diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index a870c46e29a0a57e48fedecf04e23e0f56fe66cb..ee271b58f4444c5e16def47dbb5011a0d659bdbb 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -23,130 +23,20 @@
*/
package uk.ac.sanger.artemis.components.alignment;
-import java.awt.Container;
-import java.awt.Frame;
-import java.text.DecimalFormat;
-import java.util.Arrays;
import java.util.Hashtable;
-import java.util.List;
import java.util.Vector;
-import javax.swing.JFrame;
-
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureSegmentVector;
-import uk.ac.sanger.artemis.FeatureVector;
-import uk.ac.sanger.artemis.components.EntryEdit;
-import uk.ac.sanger.artemis.components.FileViewer;
-import uk.ac.sanger.artemis.components.MultiComparator;
import uk.ac.sanger.artemis.io.Range;
class BamUtils
{
- /**
- * Read count for selected reads.
- * @param features
- * @param refName
- * @param samFileReaderHash
- * @param bamList
- * @param seqNames
- * @param offsetLengths
- * @param concatSequences
- * @param seqLengths
- * @param samRecordFlagPredicate
- * @param samRecordMapQPredicate
- * @param contained
- * @param useIntrons
- * @param mappedReads
- */
- protected static void countReads(final FeatureVector features,
- final String refName,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final List<String> bamList,
- final Vector<String> seqNames,
- final Hashtable<String, Integer> offsetLengths,
- final boolean concatSequences,
- final Hashtable<String, Integer> seqLengths,
- final SAMRecordPredicate samRecordFlagPredicate,
- final SAMRecordMapQPredicate samRecordMapQPredicate,
- final boolean contained,
- final boolean useIntrons,
- final int mappedReads[])
- {
- Hashtable<String, List<Float>> featureReadCount = new Hashtable<String, List<Float>>();
-
- for(int i=0; i<features.size(); i++)
- {
- Feature f = features.elementAt(i);
-
- int start = f.getRawFirstBase();
- int end = f.getRawLastBase();
- float fLen = getFeatureLength(f);
- List<Float> sampleCounts = new Vector<Float>();
-
- for(int j=0; j<bamList.size(); j++)
- {
- String bam = bamList.get(j);
- float cnt = 0;
- if(!useIntrons && f.getSegments().size() > 1)
- {
- for(int k=0; k<f.getSegments().size(); k++)
- {
- start = f.getSegments().elementAt(k).getRawRange().getStart();
- end = f.getSegments().elementAt(k).getRawRange().getEnd();
- cnt += getCount(start, end, bam, refName, samFileReaderHash,
- seqNames, offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate, contained);
- }
- }
- else
- cnt = getCount(start, end, bam, refName, samFileReaderHash,
- seqNames, offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate, contained);
- if(mappedReads != null)
- cnt = (cnt / ( ((float)mappedReads[j]/1000000.f) * (fLen/1000.f) )) ;
-
- sampleCounts.add(cnt);
- }
- featureReadCount.put(f.getSystematicName(), sampleCounts);
- }
-
- DecimalFormat df = new DecimalFormat("0.00##");
- StringBuffer buff = new StringBuffer();
- for(int j=0; j<bamList.size(); j++)
- {
- String bam = bamList.get(j);
- buff.append("#BAM: "+bam);
- if(mappedReads != null)
- buff.append(" Mapped Reads/million: "+ df.format( ((float)mappedReads[j]) / 1000000.f) );
- buff.append("\n");
- }
- buff.append("\n");
-
- Object[] readKey = featureReadCount.keySet().toArray();
- Arrays.sort(readKey);
-
- for (Object fId : readKey ) {
- buff.append(fId+"\t");
- List<Float> cnts = featureReadCount.get(fId);
- for(int i=0; i<cnts.size(); i++)
- buff.append(df.format(cnts.get(i)) + (i<cnts.size()-1 ? "\t" : ""));
- buff.append("\n");
- }
-
- FileViewer viewer;
- if(mappedReads != null)
- viewer = new FileViewer ("RPKM", true, false, true);
- else
- viewer = new FileViewer ("Read Count", true, false, true);
- viewer.getTextPane().setText(buff.toString());
- }
-
- private static float getFeatureLength(Feature f)
+ protected static float getFeatureLength(Feature f)
{
FeatureSegmentVector segs = f.getSegments();
int len = 0;
@@ -174,7 +64,7 @@ class BamUtils
* @param contained
* @return
*/
- private static int getCount(
+ protected static int getCount(
final int start,
final int end,
final String bam,
@@ -226,82 +116,7 @@ class BamUtils
return cnt;
}
- /**
- * Calculate the total number of mapped reads.
