From 32084443f59b052b28cb372d3ae0840abf48dc9d Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 17 Nov 2005 16:50:50 +0000
Subject: [PATCH] implement match flipping on contig reverse complement
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3826 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/AlignMatch.java | 37 ++++++-
.../sanger/artemis/SimpleComparisonData.java | 5 +-
.../artemis/components/AlignmentViewer.java | 100 +++++++++++++++++-
.../artemis/components/ComparatorGlue.java | 50 ++++++---
.../components/DisplayAdjustmentEvent.java | 12 ++-
.../artemis/components/FeatureDisplay.java | 17 ++-
uk/ac/sanger/artemis/sequence/Bases.java | 7 +-
7 files changed, 201 insertions(+), 27 deletions(-)
diff --git a/uk/ac/sanger/artemis/AlignMatch.java b/uk/ac/sanger/artemis/AlignMatch.java
index b09a9cbca..a3c1d484a 100644
--- a/uk/ac/sanger/artemis/AlignMatch.java
+++ b/uk/ac/sanger/artemis/AlignMatch.java
@@ -20,18 +20,19 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/AlignMatch.java,v 1.5 2005-07-12 10:39:45 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/AlignMatch.java,v 1.6 2005-11-17 16:50:50 tjc Exp $
*/
package uk.ac.sanger.artemis;
import uk.ac.sanger.artemis.io.Range;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
/**
* Each object of this class represents a single match from an alignment.
*
* @author Kim Rutherford
- * @version $Id: AlignMatch.java,v 1.5 2005-07-12 10:39:45 tjc Exp $
+ * @version $Id: AlignMatch.java,v 1.6 2005-11-17 16:50:50 tjc Exp $
**/
public class AlignMatch
@@ -148,6 +149,38 @@ public class AlignMatch
return query_sequence_range;
}
+ /**
+ * Set the range for either the query or the subject match. This
+ * is used when flipping contigs round.
+ * @param start
+ * @param end
+ * @param subject
+ */
+ public void setRange(final int start, final int end, boolean subject)
+ {
+ try
+ {
+ if(subject)
+ {
+ if(start < end)
+ this.subject_sequence_range = new Range(start, end);
+ else
+ this.subject_sequence_range = new Range(end, start);
+ }
+ else
+ {
+ if(start < end)
+ this.query_sequence_range = new Range(start, end);
+ else
+ this.query_sequence_range = new Range(end, start);
+ }
+ }
+ catch(OutOfRangeException ex)
+ {
+ ex.printStackTrace();
+ }
+ this.rev_match = !this.rev_match;
+ }
/**
* Returns true if and only if the query hits the reverse complement of the
* subject.
diff --git a/uk/ac/sanger/artemis/SimpleComparisonData.java b/uk/ac/sanger/artemis/SimpleComparisonData.java
index 194d7429f..48d617b5f 100644
--- a/uk/ac/sanger/artemis/SimpleComparisonData.java
+++ b/uk/ac/sanger/artemis/SimpleComparisonData.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/SimpleComparisonData.java,v 1.2 2004-12-14 10:41:42 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/SimpleComparisonData.java,v 1.3 2005-11-17 16:50:50 tjc Exp $
*/
package uk.ac.sanger.artemis;
@@ -41,7 +41,7 @@ import java.util.Hashtable;
* objects. In particular it has methods for managing AlignMatch objects.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: SimpleComparisonData.java,v 1.2 2004-12-14 10:41:42 tjc Exp $
+ * @version $Id: SimpleComparisonData.java,v 1.3 2005-11-17 16:50:50 tjc Exp $
**/
abstract class SimpleComparisonData implements ComparisonData
@@ -111,6 +111,7 @@ abstract class SimpleComparisonData implements ComparisonData
return matches;
}
+
/**
* If this object contains only valid matches for a comparison between
* subject_sequence and query_sequence return null (subject_sequence is the
diff --git a/uk/ac/sanger/artemis/components/AlignmentViewer.java b/uk/ac/sanger/artemis/components/AlignmentViewer.java
index 021f87447..1d62e5539 100644
--- a/uk/ac/sanger/artemis/components/AlignmentViewer.java
+++ b/uk/ac/sanger/artemis/components/AlignmentViewer.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AlignmentViewer.java,v 1.30 2005-11-01 12:01:04 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AlignmentViewer.java,v 1.31 2005-11-17 16:50:50 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -47,7 +47,7 @@ import javax.swing.*;
* ComparisonData object.
