for multiple bam files draw a coverage plot for each

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13367 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/alignment/CoveragePanel.java

@@ -24,14 +24,23 @@
 
 package uk.ac.sanger.artemis.components.alignment;
 
+import java.awt.AlphaComposite;
 import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.awt.geom.GeneralPath;
+import java.util.Enumeration;
+import java.util.Hashtable;
 import java.util.List;
 
+import javax.swing.JMenuItem;
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
 
 import net.sf.samtools.SAMRecord;
 
@@ -42,14 +51,29 @@ import net.sf.samtools.SAMRecord;
     private int start;
     private int end;
     private float pixPerBase;
-    private Color lightBlue = new Color(30,144,255);
     private BamView jamView;
+    private JPopupMenu popup;
+    private LineAttributes lines[];
     
-    public CoveragePanel(BamView jamView)
+    public CoveragePanel(final BamView jamView)
     {
       super();
       setBackground(Color.white);
       this.jamView = jamView;
+      
+      popup = new JPopupMenu();
+      JMenuItem configure = new JMenuItem("Configure...");
+      configure.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          lines =
+            LineAttributes.configurePlots(jamView.bamList, lines, CoveragePanel.this);
+        }
+      });
+      popup.add(configure);
+      
+      addMouseListener(new PopupListener());
     }
     
     /**
@@ -69,9 +93,23 @@ import net.sf.samtools.SAMRecord;
         windowSize = 5;
 
       int nBins = Math.round((end-start+1.f)/windowSize);
-      int coverage[] = new int[nBins];
-      for(int i=0; i<coverage.length; i++)
-        coverage[i] = 0;
+      int max = drawPlot(g2, nBins, windowSize);
+      
+      String maxStr = Float.toString(max/windowSize);
+      FontMetrics fm = getFontMetrics(getFont());
+      g2.setColor(Color.black);
+      
+      int xpos = getWidth() - fm.stringWidth(maxStr) - 
+                 jamView.getJspView().getVerticalScrollBar().getWidth();
+      g2.drawString(maxStr, xpos, fm.getHeight());
+    }
+    
+    
+    private int drawPlot(Graphics2D g2, int nBins, int windowSize)
+    {
+      List<SAMRecord> readsInView = jamView.getReadsInView();
+      List<String> bamList = jamView.bamList;
+      final Hashtable<String, Integer[]> plots = new Hashtable<String, Integer[]>();
       
       int max = 0;
       for(int i=0; i<readsInView.size(); i++)
@@ -79,42 +117,84 @@ import net.sf.samtools.SAMRecord;
         SAMRecord thisRead = readsInView.get(i);
         int offset = jamView.getSequenceOffset(thisRead.getReferenceName());
         int length = thisRead.getReadLength();
-        
+
         for(int j=0; j<length;j++)
         {
           int bin = 
             (int)(((thisRead.getAlignmentStart()-start) + j + offset) / windowSize);
 
-          if(bin < 0 || bin > coverage.length-1)
-            continue;   
+          if(bin < 0 || bin > nBins-1)
+            continue;
+
+          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);
+          }         
+ 
           coverage[bin]+=1;
           if(coverage[bin] > max)
             max = coverage[bin];
         }
       }
-      
-      g2.setColor(lightBlue);
-      GeneralPath shape = new GeneralPath();
-      shape.moveTo(0,getHeight());
-      for(int i=0; i<coverage.length; i++)
+
+      lines = getLineAttributes();
+      Enumeration<String> plotEum = plots.keys();
+      while(plotEum.hasMoreElements())
       {
-        float xpos = ((i*(windowSize)) - windowSize/2.f)*pixPerBase;
-        shape.lineTo(xpos,
-            getHeight() - (((float)coverage[i]/(float)max)*getHeight()));
-      }
+        String fileName = (String) plotEum.nextElement();
+        Integer[] thisPlot = plots.get(fileName);
+        
+        g2.setColor(lines[bamList.indexOf(fileName)].getLineColour());
+        
+        if(lines[bamList.indexOf(fileName)].getPlotType() == LineAttributes.PLOT_TYPES[0])
+        {
+          g2.setStroke(lines[bamList.indexOf(fileName)].getStroke());
+          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 x1 = (int) (((i*(windowSize)) - windowSize/2.f)*pixPerBase);
+            int y1 = (int) (getHeight() - (((float)thisPlot[i]/(float)max)*getHeight()));
+            
+            g2.drawLine(x0, y0, x1, y1);
+          }
+        }
+        else // filled plots
+        {
+          g2.setComposite(makeComposite(0.75f));
 
