X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;fp=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=7052f348d08539ae03b8a075934fdb9219aed0dd;hb=4f77328104498504339216829abf5ea87e2791ec;hp=6f514203088bf246329d5d629b62cd0bbfeaa165;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 6f51420..7052f34 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -35,8 +35,6 @@ import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; -import intervalstore.api.IntervalI; - /** * A class that models a single contiguous feature on a sequence. If flag * 'contactFeature' is true, the start and end positions are interpreted instead @@ -219,20 +217,10 @@ public class SequenceFeature implements FeatureLocationI @Override public boolean equals(Object o) { - return (o != null && (o instanceof SequenceFeature) - && equalsInterval((SequenceFeature) o)); + return equals(o, false); } /** - * Having determined that this is in fact a SequenceFeature, now check it for - * equivalence. Overridden in CrossRef; used by IntervalStore (possibly). - */ - @Override - public boolean equalsInterval(IntervalI sf) - { - return equals((SequenceFeature) sf, false); - } - /** * Overloaded method allows the equality test to optionally ignore the * 'Parent' attribute of a feature. This supports avoiding adding many * superficially duplicate 'exon' or CDS features to genomic or protein @@ -242,8 +230,14 @@ public class SequenceFeature implements FeatureLocationI * @param ignoreParent * @return */ - public boolean equals(SequenceFeature sf, boolean ignoreParent) + public boolean equals(Object o, boolean ignoreParent) { + if (o == null || !(o instanceof SequenceFeature)) + { + return false; + } + + SequenceFeature sf = (SequenceFeature) o; boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score) : score == sf.score; if (begin != sf.begin || end != sf.end || !sameScore) @@ -742,8 +736,6 @@ public class SequenceFeature implements FeatureLocationI { source = theSource; } - - } class SFSortByEnd implements Comparator