add graphs

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15609 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/variant/GraphPanel.java

+package uk.ac.sanger.artemis.components.variant;
+
+import java.awt.BasicStroke;
+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.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.geom.GeneralPath;
+import java.io.IOException;
+import java.text.DecimalFormat;
+
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JTextField;
+
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.components.variant.BCFReader.BCFReaderIterator;
+
+
+public class GraphPanel extends JPanel
+{
+  private static final long serialVersionUID = 1L;
+
+  
+  protected boolean autoWinSize = true;
+  protected int userWinSize = 1;
+  protected JPopupMenu popup = new JPopupMenu();
+  private VCFview vcfView;
+  
+  private static String TYPES[] = { "SNP", "DP" };
+  private int type = 0;  // 0 - SNP; 1 - DP
+  
+  public GraphPanel(final VCFview vcfView)
+  {
+    super();
+    this.vcfView = vcfView;
+    setBackground(Color.white);
+    initPopupMenu(this);
+  }
+  
+  /**
+   * Override
+   */
+  protected void paintComponent(Graphics g)
+  {
+    super.paintComponent(g);
+    Graphics2D g2 = (Graphics2D)g;  
+    
+    float pixPerBase = vcfView.getPixPerBaseByWidth();
+    int sbeg = vcfView.getBaseAtStartOfView();
+    int send = sbeg+vcfView.getBasesInView();
+    
+    int windowSize;
+    if(autoWinSize)
+    {
+      windowSize = (vcfView.getBasesInView()/300);
+      userWinSize = windowSize;
+    }
+    else
+      windowSize = userWinSize;
+    if(windowSize < 1)
+      windowSize = 1;
+
+    int nBins = Math.round((send-sbeg+1.f)/windowSize);
+    int snpCount[] = new int[nBins];
+    int max = 0;
+    for(int i=0; i<snpCount.length; i++)
+      snpCount[i] = 0;
+    
+    AbstractVCFReader readers[] = vcfView.getVcfReaders();
+    FeatureVector features = vcfView.getCDSFeaturesInRange(sbeg, send);
+    for(int i=0; i<readers.length; i++)
+    {
+      max = countAll(readers[i], sbeg, send, windowSize, nBins, features, snpCount, max);
+    }
+    
+    g2.setColor(Color.red);
+    g2.setStroke(new BasicStroke(1.f));
+    
+    if(windowSize == 1)
+    {
+      GeneralPath shape = new GeneralPath();
+      shape.moveTo(0,getHeight());
+      for(int i=0; i<snpCount.length; i++)
+      {
+        float xpos1 = ((i*windowSize) )*pixPerBase;
+        float xpos2 = ((i*windowSize) + windowSize)*pixPerBase;
+        
+        shape.lineTo(xpos1,getHeight());
+        shape.lineTo(xpos1,
+            getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
+        shape.lineTo(xpos2,
+            getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
+        
+        shape.lineTo(xpos2,getHeight());
+      }
+
+      shape.lineTo(getWidth(),getHeight());
+      g2.fill(shape);
+    }
+    else
+    {
+      for(int i=1; i<snpCount.length; i++)
+      {
+        int x0 = (int) (((i*windowSize) - windowSize/2.f)*pixPerBase);
+        int y0 = (int) (getHeight() - (((float)snpCount[i-1]/(float)max)*getHeight()));
+        int x1 = (int) ((((i+1)*windowSize) - windowSize/2.f)*pixPerBase);
+        int y1 = (int) (getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
+      
+        g2.drawLine(x0, y0, x1, y1);
+      }
+    }
+
+    DecimalFormat df = new DecimalFormat("0.00##");
+    String maxStr = TYPES[type]+" : "+df.format((float)max/(float)windowSize);
+    FontMetrics fm = getFontMetrics(getFont());
+    g2.setColor(Color.black);
+    
+    int xpos = getWidth() - fm.stringWidth(maxStr) - 10;
+    g2.drawString(maxStr, xpos, fm.getHeight());
+  }
+  
+  private int countAll(AbstractVCFReader reader, int sbeg, int send, int windowSize, 
+      int nBins, FeatureVector features, int snpCount[], int max)
+  {
+    if(vcfView.isConcatenate())
+    {
+      String[] contigs = reader.getSeqNames();
+      for(int j=0; j<contigs.length; j++)
+      {
+        int offset = vcfView.getSequenceOffset(contigs[j]);
+        int nextOffset;
+        if(j<contigs.length-1)
+          nextOffset = vcfView.getSequenceOffset(contigs[j+1]);
+        else
+          nextOffset = vcfView.seqLength;
+        
+        if( (offset >= sbeg && offset < send) ||
+            (offset < sbeg && sbeg < nextOffset) )