-      shape.lineTo(getWidth(),getHeight());
-      g2.fill(shape);
+          GeneralPath shape = new GeneralPath();
+          shape.moveTo(0,getHeight());
+          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()));
+          }
 
-      String maxStr = Float.toString(max/windowSize);
-      FontMetrics fm = getFontMetrics(getFont());
-      g2.setColor(Color.black);
-      
-      int xpos = getWidth() - fm.stringWidth(maxStr) - 
-                 jamView.getJspView().getVerticalScrollBar().getWidth();
-      g2.drawString(maxStr, xpos, fm.getHeight());
+          shape.lineTo(getWidth(),getHeight());
+          g2.fill(shape);
+        }
+      }
+      return max;
     }
     
+    private AlphaComposite makeComposite(float alpha)
+    {
+      int type = AlphaComposite.SRC_OVER;
+      return(AlphaComposite.getInstance(type, alpha));
+     }
+
     protected void setStartAndEnd(int start, int end)
     {
       this.start = start;
@@ -125,4 +205,45 @@ import net.sf.samtools.SAMRecord;
     {
       this.pixPerBase = pixPerBase;
     }
+    
+    
+    private LineAttributes[] getLineAttributes()
+    {
+      if(lines == null)
+        lines = LineAttributes.init(jamView.bamList.size());
+      return lines;
+    }
+  
+  
+  /**
+   * Popup menu listener
+   */
+   class PopupListener extends MouseAdapter
+   {
+     JMenuItem gotoMateMenuItem;
+     JMenuItem showDetails;
+     
+     public void mouseClicked(MouseEvent e)
+     {
+     }
+     
+     public void mousePressed(MouseEvent e)
+     {
+       maybeShowPopup(e);
+     }
+
+     public void mouseReleased(MouseEvent e)
+     {
+       maybeShowPopup(e);
+     }
+
+     private void maybeShowPopup(MouseEvent e)
+     {
+       if(e.isPopupTrigger())
+       {
+         popup.show(e.getComponent(),
+                 e.getX(), e.getY());
+       }
+     }
+   }
   }
\ No newline at end of file

