X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=ad0e472f36f9bb9bf1deafd3389f1b4e3272e83d;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=3948ba0bf852ee0cd2798b8a85d3bd9c007c846f;hpb=0c37e7cea9a7028130b6f2164961af24c3c48ec2;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 3948ba0..ad0e472 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -87,18 +87,27 @@ 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 +232,7 @@ public class SearchResults
 
           if (result == null)
           {
-            result = new int[]
-            { matchStart, matchEnd };
+            result = new int[] { matchStart, matchEnd };
           }
           else
           {
@@ -300,9 +308,9 @@ 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 +326,23 @@ 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.