JAL-2759 Changes to StartRegionIterator after review

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 509bd73..a9cd4d7 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1062,7 +1062,7 @@ public class HiddenColumns
       HiddenCursorPosition pos = cursor
               .findRegionForColumn(absoluteStart - 1, false);
 
-      return new BoundedStartRegionIterator(pos, start, end,
+      return new StartRegionIterator(pos, start, end,
               hiddenColumns);
     } finally
     {

diff --git a/src/jalview/datamodel/BoundedStartRegionIterator.java b/src/jalview/datamodel/StartRegionIterator.java
similarity index 71%
rename from src/jalview/datamodel/BoundedStartRegionIterator.java
rename to src/jalview/datamodel/StartRegionIterator.java
index d68eeeb..bd036e4 100644 (file)
--- a/src/jalview/datamodel/BoundedStartRegionIterator.java
+++ b/src/jalview/datamodel/StartRegionIterator.java
@@ -8,7 +8,7 @@ import java.util.List;
  * An iterator which iterates over visible start positions of hidden column
  * regions in a range.
  */
-public class BoundedStartRegionIterator implements Iterator<Integer>
+public class StartRegionIterator implements Iterator<Integer>
 {
   // start position to iterate from
   private int start;
@@ -33,43 +33,10 @@ public class BoundedStartRegionIterator implements Iterator<Integer>
    *          whether to make a local copy of hiddenColumns for iteration (set
    *          to true if calling from outwith the HiddenColumns class)
    */
-  BoundedStartRegionIterator(int lowerBound, int upperBound,
+  StartRegionIterator(int lowerBound, int upperBound,
           List<int[]> hiddenColumns)
   {
-    start = lowerBound;
-    end = upperBound;
-
-    if (hiddenColumns != null)
-    {
-      positions = new ArrayList<>(hiddenColumns.size());
-
-      // navigate to start, keeping count of hidden columns
-      int i = 0;
-      int hiddenSoFar = 0;
-      while ((i < hiddenColumns.size())
-              && (hiddenColumns.get(i)[0] < start + hiddenSoFar))
-      {
-        int[] region = hiddenColumns.get(i);
-        hiddenSoFar += region[1] - region[0] + 1;
-        i++;
-      }
-
-      // iterate from start to end, adding start positions of each
-      // hidden region. Positions are visible columns count, not absolute
-      while (i < hiddenColumns.size()
-              && (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
-      {
-        int[] region = hiddenColumns.get(i);
-        positions.add(region[0] - hiddenSoFar);
-        hiddenSoFar += region[1] - region[0] + 1;
-        i++;
-      }
-    }
-    else
-    {
-      positions = new ArrayList<>();
-    }
-
+    this(null, lowerBound, upperBound, hiddenColumns);
   }
 
   /**
@@ -84,7 +51,7 @@ public class BoundedStartRegionIterator implements Iterator<Integer>
    * @param hiddenColumns
    *          the hidden columns collection to use
    */
-  BoundedStartRegionIterator(HiddenCursorPosition pos, int lowerBound,
+  StartRegionIterator(HiddenCursorPosition pos, int lowerBound,
           int upperBound, List<int[]> hiddenColumns)
   {
     start = lowerBound;

diff --git a/test/jalview/datamodel/BoundedStartRegionIteratorTest.java b/test/jalview/datamodel/StartRegionIteratorTest.java
similarity index 79%
rename from test/jalview/datamodel/BoundedStartRegionIteratorTest.java
rename to test/jalview/datamodel/StartRegionIteratorTest.java
index 77b4fd2..23d0b00 100644 (file)
--- a/test/jalview/datamodel/BoundedStartRegionIteratorTest.java
+++ b/test/jalview/datamodel/StartRegionIteratorTest.java
@@ -30,7 +30,7 @@ import java.util.List;
 
 import org.testng.annotations.Test;
 
-public class BoundedStartRegionIteratorTest
+public class StartRegionIteratorTest
 {
   /**
    * Test the start region iterator
@@ -41,39 +41,39 @@ public class BoundedStartRegionIteratorTest
     List<int[]> hiddenColumns = null;
 
