diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index e464b4267201f31cc0abbebed0b0fe89a7851f66..077ad23d3cd5e4be1da583f67e5cdf516a21b9c3 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -26,6 +26,7 @@ package uk.ac.sanger.artemis.components.alignment;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Graphics;
@@ -53,20 +54,32 @@ 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;
import java.util.Vector;
+import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.JTextField;
import javax.swing.Scrollable;
import javax.swing.SwingConstants;
import javax.swing.UIManager;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordQueryNameComparator;
+import net.sf.samtools.SAMSequenceRecord;
+import net.sf.samtools.SAMFileReader.ValidationStringency;
+import net.sf.samtools.util.CloseableIterator;
+
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Options;
@@ -85,7 +98,7 @@ public class JamView extends JPanel
implements Scrollable
{
private static final long serialVersionUID = 1L;
- private List<Read> readsInView;
+ private List<SAMRecord> readsInView;
private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
private Vector<String> seqNames = new Vector<String>();
private String bam;
@@ -94,13 +107,17 @@ public class JamView extends JPanel
private JScrollPane jspView;
private JComboBox combo;
private JCheckBox checkBoxSingle;
-
+ private JCheckBox checkBoxSNPs;
+
Ruler ruler = new Ruler();
private int nbasesInView;
private int laststart;
private int lastend;
private int maxUnitIncrement = 4;
+ private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
+ private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
private int ALIGNMENT_PIX_PER_BASE;
+ public static boolean PICARD = true;
public JamView(String bam,
@@ -125,7 +142,10 @@ public class JamView extends JPanel
}
}
- readHeader();
+ if(PICARD)
+ readHeaderPicard();
+ else
+ readHeader();
// set font size
setFont(getFont().deriveFont(12.f));
@@ -133,7 +153,7 @@ public class JamView extends JPanel
new javax.swing.plaf.FontUIResource(getFont());
// Options.getOptions().getFontUIResource();
- java.util.Enumeration keys = UIManager.getDefaults().keys();
+ Enumeration<Object> keys = UIManager.getDefaults().keys();
while(keys.hasMoreElements())
{
Object key = keys.nextElement();
@@ -193,7 +213,24 @@ public class JamView extends JPanel
e.printStackTrace();
}
}
-
+
+ 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
@@ -217,7 +254,7 @@ public class JamView extends JPanel
System.out.println();
if(readsInView == null)
- readsInView = new Vector<Read>();
+ readsInView = new Vector<SAMRecord>();
else
readsInView.clear();
RunSamTools samtools = new RunSamTools(cmd, null, null, readsInView);
@@ -228,6 +265,39 @@ public class JamView extends JPanel
samtools.waitForStdout();
}
+ /**
+ * Read a SAM or BAM file.
+ */
+ private void readFromBamPicard(int start, int end)
+ {
+ // Open the input file. Automatically detects whether input is SAM or BAM
+ // and delegates to a reader implementation for the appropriate format.
+ File bamFile = new File(bam);
+ File indexFile = new File(bam+".bai");
+ final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
+ inputSam.setValidationStringency(ValidationStringency.SILENT);
+
+ if(readsInView == null)
+ readsInView = new Vector<SAMRecord>();
+ else
+ readsInView.clear();
+ String refName = (String) combo.getSelectedItem();
+ CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
+ while ( it.hasNext() )
+ {
+ try
+ {
+ SAMRecord samRecord = it.next();
+ readsInView.add(samRecord);
+ }
+ catch(Exception e)
+ {
+ System.out.println(e.getMessage());
+ }
+ }
+ inputSam.close();
+ }
+
/**
* Override
*/
@@ -251,9 +321,13 @@ public class JamView extends JPanel
{
try
{
- readFromBam(start, end);
- if(pixPerBase < ALIGNMENT_PIX_PER_BASE)
- Collections.sort(readsInView, new ReadComparator());
+ setCursor(cbusy);
+
+ if(PICARD)
+ readFromBamPicard(start, end);
+ else
+ readFromBam(start, end);
+ setCursor(cdone);
}
catch(OutOfMemoryError ome)
{
@@ -267,21 +341,33 @@ public class JamView extends JPanel
if(pixPerBase >= ALIGNMENT_PIX_PER_BASE)
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
- drawLineView(g2, seqLength, pixPerBase, start, end);
+ {
+ Collections.sort(readsInView, new ReadComparator());
+ drawLineView(g2, seqLength, pixPerBase, start, end);
+ }
}
+ /**
+ * Draw the zoomed-in base view.
