNMENT_PIX_PER_BASE;
insertions.put(xscreen,
@@ -1001,9 +1035,9 @@ public class BamView extends JPanel
if (baseQuality < 10)
g2.setColor(Color.blue);
else if (baseQuality < 20)
- g2.setColor(darkGreen);
+ g2.setColor(DARK_GREEN);
else if (baseQuality < 30)
- g2.setColor(darkOrange);
+ g2.setColor(DARK_ORANGE);
else
g2.setColor(Color.black);
}
@@ -1189,7 +1223,7 @@ public class BamView extends JPanel
ypos = ypos-2;
}
else
- g2.setColor(darkGreen);
+ g2.setColor(DARK_GREEN);
lstStart = recordStart;
lstEnd = recordEnd;
@@ -1283,7 +1317,7 @@ public class BamView extends JPanel
ypos = ypos + ystep;
}
else
- g2.setColor(darkGreen);
+ g2.setColor(DARK_GREEN);
lstStart = recordStart;
lstEnd = recordEnd;
@@ -1494,7 +1528,7 @@ public class BamView extends JPanel
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(samRecord));
else if(offTheTop)
- g2.setColor(darkOrange);
+ g2.setColor(DARK_ORANGE);
else if(samRecord.getReadNegativeStrandFlag() &&
samRecord.getMateNegativeStrandFlag()) // strand of the query (1 for reverse)
g2.setColor(Color.red);
@@ -2143,104 +2177,83 @@ public class BamView extends JPanel
menu.add(new JSeparator());
JMenu viewMenu = new JMenu("Views");
- 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", false);
- checkBoxStackView.setFont(checkIsizeStackView.getFont());
- baseQualityColour.setFont(checkIsizeStackView.getFont());
- colourByCoverageColour.setFont(checkIsizeStackView.getFont());
- markInsertions.setFont(checkIsizeStackView.getFont());
-
- group.add(checkBoxStackView);
- group.add(checkBoxPairedStackView);
- group.add(checkBoxStrandStackView);
- group.add(checkIsizeStackView);
-
- checkIsizeStackView.addActionListener(new ActionListener()
+ cbStackView.setFont(cbIsizeStackView.getFont());
+ baseQualityColour.setFont(cbIsizeStackView.getFont());
+ colourByCoverageColour.setFont(cbIsizeStackView.getFont());
+ markInsertions.setFont(cbIsizeStackView.getFont());
+
+ cbIsizeStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
- if(checkIsizeStackView.isSelected())
- {
- isStackView = false;
- isPairedStackView = false;
- isStrandStackView = false;
+ if(isIsizeStackView())
logMenuItem.setEnabled(true);
- }
repaint();
}
});
- viewMenu.add(checkIsizeStackView);
+ viewMenu.add(cbIsizeStackView);
- checkBoxStackView.addActionListener(new ActionListener()
+ cbStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
- isStackView = !isStackView;
-
- if(isStackView)
- {
- isPairedStackView = !isStackView;
- isStrandStackView = !isStackView;
- checkBoxPairedStackView.setSelected(!isStackView);
- checkBoxStrandStackView.setSelected(!isStackView);
+
+ if(isStackView())
logMenuItem.setEnabled(false);
- }
repaint();
}
});
- viewMenu.add(checkBoxStackView);
+ viewMenu.add(cbStackView);
- checkBoxPairedStackView.addActionListener(new ActionListener()
+ cbPairedStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
- isPairedStackView = !isPairedStackView;
- if(isPairedStackView)
- {
- isStackView = !isPairedStackView;
- isStrandStackView = !isPairedStackView;
- checkBoxStackView.setSelected(!isPairedStackView);
- checkBoxStrandStackView.setSelected(!isPairedStackView);
+ if(cbPairedStackView.isSelected())
logMenuItem.setEnabled(false);
- }
repaint();
}
});
- viewMenu.add(checkBoxPairedStackView);
+ viewMenu.add(cbPairedStackView);
- checkBoxStrandStackView.addActionListener(new ActionListener()
+ cbStrandStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
- isStrandStackView = !isStrandStackView;
-
- if(isStrandStackView)
+
+ if(isStrandStackView())
{
- isStackView = !isStrandStackView;
- isPairedStackView = !isStrandStackView;
- checkBoxStackView.setSelected(!isStrandStackView);
- checkBoxPairedStackView.setSelected(!isStrandStackView);
