X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FVisibleContigsIterator.java;h=9198de8086ebc42f73416554f7b83dc6874efa24;hb=b3fb6325a8bc315c5c938faf10ffd2e73d965f16;hp=ff060ac2aa56ee88a1261f3592eeca895b310e4a;hpb=fa20ec4effe2fb9205d844fd85befbe785bf1a2e;p=jalview.git

diff --git a/src/jalview/datamodel/VisibleContigsIterator.java b/src/jalview/datamodel/VisibleContigsIterator.java
index ff060ac..9198de8 100644
--- a/src/jalview/datamodel/VisibleContigsIterator.java
+++ b/src/jalview/datamodel/VisibleContigsIterator.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import java.util.ArrayList;
@@ -5,7 +25,9 @@ import java.util.Iterator;
 import java.util.List;
 
 /**
- * An iterator which iterates over visible regions in a range.
+ * An iterator which iterates over visible regions in a range. Provides a
+ * special "endsAtHidden" indicator to allow callers to determine if the final
+ * visible column is adjacent to a hidden region.
  */
 public class VisibleContigsIterator implements Iterator<int[]>
 {
@@ -15,8 +37,7 @@ public class VisibleContigsIterator implements Iterator<int[]>
 
   private boolean endsAtHidden = false;
 
-  VisibleContigsIterator(int start, int end,
-          List<int[]> hiddenColumns)
+  VisibleContigsIterator(int start, int end, List<int[]> hiddenColumns)
   {
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
@@ -37,9 +58,17 @@ public class VisibleContigsIterator implements Iterator<int[]>
         }
         if (hideStart > vstart)
         {
-          int[] contig = new int[] { vstart, hideStart - 1 };
-          vcontigs.add(contig);
-          endsAtHidden = true;
+          if (end - 1 > hideStart - 1)
+          {
+            int[] contig = new int[] { vstart, hideStart - 1 };
+            vcontigs.add(contig);
+            endsAtHidden = true;
+          }
+          else
+          {
+            int[] contig = new int[] { vstart, end - 1 };
+            vcontigs.add(contig);
+          }
         }
         vstart = hideEnd + 1;
 
@@ -83,4 +112,3 @@ public class VisibleContigsIterator implements Iterator<int[]>
     return endsAtHidden;
   }
 }
-