Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 35efe4f..5e75725 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,23 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.datamodel;
 
+import jalview.util.MessageManager;
+
 import java.util.*;
 
 /**
@@ -110,7 +114,7 @@ public class Alignment implements AlignmentI
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
-    throw new Error("Alignment(CigarArray) not yet implemented");
+    throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
@@ -446,7 +450,8 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(null);
       }
-      for (SequenceGroup sg:groups) {
+      for (SequenceGroup sg : groups)
+      {
         sg.setContext(null);
       }
       groups.clear();
@@ -1484,32 +1489,38 @@ public class Alignment implements AlignmentI
 
     }
   }
- @Override
- public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
- {
-   alignmentAnnotation.validateRangeAndDisplay();
-   if (isNucleotide() && alignmentAnnotation.isValidStruc())
-   {
-     hasRNAStructure = true;
-   }
- }
- @Override
-public int getEndRes()
-{
-  return getWidth()-1;
-}@Override
-public int getStartRes()
-{
-  return 0;
-}
 
-/* In the case of AlignmentI - returns the dataset for the alignment, if set
- * (non-Javadoc)
- * @see jalview.datamodel.AnnotatedCollectionI#getContext()
- */
-@Override
-public AnnotatedCollectionI getContext()
-{
-  return dataset;
-}
+  @Override
+  public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    alignmentAnnotation.validateRangeAndDisplay();
+    if (isNucleotide() && alignmentAnnotation.isValidStruc())
+    {
+      hasRNAStructure = true;
+    }
+  }
+
+  @Override
+  public int getEndRes()
+  {
+    return getWidth() - 1;
+  }
+
+  @Override
+  public int getStartRes()
+  {
+    return 0;
+  }
+
+  /*
+   * In the case of AlignmentI - returns the dataset for the alignment, if set
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+   */
+  @Override
+  public AnnotatedCollectionI getContext()
+  {
+    return dataset;
+  }
 }