diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index e73eaf3171c5020bd8b485f0098686d824e6c81b..8d8f33cde2905461f152144f71a464c2516a2f90 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -5,9 +5,11 @@ import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
+import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Point;
+import java.awt.Rectangle;
import java.awt.Stroke;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
@@ -28,6 +30,9 @@ import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.Scrollable;
+import javax.swing.SwingConstants;
+import javax.swing.UIManager;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
@@ -43,6 +48,7 @@ import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;
public class JamView extends JPanel
+ implements Scrollable
{
private static final long serialVersionUID = 1L;
private List<Read> readsInView;
@@ -54,6 +60,11 @@ public class JamView extends JPanel
private JScrollPane jspView;
private JComboBox combo;
private int nbasesInView;
+ private int laststart;
+ private int lastend;
+ private int maxUnitIncrement = 4;
+ private int ALIGNMENT_PIX_PER_BASE;
+
public JamView(String bam,
String reference,
@@ -77,6 +88,23 @@ public class JamView extends JPanel
}
}
readHeader();
+
+ final javax.swing.plaf.FontUIResource font_ui_resource =
+ Options.getOptions().getFontUIResource();
+
+ java.util.Enumeration keys = UIManager.getDefaults().keys();
+ while(keys.hasMoreElements())
+ {
+ Object key = keys.nextElement();
+ Object value = UIManager.get(key);
+ if(value instanceof javax.swing.plaf.FontUIResource)
+ UIManager.put(key, font_ui_resource);
+ }
+ FontMetrics fm = getFontMetrics(getFont());
+ int boundWidth = fm.stringWidth("A")/5;
+ ALIGNMENT_PIX_PER_BASE = fm.stringWidth("A")+boundWidth;
+
+ System.out.println(getFont().getFontName());
}
private void readHeader()
@@ -122,7 +150,7 @@ public class JamView extends JPanel
}
}
- private void readFromBam(int start, int end)
+ private void readFromBam(int start, int end, boolean pair_sort)
{
String refName = (String) combo.getSelectedItem();
String cmd[] = { "/Users/tjc/BAM/samtools-0.1.5c/samtools",
@@ -162,8 +190,9 @@ public class JamView extends JPanel
pread.seq = fields[9];
readsInView.add(pread);
}
-
- Collections.sort(readsInView, new ReadComparator());
+
+ if(pair_sort)
+ Collections.sort(readsInView, new ReadComparator());
}
catch (IOException e)
{
@@ -183,41 +212,121 @@ public class JamView extends JPanel
int seqLength = seqLengths.get(refName);
float pixPerBase = ((float)getWidth())/(float)(seqLength);
- double x = jspView.getViewport().getViewRect().getX();
-
- int start = (int) (seqLength * ( x / getWidth()));
- int end = (int) (start + (jspView.getViewport().getWidth() / pixPerBase));
- int scaleHeight = 15;
- readFromBam(start, end);
-
- drawScale(g2, start, end, pixPerBase);
-
- Stroke originalStroke = g2.getStroke();
- Stroke stroke =
- new BasicStroke (2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ if(pixPerBase >= ALIGNMENT_PIX_PER_BASE)
+ drawAlignment(g2, seqLength, pixPerBase);
+ else
+ drawLineView(g2, seqLength, pixPerBase);
+ }
+
+ private void drawAlignment(Graphics2D g2, int seqLength, float pixPerBase)
+ {
+ double x = jspView.getViewport().getViewRect().getX();
+ int start = (int) (seqLength * ( (float)x / (float)getWidth()));
+ int end = (int) (start + ((float)jspView.getViewport().getWidth() /
+ (float)pixPerBase));
- for(int i=0; i<readsInView.size(); i++)
- {
+ if(laststart != start ||
+ lastend != end)
+ readFromBam(start, end, false);
+
+ laststart = start;
+ lastend = end;
+
+ int ypos = 1;
+
+ boolean draw[] = new boolean[readsInView.size()];
+ for(int i=0; i<readsInView.size(); i++)
+ draw[i] = false;
+
+ for(int i=0; i<readsInView.size(); i++)
+ {
+ if (!draw[i])
+ {
+ Read thisRead = readsInView.get(i);
+ ypos = ypos + 10;
+
+ drawSequence(g2, thisRead, pixPerBase, ypos);
+ draw[i] = true;
+
+ int thisEnd = thisRead.pos+thisRead.seq.length();
+ for(int j=i+1; j<readsInView.size(); j++)
+ {
+ if (!draw[j])
+ {
+ Read nextRead = readsInView.get(j);
+ if(nextRead.pos > thisEnd+1)
+ {
+ drawSequence(g2, nextRead, pixPerBase, ypos);
+ draw[j] = true;
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ private void drawSequence(Graphics2D g2, Read read, float pixPerBase, int ypos)
+ {
+ if ((read.flag & 0x0001) != 0x0001 ||
+ (read.flag & 0x0008) == 0x0008)
+ g2.setColor(Color.black);
+ else
+ g2.setColor(Color.blue);
+
+ int xpos;
+
+ for(int i=0;i<read.seq.length(); i++)
+ {
+ xpos = ((read.pos-1) + i)*ALIGNMENT_PIX_PER_BASE;
+ g2.drawString(read.seq.substring(i, i+1), xpos, ypos);
+ }
+
+ }
+
+ private void drawLineView(Graphics2D g2, int seqLength, float pixPerBase)
+ {
+ double x = jspView.getViewport().getViewRect().getX();
