Merge hack/JAL-1617 fake DBRef to develop

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 7a241fd..e62e58a 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -39,10 +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;
@@ -64,6 +81,19 @@ public class SearchResults
     {
       return end;
     }
+
+    /**
+     * Returns the string of characters in the matched region.
+     */
+    @Override
+    public String toString()
+    {
+      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));
+    }
   }
 
   /**
@@ -228,4 +258,22 @@ public class SearchResults
   {
     return matches;
   }
+
+  /**
+   * 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
+   */
+  @Override
+  public String toString()
+  {
+    StringBuilder result = new StringBuilder(256);
+    for (Match m : matches)
+    {
+      result.append(m.toString());
+    }
+    return result.toString();
+  }
 }