+        {
+          int thisStart = sbeg - offset;
+          if(thisStart < 1)
+            thisStart = 1;
+          int thisEnd   = send - offset;
+          
+          max = count(reader, contigs[j], thisStart, thisEnd, windowSize, nBins, features, snpCount, max);
+        }
+      }
+      return max;
+    }
+    else
+      return count(reader, vcfView.getChr(), sbeg, send, windowSize, nBins, features, snpCount, max);
+  }
+  
+  private int count(AbstractVCFReader reader, String chr, int sbeg, int send, int windowSize, 
+      int nBins, FeatureVector features, int snpCount[], int max)
+  {
+    if(reader instanceof BCFReader)
+    {
+      try
+      {
+        BCFReader bcfReader = (BCFReader)reader;
+        BCFReaderIterator it = bcfReader.query(chr, sbeg, send);
+
+        VCFRecord record;
+        while((record = it.next()) != null)
+        {
+          max = calc(record, features, reader, windowSize, nBins, snpCount, max);
+        }
+      }
+      catch (IOException e)
+      {
+        e.printStackTrace();
+      }
+    }
+    else
+    {
+      TabixReader.Iterator iter = 
+        ((TabixReader)reader).query(chr+":"+sbeg+"-"+send); // get the iterator
+      if (iter == null)
+        return max;
+      try
+      {
+        String s;
+        while ((s = iter.next()) != null)
+        {
+          VCFRecord record = VCFRecord.parse(s);
+          max = calc(record, features, reader, windowSize, nBins, snpCount, max);
+        }
+      }
+      catch (IOException e)
+      {
+        e.printStackTrace();
+      }
+    }
+    return max;
+  }
+  
+  private int calc(VCFRecord record, FeatureVector features,
+      AbstractVCFReader reader, int windowSize, int nBins, int snpCount[], int max)
+  {
+    int pos = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
+    if(!vcfView.showVariant(record, features, pos, reader.isVcf_v4()))
+      return max;
+    
+    int bin = (int)((pos-vcfView.getBaseAtStartOfView()) / windowSize);
+    if(bin < 0 || bin > nBins-1)
+      return max;
+
+    if(type == 1)
+    {
+      int dp = 0;
+      try
+      {
+        dp = Integer.parseInt(record.getInfoValue("DP"));
+      }
+      catch(Exception e){ e.printStackTrace(); }
+      snpCount[bin]+=dp;
+    }
+    else
+      snpCount[bin]+=1;
+    
+    if(snpCount[bin] > max)
+      max = snpCount[bin];
+
+    return max;
+  }
+  
+  private void initPopupMenu(final JPanel graphPanel)
+  {
+    final JMenuItem setScale = new JMenuItem("Set the Window Size...");
+    setScale.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent _)
+      {
+        GridBagLayout gridbag = new GridBagLayout();
+        GridBagConstraints c = new GridBagConstraints();
+        JPanel pane = new JPanel(gridbag);
+        final JTextField newWinSize = new JTextField(Integer.toString(userWinSize), 10);
+        final JLabel lab = new JLabel("Window size:");
+        c.gridy = 0;
+        pane.add(lab, c);
+        pane.add(newWinSize, c);
+
+        final JCheckBox autoSet = new JCheckBox("Automatically set window size", false);
+        autoSet.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            lab.setEnabled(!autoSet.isSelected());
+            newWinSize.setEnabled(!autoSet.isSelected());
+          }
+        });
+        c.gridy = 1;
+        c.gridwidth = GridBagConstraints.REMAINDER;
+        pane.add(autoSet, c);
+
+        String window_options[] = { "OK", "Cancel" };
+        int select = JOptionPane.showOptionDialog(null, pane, "Window Size",
+            JOptionPane.DEFAULT_OPTION, JOptionPane.QUESTION_MESSAGE, null,
+            window_options, window_options[0]);
+
+        if (select == 1)
+          return;
+        autoWinSize = autoSet.isSelected();
+        try
+        {
+          userWinSize = Integer.parseInt(newWinSize.getText().trim());
+        }
+        catch (NumberFormatException nfe)
+        {
+          return;
+        }
+        graphPanel.repaint();
+      }
+    });
+    popup.add(setScale);
+    
+    addMouseListener(new PopupListener());
+  }
+  
+  /**
+   * @param type the type to set
+   */
+  protected void setType(int type)
+  {
+    this.type = type;
+  }
+
+  /**
+   * 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/variant/VCFview.java