setViewportMidPoint();
logMenuItem.setEnabled(false);
}
repaint();
}
});
- viewMenu.add(checkBoxStrandStackView);
+ viewMenu.add(cbStrandStackView);
+
+ cbCoverageView.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ laststart = -1;
+ lastend = -1;
+ repaint();
+ }
+ });
+ viewMenu.add(cbCoverageView);
+
menu.add(viewMenu);
final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks");
@@ -2325,6 +2338,8 @@ public class BamView extends JPanel
{
isCoverage = !isCoverage;
coveragePanel.setVisible(isCoverage);
+ laststart = -1;
+ lastend = -1;
repaint();
}
});
@@ -2387,7 +2402,7 @@ public class BamView extends JPanel
}
menu.add(new JSeparator());
- logMenuItem.setFont(checkIsizeStackView.getFont());
+ logMenuItem.setFont(cbIsizeStackView.getFont());
menu.add(logMenuItem);
logMenuItem.addActionListener(new ActionListener()
{
@@ -2407,7 +2422,13 @@ public class BamView extends JPanel
new SAMRecordFilter(BamView.this);
}
});
- menu.add(new JSeparator());
+
+ //
+ JMenu coverageMenu = new JMenu("Coverage Options");
+ coverageView.init(this, 0.f, 0, 0);
+ coverageView.createMenus(coverageMenu, BamView.this);
+ viewMenu.add(new JSeparator());
+ viewMenu.add(coverageMenu);
}
public void setVisible(boolean visible)
@@ -2442,7 +2463,7 @@ public class BamView extends JPanel
this.nbasesInView = nbasesInView;
float pixPerBase = getPixPerBaseByWidth();
- if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
+ if(isBaseAlignmentView(pixPerBase))
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
this.nbasesInView = (int)(mainPanel.getWidth()/pixPerBase);
@@ -2457,9 +2478,20 @@ public class BamView extends JPanel
}
else if(jspView != null)
{
+ if(!cbCoverageView.isSelected() && nbasesInView >= MAX_BASES)
+ {
+ cbLastSelected = getSelectedCheckBoxMenuItem();
+ cbCoverageView.setSelected(true);
+ }
+ else if(cbCoverageView.isSelected() && nbasesInView < MAX_BASES && cbLastSelected != null)
+ {
+ cbLastSelected.setSelected(true);
+ cbLastSelected = null;
+ }
+
jspView.setColumnHeaderView(null);
- if(!isStrandStackView)
+ if(!isStrandStackView())
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
showBaseAlignment = false;
@@ -2661,6 +2693,63 @@ public class BamView extends JPanel
fileIndex = (Integer) samRecord.getAttribute("FL");
return lines[fileIndex].getLineColour();
}
+
+ protected int getMaxBases()
+ {
+ return MAX_BASES;
+ }
+
+ protected void setMaxBases(int max)
+ {
+ MAX_BASES = max;
+ }
+
+ private boolean isStackView()
+ {
+ return cbStackView.isSelected();
+ }
+
+ private boolean isPairedStackView()
+ {
+ return cbPairedStackView.isSelected();
+ }
+
+ private boolean isStrandStackView()
+ {
+ return cbStrandStackView.isSelected();
+ }
+
+ private boolean isCoverageView(float pixPerBase)
+ {
+ if(isBaseAlignmentView(pixPerBase))
+ return false;
+ return cbCoverageView.isSelected();
+ }
+
+ private boolean isIsizeStackView()
+ {
+ return cbIsizeStackView.isSelected();
+ }
+
+ private boolean isBaseAlignmentView(float pixPerBase)
+ {
+ if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
+ return true;
+ return false;
+ }
+
+ private JCheckBoxMenuItem getSelectedCheckBoxMenuItem()
+ {
+ if(isStackView())
+ return cbStackView;
+ if(isPairedStackView())
+ return cbPairedStackView;
+ if(isStrandStackView())
+ return cbStrandStackView;
+ if(isIsizeStackView())
+ return cbIsizeStackView;
+ return cbCoverageView;
+ }
private Selection getSelection()
{
@@ -2672,6 +2761,11 @@ public class BamView extends JPanel
return readsInView;
}
+ protected Hashtable<String, int[]> getCoveragePlotData()
+ {
+ return coverageView.getPlotData();
+ }
+
protected int getBasesInView()
{
return nbasesInView;
