diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..46a488a58298b3fe87458b03109d64948db760ac
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -0,0 +1,125 @@
+/* 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
diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index 71ec5b5ae3a1cdbb34ef624b7459b935629d3c5b..5556e681d6960b6db289fba84bacdef64991db0d 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -40,6 +40,8 @@ import java.awt.Rectangle;
import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.awt.event.ItemEvent;
@@ -51,13 +53,8 @@ import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionListener;
import java.awt.event.WindowEvent;
import java.awt.event.WindowFocusListener;
-import java.awt.geom.GeneralPath;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
import java.util.Collections;
-import java.util.Comparator;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
@@ -75,6 +72,7 @@ import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
+import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
import javax.swing.JTextField;
@@ -125,6 +123,8 @@ public class JamView extends JPanel
private Bases bases;
private JScrollPane jspView;
+ private JScrollBar scrollBar;
+
private JComboBox combo;
private boolean isSingle = false;
private boolean isSNPs = false;
@@ -156,7 +156,6 @@ public class JamView extends JPanel
/** Used to colour the frames. */
private Color lightGrey = new Color(200, 200, 200);
private Color darkGreen = new Color(0, 150, 0);
- private Color lightBlue = new Color(30,144,255);
private Color darkOrange = new Color(255,140,0);
private Point lastMousePoint = null;
@@ -166,11 +165,10 @@ public class JamView extends JPanel
private int maxHeight = 800;
+ private boolean concatSequences = false;
private int ALIGNMENT_PIX_PER_BASE;
private JPopupMenu popup;
- // use the picard library otherwise call samtools
- public static boolean PICARD = true;
public JamView(String bam,
@@ -195,10 +193,7 @@ public class JamView extends JPanel
}
}
- if(PICARD)
- readHeaderPicard();
- else
- readHeader();
+ readHeaderPicard();
// set font size
//setFont(getFont().deriveFont(12.f));
@@ -233,12 +228,11 @@ public class JamView extends JPanel
mouseOverSAMRecord.getReadName() + "\n" +
mouseOverSAMRecord.getAlignmentStart() + ".." +
mouseOverSAMRecord.getAlignmentEnd() + "\nisize=" +
- mouseOverSAMRecord.getInferredInsertSize(): null);
+ mouseOverSAMRecord.getInferredInsertSize() + "\nrname=" +
+ mouseOverSAMRecord.getReferenceName(): null);
}
-
- /**
- * Read the BAM/SAM header
- */
+
+ /*
private void readHeader()
{
String samtoolCmd = "";
@@ -285,29 +279,6 @@ public class JamView extends JPanel
}
}
- private void readHeaderPicard()
- {
- File bamFile = new File(bam);
- File indexFile = new File(bam+".bai");
- final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
- SAMFileHeader header = inputSam.getFileHeader();
- List<SAMSequenceRecord> readGroups = header.getSequenceDictionary().getSequences();
-
- for(int i=0; i<readGroups.size(); i++)
- {
- seqLengths.put(readGroups.get(i).getSequenceName(),
- readGroups.get(i).getSequenceLength());
- seqNames.add(readGroups.get(i).getSequenceName());
- }
- inputSam.close();
- }
-
- /**
- * Read data from BAM/SAM file for a region.
