X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=4a38ec0f5b76a4263457fdc980ecce2daf33d83d;hb=6c36212c1e16557e6afb1b4dba9c28864d52ad4a;hp=db83e76c485faa593084cbdeaacaf4a6aae7482f;hpb=457478300feb669620d4d18b8e4ce77ebbfdc4ae;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index db83e76..4a38ec0 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -278,6 +278,27 @@ 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
+   */
+  public void addRangeOfElements(int[] rng, boolean baseOne)
+  {
+    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);
+      }
+    }
+
+  }
+
+  /**
    * clears column selection
    */
   public void clear()
@@ -567,7 +588,7 @@ public class ColumnSelection
     // viewmodel package
     this.clear();
 
-    if (ann_row.graph == AlignmentAnnotation.CUSTOMRENDERER && (filterParams
+    if (ann_row.graph == AlignmentAnnotation.CONTACT_MAP && (filterParams
             .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
             || filterParams
                     .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD))
@@ -586,8 +607,8 @@ 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