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 62336f11c..130ddaf4c 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -29,6 +29,8 @@ import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.geom.GeneralPath;
@@ -36,8 +38,13 @@ import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
-import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMRecord;
@@ -45,46 +52,62 @@ import net.sf.samtools.SAMRecord;
public class CoveragePanel extends AbstractGraphPanel
{
private static final long serialVersionUID = 1L;
- private BamView jamView;
+ private BamView bamView;
private static LineAttributes lines[];
private boolean includeCombined = false;
+ private Hashtable<String, int[]> plots;
+ private int combinedCoverage[];
+ private int nBins;
+ private int windowSize;
+ private int max;
+ private boolean redraw = false;
+ private boolean setMaxBases = false;
- public CoveragePanel(final BamView jamView)
+ protected CoveragePanel(final BamView bamView)
+ {
+ this();
+ this.bamView = bamView;
+ //initPopupMenu(this, popup);
+ createMenus(popup, this);
+ addMouseListener(new PopupListener());
+ }
+
+ protected CoveragePanel()
{
super();
setBackground(Color.white);
- this.jamView = jamView;
- initPopupMenu(this);
-
- JMenuItem configure = new JMenuItem("Configure...");
+ addMouseListener(new PopupListener());
+ setMaxBases = true;
+ }
+
+ protected void createMenus(JComponent menu, final JPanel panel)
+ {
+ JMenuItem configure = new JMenuItem("Configure Line(s)...");
configure.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- int size = jamView.bamList.size();
+ int size = bamView.bamList.size();
if(includeCombined)
size++;
lines =
- LineAttributes.configurePlots(jamView.bamList,
+ LineAttributes.configurePlots(bamView.bamList,
getLineAttributes(size), CoveragePanel.this);
}
});
- popup.add(configure);
+ menu.add(configure);
- if(jamView.bamList.size() > 1)
+ JMenuItem optMenu = new JMenuItem("Options...");
+ optMenu.addActionListener(new ActionListener()
{
- final JCheckBoxMenuItem showCombined = new JCheckBoxMenuItem("Show Combined Plot", false);
- showCombined.addActionListener(new ActionListener()
+ public void actionPerformed(ActionEvent e)
{
- public void actionPerformed(ActionEvent e)
- {
- includeCombined = showCombined.isSelected();
- repaint();
- }
- });
- popup.add(showCombined);
- }
+ defineOpts();
+ panel.repaint();
+ }
+ });
+ menu.add(optMenu);
}
/**
@@ -94,15 +117,27 @@ import net.sf.samtools.SAMRecord;
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
-
- List<SAMRecord> readsInView = jamView.getReadsInView();
+ List<SAMRecord> readsInView = bamView.getReadsInView();
if(readsInView == null)
return;
-
- int windowSize;
+ drawPlot(g2);
+ drawMax(g2);
+ }
+
+ protected void init(BamView bamView, float pixPerBase, int start, int end)
+ {
+ this.bamView = bamView;
+ setPixPerBase(pixPerBase);
+ setStartAndEnd(start, end);
+ init();
+ redraw = false;
+ }
+
+ private void init()
+ {
if(autoWinSize)
{
- windowSize = (jamView.getBasesInView()/200);
+ windowSize = (bamView.getBasesInView()/300);
userWinSize = windowSize;
}
else
@@ -110,84 +145,97 @@ import net.sf.samtools.SAMRecord;
if(windowSize < 1)
windowSize = 1;
+ nBins = Math.round((end-start+1.f)/windowSize);
- int nBins = Math.round((end-start+1.f)/windowSize);
- int max = drawPlot(g2, nBins, windowSize);
-
+ plots = new Hashtable<String, int[]>();
+ combinedCoverage = null;
+ if(includeCombined)
+ {
+ combinedCoverage = new int[nBins];
+ for(int k=0; k<combinedCoverage.length; k++)
+ combinedCoverage[k] = 0;
+ plots.put("-1", combinedCoverage);
+ }
+ max = 0;
+ }
+
+ protected void drawMax(Graphics2D g2)
+ {
String maxStr = Float.toString(max/windowSize);
