Initial BAM View changes to fix selection issues, zooming into secondary...

Initial BAM View changes to fix selection issues, zooming into secondary alignments, erroneous collapsing of reads with same start/end position and display of SNPs - related to RT ticket 597652

test/build-test.xml

@@ -350,6 +350,9 @@
 				<jvmarg value="-Djava.awt.headless=true" />
 				<batchtest fork="yes" todir="${junit.reports.dir}">
 					<fileset dir="${evosuite.tests.src.dir}">
+						
+						<!--include name="**/*BamView_ESTest.java" if="${do.run.evosuite.tests}" /-->
+						
 						<include name="**/*_ESTest.java" if="${do.run.evosuite.tests}" />
 						
 						<!-- Exclude classes that currently produce broken tests -->
@@ -382,7 +385,7 @@
 	</target>
 	
 	<!-- Create Jacoco reports -->
-	<target name="jacoco-coverage-report">
+	<target name="jacoco-coverage-report" depends="run-manual-tests">
 
 		<delete dir="${coverage.report.jacoco.dir}" />
 		<mkdir dir="${coverage.report.jacoco.dir}" />

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

@@ -362,5 +362,28 @@ class BamUtils
     }
     return featureReadCount;
   }
+  
+  /**
+   * Check whether two SAM records are the same.
+   * @param bamRec1 SamViewRecord
+   * @param bamRec2 SamViewRecord
+   * @return boolean - true if equality holds.
+   */
+  public static boolean samRecordEqualityCheck(SAMRecord rec1, SAMRecord rec2)
+  {
+	  boolean result = false;
+	  
+	  if (rec1 == null && rec2 == null)
+		  return true;
+	  
+	  result = (
+		(rec1.getReadName().equals(rec2.getReadName())) &&
+		(rec1.getAlignmentStart() == rec2.getAlignmentStart()) &&
+		(rec1.getAlignmentEnd() == rec2.getAlignmentEnd()) &&
+		(rec1.getFlags() == rec2.getFlags())
+	  );
+	  
+	  return result;
+  }
 }
 

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

@@ -220,6 +220,7 @@ public class BamView extends JPanel
   private JCheckBoxMenuItem colourByCoverageColour = new JCheckBoxMenuItem("Coverage Plot Colours");
   private JCheckBoxMenuItem baseQualityColour = new JCheckBoxMenuItem("Base Quality");
   private JCheckBoxMenuItem markInsertions = new JCheckBoxMenuItem("Mark Insertions", true);
+  
   private AlphaComposite translucent = 
     AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
   
@@ -234,9 +235,11 @@ public class BamView extends JPanel
   private static Color DARK_ORANGE = new Color(255,140,0);
   private static Color DEEP_PINK   = new Color(139,10,80);
   
+  private static Color NON_SELECTED_READ_HIGHLIGHT_COLOUR = new Color(189,103,107);
+  
   private Point lastMousePoint = null;
-  private BamViewRecord mouseOverSAMRecord = null;
-  private BamViewRecord highlightSAMRecord = null;
+  private volatile BamViewRecord mouseOverSAMRecord = null;
+  private volatile BamViewRecord highlightSAMRecord = null;
   private String mouseOverInsertion;
   // record of where a mouse drag starts
   protected int dragStart = -1;
@@ -1202,7 +1205,7 @@ public class BamView extends JPanel
     int xpos;
     int len    = 0;
     int refPos = 0;
-    final String readSeq = samRecord.getReadString();
+    SAMRecordSequenceString readSeq = new SAMRecordSequenceString(samRecord.getReadString());
     final int offset = getSequenceOffset(samRecord.getReferenceName());
 
     byte[] phredQuality = null;
@@ -1222,12 +1225,15 @@ public class BamView extends JPanel
         xpos = block.getReferenceStart() - 1 + j + offset;
         refPos = xpos - refSeqStart + 1;
 
-        if(phredQuality != null)
+        if(phredQuality != null && phredQuality.length > 0)
           setColourByBaseQuality(g2, phredQuality[readPos]);
 
         if(isSNPs && refSeq != null && refPos > 0 && refPos < refSeq.length())
         { 
-          if(Character.toUpperCase(readSeq.charAt(readPos)) != refSeq.charAt(refPos))
+          if( 
+        		  (!readSeq.isSecondaryAlignment()) && 
+        		  (Character.toUpperCase(readSeq.charAt(readPos)) != refSeq.charAt(refPos)) 
+        	  )
             g2.setColor(Color.red);
           else
             g2.setColor(col);
@@ -1266,15 +1272,26 @@ public class BamView extends JPanel
         }
       }
 