uk/ac/sanger/artemis/components/alignment/LineAttributes.java

+/* LineAttributes.java
+ *
+ * created: 2010
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2010  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ **/
+
+
+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSlider;
+import javax.swing.ListCellRenderer;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+/**
+ * Define line attributes for graphs lines
+ */
+public class LineAttributes
+{
+  /** defines the colour */
+  private Color lineColour = Color.black;
+  /** defines the line Stroke - size and style */
+  private BasicStroke stroke;
+  
+  private static float dotDash[] = {10.f, 5.f, 3.f, 5.f};
+  private static float dash[] = {10.f};
+  
+  private static BasicStroke style1 = 
+      new BasicStroke(1.f);
+  private static BasicStroke style2 = 
+      new BasicStroke(1.f, BasicStroke.CAP_BUTT,
+                      BasicStroke.JOIN_MITER, 
+                      1.f, dash, 0.f);
+  private static BasicStroke style3 = 
+      new BasicStroke(1.f, BasicStroke.CAP_BUTT, 
+                      BasicStroke.JOIN_MITER, 
+                      1.f, dotDash, 0.f);
+  
+  /** available stroke types */
+  private static BasicStroke[] STROKES = 
+       new BasicStroke[]{ style1, style2, style3 };
+  
+  /** fill in underneath wiggle plots */
+  public static String PLOT_TYPES[]    = 
+          { "Open", "Filled" };
+  private String plotType = PLOT_TYPES[0];
+
+  /**
+   * Contruct a LineAttributes instance
+   * @param lineColour
+   */
+  public LineAttributes(Color lineColour)
+  {
+    this.lineColour = lineColour;
+    this.stroke = new BasicStroke(1.f);
+  }
+  
+  public Color getLineColour()
+  {
+    return lineColour;
+  }
+
+  public void setLineColour(Color lineColour)
+  {
+    this.lineColour = lineColour;
+  }
+
+  public BasicStroke getStroke()
+  {
+    return stroke;
+  }
+
+  public void setStroke(BasicStroke stroke)
+  {
+    this.stroke = stroke;
+  }
+  
+  protected static BasicStroke[] getStrokes()
+  {
+    return STROKES;
+  }
+  
+  /**
+   * Given a stroke return the index for it based on the style.
+   * @param stroke
+   * @return
+   */
+  private static int getStyleIndex(BasicStroke stroke)
+  {
+    float myDash[] = stroke.getDashArray();
+    if(myDash != null && 
+       myDash.length == dotDash.length)
+      return 2;
+    else if(myDash != null && 
+            myDash.length == dash.length &&
+            myDash[0] == dash[0])
+      return 1;
+    else
+      return 0;
+  }
+  
+  public String getPlotType()
+  {
+    return plotType;
+  }
+
+  public static LineAttributes[]  init(int numPlots)
+  {
+    final Color frameColour[] = { 
+        Color.red, 
+        new Color(0,200,0), 
+        Color.blue,
+        Color.magenta,
+        new Color(50, 255, 255),
+        Color.yellow,
+        Color.black };
+    LineAttributes lines[] = new LineAttributes[numPlots];
+    
+    if(numPlots == 1)
+    {
+      lines[0] = new LineAttributes(Color.black);
+      return lines;
+    }
+    
+    for(int i=0; i<numPlots; i++)
+    {
+      if(i < frameColour.length)
+        lines[i] = new LineAttributes(frameColour[i]);
+      else
+        lines[i] = new LineAttributes(Color.black);
+    }
+    return lines;
+  }
+
+  
+  /**
+   * Utility used by uk.ac.sanger.artemis.components.Plot
+   * @param numPlots
+   * @param lines
+   * @param plot
+   * @return
+   */
+  public static LineAttributes[] configurePlots(
+                                    final List<String> bamList, 
+                                    final LineAttributes[] lines,
+                                    final JPanel covergePanel)
+  {
+    JPanel panel = new JPanel(new GridBagLayout());
+    GridBagConstraints c = new GridBagConstraints();
+
+    final int numPlots = bamList.size();
+    final LineAttributes[] thislines;
+    if(lines.length < numPlots)
+      thislines = init(numPlots);
+    else
+      thislines = lines;
+    
+    int gridx = 0;
+    int gridy = 0;
+    c.gridy = gridy++;
+    c.gridx = gridx;
+    // open / filled    
+    panel.add(new JLabel("Plot Options:"), c);
+    final JComboBox openPlot = new JComboBox(PLOT_TYPES);
+    openPlot.setSelectedItem(thislines[0].plotType);
+    openPlot.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        for(int i=0; i<numPlots; i++)
+          thislines[i].plotType =    
+            (String) openPlot.getSelectedItem();
+        covergePanel.repaint();
+      }
+    });
+    c.gridy = gridy++;
+    panel.add(openPlot, c);
+    
+    c.gridy = gridy++;
+    panel.add(new JLabel("Line Options:"), c);
+    c.gridx = gridx++;
+    c.gridy = gridy++;
+    gridx++;
+    
+    final JCheckBox applyToAll = new JCheckBox("Apply colour to all");
+
+    panel.add(new JLabel("Colour"), c);
+    c.gridx = gridx++;
+    panel.add(new JLabel("Line style"), c);