+ * @param g2
+ * @param seqLength
+ * @param pixPerBase
+ * @param start
+ * @param end
+ */
private void drawBaseAlignment(Graphics2D g2, int seqLength,
float pixPerBase, final int start, final int end)
{
- FontMetrics fm = getFontMetrics(getFont());
int ypos = 0;
ruler.start = start;
ruler.end = end;
ruler.repaint();
- //drawBaseScale(g2, start, end, ypos);
ypos+=6;
+
+ char[] refSeq = null;
+ int refSeqStart = start;
if(bases != null)
{
// draw the reference sequence
@@ -291,20 +377,19 @@ public class JamView extends JPanel
int seqEnd = end+1;
if(seqEnd > bases.getLength())
seqEnd = bases.getLength();
-
- int seqStart = start;
- if(seqStart < 1)
- seqStart = 1;
- String seq = bases.getSubSequence(new Range(seqStart, seqEnd), Bases.FORWARD);
+
+ if(refSeqStart < 1)
+ refSeqStart = 1;
+ refSeq =
+ bases.getSubSequenceC(new Range(refSeqStart, seqEnd), Bases.FORWARD);
int xpos;
- for(int i=0;i<seq.length(); i++)
+ for(int i=0;i<refSeq.length; i++)
{
- xpos = ((seqStart-1) + i)*ALIGNMENT_PIX_PER_BASE;
- g2.drawString(seq.substring(i, i+1).toUpperCase(), xpos, ypos);
- System.out.print(seq.substring(i, i+1).toUpperCase());
+ xpos = ((refSeqStart-1) + i)*ALIGNMENT_PIX_PER_BASE;
+ refSeq[i] = Character.toUpperCase(refSeq[i]);
+ g2.drawChars(refSeq, i, 1, xpos, ypos);
}
- System.out.println();
}
catch (OutOfRangeException e)
{
@@ -312,33 +397,36 @@ public class JamView extends JPanel
}
}
- boolean draw[] = new boolean[readsInView.size()];
+ boolean drawn[] = new boolean[readsInView.size()];
for(int i=0; i<readsInView.size(); i++)
- draw[i] = false;
-
-
+ drawn[i] = false;
for(int i=0; i<readsInView.size(); i++)
{
- if (!draw[i])
+ if (!drawn[i])
{
- Read thisRead = readsInView.get(i);
+ SAMRecord thisRead = readsInView.get(i);
ypos+=11;
- drawSequence(g2, thisRead, pixPerBase, ypos);
- draw[i] = true;
+ drawSequence(g2, thisRead, pixPerBase, ypos, refSeq, refSeqStart);
+ drawn[i] = true;
+
+ int thisEnd = thisRead.getAlignmentEnd();
+ if(thisEnd == 0)
+ thisEnd = thisRead.getAlignmentStart()+thisRead.getReadLength();
- int thisEnd = thisRead.pos+thisRead.seq.length();
for(int j=i+1; j<readsInView.size(); j++)
{
- if (!draw[j])
+ if (!drawn[j])
{
- Read nextRead = readsInView.get(j);
- if(nextRead.pos > thisEnd+1)
+ SAMRecord nextRead = readsInView.get(j);
+ if(nextRead.getAlignmentStart() > thisEnd+1)
{
- drawSequence(g2, nextRead, pixPerBase, ypos);
- draw[j] = true;
- thisEnd = nextRead.pos+nextRead.seq.length();
+ drawSequence(g2, nextRead, pixPerBase, ypos, refSeq, refSeqStart);
+ drawn[j] = true;
+ thisEnd = nextRead.getAlignmentEnd();
+ if(thisEnd == 0)
+ thisEnd = nextRead.getAlignmentStart()+nextRead.getReadLength();
}
}
}
@@ -359,24 +447,44 @@ public class JamView extends JPanel
* @param pixPerBase
* @param ypos
*/
- private void drawSequence(Graphics2D g2, Read read, float pixPerBase, int ypos)
+ private void drawSequence(Graphics2D g2, SAMRecord samRecord,
+ float pixPerBase, int ypos, char[] refSeq, int refSeqStart)
{
- if ((read.flag & 0x0001) != 0x0001 ||
- (read.flag & 0x0008) == 0x0008)
+ if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
+ samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
g2.setColor(Color.black);
else
g2.setColor(Color.blue);
+ Color col = g2.getColor();
int xpos;
-
- for(int i=0;i<read.seq.length(); i++)
+ String seq = samRecord.getReadString();
+