- * @param refName
- * @param samFileReaderHash
- * @param bamList
- * @param seqNames
- * @param offsetLengths
- * @param concatSequences
- * @param seqLengths
- * @param sequenceLength
- * @return
- */
- protected static int[] getTotalMappedReads(
- final String refName,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final List<String> bamList,
- final Vector<String> seqNames,
- final Hashtable<String, Integer> offsetLengths,
- final boolean concatSequences,
- final Hashtable<String, Integer> seqLengths,
- final int sequenceLength,
- final SAMRecordPredicate samRecordFlagPredicate,
- SAMRecordMapQPredicate samRecordMapQPredicate)
- {
- int MAX_BASE_CHUNK = 2000*60;
- int mapped[] = new int[bamList.size()];
- boolean contained = false;
-
- for (int i = 0; i < sequenceLength; i += MAX_BASE_CHUNK)
- {
- int sbegc = i;
- int sendc = i + MAX_BASE_CHUNK - 1;
-
- for (int j=0; j<bamList.size(); j++)
- {
- String bam = bamList.get(j);
- if (concatSequences)
- {
- int len = 0;
- int lastLen = 1;
- for (String name : seqNames)
- {
- int thisLength = seqLengths.get(name);
- len += thisLength;
-
- if ((lastLen >= sbegc && lastLen < sendc)
- || (len >= sbegc && len < sendc)
- || (sbegc >= lastLen && sbegc < len)
- || (sendc >= lastLen && sendc < len))
- {
- int offset = offsetLengths.get(name);
- int thisStart = sbegc - offset;
- if (thisStart < 1)
- thisStart = 1;
- int thisEnd = sendc - offset;
- if (thisEnd > thisLength)
- thisEnd = thisLength;
-
- mapped[j] += count(bam, samFileReaderHash, name, thisStart, thisEnd,
- samRecordFlagPredicate, samRecordMapQPredicate, contained);
-
- }
- lastLen = len;
- }
- }
- else
- {
- mapped[j] += count(bam, samFileReaderHash, refName, sbegc, sendc,
- samRecordFlagPredicate, samRecordMapQPredicate, contained);
- }
- }
- }
- return mapped;
- }
-
- private static int count(String bam,
+ protected static int count(String bam,
Hashtable<String, SAMFileReader> samFileReaderHash,
String refName,
int start,
@@ -330,18 +145,6 @@ class BamUtils
it.close();
return cnt;
}
-
- protected static Container getBamContainer(BamView bamView)
- {
- Frame fs[] = JFrame.getFrames();
- for(Frame f: fs)
- {
- if( f instanceof JFrame &&
- ((JFrame)f) instanceof EntryEdit ||
- ((JFrame)f) instanceof MultiComparator)
- return ((JFrame)f).getContentPane();
- }
- return bamView;
- }
+
}
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 608c75128fba7d8d6f25e3f0ccb707037d735eb7..ace4e38e56d0098403eb1a76f20ef330186ddf14 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -29,8 +29,6 @@ import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Composite;
-import java.awt.Container;
-import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.FontMetrics;
@@ -2016,10 +2014,8 @@ public class BamView extends JPanel
{
public void actionPerformed(ActionEvent e)
{
- Container c = BamUtils.getBamContainer(BamView.this);
- c.setCursor(new Cursor(Cursor.WAIT_CURSOR));
FeatureVector features = feature_display.getSelection().getAllFeatures();
-
+
JCheckBox overlap = new JCheckBox("Include all overlapping reads", true);
overlap.setToolTipText("Include reads that partially overlap the feature");
JCheckBox spliced = new JCheckBox("Introns included", true);
@@ -2028,11 +2024,10 @@ public class BamView extends JPanel
yBox.add(spliced);
JOptionPane.showMessageDialog(null, yBox, "Read Count Option", JOptionPane.INFORMATION_MESSAGE);
- BamUtils.countReads(features, (String)combo.getSelectedItem(), samFileReaderHash, bamList,
+ new MappedReads(features, (String)combo.getSelectedItem(), samFileReaderHash, bamList,
seqNames, offsetLengths, concatSequences, seqLengths,
samRecordFlagPredicate, samRecordMapQPredicate,
- !overlap.isSelected(), spliced.isSelected(), null);
- c.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ !overlap.isSelected(), spliced.isSelected());
}
});
@@ -2044,10 +2039,8 @@ public class BamView extends JPanel
{
public void actionPerformed(ActionEvent e)
{
- Container c = BamUtils.getBamContainer(BamView.this);
- c.setCursor(new Cursor(Cursor.WAIT_CURSOR));
FeatureVector features = feature_display.getSelection().getAllFeatures();
-
+
JCheckBox overlap = new JCheckBox("Include all overlapping reads", true);
overlap.setToolTipText("Include reads that partially overlap the feature");
JCheckBox spliced = new JCheckBox("Introns included", true);
@@ -2061,18 +2054,11 @@ public class BamView extends JPanel
seqlen = feature_display.getSequenceLength();
else if(bases != null)
seqlen = bases.getLength();
-
- int mappedReads[] =
- BamUtils.getTotalMappedReads((String)combo.getSelectedItem(),
- samFileReaderHash, bamList, seqNames, offsetLengths, concatSequences,
- offsetLengths, seqlen, samRecordFlagPredicate, samRecordMapQPredicate);
-
- logger4j.debug("TOTAL MAPPED READS "+mappedReads);
- BamUtils.countReads(features, (String)combo.getSelectedItem(), samFileReaderHash, bamList,
- seqNames, offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate,
- !overlap.isSelected(), spliced.isSelected(), mappedReads);
- c.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+
+ new MappedReads(features, (String)combo.getSelectedItem(),
+ samFileReaderHash, bamList, seqNames, offsetLengths, concatSequences,
+ offsetLengths, seqlen, samRecordFlagPredicate, samRecordMapQPredicate,
+ !overlap.isSelected(), spliced.isSelected());
}
});
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
new file mode 100644
index 0000000000000000000000000000000000000000..ca71b7e99a375667375f9ebfb4951cef8f00231e
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -0,0 +1,327 @@
+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.Point;
+import java.awt.Toolkit;
+import java.text.DecimalFormat;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.components.FileViewer;
+import uk.ac.sanger.artemis.components.SwingWorker;
+
+import net.sf.samtools.SAMFileReader;
+
+public class MappedReads
+{
+ private JProgressBar progressBar;
+ private JLabel progressTxt = new JLabel();
+
+ private FeatureVector features;
+ private String refName;
+ private Hashtable<String, SAMFileReader> samFileReaderHash;
+ private List<String> bamList;
+ private Vector<String> seqNames;
+ private Hashtable<String, Integer> offsetLengths;
+ private boolean concatSequences;
+ private Hashtable<String, Integer> seqLengths;
+ private int sequenceLength;
+ private SAMRecordPredicate samRecordFlagPredicate;
+ private SAMRecordMapQPredicate samRecordMapQPredicate;
+ private boolean contained;
+ private boolean useIntrons;
+ private JDialog dialog = new JDialog((JFrame)null, "Calculating", true);;
+
+ private int mappedReads[];
+
+ /**
+ * Calculate the total number of mapped reads.