-      // highlight
       if(highlightSAMRecord != null && 
-         highlightSAMRecord.sam.getReadName().equals(samRecord.getReadName()))
+    	       highlightSAMRecord.sam.getReadName().equals(bamViewRecord.sam.getReadName()))
       {
         refPos =  block.getReferenceStart() + offset - refSeqStart;
         int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
         int width  = block.getLength()*ALIGNMENT_PIX_PER_BASE;
         Color col1 = g2.getColor();
-        g2.setColor(Color.red);
+        //g2.setColor(Color.red);
+        
+        if (isThisBamRecordHighlighted(bamViewRecord) )
+		{
+			// Selected read alignment
+			g2.setColor(Color.black);
+		}
+		else 
+		{
+			// For a read with the same name as selected one.
+			g2.setColor(NON_SELECTED_READ_HIGHLIGHT_COLOUR);
+		}
+        
         g2.drawRect(xstart, ypos-BASE_HEIGHT, width, BASE_HEIGHT);        
         if(i < blocks.size()-1)
         {
@@ -1494,8 +1511,6 @@ public class BamView extends JPanel
     if(isOrientation)
       ydiff= 2*ydiff;
     int maxEnd = 0;
-    int lstStart = 0;
-    int lstEnd = 0;
     final int baseAtStartOfView = getBaseAtStartOfView();
     g2.setColor(Color.blue);
     final Rectangle r = jspView.getViewport().getViewRect();
@@ -1503,6 +1518,7 @@ public class BamView extends JPanel
     for(BamViewRecord bamViewRecord: readsInView)
     {
       SAMRecord samRecord = bamViewRecord.sam;
+      
       int offset = getSequenceOffset(samRecord.getReferenceName());
 
       int recordStart = samRecord.getAlignmentStart()+offset;
@@ -1510,11 +1526,6 @@ public class BamView extends JPanel
       
       List<Integer> snps = getSNPs(samRecord);
       
-      if(colourByCoverageColour.isSelected() || 
-         colourByStrandTag.isSelected() ||
-         colourByReadGrp.isSelected() ||
-         lstStart != recordStart || lstEnd != recordEnd || snps != null)
-      {
       if(colourByStrandTag.isSelected())
 	  {
 	      if(samRecord.getAttribute("XS") == null)
@@ -1530,6 +1541,8 @@ public class BamView extends JPanel
 	      g2.setColor(getColourByCoverageColour(bamViewRecord));
 	  else if(colourByReadGrp.isSelected())
 	      g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, samRecord.getReadGroup()));
+	  else if (samRecord.getDuplicateReadFlag())
+			g2.setColor(DARK_GREEN); // Duplicate
 	  else if (!samRecord.getReadPairedFlag() ||   // read is not paired in sequencing
 	              samRecord.getMateUnmappedFlag() )  // mate is unmapped )  // mate is unmapped 
 	      g2.setColor(Color.black);
@@ -1543,20 +1556,10 @@ public class BamView extends JPanel
       }
       else
         ypos = ypos-ydiff;
-      }
-      else
-        g2.setColor(DARK_GREEN);
-      
-      if(snps != null)
-        lstStart = -1;
-      else
-      {
-        lstStart = recordStart;
-        lstEnd   = recordEnd;
-      }
       
       if(ypos > r.getMaxY() || ypos < r.getMinY())
         continue;
+      
       drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
     }
   }
@@ -1614,8 +1617,6 @@ public class BamView extends JPanel
     int hgt = getHeight();
     int ypos = (hgt - scaleHeight);
     int maxEnd = 0;
-    int lstStart = 0;
-    int lstEnd = 0;
     int baseAtStartOfView = getBaseAtStartOfView();
     g2.setColor(Color.blue);
     Rectangle r = jspView.getViewport().getViewRect();
@@ -1623,6 +1624,7 @@ public class BamView extends JPanel
     for(BamViewRecord bamViewRecord: readsInView)
     {
       SAMRecord samRecord = bamViewRecord.sam;
+      
       if( isNegativeStrand(samRecord, colourByStrandTag.isSelected()) == isStrandNegative )
       {
         final int offset = getSequenceOffset(samRecord.getReferenceName());
@@ -1630,11 +1632,6 @@ public class BamView extends JPanel
         final int recordEnd   = samRecord.getAlignmentEnd()+offset;
         List<Integer> snps = getSNPs(samRecord);
         
