JAL-2759 Remove getVisibleBlocksIterator call

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2c90047..076b0a3 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
-              .getVisibleBlocksIterator(startRes, endRes, true);
+              .getVisContigsIterator(startRes, endRes, true);
 
       while (regions.hasNext())
       {

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index a81d3bd..5ac0abb 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -26,6 +26,28 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 
+/**
+ * This class manages the collection of hidden columns associated with an
+ * 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
+ * 
+ * - getBoundedStartIterator: iterate over the start positions of hidden
+ * regions, within some bounds
+ * 
+ * - getVisContigsIterator: iterate over visible regions in a range, returning
+ * absolute positions
+ * 
+ * - getVisibleBlocksIterator
+ * 
+ * - getVisibleColsIterator: iterate over the visible *columns*
+ * 
+ * For performance reasons, provide bounds where possible.
+ * 
+ * @author kmourao
+ *
+ */
 public class HiddenColumns
 {
   private static final int HASH_MULTIPLIER = 31;
@@ -1466,35 +1488,14 @@ public class HiddenColumns
    * boundaries
    * 
    * @param start
-   *          first column, inclusive from 0, absolute value
+   *          first column, inclusive from 0
    * @param end
-   *          last column - not inclusive, absolute value
-   */
-  public Iterator<int[]> getVisContigsIterator(int start, int end)
-  {
-    try
-    {
-      LOCK.readLock().lock();
-      return new VisibleContigsIterator(start, end, hiddenColumns);
-    } finally
-    {
-      LOCK.readLock().unlock();
-    }
-  }
-
-  /**
-   * return an iterator over visible segments between the given start and end
-   * boundaries
-   * 
-   * @param start
-   *          (first column - inclusive from 0)
-   * @param end
-   *          (last column - inclusive)
+   *          last column - not inclusive
    * @param useVisibleCoords
    *          if true, start and end are visible column positions, not absolute
-   *          positions
+   *          positions*
    */
-  public Iterator<int[]> getVisibleBlocksIterator(int start, int end,
+  public Iterator<int[]> getVisContigsIterator(int start, int end,
           boolean useVisibleCoords)
   {
     int adjstart = start;
@@ -1508,9 +1509,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-
-      return new VisibleContigsIterator(adjstart, adjend + 1,
-              hiddenColumns);
+      return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 0e93da9..7e77bec 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -463,7 +463,8 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end));
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
   }
 
   /**

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 10c60c1..5c5fbbe 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
-              .getVisibleBlocksIterator(startRes, endRes, true);
+              .getVisContigsIterator(startRes, endRes, true);
 
       while (regions.hasNext())
       {
@@ -1365,7 +1365,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleContigsIterator regions = (VisibleContigsIterator) hidden
-              .getVisibleBlocksIterator(startRes, endRes, true);
+              .getVisContigsIterator(startRes, endRes, true);
       while (regions.hasNext())
       {
         int[] region = regions.next();

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index ac72e93..973cfe8 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1076,7 +1076,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     Iterator<int[]> intervals = hidden
                             .getVisContigsIterator(seqsel.getStartRes(),
-                                    seqsel.getEndRes() + 1);
+                                    seqsel.getEndRes() + 1, false);
                     while (intervals.hasNext())
                     {
                       int[] region = intervals.next();

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 1ed846a..6a31b31 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -136,7 +136,8 @@ public class DnaTest
             FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     assertNotNull("Couldn't do a full width translation of test data.",
@@ -166,7 +167,7 @@ public class DnaTest
       }
       cs.hideColumns(ipos + vwidth, alf.getWidth());
       Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
-              alf.getWidth());
+              alf.getWidth(), false);
       AlignViewportI av = new AlignViewport(alf, cs);
       Dna dna = new Dna(av, vcontigs);
       AlignmentI transAlf = dna.translateCdna();
@@ -193,7 +194,8 @@ public class DnaTest
             DataSourceType.PASTE, FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     String aa = translated.getSequenceAt(0).getSequenceAsString();
@@ -217,7 +219,8 @@ public class DnaTest
     cs.hideColumns(24, 35); // hide codons 9-12
     cs.hideColumns(177, 191); // hide codons 60-64
     AlignViewportI av = new AlignViewport(alf, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     String aa = translated.getSequenceAt(0).getSequenceAsString();
@@ -303,7 +306,8 @@ public class DnaTest
             .generate(12, 8, 97, 5, 5);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(cdna, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
 
@@ -319,7 +323,7 @@ public class DnaTest
     }
     AlignmentI cdnaReordered = new Alignment(sorted);
     av = new AlignViewport(cdnaReordered, cs);
-    contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+    contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
     dna = new Dna(av, contigs);
     AlignmentI translated2 = dna.translateCdna();
 