+ * @param refName
+ * @param samFileReaderHash
+ * @param bamList
+ * @param seqNames
+ * @param offsetLengths
+ * @param concatSequences
+ * @param seqLengths
+ * @param sequenceLength
+ */
+ public MappedReads(
+ final FeatureVector features,
+ final String refName,
+ final Hashtable<String, SAMFileReader> samFileReaderHash,
+ final List<String> bamList,
+ final Vector<String> seqNames,
+ final Hashtable<String, Integer> offsetLengths,
+ final boolean concatSequences,
+ final Hashtable<String, Integer> seqLengths,
+ final int sequenceLength,
+ final SAMRecordPredicate samRecordFlagPredicate,
+ SAMRecordMapQPredicate samRecordMapQPredicate,
+ final boolean contained,
+ final boolean useIntrons)
+ {
+ this.features = features;
+ this.refName = refName;
+ this.samFileReaderHash = samFileReaderHash;
+ this.bamList = bamList;
+ this.seqNames = seqNames;
+ this.offsetLengths = offsetLengths;
+ this.concatSequences = concatSequences;
+ this.seqLengths = seqLengths;
+ this.sequenceLength = sequenceLength;
+ this.samRecordFlagPredicate = samRecordFlagPredicate;
+ this.samRecordMapQPredicate = samRecordMapQPredicate;
+ this.contained = contained;
+ this.useIntrons = useIntrons;
+
+ progressBar = new JProgressBar(0, sequenceLength);
+ progressBar.setValue(0);
+ progressBar.setStringPainted(true);
+
+ JPanel panel = new JPanel(new BorderLayout());
+ progressTxt.setText("Total number of mapped reads");
+ panel.add(progressTxt, BorderLayout.NORTH);
+ panel.add(progressBar, BorderLayout.CENTER);
+
+ dialog.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ panel.setOpaque(true);
+ dialog.setContentPane(panel);
+ dialog.pack();
+ centerDialog();
+
+ CalculateTotalMappedReads cmr = new CalculateTotalMappedReads();
+ cmr.start();
+ dialog.setVisible(true);
+ }
+
+ /**
+ * Read count for selected features.
+ * @param features
+ * @param refName
+ * @param samFileReaderHash
+ * @param bamList
+ * @param seqNames
+ * @param offsetLengths
+ * @param concatSequences
+ * @param seqLengths
+ * @param samRecordFlagPredicate
+ * @param samRecordMapQPredicate
+ * @param contained
+ * @param useIntrons
+ */
+ public MappedReads(
+ final FeatureVector features,
+ final String refName,
+ final Hashtable<String, SAMFileReader> samFileReaderHash,
+ final List<String> bamList,
+ final Vector<String> seqNames,
+ final Hashtable<String, Integer> offsetLengths,
+ final boolean concatSequences,
+ final Hashtable<String, Integer> seqLengths,
+ final SAMRecordPredicate samRecordFlagPredicate,
+ final SAMRecordMapQPredicate samRecordMapQPredicate,
+ final boolean contained,
+ final boolean useIntrons)
+ {
+ this.features = features;
+ this.refName = refName;
+ this.samFileReaderHash = samFileReaderHash;
+ this.bamList = bamList;
+ this.seqNames = seqNames;
+ this.offsetLengths = offsetLengths;
+ this.concatSequences = concatSequences;
+ this.seqLengths = seqLengths;
+ this.samRecordFlagPredicate = samRecordFlagPredicate;
+ this.samRecordMapQPredicate = samRecordMapQPredicate;
+ this.contained = contained;
+ this.useIntrons = useIntrons;
+
+ progressBar = new JProgressBar(0, features.size());
+ progressBar.setValue(0);
+ progressBar.setStringPainted(true);
+
+ JPanel panel = new JPanel(new BorderLayout());
+ progressTxt.setText("Number of mapped reads for "+features.size()+" features");
+ panel.add(progressTxt, BorderLayout.NORTH);
+ panel.add(progressBar, BorderLayout.CENTER);
+
+ panel.setOpaque(true);
+ dialog.setContentPane(panel);
+ dialog.pack();
+ centerDialog();
+
+ CalculateMappedReads cmr = new CalculateMappedReads();
+ cmr.start();
+ dialog.setVisible(true);
+ }
+
+ private void centerDialog()
+ {
+ final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ final int x_position =(screen.width - dialog.getSize().width) / 2;
+ int y_position =(screen.height - dialog.getSize().height) / 2;
+
+ if(y_position < 10)
+ y_position = 10;
+ dialog.setLocation(new Point(x_position, y_position));
