X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FVisibleRowsIteratorTest.java;fp=test%2Fjalview%2Fdatamodel%2FVisibleRowsIteratorTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=4a021c5623f5b7586fad03b80c7638134ade8ae9;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/datamodel/VisibleRowsIteratorTest.java b/test/jalview/datamodel/VisibleRowsIteratorTest.java
deleted file mode 100644
index 4a021c5..0000000
--- a/test/jalview/datamodel/VisibleRowsIteratorTest.java
+++ /dev/null
@@ -1,233 +0,0 @@
-/*
- * 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);
-  }
-}