@@ -551,7 +555,8 @@ public class DnaTest
 
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(al, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+            false);
     Dna testee = new Dna(av, contigs);
     AlignmentI reversed = testee.reverseCdna(false);
     assertEquals(1, reversed.getHeight());

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 57d716d..e66367b 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -119,7 +119,7 @@ public class HiddenColumnsTest
   {
     HiddenColumns cs = new HiddenColumns();
 
-    Iterator<int[]> visible = cs.getVisContigsIterator(3, 10);
+    Iterator<int[]> visible = cs.getVisContigsIterator(3, 10, false);
     int[] region = visible.next();
     assertEquals("[3, 9]", Arrays.toString(region));
     assertFalse(visible.hasNext());
@@ -131,7 +131,7 @@ public class HiddenColumnsTest
     // Test both ends visible region
 
     // start position is inclusive, end position exclusive
-    visible = cs.getVisContigsIterator(1, 13);
+    visible = cs.getVisContigsIterator(1, 13, false);
     region = visible.next();
     assertEquals("[1, 2]", Arrays.toString(region));
     region = visible.next();
@@ -141,7 +141,7 @@ public class HiddenColumnsTest
     assertFalse(visible.hasNext());
 
     // Test start hidden, end visible
-    visible = cs.getVisContigsIterator(4, 14);
+    visible = cs.getVisContigsIterator(4, 14, false);
     region = visible.next();
     assertEquals("[7, 7]", Arrays.toString(region));
     region = visible.next();
@@ -151,13 +151,13 @@ public class HiddenColumnsTest
     assertFalse(visible.hasNext());
 
     // Test start hidden, end hidden
-    visible = cs.getVisContigsIterator(3, 10);
+    visible = cs.getVisContigsIterator(3, 10, false);
     region = visible.next();
     assertEquals("[7, 7]", Arrays.toString(region));
     assertFalse(visible.hasNext());
 
     // Test start visible, end hidden
-    visible = cs.getVisContigsIterator(0, 13);
+    visible = cs.getVisContigsIterator(0, 13, false);
     region = visible.next();
     assertEquals("[0, 2]", Arrays.toString(region));
     region = visible.next();
@@ -167,7 +167,7 @@ public class HiddenColumnsTest
     assertFalse(visible.hasNext());
 
     // Test empty result
-    visible = cs.getVisContigsIterator(4, 6);
+    visible = cs.getVisContigsIterator(4, 6, false);
     assertFalse(visible.hasNext());
   }
 
@@ -796,7 +796,7 @@ public class HiddenColumnsTest
             false);
 
     // confirm that original contigs are as expected
-    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25);
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
     int[] region = visible.next();
     assertEquals("[0, 14]", Arrays.toString(region));
     region = visible.next();
@@ -807,7 +807,7 @@ public class HiddenColumnsTest
             view);
 
     // confirm that the contigs have changed to account for the gaps
-    visible = result.getVisContigsIterator(0, 25);
+    visible = result.getVisContigsIterator(0, 25, false);
     region = visible.next();
     assertEquals("[0, 10]", Arrays.toString(region));
     region = visible.next();
@@ -854,7 +854,7 @@ public class HiddenColumnsTest
             false);
 
     // confirm that original contigs are as expected
-    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20);
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
     int[] region = visible.next();
     assertEquals("[0, 6]", Arrays.toString(region));
     region = visible.next();
@@ -866,7 +866,7 @@ public class HiddenColumnsTest
             view);
 
     // confirm that the contigs have changed to account for the gaps
-    visible = result.getVisContigsIterator(0, 20);
+    visible = result.getVisContigsIterator(0, 20, false);
     region = visible.next();
     assertEquals("[0, 4]", Arrays.toString(region));
     region = visible.next();
@@ -1322,7 +1322,7 @@ public class HiddenColumnsTest
   public void testVisibleBlocksVisBoundsIterator()
   {
     HiddenColumns h = new HiddenColumns();
-    Iterator<int[]> regions = h.getVisibleBlocksIterator(0, 30, true);
+    Iterator<int[]> regions = h.getVisContigsIterator(0, 30, 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.getVisibleBlocksIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 30, 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.getVisibleBlocksIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 30, 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.getVisibleBlocksIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 30, 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.getVisibleBlocksIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 30, 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.getVisibleBlocksIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 30, 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.getVisibleBlocksIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 30, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();
@@ -1426,7 +1426,7 @@ public class HiddenColumnsTest
     h.hideColumns(9, 11);
     h.hideColumns(22, 26);
 
-    regions = h.getVisibleBlocksIterator(0, 30, true);
+    regions = h.getVisContigsIterator(0, 30, true);
 
     assertTrue(regions.hasNext());
     region = regions.next();