+ for(int i=0;i<seq.length(); i++)
{
- xpos = ((read.pos-1) + i)*ALIGNMENT_PIX_PER_BASE;
- g2.drawString(read.seq.substring(i, i+1), xpos, ypos);
+ xpos = ((samRecord.getAlignmentStart()-1) + i)*ALIGNMENT_PIX_PER_BASE;
+
+ if(checkBoxSNPs.isSelected() && refSeq != null)
+ {
+ int refPos = samRecord.getAlignmentStart()-refSeqStart+i;
+
+ if(refPos >= 0 && refPos < refSeq.length && seq.charAt(i) != refSeq[refPos])
+ g2.setColor(Color.red);
+ else
+ g2.setColor(col);
+ }
+ g2.drawString(seq.substring(i, i+1), xpos, ypos);
}
-
}
+ /**
+ * Draw zoomed-out view.
+ * @param g2
+ * @param seqLength
+ * @param pixPerBase
+ * @param start
+ * @param end
+ */
private void drawLineView(Graphics2D g2, int seqLength, float pixPerBase, int start, int end)
{
drawScale(g2, start, end, pixPerBase);
@@ -388,53 +496,55 @@ public class JamView extends JPanel
for(int i=0; i<readsInView.size(); i++)
{
- Read thisRead = readsInView.get(i);
- Read nextRead = null;
+ SAMRecord samRecord = readsInView.get(i);
+ SAMRecord samNextRecord = null;
- if( (thisRead.flag & 0x0001) != 0x0001 || // read is not paired in sequencing
- (thisRead.flag & 0x0008) == 0x0008 ) // mate is unmapped
+ if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
+ samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
{
if(checkBoxSingle.isSelected())
{
- int ypos = (getHeight() - scaleHeight) - thisRead.seq.length();
+ int ypos = (getHeight() - scaleHeight) - samRecord.getReadString().length();
g2.setColor(Color.orange);
- drawRead(g2, thisRead, pixPerBase, stroke, ypos);
+ drawRead(g2, samRecord, pixPerBase, stroke, ypos);
}
continue;
}
- int ypos = (getHeight() - scaleHeight) - ( Math.abs(thisRead.isize) );
+ int ypos = (getHeight() - scaleHeight) - ( Math.abs(samRecord.getInferredInsertSize()) );
if(i < readsInView.size()-1)
{
- nextRead = readsInView.get(++i);
+ samNextRecord = readsInView.get(++i);
- if(thisRead.qname.equals(nextRead.qname))
+ if(samRecord.getReadName().equals(samNextRecord.getReadName()))
{
- if( (thisRead.flag & 0x0010) == 0x0010 && // strand of the query (1 for reverse)
- (nextRead.flag & 0x0010) == 0x0010 )
+ if( samRecord.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
+ samNextRecord.getReadNegativeStrandFlag() )
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
- int thisEnd = drawRead(g2, thisRead, pixPerBase, stroke, ypos)[1];
- int nextStart = drawRead(g2, nextRead, pixPerBase, stroke, ypos)[0];
+ drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+ drawRead(g2, samNextRecord, pixPerBase, stroke, ypos);
- if(thisEnd < nextStart && (nextStart-thisEnd)*pixPerBase > 2.f)
+ if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() &&
+ (samNextRecord.getAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
{
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
- g2.drawLine((int)(thisEnd*pixPerBase), ypos, (int)(nextStart*pixPerBase), ypos);
+ g2.drawLine((int)(samRecord.getAlignmentEnd()*pixPerBase), ypos,
+ (int)(samNextRecord.getAlignmentStart()*pixPerBase), ypos);
}
}
else
{
- drawLoneRead(g2, thisRead, ypos, pixPerBase, originalStroke, stroke);
+ drawLoneRead(g2, samRecord, ypos, pixPerBase, originalStroke, stroke);
i--;
}
}
else
{
- drawLoneRead(g2, thisRead, ypos, pixPerBase, originalStroke, stroke);
+ drawLoneRead(g2, samRecord, ypos, pixPerBase, originalStroke, stroke);
}
}
}
@@ -448,45 +558,34 @@ public class JamView extends JPanel
* @param originalStroke
* @param stroke
*/
- private void drawLoneRead(Graphics2D g2, Read thisRead, int ypos,
+ private void drawLoneRead(Graphics2D g2, SAMRecord samRecord, int ypos,
float pixPerBase, Stroke originalStroke, Stroke stroke)
{
boolean drawLine = true;
- if( (thisRead.flag & 0x0010) == 0x0010 ) // strand of the query (1 for reverse)
+ if(samRecord.getReadNegativeStrandFlag()) // strand of the query (1 for reverse)
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
if(ypos <= 0)
{
- ypos = thisRead.seq.length();
+ ypos = samRecord.getReadString().length();
drawLine = false;
g2.setColor(Color.orange);
}
- int thisEnd = drawRead(g2, thisRead, pixPerBase, stroke, ypos)[1];
+ int thisStart = samRecord.getAlignmentStart()-1;
+ int thisEnd = thisStart + samRecord.getReadString().length();
+ drawRead(g2, samRecord, pixPerBase, stroke, ypos);
if(drawLine)
{
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
- int nextStart = (int) ((thisRead.mpos-1)*pixPerBase);
+ int nextStart = (int) ((samRecord.getMateAlignmentStart()-1)*pixPerBase);
g2.drawLine((int)(thisEnd*pixPerBase), ypos, nextStart, ypos);
}
}
-
- private void drawBaseScale(Graphics2D g2, int start, int end, int ypos)
- {
- int startMark = (((int)(start/10))*10)+1;
- for(int i=startMark; i<end; i+=10)
- {
- int xpos = (i-1-start)*ALIGNMENT_PIX_PER_BASE;
- g2.drawString(Integer.toString(i), xpos, ypos);
-
- xpos+=(ALIGNMENT_PIX_PER_BASE/2);
- g2.drawLine(xpos, ypos+1, xpos, ypos+5);
- }
- }
private void drawScale(Graphics2D g2, int start, int end, float pixPerBase)
{
@@ -536,14 +635,41 @@ public class JamView extends JPanel
}
}
- private int[] drawRead(Graphics2D g2, Read read,
+ private void drawRead(Graphics2D g2, SAMRecord thisRead,
float pixPerBase, Stroke stroke, int ypos)
{
- int thisStart = read.pos-1;
- int thisEnd = thisStart + read.seq.length();
+ int thisStart = thisRead.getAlignmentStart()-1;
+ int thisEnd = thisRead.getAlignmentEnd();
g2.setStroke(stroke);
- g2.drawLine((int)(thisStart*pixPerBase), ypos, (int)(thisEnd*pixPerBase), ypos);
- return new int[] { thisStart, thisEnd };
+ g2.drawLine((int) (thisStart * pixPerBase), ypos,
+ (int) (thisEnd * pixPerBase), ypos);
+
+ if (checkBoxSNPs.isSelected())
+ {
+ try
+ {
+ char[] refSeq = bases.getSubSequenceC(
+ new Range(thisStart + 1, thisEnd), Bases.FORWARD);
+ byte[] readSeq = thisRead.getReadBases();
+
+ Color col = g2.getColor();
+
+ g2.setColor(Color.red);
+ for (int i = 0; i < refSeq.length && i < readSeq.length; i++)
+ {
+ if (Character.toUpperCase(refSeq[i]) != readSeq[i])
+ {
+ g2.drawLine((int) ((thisStart + i) * pixPerBase), ypos + 1,
+ (int) ((thisStart + i) * pixPerBase), ypos - 1);
+ }
+ }
+ g2.setColor(col);
+ }
+ catch (OutOfRangeException e)
+ {
+ e.printStackTrace();
+ }
+ }
}
public void addToPanel(final JPanel panel)
@@ -563,7 +689,7 @@ public class JamView extends JPanel
}
});
gc.fill = GridBagConstraints.NONE;
- gc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gc.anchor = GridBagConstraints.NORTHWEST;
topPanel.add(combo, gc);
checkBoxSingle = new JCheckBox("Single Reads");
@@ -576,19 +702,53 @@ public class JamView extends JPanel
});
topPanel.add(checkBoxSingle, gc);
+
+ checkBoxSNPs = new JCheckBox("SNPs");
+ checkBoxSNPs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ repaint();
+ }
+ });