- * @param start
- * @param end
- * @param pair_sort
- */
private void readFromBam(int start, int end)
{
String refName = (String) combo.getSelectedItem();
@@ -334,6 +305,24 @@ public class JamView extends JPanel
System.out.println(samtools.getProcessStderr());
samtools.waitForStdout();
+ }*/
+
+
+ private void readHeaderPicard()
+ {
+ File bamFile = new File(bam);
+ File indexFile = new File(bam+".bai");
+ final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
+ SAMFileHeader header = inputSam.getFileHeader();
+ List<SAMSequenceRecord> readGroups = header.getSequenceDictionary().getSequences();
+
+ for(int i=0; i<readGroups.size(); i++)
+ {
+ seqLengths.put(readGroups.get(i).getSequenceName(),
+ readGroups.get(i).getSequenceLength());
+ seqNames.add(readGroups.get(i).getSequenceName());
+ }
+ inputSam.close();
}
/**
@@ -352,7 +341,56 @@ public class JamView extends JPanel
readsInView = new Vector<SAMRecord>();
else
readsInView.clear();
- String refName = (String) combo.getSelectedItem();
+
+ if(concatSequences)
+ {
+ int len = 0;
+ int lastLen = 1;
+ for(int i=0; i<seqNames.size(); i++)
+ {
+ int thisLength = seqLengths.get(seqNames.get(i));
+ len += thisLength;
+
+ if( (lastLen >= start && lastLen < end) ||
+ (len >= start && len < end) ||
+ (start >= lastLen && start < len) ||
+ (end >= lastLen && end < len) )
+ {
+ int offset = getSequenceOffset(seqNames.get(i));
+ int thisStart = start - offset;
+ if(thisStart < 1)
+ thisStart = 1;
+ int thisEnd = end - offset;
+ if(thisEnd > thisLength)
+ thisEnd = thisLength;
+
+ System.out.println("READ "+seqNames.get(i)+" "+thisStart+".."+thisEnd);
+ iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd);
+ }
+ lastLen = len;
+ }
+ }
+ else
+ {
+ String refName = (String) combo.getSelectedItem();
+ iterateOverBam(inputSam, refName, start, end);
+ }
+
+ inputSam.close();
+ //System.out.println("readFromBamPicard "+start+".."+end);
+ }
+
+ /**
+ * Iterate over BAM file and load into the <code>List</code> of
+ * <code>SAMRecord</code>.
+ * @param inputSam
+ * @param refName
+ * @param start
+ * @param end
+ */
+ private void iterateOverBam(final SAMFileReader inputSam,
+ String refName, int start, int end)
+ {
CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
while ( it.hasNext() )
{
@@ -366,8 +404,36 @@ public class JamView extends JPanel
System.out.println(e.getMessage());
}
}
- inputSam.close();
- //System.out.println("readFromBamPicard "+start+".."+end);
+ it.close();
+ }
+
+ private int getSequenceLength()
+ {
+ if(concatSequences)
+ {
+ int len = 0;
+ for(int i=0; i<seqNames.size(); i++)
+ len += seqLengths.get(seqNames.get(i));
+ return len;
+ }
+ else
+ return seqLengths.get((String) combo.getSelectedItem());
+ }
+
+ protected int getSequenceOffset(String refName)
+ {
+ if(!concatSequences)
+ return 0;
+ int offset = 0;
+ for(int i=0; i<combo.getItemCount(); i++)
+ {
+ String thisSeqName = (String) combo.getItemAt(i);
+ if(refName.equals(thisSeqName))
+ return offset;
+
+ offset += seqLengths.get(combo.getItemAt(i));
+ }
+ return offset;
}
/**
@@ -379,48 +445,42 @@ public class JamView extends JPanel
Graphics2D g2 = (Graphics2D)g;
mouseOverSAMRecord = null;
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
+ int seqLength = getSequenceLength();
float pixPerBase = getPixPerBaseByWidth();
int start;
- final int end;
+ int end;
if(startBase > 0)
start = startBase;
else
- {
- double x = jspView.getViewport().getViewRect().getX();
- start = 1 + (int) (getMaxBasesInPanel(seqLength) * ( (float)x / (float)getPreferredSize().getWidth() ));
- }
+ start = getBaseAtStartOfView();
if(endBase > 0)
end = endBase;
else
{
- int width = jspView.getViewport().getViewRect().width;
- if(jspView.getVerticalScrollBar() != null)
- width += jspView.getVerticalScrollBar().getWidth();
- end = (int) (start + ((float)width / (float)pixPerBase));
+ end = start + nbasesInView - 1;
+ if(end > seqLength)
