diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index e610135d095c1a6f217884ff079058ddecc3565d..3ead683c1405093fa72b98e77e1f4772b395a765 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -35,6 +35,8 @@ import java.awt.FlowLayout;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
import java.awt.Insets;
import java.awt.Point;
import java.awt.Rectangle;
@@ -87,6 +89,7 @@ import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
+import javax.swing.JRadioButton;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
@@ -152,7 +155,7 @@ public class BamView extends JPanel
private HashMap<String, Integer> offsetLengths;
private Vector<String> seqNames = new Vector<String>();
protected List<String> bamList;
- private List<Integer> hideBamList = new Vector<Integer>();
+ protected List<Integer> hideBamList = new Vector<Integer>();
private SAMRecordPredicate samRecordFlagPredicate;
private SAMRecordMapQPredicate samRecordMapQPredicate;
@@ -2352,36 +2355,7 @@ 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();
- final TextFieldInt minBams = new TextFieldInt();
-
- threshold.setValue(6);
- minSize.setValue(6);
- minBams.setValue(bamList.size());
-
- yBox.add(new JLabel("Minimum number of reads:"));
- yBox.add(threshold);
- yBox.add(new JLabel("Minimum number of BAMs for reads to be present in:"));
- yBox.add(minBams);
- 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;
-
- if(minBams.getValue() > bamList.size())
- minBams.setValue(bamList.size());
-
- new MappedReads(feature_display, (String)combo.getSelectedItem(),
- samFileReaderHash, bamList, seqNames, offsetLengths,
- concatSequences, seqLengths, samRecordFlagPredicate, samRecordMapQPredicate,
- threshold.getValue(), minSize.getValue(), minBams.getValue(), true);
+ new CreateFeatures(groupsFrame);
}
});
@@ -3690,7 +3664,101 @@ public class BamView extends JPanel
{
SAMRecord sam1;
SAMRecord sam2;
- }
+ }
+
+ class CreateFeatures
+ {
+ CreateFeatures(final GroupBamFrame groupsFrame)
+ {
+ final TextFieldInt threshold = new TextFieldInt();
+ final TextFieldInt minSize = new TextFieldInt();
+ final TextFieldInt minBams = new TextFieldInt();
+
+ threshold.setValue(6);
+ minSize.setValue(6);
+ minBams.setValue( (groupsFrame.getNumberOfGroups() == 1 ?
+ bamList.size() : groupsFrame.getMaximumBamsInGroup()) );
+
+ final JPanel gridPanel = new JPanel(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.gridx = 0;
+ c.gridy = 0;
+
+ gridPanel.add(new JLabel("Minimum number of reads:"), c);
+ c.gridy++;
+ gridPanel.add(threshold, c);
+
+ c.gridy++;
+ gridPanel.add(new JSeparator(), c);
+ c.gridy++;
+ gridPanel.add(new JLabel("Minimum number of BAMs for reads to be present in:"), c);
+ c.gridy++;
+ gridPanel.add(minBams, c);
+
+ JRadioButton useAllBams = new JRadioButton("out of all BAMs", (groupsFrame.getNumberOfGroups() == 1));
+ JRadioButton useGroup = new JRadioButton("within a group", (groupsFrame.getNumberOfGroups() != 1));
+
+ if(groupsFrame.getNumberOfGroups() == 1)
+ useGroup.setEnabled(false);
+
+ ButtonGroup group = new ButtonGroup();
+ group.add(useAllBams);
+ group.add(useGroup);
+
+ Box xBox = Box.createHorizontalBox();
+ xBox.add(useAllBams);
+ xBox.add(useGroup);
+ xBox.add(Box.createHorizontalGlue());
+ c.gridy++;
+ gridPanel.add(xBox, c);
+
+ c.gridy++;
+ gridPanel.add(new JSeparator(), c);
+ c.gridy++;
+ gridPanel.add(new JLabel("Minimum feature size:"), c);
+ c.gridy++;
+ gridPanel.add(minSize, c);
+
+ int status =
+ JOptionPane.showConfirmDialog(feature_display, gridPanel,
+ "Options", JOptionPane.OK_CANCEL_OPTION);
+ if(status == JOptionPane.CANCEL_OPTION)
+ return;
+
+ if(!useGroup.isSelected() && minBams.getValue() > bamList.size())
+ {
+ status =
+ JOptionPane.showConfirmDialog(feature_display,
+ "The minimum number of BAMs setting can not be\n"+
+ "greater than the total number of BAM files.\n"+
+ "Set this to the number of BAMs (i.e. "+bamList.size()+").",
