JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / datamodel / SearchResults.java

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 3948ba0..b9db461 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -67,8 +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()
@@ -87,18 +101,27 @@ 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);
       final int to = Math.min(end, chars.length + 1);
-      // return String.valueOf(Arrays.copyOfRange(chars, from, to));
-      return String.valueOf(from)
-              + String.valueOf(Arrays.copyOfRange(chars, from, to));
+      return String.valueOf(Arrays.copyOfRange(chars, from, to));
     }
 
     public void setSequence(SequenceI seq)
@@ -223,8 +246,7 @@ public class SearchResults
 
           if (result == null)
           {
-            result = new int[]
-            { matchStart, matchEnd };
+            result = new int[] { matchStart, matchEnd };
           }
           else
           {
@@ -300,9 +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
    */
@@ -318,6 +340,23 @@ public class SearchResults
   }
 
   /**
+   * 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.