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Commit e6d8d32e authored by tjc's avatar tjc
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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
parent 3e59baab
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uk/ac/sanger/artemis/components/AddMenu.java
+ 101
− 33
View file @ e6d8d32e
......@@ -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);
cdsFeatures = cdsFeatures.sort(feature_comparator);
//if (cds_location.isComplement ()) {
// cds_ranges.reverse ();
//}
}
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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