X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=89fb1ab21b2246e1dd61aaf3fec356e731ef2672;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=2d43f025f7bc6746b216f37d9aee2feb13330bb1;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 2d43f02..89fb1ab 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -135,9 +135,9 @@ public class HiddenColumns
           // all overlapping regions and we need contained regions
           if (region[0] >= start && region[1] <= end)
           {
-            hiddenColumns.add(
-                    new int[]
-            { region[0] - offset, region[1] - offset });
+            hiddenColumns
+                    .add(new int[]
+                    { region[0] - offset, region[1] - offset });
             numColumns += region[1] - region[0] + 1;
           }
         }
@@ -169,7 +169,8 @@ public class HiddenColumns
       if (!hiddenColumns.isEmpty())
       {
         // set up cursor reset values
-        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start, false);
+        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start,
+                false);
         regionindex = cursorPos.getRegionIndex();
 
         if (regionindex > 0)
@@ -252,7 +253,7 @@ public class HiddenColumns
       int oldstart = region[0];
       region[0] = Math.min(region[0], start);
       numColumns += oldstart - region[0]; // new columns are between old and
-                                              // adjusted starts
+                                          // adjusted starts
       added = true;
     }
     else if (start <= region[1] + 1)
@@ -528,8 +529,7 @@ public class HiddenColumns
 
       if (!hiddenColumns.isEmpty())
       {
-        result += cursor.findRegionForColumn(column, true)
-                .getHiddenSoFar();
+        result += cursor.findRegionForColumn(column, true).getHiddenSoFar();
       }
 
       return result;
@@ -562,11 +562,11 @@ public class HiddenColumns
                 .findRegionForColumn(hiddenColumn, false);
         int index = cursorPos.getRegionIndex();
         int hiddenBeforeCol = cursorPos.getHiddenSoFar();
-    
+
         // just subtract hidden cols count - this works fine if column is
         // visible
         result = hiddenColumn - hiddenBeforeCol;
-    
+
         // now check in case column is hidden - it will be in the returned
         // hidden region
         if (index < hiddenColumns.size())
@@ -744,7 +744,6 @@ public class HiddenColumns
     }
   }
 
-
   /**
    * Returns a hashCode built from hidden column ranges
    */
@@ -798,7 +797,7 @@ public class HiddenColumns
       for (int firstSet = tohide
               .nextSetBit(start), lastSet = start; firstSet >= start
                       && lastSet <= end; firstSet = tohide
-                      .nextSetBit(lastSet))
+                              .nextSetBit(lastSet))
       {
         lastSet = tohide.nextClearBit(firstSet);
         if (lastSet <= end)
@@ -848,7 +847,7 @@ public class HiddenColumns
     try
     {
       LOCK.writeLock().lock();
-      
+
       if (!hiddenColumns.isEmpty())
       {
         HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
@@ -1066,8 +1065,7 @@ public class HiddenColumns
       HiddenCursorPosition pos = cursor
               .findRegionForColumn(absoluteStart - 1, false);
 
-      return new StartRegionIterator(pos, start, end,
-              hiddenColumns);
+      return new StartRegionIterator(pos, start, end, hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
@@ -1108,8 +1106,7 @@ public class HiddenColumns
    *          if true, start and end are visible column positions, not absolute
    *          positions*
    */
-  public VisibleContigsIterator getVisContigsIterator(int start,
-          int end,
+  public VisibleContigsIterator getVisContigsIterator(int start, int end,
           boolean useVisibleCoords)
   {
     int adjstart = start;