From e930678ad2370a510a7fe5177aa826473cf3291f Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 31 Jan 2014 13:58:32 +0000
Subject: [PATCH] add the ability to find features contained by ranges defined
by selected features as well as selected base ranges
---
.../sanger/artemis/components/SelectMenu.java | 68 +++++++++++++------
1 file changed, 48 insertions(+), 20 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/SelectMenu.java b/uk/ac/sanger/artemis/components/SelectMenu.java
index 4d801fa1f..c2ac0e93e 100644
--- a/uk/ac/sanger/artemis/components/SelectMenu.java
+++ b/uk/ac/sanger/artemis/components/SelectMenu.java
@@ -1000,37 +1000,65 @@ public class SelectMenu extends SelectionMenu
}
}
}
-
/**
- * If there are some selected bases select the features that are
+ * If there are some selected bases or features select the features that are
* fully contained within that selection.
**/
private void selectContainedFeatures () {
final MarkerRange selected_marker_range =
getSelection ().getMarkerRange ();
- if (selected_marker_range == null) {
- new MessageDialog (getParentFrame (), "sequence range is not selected");
- return;
- } else {
- try {
- final FeatureVector featuresInRange =
- getEntryGroup ().getFeaturesInRange (selected_marker_range.getRawRange ());
- final FeatureVector featuresContainedByRange = new FeatureVector();
- for(int i=0; i<featuresInRange.size(); i++)
- {
- Feature f = featuresInRange.elementAt(i);
- Range maxR = f.getMaxRawRange();
- if(selected_marker_range.getRawStart().getRawPosition() <= maxR.getStart() &&
- selected_marker_range.getRawEnd().getRawPosition() >= maxR.getEnd())
- featuresContainedByRange.add(f);
+ final FeatureVector featuresContainedByRange;
+ try
+ {
+ if (selected_marker_range == null) {
+ final FeatureVector selected_features = getSelection ().getAllFeatures ();
+ if (selected_features.size () == 0) {
+ new MessageDialog (getParentFrame (), "nothing selected");
+ return;
}
- getSelection ().set (featuresContainedByRange);
- } catch (OutOfRangeException e) {
- throw new Error ("internal error - unexpected exception: " + e);
+
+ featuresContainedByRange = new FeatureVector();
+ for(int i=0; i<selected_features.size(); i++) {
+ Range r = selected_features.elementAt(i).getMaxRawRange();
+ final FeatureVector featuresContained = getFeaturesContainedByRange(r);
+ for(int j=0; j<featuresContained.size(); j++) {
+ final Feature f = featuresContained.elementAt(j);
+ if(!featuresContainedByRange.contains(f) && !selected_features.contains(f))
+ featuresContainedByRange.add(f);
+ }
+ }
+ } else {
+ featuresContainedByRange = getFeaturesContainedByRange(
+ selected_marker_range.getRawRange());
}
+ } catch (OutOfRangeException e) {
+ throw new Error ("internal error - unexpected exception: " + e);
+ }
+ getSelection ().set (featuresContainedByRange);
+ }
+
+ /**
+ * Return the features that are contained by a given range
+ * @param r
+ * @return
+ * @throws OutOfRangeException
+ */
+ private FeatureVector getFeaturesContainedByRange(Range r) throws OutOfRangeException
+ {
+ final FeatureVector featuresInRange =
+ getEntryGroup ().getFeaturesInRange (r);
+ final FeatureVector featuresContainedByRange = new FeatureVector();
+ for(int i=0; i<featuresInRange.size(); i++)
+ {
+ Feature f = featuresInRange.elementAt(i);
+ Range maxR = f.getMaxRawRange();
+ if(r.getStart() <= maxR.getStart() &&
+ r.getEnd() >= maxR.getEnd())
+ featuresContainedByRange.add(f);
}
+ return featuresContainedByRange;
}
/**
--
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