X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=b9db46123c335bd5f703045adbecd9f6e0107c84;hb=51e084651cb62b4d7597b2b448c8529d3ab60cca;hp=2a33f6c9afc3f61e400a2f2aada814b1ade65a78;hpb=9612728299dc4c2242a6a968875a194624983920;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 2a33f6c..b9db461 100755
--- 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;
@@ -63,8 +67,22 @@ public class SearchResults
     public Match(SequenceI seq, int start, int end)
     {
       sequence = seq;
-      this.start = start;
-      this.end = end;
+
+      /*
+       * always hold in forwards order, even if given in reverse order
+       * (such as from a mapping to a reverse strand); this avoids
+       * trouble for routines that highlight search results etc
+       */
+      if (start <= end)
+      {
+        this.start = start;
+        this.end = end;
+      }
+      else
+      {
+        this.start = end;
+        this.end = start;
+      }
     }
 
     public SequenceI getSequence()
@@ -83,11 +101,22 @@ public class SearchResults
     }
 
     /**
-     * Returns the string of characters in the matched region.
+     * Returns the string of characters in the matched region, prefixed by the
+     * start position, e.g. "12CGT" or "208K"
      */
     @Override
     public String toString()
     {
+      final int from = Math.max(start - 1, 0);
+      String startPosition = String.valueOf(from);
+      return startPosition + getCharacters();
+    }
+
+    /**
+     * Returns the string of characters in the matched region.
+     */
+    public String getCharacters()
+    {
       char[] chars = sequence.getSequence();
       // convert start/end to base 0 (with bounds check)
       final int from = Math.max(start - 1, 0);
@@ -99,6 +128,35 @@ public class SearchResults
     {
       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);
+    }
   }
 
   /**
@@ -188,8 +246,7 @@ public class SearchResults
 
           if (result == null)
           {
-            result = new int[]
-            { matchStart, matchEnd };
+            result = new int[] { matchStart, matchEnd };
           }
           else
           {
@@ -265,9 +322,9 @@ public class SearchResults
   }
 
   /**
-   * Return the results as a string of characters. Meant for use when the
-   * context ensures that all matches are to regions of the same sequence
-   * (otherwise the result is meaningless).
+   * Return the results as a string of characters (bases) prefixed by start
+   * position(s). Meant for use when the context ensures that all matches are to
+   * regions of the same sequence (otherwise the result is meaningless).
    * 
    * @return
    */
@@ -281,4 +338,47 @@ public class SearchResults
     }
     return result.toString();
   }
+
+  /**
+   * Return the results as a string of characters (bases). Meant for use when
+   * the context ensures that all matches are to regions of the same sequence
+   * (otherwise the result is meaningless).
+   * 
+   * @return
+   */
+  public String getCharacters()
+  {
+    StringBuilder result = new StringBuilder(256);
+    for (Match m : matches)
+    {
+      result.append(m.getCharacters());
+    }
+    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);
+  }
 }