+ end = seqLength;
}
- //System.out.println("paintComponent "+start+".."+end+" "+startBase+".."+endBase+
- // " pixPerBase="+pixPerBase+" getPreferredSize().getWidth()="+getPreferredSize().getWidth());
+
+ //System.out.println(start+".."+end+" " +
+ // "sequence length = "+getSequenceLength()+
+ // " pixPerBase="+pixPerBase);
+
if(laststart != start ||
lastend != end)
{
+ setCursor(cbusy);
try
{
- setCursor(cbusy);
-
- if(PICARD)
- readFromBamPicard(start, end);
- else
- readFromBam(start, end);
-
+ readFromBamPicard(start, end);
if(!isStackView || pixPerBase*3 >= ALIGNMENT_PIX_PER_BASE)
Collections.sort(readsInView, new SAMRecordComparator());
+
setCursor(cdone);
}
catch(OutOfMemoryError ome)
@@ -454,26 +514,16 @@ public class JamView extends JPanel
private float getPixPerBaseByWidth()
{
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
- return ((float)getPreferredSize().getWidth())/(getMaxBasesInPanel(seqLength));
+ return (float)( getPreferredSize().getWidth() /nbasesInView);
}
- private float getPixPerBaseByBasesInView()
- {
- int width = jspView.getViewport().getViewRect().width;
- if(jspView.getVerticalScrollBar() != null)
- width += jspView.getVerticalScrollBar().getWidth();
-
- return ((float)width)/(float)(nbasesInView);
- }
- private float getMaxBasesInPanel(int seqLength)
+ private int getMaxBasesInPanel(int seqLength)
{
if(feature_display == null)
- return (float)(seqLength);
+ return seqLength+nbasesInView/2;
else
- return (float)(seqLength+nbasesInView);
+ return seqLength+nbasesInView;
}
/**
@@ -513,20 +563,14 @@ public class JamView extends JPanel
refSeqStart = 1;
refSeq =
bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
- int xpos = (refSeqStart-1)*ALIGNMENT_PIX_PER_BASE;
+
+ System.out.println(refSeqStart +" "+ seqEnd+" "+refSeq);
g2.setColor(lightGrey);
- g2.fillRect(xpos, ypos-11,
- jspView.getViewport().getWidth()+(ALIGNMENT_PIX_PER_BASE*2), 11);
+ g2.fillRect(0, ypos-11, getPreferredSize().width, 11);
drawSelectionRange(g2, pixPerBase, start, end);
g2.setColor(Color.black);
- g2.drawString(refSeq, xpos, ypos);
-
- //for(int i=0;i<refSeq.length(); i++)
- //{
- //xpos = ((refSeqStart-1) + i)*ALIGNMENT_PIX_PER_BASE;
- //g2.drawString(refSeq.substring(i, i+1), xpos, ypos);
- //}
+ g2.drawString(refSeq, 0, ypos);
}
catch (OutOfRangeException e)
{
@@ -603,7 +647,8 @@ public class JamView extends JPanel
int xpos;
int len = 0;
String readSeq = samRecord.getReadString();
-
+ int offset = getSequenceOffset(samRecord.getReferenceName());
+
List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
for(int i=0; i<blocks.size(); i++)
{
@@ -612,7 +657,7 @@ public class JamView extends JPanel
for(int j=0; j<block.getLength(); j++)
{
int readPos = block.getReadStart()-1+j;
- xpos = block.getReferenceStart()-1+j;
+ xpos = block.getReferenceStart()-1+j+offset;
int refPos = xpos-refSeqStart+1;
if(isSNPs && refSeq != null && refPos > 0 && refPos < refSeq.length())
@@ -623,14 +668,16 @@ public class JamView extends JPanel
g2.setColor(col);
}
- g2.drawString(readSeq.substring(readPos, readPos+1), xpos*ALIGNMENT_PIX_PER_BASE, ypos);
+ g2.drawString(readSeq.substring(readPos, readPos+1),
+ refPos*ALIGNMENT_PIX_PER_BASE, ypos);
}
}
if(lastMousePoint != null)
{
- int xstart = (blocks.get(0).getReferenceStart()-1)*ALIGNMENT_PIX_PER_BASE;
- int xend = (blocks.get(0).getReferenceStart()-1+len)*ALIGNMENT_PIX_PER_BASE;
+ int refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
+ int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
+ int xend = (refPos+len)*ALIGNMENT_PIX_PER_BASE;
if(lastMousePoint.getY() > ypos-11 && lastMousePoint.getY() < ypos)
if(lastMousePoint.getX() > xstart &&
@@ -697,8 +744,8 @@ public class JamView extends JPanel
g2.setColor(Color.LIGHT_GRAY);
drawTranslucentLine(g2,
- (int)(samRecord.getAlignmentEnd()*pixPerBase),
- (int)(samNextRecord.getAlignmentStart()*pixPerBase), ypos);