FontMetrics fm = getFontMetrics(getFont());
g2.setColor(Color.black);
- int xpos = getWidth() - fm.stringWidth(maxStr) -
- jamView.getJspView().getVerticalScrollBar().getWidth();
+ int xpos = bamView.getJspView().getVisibleRect().width - fm.stringWidth(maxStr) -
+ bamView.getJspView().getVerticalScrollBar().getWidth();
g2.drawString(maxStr, xpos, fm.getHeight());
}
+ private void drawPlot(Graphics2D g2)
+ {
+ init();
+ max = 0;
+ plots = bamView.getCoveragePlotData();
+ Enumeration<String> plotEum = plots.keys();
+ while(plotEum.hasMoreElements())
+ {
+ String fileName = (String) plotEum.nextElement();
+ int[] thisPlot = plots.get(fileName);
+ for(int i=1; i<thisPlot.length; i++)
+ if(max < thisPlot[i])
+ max = thisPlot[i];
+ }
+
+ draw(g2, getWidth(), getHeight());
+ }
- private int drawPlot(Graphics2D g2, int nBins, int windowSize)
+ protected void addRecord(SAMRecord thisRead)
{
- List<SAMRecord> readsInView = jamView.getReadsInView();
- List<String> bamList = jamView.bamList;
- final Hashtable<String, Integer[]> plots = new Hashtable<String, Integer[]>();
+ 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);
- Integer combinedCoverage[] = null;
- if(includeCombined)
+ if(coverage == null)
{
- combinedCoverage = new Integer[nBins];
- for(int k=0; k<combinedCoverage.length; k++)
- combinedCoverage[k] = 0;
- plots.put("-1", combinedCoverage);
- }
+ coverage = new int[nBins];
+ for(int k=0; k<coverage.length; k++)
+ coverage[k] = 0;
+ plots.put(fileName, coverage);
+ }
- int max = 0;
- for(int i=0; i<readsInView.size(); i++)
+ List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
+ for(int j=0; j<blocks.size(); j++)
{
- SAMRecord thisRead = readsInView.get(i);
- int offset = jamView.getSequenceOffset(thisRead.getReferenceName());
- offset = offset - jamView.getBaseAtStartOfView();
-
- String fileName;
- if(bamList.size() > 1)
- fileName = bamList.get((Integer) thisRead.getAttribute("FL"));
- else
- fileName = bamList.get(0);
- Integer coverage[] = plots.get(fileName);
-
- if(coverage == null)
- {
- coverage = new Integer[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);
+ for(int k=0; k<block.getLength(); k++)
{
- AlignmentBlock block = blocks.get(j);
-
- for(int k=0; k<block.getLength(); k++)
+ int pos = block.getReferenceStart() + 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)
{
- int pos = block.getReferenceStart() + 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;
- if(combinedCoverage[bin] > max)
- max = combinedCoverage[bin];
- }
- }
- }
+ combinedCoverage[bin]+=1;
+ if(combinedCoverage[bin] > max)
+ max = combinedCoverage[bin];
+ }
+ }
}
-
- int size = jamView.bamList.size();
+ }
+
+ protected void draw(Graphics2D g2, int wid, int hgt)
+ {
+ int size = bamView.bamList.size();
if(includeCombined)
{
lines = getLineAttributes(size+1);
@@ -200,13 +248,13 @@ import net.sf.samtools.SAMRecord;
while(plotEum.hasMoreElements())
{
String fileName = (String) plotEum.nextElement();
- Integer[] thisPlot = plots.get(fileName);
-
+ int[] thisPlot = plots.get(fileName);
+
int index;
if(fileName.equals("-1"))
index = lines.length-1;
else
- index = bamList.indexOf(fileName);
+ index = bamView.bamList.indexOf(fileName);
g2.setColor(lines[index].getLineColour());
@@ -216,10 +264,10 @@ import net.sf.samtools.SAMRecord;
for(int i=1; i<thisPlot.length; i++)
{
int x0 = (int) ((((i-1)*(windowSize)) - windowSize/2.f)*pixPerBase);
- int y0 = (int) (getHeight() - (((float)thisPlot[i-1]/(float)max)*getHeight()));
+ int y0 = (int) (hgt - (((float)thisPlot[i-1]/(float)max)*hgt));
int x1 = (int) (((i*(windowSize)) - windowSize/2.f)*pixPerBase);
- int y1 = (int) (getHeight() - (((float)thisPlot[i]/(float)max)*getHeight()));
-