-        if(colourByCoverageColour.isSelected() || 
-           colourByStrandTag.isSelected() ||
-           colourByReadGrp.isSelected() ||
-           lstStart != recordStart || lstEnd != recordEnd || snps != null)
-        {
         if(colourByStrandTag.isSelected())
         {
             if(samRecord.getAttribute("XS") == null)
@@ -1650,6 +1647,8 @@ public class BamView extends JPanel
             g2.setColor(getColourByCoverageColour(bamViewRecord));
         else if(colourByReadGrp.isSelected())
             g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, samRecord.getReadGroup()));
+        else if (samRecord.getDuplicateReadFlag())
+			g2.setColor(DARK_GREEN); // Duplicate
         else if (!samRecord.getReadPairedFlag() ||   // read is not paired in sequencing
                     samRecord.getMateUnmappedFlag() )  // mate is unmapped 
             g2.setColor(Color.black);
@@ -1663,17 +1662,6 @@ public class BamView extends JPanel
         }
         else
           ypos = ypos + ystep;
-        }
-        else
-          g2.setColor(DARK_GREEN);
-
-        if(snps != null)
-          lstStart = -1;
-        else
-        {
-          lstStart = recordStart;
-          lstEnd   = recordEnd;
-        }
 
         if(ypos > r.getMaxY() || ypos < r.getMinY())
           continue;
@@ -2142,13 +2130,25 @@ public class BamView extends JPanel
 		  new BasicStroke (readLnHgt*1.6f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
 		g2.setStroke(stroke);
 		Color c = g2.getColor();
+
+		if (isThisBamRecordHighlighted(bamViewRecord) )
+		{
+			// Selected read alignment
 			g2.setColor(Color.black);
+		}
+		else 
+		{
+			// For a read with the same name as selected one.
+			g2.setColor(NON_SELECTED_READ_HIGHLIGHT_COLOUR);
+		}
+		
 		g2.drawLine((int)( thisStart * pixPerBase), ypos,
 		            (int)( thisEnd * pixPerBase), ypos);
 		g2.setColor(c);
 		g2.setStroke(originalStroke);
 	}
     
+    
     if(thisRead.getCigar().getCigarElements().size() == 1)
       g2.drawLine((int)( thisStart * pixPerBase), ypos,
                   (int)( thisEnd * pixPerBase), ypos);
@@ -2182,15 +2182,17 @@ public class BamView extends JPanel
     // test if the mouse is over this read
     if(lastMousePoint != null)
     {
-      if(lastMousePoint.getY()+2 > ypos && lastMousePoint.getY()-2 < ypos)
+	    	if(lastMousePoint.getY() > ypos-(Math.abs(ydiff)/2) && lastMousePoint.getY() < ypos+(Math.abs(ydiff)/2))
+	    	{
 		      if(lastMousePoint.getX() > thisStart * pixPerBase &&
 		         lastMousePoint.getX() < thisEnd * pixPerBase)
 		      {
 		    	  	mouseOverSAMRecord = bamViewRecord;
 		      }
 	    }
+    }
     
-    if (isSNPs && snps != null)
+    if (isSNPs && snps != null && snps.size() > 0)
       showSNPsOnReads(snps, g2, pixPerBase, ypos);
   }
   
@@ -2341,6 +2343,12 @@ public class BamView extends JPanel
           new Range(rbeg+offset, rend+offset), Bases.FORWARD);
       final byte[] readSeq = samRecord.getReadBases();
 
+      if (readSeq == null || readSeq.length == 0) 
+      {
+    	  	// Can occur for secondary alignments
+    	  	return null;
+      }
+      
       offset = offset - getBaseAtStartOfView();
       final List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
       for(AlignmentBlock block: blocks)
@@ -2843,8 +2851,12 @@ public class BamView extends JPanel
     colourMenu.add(baseQualityColour);
     menu.add(colourMenu);
     
-    //
+    // =============
+    // Show Menu 
+    // =============
+    
     JMenu showMenu = new JMenu("Show");
+
     JCheckBoxMenuItem checkBoxOrientation = new JCheckBoxMenuItem("Orientation");
     checkBoxOrientation.addActionListener(new ActionListener()
     {
@@ -3199,6 +3211,10 @@ public class BamView extends JPanel
           if (buttonAutoHide.isSelected() && topPanel.isVisible())
             topPanel.setVisible(false); 
         }
+        
+        // KJP - added these to make selecting work properly.
+        mainPanel.repaint();
+        mainPanel.revalidate();
       }
     };
     addMouseMotionListener(mouseMotionListener);
@@ -3506,7 +3522,10 @@ public class BamView extends JPanel
     if(event.getButton() == MouseEvent.BUTTON3 || bases == null) 
       return;
     