+ (int)((samRecord.getAlignmentEnd()-getBaseAtStartOfView())*pixPerBase),
+ (int)((samNextRecord.getAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
}
if( samRecord.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
@@ -722,7 +769,7 @@ public class JamView extends JPanel
}
}
- drawYScale(g2, start, pixPerBase, scaleHeight);
+ drawYScale(g2, scaleHeight);
}
/**
@@ -770,7 +817,7 @@ public class JamView extends JPanel
{
SAMRecord samRecord = readsInView.get(i);
- int recordStart = samRecord.getAlignmentStart();;
+ int recordStart = samRecord.getAlignmentStart();
int recordEnd = samRecord.getAlignmentEnd();
if(lstStart != recordStart || lstEnd != recordEnd)
@@ -898,8 +945,8 @@ public class JamView extends JPanel
if(pr.sam2 != null)
{
drawTranslucentJointedLine(g2,
- (int)(pr.sam1.getAlignmentEnd()*pixPerBase),
- (int)(pr.sam2.getAlignmentStart()*pixPerBase), ypos);
+ (int)((pr.sam1.getAlignmentEnd()-getBaseAtStartOfView())*pixPerBase),
+ (int)((pr.sam2.getAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
}
else
{
@@ -913,8 +960,8 @@ public class JamView extends JPanel
prStart = pr.sam1.getAlignmentStart();
drawTranslucentJointedLine(g2,
- (int)(prStart*pixPerBase),
- (int)(pr.sam1.getMateAlignmentStart()*pixPerBase), ypos);
+ (int)( (prStart-getBaseAtStartOfView())*pixPerBase),
+ (int)( (pr.sam1.getMateAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
}
}
@@ -944,7 +991,8 @@ public class JamView extends JPanel
float pixPerBase, Stroke originalStroke, Stroke stroke)
{
boolean offTheTop = false;
- int thisStart = samRecord.getAlignmentStart()-1;
+ int offset = getSequenceOffset(samRecord.getReferenceName());
+ int thisStart = samRecord.getAlignmentStart()-1+offset;
int thisEnd = thisStart + samRecord.getReadString().length();
if(ypos <= 0)
@@ -960,15 +1008,17 @@ public class JamView extends JPanel
if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
{
- int nextStart = (int) ((samRecord.getMateAlignmentStart()-1)*pixPerBase);
+ int nextStart =
+ (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
- (int)(thisStart*pixPerBase), nextStart, ypos);
+ (int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
}
else
{
- int nextStart = (int) ((samRecord.getMateAlignmentStart()-1)*pixPerBase);
+ int nextStart =
+ (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
- (int)(thisEnd*pixPerBase), nextStart, ypos);
+ (int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
}
}
@@ -983,15 +1033,15 @@ public class JamView extends JPanel
drawRead(g2, samRecord, pixPerBase, stroke, ypos);
if (isSNPs)
- showSNPsOnReads(g2, samRecord, pixPerBase, ypos);
+ showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);
}
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( 0, getHeight()-14,
+ (int)((end - getBaseAtStartOfView())*pixPerBase), getHeight()-14);
int interval = end-start;
if(interval > 256000)
@@ -1016,19 +1066,26 @@ public class JamView extends JPanel
markStart = 1;
int sm = markStart-(division/2);
-
+ float x;
if(sm > start)
- g2.drawLine((int)(sm*pixPerBase), getHeight()-14,(int)(sm*pixPerBase), getHeight()-12);
+ {
+ x = (sm-getBaseAtStartOfView())*pixPerBase;
+ g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-12);
+ }
for(int m=markStart; m<end; m+=division)
{
- g2.drawString(Integer.toString(m), m*pixPerBase, getHeight()-1);
- g2.drawLine((int)(m*pixPerBase), getHeight()-14,(int)(m*pixPerBase), getHeight()-11);
+ x = (m-getBaseAtStartOfView())*pixPerBase;
+ g2.drawString(Integer.toString(m), x, getHeight()-1);
+ g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-11);
sm = m+(division/2);
if(sm < end)
- g2.drawLine((int)(sm*pixPerBase), getHeight()-14,(int)(sm*pixPerBase), getHeight()-12);
+ {
+ x = (sm-getBaseAtStartOfView())*pixPerBase;
+ g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-12);
+ }
if(m == 1)
m = 0;
@@ -1038,21 +1095,18 @@ public class JamView extends JPanel
/**
* Draw a y-scale for inferred size (isize) of reads.
