+/*
+ * 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.gui;
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotSame;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.io.Jalview2xmlTests;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.util.MessageManager;
+import java.awt.Color;
import java.util.List;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AlignFrameTest
{
+ AlignFrame af;
- @Test
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = "Functional")
public void testHideFeatureColumns()
{
SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
Float.NaN, null));
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
- AlignFrame af = new AlignFrame(al, al.getWidth(), al.getHeight());
+ AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), al.getHeight());
/*
* hiding a feature not present does nothing
*/
- assertFalse(af.hideFeatureColumns("exon", true));
- assertTrue(af.getViewport().getColumnSelection().isEmpty());
- assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+ assertFalse(alignFrame.hideFeatureColumns("exon", true));
+ assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+ assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy()
.isEmpty());
- assertFalse(af.hideFeatureColumns("exon", false));
- assertTrue(af.getViewport().getColumnSelection().isEmpty());
- assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+ assertFalse(alignFrame.hideFeatureColumns("exon", false));
+ assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+ assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy()
.isEmpty());
/*
* hiding a feature in all columns does nothing
*/
- assertFalse(af.hideFeatureColumns("Metal", true));
- assertTrue(af.getViewport().getColumnSelection().isEmpty());
- List<int[]> hidden = af.getViewport().getColumnSelection()
- .getHiddenColumns();
+ assertFalse(alignFrame.hideFeatureColumns("Metal", true));
+ assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+ List<int[]> hidden = alignFrame.getViewport().getAlignment()
+ .getHiddenColumns()
+ .getHiddenColumnsCopy();
assertTrue(hidden.isEmpty());
/*
* sequence positions [2-4], [7-9] are column positions
* [1-3], [6-8] base zero
*/
- assertTrue(af.hideFeatureColumns("Turn", true));
- hidden = af.getViewport().getColumnSelection().getHiddenColumns();
- assertEquals(2, hidden.size());
- assertEquals(1, hidden.get(0)[0]);
- assertEquals(3, hidden.get(0)[1]);
- assertEquals(6, hidden.get(1)[0]);
- assertEquals(8, hidden.get(1)[1]);
+ assertTrue(alignFrame.hideFeatureColumns("Turn", true));
+ hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
+ assertEquals(hidden.size(), 2);
+ assertEquals(hidden.get(0)[0], 1);
+ assertEquals(hidden.get(0)[1], 3);
+ assertEquals(hidden.get(1)[0], 6);
+ assertEquals(hidden.get(1)[1], 8);
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ /*
+ * 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)
+ {
+ }
+ }
+ }
+ }
+
+ /**
+ * Test that changing background (alignment) colour scheme
+ * <ul>
+ * <li>with Apply Colour to All Groups not selected, does not change group
+ * colours</li>
+ * <li>with Apply Colour to All Groups selected, does change group colours</li>
+ * <li>in neither case, changes alignment or group colour thresholds (PID or
+ * Conservation)</li>
+ * </ul>
+ */
+ @Test(groups = "Functional")
+ public void testChangeColour_background_groupsAndThresholds()
+ {
+ AlignViewport av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+
+ /*
+ * Colour alignment by Buried Index
+ */
+ af.applyToAllGroups_actionPerformed(false);
+ af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
+ assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
+ assertFalse(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getThreshold(), 0);
+
+ /*
+ * Apply Conservation 20%
+ */
+ af.conservationMenuItem_actionPerformed(true);
+ SliderPanel sp = SliderPanel.getSliderPanel();
+ assertEquals(sp.getTitle(), MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { "Background" }));
+ assertTrue(sp.isForConservation());
+ sp.valueChanged(20);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
+
+ /*
+ * Apply PID threshold 10% (conservation still applies as well)
+ */
+ af.abovePIDThreshold_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ assertEquals(sp.getTitle(), MessageManager.formatMessage(
+ "label.percentage_identity_threshold",
+ new String[] { "Background" }));
+ sp.valueChanged(10);
+ assertEquals(av.getResidueShading().getThreshold(), 10);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
+
+ /*
+ * create a group with Strand colouring, 30% Conservation
+ * and 40% PID threshold
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(al.getSequenceAt(0), false);
+ sg.setStartRes(15);
+ sg.setEndRes(25);
+ av.setSelectionGroup(sg);
+
+ /*
+ * apply 30% Conservation to group
+ */
+ PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+ popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
+ .toString());
+ assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
+ assertEquals(al.getGroups().size(), 1);
+ assertSame(al.getGroups().get(0), sg);
+ popupMenu.conservationMenuItem_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ assertEquals(sp.getTitle(), MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { sg.getName() }));
+ sp.valueChanged(30);
+ assertTrue(sg.getGroupColourScheme().conservationApplied());
+ assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
+
+ /*
+ * apply 40% PID threshold to group
+ */
+ popupMenu.abovePIDColour_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ assertEquals(sp.getTitle(), MessageManager.formatMessage(
+ "label.percentage_identity_threshold",
+ new String[] { sg.getName() }));
+ sp.valueChanged(40);
+ assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
+ // conservation threshold is unchanged:
+ assertTrue(sg.getGroupColourScheme().conservationApplied());
+ assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
+
+ /*
+ * change alignment colour - group colour, and all thresholds,
+ * should be unaffected
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
+ assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
+ assertEquals(av.getResidueShading().getThreshold(), 10);
+ assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
+ assertTrue(sg.getGroupColourScheme().conservationApplied());
+ assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
+ assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
+
+ /*
+ * Now change alignment colour with Apply Colour To All Groups
+ * - group colour should change, but not colour thresholds
+ */
+ af.applyToAllGroups_actionPerformed(true);
+ af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
+ assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
+ assertEquals(av.getResidueShading().getThreshold(), 10);
+ assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
+ assertTrue(sg.getGroupColourScheme().conservationApplied());
+ assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
+ assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
+ }
+
+ /**
+ * Test residue colouring with various options
+ * <ol>
+ * <li>no PID or Conservation threshold</li>
+ * <li>colour by Conservation applied</li>
+ * <li>colour by Conservation removed</li>
+ * <li>colour above PID - various values</li>
+ * <li>colour above PID removed</li>
+ * <li>Above PID plus By Conservation combined</li>
+ * <li>remove Above PID to leave just By Conservation</li>
+ * <li>re-add Above PID</li>
+ * <li>remove By Conservation to leave just Above PID</li>
+ * <li>remove Above PID to leave original colours</li>
+ * </ol>
+ */
+ @Test(groups = "Functional")
+ public void testColourThresholdActions()
+ {
+ AlignViewport av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+
+ /*
+ * Colour alignment by Helix Propensity, no thresholds
+ */
+ af.applyToAllGroups_actionPerformed(false);
+ af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
+ assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
+ assertFalse(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getThreshold(), 0);
+
+ /*
+ * inspect the colour of
+ * FER_CAPAN.9(I), column 14 (14 base 0)
+ * FER_CAPAN.10(SER), column 16 (15 base 0)
+ */
+ SequenceI ferCapan = al.findName("FER_CAPAN");
+ ResidueShaderI rs = av.getResidueShading();
+ Color c = rs.findColour('I', 14, ferCapan);
+ Color i_original = new Color(138, 117, 138);
+ assertEquals(c, i_original);
+ c = rs.findColour('S', 15, ferCapan);
+ Color s_original = new Color(54, 201, 54);
+ assertEquals(c, s_original);
+
+ /*
+ * colour by conservation with increment 10
+ */
+ af.conservationMenuItem_actionPerformed(true);
+ SliderPanel sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ assertEquals(sp.getValue(), 30); // initial slider setting
+ sp.valueChanged(10);
+ assertSame(rs, av.getResidueShading());
+ c = rs.findColour('I', 14, ferCapan);
+ Color i_faded = new Color(196, 186, 196);
+ assertEquals(c, i_faded);
+ c = rs.findColour('S', 15, ferCapan);
+ Color s_faded = new Color(144, 225, 144);
+ assertEquals(c, s_faded);
+
+ /*
+ * deselect By Conservation - colour should revert
+ */
+ af.conservationMenuItem_actionPerformed(false);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_original);
+
+ /*
+ * now Above PID, threshold = 0%
+ * should be no change
+ */
+ af.abovePIDThreshold_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ assertEquals(sp.getValue(), 0); // initial slider setting
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, i_original);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_original);
+
+ /*
+ * Above PID, threshold = 1%
+ * 15.I becomes White because no match to consensus (V)
+ * 16.S remains coloured as matches 66.66% consensus
+ */
+ sp.valueChanged(1);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, Color.white);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_original);
+
+ /*
+ * threshold 66% - no further change yet...
