Added IntervalFileFeature interface for common interface for bed and …

…interval_list

src/main/java/htsjdk/samtools/util/Interval.java

@@ -24,7 +24,7 @@
 package htsjdk.samtools.util;
 
 import htsjdk.samtools.SAMException;
-import htsjdk.tribble.Feature;
+import htsjdk.tribble.IntervalFileFeature;
 import htsjdk.tribble.annotation.Strand;
 
 import java.util.Collection;
@@ -34,7 +34,7 @@
  *
  * @author Tim Fennell
  */
-public class Interval implements Comparable<Interval>, Cloneable, Feature {
+public class Interval implements Comparable<Interval>, Cloneable, IntervalFileFeature {
     private final boolean negativeStrand;
     private final String name;
     private final String contig;

src/main/java/htsjdk/tribble/IntervalFileFeature.java

@@ -0,0 +1,34 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2023 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package htsjdk.tribble;
+
+
+/**
+ * An interface for features provided via an interval file, e.g. bed or interval_list.
+ * Provides a common interface for accessing the name column for both of these file types.
+ */
+public interface IntervalFileFeature extends Feature {
+    String getName();
+
+}

src/main/java/htsjdk/tribble/bed/BEDFeature.java

@@ -23,7 +23,7 @@
  */
 package htsjdk.tribble.bed;
 
-import htsjdk.tribble.Feature;
+import htsjdk.tribble.IntervalFileFeature;
 import htsjdk.tribble.annotation.Strand;
 
 import java.awt.*;
@@ -36,7 +36,7 @@
  * This is different than the 0-based representation in a BED file.  This conversion is handled by {@link BEDCodec}.
  * Anyone writing a bed file should be aware of this difference.
  */
-public interface BEDFeature extends Feature {
+public interface BEDFeature extends IntervalFileFeature {
     Strand getStrand();
 
     String getType();
@@ -47,8 +47,6 @@ public interface BEDFeature extends Feature {
 
     java.util.List<FullBEDFeature.Exon> getExons();
 
-    String getName();
-
     float getScore();
 
     String getLink();