X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=454ff610f3c62db8c5c53f00a8fb92d23cae0466;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=60db9dd432e04bd16055acf3f8f15b16134c151d;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index 60db9dd..454ff61 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -20,23 +20,46 @@ */ package jalview.gui; -import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertFalse; -import static org.testng.AssertJUnit.assertTrue; +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.util.List; +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() @@ -50,49 +73,554 @@ public class AlignFrameTest { SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ"); SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ"); - seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, - Float.NaN, null)); - seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, - Float.NaN, null)); + 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 af = new AlignFrame(al, al.getWidth(), al.getHeight()); + 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(af.hideFeatureColumns("exon", true)); - assertTrue(af.getViewport().getColumnSelection().isEmpty()); - assertTrue(af.getViewport().getColumnSelection().getHiddenColumns() - .isEmpty()); - assertFalse(af.hideFeatureColumns("exon", false)); - assertTrue(af.getViewport().getColumnSelection().isEmpty()); - assertTrue(af.getViewport().getColumnSelection().getHiddenColumns() - .isEmpty()); + 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(af.hideFeatureColumns("Metal", true)); - assertTrue(af.getViewport().getColumnSelection().isEmpty()); - List hidden = af.getViewport().getColumnSelection() - .getHiddenColumns(); - assertTrue(hidden.isEmpty()); + 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(null, Color.red, Color.blue, null, + 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 */ - 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]); + 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. + *
  2. colour by Conservation applied
    3. + *
  3. colour by Conservation removed
    4. + *
  4. colour above PID - various values
    5. + *
  5. colour above PID removed
    6. + *
  6. Above PID plus By Conservation combined
    7. + *
  7. remove Above PID to leave just By Conservation
    8. + *
  8. re-add Above PID
    9. + *
  9. remove By Conservation to leave just Above PID
    10. + *
  10. remove Above PID to leave original colours
    11. + *
+ */ + @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"); } }