X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=d362d35c1d5a2ee1bcb58f3f6db121fcaa2ae28e;hb=bf5bc203579d7a291844f3b34d5e8431984ee8e2;hp=fed5992fec0b6c0a0571656c1120bd57e3caef4b;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index fed5992..d362d35 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -20,45 +20,92 @@ */ 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 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; + +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.io.Jalview2xmlTests; +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.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; @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 + */ + do + { + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { + } + } while (af.getViewport().getCalcManager().isWorking()); + } + + public static void setUpJvOptionPane() { JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); @@ -69,100 +116,82 @@ 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 alignFrame = 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(alignFrame.hideFeatureColumns("exon", true)); assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); - assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns() - .getHiddenRegions() - .isEmpty()); + + assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() + .getNumberOfRegions(), 0); + assertFalse(alignFrame.hideFeatureColumns("exon", false)); assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); - assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns() - .getHiddenRegions() - .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()); - List hidden = alignFrame.getViewport().getAlignment() - .getHiddenColumns() - .getHiddenRegions(); - assertTrue(hidden.isEmpty()); - /* - * hide a feature present in some columns - * sequence positions [2-4], [7-9] are column positions - * [1-3], [6-8] base zero - */ - assertTrue(alignFrame.hideFeatureColumns("Turn", true)); - hidden = alignFrame.getViewport().getAlignment().getHiddenColumns() - .getHiddenRegions(); - 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); - } + assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() + .getNumberOfRegions(), 0); + - @BeforeClass(alwaysRun = true) - public static void setUpBeforeClass() throws Exception - { /* - * use read-only test properties file + * threshold Metal to hide features where score < 5 + * seq1 feature in columns 1-5 is hidden + * seq2 feature in columns 6-10 is shown */ - 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); + 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); /* - * wait for Consensus thread to complete + * hide a feature present in some columns + * sequence positions [2-4], [7-9] are column positions + * [1-3], [6-8] base zero */ - synchronized (this) - { - while (af.getViewport().getConsensusSeq() == null) - { - try - { - wait(50); - } catch (InterruptedException e) - { - } - } - } + 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); } /** @@ -229,8 +258,11 @@ public class AlignFrameTest /* * apply 30% Conservation to group + * (notice menu action applies to selection group even if mouse click + * is at a sequence not in the group) */ - PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); + PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), + null); popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand .toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); @@ -323,7 +355,7 @@ public class AlignFrameTest /* * inspect the colour of - * FER_CAPAN.9(I), column 14 (14 base 0) + * FER_CAPAN.9(I), column 15 (14 base 0) * FER_CAPAN.10(SER), column 16 (15 base 0) */ SequenceI ferCapan = al.findName("FER_CAPAN"); @@ -342,10 +374,14 @@ public class AlignFrameTest SliderPanel sp = SliderPanel.getSliderPanel(); assertTrue(sp.isForConservation()); assertEquals(sp.getValue(), 30); // initial slider setting + c = rs.findColour('I', 14, ferCapan); + Color i_faded = new Color(255, 255, 255); + assertEquals(c, i_faded); sp.valueChanged(10); assertSame(rs, av.getResidueShading()); + assertEquals(rs.getConservationInc(), 10); c = rs.findColour('I', 14, ferCapan); - Color i_faded = new Color(196, 186, 196); + 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); @@ -508,7 +544,8 @@ public class AlignFrameTest sg.setStartRes(15); sg.setEndRes(25); av.setSelectionGroup(sg); - PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); + PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0), + null); popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand .toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); @@ -544,10 +581,11 @@ public class AlignFrameTest 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()); + assertTrue(rs.conservationApplied(), rs.toString()); assertEquals(rs.getConservationInc(), 20); assertEquals(av2.getAlignment().getGroups().size(), 1); sg = av2.getAlignment().getGroups().get(0); @@ -568,4 +606,26 @@ public class AlignFrameTest 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"); + } }