@@ -54,6 +54,7 @@ import java.util.List;
 import java.util.Vector;
 import java.util.regex.Pattern;
 
+import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
@@ -131,6 +132,8 @@ public class VCFview extends JPanel
   private String chr;
   private VCFRecord mouseVCF;
   private int mouseOverIndex = -1;
+  
+  private GraphPanel graphPanel;
 
 //record of where a mouse drag starts
   private int dragStart = -1;
@@ -222,7 +225,8 @@ public class VCFview extends JPanel
     vcfPanel.add(jspView, BorderLayout.CENTER);
     
     JPanel bottomPanel = new JPanel(new BorderLayout());
-    GraphPanel graphPanel = new GraphPanel(this);
+    graphPanel = new GraphPanel(this);
+    graphPanel.setBorder(BorderFactory.createMatteBorder(1, 0, 1, 0, Color.gray));
     graphPanel.setPreferredSize(new Dimension(900, 100));
     graphPanel.setVisible(false);
     
@@ -565,6 +569,33 @@ public class VCFview extends JPanel
       }
     });
     view.add(viewFasta);
+    
+    JMenu graph = new JMenu("Graph");
+    popup.add(graph);
+    
+    final JCheckBoxMenuItem graphSNP = new JCheckBoxMenuItem("SNP");
+    final JCheckBoxMenuItem graphDP = new JCheckBoxMenuItem("Depth (DP)");
+    graph.add(graphSNP);
+    graphSNP.addActionListener(new ActionListener(){
+      public void actionPerformed(ActionEvent e)
+      {
+        graphPanel.setVisible(graphSNP.isSelected());
+        graphDP.setSelected(false);
+        graphPanel.setType(0);
+        graphPanel.repaint();
+      }
+    });
+    
+    graph.add(graphDP);
+    graphDP.addActionListener(new ActionListener(){
+      public void actionPerformed(ActionEvent e)
+      {
+        graphPanel.setVisible(graphDP.isSelected());
+        graphSNP.setSelected(false);
+        graphPanel.setType(1);
+        graphPanel.repaint();
+      }
+    });
   }
 
   private static EntryGroup getReference(String reference)
@@ -616,13 +647,21 @@ public class VCFview extends JPanel
    * @param fileName
    * @return
    */
-  private String testForURL(String fileName)
+  private String testForURL(String fileName, boolean isBCF)
   {
     if(!fileName.startsWith("http:"))
       return fileName;
 
-    String newFileName = download(fileName, null, ".bcf");
-    download(fileName+".bci", newFileName, ".bci");
+    if(isBCF)
+    {
+      String newFileName = download(fileName, null, ".bcf");
+      download(fileName+".bci", newFileName, ".bci");
+      return newFileName;
+    }
+
+    String newFileName = download(fileName, null, ".vcf.gz");
+    download(fileName+".tbi", newFileName, ".tbi");
+
     return newFileName;
   }
   
@@ -673,7 +712,7 @@ public class VCFview extends JPanel
     {
       if(IOUtils.isBCF(fileName))
       {
-        fileName = testForURL(fileName);
+        fileName = testForURL(fileName, true);
         vcfReaders[index] = new BCFReader(new File(fileName));
   
         String hdr = ((BCFReader)vcfReaders[index]).headerToString();
@@ -682,6 +721,7 @@ public class VCFview extends JPanel
         return hdr;
       }
 
+      fileName = testForURL(fileName, false);
       BlockCompressedInputStream is = 
         new BlockCompressedInputStream(new FileInputStream(fileName));
       vcfReaders[index] = new TabixReader(fileName);
@@ -790,6 +830,13 @@ public class VCFview extends JPanel
     return offsetLengths.get(refName);
   }
   
+  public void repaint()
+  {
+    super.repaint();
+    if(graphPanel != null && graphPanel.isVisible())
+      graphPanel.repaint();
+  }
+  
   protected void paintComponent(Graphics g)
   {
     super.paintComponent(g);
@@ -892,7 +939,7 @@ public class VCFview extends JPanel
     }
   }
   
-  private FeatureVector getCDSFeaturesInRange(int start, int end)
+  protected FeatureVector getCDSFeaturesInRange(int start, int end)
   {
     if(entryGroup == null)
       return null;