JAL-2759 corrected old getVisibleBlocksIterator calls for new call

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 076b0a3..9d9ee2c 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -566,7 +566,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleContigsIterator regions = (VisibleContigsIterator) hidden
-              .getVisContigsIterator(startRes, endRes, true);
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())
       {

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 5ac0abb..7862975 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -31,17 +31,16 @@ import java.util.concurrent.locks.ReentrantReadWriteLock;
  * alignment. To iterate over the collection, or over visible columns/regions,
  * use an iterator obtained from one of:
  * 
- * - getBoundedIterator: iterate over the hidden regions, within some bounds
+ * - getBoundedIterator: iterates over the hidden regions, within some bounds,
+ * returning absolute positions
  * 
- * - getBoundedStartIterator: iterate over the start positions of hidden
- * regions, within some bounds
+ * - getBoundedStartIterator: iterates over the start positions of hidden
+ * regions, within some bounds, returning visible positions
  * 
- * - getVisContigsIterator: iterate over visible regions in a range, returning
+ * - getVisContigsIterator: iterates over visible regions in a range, returning
  * absolute positions
  * 
- * - getVisibleBlocksIterator
- * 
- * - getVisibleColsIterator: iterate over the visible *columns*
+ * - getVisibleColsIterator: iterates over the visible *columns*
  * 
  * For performance reasons, provide bounds where possible.
  * 
@@ -82,7 +81,8 @@ public class HiddenColumns
    * Methods which change the hiddenColumns collection. These methods should 
    * use a writeLock to prevent other threads accessing the hiddenColumns
    * collection while changes are being made. They should also reset the hidden
-   * columns cursor, and either update the hidden columns count, or set it to 0.
+   * columns cursor, and either update the hidden columns count, or set it to 0 
+   * (so that it will later be updated when needed).
    */
 
   /**

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 5c5fbbe..2a43e85 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1031,7 +1031,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleContigsIterator regions = (VisibleContigsIterator) hidden
-              .getVisContigsIterator(startRes, endRes, true);
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())
       {
@@ -1365,7 +1365,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleContigsIterator regions = (VisibleContigsIterator) hidden
-              .getVisContigsIterator(startRes, endRes, true);
+              .getVisContigsIterator(startRes, endRes + 1, true);
       while (regions.hasNext())
       {
         int[] region = regions.next();

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index e66367b..7b0e8af 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -1322,7 +1322,7 @@ public class HiddenColumnsTest
   public void testVisibleBlocksVisBoundsIterator()
   {
     HiddenColumns h = new HiddenColumns();
-    Iterator<int[]> regions = h.getVisContigsIterator(0, 30, true);
+    Iterator<int[]> regions = h.getVisContigsIterator(0, 31, true);
 
     // only 1 visible region spanning 0-30 if nothing is hidden
     assertTrue(regions.hasNext());
@@ -1335,7 +1335,7 @@ public class HiddenColumnsTest
     // 2 regions one on either side
     // second region boundary accounts for hidden columns
     h.hideColumns(10, 15);
-    regions = h.getVisContigsIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 31, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();
@@ -1349,7 +1349,7 @@ public class HiddenColumnsTest
     // single hidden region at left
     h = new HiddenColumns();
     h.hideColumns(0, 5);
-    regions = h.getVisContigsIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 31, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();
@@ -1360,7 +1360,7 @@ public class HiddenColumnsTest
     // single hidden region at right
     h = new HiddenColumns();
     h.hideColumns(27, 30);
-    regions = h.getVisContigsIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 31, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();
@@ -1375,7 +1375,7 @@ public class HiddenColumnsTest
     h = new HiddenColumns();
     h.hideColumns(0, 5);
     h.hideColumns(23, 25);
-    regions = h.getVisContigsIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 31, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();
@@ -1390,7 +1390,7 @@ public class HiddenColumnsTest
     h = new HiddenColumns();
     h.hideColumns(27, 30);
     h.hideColumns(11, 14);
-    regions = h.getVisContigsIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 31, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();
@@ -1408,7 +1408,7 @@ public class HiddenColumnsTest
     h = new HiddenColumns();
     h.hideColumns(27, 35);
     h.hideColumns(0, 4);
-    regions = h.getVisContigsIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 31, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();
@@ -1426,7 +1426,7 @@ public class HiddenColumnsTest
     h.hideColumns(9, 11);
     h.hideColumns(22, 26);
 
-    regions = h.getVisContigsIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 31, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();