+ int start = (int) (seqLength * ( (float)x / (float)getWidth()));
+ int end = (int) (start + ((float)jspView.getViewport().getWidth() /
+ (float)pixPerBase));
+
+ if(laststart != start ||
+ lastend != end)
+ readFromBam(start, end, true);
+
+ laststart = start;
+ lastend = end;
+
+ drawScale(g2, start, end, pixPerBase);
+
+ Stroke originalStroke = g2.getStroke();
+ Stroke stroke =
+ new BasicStroke (2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ int scaleHeight = 15;
+
+ for(int i=0; i<readsInView.size(); i++)
+ {
Read thisRead = readsInView.get(i);
Read nextRead = null;
if( (thisRead.flag & 0x0001) != 0x0001 ||
- (thisRead.flag & 0x0008) == 0x0008 ) // not single read
- continue;
+ (thisRead.flag & 0x0008) == 0x0008 ) // not single read
+ continue;
if(i < readsInView.size()-1)
{
- nextRead = readsInView.get(i+1);
- i++;
+ nextRead = readsInView.get(i+1);
+ i++;
}
if(nextRead != null &&
(nextRead.flag & 0x0001) == 0x0001 &&
(nextRead.flag & 0x0008) != 0x0008 )
{
- if(thisRead.qname.equals(nextRead.qname))
- {
+ if(thisRead.qname.equals(nextRead.qname))
+ {
if( (thisRead.flag & 0x0010) == 0x0010 &&
(nextRead.flag & 0x0010) == 0x0010 )
g2.setColor(Color.red);
@@ -226,29 +335,23 @@ public class JamView extends JPanel
int ypos = (getHeight() - scaleHeight) - ( Math.abs(thisRead.isize) );
int thisStart = drawRead(g2, thisRead, pixPerBase, stroke, ypos);
- int nextStart = drawRead(g2, nextRead, pixPerBase, stroke, ypos);
- g2.setStroke(originalStroke);
- g2.setColor(Color.LIGHT_GRAY);
- g2.drawLine(thisStart, ypos, nextStart, ypos);
- }
- else
- i--;
+ int nextStart = drawRead(g2, nextRead, pixPerBase, stroke, ypos);
+ g2.setStroke(originalStroke);
+ g2.setColor(Color.LIGHT_GRAY);
+ g2.drawLine(thisStart, ypos, nextStart, ypos);
+ }
+ else
+ i--;
}
- }
+ }
}
- private int getBaseAtStartOfView()
- {
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
- double x = jspView.getViewport().getViewRect().getX();
- return (int) (seqLength * ( x / getWidth()));
- }
private void drawScale(Graphics2D g2, int start, int end, float pixPerBase)
{
g2.setColor(Color.black);
- g2.drawLine( (int)(start*pixPerBase), getHeight()-14, (int)(end*pixPerBase), getHeight()-14);
+ g2.drawLine( (int)(start*pixPerBase), getHeight()-14,
+ (int)(end*pixPerBase), getHeight()-14);
int interval = end-start;
if(interval > 256000)
@@ -261,11 +364,17 @@ public class JamView extends JPanel
drawTicks(g2, start, end, pixPerBase, 800);
else if(interval > 1000)
drawTicks(g2, start, end, pixPerBase, 200);
+ else
+ drawTicks(g2, start, end, pixPerBase, 50);
}
private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division)
{
- int markStart = (Math.round(start/division)*division)+division;
+ int markStart = (Math.round(start/division)*division);
+
+ if(markStart < 1)
+ markStart = 1;
+
int sm = markStart-(division/2);
if(sm > start)
@@ -280,25 +389,24 @@ public class JamView extends JPanel
if(sm < end)
g2.drawLine((int)(sm*pixPerBase), getHeight()-14,(int)(sm*pixPerBase), getHeight()-12);
+
+ if(m == 1)
+ m = 0;
}
}
private int drawRead(Graphics2D g2, Read read,
- float pixPerBase, Stroke stroke, int ypos)
+ float pixPerBase, Stroke stroke, int ypos)
{
- int thisStart = (int) (read.pos*pixPerBase);
+ int thisStart = (int) ((read.pos-1)*pixPerBase);
int thisEnd = (int) (thisStart + (read.seq.length()*pixPerBase));
g2.setStroke(stroke);
g2.drawLine(thisStart, ypos, thisEnd, ypos);
return thisStart;
}
-
-
-
public void showJFrame()
{
- this.nbasesInView = nbasesInView;
JFrame frame = new JFrame("JamTool");
combo = new JComboBox(seqNames);
@@ -311,10 +419,10 @@ public class JamView extends JPanel
}
});
- frame.setPreferredSize(new Dimension(1000,800));
+ frame.setPreferredSize(new Dimension(1000,500));
setLength(nbasesInView);
- jspView = new JScrollPane(this, JScrollPane.VERTICAL_SCROLLBAR_NEVER,
+ jspView = new JScrollPane(this, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
JPanel panel = (JPanel) frame.getContentPane();
@@ -334,11 +442,15 @@ public class JamView extends JPanel
switch(event.getKeyCode())
{
case KeyEvent.VK_UP:
+ int startBase = getBaseAtStartOfView();
setZoomLevel( (int) (JamView.this.nbasesInView*1.1) );
+ setViewToBasePosition(startBase);
repaint();
break;
case KeyEvent.VK_DOWN:
+ startBase = getBaseAtStartOfView();
setZoomLevel( (int) (JamView.this.nbasesInView*.9) );
+ setViewToBasePosition(startBase);
repaint();
break;
default:
@@ -356,37 +468,57 @@ public class JamView extends JPanel
frame.setVisible(true);
}
+ private int getBaseAtStartOfView()
+ {
+ String refName = (String) combo.getSelectedItem();
+ int seqLength = seqLengths.get(refName);
+ double x = jspView.getViewport().getViewRect().getX();
+ return (int) (seqLength * ( x / getWidth()));
+ }
+
+ /**
+ * Set the panel size based on the number of bases visible
+ * and repaint.
