From 46f1f348ce62e2f630ed518344626be6f41f5538 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 26 Oct 2012 15:57:12 +0100
Subject: [PATCH] select BAM file in heatmap view
---
.../artemis/components/alignment/BamView.java | 59 +++++++++++--
.../components/alignment/CoveragePanel.java | 87 ++++++++++++++++---
2 files changed, 126 insertions(+), 20 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 3e3ef70d4..d77f92a96 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1829,7 +1829,8 @@ public class BamView extends JPanel
coverageView.drawSelectionRange(g2, pixPerBase, start, end, getHeight(), Color.PINK);
coverageView.draw(g2, getWidth(), hgt, hideBamList);
- coverageView.drawMax(g2);
+ if(!coverageView.isPlotHeatMap())
+ coverageView.drawMax(g2);
}
/**
@@ -3627,8 +3628,10 @@ public class BamView extends JPanel
*/
class PopupListener extends MouseAdapter
{
- JMenuItem gotoMateMenuItem;
- JMenuItem showDetails;
+ private JMenuItem gotoMateMenuItem;
+ private JMenuItem showDetails;
+ private JMenu coverageMenu;
+ private JMenuItem createGroup;
public void mouseClicked(MouseEvent e)
{
@@ -3641,7 +3644,13 @@ public class BamView extends JPanel
if(e.getClickCount() > 1)
getSelection().clear();
else if(e.getButton() == MouseEvent.BUTTON1)
- highlightSAMRecord = mouseOverSAMRecord;
+ {
+ if(isCoverageView(getPixPerBaseByWidth()))
+ coverageView.singleClick(e.isShiftDown(),
+ e.getPoint().y-getJspView().getViewport().getViewPosition().y);
+ else
+ highlightSAMRecord = mouseOverSAMRecord;
+ }
else
highlightRange(e, MouseEvent.BUTTON2_DOWN_MASK);
repaint();
@@ -3661,19 +3670,53 @@ public class BamView extends JPanel
private void maybeShowPopup(MouseEvent e)
{
if(e.isPopupTrigger())
- {
+ {
+ //
+ // main menu options
if(popup == null)
{
popup = new JPopupMenu();
createMenus(popup);
}
-
+
+ //
+ // coverage heatmap menu options
+ if(coverageMenu != null)
+ popup.remove(coverageMenu);
+ if(isCoverageView(getPixPerBaseByWidth()) && coverageView.isPlotHeatMap())
+ {
+ if(coverageMenu == null)
+ {
+ coverageMenu = new JMenu("Coverage HeatMap");
+ final JCheckBoxMenuItem coverageGrid = new JCheckBoxMenuItem("Heatmap grid", false);
+ coverageGrid.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ coverageView.showLabels(coverageGrid.isSelected());
+ }
+ });
+ coverageMenu.add(coverageGrid);
+
+ createGroup = new JMenuItem("Create group from selected BAMs");
+ createGroup.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+
+ }
+ });
+ coverageMenu.add(createGroup);
+ }
+ createGroup.setEnabled(coverageView.hasSelectedBams());
+ popup.add(coverageMenu);
+ }
+
if(gotoMateMenuItem != null)
popup.remove(gotoMateMenuItem);
-
if(showDetails != null)
popup.remove(showDetails);
-
+
if( mouseOverSAMRecord != null &&
mouseOverSAMRecord.sam.getReadPairedFlag() &&
!mouseOverSAMRecord.sam.getMateUnmappedFlag() )
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 19b5188d9..1f3c6e0a4 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -25,11 +25,13 @@
package uk.ac.sanger.artemis.components.alignment;
import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
+import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.geom.GeneralPath;
@@ -62,10 +64,12 @@ import net.sf.samtools.SAMRecord;
private static boolean redraw = false;