     // null hidden columns
-    Iterator<Integer> it = new BoundedStartRegionIterator(3, 10,
+    Iterator<Integer> it = new StartRegionIterator(3, 10,
             hiddenColumns);
     assertFalse(it.hasNext());
 
     hiddenColumns = new ArrayList<>();
 
     // no hidden columns
-    it = new BoundedStartRegionIterator(3, 10, hiddenColumns);
+    it = new StartRegionIterator(3, 10, hiddenColumns);
     assertFalse(it.hasNext());
 
     // add some hidden columns
     hiddenColumns.add(new int[] { 5, 10 });
     hiddenColumns.add(new int[] { 25, 40 });
 
-    it = new BoundedStartRegionIterator(3, 10, hiddenColumns);
+    it = new StartRegionIterator(3, 10, hiddenColumns);
     assertTrue(it.hasNext());
     Integer result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(3, 15, hiddenColumns);
+    it = new StartRegionIterator(3, 15, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(3, 18, hiddenColumns);
+    it = new StartRegionIterator(3, 18, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(3, 19, hiddenColumns);
+    it = new StartRegionIterator(3, 19, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
@@ -84,7 +84,7 @@ public class BoundedStartRegionIteratorTest
 
     hiddenColumns.add(new int[] { 47, 50 });
 
-    it = new BoundedStartRegionIterator(15, 60, hiddenColumns);
+    it = new StartRegionIterator(15, 60, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(19, (int) result);
@@ -104,39 +104,39 @@ public class BoundedStartRegionIteratorTest
     HiddenCursorPosition pos = null;
 
     // null hidden columns
-    Iterator<Integer> it = new BoundedStartRegionIterator(pos, 3, 10,
+    Iterator<Integer> it = new StartRegionIterator(pos, 3, 10,
             hiddenColumns);
     assertFalse(it.hasNext());
 
     hiddenColumns = new ArrayList<>();
 
     // no hidden columns
-    it = new BoundedStartRegionIterator(pos, 3, 10, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 10, hiddenColumns);
     assertFalse(it.hasNext());
 
     // add some hidden columns
     hiddenColumns.add(new int[] { 5, 10 });
     hiddenColumns.add(new int[] { 25, 40 });
 
-    it = new BoundedStartRegionIterator(pos, 3, 10, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 10, hiddenColumns);
     assertTrue(it.hasNext());
     Integer result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(pos, 3, 15, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 15, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(pos, 3, 18, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 18, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(pos, 3, 19, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 19, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
@@ -147,7 +147,7 @@ public class BoundedStartRegionIteratorTest
 
     hiddenColumns.add(new int[] { 47, 50 });
 
-    it = new BoundedStartRegionIterator(pos, 15, 60, hiddenColumns);
+    it = new StartRegionIterator(pos, 15, 60, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(19, (int) result);
@@ -171,26 +171,26 @@ public class BoundedStartRegionIteratorTest
 
     HiddenCursorPosition pos = new HiddenCursorPosition(0, 0);
 
-    Iterator<Integer> it = new BoundedStartRegionIterator(pos, 3, 10,
+    Iterator<Integer> it = new StartRegionIterator(pos, 3, 10,
             hiddenColumns);
     assertTrue(it.hasNext());
     Integer result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(pos, 3, 15, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 15, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(pos, 3, 18, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 18, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
     assertFalse(it.hasNext());
 
-    it = new BoundedStartRegionIterator(pos, 3, 19, hiddenColumns);
+    it = new StartRegionIterator(pos, 3, 19, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(5, (int) result);
@@ -202,7 +202,7 @@ public class BoundedStartRegionIteratorTest
     pos = new HiddenCursorPosition(1, 6);
     hiddenColumns.add(new int[] { 47, 50 });
 
-    it = new BoundedStartRegionIterator(pos, 15, 60, hiddenColumns);
+    it = new StartRegionIterator(pos, 15, 60, hiddenColumns);
     assertTrue(it.hasNext());
     result = it.next();
     assertEquals(19, (int) result);