X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FVisibleRowsIteratorTest.java;fp=test%2Fjalview%2Fdatamodel%2FVisibleRowsIteratorTest.java;h=4a021c5623f5b7586fad03b80c7638134ade8ae9;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git

diff --git a/test/jalview/datamodel/VisibleRowsIteratorTest.java b/test/jalview/datamodel/VisibleRowsIteratorTest.java
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+/*
+ * 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 static org.testng.Assert.assertTrue;
+
+import jalview.analysis.AlignmentGenerator;
+
+import java.util.Hashtable;
+import java.util.NoSuchElementException;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class VisibleRowsIteratorTest
+{
+  AlignmentI al;
+
+  AlignmentI al2;
+
+  AlignmentI al3;
+
+  Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+
+  Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences2 = new Hashtable<SequenceI, SequenceCollectionI>();
+
+  @BeforeClass(groups = { "Functional" })
+  public void setup()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    al = gen.generate(20, 15, 123, 5, 5);
+    if (!hiddenRepSequences.isEmpty())
+    {
+      al.getHiddenSequences().showAll(hiddenRepSequences);
+    }
+    hideSequences(al, hiddenRepSequences, 2, 4);
+
+    al2 = gen.generate(20, 15, 123, 5, 5);
+    if (!hiddenRepSequences2.isEmpty())
+    {
+      al2.getHiddenSequences().showAll(hiddenRepSequences2);
+    }
+    hideSequences(al2, hiddenRepSequences2, 0, 2);
+
+    al3 = gen.generate(20, 15, 123, 5, 5);
+  }
+
+  /*
+   * Test iterator iterates correctly through the rows
+   * when alignment has hidden rows
+   */
+  @Test(groups = { "Functional" })
+  public void testHasNextAndNextWithHidden()
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al);
+    int count = 0;
+    while (it.hasNext())
+    {
+      it.next();
+      count++;
+    }
+    assertTrue(count == 4, "hasNext() is false after 4 iterations");
+  }
+
+  /*
+   * Test iterator iterates correctly through the rows
+   * when alignment has no hidden rows
+   */
+  @Test(groups = { "Functional" })
+  public void testHasNextAndNextNoHidden()
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3);
+    int count = 0;
+    while (it.hasNext())
+    {
+      it.next();
+      count++;
+    }
+    assertTrue(count == 4, "hasNext() is false after 4 iterations");
+  }
+
+  /*
+   * Test iterator iterates correctly through the rows
+   * when alignment has hidden rows at start
+   */
+  @Test(groups = { "Functional" })
+  public void testHasNextAndNextStartHidden()
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al2);
+    int count = 0;
+    while (it.hasNext())
+    {
+      it.next();
+      count++;
+    }
+    assertTrue(count == 4, "hasNext() is false after 4 iterations");
+  }
+
+  /*
+   * Test iterator iterates correctly through the rows
+   * when alignment has hidden rows at end
+   */
+  @Test(groups = { "Functional" })
+  public void testHasNextAndNextEndHidden()
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al);
+    int count = 0;
+    while (it.hasNext())
+    {
+      it.next();
+      count++;
+    }
+    assertTrue(count == 2, "hasNext() is false after 2 iterations");
+  }
+
+  /*
+   * Test iterator always throws NoSuchElementException at end of iteration
+   * when alignment has hidden rows
+   */
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { NoSuchElementException.class })
+  public void testLastNextWithHidden() throws NoSuchElementException
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al);
+    while (it.hasNext())
+    {
+      it.next();
+    }
+    it.next();
+  }
+
+  /*
+   * Test iterator always throws NoSuchElementException at end of iteration
+   * when alignment has no hidden rows
+   */
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { NoSuchElementException.class })
+  public void testLastNextNoHidden() throws NoSuchElementException
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3);
+    while (it.hasNext())
+    {
+      it.next();
+    }
+    it.next();
+  }
+
+  /*
+   * Test iterator always throws NoSuchElementException at end of iteration
+   * when alignment has hidden rows at start
+   */
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { NoSuchElementException.class })
+  public void testLastNextStartHidden() throws NoSuchElementException
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al2);
+    while (it.hasNext())
+    {
+      it.next();
+    }
+    it.next();
+  }
+
+  /*
+   * Test iterator always throws NoSuchElementException at end of iteration
+   * when alignment has hidden rows at end
+   */
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { NoSuchElementException.class })
+  public void testLastNextEndHidden() throws NoSuchElementException
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al);
+    while (it.hasNext())
+    {
+      it.next();
+    }
+    it.next();
+  }
+
+  /*
+   * Test calls to remove throw UnsupportedOperationException
+   */
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { UnsupportedOperationException.class })
+  public void testRemove() throws UnsupportedOperationException
+  {
+    VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al);
+    it.remove();
+  }
+
+  /*
+   * Hide sequences between start and end
+   */
+  private void hideSequences(AlignmentI alignment,
+          Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences,
+          int start, int end)
+  {
+    SequenceI[] allseqs = alignment.getSequencesArray();
+    SequenceGroup theseSeqs = new SequenceGroup();
+
+    for (int i = start; i <= end; i++)
+    {
+      theseSeqs.addSequence(allseqs[i], false);
+      alignment.getHiddenSequences().hideSequence(allseqs[i]);
+    }
+
+    hiddenRepSequences.put(allseqs[start], theseSeqs);
+  }
+}