+ */
+ sp.valueChanged(66);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, Color.white);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_original);
+
+ /*
+ * threshold 67% - now both residues are white
+ */
+ sp.valueChanged(67);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, Color.white);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, Color.white);
+
+ /*
+ * deselect Above PID - colours should revert
+ */
+ af.abovePIDThreshold_actionPerformed(false);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, i_original);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_original);
+
+ /*
+ * Now combine Above 50% PID and By Conservation 10%
+ * 15.I is White because no match to consensus (V)
+ * 16.S is coloured but faded
+ */
+ af.abovePIDThreshold_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ sp.valueChanged(50);
+ af.conservationMenuItem_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ sp.valueChanged(10);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, Color.white);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_faded);
+
+ /*
+ * turn off Above PID - should just leave Conservation fading as before
+ */
+ af.abovePIDThreshold_actionPerformed(false);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, i_faded);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_faded);
+
+ /*
+ * Now add Above 50% PID to conservation colouring
+ * - should give the same as PID followed by conservation (above)
+ */
+ af.abovePIDThreshold_actionPerformed(true);
+ SliderPanel.getSliderPanel().valueChanged(50);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, Color.white);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_faded);
+
+ /*
+ * turn off By Conservation
+ * should leave I white, S original (unfaded) colour
+ */
+ af.conservationMenuItem_actionPerformed(false);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, Color.white);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_original);
+
+ /*
+ * finally turn off Above PID to leave original colours
+ */
+ af.abovePIDThreshold_actionPerformed(false);
+ c = rs.findColour('I', 14, ferCapan);
+ assertEquals(c, i_original);
+ c = rs.findColour('S', 15, ferCapan);
+ assertEquals(c, s_original);
+ }
+
+ /**
+ * Verify that making a New View transfers alignment and group colour schemes,
+ * including any thresholds, to the new view. Because New View is performed by
+ * saving and reloading a 'project' file, this is similar to verifying a
+ * project save and reload.
+ *
+ * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
+ */
+ @Test(groups = "Functional")
+ public void testNewView_colourThresholds()
+ {
+ AlignViewport av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+
+ /*
+ * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
+ assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
+ af.abovePIDThreshold_actionPerformed(true);
+ SliderPanel sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ sp.valueChanged(10);
+ af.conservationMenuItem_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ sp.valueChanged(20);
+ ResidueShaderI rs = av.getResidueShading();
+ assertEquals(rs.getThreshold(), 10);
+ assertTrue(rs.conservationApplied());
+ assertEquals(rs.getConservationInc(), 20);
+
+ /*
+ * create a group with Strand colouring, 30% Conservation
+ * and 40% PID threshold
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(al.getSequenceAt(0), false);
+ sg.setStartRes(15);
+ sg.setEndRes(25);
+ av.setSelectionGroup(sg);
+ PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+ popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
+ .toString());
+ assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
+ assertEquals(al.getGroups().size(), 1);
+ assertSame(al.getGroups().get(0), sg);
+ popupMenu.conservationMenuItem_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ sp.valueChanged(30);
+ popupMenu.abovePIDColour_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ sp.valueChanged(40);
+ rs = sg.getGroupColourScheme();
+ assertTrue(rs.conservationApplied());
+ assertEquals(rs.getConservationInc(), 30);
+ assertEquals(rs.getThreshold(), 40);
+
+ /*
+ * set slider panel focus to the background alignment
+ */
+ af.conservationMenuItem_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ assertEquals(sp.getTitle(), MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { "Background" }));
+
+ /*
+ * make a new View, verify alignment and group colour schemes
+ */
+ af.newView_actionPerformed(null);
+ assertEquals(af.alignPanel.getViewName(), "View 1");
+ AlignViewport av2 = af.getViewport();
+ assertNotSame(av, av2);
+ assertSame(av2, af.alignPanel.av);
+ rs = av2.getResidueShading();
+ assertNotSame(av.getResidueShading(), rs);
+ assertEquals(rs.getThreshold(), 10);
+ assertTrue(rs.conservationApplied(), rs.toString());
+ assertEquals(rs.getConservationInc(), 20);
+ assertEquals(av2.getAlignment().getGroups().size(), 1);
+ sg = av2.getAlignment().getGroups().get(0);
+ rs = sg.getGroupColourScheme();
+ assertTrue(rs.conservationApplied());
+ assertEquals(rs.getConservationInc(), 30);
+ assertEquals(rs.getThreshold(), 40);
+
+ /*
+ * check the Conservation SliderPanel (still open) is linked to
+ * and updates the new view (JAL-2385)
+ */
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ assertEquals(sp.getTitle(), MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { "View 1" }));
+ sp.valueChanged(22);
+ assertEquals(av2.getResidueShading().getConservationInc(), 22);
}
}
git://source.jalview.org / jalview.git / blobdiff