X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=b813dcfa13cc6d6a551ff7cb8dd96cf2ef35563e;hb=298d676e11b2664a99a56b6c1d2a216e40727e9e;hp=9eaeb7a9e5aae02989bae9c1e290c4e5597dd226;hpb=bcd69929dba447593c10ed661545751727ad0b77;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 9eaeb7a..b813dcf 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -114,7 +114,7 @@ public class EditCommand implements CommandI
     public abstract Action getUndoAction();
   };
 
-  private List<Edit> edits = new ArrayList<Edit>();
+  private List<Edit> edits = new ArrayList<>();
 
   String description;
 
@@ -222,14 +222,16 @@ public class EditCommand implements CommandI
     /**
      * Check a contiguous edit; either
      * <ul>
-     * <li>a new Insert <n> positions to the right of the last <insert n>, or</li>
+     * <li>a new Insert <n> positions to the right of the last <insert n>,
+     * or</li>
      * <li>a new Delete <n> gaps which is <n> positions to the left of the last
      * delete.</li>
      * </ul>
      */
-    boolean contiguous = (action == Action.INSERT_GAP && e.position == lastEdit.position
-            + lastEdit.number)
-            || (action == Action.DELETE_GAP && e.position + e.number == lastEdit.position);
+    boolean contiguous = (action == Action.INSERT_GAP
+            && e.position == lastEdit.position + lastEdit.number)
+            || (action == Action.DELETE_GAP
+                    && e.position + e.number == lastEdit.position);
     if (contiguous)
     {
       /*
@@ -475,7 +477,8 @@ public class EditCommand implements CommandI
     {
       command.seqs[s].insertCharAt(command.position, command.number,
               command.gapChar);
-      // System.out.println("pos: "+command.position+" number: "+command.number);
+      // System.out.println("pos: "+command.position+" number:
+      // "+command.number);
     }
 
     adjustAnnotations(command, true, false, null);
@@ -504,8 +507,8 @@ public class EditCommand implements CommandI
   {
     for (int s = 0; s < command.seqs.length; s++)
     {
-      command.seqs[s].deleteChars(command.position, command.position
-              + command.number);
+      command.seqs[s].deleteChars(command.position,
+              command.position + command.number);
     }
 
     adjustAnnotations(command, false, false, null);
@@ -536,8 +539,8 @@ public class EditCommand implements CommandI
           // we are redoing an undone cut.
           sequence.setDatasetSequence(null);
         }
-        sequence.deleteChars(command.position, command.position
-                + command.number);
+        sequence.deleteChars(command.position,
+                command.position + command.number);
         if (command.oldds != null && command.oldds[i] != null)
         {
           // oldds entry contains the cut dataset sequence.
@@ -602,8 +605,8 @@ public class EditCommand implements CommandI
         // readd it to the alignment
         if (command.alIndex[i] < command.al.getHeight())
         {
-          List<SequenceI> sequences;
-          synchronized (sequences = command.al.getSequences())
+          List<SequenceI> sequences = command.al.getSequences();
+          synchronized (sequences)
           {
             if (!(command.alIndex[i] < 0))
             {
@@ -647,8 +650,8 @@ public class EditCommand implements CommandI
             {
               newDSNeeded = true;
               start = command.seqs[i].findPosition(command.position);
-              end = command.seqs[i].findPosition(command.position
-                      + command.number);
+              end = command.seqs[i]
+                      .findPosition(command.position + command.number);
             }
             if (command.seqs[i].getStart() == start)
             {
@@ -732,16 +735,16 @@ public class EditCommand implements CommandI
       tmp = new StringBuffer(oldstring.substring(0, start));
       tmp.append(command.string[i]);
       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, new String(
-                      command.string[i]));
+              jalview.util.Comparison.GapChars,
+              new String(command.string[i]));
       int ipos = command.seqs[i].findPosition(start)
               - command.seqs[i].getStart();
       tmp.append(oldstring.substring(end));
       command.seqs[i].setSequence(tmp.toString());
       command.string[i] = oldstring.substring(start, end).toCharArray();
       String nogapold = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, new String(
-                      command.string[i]));
+              jalview.util.Comparison.GapChars,
+              new String(command.string[i]));
       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
       {
         if (newDSWasNeeded)
@@ -786,7 +789,7 @@ public class EditCommand implements CommandI
     if (modifyVisibility && !insert)
     {
       // only occurs if a sequence was added or deleted.
-      command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
+      command.deletedAnnotationRows = new Hashtable<>();
     }
     if (command.fullAlignmentHeight)
     {
@@ -836,7 +839,8 @@ public class EditCommand implements CommandI
                 tmp = saved;
                 command.deletedAnnotationRows.put(command.seqs[s], saved);
                 // and then remove any annotation in the other views
-                for (int alview = 0; views != null && alview < views.length; alview++)
+                for (int alview = 0; views != null
+                        && alview < views.length; alview++)
                 {
                   if (views[alview] != command.al)
                   {
@@ -888,7 +892,8 @@ public class EditCommand implements CommandI
                 }
                 // and then duplicate added annotation on every other alignment
                 // view
-                for (int vnum = 0; views != null && vnum < views.length; vnum++)
+                for (int vnum = 0; views != null
+                        && vnum < views.length; vnum++)
                 {
                   if (views[vnum] != command.al)
                   {
@@ -943,7 +948,7 @@ public class EditCommand implements CommandI
 