+ "Options", JOptionPane.OK_CANCEL_OPTION);
+ if(status == JOptionPane.CANCEL_OPTION)
+ return;
+ minBams.setValue(bamList.size());
+ }
+ else if(useGroup.isSelected() && minBams.getValue() > groupsFrame.getMaximumBamsInGroup())
+ {
+ status =
+ JOptionPane.showConfirmDialog(feature_display,
+ "Minimum number of BAMs setting can not be greater than\n"+
+ "the total number of BAM files found in any of the groups.\n"+
+ "Set this to the greatest number of BAM files in any\n"+
+ "group (i.e. "+groupsFrame.getMaximumBamsInGroup()+").",
+ "Options", JOptionPane.OK_CANCEL_OPTION);
+ if(status == JOptionPane.CANCEL_OPTION)
+ return;
+ minBams.setValue(groupsFrame.getMaximumBamsInGroup());
+ }
+
+ new MappedReads((String)combo.getSelectedItem(),BamView.this, samFileReaderHash,
+ seqNames, offsetLengths, concatSequences, seqLengths,
+ (useGroup.isSelected() ? groupsFrame : null),
+ threshold.getValue(), minSize.getValue(), minBams.getValue(), true);
+ }
+ }
public static void main(String[] args)
{
diff --git a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
index f953cf0e2ce56c880cc3c4a1269e9355b3d063fe..148a80d90a4ed68ec98c554fea6bd47aa9e29caa 100644
--- a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
+++ b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
@@ -191,18 +191,73 @@ class GroupBamFrame extends JFrame
bamPanel.add(new JLabel(bamView.getImageIcon(col)), c);
c.gridx = 2;
- JComboBox groupList = new JComboBox( groups );
- bamPanel.add(groupList, c);
+ JComboBox groupCombo = new JComboBox( groups );
+ bamPanel.add(groupCombo, c);
if(bamGroupMap.containsKey(cbBam))
- groupList.setSelectedItem(
+ groupCombo.setSelectedItem(
(String) bamGroupMap.get(cbBam).getSelectedItem());
- bamGroupMap.put(cbBam, groupList);
+ bamGroupMap.put(cbBam, groupCombo);
}
}
}
+ /**
+ * For a give BAM file return the group it belongs to.
+ * @param bamName
+ * @return
+ */
+ protected String getGroupName(final String bamName)
+ {
+ Iterator<JCheckBoxMenuItem> it = bamGroupMap.keySet().iterator();
+ while(it.hasNext())
+ {
+ JCheckBoxMenuItem cbs = it.next();
+ if(cbs.getText().equals(bamName))
+ return (String) bamGroupMap.get(cbs).getSelectedItem();
+ }
+ return null;
+ }
+
+ protected int getNumberOfGroups()
+ {
+ return groups.length;
+ }
+
+ /**
+ * Find the maximum number of BAM files found in the groups.
+ * @return
+ */
+ protected int getMaximumBamsInGroup()
+ {
+ int max = 1;
+ int grpMax[] = new int[getNumberOfGroups()];
+ for(int i=0; i<grpMax.length; i++)
+ grpMax[i] = 0;
+ Iterator<JCheckBoxMenuItem> it = bamGroupMap.keySet().iterator();
+ while(it.hasNext())
+ {
+ JCheckBoxMenuItem cbs = it.next();
+ String grp = (String) bamGroupMap.get(cbs).getSelectedItem();
+ for(int i=0; i<groups.length; i++)
+ {
+ if(grp.equals(groups[i]))
+ {
+ grpMax[i]++;
+ break;
+ }
+ }
+ }
+
+ for(int i=0; i<grpMax.length; i++)
+ {
+ if(grpMax[i] > max)
+ max = grpMax[i];
+ }
+ return max;
+ }
+
private void updateGroupPanel()
{
groupPanel.removeAll();
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index a6ca6f05e2356c85efc4e496de2d58f0842e37be..94fa5a864f6d8537de1725f731b7be5aee20330f 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -4,6 +4,7 @@ import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.Point;
import java.awt.Toolkit;
+import java.io.File;
import java.text.DecimalFormat;
import java.util.Arrays;
import java.util.HashMap;
@@ -45,6 +46,7 @@ public class MappedReads
private String refName;
private Hashtable<String, SAMFileReader> samFileReaderHash;
private List<String> bamList;
+ private List<Integer> hideBamList;
private Vector<String> seqNames;
private HashMap<String, Integer> offsetLengths;
private boolean concatSequences;
@@ -187,32 +189,29 @@ public class MappedReads
* and anti-sense regions of existing annotations. This should exclude rRNA and
* tRNA regions. If two or more BAM files are loaded it should create features
* based on the combined read peak span.
