From e6d8d32e97089253c2fa9aee1fd73d10b296ff0f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 13 Mar 2008 15:20:32 +0000
Subject: [PATCH] fixes for creating intergenic region
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@7229 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/AddMenu.java | 134 ++++++++++++++-----
1 file changed, 101 insertions(+), 33 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/AddMenu.java b/uk/ac/sanger/artemis/components/AddMenu.java
index 5c70b1188..32c019647 100644
--- a/uk/ac/sanger/artemis/components/AddMenu.java
+++ b/uk/ac/sanger/artemis/components/AddMenu.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/AddMenu.java,v 1.37 2008-03-13 09:51:17 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AddMenu.java,v 1.38 2008-03-13 15:20:32 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -55,6 +55,7 @@ import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.util.Comparator;
import java.util.Vector;
import java.util.Enumeration;
@@ -73,7 +74,7 @@ import javax.swing.KeyStroke;
* should have been called CreateMenu.
*
* @author Kim Rutherford
- * @version $Id: AddMenu.java,v 1.37 2008-03-13 09:51:17 tjc Exp $
+ * @version $Id: AddMenu.java,v 1.38 2008-03-13 15:20:32 tjc Exp $
**/
public class AddMenu extends SelectionMenu
{
@@ -855,17 +856,28 @@ public class AddMenu extends SelectionMenu
static void createIntergenicFeatures (final JFrame frame,
final EntryGroup entry_group)
{
- try {
+ try
+ {
entry_group.getActionController ().startAction ();
- final FeatureKeyPredicate predicate;
+ final FeaturePredicate predicate;
if(GeneUtils.isDatabaseEntry(entry_group))
predicate = new FeatureKeyPredicate(new Key("gene"));
else
- predicate = new FeatureKeyPredicate(Key.CDS);
- final FeatureVector cdsFeatures = new FeatureVector ();
-
+ {
+ final FeaturePredicateVector temp_predicates =
+ new FeaturePredicateVector();
+
+ temp_predicates.add(new FeatureKeyPredicate(Key.CDS));
+ temp_predicates.add(new FeatureKeyPredicate(new Key("tRNA")));
+
+ predicate =
+ new FeaturePredicateConjunction(temp_predicates,
+ FeaturePredicateConjunction.OR);
+ }
+
+ FeatureVector cdsFeatures = new FeatureVector ();
final FeatureEnumeration feature_enum = entry_group.features ();
while (feature_enum.hasMoreFeatures ())
{
@@ -874,39 +886,33 @@ public class AddMenu extends SelectionMenu
cdsFeatures.add (current_feature);
}
- RangeVector cdsRanges = new RangeVector();
- for (int i = 0; i < cdsFeatures.size (); ++i)
- {
- final Feature selection_feature = cdsFeatures.elementAt(i);
- final Location cds_location = selection_feature.getLocation();
- final Range cds_range = cds_location.getTotalRange();
-
- cdsRanges.add(cds_range);
-
- //if (cds_location.isComplement ()) {
- // cds_ranges.reverse ();
- //}
- }
+ cdsFeatures = cdsFeatures.sort(feature_comparator);
- int prevEnd = 1;
+ int prevEnd = 0;
Entry newEntry = null;
+ boolean prevForward = true;
- for(int i=0; i < cdsRanges.size(); i++)
+ for(int i=0; i < cdsFeatures.size (); i++)
{
- Range r = (Range)cdsRanges.get(i);
+ final Feature this_feature = cdsFeatures.elementAt(i);
+ final Location cds_location = this_feature.getLocation();
+ final Range r = cds_location.getTotalRange();
+
int currentStart = r.getStart();
if(i==0 && r.getStart()==1)
{
prevEnd = r.getEnd();
-
+ prevForward = this_feature.isForwardFeature();
