/* * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; import jalview.api.FeatureColourI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; 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.project.Jalview2xmlTests; import jalview.renderer.ResidueShaderI; import jalview.schemes.BuriedColourScheme; import jalview.schemes.FeatureColour; 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.Iterator; 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; @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"); 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)); AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), al.getHeight()); /* * make all features visible (select feature columns checks visibility) */ alignFrame.getFeatureRenderer().findAllFeatures(true); /* * hiding a feature not present does nothing */ assertFalse(alignFrame.hideFeatureColumns("exon", true)); assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() .getNumberOfRegions(), 0); assertFalse(alignFrame.hideFeatureColumns("exon", false)); 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)); 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 */ FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f); fc.setAboveThreshold(true); fc.setThreshold(5f); alignFrame.getFeatureRenderer().setColour("Metal", fc); assertTrue(alignFrame.hideFeatureColumns("Metal", true)); HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns(); assertEquals(hidden.getNumberOfRegions(), 1); Iterator regions = hidden.iterator(); int[] next = regions.next(); assertEquals(next[0], 5); assertEquals(next[1], 9); /* * hide a feature present in some columns * sequence positions [2-4], [7-9] are column positions * [1-3], [6-8] base zero */ alignFrame.getViewport().showAllHiddenColumns(); assertTrue(alignFrame.hideFeatureColumns("Turn", true)); 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 { /* * 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 * */ @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 *
    *
  1. no PID or Conservation threshold
  2. *
  3. colour by Conservation applied
  4. *
  5. colour by Conservation removed
  6. *
  7. colour above PID - various values
  8. *
  9. colour above PID removed
  10. *
  11. Above PID plus By Conservation combined
  12. *
  13. remove Above PID to leave just By Conservation
  14. *
  15. re-add Above PID
  16. *
  17. remove By Conservation to leave just Above PID
  18. *
  19. remove Above PID to leave original colours
  20. *
*/ @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); } /** * 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"); } }