- * @param feature_display
* @param refName
+ * @param bamView
* @param samFileReaderHash
* @param bamList
* @param seqNames
* @param offsetLengths
* @param concatSequences
* @param seqLengths
- * @param samRecordFlagPredicate
- * @param samRecordMapQPredicate
+ * @param groupsFrame
* @param threshold
* @param minSize
* @param minBams
* @param contained
*/
- public MappedReads(
- final FeatureDisplay feature_display,
+ public MappedReads(
final String refName,
+ final BamView bamView,
final Hashtable<String, SAMFileReader> samFileReaderHash,
- final List<String> bamList,
final Vector<String> seqNames,
final HashMap<String, Integer> offsetLengths,
final boolean concatSequences,
final HashMap<String, Integer> seqLengths,
- final SAMRecordPredicate samRecordFlagPredicate,
- final SAMRecordMapQPredicate samRecordMapQPredicate,
+ final GroupBamFrame groupsFrame,
final int threshold,
final int minSize,
final int minBams,
@@ -220,15 +219,18 @@ public class MappedReads
{
this.refName = refName;
this.samFileReaderHash = samFileReaderHash;
- this.bamList = bamList;
+ this.bamList = bamView.bamList;
+ this.hideBamList = bamView.hideBamList;
this.seqNames = seqNames;
this.offsetLengths = offsetLengths;
this.concatSequences = concatSequences;
this.seqLengths = seqLengths;
- this.samRecordFlagPredicate = samRecordFlagPredicate;
- this.samRecordMapQPredicate = samRecordMapQPredicate;
+ this.samRecordFlagPredicate = bamView.getSamRecordFlagPredicate();
+ this.samRecordMapQPredicate = bamView.getSamRecordMapQPredicate();
+
this.contained = contained;
+ final FeatureDisplay feature_display = bamView.getFeatureDisplay();
progressBar = new JProgressBar(0, feature_display.getSequenceLength());
progressBar.setValue(0);
progressBar.setStringPainted(true);
@@ -245,7 +247,7 @@ public class MappedReads
centerDialog();
final CalculateNewFeatures cmr = new CalculateNewFeatures(
- feature_display, refName, threshold, minSize, minBams);
+ feature_display, refName, groupsFrame, threshold, minSize, minBams);
cmr.start();
dialog.setVisible(true);
}
@@ -443,15 +445,19 @@ public class MappedReads
private int threshold;
private int minSize;
private int minBams;
+ private GroupBamFrame groupsFrame;
- CalculateNewFeatures(final FeatureDisplay feature_display,
- final String refSeq, final int threshold,
+ CalculateNewFeatures(final FeatureDisplay feature_display,
+ final String refSeq,
+ final GroupBamFrame groupsFrame,
+ final int threshold,
final int minSize,
final int minBams)
{
entryGroup = feature_display.getEntryGroup();
bases = feature_display.getBases();
this.refSeq = refSeq;
+ this.groupsFrame = groupsFrame;
this.threshold = threshold;
this.minSize = minSize;
this.minBams = minBams;
@@ -470,12 +476,11 @@ public class MappedReads
public Object construct()
{
- int MAX_BASE_CHUNK = 2000 * 60;
+ final int MAX_BASE_CHUNK = 2000 * 60;
Key excluseKeys[] = { new Key("rRNA"), new Key("tRNA") };
- int seqlen = bases.getLength();
final int beg = 1;
- final int end = seqlen;
+ final int end = bases.getLength();
int fwdStart = -1;
int revStart = -1;
@@ -483,6 +488,9 @@ public class MappedReads
final List<MarkerObj> revMarkers = new Vector<MarkerObj>();
for (int i = 0; i < bamList.size(); i++)
{
+ if(hideBamList.contains(i))
+ continue;
+
for(int j=beg; j<end; j+=MAX_BASE_CHUNK)
{
progressBar.setValue((j + (i*end)) / bamList.size());
@@ -594,6 +602,31 @@ public class MappedReads
if(bamIdxList.size() >= minBams)
{
+ if(groupsFrame != null && minBams > 1)
+ {
+ boolean foundMinBams = false;
+ Hashtable<String, Integer> groupCluster = new Hashtable<String, Integer>();
+ for(int j=0; j<bamIdxList.size(); j++)
+ {
+ File f = new File(bamList.get(j));
+ String grp = groupsFrame.getGroupName( f.getName() );
+ if(groupCluster.containsKey(grp))
+ {
+ int val = groupCluster.get(grp)+1;
+ if(val >= minBams)
+ {
+ foundMinBams = true;
+ break;
+ }
+ groupCluster.put(grp, val);
+ }
+ else
+ groupCluster.put(grp, 1);
+ }
+ if(!foundMinBams)
+ continue;
+ }
+
// create a new feature
try
{
@@ -638,7 +671,7 @@ public class MappedReads
final EntryGroup entryGroup,
final int bamIdx)
{
- if(cnt > threshold && fStart == -1) // START FEATURE
+ if(cnt >= threshold && fStart == -1) // START FEATURE
{
boolean exclude = false;
try