     if (!insert)
     {
-      command.deletedAnnotations = new Hashtable<String, Annotation[]>();
+      command.deletedAnnotations = new Hashtable<>();
     }
 
     int aSize;
@@ -1015,8 +1020,8 @@ public class EditCommand implements CommandI
           }
 
           System.arraycopy(annotations[a].annotations, command.position,
-                  temp, command.position + command.number, aSize
-                          - command.position);
+                  temp, command.position + command.number,
+                  aSize - command.position);
         }
         else
         {
@@ -1059,8 +1064,8 @@ public class EditCommand implements CommandI
                     annotations[a].annotations.length - command.position);
             if (copylen > 0)
             {
-              System.arraycopy(annotations[a].annotations,
-                      command.position, deleted, 0, copylen); // command.number);
+              System.arraycopy(annotations[a].annotations, command.position,
+                      deleted, 0, copylen); // command.number);
             }
           }
 
@@ -1069,10 +1074,10 @@ public class EditCommand implements CommandI
           if (annotations[a].annotations.length > command.position
                   + command.number)
           {
-            System.arraycopy(annotations[a].annotations, command.position
-                    + command.number, temp, command.position,
-                    annotations[a].annotations.length - command.position
-                            - command.number); // aSize
+            System.arraycopy(annotations[a].annotations,
+                    command.position + command.number, temp,
+                    command.position, annotations[a].annotations.length
+                            - command.position - command.number); // aSize
           }
         }
         else
@@ -1133,7 +1138,7 @@ public class EditCommand implements CommandI
       return;
     }
 
-    List<SequenceFeature> oldsf = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> oldsf = new ArrayList<>();
 
     int cSize = j - i;
 
@@ -1191,7 +1196,7 @@ public class EditCommand implements CommandI
 
     if (command.editedFeatures == null)
     {
-      command.editedFeatures = new Hashtable<SequenceI, List<SequenceFeature>>();
+      command.editedFeatures = new Hashtable<>();
     }
 
     command.editedFeatures.put(seq, oldsf);
@@ -1228,7 +1233,7 @@ public class EditCommand implements CommandI
    */
   public Map<SequenceI, SequenceI> priorState(boolean forUndo)
   {
-    Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
+    Map<SequenceI, SequenceI> result = new HashMap<>();
     if (getEdits() == null)
     {
       return result;
@@ -1261,7 +1266,7 @@ public class EditCommand implements CommandI
      * Work backwards through the edit list, deriving the sequences before each
      * was applied. The final result is the sequence set before any edits.
      */
-    Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
+    Iterator<Edit> editList = new ReverseListIterator<>(getEdits());
     while (editList.hasNext())
     {
       Edit oldEdit = editList.next();
@@ -1422,7 +1427,7 @@ public class EditCommand implements CommandI
     }
     else
     {
-      return new ReverseListIterator<Edit>(getEdits());
+      return new ReverseListIterator<>(getEdits());
     }
   }
 }