Merge branch 'documentation/JAL-2675_release2102b1' into feature/JAL-2611

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

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 21ff841..d319249 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -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.
@@ -555,11 +558,10 @@ public class EditCommand implements CommandI
               command.oldds = new SequenceI[command.seqs.length];
             }
             command.oldds[i] = oldds;
-            adjustFeatures(
-                    command,
-                    i,
+            adjustFeatures(command, i,
                     sequence.findPosition(command.position),
-                    sequence.findPosition(command.position + command.number),
+                    sequence.findPosition(
+                            command.position + command.number),
                     false);
           }
         }
@@ -646,8 +648,8 @@ 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)
             {
@@ -731,16 +733,16 @@ 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)
@@ -833,7 +835,8 @@ 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)
                   {
@@ -885,7 +888,8 @@ 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)
                   {
@@ -1012,8 +1016,8 @@ 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
         {
@@ -1056,8 +1060,8 @@ 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);
             }
           }
 
@@ -1066,10 +1070,10 @@ 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