+   
+    c.gridx = gridx;
+    panel.add(new JLabel("Line size"), c);
+    
+    for(int i=0; i<numPlots; i++)
+    {
+      c.gridy = gridy++;
+      final int colourNumber = i;
+      gridx = 0;
+
+      c.gridx = 0;
+      c.gridwidth = GridBagConstraints.REMAINDER;
+      c.anchor = GridBagConstraints.NORTHWEST;
+      final JLabel bamFileName = new JLabel(bamList.get(i));
+      panel.add(bamFileName,c);
+      
+      c.gridwidth = 1;
+      c.gridy = gridy++;
+      final JLabel colourLabel = new JLabel("   ");
+      colourLabel.setBackground(thislines[i].getLineColour());
+      colourLabel.setOpaque(true);
+      c.gridx = gridx++;
+      panel.add(colourLabel,c);
+
+      JButton butt = new JButton("Select");
+      butt.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent _)
+        {
+          Color newColour = JColorChooser.showDialog(null, "Colour Chooser",
+              thislines[colourNumber].getLineColour());
+          
+          if(applyToAll.isSelected())
+          {
+            for(int iplot=0; iplot<numPlots; iplot++)
+              thislines[iplot].setLineColour(newColour);
+          }
+          else
+            thislines[colourNumber].setLineColour(newColour); 
+          colourLabel.setBackground(thislines[colourNumber].getLineColour());
+          covergePanel.repaint();
+        }
+      });
+      c.gridx = gridx++;
+      panel.add(butt, c);
+      
+      // line style
+      final JSlider slider = new JSlider(1, 10, 
+          (int)lines[colourNumber].getStroke().getLineWidth());
+      Integer index[] = new Integer[STROKES.length];
+      for(int j=0; j<index.length; j++)
+        index[j] = j;
+      final JComboBox lineStyle = new JComboBox(index);
+      lineStyle.setRenderer(new LineStyleListRenderer());
+      lineStyle.setSelectedIndex(
+          LineAttributes.getStyleIndex(thislines[colourNumber].getStroke()));
+      lineStyle.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
+        {
+          thislines[colourNumber].setStroke(
+              STROKES[lineStyle.getSelectedIndex()]);
+          setLineSize(covergePanel, slider, thislines, colourNumber);
+        }
+      });
+      c.gridx = gridx++;
+      panel.add(lineStyle, c);
+      
+      
+      // line size
+      slider.addChangeListener(new ChangeListener()
+      {
+        public void stateChanged(ChangeEvent e)
+        {
+          setLineSize(covergePanel, slider, thislines, colourNumber);
+        }
+      });
+      c.gridx = gridx;
+      panel.add(slider, c);
+      
+    }
+    
+    c.gridx = 0;
+    c.gridy = gridy++;
+    c.gridwidth = GridBagConstraints.REMAINDER;
+    c.anchor = GridBagConstraints.WEST;
+    panel.add(applyToAll, c);
+
+    JScrollPane jsp = new JScrollPane(panel, 
+        JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+        JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+    Dimension d = Toolkit.getDefaultToolkit().getScreenSize();
+    
+    if(panel.getPreferredSize().height > d.height/2)
+    {
+      d.setSize(jsp.getPreferredSize().width, d.height/2);
+      jsp.setPreferredSize(d);
+    }
+    
+    String config_options[] = { "OK" };
+    JOptionPane.showOptionDialog(null,
+                                 jsp, "Configure Lines",
+                                 JOptionPane.DEFAULT_OPTION,
+                                 JOptionPane.QUESTION_MESSAGE,
+                                 null, config_options, config_options[0]);
+    return thislines;
+  }
+  
+  
+  private static void setLineSize(JPanel covergePanel, JSlider slider,
+                           LineAttributes[] thislines, int number)
+  {
+    BasicStroke oldStroke = thislines[number].getStroke();
+    BasicStroke newStroke = new BasicStroke(slider.getValue(),
+        BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER, 
+        1.f, oldStroke.getDashArray(), 0.f);
+    thislines[number].setStroke(newStroke);
+    covergePanel.repaint();
+  }
+}
+
+
+/**
+ * Renderer for the JComboBox to define different line styles.
+ */
+class LineStyleListRenderer extends JComponent implements ListCellRenderer
+{
+  private static final long serialVersionUID = 1L;
+  private int selectedIndex = 0;
+  public LineStyleListRenderer()
+  {
+    super();
+    setMinimumSize(new Dimension(100, 20));
+    setPreferredSize(new Dimension(100, 20));
+  }
+
+  /**
+   * This method finds the selected index.
+   */
+  public Component getListCellRendererComponent(JList list, Object value,
+      int index, boolean isSelected, boolean cellHasFocus)
+  {
+    selectedIndex = ((Integer) value).intValue();
+    return this;
+  }
+  
+  public void paintComponent(Graphics g)
+  {
+    super.paintComponent(g);
+    Graphics2D g2 = (Graphics2D)g;
+    g2.setStroke(LineAttributes.getStrokes()[selectedIndex]);
+    g2.drawLine(10, 10, 90, 10);
+  }
+}
\ No newline at end of file