* @param g2
- * @param start
- * @param pixPerBase
* @param xScaleHeight
*/
- private void drawYScale(Graphics2D g2, int start, float pixPerBase, int xScaleHeight)
+ private void drawYScale(Graphics2D g2, int xScaleHeight)
{
g2.setColor(Color.black);
int maxY = getPreferredSize().height-xScaleHeight;
- int xpos = (int) (pixPerBase*start);
for(int i=100; i<maxY; i+=100)
{
int ypos = getHeight()-i-xScaleHeight;
- g2.drawLine(xpos, ypos, xpos+2, ypos);
- g2.drawString(Integer.toString(i), xpos+3, ypos);
+ g2.drawLine(0, ypos, 2, ypos);
+ g2.drawString(Integer.toString(i), 3, ypos);
}
}
@@ -1067,11 +1121,13 @@ public class JamView extends JPanel
private void drawRead(Graphics2D g2, SAMRecord thisRead,
float pixPerBase, Stroke stroke, int ypos)
{
- int thisStart = thisRead.getAlignmentStart()-1;
- int thisEnd = thisRead.getAlignmentEnd()-1;
+ int offset = getSequenceOffset(thisRead.getReferenceName());
+
+ int thisStart = thisRead.getAlignmentStart()+offset-getBaseAtStartOfView();
+ int thisEnd = thisRead.getAlignmentEnd()+offset-getBaseAtStartOfView();
g2.setStroke(stroke);
- g2.drawLine((int)(thisStart * pixPerBase), ypos,
- (int)(thisEnd * pixPerBase), ypos);
+ g2.drawLine((int)( thisStart * pixPerBase), ypos,
+ (int)( thisEnd * pixPerBase), ypos);
// test if the mouse is over this read
if(lastMousePoint != null)
@@ -1085,7 +1141,7 @@ public class JamView extends JPanel
}
if (isSNPs)
- showSNPsOnReads(g2, thisRead, pixPerBase, ypos);
+ showSNPsOnReads(g2, thisRead, pixPerBase, ypos, offset);
}
/**
@@ -1109,7 +1165,7 @@ public class JamView extends JPanel
if(end < rangeStart || start > rangeEnd)
return;
- int x = (int) (pixPerBase*(rangeStart-1));
+ int x = (int) (pixPerBase*(rangeStart-getBaseAtStartOfView()));
int width = (int) (pixPerBase*(rangeEnd-rangeStart+1));
g2.setColor(Color.pink);
@@ -1160,7 +1216,7 @@ public class JamView extends JPanel
* @param ypos
*/
private void showSNPsOnReads(Graphics2D g2, SAMRecord thisRead,
- float pixPerBase, int ypos)
+ float pixPerBase, int ypos, int offset)
{
int thisStart = thisRead.getAlignmentStart();
int thisEnd = thisRead.getAlignmentEnd();
@@ -1171,7 +1227,7 @@ public class JamView extends JPanel
try
{
char[] refSeq = bases.getSubSequenceC(
- new Range(thisStart, thisEnd), Bases.FORWARD);
+ new Range(thisStart+offset, thisEnd+offset), Bases.FORWARD);
byte[] readSeq = thisRead.getReadBases();
Color col = g2.getColor();
@@ -1187,8 +1243,8 @@ public class JamView extends JPanel
if (Character.toUpperCase(refSeq[refPos-thisStart]) != readSeq[readPos])
{
- g2.drawLine((int) ((refPos) * pixPerBase), ypos + 2,
- (int) ((refPos) * pixPerBase), ypos - 2);
+ g2.drawLine((int) ((refPos+offset-getBaseAtStartOfView()) * pixPerBase), ypos + 2,
+ (int) ((refPos+offset-getBaseAtStartOfView()) * pixPerBase), ypos - 2);
}
}
@@ -1220,6 +1276,16 @@ public class JamView extends JPanel
this.feature_display = feature_display;
this.selection = feature_display.getSelection();
topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
+
+ if(seqNames.size() > 1)
+ {
+ int len = 0;
+ for(int i=0; i<seqNames.size(); i++)
+ len += seqLengths.get(seqNames.get(i));
+
+ if(len == feature_display.getSequenceLength())
+ concatSequences = true;
+ }
}
else
{
@@ -1286,7 +1352,7 @@ public class JamView extends JPanel
try
{
int basePosition = Integer.parseInt(baseText.getText());
