JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 3916b7d..15bbffa 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -486,6 +486,7 @@ public class ColumnSelection
 
   /**
    * This Method is used to return all the HiddenColumn regions
+   * 
    * @return empty list or List of hidden column intervals
    */
   public List<int[]> getHiddenColumns()
@@ -666,8 +667,7 @@ public class ColumnSelection
       }
       else if (end < region[0] && start < region[0])
       {
-        hiddenColumns.insertElementAt(new int[]
-        { start, end }, i);
+        hiddenColumns.insertElementAt(new int[] { start, end }, i);
         added = true;
         break;
       }
@@ -679,8 +679,7 @@ public class ColumnSelection
     }
     else if (!added)
     {
-      hiddenColumns.addElement(new int[]
-      { start, end });
+      hiddenColumns.addElement(new int[] { start, end });
     }
 
   }
@@ -909,16 +908,14 @@ public class ColumnSelection
         }
         if (hideStart > vstart)
         {
-          visiblecontigs.add(new int[]
-          { vstart, hideStart - 1 });
+          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
       }
 
       if (vstart < end)
       {
-        visiblecontigs.add(new int[]
-        { vstart, end - 1 });
+        visiblecontigs.add(new int[] { vstart, end - 1 });
       }
       int[] vcontigs = new int[visiblecontigs.size() * 2];
       for (int i = 0, j = visiblecontigs.size(); i < j; i++)
@@ -933,8 +930,7 @@ public class ColumnSelection
     }
     else
     {
-      return new int[]
-      { start, end - 1 };
+      return new int[] { start, end - 1 };
     }
   }
 
@@ -975,7 +971,7 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       // then mangle the alignmentAnnotation annotation array
-      Vector<Annotation []> annels = new Vector<Annotation []>();
+      Vector<Annotation[]> annels = new Vector<Annotation[]>();
       Annotation[] els = null;
       List<int[]> regions = getHiddenColumns();
       int blockStart = start, blockEnd = end;
@@ -1035,7 +1031,7 @@ public class ColumnSelection
       alignmentAnnotation.annotations = new Annotation[w];
       w = 0;
 
-        for (Annotation [] chnk : annels)
+      for (Annotation[] chnk : annels)
       {
         System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
                 chnk.length);
@@ -1284,7 +1280,7 @@ public class ColumnSelection
   {
     return hiddenColumns != null && hiddenColumns.size() > 0;
   }
-  
+
   /**
    * 
    * @return true if there are more than one set of columns hidden
@@ -1308,7 +1304,7 @@ public class ColumnSelection
       hideColumns(r[0], r[1]);
     }
   }
-  
+
   public boolean filterAnnotations(Annotation[] annotations,
           AnnotationFilterParameter filterParams)
   {