From 4b41478373a5c4b90a106af7351ace054f476c67 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 30 Jun 2017 08:44:08 +0100 Subject: [PATCH] JAL-2574 renamed findFeatures as findOverlappingFeatures to minimise confusion --- src/jalview/analysis/AlignmentSorter.java | 2 +- src/jalview/commands/EditCommand.java | 3 ++- src/jalview/controller/AlignViewController.java | 2 +- src/jalview/datamodel/Sequence.java | 2 +- src/jalview/datamodel/SequenceI.java | 2 +- src/jalview/gui/AlignmentPanel.java | 2 +- src/jalview/renderer/seqfeatures/FeatureRenderer.java | 2 +- .../viewmodel/seqfeatures/FeatureRendererModel.java | 2 +- test/jalview/datamodel/SequenceTest.java | 12 ++++++------ 9 files changed, 15 insertions(+), 14 deletions(-) diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 9943a22..edf2599 100755 --- 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 sfs = seqs[i].findFeatures(startCol + 1, + List 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 --- 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 sfs = seq.findFeatures(start, start); + List 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 --- 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 sfs = sq.findFeatures(startColumn, + List 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 --- 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 findFeatures(int fromColumn, int toColumn, + public List 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 --- 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 findFeatures(int fromCol, int toCol, String... types); + List 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 --- 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 features = seq.findFeatures(column, column); + List 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 --- 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 overlaps = seq.findFeatures(column, column, + List 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 --- 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 features = sequence.findFeatures(column, column, + List 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 --- 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 found = sq.findFeatures(1, 2); + List 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()); } -- 1.7.10.2