- goToBasePosition(basePosition);
+ scrollBar.setValue(basePosition);
}
catch (NumberFormatException nfe)
{
@@ -1306,9 +1372,7 @@ public class JamView extends JPanel
{
public void actionPerformed(ActionEvent e)
{
- int startBase = getBaseAtStartOfView();
setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
- goToBasePosition(startBase);
}
});
topPanel.add(zoomIn);
@@ -1321,9 +1385,7 @@ public class JamView extends JPanel
{
if (showBaseAlignment)
return;
- int startBase = getBaseAtStartOfView();
setZoomLevel((int) (JamView.this.nbasesInView * .9));
- goToBasePosition(startBase);
}
});
topPanel.add(zoomOut);
@@ -1335,7 +1397,7 @@ public class JamView extends JPanel
jspView = new JScrollPane(this,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
- JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
+ JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
setDisplay(1, nbasesInView, null);
mainPanel.setLayout(new BorderLayout());
@@ -1344,8 +1406,27 @@ public class JamView extends JPanel
mainPanel.add(topPanel, BorderLayout.NORTH);
mainPanel.add(jspView, BorderLayout.CENTER);
- coveragePanel = new CoveragePanel();
- mainPanel.add(coveragePanel, BorderLayout.SOUTH);
+ JPanel bottomPanel = new JPanel(new BorderLayout());
+
+
+ coveragePanel = new CoveragePanel(this);
+ bottomPanel.add(coveragePanel, BorderLayout.CENTER);
+
+ if(feature_display == null)
+ {
+ scrollBar = new JScrollBar(JScrollBar.HORIZONTAL, 1, nbasesInView, 1,
+ getMaxBasesInPanel(getSequenceLength()));
+ scrollBar.addAdjustmentListener(new AdjustmentListener()
+ {
+ public void adjustmentValueChanged(AdjustmentEvent e)
+ {
+ repaint();
+ }
+ });
+ bottomPanel.add(scrollBar, BorderLayout.SOUTH);
+ }
+
+ mainPanel.add(bottomPanel, BorderLayout.SOUTH);
coveragePanel.setPreferredSize(new Dimension(900, 100));
coveragePanel.setVisible(false);
@@ -1361,16 +1442,12 @@ public class JamView extends JPanel
switch (event.getKeyCode())
{
case KeyEvent.VK_UP:
- int startBase = getBaseAtStartOfView();
setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
- goToBasePosition(startBase);
break;
case KeyEvent.VK_DOWN:
if (showBaseAlignment)
break;
- startBase = getBaseAtStartOfView();
setZoomLevel((int) (JamView.this.nbasesInView * .9));
- goToBasePosition(startBase);
break;
default:
break;
@@ -1388,6 +1465,7 @@ public class JamView extends JPanel
public void focusLost(FocusEvent fe){}
});
}
+
private void createViewMenu(JComponent view)
{
@@ -1508,10 +1586,10 @@ public class JamView extends JPanel
private int getBaseAtStartOfView()
{
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
- double x = jspView.getViewport().getViewRect().getX();
- return (int) (getMaxBasesInPanel(seqLength) * ( x / getWidth())) + 1;
+ if(feature_display != null)
+ return feature_display.getForwardBaseAtLeftEdge();
+ else
+ return scrollBar.getValue();
}
/**
@@ -1521,16 +1599,15 @@ public class JamView extends JPanel
*/
private void setZoomLevel(final int nbasesInView)
{
+ int startValue = getBaseAtStartOfView();
this.nbasesInView = nbasesInView;
-
- //System.out.println("setZoomLevel "+nbasesInView+" "+getBaseAtStartOfView());
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
- float pixPerBase = getPixPerBaseByBasesInView();
+
+ float pixPerBase = getPixPerBaseByWidth();
if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
+ this.nbasesInView = (int)(getPreferredSize().getWidth()/pixPerBase);