*
* @author Kim Rutherford
- * @version $Id: AlignmentViewer.java,v 1.30 2005-11-01 12:01:04 tjc Exp $
+ * @version $Id: AlignmentViewer.java,v 1.31 2005-11-17 16:50:50 tjc Exp $
**/
public class AlignmentViewer extends CanvasPanel
@@ -1524,6 +1524,102 @@ public class AlignmentViewer extends CanvasPanel
return match.getQuerySequenceEnd();
}
+ /**
+ * Remove an AlignMatch from the all_matches array
+ * @param index for the array
+ */
+ public void removeMatch(final int index)
+ {
+ AlignMatch tmp_matches[] = new AlignMatch[all_matches.length - 1];
+ System.arraycopy(all_matches,0,tmp_matches,0,index);
+
+ if(index < tmp_matches.length -1)
+ {
+ System.out.println("removeMatch() ");
+
+ System.arraycopy(all_matches,index+1,tmp_matches,
+ index,all_matches.length-index);
+ }
+ this.all_matches = new AlignMatch[tmp_matches.length];
+ this.all_matches = tmp_matches;
+ }
+
+ /**
+ * Flip the matches within a contig and deleted those that overlap
+ * with other contigs
+ * @param subject true if flipping the subject
+ * @param start of the contig
+ * @param end of the contig
+ */
+ protected void flippingContig(boolean subject, int start, int end)
+ {
+ int match_start;
+ int match_end;
+ int delete_overlaps = -1;
+
+ for(int i = 0; i < all_matches.length; ++i)
+ {
+ if(subject)
+ {
+ match_start = all_matches[i].getSubjectSequenceStart();
+ match_end = all_matches[i].getSubjectSequenceEnd();
+
+ if(match_start >= start &&
+ match_end <= end)
+ {
+ match_start = end - (match_start - start);
+ match_end = end - (match_end -start);
+ all_matches[i].setRange(match_start, match_end, subject);
+ }
+ else if( (match_start >= start && match_start <= end) ||
+ (match_end <= end && match_end >= start) )
+ {
+ // this match extends past end of contig
+ if(delete_overlaps == -1)
+ delete_overlaps = JOptionPane.showConfirmDialog(null,
+ "Found a match extending past the boundary of the contig:\n"+
+ match_start+".."+match_end+
+ "\nDelete all such matches?",
+ "Delete Overlapping Matches",
+ JOptionPane.YES_NO_OPTION);
+
+
+ if(delete_overlaps == JOptionPane.YES_OPTION)
+ removeMatch(i);
+ }
+ }
+ else
+ {
+ match_start = all_matches[i].getQuerySequenceStart();
+ match_end = all_matches[i].getQuerySequenceEnd();
+
+ if(match_start >= start &&
+ match_end <= end)
+ {
+ match_start = end - (match_start - start);
+ match_end = end - (match_end -start);
+ all_matches[i].setRange(match_start, match_end, subject);
+ }
+ else if( (match_start >= start && match_start <= end) ||
+ (match_end <= end && match_end >= start) )
+ {
+ // this match extends past end of contig
+ if(delete_overlaps == -1)
+ delete_overlaps = JOptionPane.showConfirmDialog(null,
+ "Found a match extending past the boundary of the contig:\n"+
+ match_start+".."+match_end+
+ "\nDelete all such matches?",
+ "Delete Overlapping Matches",
+ JOptionPane.YES_NO_OPTION);
+
+
+ if(delete_overlaps == JOptionPane.YES_OPTION)
+ removeMatch(i);
+ }
+ }
+ }
+ }
+
/**
*
* Find regions where there are no matches.
