JAL-2574 renamed findFeatures as findOverlappingFeatures to minimise

confusion

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 9943a22..edf2599 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -757,7 +757,7 @@ public class AlignmentSorter
        */
       String[] types = featureTypes == null ? null : featureTypes
               .toArray(new String[featureTypes.size()]);
-      List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
+      List<SequenceFeature> sfs = seqs[i].findOverlappingFeatures(startCol + 1,
               endCol + 1, types);
 
       seqScores[i] = 0;

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 0d3b702..a4a3ac1 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1159,7 +1159,8 @@ public class EditCommand implements CommandI
        * shift right any features that start at the cut position,
        * unless they were truncated
        */
-      List<SequenceFeature> sfs = seq.findFeatures(start, start);
+      List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
+              start);
       for (SequenceFeature sf : sfs)
       {
         if (sf.getBegin() == start)

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 5c1f403..7555e3f 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -241,7 +241,7 @@ public class AlignViewController implements AlignViewControllerI
       if (sq != null)
       {
         // int ist = sq.findPosition(sqcol.getStartRes());
-        List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+        List<SequenceFeature> sfs = sq.findOverlappingFeatures(startColumn,
                 endColumn, featureType);
 
         if (!sfs.isEmpty())

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 15718f9..0aacc39 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1806,7 +1806,7 @@ public class Sequence extends ASequence implements SequenceI
    * {@inheritDoc}
    */
   @Override
-  public List<SequenceFeature> findFeatures(int fromColumn, int toColumn,
+  public List<SequenceFeature> findOverlappingFeatures(int fromColumn, int toColumn,
           String... types)
   {
     int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index d76c5a7..4f00760 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -510,7 +510,7 @@ public interface SequenceI extends ASequenceI
    *          optional feature types to restrict results to
    * @return
    */
-  List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+  List<SequenceFeature> findOverlappingFeatures(int fromCol, int toCol, String... types);
 
   /**
    * Method to call to indicate that the sequence (characters or alignment/gaps)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 3994c29..2732f8c 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1515,7 +1515,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
             }
             if (!Comparison.isGap(seq.getCharAt(column)))
             {
-              List<SequenceFeature> features = seq.findFeatures(column, column);
+              List<SequenceFeature> features = seq.findOverlappingFeatures(column, column);
               for (SequenceFeature sf : features)
               {
                 if (sf.isContactFeature())

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 541288e..cf4fe9b 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -421,7 +421,7 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      List<SequenceFeature> overlaps = seq.findFeatures(column, column,
+      List<SequenceFeature> overlaps = seq.findOverlappingFeatures(column, column,
               type);
       for (SequenceFeature sequenceFeature : overlaps)
       {

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index de1ee5e..f8b6d33 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -280,7 +280,7 @@ public abstract class FeatureRendererModel implements
             .getVisibleFeatures();
     String[] visibleTypes = visibleFeatures
             .toArray(new String[visibleFeatures.size()]);
-    List<SequenceFeature> features = sequence.findFeatures(column, column,
+    List<SequenceFeature> features = sequence.findOverlappingFeatures(column, column,
             visibleTypes);
 
     for (SequenceFeature sf : features)

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 3f9750c..c047ca5 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1412,7 +1412,7 @@ public class SequenceTest
     SequenceI sq = new Sequence("test/8-16", "-ABC--DEF--GHI--");
     sq.createDatasetSequence();
 
-    assertTrue(sq.findFeatures(1, 99).isEmpty());
+    assertTrue(sq.findOverlappingFeatures(1, 99).isEmpty());
 
     // add non-positional feature
     SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f,
@@ -1437,29 +1437,29 @@ public class SequenceTest
     sq.addSequenceFeature(sfContactFG);
 
     // no features in columns 1-2 (-A)
-    List<SequenceFeature> found = sq.findFeatures(1, 2);
+    List<SequenceFeature> found = sq.findOverlappingFeatures(1, 2);
     assertTrue(found.isEmpty());
 
     // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
-    found = sq.findFeatures(1, 6);
+    found = sq.findOverlappingFeatures(1, 6);
     assertEquals(2, found.size());
     assertTrue(found.contains(sfBCD));
     assertTrue(found.contains(sfContactBH));
 
     // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
-    found = sq.findFeatures(5, 6);
+    found = sq.findOverlappingFeatures(5, 6);
     assertEquals(1, found.size());
     assertTrue(found.contains(sfBCD));
 
     // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
-    found = sq.findFeatures(7, 10);
+    found = sq.findOverlappingFeatures(7, 10);
     assertEquals(3, found.size());
     assertTrue(found.contains(sfBCD));
     assertTrue(found.contains(sfDE));
     assertTrue(found.contains(sfContactFG));
 
     // columns 10-11 (--) should find nothing
-    found = sq.findFeatures(10, 11);
+    found = sq.findOverlappingFeatures(10, 11);
     assertEquals(0, found.size());
   }