-    highlightSAMRecord = null;
+    // KJP: Removed this as it causes selection issues and
+    // doesn't seems strictly necessary.
+    // highlightSAMRecord = null;
+    
     if(event.getClickCount() > 1)
     {
       getSelection().clear();
@@ -3906,18 +3925,30 @@ public class BamView extends JPanel
         if(isCoverageView(getPixPerBaseByWidth()))
           coverageView.singleClick(e.isShiftDown(),
               e.getPoint().y-getJspView().getViewport().getViewPosition().y);
-        else
-          highlightSAMRecord = mouseOverSAMRecord;
+        //else
+        //{
+        	//	mouseHighlightSelectionMade.set(true);
+        	//	highlightSAMRecord = null;
+        //}
       }
       else
         highlightRange(e, MouseEvent.BUTTON2_DOWN_MASK);
-      repaint();
+      //repaint();
     }
     
-    public void mousePressed(MouseEvent e)
+    public void mousePressed(final MouseEvent e)
     {
+      highlightSAMRecord = mouseOverSAMRecord;
+
+    	  repaint();
+    	  
+    	  javax.swing.SwingUtilities.invokeLater(new Runnable() {
+    	        public void run() {
     	        		maybeShowPopup(e);
     	        }
+    	    });
+      
+    }
 
     public void mouseReleased(MouseEvent e)
     {
@@ -3988,6 +4019,9 @@ public class BamView extends JPanel
         		mouseOverSAMRecord.sam.getReadPairedFlag() &&
            !mouseOverSAMRecord.sam.getMateUnmappedFlag() )
         {
+        	  // KJP: new
+      	  highlightSAMRecord = mouseOverSAMRecord;
+      	  
           final BamViewRecord thisSAMRecord = mouseOverSAMRecord;
           gotoMateMenuItem = new JMenuItem("Go to mate of : "+
               thisSAMRecord.sam.getReadName());
@@ -4015,6 +4049,9 @@ public class BamView extends JPanel
           
         if( mouseOverSAMRecord != null)
         {
+        	  // KJP: new
+        	  highlightSAMRecord = mouseOverSAMRecord;
+        	  
           final BamViewRecord thisSAMRecord = mouseOverSAMRecord;
           showDetails = new JMenuItem("Show details of : "+
               thisSAMRecord.sam.getReadName());
@@ -4195,6 +4232,21 @@ public class BamView extends JPanel
     return concatSequences;
   }
   
+  /**
+   * Check whether the given BAM record is highlighted currently.
+   * @param bamRec BamViewRecord
+   * @return boolean - true if highlighted
+   */
+  protected boolean isThisBamRecordHighlighted(BamViewRecord bamRec)
+  {
+	  if (highlightSAMRecord == null) 
+	  {
+		  return false;
+	  }
+	  
+	  return BamUtils.samRecordEqualityCheck(highlightSAMRecord.sam, bamRec.sam);
+  }
+
   class PairedRead
   {
     BamViewRecord sam1;

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

+package uk.ac.sanger.artemis.components.alignment;
+
+/**
+ * Utility class that handles operations on an alignment block
+ * string taking into account the possibility that it could be
+ * a secondary alignment.
+ * 
+ * @author kp11
+ *
+ */
+public class SAMRecordSequenceString 
+{
+
+	public final static char SECONDARY_ALIGNMENT_BASE_CHAR = '=';
+	public final static char SECONDARY_ALIGNMENT_MARKER = '*';
+	
+	private String sequence;
+	private boolean isSecondaryAlignment;
+	
+	public SAMRecordSequenceString(String sequence) 
+	{
+		this.sequence = sequence;
+		this.isSecondaryAlignment = (String.valueOf(SECONDARY_ALIGNMENT_MARKER).equals(sequence));
+	}
+
+	public String substring(int beginIdx, int endIdx) 
+	{
+		
+		String result = null;
+		
+		if (!isSecondaryAlignment()) 
+		{
+			result = sequence.substring(beginIdx, endIdx);
+		} 
+		else
+		{
+			result =  new String(new char[endIdx-beginIdx]).replace('\0', SECONDARY_ALIGNMENT_BASE_CHAR);
+		}
+		
+		return result;
+
+	}
+	
+	public char charAt(int idx) 
+	{
+		
+		char result;
+		
+		if (!isSecondaryAlignment()) 
+		{
+			result = sequence.charAt(idx);
+		}
+		else
+		{
+			result = SECONDARY_ALIGNMENT_BASE_CHAR;
+		}
+		
+		return result;
+	}
+
+	public String getSequence() 
+	{
+		return sequence;
+	}
+	
+	public int length() 
+	{
+		return sequence.length();
+	}
+	
+	public boolean isSecondaryAlignment() {
+		return isSecondaryAlignment;
+	}
+}