JAL-2611 reinstated missed commit

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

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index eb2d174..6d620b4 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -401,7 +401,6 @@ public class ColumnSelection
 
   }
 
-
   /**
    * Hides the specified column and any adjacent selected columns
    * 
@@ -444,10 +443,6 @@ public class ColumnSelection
     hidden.hideColumns(min, max);
   }
 
-
-
-
-
   /**
    * Copy constructor
    * 
@@ -468,11 +463,6 @@ public class ColumnSelection
   {
   }
 
-
-
-
-
-
   /**
    * Invert the column selection from first to end-1. leaves hiddenColumns
    * untouched (and unselected)
@@ -482,7 +472,7 @@ public class ColumnSelection
    */
   public void invertColumnSelection(int first, int width, AlignmentI al)
   {
-    boolean hasHidden = al.getHiddenColumns().hasHidden();
+    boolean hasHidden = al.getHiddenColumns().hasHiddenColumns();
     for (int i = first; i < width; i++)
     {
       if (contains(i))
@@ -511,7 +501,7 @@ public class ColumnSelection
     selection = new IntList();
     if (colsel.selection != null && colsel.selection.size() > 0)
     {
-      if (hiddenColumns.hasHidden())
+      if (hiddenColumns.hasHiddenColumns())
       {
         // only select visible columns in this columns selection
         for (Integer col : colsel.getSelected())
@@ -534,7 +524,6 @@ public class ColumnSelection
     }
   }
 
-
   /**
    * 
    * @return true if there are columns marked
@@ -544,8 +533,6 @@ public class ColumnSelection
     return (selection != null && selection.size() > 0);
   }
 
-
-
   public boolean filterAnnotations(Annotation[] annotations,
           AnnotationFilterParameter filterParams)
   {
@@ -560,13 +547,15 @@ public class ColumnSelection
 
         boolean itemMatched = false;
 
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+        if (filterParams
+                .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
                 && annotations[count].value >= filterParams
                         .getThresholdValue())
         {
           itemMatched = true;
         }
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+        if (filterParams
+                .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
                 && annotations[count].value <= filterParams
                         .getThresholdValue())
         {
@@ -691,8 +680,8 @@ public class ColumnSelection
    * 
    * @return
    */
-  public boolean markColumns(BitSet markedColumns, int startCol,
-          int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+  public boolean markColumns(BitSet markedColumns, int startCol, int endCol,
+          boolean invert, boolean extendCurrent, boolean toggle)
   {
     boolean changed = false;
     if (!extendCurrent && !toggle)