+ }
+
+ class CalculateMappedReads extends SwingWorker
+ {
+ Hashtable<String, List<Float>> featureReadCount;
+ public Object construct()
+ {
+ featureReadCount = new Hashtable<String, List<Float>>();
+ for (int i = 0; i < features.size(); i++)
+ {
+ Feature f = features.elementAt(i);
+ progressBar.setValue(i);
+
+ int start = f.getRawFirstBase();
+ int end = f.getRawLastBase();
+ float fLen = BamUtils.getFeatureLength(f);
+ List<Float> sampleCounts = new Vector<Float>();
+
+ for (int j = 0; j < bamList.size(); j++)
+ {
+ String bam = bamList.get(j);
+ float cnt = 0;
+ if (!useIntrons && f.getSegments().size() > 1)
+ {
+ for (int k = 0; k < f.getSegments().size(); k++)
+ {
+ start = f.getSegments().elementAt(k).getRawRange().getStart();
+ end = f.getSegments().elementAt(k).getRawRange().getEnd();
+ cnt += BamUtils.getCount(start, end, bam, refName, samFileReaderHash,
+ seqNames, offsetLengths, concatSequences, seqLengths,
+ samRecordFlagPredicate, samRecordMapQPredicate, contained);
+ }
+ }
+ else
+ cnt = BamUtils.getCount(start, end, bam, refName, samFileReaderHash, seqNames,
+ offsetLengths, concatSequences, seqLengths,
+ samRecordFlagPredicate, samRecordMapQPredicate, contained);
+
+ if (mappedReads != null)
+ cnt = (cnt / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
+
+ sampleCounts.add(cnt);
+ }
+ featureReadCount.put(f.getSystematicName(), sampleCounts);
+ }
+ return null;
+ }
+
+ public void finished()
+ {
+ DecimalFormat df = new DecimalFormat("0.00##");
+ StringBuffer buff = new StringBuffer();
+ for (int j = 0; j < bamList.size(); j++)
+ {
+ String bam = bamList.get(j);
+ buff.append("#BAM: " + bam);
+ if (mappedReads != null)
+ buff.append(" Mapped Reads/million: "
+ + df.format(((float) mappedReads[j]) / 1000000.f));
+ buff.append("\n");
+ }
+ buff.append("\n");
+
+ Object[] readKey = featureReadCount.keySet().toArray();
+ Arrays.sort(readKey);
+
+ for (Object fId : readKey)
+ {
+ buff.append(fId + "\t");
+ List<Float> cnts = featureReadCount.get(fId);
+ for (int i = 0; i < cnts.size(); i++)
+ buff.append(df.format(cnts.get(i)) + (i < cnts.size() - 1 ? "\t" : ""));
+ buff.append("\n");
+ }
+
+ FileViewer viewer;
+ if (mappedReads != null)
+ viewer = new FileViewer("RPKM", true, false, true);
+ else
+ viewer = new FileViewer("Read Count", true, false, true);
+ viewer.getTextPane().setText(buff.toString());
+
+ dialog.dispose();
+ }
+ }
+
+ class CalculateTotalMappedReads extends SwingWorker
+ {
+ public Object construct()
+ {
+ int MAX_BASE_CHUNK = 2000 * 60;
+ mappedReads = new int[bamList.size()];
+ boolean contained = false;
+ for (int i = 0; i < sequenceLength; i += MAX_BASE_CHUNK)
+ {
+ progressBar.setValue(i);
+ int sbegc = i;
+ int sendc = i + MAX_BASE_CHUNK - 1;
+
+ for (int j = 0; j < bamList.size(); j++)
+ {
+ String bam = bamList.get(j);
+ if (concatSequences)
+ {
+ int len = 0;
+ int lastLen = 1;
+ for (String name : seqNames)
+ {
+ int thisLength = seqLengths.get(name);
+ len += thisLength;
+
+ if ((lastLen >= sbegc && lastLen < sendc)
+ || (len >= sbegc && len < sendc)
+ || (sbegc >= lastLen && sbegc < len)
+ || (sendc >= lastLen && sendc < len))
+ {
+ int offset = offsetLengths.get(name);
+ int thisStart = sbegc - offset;
+ if (thisStart < 1)
+ thisStart = 1;
+ int thisEnd = sendc - offset;
+ if (thisEnd > thisLength)
+ thisEnd = thisLength;
+
+ mappedReads[j] += BamUtils.count(bam, samFileReaderHash, name,
+ thisStart, thisEnd, samRecordFlagPredicate,
+ samRecordMapQPredicate, contained);
+
+ }
+ lastLen = len;
+ }
+ }
+ else
+ {
+ mappedReads[j] += BamUtils.count(bam, samFileReaderHash, refName, sbegc,
+ sendc, samRecordFlagPredicate, samRecordMapQPredicate,
+ contained);
+ }
+ }
+ }
+
+ progressBar.setValue(0);
+ progressBar.setMaximum(features.size());
+ progressTxt.setText("RPKM values for "+features.size()+" features");
+ CalculateMappedReads cmr = new CalculateMappedReads();
+ cmr.start();
+ return null;
+ }
+ }
+}