diff --git a/uk/ac/sanger/artemis/components/ComparatorGlue.java b/uk/ac/sanger/artemis/components/ComparatorGlue.java
index 8da6a0ab9..556999ba4 100644
--- a/uk/ac/sanger/artemis/components/ComparatorGlue.java
+++ b/uk/ac/sanger/artemis/components/ComparatorGlue.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ComparatorGlue.java,v 1.1 2004-06-09 09:46:10 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ComparatorGlue.java,v 1.2 2005-11-17 16:50:50 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -41,7 +41,7 @@ import javax.swing.*;
* and an AlignmentViewer.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ComparatorGlue.java,v 1.1 2004-06-09 09:46:10 tjc Exp $
+ * @version $Id: ComparatorGlue.java,v 1.2 2005-11-17 16:50:50 tjc Exp $
**/
public class ComparatorGlue {
@@ -75,11 +75,21 @@ public class ComparatorGlue {
* Wire-up the two FeatureDisplay objects with DisplayAdjustmentListeners.
**/
private void addDisplayListeners (final FeatureDisplay subject_display,
- final FeatureDisplay query_display) {
-
- subject_listener = new DisplayAdjustmentListener () {
- public void displayAdjustmentValueChanged (DisplayAdjustmentEvent e) {
- if (e.getType () == DisplayAdjustmentEvent.REV_COMP_EVENT) {
+ final FeatureDisplay query_display)
+ {
+
+ subject_listener = new DisplayAdjustmentListener ()
+ {
+ public void displayAdjustmentValueChanged (DisplayAdjustmentEvent e)
+ {
+ if (e.getType () == DisplayAdjustmentEvent.REV_COMP_EVENT)
+ {
+ getAlignmentViewer ().unlockDisplays ();
+ return;
+ }
+ else if (e.getType () == DisplayAdjustmentEvent.CONTIG_REV_COMP_EVENT)
+ {
+ getAlignmentViewer().flippingContig(true, e.getStart(), e.getEnd());
getAlignmentViewer ().unlockDisplays ();
return;
}
@@ -107,10 +117,19 @@ public class ComparatorGlue {
}
};
- query_listener = new DisplayAdjustmentListener () {
- public void displayAdjustmentValueChanged (DisplayAdjustmentEvent e) {
- if (e.getType () == DisplayAdjustmentEvent.REV_COMP_EVENT) {
- getAlignmentViewer ().unlockDisplays ();
+ query_listener = new DisplayAdjustmentListener ()
+ {
+ public void displayAdjustmentValueChanged (DisplayAdjustmentEvent e)
+ {
+ if (e.getType () == DisplayAdjustmentEvent.REV_COMP_EVENT)
+ {
+ getAlignmentViewer().unlockDisplays();
+ return;
+ }
+ else if (e.getType () == DisplayAdjustmentEvent.CONTIG_REV_COMP_EVENT)
+ {
+ getAlignmentViewer().flippingContig(false, e.getStart(), e.getEnd());
+ getAlignmentViewer().unlockDisplays();
return;
}
@@ -121,7 +140,8 @@ public class ComparatorGlue {
if (getAlignmentViewer ().displaysAreLocked () &&
(e.getType () == DisplayAdjustmentEvent.SCROLL_ADJUST_EVENT ||
- e.getType () == DisplayAdjustmentEvent.ALL_CHANGE_ADJUST_EVENT)) {
+ e.getType () == DisplayAdjustmentEvent.ALL_CHANGE_ADJUST_EVENT))
+ {
final int difference = e.getStart () - query_first_base_position;
subject_first_base_position =
@@ -141,8 +161,10 @@ public class ComparatorGlue {
query_display.addDisplayAdjustmentListener (query_listener);
final DisplayAdjustmentListener subject_align_listener =
- new DisplayAdjustmentListener () {
- public void displayAdjustmentValueChanged (DisplayAdjustmentEvent e) {
+ new DisplayAdjustmentListener ()
+ {
+ public void displayAdjustmentValueChanged (DisplayAdjustmentEvent e)
+ {
getAlignmentViewer ().setSubjectSequencePosition (e);
}
};
diff --git a/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java b/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java
index fa70a88ba..4be835f85 100644
--- a/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java
+++ b/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java,v 1.1 2004-06-09 09:46:13 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java,v 1.2 2005-11-17 16:50:50 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
@@ -31,7 +31,7 @@ import uk.ac.sanger.artemis.ChangeEvent;
* This event is sent when a FeatureDisplay is scrolled.