jspView.getVerticalScrollBar().setValue(0);
jspView.setColumnHeaderView(ruler);
showBaseAlignment = true;
@@ -1543,28 +1620,12 @@ public class JamView extends JPanel
showBaseAlignment = false;
}
- Dimension d = new Dimension();
- d.setSize((getMaxBasesInPanel(seqLength)*pixPerBase), maxHeight);
- setPreferredSize(d);
- revalidate();
+ if(scrollBar != null)
+ scrollBar.setValues(startValue, nbasesInView, 1,
+ getMaxBasesInPanel(getSequenceLength()));
}
- /**
- * Set the ViewPort so it starts at the given base position.
- * @param base
- */
- private void goToBasePosition(int base)
- {
- Point p = jspView.getViewport().getViewPosition();
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
-
- float width = (float) getPreferredSize().getWidth();
-
- p.x = Math.round(width*((float)(base-1)/(getMaxBasesInPanel(seqLength))));
- //System.out.println("goToBasePosition "+base);
- jspView.getViewport().setViewPosition(p);
- }
+
/**
* Set the start and end base positions to display.
@@ -1580,13 +1641,10 @@ public class JamView extends JPanel
this.endBase = end;
this.nbasesInView = end-start+1;
lastMousePoint = null;
-
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
float pixPerBase;
if(jspView.getViewport().getViewRect().width > 0)
- pixPerBase = this.getPixPerBaseByWidth(); // getPixPerBaseByBasesInView();
+ pixPerBase = getPixPerBaseByWidth();
else
{
if(feature_display == null)
@@ -1609,11 +1667,8 @@ public class JamView extends JPanel
}
Dimension d = new Dimension();
- d.setSize((getMaxBasesInPanel(seqLength)*pixPerBase), maxHeight);
-
- //System.out.println("setDisplay() "+d.getWidth());
+ d.setSize(nbasesInView*pixPerBase, maxHeight);
setPreferredSize(d);
- goToBasePosition(startBase);
if(event == null)
{
@@ -1704,7 +1759,8 @@ public class JamView extends JPanel
**/
private void handleCanvasMouseDragOrClick(final MouseEvent event)
{
- if(event.isShiftDown() || event.getButton() == MouseEvent.BUTTON3)
+ if(event.isShiftDown() || event.getButton() == MouseEvent.BUTTON3
+ || bases == null)
return;
if(event.getClickCount() > 1)
@@ -1715,10 +1771,9 @@ public class JamView extends JPanel
}
int onmask = MouseEvent.BUTTON1_DOWN_MASK;
- String refName = (String) combo.getSelectedItem();
- int seqLength = seqLengths.get(refName);
+ int seqLength = getSequenceLength();
float pixPerBase = getPixPerBaseByWidth();
- int start = (int) ( (event.getPoint().getX()/pixPerBase) + 1.f );
+ int start = (int) ( ( (event.getPoint().getX())/pixPerBase) + getBaseAtStartOfView() );
if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
dragStart = start;
@@ -1751,88 +1806,89 @@ public class JamView extends JPanel
return selection;
}
- private class CoveragePanel extends JPanel
+ public List<SAMRecord> getReadsInView()
{
- private static final long serialVersionUID = 1L;
+ return readsInView;
+ }
- private int start;
- private int end;
- private float pixPerBase;
-
- public CoveragePanel()
- {
- super();
- setBackground(Color.white);
- }
-
- /**
- * Override
- */
- protected void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
-
- 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 length = thisRead.getReadLength();
-
- for(int j=0; j<length;j++)
- {
- int bin =
- Math.round(((thisRead.getAlignmentStart()-start) + j) / 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()));
- }
