Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index a9cd4d7..89fb1ab 100644 (file)
--- 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)
@@ -469,6 +470,10 @@ public class HiddenColumns
     }
   }
 
+  /**
+   * Answers true if obj is an instance of HiddenColumns, and holds the same
+   * array of start-end column ranges as this, else answers false
+   */
   @Override
   public boolean equals(Object obj)
   {
@@ -524,8 +529,7 @@ public class HiddenColumns
 
       if (!hiddenColumns.isEmpty())
       {
-        result += cursor.findRegionForColumn(column, true)
-                .getHiddenSoFar();
+        result += cursor.findRegionForColumn(column, true).getHiddenSoFar();
       }
 
       return result;
@@ -558,11 +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())
@@ -740,7 +744,6 @@ public class HiddenColumns
     }
   }
 
-
   /**
    * Returns a hashCode built from hidden column ranges
    */
@@ -794,7 +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)
@@ -844,7 +847,7 @@ public class HiddenColumns
     try
     {
       LOCK.writeLock().lock();
-      
+
       if (!hiddenColumns.isEmpty())
       {
         HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
@@ -1045,7 +1048,7 @@ public class HiddenColumns
    * @param end
    *          position to end at (inclusive, visible column position)
    */
-  public Iterator<Integer> getBoundedStartIterator(int start, int end)
+  public Iterator<Integer> getStartRegionIterator(int start, int end)
   {
     try
     {
@@ -1062,8 +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();
@@ -1084,7 +1086,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      return new RangeElementsIterator(start, end,
+      return new RangeElementsIterator(
               new VisibleContigsIterator(start, end + 1, hiddenColumns));
     } finally
     {
@@ -1104,8 +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;