JAL-845 implement alignment of protein to match cDNA alignment

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index a53d103..fb420b9 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -40,16 +40,26 @@ public class SearchResults
   {
     SequenceI sequence;
 
-    /*
+    /**
      * Start position of match in sequence (base 1)
      */
     int start;
 
-    /*
+    /**
      * End position (inclusive) (base 1)
      */
     int end;
 
+    /**
+     * Constructor
+     * 
+     * @param seq
+     *          a sequence
+     * @param start
+     *          start position of matched range (base 1)
+     * @param end
+     *          end of matched range (inclusive, base 1)
+     */
     public Match(SequenceI seq, int start, int end)
     {
       sequence = seq;
@@ -79,7 +89,10 @@ public class SearchResults
     public String toString()
     {
       char[] chars = sequence.getSequence();
-      return String.valueOf(Arrays.copyOfRange(chars, start - 1, end));
+      // 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));
     }
   }