JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...

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

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4882597..b427739 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -278,22 +278,26 @@ public class ColumnSelection
   }
 
   /**
-   * add a series of start,end (inclusive) ranges to the column selection 
-   * @param rng [start_0, end_0, start_1, end_1, ... ]
-   * @param baseOne - when true, ranges are base 1 and will be mapped to base 0
+   * add a series of start,end (inclusive) ranges to the column selection
+   * 
+   * @param rng
+   *          [start_0, end_0, start_1, end_1, ... ]
+   * @param baseOne
+   *          - when true, ranges are base 1 and will be mapped to base 0
    */
-  public void addRangeOfElements(int[] rng,boolean baseOne)
+  public void addRangeOfElements(int[] rng, boolean baseOne)
   {
-    int base=baseOne ? -1 : 0;
+    int base = baseOne ? -1 : 0;
     for (int c = 0; c < rng.length; c += 2)
     {
       for (int p = rng[c]; p <= rng[c + 1]; p++)
       {
-        selection.add(base+p);
+        selection.add(base + p);
       }
     }
-    
+
   }
+
   /**
    * clears column selection
    */
@@ -336,10 +340,12 @@ public class ColumnSelection
 
   /**
    * Returns a read-only view of the (possibly empty) list of selected columns
+   * (base 1)
    * <p>
-   * The list contains no duplicates but is not necessarily ordered. It also may
-   * include columns hidden from the current view. To modify (for example sort)
-   * the list, you should first make a copy.
+   * The list contains no duplicates but is not necessarily ordered. Columns are
+   * reported in alignment coordinates (base 1), so may also include columns
+   * hidden from the current view. To modify (for example sort) the list, you
+   * should first make a copy.
    * <p>
    * The list is not thread-safe: iterating over it could result in
    * ConcurrentModificationException if it is modified by another thread.
@@ -603,8 +609,8 @@ public class ColumnSelection
           int cpos = ann_row.sequenceRef.findPosition(column) - 1;
           ContactListI clist = ann_row.sequenceRef
                   .getContactListFor(ann_row, cpos);
-          for (int row = column + 8,
-                  rowEnd = clist.getContactHeight(); row < rowEnd; row++)
+          for (int row = column + 8, rowEnd = clist
+                  .getContactHeight(); row < rowEnd; row++)
           {
             if (filterParams
                     .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD