move drawMax() to AbstractGraphPanel

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15671 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

@@ -23,12 +23,16 @@
  */
 package uk.ac.sanger.artemis.components.alignment;
 
+import java.awt.Color;
+import java.awt.FontMetrics;
+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.text.DecimalFormat;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComponent;
@@ -46,6 +50,9 @@ public class AbstractGraphPanel extends JPanel
   protected int end;
   protected float pixPerBase;
   
+  protected BamView bamView;
+  protected int windowSize;
+  protected int max;
   protected boolean autoWinSize = true;
   protected int userWinSize = 1;
   protected JPopupMenu popup = new JPopupMenu();
@@ -61,12 +68,13 @@ public class AbstractGraphPanel extends JPanel
         GridBagConstraints c = new GridBagConstraints();
         JPanel pane = new JPanel(gridbag);
         final JTextField newWinSize = new JTextField(Integer.toString(userWinSize), 10);
+        newWinSize.setEnabled(!autoWinSize);
         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);
+        final JCheckBox autoSet = new JCheckBox("Automatically set window size", autoWinSize);
         autoSet.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -102,6 +110,23 @@ public class AbstractGraphPanel extends JPanel
     
     addMouseListener(new PopupListener());
   }
+  
+  /**
+   * Draw maximum average value.
+   * @param g2
+   */
+  protected void drawMax(Graphics2D g2)
+  {
+    DecimalFormat df = new DecimalFormat("0.#");
+    String maxStr = df.format((float)max/(float)windowSize);
+
+    FontMetrics fm = getFontMetrics(getFont());
+    g2.setColor(Color.black);
+    
+    int xpos = bamView.getJspView().getVisibleRect().width - fm.stringWidth(maxStr) - 
+               bamView.getJspView().getVerticalScrollBar().getWidth();
+    g2.drawString(maxStr, xpos, fm.getHeight());
+  }
 
   protected void setStartAndEnd(int start, int end)
   {

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

@@ -26,7 +26,6 @@ package uk.ac.sanger.artemis.components.alignment;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
-import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 
@@ -49,10 +48,10 @@ import net.sf.samtools.SAMRecord;
   public class SnpPanel extends AbstractGraphPanel
   {
     private static final long serialVersionUID = 1L;
-    private BamView bamView;
-
     private Bases bases;
     private float minBaseQualityFilter = 0;
+    private int nBins;
+    private int snpCount[];
        
     public SnpPanel(final BamView bamView, Bases bases)
     {
@@ -96,16 +95,18 @@ import net.sf.samtools.SAMRecord;
     {
       super.paintComponent(g);
       Graphics2D g2 = (Graphics2D)g;
-      
-      if(bases == null)
-        return;
-      
-      List<SAMRecord> readsInView = bamView.getReadsInView();
-      if(readsInView == null)
+
+      if(bases == null || nBins == 0 || bamView.getReadsInView() == null)
         return;
-      
-      int windowSize;
-      
+      draw(g2);
+      drawMax(g2);
+    }
+    
+    protected void init(BamView bamView, float pixPerBase, int start, int end)
+    {
+      this.bamView = bamView;
+      setPixPerBase(pixPerBase);
+      setStartAndEnd(start, end);
       if(autoWinSize)
       {
         windowSize = (bamView.getBasesInView()/300);
@@ -116,36 +117,13 @@ import net.sf.samtools.SAMRecord;
       
       if(windowSize < 1)
         windowSize = 1;
-
-      int nBins = Math.round((end-start+1.f)/windowSize);
-      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) - 
-      bamView.getJspView().getVerticalScrollBar().getWidth();
-      g2.drawString(maxStr, xpos, fm.getHeight());
+      nBins = Math.round((end-start+1.f)/windowSize);
+      max = 0;
+      snpCount = null;
     }
-    
-    
-    private int drawPlot(Graphics2D g2, int nBins, int windowSize)
-    {
-      //lines = CoveragePanel.getLineAttributes(bamView.bamList.size());
-      List<SAMRecord> readsInView = bamView.getReadsInView();
-      
-      int snpCount[] = new int[nBins];
-      for(int i=0; i<snpCount.length; i++)
-        snpCount[i] = 0;
-      
-      int max = 0;
-      for(int i=0; i<readsInView.size(); i++)
-      {
-        SAMRecord thisRead = readsInView.get(i);
-        max = calculateSNPs(thisRead, windowSize, nBins, snpCount, max);
-      }
 
+    protected void draw(Graphics2D g2)
+    {
       g2.setColor(Color.red);
       g2.setStroke(new BasicStroke(1.f));
       
@@ -182,8 +160,6 @@ import net.sf.samtools.SAMRecord;
           g2.drawLine(x0, y0, x1, y1);
         }
       }
-
-      return max;
     }
     
     /**
@@ -193,12 +169,15 @@ import net.sf.samtools.SAMRecord;
      * @param pixPerBase
      * @param ypos
      */
-    private int calculateSNPs(SAMRecord thisRead,
-                               int windowSize, 
-                               int nBins,
-                               int[] snpCount,
-                               int max)
+    protected void addRecord(SAMRecord thisRead)
     {
+      if(snpCount == null)
+      {
+        snpCount = new int[nBins];
+        for(int i=0; i<snpCount.length; i++)
+          snpCount[i] = 0;
+      }
+
       int thisStart = thisRead.getAlignmentStart();
       int thisEnd   = thisRead.getAlignmentEnd();
       int offset    = bamView.getSequenceOffset(thisRead.getReferenceName());
@@ -241,7 +220,5 @@ import net.sf.samtools.SAMRecord;
       {
         e.printStackTrace();
       }
-      return max;
     }
-   
   }
\ No newline at end of file