X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=568d285c6be70abeee7861f9d089cd40149cfcbc;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=fed5992fec0b6c0a0571656c1120bd57e3caef4b;hpb=14985603cea28569e295ddabb219da8034f1c7b2;p=jalview.git diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index fed5992..568d285 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -20,25 +20,29 @@ */ 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.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; @@ -46,7 +50,7 @@ import jalview.schemes.TurnColourScheme; import jalview.util.MessageManager; import java.awt.Color; -import java.util.List; +import java.util.Iterator; import org.testng.annotations.AfterMethod; import org.testng.annotations.BeforeClass; @@ -62,6 +66,9 @@ public class AlignFrameTest { JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + + // BH 2020.03.22 solved the assertEquals(c, i_faded) problem below + Jalview.setSynchronous(true); } @Test(groups = "Functional") @@ -69,54 +76,82 @@ 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()); + + 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 */ + alignFrame.getViewport().showAllHiddenColumns(); 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); + 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) @@ -132,7 +167,7 @@ public class AlignFrameTest @AfterMethod(alwaysRun = true) public void tearDown() { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); } /** @@ -143,7 +178,7 @@ public class AlignFrameTest public void setUp() { Cache.loadProperties("test/jalview/io/testProps.jvprops"); - Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Cache.getInstance().applicationProperties.setProperty("SHOW_IDENTITY", Boolean.TRUE.toString()); af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa", DataSourceType.FILE); @@ -544,10 +579,11 @@ 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 +604,26 @@ 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"); + } }