JAL-1800 SearchResults.equals() to allow smarter mouseover of codons

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 2a33f6c..3948ba0 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -36,6 +36,10 @@ public class SearchResults
 
   private List<Match> matches = new ArrayList<Match>();
 
+  /**
+   * One match consists of a sequence reference, start and end positions.
+   * Discontiguous ranges in a sequence require two or more Match objects.
+   */
   public class Match
   {
     SequenceI sequence;
@@ -92,13 +96,44 @@ public class SearchResults
       // convert start/end to base 0 (with bounds check)
       final int from = Math.max(start - 1, 0);
       final int to = Math.min(end, chars.length + 1);
-      return String.valueOf(Arrays.copyOfRange(chars, from, to));
+      // return String.valueOf(Arrays.copyOfRange(chars, from, to));
+      return String.valueOf(from)
+              + String.valueOf(Arrays.copyOfRange(chars, from, to));
     }
 
     public void setSequence(SequenceI seq)
     {
       this.sequence = seq;
     }
+
+    /**
+     * Hashcode is the hashcode of the matched sequence plus a hash of start and
+     * end positions. Match objects that pass the test for equals are guaranteed
+     * to have the same hashcode.
+     */
+    @Override
+    public int hashCode()
+    {
+      int hash = sequence == null ? 0 : sequence.hashCode();
+      hash += 31 * start;
+      hash += 67 * end;
+      return hash;
+    }
+
+    /**
+     * Two Match objects are equal if they are for the same sequence, start and
+     * end positions
+     */
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (obj == null || !(obj instanceof Match))
+      {
+        return false;
+      }
+      Match m = (Match) obj;
+      return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
+    }
   }
 
   /**
@@ -281,4 +316,30 @@ public class SearchResults
     }
     return result.toString();
   }
+
+  /**
+   * Hashcode is has derived from the list of matches. This ensures that when
+   * two SearchResults objects satisfy the test for equals(), then they have the
+   * same hashcode.
+   */
+  @Override
+  public int hashCode()
+  {
+    return matches.hashCode();
+  }
+
+  /**
+   * Two SearchResults are considered equal if they contain the same matches in
+   * the same order.
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (obj == null || !(obj instanceof SearchResults))
+    {
+      return false;
+    }
+    SearchResults sr = (SearchResults) obj;
+    return ((ArrayList<Match>) this.matches).equals(sr.matches);
+  }
 }

diff --git a/test/jalview/datamodel/MatchTest.java b/test/jalview/datamodel/MatchTest.java
new file mode 100644 (file)
index 0000000..9b5e97b
--- /dev/null
+++ b/test/jalview/datamodel/MatchTest.java
@@ -0,0 +1,67 @@
+package jalview.datamodel;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.SearchResults.Match;
+
+import org.testng.annotations.Test;
+
+public class MatchTest
+{
+
+  @Test(groups = { "Functional" })
+  public void testToString()
+  {
+    SequenceI seq = new Sequence("", "abcdefghijklm");
+    Match m = new SearchResults().new Match(seq, 3, 5);
+    assertEquals("2cde", m.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testEquals()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    assertFalse(sr1.equals(null));
+    assertFalse(sr1.equals(seq1));
+    assertTrue(sr1.equals(sr1));
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+
+    sr1.addResult(seq1, 1, 1);
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+
+    sr2.addResult(seq1, 1, 1);
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+
+    /*
+     * same match but on different sequences - not equal
+     */
+    SearchResults sr3 = new SearchResults();
+    sr3.addResult(seq2, 1, 1);
+    assertFalse(sr1.equals(sr3));
+    assertFalse(sr3.equals(sr1));
+
+    /*
+     * same sequence but different end position - not equal
+     */
+    sr1.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 3, 5);
+    assertFalse(sr1.equals(sr2));
+
+    /*
+     * same sequence but different start position - not equal
+     */
+    sr1 = new SearchResults();
+    sr2 = new SearchResults();
+    sr1.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 2, 4);
+    assertFalse(sr1.equals(sr2));
+  }
+}

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index b576569..983bd34 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -1,6 +1,8 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
 
 import org.testng.annotations.Test;
 
@@ -13,12 +15,120 @@ public class SearchResultsTest
     SequenceI seq = new Sequence("", "abcdefghijklm");
     SearchResults sr = new SearchResults();
     sr.addResult(seq, 1, 1);
-    assertEquals("a", sr.toString());
+    assertEquals("0a", sr.toString());
     sr.addResult(seq, 3, 5);
-    assertEquals("acde", sr.toString());
+    assertEquals("0a2cde", sr.toString());
 
     seq = new Sequence("", "pqrstuvwxy");
     sr.addResult(seq, 6, 7);
-    assertEquals("acdeuv", sr.toString());
+    assertEquals("0a2cde5uv", sr.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testEquals()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    assertFalse(sr1.equals(null)); // null object
+    assertFalse(sr1.equals(seq1)); // wrong type
+    assertTrue(sr1.equals(sr1)); // self
+    assertTrue(sr1.equals(sr2)); // empty
+    assertTrue(sr2.equals(sr1)); // reflexive
+
+    /*
+     * only one result is not empty
+     */
+    sr1.addResult(seq1, 1, 1);
+    assertTrue(sr1.equals(sr1));
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+
+    /*
+     * both the same
+     */
+    sr2.addResult(seq1, 1, 1);
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+
+    /*
+     * both have three matches
+     */
+    sr1.addResult(seq1, 3, 4);
+    sr1.addResult(seq1, 6, 8);
+    sr2.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 6, 8);
+    assertTrue(sr1.equals(sr1));
+    assertTrue(sr2.equals(sr2));
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+  }
+
+  /**
+   * Matches that are similar but for distinct sequences are not equal
+   */
+  @Test(groups = { "Functional" })
+  public void testEquals_distinctSequences()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    sr1.addResult(seq1, 1, 1);
+    sr2.addResult(seq2, 1, 1);
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+  }
+
+  /**
+   * Matches that are the same except for ordering are not equal
+   */
+  @Test(groups = { "Functional" })
+  public void testEquals_orderDiffers()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    sr1.addResult(seq1, 1, 1);
+    sr1.addResult(seq1, 2, 2);
+    sr2.addResult(seq1, 2, 2);
+    sr2.addResult(seq1, 1, 1);
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+  }
+
+  /**
+   * Verify that hashCode matches for equal objects
+   */
+  @Test(groups = { "Functional" })
+  public void testHashcode()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    /*
+     * both empty
+     */
+    assertEquals(sr1.hashCode(), sr2.hashCode());
+
+    /*
+     * both one match
+     */
+    sr1.addResult(seq1, 1, 1);
+    sr2.addResult(seq1, 1, 1);
+    assertEquals(sr1.hashCode(), sr2.hashCode());
+
+    /*
+     * both three matches
+     */
+    sr1.addResult(seq1, 3, 4);
+    sr1.addResult(seq1, 6, 8);
+    sr2.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 6, 8);
+    assertEquals(sr1.hashCode(), sr2.hashCode());
   }
 }