*/
package jalview.gui;
+import static org.junit.Assert.assertNotEquals;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotSame;
AlignFrame af;
@BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
+ public static void setUpBeforeClass() throws Exception
+ {
+ setUpJvOptionPane();
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /**
+ * configure (read-only) properties for test to ensure Consensus is computed for
+ * colour Above PID testing
+ */
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.TRUE.toString());
+ af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+ DataSourceType.FILE);
+
+ /*
+ * wait for Consensus thread to complete
+ */
+ synchronized (this)
+ {
+ while (af.getViewport().getConsensusSeq() == null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ }
+
+ public static void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
@Test(groups = "Functional")
public void testHideFeatureColumns()
{
- SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
- SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
- seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
- null));
- seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
- Float.NaN, null));
- seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
- Float.NaN, null));
+ SequenceI seq1 = new Sequence("Seq1/01-10", "A---BCDEFG-HIJ");
+ SequenceI seq2 = new Sequence("Seq2/11-20", "-AB-CDEF--GHIJ");
+ String METAL = "Metal";
+ String TURN = "Turn";
+ seq1.addSequenceFeature(
+ new SequenceFeature(METAL, "", 1, 5, 0f, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature(METAL, "", 16, 20, 10f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature(TURN, "", 2, 4, Float.NaN, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature(TURN, "", 17, 19, Float.NaN, null));
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
al.getHeight());
/*
* hiding a feature not present does nothing
*/
- assertFalse(alignFrame.hideFeatureColumns("exon", true));
+ assertFalse(alignFrame.hideFeatureColumns(true, "exon"));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
- assertFalse(alignFrame.hideFeatureColumns("exon", false));
+ assertFalse(alignFrame.hideFeatureColumns(false, "exon"));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
/*
* hiding a feature in all columns does nothing
*/
- assertFalse(alignFrame.hideFeatureColumns("Metal", true));
+ assertFalse(alignFrame.hideFeatureColumns(true, METAL));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
/*
* threshold Metal to hide features where score < 5
- * seq1 feature in columns 1-5 is hidden
- * seq2 feature in columns 6-10 is shown
+ * seq1 feature in columns 1-8 is hidden
+ * seq2 feature in columns 8-14 is shown
+ * result: columns 8-14 are hidden
+ * note this includes gapped columns spanned by the feature
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
- alignFrame.getFeatureRenderer().setColour("Metal", fc);
- assertTrue(alignFrame.hideFeatureColumns("Metal", true));
+ alignFrame.getFeatureRenderer().setColour(METAL, fc);
+ assertTrue(alignFrame.hideFeatureColumns(true, METAL));
HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
assertEquals(hidden.getNumberOfRegions(), 1);
Iterator<int[]> regions = hidden.iterator();
- int[] next = regions.next();
- assertEquals(next[0], 5);
- assertEquals(next[1], 9);
+ assertEquals(regions.next(), new int[] { 7, 13 }); // base 0
+ assertFalse(regions.hasNext());
/*
* hide a feature present in some columns
- * sequence positions [2-4], [7-9] are column positions
- * [1-3], [6-8] base zero
+ * seq1 positions [2-4] are column positions [4-6] base zero
+ * seq2 positions [17-19] are column positions [10-12] base zero
*/
alignFrame.getViewport().showAllHiddenColumns();
- assertTrue(alignFrame.hideFeatureColumns("Turn", true));
+ assertTrue(alignFrame.hideFeatureColumns(true, TURN));
regions = alignFrame.getViewport().getAlignment()
.getHiddenColumns().iterator();
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 2);
- next = regions.next();
- assertEquals(next[0], 1);
- assertEquals(next[1], 3);
- next = regions.next();
- assertEquals(next[0], 6);
- assertEquals(next[1], 8);
- }
-
- @BeforeClass(alwaysRun = true)
- public static void setUpBeforeClass() throws Exception
- {
+ assertEquals(regions.next(), new int[] { 4, 6 });
+ assertEquals(regions.next(), new int[] { 10, 12 });
+ assertFalse(regions.hasNext());
+
/*
- * use read-only test properties file
+ * hiding a contact feature should only hide start and end positions,
+ * not the intermediate columns
*/
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Jalview.main(new String[] { "-nonews" });
- }
-
- @AfterMethod(alwaysRun = true)
- public void tearDown()
- {
- Desktop.instance.closeAll_actionPerformed(null);
- }
-
- /**
- * configure (read-only) properties for test to ensure Consensus is computed
- * for colour Above PID testing
- */
- @BeforeMethod(alwaysRun = true)
- public void setUp()
- {
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.TRUE.toString());
- af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
- DataSourceType.FILE);
+ String DISULFIDE = "Disulfide Bond";
+ seq1.addSequenceFeature(
+ new SequenceFeature(DISULFIDE, "", 1, 5, 0f, null));
+ alignFrame.getViewport().showAllHiddenColumns();
+ assertTrue(alignFrame.hideFeatureColumns(true, DISULFIDE));
+ regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 2);
+ assertEquals(regions.next(), new int[] { 0, 0 });
+ assertEquals(regions.next(), new int[] { 7, 7 });
+ assertFalse(regions.hasNext());
/*
- * wait for Consensus thread to complete
+ * hide multiple feature types:
+ * TURN columns hides 4-6, 10-12
+ * DISULFIDE columns hides 0, 7
+ * combined is { 0-0, 4-7, 10-12 }
*/
- synchronized (this)
- {
- while (af.getViewport().getConsensusSeq() == null)
- {
- try
- {
- wait(50);
- } catch (InterruptedException e)
- {
- }
- }
- }
+ alignFrame.getViewport().showAllHiddenColumns();
+ assertTrue(alignFrame.hideFeatureColumns(true, TURN, DISULFIDE));
+ regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 3);
+ assertEquals(regions.next(), new int[] { 0, 0 });
+ assertEquals(regions.next(), new int[] { 4, 7 });
+ assertEquals(regions.next(), new int[] { 10, 12 });
+ assertFalse(regions.hasNext());
}
/**
sp.valueChanged(22);
assertEquals(av2.getResidueShading().getConservationInc(), 22);
}
+
+ /**
+ * Verify that making a New View preserves the dataset reference for the
+ * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
+ * save alignments with multiple views, and codon mappings will not be shared
+ * across all panels in a split frame.
+ *
+ * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
+ */
+ @Test(groups = "Functional")
+ public void testNewView_dsRefPreserved()
+ {
+ AlignViewport av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+ AlignmentI original_ds = al.getDataset();
+ af.newView_actionPerformed(null);
+ assertNotEquals("New view didn't select the a new panel", av,
+ af.getViewport());
+ org.testng.Assert.assertEquals(original_ds,
+ af.getViewport().getAlignment().getDataset(),
+ "Dataset was not preserved in new view");
+ }
}
git://source.jalview.org / jalview.git / blobdiff