+++ /dev/null
-/*
- * 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);
- }
-}
git://source.jalview.org / jalview.git / blobdiff