+ * @param nbasesInView
+ */
private void setZoomLevel(final int nbasesInView)
{
- int startBase = getBaseAtStartOfView();
-
this.nbasesInView = nbasesInView;
setLength(this.nbasesInView);
revalidate();
repaint();
- System.out.println(startBase+" "+getBaseAtStartOfView());
+ }
+
+ /**
+ * Set the ViewPort so it starts at the given base position.
+ * @param base
+ */
+ private void setViewToBasePosition(int base)
+ {
+ Point p = jspView.getViewport().getViewPosition();
String refName = (String) combo.getSelectedItem();
int seqLength = seqLengths.get(refName);
-
-
- float pixPerBase = ((float)getWidth())/(float)(seqLength);
- Point p = jspView.getViewport().getViewPosition();
- p.x = (int)(startBase*pixPerBase);
+ p.x = (int) ((getPreferredSize().width)*(((float)base)/(float)seqLength));
jspView.getViewport().setViewPosition(p);
- revalidate();
- repaint();
-
- System.out.println(startBase+" "+getBaseAtStartOfView());
}
+ /**
+ * Set the panel size based on the number of bases visible.
+ * @param nbasesInView
+ */
private void setLength(int basesToShow)
{
String refName = (String) combo.getSelectedItem();
int seqLength = seqLengths.get(refName);
- float pixPerBase = 1000.f/(float)(basesToShow);
- setPreferredSize( new Dimension((int) (seqLength*pixPerBase),
- getSize().height) );
+ double pixPerBase = 1000.d/(double)(basesToShow);
+
+ System.out.println(pixPerBase+" "+ALIGNMENT_PIX_PER_BASE);
+ if(pixPerBase > ALIGNMENT_PIX_PER_BASE)
+ pixPerBase = ALIGNMENT_PIX_PER_BASE;
+ Dimension d = new Dimension();
+ d.setSize((seqLength*pixPerBase), 800.d);
+ setPreferredSize(d);
}
/**
@@ -458,16 +590,67 @@ public class JamView extends JPanel
return pr1.qname.compareTo(pr2.qname);
}
}
+
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ return getPreferredSize();
+ }
+
+ public int getScrollableBlockIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ if (orientation == SwingConstants.HORIZONTAL)
+ return visibleRect.width - maxUnitIncrement;
+ else
+ return visibleRect.height - maxUnitIncrement;
+ }
+
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
+
+ public boolean getScrollableTracksViewportWidth()
+ {
+ return false;
+ }
+
+ public int getScrollableUnitIncrement(Rectangle visibleRect, int orientation,
+ int direction)
+ {
+ //Get the current position.
+ int currentPosition = 0;
+ if (orientation == SwingConstants.HORIZONTAL)
+ currentPosition = visibleRect.x;
+ else
+ currentPosition = visibleRect.y;
+
+ //Return the number of pixels between currentPosition
+ //and the nearest tick mark in the indicated direction.
+ if (direction < 0)
+ {
+ int newPosition = currentPosition -
+ (currentPosition / maxUnitIncrement)
+ * maxUnitIncrement;
+ return (newPosition == 0) ? maxUnitIncrement : newPosition;
+ }
+ else
+ {
+ return ((currentPosition / maxUnitIncrement) + 1)
+ * maxUnitIncrement
+ - currentPosition;
+ }
+ }
public static void main(String[] args)
{
String bam = args[0];
int nbasesInView = Integer.parseInt(args[1]);
String reference = null;
- if(args.length > 2)
- reference = args[2];
+ //if(args.length > 2)
+ // reference = args[2];
- JamView view = new JamView(bam, reference, nbasesInView);
- view.showJFrame();
+ JamView view = new JamView(bam, reference, nbasesInView);
+ view.showJFrame();
}
}