diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index 46f60f9d910a3e704555eebe93b43c7ab0e35b72..8ad6da6ce670d76fdf208fb781b63205133b2fff 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -165,15 +165,12 @@ class BamUtils
final Hashtable<String, SAMFileReader> samFileReaderHash,
final String refName,
final int start,
- final int end,
+ final int end,
+ final int cnt[][],
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordPredicate samRecordMapQPredicate)
{
- final int cnt[][] = new int[end-start+1][2];
- for (int i = 0; i < cnt.length; i++)
- for (int j = 0; j < 2; j++)
- cnt[i][j] = 0;
SAMFileReader inputSam = samFileReaderHash.get(bamFile);
final CloseableIterator<SAMRecord> it =
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 1a116ea0043aa74b63750279f5ae9d8457c3c171..5f394637f873969dc8e786fd45ece5ebde04efc9 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -80,6 +80,7 @@ import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JFrame;
+import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
@@ -117,6 +118,7 @@ import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.SelectionChangeEvent;
import uk.ac.sanger.artemis.SelectionChangeListener;
import uk.ac.sanger.artemis.SimpleEntryGroup;
+import uk.ac.sanger.artemis.circular.TextFieldInt;
import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.EntryEdit;
@@ -2348,10 +2350,26 @@ public class BamView extends JPanel
if(feature_display == null)
return;
+ final Box yBox = Box.createVerticalBox();
+ final TextFieldInt threshold = new TextFieldInt();
+ final TextFieldInt minSize = new TextFieldInt();
+ threshold.setValue(6);
+ minSize.setValue(6);
+ yBox.add(new JLabel("Minimum number of reads:"));
+ yBox.add(threshold);
+ yBox.add(new JLabel("Minimum feature size:"));
+ yBox.add(minSize);
+
+ int status =
+ JOptionPane.showConfirmDialog(BamView.this, yBox,
+ "Options", JOptionPane.OK_CANCEL_OPTION);
+ if(status == JOptionPane.CANCEL_OPTION)
+ return;
+
new MappedReads(feature_display, (String)combo.getSelectedItem(),
samFileReaderHash, bamList, seqNames, offsetLengths,
concatSequences, seqLengths, samRecordFlagPredicate, samRecordMapQPredicate,
- true);
+ threshold.getValue(), minSize.getValue(), true);
}
});
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index 96e32b6bfc6b3856786e390f912af3e37eca427c..f065b85bbfa9369949e1fc0cd99fd1be44ebd164 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -208,6 +208,8 @@ public class MappedReads
final HashMap<String, Integer> seqLengths,
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordMapQPredicate samRecordMapQPredicate,
+ final int threshold,
+ final int minSize,
final boolean contained)
{
this.refName = refName;
@@ -226,16 +228,17 @@ public class MappedReads
progressBar.setStringPainted(true);
JPanel panel = new JPanel(new BorderLayout());
- progressTxt.setText("Search for new features");
+ progressTxt.setText("");
panel.add(progressTxt, BorderLayout.NORTH);
panel.add(progressBar, BorderLayout.CENTER);
panel.setOpaque(true);
+ dialog.setTitle("Search");
dialog.setContentPane(panel);
dialog.pack();
centerDialog();
- CalculateNewFeatures cmr = new CalculateNewFeatures(feature_display, refName);
+ CalculateNewFeatures cmr = new CalculateNewFeatures(feature_display, refName, threshold, minSize);
cmr.start();
dialog.setVisible(true);
}
@@ -422,34 +425,37 @@ public class MappedReads
}
}
+ /**
+ * Find new features from read count peaks.