+ topPanel.add(checkBoxSNPs, gc);
+
+ final JTextField baseText = new JTextField(10);
+ JButton goTo = new JButton("GoTo:");
+ goTo.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ int basePosition = Integer.parseInt(baseText.getText());
+ goToBasePosition(basePosition);
+ }
+ catch(NumberFormatException nfe)
+ {
+ JOptionPane.showMessageDialog(JamView.this,
+ "Expecting a base number!",
+ "Number Format", JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ topPanel.add(goTo, gc);
+ topPanel.add(baseText, gc);
+
panel.setPreferredSize(new Dimension(1000,500));
setLength(nbasesInView);
-
- jspView = new JScrollPane(this, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
- JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
-
+
+ jspView = new JScrollPane(this,
+ JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+ JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
+
panel.setLayout(new BorderLayout());
panel.add(topPanel, BorderLayout.NORTH);
panel.add(jspView, BorderLayout.CENTER);
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
-
+
addMouseListener(new MouseAdapter()
{
public void mouseClicked(MouseEvent e)
@@ -606,13 +766,13 @@ public class JamView extends JPanel
case KeyEvent.VK_UP:
int startBase = getBaseAtStartOfView();
setZoomLevel( (int) (JamView.this.nbasesInView*1.1) );
- setViewToBasePosition(startBase);
+ goToBasePosition(startBase);
repaint();
break;
case KeyEvent.VK_DOWN:
startBase = getBaseAtStartOfView();
setZoomLevel( (int) (JamView.this.nbasesInView*.9) );
- setViewToBasePosition(startBase);
+ goToBasePosition(startBase);
repaint();
break;
default:
@@ -655,7 +815,7 @@ public class JamView extends JPanel
* Set the ViewPort so it starts at the given base position.
* @param base
*/
- private void setViewToBasePosition(int base)
+ private void goToBasePosition(int base)
{
Point p = jspView.getViewport().getViewPosition();
@@ -692,7 +852,7 @@ public class JamView extends JPanel
d.setSize((seqLength*pixPerBase), 800.d);
setPreferredSize(d);
}
-
+
/**
* Return an Artemis entry from a file
* @param entryFileName
@@ -741,11 +901,13 @@ public class JamView extends JPanel
return entry;
}
+
class Ruler extends JPanel
{
+ private static final long serialVersionUID = 1L;
int start;
int end;
-
+
public Ruler()
{
super();
@@ -753,26 +915,41 @@ public class JamView extends JPanel
setBackground(Color.white);
setFont(getFont().deriveFont(11.f));
}
-
+
public void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
drawBaseScale(g2, start, end, 12);
}
+
+ private void drawBaseScale(Graphics2D g2, int start, int end, int ypos)
+ {
+ int startMark = (((int)(start/10))*10)+1;
+
+ for(int i=startMark; i<end; i+=10)
+ {
+ int xpos = (i-1-start)*ALIGNMENT_PIX_PER_BASE;
+ g2.drawString(Integer.toString(i), xpos, ypos);
+
+ xpos+=(ALIGNMENT_PIX_PER_BASE/2);
+ g2.drawLine(xpos, ypos+1, xpos, ypos+5);
+ }
+ }
}
- class ReadComparator implements Comparator
+ class ReadComparator implements Comparator<Object>
{
public int compare(Object o1, Object o2)
{
- Read pr1 = (Read) o1;
- Read pr2 = (Read) o2;
+ SAMRecord pr1 = (SAMRecord) o1;
+ SAMRecord pr2 = (SAMRecord) o2;
- return pr1.qname.compareTo(pr2.qname);
+ return pr1.getReadName().compareTo(pr2.getReadName());
}
}
+
public Dimension getPreferredScrollableViewportSize()
{
return getPreferredSize();
@@ -867,8 +1044,8 @@ public class JamView extends JPanel