+ int y1 = (int) (hgt - (((float)thisPlot[i]/(float)max)*hgt));
+
g2.drawLine(x0, y0, x1, y1);
}
}
@@ -228,28 +276,26 @@ import net.sf.samtools.SAMRecord;
g2.setComposite(makeComposite(0.75f));
GeneralPath shape = new GeneralPath();
- shape.moveTo(0,getHeight());
+ shape.moveTo(0,hgt);
for(int i=0; i<thisPlot.length; i++)
{
float xpos = ((i*(windowSize)) - windowSize/2.f)*pixPerBase;
shape.lineTo(xpos,
- getHeight() - (((float)thisPlot[i]/(float)max)*getHeight()));
+ hgt - (((float)thisPlot[i]/(float)max)*hgt));
}
- shape.lineTo(getWidth(),getHeight());
+ shape.lineTo(wid,hgt);
g2.fill(shape);
}
}
- return max;
}
private AlphaComposite makeComposite(float alpha)
{
int type = AlphaComposite.SRC_OVER;
return(AlphaComposite.getInstance(type, alpha));
- }
-
-
+ }
+
protected static LineAttributes[] getLineAttributes(int nsize)
{
if(lines == null)
@@ -263,4 +309,88 @@ import net.sf.samtools.SAMRecord;
}
return lines;
}
+
+ /**
+ * @return the redraw
+ */
+ protected boolean isRedraw()
+ {
+ return redraw;
+ }
+
+ private void defineOpts()
+ {
+ final JPanel opts = new JPanel(new GridBagLayout());
+ final GridBagConstraints c = new GridBagConstraints();
+
+ final JTextField newBaseMax = new JTextField(Integer.toString(bamView.getMaxBases()), 10);
+ c.gridy = 0;
+ if(setMaxBases)
+ {
+ final JLabel labMax1 = new JLabel("Zoom level before switching");
+ final JLabel labMax2 = new JLabel("to coverage view (in bases):");
+ c.anchor = GridBagConstraints.WEST;
+ opts.add(labMax1, c);
+ c.gridy = c.gridy+1;
+ opts.add(labMax2, c);
+ opts.add(newBaseMax, c);
+ }
+
+ final JTextField newWinSize = new JTextField(Integer.toString(userWinSize), 10);
+ final JLabel lab = new JLabel("Window size:");
+ lab.setEnabled(!autoWinSize);
+ newWinSize.setEnabled(!autoWinSize);
+
+ c.gridy = c.gridy+1;
+ c.anchor = GridBagConstraints.EAST;
+ opts.add(lab, c);
+ opts.add(newWinSize, c);
+
+ final JCheckBox autoSet = new JCheckBox("Automatically set window size", autoWinSize);
+ autoSet.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ lab.setEnabled(!autoSet.isSelected());
+ newWinSize.setEnabled(!autoSet.isSelected());
+ }
+ });
+ c.anchor = GridBagConstraints.WEST;
+ c.gridy = c.gridy+1;
+ c.gridwidth = GridBagConstraints.REMAINDER;
+ opts.add(autoSet, c);
+
+ final JCheckBox showCombined = new JCheckBox("Show Combined Plot", includeCombined);
+ if(bamView.bamList.size() == 1)
+ showCombined.setEnabled(false);
+ c.gridy = c.gridy+1;
+ opts.add(showCombined, c);
+
+ String window_options[] = { "OK", "Cancel" };
+ int select = JOptionPane.showOptionDialog(null, opts, "Coverage Options",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.QUESTION_MESSAGE, null,
+ window_options, window_options[0]);
+
+ if(select == 1)
+ return;
+
+ redraw = true;
+ autoWinSize = autoSet.isSelected();
+ includeCombined = showCombined.isSelected();
+ try
+ {
+ userWinSize = Integer.parseInt(newWinSize.getText().trim());
+ if(setMaxBases)
+ bamView.setMaxBases(Integer.parseInt(newBaseMax.getText().trim()));
+ }
+ catch (NumberFormatException nfe)
+ {
+ return;
+ }
+ }
+
+ protected Hashtable<String, int[]> getPlotData()
+ {
+ return plots;
+ }
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/SnpPanel.java b/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
index 80b4349bd..453ae6fae 100644
--- a/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
@@ -60,7 +60,7 @@ import net.sf.samtools.SAMRecord;
setBackground(Color.white);
this.bamView = bamView;
this.bases = bases;
- initPopupMenu(this);
+ initPopupMenu(this, popup);
JMenuItem configure = new JMenuItem("Filter by Base Quality...");
configure.addActionListener(new ActionListener()
--
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