JAL-1686 JAL-2110 equals and/or hashCode method added

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 6d6cdb5..5d00b6b 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -23,6 +23,7 @@ package jalview.datamodel;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.AbstractList;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -36,7 +37,7 @@ public class AlignedCodonFrame
   /*
    * Data bean to hold mappings from one sequence to another
    */
-  private class SequenceToSequenceMapping
+  public class SequenceToSequenceMapping
   {
     private SequenceI fromSeq;
 
@@ -57,6 +58,48 @@ public class AlignedCodonFrame
       return String.format("From %s %s", fromSeq.getName(),
               mapping.toString());
     }
+
+    /**
+     * Returns a hashCode derived from the hashcodes of the mappings
+     * 
+     * @see SequenceToSequenceMapping#hashCode()
+     */
+    @Override
+    public int hashCode()
+    {
+      return mappings.hashCode();
+    }
+
+    /**
+     * Answers true if the objects hold the same mapping between the same two
+     * sequences
+     * 
+     * @see Mapping#equals
+     */
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (!(obj instanceof SequenceToSequenceMapping))
+      {
+        return false;
+      }
+      SequenceToSequenceMapping that = (SequenceToSequenceMapping) obj;
+      if (this.mapping == null)
+      {
+        return that.mapping == null;
+      }
+      return this.mapping.equals(that.mapping);
+    }
+
+    public SequenceI getFromSeq()
+    {
+      return fromSeq;
+    }
+
+    public Mapping getMapping()
+    {
+      return mapping;
+    }
   }
 
   private List<SequenceToSequenceMapping> mappings;
@@ -90,6 +133,8 @@ public class AlignedCodonFrame
 
     /*
      * if we already hold a mapping between these sequences, just add to it 
+     * note that 'adding' a duplicate map does nothing; this protects against
+     * creating duplicate mappings in AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
@@ -674,4 +719,37 @@ public class AlignedCodonFrame
     }
     return null;
   }
+
+  /**
+   * Returns a hashcode derived from the list of sequence mappings
+   * 
+   * @see SequenceToSequenceMapping#hashCode()
+   * @see AbstractList#hashCode()
+   */
+  @Override
+  public int hashCode()
+  {
+    return this.mappings.hashCode();
+  }
+
+  /**
+   * Two AlignedCodonFrame objects are equal if they hold the same ordered list
+   * of mappings
+   * 
+   * @see SequenceToSequenceMapping#
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (!(obj instanceof AlignedCodonFrame))
+    {
+      return false;
+    }
+    return this.mappings.equals(((AlignedCodonFrame) obj).mappings);
+  }
+
+  public List<SequenceToSequenceMapping> getMappings()
+  {
+    return mappings;
+  }
 }

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index bd83fe9..b4489e2 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -356,14 +356,13 @@ public class Mapping
   /**
    * Equals that compares both the to references and MapList mappings.
    * 
-   * @param other
+   * @param o
    * @return
+   * @see MapList#equals
    */
   @Override
   public boolean equals(Object o)
   {
-    // TODO should override Object.hashCode() to ensure that equal objects have
-    // equal hashcodes
     if (o == null || !(o instanceof Mapping))
     {
       return false;
@@ -390,6 +389,21 @@ public class Mapping
   }
 
   /**
+   * Returns a hashCode made from the sequence and maplist
+   */
+  @Override
+  public int hashCode()
+  {
+    int hashCode = (this.to == null ? 1 : this.to.hashCode());
+    if (this.map != null)
+    {
+      hashCode = hashCode * 31 + this.map.hashCode();
+    }
+
+    return hashCode;
+  }
+
+  /**
    * get the 'initial' position in the associated sequence for a position in the
    * mapped reference frame
    * 

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index ab811a9..cae968e 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -88,8 +88,6 @@ public class MapList
   @Override
   public boolean equals(Object o)
   {
-    // TODO should also override hashCode to ensure equal objects have equal
-    // hashcodes
     if (o == null || !(o instanceof MapList))
     {
       return false;
@@ -112,6 +110,19 @@ public class MapList
   }
 
   /**
+   * Returns a hashcode made from the fromRatio, toRatio, and from/to ranges
+   */
+  @Override
+  public int hashCode()
+  {
+    int hashCode = 31 * fromRatio;
+    hashCode = 31 * hashCode + toRatio;
+    hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
+    hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+    return hashCode;
+  }
+
+  /**
    * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
    * 
    * @return
@@ -992,6 +1003,10 @@ public class MapList
    */
   public void addMapList(MapList map)
   {
+    if (this.equals(map))
+    {
+      return;
+    }
     this.fromLowest = Math.min(fromLowest, map.fromLowest);
     this.toLowest = Math.min(toLowest, map.toLowest);
     this.fromHighest = Math.max(fromHighest, map.fromHighest);
@@ -1087,4 +1102,5 @@ public class MapList
     }
     return forwardStrand;
   }
+
 }

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index cd8a1e3..f2dd968 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -451,4 +451,30 @@ public class AlignedCodonFrameTest
     assertArrayEquals(new int[] { 2, 2 },
             acf.getMappedRegion(seq2, seq1, 6));
   }
+
+  /**
+   * Tests for addMap. See also tests for MapList.addMapList
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMap()
+  {
+    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+    seq1.createDatasetSequence();
+    final Sequence aseq1 = new Sequence("Seq1", "-V-L");
+    aseq1.createDatasetSequence();
+  
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+        1, 2 }, 3, 1);
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+    Mapping before = acf.getMappingsFromSequence(seq1).get(0);
+
+    /*
+     * add the same map again, verify it doesn't get duplicated
+     */
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+    assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
+  }
 }

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index d4ed0ea..ba298c5 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -563,6 +563,21 @@ public class MapListTest
             s);
   }
 
+  /**
+   * Test that confirms adding a map twice does nothing
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMapList_sameMap()
+  {
+    MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
+            new int[] { 72, 22 }, 1, 3);
+    String before = ml.toString();
+    ml.addMapList(ml);
+    assertEquals(before, ml.toString());
+    ml.addMapList(new MapList(ml));
+    assertEquals(before, ml.toString());
+  }
+
   @Test(groups = { "Functional" })
   public void testAddMapList_contiguous()
   {