change to using a JScrollBar

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11936 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

+/* CoveragePanel
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009  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.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.geom.GeneralPath;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+import net.sf.samtools.SAMRecord;
+
+  public class CoveragePanel extends JPanel
+  {
+    private static final long serialVersionUID = 1L;
+
+    private int start;
+    private int end;
+    private float pixPerBase;
+    private Color lightBlue = new Color(30,144,255);
+    private JamView jamView;
+    
+    public CoveragePanel(JamView jamView)
+    {
+      super();
+      setBackground(Color.white);
+      this.jamView = jamView;
+    }
+    
+    /**
+     * Override
+     */
+    protected void paintComponent(Graphics g)
+    {
+      super.paintComponent(g);
+      Graphics2D g2 = (Graphics2D)g;
+      
+      List<SAMRecord> readsInView = jamView.getReadsInView();
+      if(readsInView == null)
+        return;
+      
+      int windowSize = 10;
+      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 = 0;
+      for(int i=0; i<readsInView.size(); i++)
+      {
+        SAMRecord thisRead = readsInView.get(i);
+        int offset = jamView.getSequenceOffset(thisRead.getReferenceName());
+        int length = thisRead.getReadLength();
+        
+        for(int j=0; j<length;j++)
+        {
+          int bin = 
+            Math.round(((thisRead.getAlignmentStart()-start) + j + offset) / windowSize);
+
+          if(bin < 0 || bin > coverage.length-1)
+            continue;   
+          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++)
+      {
+        float xpos = ((i*(windowSize)) - windowSize/2.f)*pixPerBase;
+        shape.lineTo(xpos,
+            getHeight() - (((float)coverage[i]/(float)max)*getHeight()));
+      }
+
+      shape.lineTo(getWidth(),getHeight());
+      g2.fill(shape);
+
+      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());
+    }
+    
+    protected void setStartAndEnd(int start, int end)
+    {
+      this.start = start;
+      this.end = end;
+    }
+
+    protected void setPixPerBase(float pixPerBase)
+    {
+      this.pixPerBase = pixPerBase;
+    }
+  }
\ No newline at end of file

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

+/* SAMRecordComparator
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009  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.util.Comparator;
+
+import uk.ac.sanger.artemis.components.alignment.JamView.PairedRead;
+
+
+  class PairedReadComparator implements Comparator<Object>
+  {
+    public int compare(Object o1, Object o2) 
+    {
+      PairedRead pr1 = (PairedRead) o1;
+      PairedRead pr2 = (PairedRead) o2;
+      
+      int start1 = pr1.sam1.getAlignmentStart();
+      if(pr1.sam1.getAlignmentEnd() < start1)
+        start1 = pr1.sam1.getAlignmentEnd();
+      
+      int start2 = pr2.sam1.getAlignmentStart();
+      if(pr2.sam1.getAlignmentEnd() < start2)
+        start2 = pr1.sam1.getAlignmentEnd();
+        
+      return start1-start2;
+    }
+  }
\ No newline at end of file

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

+/* SAMRecordComparator
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009  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.util.Comparator;
+
+import net.sf.samtools.SAMRecord;
+
+ class SAMRecordComparator implements Comparator<Object>
+  {
+    public int compare(Object o1, Object o2) 
+    {
+      SAMRecord pr1 = (SAMRecord) o1;
+      SAMRecord pr2 = (SAMRecord) o2;
+      
+      int cmp = pr1.getReadName().compareTo(pr2.getReadName());
+      if(cmp == 0)
+      {
+        if(pr1.getAlignmentStart() < pr2.getAlignmentStart())
+          return -1;
+        else
+          return 1;
+      }   
+      return cmp;
+    }
+  }
\ No newline at end of file