Merge branch 'bug/JAL-2829deleteCharsWithGaps' into

[jalview.git] / src / jalview / commands / EditCommand.java

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index d603a0d..f71fb79 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1415,43 +1415,45 @@ public class EditCommand implements CommandI
 
   public class Edit
   {
-    public SequenceI[] oldds;
+    private SequenceI[] oldds;
 
     /**
      * start and end of sequence prior to edit
      */
-    public Range[] oldStartEnd;
+    private Range[] oldStartEnd;
 
-    boolean fullAlignmentHeight = false;
+    private boolean fullAlignmentHeight = false;
 
-    Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+    private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
 
-    Map<String, Annotation[]> deletedAnnotations;
+    private Map<String, Annotation[]> deletedAnnotations;
 
     /*
      * features deleted by the cut (re-add on Undo)
      * (including the original of any shortened features)
      */
-    Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+    private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
 
     /*
      * shortened features added by the cut (delete on Undo)
      */
-    Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
+    private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
 
-    AlignmentI al;
+    private AlignmentI al;
 
-    Action command;
+    final private Action command;
 
     char[][] string;
 
     SequenceI[] seqs;
 
-    int[] alIndex;
+    private int[] alIndex;
 
-    int position, number;
+    private int position;
 
-    char gapChar;
+    private int number;
+
+    private char gapChar;
 
     public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
             char gap)
@@ -1479,6 +1481,16 @@ public class EditCommand implements CommandI
       fullAlignmentHeight = (align.getHeight() == sqs.length);
     }
 
+    /**
+     * Constructor given a REPLACE command and the replacement string
+     * 
+     * @param cmd
+     * @param sqs
+     * @param pos
+     * @param count
+     * @param align
+     * @param replace
+     */
     Edit(Action cmd, SequenceI[] sqs, int pos, int count,
             AlignmentI align, String replace)
     {