JAL-1517 fix copyright for 2.8.2

[jalview.git] / src / jalview / analysis / Dna.java

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5285924..16cae49 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
@@ -125,7 +128,7 @@ public class Dna
     {
       SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
               viscontigs, codons, gapCharacter,
-              (product != null) ? product[s] : null); // possibly anonymous
+              (product != null) ? product[s] : null, false); // possibly anonymous
       // product
       if (newseq != null)
       {
@@ -420,13 +423,36 @@ public class Dna
    * @param codons
    *          Definition of global ORF alignment reference frame
    * @param gapCharacter
-   * @param newSeq
    * @return sequence ready to be added to alignment.
+   * @deprecated Use {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)} instead
    */
   public static SequenceI translateCodingRegion(SequenceI selection,
           String seqstring, int[] viscontigs, AlignedCodonFrame codons,
           char gapCharacter, DBRefEntry product)
   {
+    return translateCodingRegion(selection, seqstring, viscontigs, codons,
+            gapCharacter, product, false);
+  }
+
+  /**
+   * Translate a na sequence
+   * 
+   * @param selection
+   *          sequence displayed under viscontigs visible columns
+   * @param seqstring
+   *          ORF read in some global alignment reference frame
+   * @param viscontigs
+   *          mapping from global reference frame to visible seqstring ORF read
+   * @param codons
+   *          Definition of global ORF alignment reference frame
+   * @param gapCharacter
+   * @param starForStop when true stop codons will translate as '*', otherwise as 'X'  
+   * @return sequence ready to be added to alignment.
+   */
+  public static SequenceI translateCodingRegion(SequenceI selection,
+          String seqstring, int[] viscontigs, AlignedCodonFrame codons,
+          char gapCharacter, DBRefEntry product, final boolean starForStop)
+  {
     java.util.List skip = new ArrayList();
     int skipint[] = null;
     ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
@@ -560,7 +586,7 @@ public class Dna
           }
           if (aa.equals("STOP"))
           {
-            aa = "X";
+            aa = starForStop ? "*" : "X";
           }
           resSize++;
         }