*
* @author Kim Rutherford
- * @version $Id: DisplayAdjustmentEvent.java,v 1.1 2004-06-09 09:46:13 tjc Exp $
+ * @version $Id: DisplayAdjustmentEvent.java,v 1.2 2005-11-17 16:50:50 tjc Exp $
**/
public class DisplayAdjustmentEvent extends ChangeEvent
@@ -90,6 +90,14 @@ public class DisplayAdjustmentEvent extends ChangeEvent
* the the scale has changed.
**/
final static public int ALL_CHANGE_ADJUST_EVENT = 3;
+
+ /**
+ * The type of DisplayAdjustmentEvent where the display has been reverse
+ * complemented.
+ **/
+ final static public int CONTIG_REV_COMP_EVENT = 4;
+
+
/**
* Create a new DisplayAdjustmentEvent.
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 6de6173da..051a45f57 100644
--- a/uk/ac/sanger/artemis/components/FeatureDisplay.java
+++ b/uk/ac/sanger/artemis/components/FeatureDisplay.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.31 2005-11-15 12:21:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.32 2005-11-17 16:50:50 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -47,7 +47,7 @@ import javax.swing.UIManager;
* This component is used for displaying an Entry.
*
* @author Kim Rutherford
- * @version $Id: FeatureDisplay.java,v 1.31 2005-11-15 12:21:18 tjc Exp $
+ * @version $Id: FeatureDisplay.java,v 1.32 2005-11-17 16:50:50 tjc Exp $
**/
public class FeatureDisplay extends EntryGroupPanel
@@ -967,6 +967,19 @@ public class FeatureDisplay extends EntryGroupPanel
if(event.getType() == SequenceChangeEvent.REVERSE_COMPLEMENT )
fireAdjustmentEvent(DisplayAdjustmentEvent.REV_COMP_EVENT);
+ else if(event.getType() == SequenceChangeEvent.CONTIG_REVERSE_COMPLEMENT )
+ {
+ final Range range = event.getRange();
+
+ fireAction(adjustment_listener_list,
+ new DisplayAdjustmentEvent(FeatureDisplay.this,
+ range.getStart(),
+ range.getEnd(),
+ getMaxVisibleBases(),
+ getScaleValue(), getScaleFactor(),
+ isRevCompDisplay(),
+ DisplayAdjustmentEvent.CONTIG_REV_COMP_EVENT));
+ }
else
fireAdjustmentEvent(DisplayAdjustmentEvent.SCROLL_ADJUST_EVENT);
}
diff --git a/uk/ac/sanger/artemis/sequence/Bases.java b/uk/ac/sanger/artemis/sequence/Bases.java
index 57c2b6c1a..6c7fff720 100644
--- a/uk/ac/sanger/artemis/sequence/Bases.java
+++ b/uk/ac/sanger/artemis/sequence/Bases.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.17 2005-11-15 12:21:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.18 2005-11-17 16:50:50 tjc Exp $
*/
package uk.ac.sanger.artemis.sequence;
@@ -47,7 +47,7 @@ import java.util.Iterator;
* non-base letter returns '@'.
*
* @author Kim Rutherford
- * @version $Id: Bases.java,v 1.17 2005-11-15 12:21:18 tjc Exp $ */
+ * @version $Id: Bases.java,v 1.18 2005-11-17 16:50:50 tjc Exp $ */
public class Bases
{
@@ -1224,7 +1224,8 @@ public class Bases
if (this_hash_map != null) {
final Iterator iter = this_hash_map.keySet ().iterator ();
- while (iter.hasNext()) {
+ while (iter.hasNext())
+ {
final SequenceChangeListener this_listener =
(SequenceChangeListener) iter.next();
this_listener.sequenceChanged (event);
--
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