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ return getPreferredSize();
+ }
- shape.lineTo(getWidth(),getHeight());
- g2.fill(shape);
+ public int getScrollableBlockIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ if (orientation == SwingConstants.HORIZONTAL)
+ return visibleRect.width - maxUnitIncrement;
+ else
+ return visibleRect.height - maxUnitIncrement;
+ }
- String maxStr = Integer.toString(max);
- FontMetrics fm = getFontMetrics(getFont());
- g2.setColor(Color.black);
-
- int xpos = getWidth() - fm.stringWidth(maxStr) -
- jspView.getVerticalScrollBar().getWidth();
- g2.drawString(maxStr, xpos, fm.getHeight());
- }
-
- protected void setStartAndEnd(int start, int end)
- {
- this.start = start;
- this.end = end;
- }
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
- public void setPixPerBase(float pixPerBase)
- {
- this.pixPerBase = pixPerBase;
- }
+ 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;
+ }
+ }
+
+ /**
+ * Artemis event notification
+ */
+ public void displayAdjustmentValueChanged(DisplayAdjustmentEvent event)
+ {
+ if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
+ {
+ laststart = -1;
+ lastend = -1;
+ this.startBase = event.getStart();
+ this.endBase = event.getEnd();
+
+ int width = feature_display.getMaxVisibleBases();
+ setZoomLevel(width);
+ repaint();
+ }
+ else
+ {
+ setDisplay(event.getStart(),
+ event.getStart()+feature_display.getMaxVisibleBases(), event);
+ repaint();
+ }
+ }
+
+ public void selectionChanged(SelectionChangeEvent event)
+ {
+ repaint();
}
private class Ruler extends JPanel
@@ -1907,138 +1963,12 @@ public class JamView extends JPanel
}
}
}
-
- 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;
- }
- }
-
-
- 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;
- }
- }
class PairedRead
{
SAMRecord sam1;
SAMRecord sam2;
}
-
-
- 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;
- }
- }
-
- /**
- * Artemis event notification
- */
- public void displayAdjustmentValueChanged(DisplayAdjustmentEvent event)
- {
- if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
- {
- laststart = -1;
- lastend = -1;
- this.startBase = event.getStart();
- this.endBase = event.getEnd();
-
- //int width = event.getEnd()-event.getStart()+1;
- int width = feature_display.getMaxVisibleBases();
- //System.out.println("displayAdjustmentValueChanged() "+event.getStart()+".."+event.getEnd()+" +width");
-
- setZoomLevel(width);
- goToBasePosition(event.getStart());
- setDisplay(event.getStart(), event.getEnd(), event);
- repaint();
- }
- else
- {
- setDisplay(event.getStart(), event.getEnd(), event);
- repaint();
- }
- }
-
- public void selectionChanged(SelectionChangeEvent event)
- {
- repaint();
- }
-
-
public static void main(String[] args)
{
diff --git a/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java b/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..1b652b1b855e7cebe85fbc5f2de38e8c7af8c586
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
@@ -0,0 +1,49 @@
+/* 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
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordComparator.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..c1ca3c074651ee8c73147cf4bfa9e28a2c0adcc3
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordComparator.java
@@ -0,0 +1,48 @@
+/* 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