private boolean setMaxBases = false;
-
+
private boolean plotByStrand = false;
private boolean plotHeatMap = false;
private List<HeatMapLn> heatPlots;
+ private List<String> selected = new Vector<String>();
+ private boolean showGrid = false;
protected CoveragePanel(final BamView bamView)
{
@@ -259,7 +263,8 @@ import net.sf.samtools.SAMRecord;
{
if(hideBamList != null)
idx = adjustIdx(idx, hideBamList);
- drawHeatMap(g2, hgt, line, idx, thisPlot, fName);
+ drawHeatMap(g2, hgt, line, idx, thisPlot, fName,
+ (idx == plots.size()-1));
}
else
drawLinePlot(g2, wid, hgt, line, thisPlot);
@@ -379,14 +384,14 @@ import net.sf.samtools.SAMRecord;
* @param idx
* @param thisPlot
*/
- private void drawHeatMap(final Graphics2D g2, int hgt, LineAttributes line, int idx, int[][] thisPlot, String fName)
+ private void drawHeatMap(final Graphics2D g2, int hgt, LineAttributes line, int idx, int[][] thisPlot, String fName, boolean lastPlot)
{ // heat map
- int NSHADES = 240;
- int plotHgt = hgt/plots.size();
- int plotPos = plotHgt * idx;
- Color definedColours[] = Plot.makeColours(line.getLineColour(), NSHADES);
+ final int NSHADES = 240;
+ final int plotHgt = hgt/plots.size();
+ final int plotPos = (hgt*idx)/plots.size();
+ final Color definedColours[] = Plot.makeColours(line.getLineColour(), NSHADES);
- heatPlots.add(new HeatMapLn(plotPos, plotPos+plotHgt, idx, fName));
+ heatPlots.add(new HeatMapLn(plotPos, plotPos+plotHgt, fName));
float maxVal = getValue(max);
for(int i=0; i<thisPlot.length; i++)
@@ -406,6 +411,22 @@ import net.sf.samtools.SAMRecord;
g2.setColor(definedColours[ colourIdx ]);
g2.fillRect(xpos, plotPos, (int) (windowSize*2*pixPerBase), plotHgt);
}
+
+ if(showGrid && !lastPlot)
+ {
+ g2.setColor(Color.darkGray);
+ g2.drawLine(0, plotPos+plotHgt-1, bamView.getWidth(), plotPos+plotHgt-1);
+ }
+
+ if(selected.contains(fName))
+ {
+ g2.setColor(Color.darkGray);
+ Stroke stroke = g2.getStroke();
+ g2.setStroke(new BasicStroke(2.f));
+ g2.drawLine(0, plotPos+1, bamView.getWidth(), plotPos+1);
+ g2.drawLine(0, plotPos+plotHgt-1, bamView.getWidth(), plotPos+plotHgt-1);
+ g2.setStroke(stroke);
+ }
}
private AlphaComposite makeComposite(float alpha)
@@ -483,6 +504,13 @@ import net.sf.samtools.SAMRecord;
return null;
}
+
+ protected void showLabels(boolean showLabel)
+ {
+ //
+ this.showGrid = showLabel;
+ bamView.repaint();
+ }
private void defineOpts()
{
@@ -560,16 +588,51 @@ import net.sf.samtools.SAMRecord;
return;
}
}
+
+ /**
+ * Click on heatmap
+ * @param y
+ */
+ protected void singleClick(boolean isShiftDown, int ypos)
+ {
+ if(!isPlotHeatMap())
+ return;
+
+ String sel = null;
+ for(HeatMapLn h: heatPlots)
+ {
+ if(ypos > h.yTop && ypos < h.yBtm)
+ sel = h.fName;
+ }
+
+ if(selected.contains(sel))
+ {
+ if(!isShiftDown)
+ selected.clear();
+ else
+ selected.remove(sel);
+ }
+ else
+ {
+ if(!isShiftDown)
+ selected.clear();
+ selected.add(sel);
+ }
+ }
+
+ protected boolean hasSelectedBams()
+ {
+ return (selected.size() > 0);
+ }
class HeatMapLn
{
- int yTop, yBtm, idx;
- String fName;
- HeatMapLn(int yTop, int yBtm, int idx, String fName)
+ private int yTop, yBtm;
+ private String fName;
+ HeatMapLn(int yTop, int yBtm, String fName)
{
this.yTop = yTop;
this.yBtm = yBtm;
- this.idx = idx;
this.fName = fName;
}
--
GitLab