+/*
+ * 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.analysis;
import static org.testng.AssertJUnit.assertEquals;
/*
* Set up 6 sequences and 7 annotations.
*/
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
al = buildAlignment(NUM_SEQS);
* sequence ref</li>
* </ul>
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSortBySequenceAndType_autocalcLast()
{
// @formatter:off
/**
* Variant with autocalculated annotations sorting to front
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSortBySequenceAndType_autocalcFirst()
{
// @formatter:off
* sequence ref</li>
* </ul>
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSortByTypeAndSequence_autocalcLast()
{
// @formatter:off
/**
* Variant of test with autocalculated annotations sorted to front
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSortByTypeAndSequence_autocalcFirst()
{
// @formatter:off
* Variant of test with autocalculated annotations sorted to front but
* otherwise no change.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testNoSort_autocalcFirst()
{
// @formatter:off
assertEquals("Structure", anns[6].label);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSort_timingPresorted()
{
testTiming_presorted(50, 100);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
System.out.println("Timing test for presorted " + numSeqs
- + " sequences and "
- + numAnns + " annotations took " + elapsed + "ms");
+ + " sequences and " + numAnns + " annotations took " + elapsed
+ + "ms");
}
/**
* Timing tests for sorting randomly sorted annotations for various sizes.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSort_timingUnsorted()
{
testTiming_unsorted(50, 100);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
System.out.println("Timing test for unsorted " + numSeqs
- + " sequences and "
- + numAnns + " annotations took " + elapsed + "ms");
+ + " sequences and " + numAnns + " annotations took " + elapsed
+ + "ms");
}
/**
* Timing test for sorting annotations with a limited range of types (labels).
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSort_timingSemisorted()
{
testTiming_semiSorted(50, 100);
Alignment alignment = buildAlignment(numSeqs);
AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
- String[] labels = new String[]
- { "label1", "label2", "label3", "label4", "label5", "label6" };
+ String[] labels = new String[] { "label1", "label2", "label3",
+ "label4", "label5", "label6" };
/*
* Set the annotations in sequence order with randomly assigned labels.
long endTime = System.currentTimeMillis();
long elapsed = endTime - startTime;
System.out.println("Sort by label for semisorted " + numSeqs
- + " sequences and "
- + numAnns + " annotations took " + elapsed + "ms");
+ + " sequences and " + numAnns + " annotations took " + elapsed
+ + "ms");
// now resort by sequence
startTime = System.currentTimeMillis();