+ */
class CalculateNewFeatures extends SwingWorker
{
private EntryGroup entryGroup;
private Bases bases;
private String refSeq;
+ private int threshold;
+ private int minSize;
- CalculateNewFeatures(final FeatureDisplay feature_display, final String refSeq)
+ CalculateNewFeatures(final FeatureDisplay feature_display,
+ final String refSeq, final int threshold,
+ final int minSize)
{
entryGroup = feature_display.getEntryGroup();
bases = feature_display.getBases();
this.refSeq = refSeq;
+ this.threshold = threshold;
+ this.minSize = minSize;
}
public Object construct()
{
int MAX_BASE_CHUNK = 2000 * 60;
-
- final int threshold = 4;
- final int minSize = 10;
-
Key excluseKeys[] = { new Key("rRNA"), new Key("tRNA") };
int seqlen = bases.getLength();
final int beg = 1;
final int end = seqlen;
-
- int offset = 0;
-
+
int fwdStart = -1;
int revStart = -1;
final List<MarkerRange> fwdMarkers = new Vector<MarkerRange>();
@@ -466,20 +472,24 @@ public class MappedReads
try
{
- int cnt[][] = null;
+ int cnt[][] = new int[stop-start+1][2];
+ for (int row = 0; row < cnt.length; row++)
+ for (int col = 0; col < 2; col++)
+ cnt[row][col] = 0;
+
if (concatSequences)
{
for (String name : seqNames)
{
int len = seqLengths.get(name);
- offset = offsetLengths.get(name);
+ int offset = offsetLengths.get(name);
if( (start >= offset && start <= offset+len) ||
(stop >= offset && start <= offset+len) )
{
cnt =
BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
- name, start-offset, stop-offset,
+ name, start-offset, stop-offset, cnt,
samRecordFlagPredicate, samRecordMapQPredicate);
}
}
@@ -488,7 +498,7 @@ public class MappedReads
{
cnt =
BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
- refSeq, start, stop,
+ refSeq, start, stop, cnt,
samRecordFlagPredicate, samRecordMapQPredicate);
}
@@ -496,11 +506,13 @@ public class MappedReads
{
final Range r = new Range(start+k, start+k+1);
- fwdStart = findFeatures(cnt[k][0], true, threshold, fwdStart, j+k,
- r, minSize, excluseKeys, fwdMarkers, entryGroup);
+ // find forward strand potential features
+ fwdStart = findFeatures(cnt[k][0], true, fwdStart, j+k,
+ r, excluseKeys, fwdMarkers, entryGroup);
- revStart = findFeatures(cnt[k][1], false, threshold, revStart, j+k,
- r, minSize, excluseKeys, revMarkers, entryGroup);
+ // find reverse strand potential features
+ revStart = findFeatures(cnt[k][1], false, revStart, j+k,
+ r, excluseKeys, revMarkers, entryGroup);
}
}
@@ -510,9 +522,8 @@ public class MappedReads
}
}
}
-
- System.out.println("No. of features="+fwdMarkers.size());
- final Entry newEntry = entryGroup.createEntry ("BAM_CDS");
+
+ final Entry newEntry = entryGroup.createEntry ("align_"+threshold+"_"+minSize);
createFeatures(fwdMarkers, true, newEntry);
createFeatures(revMarkers, false, newEntry);
return null;
@@ -521,6 +532,13 @@ public class MappedReads
private void createFeatures(final List<MarkerRange> markers, final boolean isFwd, final Entry newEntry)
{
+ final Key key = Key.CDS;
+/* if(entryGroup.getDefaultEntry() != null &&
+ entryGroup.getDefaultEntry().getEMBLEntry() instanceof GFFDocumentEntry)
+ key = new Key("region");
+ else
+ key = new Key("misc_feature");*/
+
// merge overlapping markers
List<MarkerRange> featureMarkers = new Vector<MarkerRange>();
List<Integer> ignoreMarkers = new Vector<Integer>();
@@ -547,7 +565,7 @@ public class MappedReads
{
try
{
- newEntry.createFeature(Key.CDS,
+ newEntry.createFeature(key,
( isFwd ? r.createLocation() : r.createLocation().getComplement()), null);
}
catch (ReadOnlyException e1)
@@ -569,11 +587,9 @@ public class MappedReads
* Search for new features based on read counts.
* @param cnt read count
* @param isFwd strand to find features on is the forward strand if true
- * @param threshold read count minimum threshold
* @param fStart start of a new feature or -1 if not identified yet
* @param pos current base position
* @param range current base range
- * @param minSize minimum feature size
* @param excluseKeys feature keys of regions to avoid looking in
* @param markers list of new features
* @param entryGroup entry group
@@ -581,11 +597,9 @@ public class MappedReads
*/
private int findFeatures(final int cnt,
final boolean isFwd,
- final int threshold,
int fStart,
final int pos,
final Range range,
- final int minSize,
final Key excluseKeys[],
final List<MarkerRange> markers,
final EntryGroup entryGroup)
@@ -617,7 +631,18 @@ public class MappedReads
{
try
{
- if((range.getStart()-fStart) >= minSize)
+ boolean exclude = false;
+ final FeatureVector features = entryGroup.getFeaturesInRange(range);
+ for(int k=0; k<features.size(); k++)
+ {
+ Feature f = features.elementAt(k);
+ for(int l=0; l<excluseKeys.length; l++)
+ if(f.getKey().equals(excluseKeys[l]))
+ exclude = true;
+ }
+
+ if(!exclude &&
+ (range.getStart()-fStart) >= minSize)
{
final MarkerRange marker = new MarkerRange(
bases.getForwardStrand(), fStart, range.getStart());
@@ -635,10 +660,16 @@ public class MappedReads
FeatureVector features = entryGroup.getFeaturesInRange(range);
for(int k=0; k<features.size(); k++)
{
+ boolean exclude = false;
Feature f = features.elementAt(k);
- if( f.isProteinFeature() && ! (isFwd ^ f.isForwardFeature()) ) // on same strand
+ for(int l=0; l<excluseKeys.length; l++)
+ if(f.getKey().equals(excluseKeys[l]))
+ exclude = true;
+
+ if( exclude ||
+ (f.isProteinFeature() && ! (isFwd ^ f.isForwardFeature())) ) // on same strand
{
- if((f.getFirstBase()-fStart) >= minSize)
+ if((f.getRawFirstBase()-fStart) >= minSize)
{
final MarkerRange marker = new MarkerRange(
bases.getForwardStrand(), fStart, f.getRawFirstBase() );