view.addToPanel((JPanel)frame.getContentPane());
frame.pack();
+ frame.setVisible(true);
view.jspView.getVerticalScrollBar().setValue(
view.jspView.getVerticalScrollBar().getMaximum());
- frame.setVisible(true);
}
}
diff --git a/uk/ac/sanger/artemis/components/alignment/Read.java b/uk/ac/sanger/artemis/components/alignment/Read.java
deleted file mode 100644
index 56d701165a16fc6635b760be290e70112e52a85e..0000000000000000000000000000000000000000
--- a/uk/ac/sanger/artemis/components/alignment/Read.java
+++ /dev/null
@@ -1,52 +0,0 @@
-/* Read
- *
- * 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;
-
-class Read
-{
- String qname; // query name
- int flag; // bitwise flag
- String rname; // reference name
- int pos; // leftmost coordinate
- short mapq; // MAPping Quality
- String cigar; // extended CIGAR string
- String mrnm; // Mate Reference sequence NaMe; Ò=Ó if the same as rname
- int mpos; // leftmost Mate POSition
- int isize; // inferred Insert SIZE
- String seq; // query SEQuence; Ò=Ó for a match to the reference; n/N/. for ambiguity
-
- public String toString()
- {
- return qname+"\t"+
- flag+"\t"+
- rname+"\t"+
- pos+"\t"+
- mapq+"\t"+
- cigar+"\t"+
- mrnm+"\t"+
- mpos+"\t"+
- isize+"\t"+
- seq;
- }
-}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/RunSamTools.java b/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
index ddad42a3287d6ac82bc9d2f9b94d85b8a4f2229c..d7da5e70af876ae3e07134857880e1dad1508a6f 100644
--- a/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
+++ b/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
@@ -26,6 +26,8 @@ package uk.ac.sanger.artemis.components.alignment;
import java.io.*;
import java.util.List;
+import net.sf.samtools.SAMRecord;
+
/**
* Used to run an samtools process this reads stdout and
* stderr in separate threads.
@@ -36,7 +38,7 @@ public class RunSamTools
/** running process */
private Process p;
/** standard out */
- private List<Read> readsInView;
+ private List<SAMRecord> readsInView;
/** standard error */
private StringBuffer stderr = new StringBuffer();
private StringBuffer stdout = new StringBuffer();
@@ -57,7 +59,7 @@ public class RunSamTools
public RunSamTools(String cmd[],
String[] envp,
File project,
- List<Read> readsInView)
+ List<SAMRecord> readsInView)
{
//this.project = project;
this.readsInView = readsInView;
@@ -156,17 +158,18 @@ public class RunSamTools
{
String fields[] = line.split("\t");
- Read pread = new Read();
- pread.qname = fields[0];
- pread.flag = Integer.parseInt(fields[1]);
- pread.rname = fields[2];
- pread.pos = Integer.parseInt(fields[3]);
- pread.mapq = Short.parseShort(fields[4]);
- pread.cigar = fields[5];
- pread.mrnm = fields[6];
- pread.mpos = Integer.parseInt(fields[7]);
- pread.isize = Integer.parseInt(fields[8]);
- pread.seq = fields[9];
+ SAMRecord pread = new SAMRecord(null);
+ pread.setReadName(fields[0]);
+ pread.setFlags(Integer.parseInt(fields[1]));
+ pread.setReferenceName(fields[2]);
+ pread.setAlignmentStart(Integer.parseInt(fields[3]));
+ pread.setMappingQuality(Integer.parseInt(fields[4]));
+ pread.setCigarString(fields[5]);
+ pread.setMateReferenceName(fields[6]);
+ pread.setMateAlignmentStart( Integer.parseInt(fields[7]));
+ pread.setInferredInsertSize(Integer.parseInt(fields[8]));
+ pread.setReadString(fields[9]);
+
readsInView.add(pread);
}
else