--- /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