// check for overlapping CDS
- if(i<cdsRanges.size()-1)
+ if(i<cdsFeatures.size()-1)
{
int next = i+1;
- while(((Range)cdsRanges.get(next)).getStart() <= prevEnd)
+ while(getTotalRange((Feature)cdsFeatures.elementAt(next)).getStart() <= prevEnd+1)
{
- prevEnd = ((Range)cdsRanges.get(next)).getEnd();
+ Feature f = (Feature)cdsFeatures.elementAt(next);
+ prevEnd = getTotalRange(f).getEnd();
+ prevForward = f.isForwardFeature();
i = next;
next++;
}
@@ -925,34 +931,62 @@ public class AddMenu extends SelectionMenu
key = new Key ("region");
else
key = new Key ("misc_feature");
+
+
+ // intergenic regions (IGR) - flanking CDS 4 possible:
+ // IGR-F (forward): cds> IGR cds>
+ // IGR-R (reverse): <cds IGR <cds
+ // IGR-B (both): <cds IGR cds>
+ // IGR-X: cds> IGR <cds
+ String note;
+
+ if(this_feature.isForwardFeature())
+ {
+ if(prevForward)
+ note = "IGR-F";
+ else
+ note = "IGR-B";
+ }
+ else
+ {
+ if(prevForward)
+ note = "IGR-X";
+ else
+ note = "IGR-R";
+ }
final QualifierVector qualifiers = new QualifierVector ();
+ final Qualifier qualifier = new Qualifier("note", note);
+ qualifiers.add(qualifier);
if(newEntry == null)
newEntry = entry_group.createEntry("intergenic");
newEntry.createFeature(key, location, qualifiers);
prevEnd = r.getEnd();
+ prevForward = this_feature.isForwardFeature();
// check for overlapping CDS
- if(i<cdsRanges.size()-1)
+ if(i<cdsFeatures.size()-1)
{
int next = i+1;
- while( next < cdsRanges.size() &&
- ((Range)cdsRanges.get(next)).getStart() <= prevEnd)
+ while( next < cdsFeatures.size() &&
+ getTotalRange((Feature)cdsFeatures.elementAt(next)).getStart() <= prevEnd+1)
{
- prevEnd = ((Range)cdsRanges.get(next)).getEnd();
+ Feature f = (Feature)cdsFeatures.elementAt(next);
+ prevEnd = getTotalRange(f).getEnd();
+ prevForward = f.isForwardFeature();
i = next;
next++;
}
}
- else if(i==cdsRanges.size()-1)
+ else if(i==cdsFeatures.size()-1)
{
if(entry_group.getSequenceLength() > r.getEnd())
{
new_range = new Range(prevEnd + 1,
entry_group.getSequenceLength());
location = new Location(new_range);
- entry_group.getDefaultEntry().createFeature(key,
+ newEntry.createFeature(key,
location, qualifiers);
}
}
@@ -969,6 +1003,40 @@ public class AddMenu extends SelectionMenu
}
}
+ private static Range getTotalRange(Feature f)
+ {
+ return ((Range) f.getLocation().getTotalRange() );
+ }
+
+ /**
+ * This is used by getSortedFeaturesInRange().
+ **/
+ final private static Comparator feature_comparator = new Comparator()
+ {
+ /**
+ * Compare two Objects with respect to ordering.
+ * @return a negative number if feature1_object is less than
+ * feature2_object ; a positive number if feature1_object is greater
+ * than feature2_object; else 0
+ **/
+ public int compare(final Object feature1_object,
+ final Object feature2_object)
+ {
+ final Feature feature1 =(Feature) feature1_object;
+ final Feature feature2 =(Feature) feature2_object;
+
+ final int feature1_start = feature1.getLocation().getTotalRange().getStart();
+ final int feature2_start = feature2.getLocation().getTotalRange().getStart();
+
+ if(feature1_start < feature2_start)
+ return -1;
+ else if(feature1_start > feature2_start)
+ return 1;
+
+ return 1;
+ }
+ };
+
/**
* Create a new exon for each FeatureSegment in the selected CDS features.
--
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