X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=b0aaab9ec03a0651dc12b8e6e7f539e303c5817f;hb=43699f9bc6ba2f390d3652f69b6db8975ff727c0;hp=8ba165ec849279d4198c7873e2d462ae8e583b36;hpb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;p=jalview.git diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index 8ba165e..b0aaab9 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -26,10 +26,12 @@ 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; @@ -39,6 +41,7 @@ import jalview.io.FileLoader; import jalview.io.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 +49,7 @@ 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; @@ -69,50 +72,81 @@ 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().getColumnSelection().getHiddenColumns() - .isEmpty()); + + assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() + .getNumberOfRegions(), 0); + assertFalse(alignFrame.hideFeatureColumns("exon", false)); assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); - assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns() - .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().getColumnSelection() - .getHiddenColumns(); - 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(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)); - hidden = alignFrame.getViewport().getColumnSelection().getHiddenColumns(); - 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) @@ -183,8 +217,8 @@ public class AlignFrameTest af.applyToAllGroups_actionPerformed(false); af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); - assertFalse(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getThreshold(), 0); + assertFalse(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getThreshold(), 0); /* * Apply Conservation 20% @@ -196,8 +230,8 @@ public class AlignFrameTest new String[] { "Background" })); assertTrue(sp.isForConservation()); sp.valueChanged(20); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); + assertTrue(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getConservationInc(), 20); /* * Apply PID threshold 10% (conservation still applies as well) @@ -209,9 +243,9 @@ public class AlignFrameTest "label.percentage_identity_threshold", new String[] { "Background" })); sp.valueChanged(10); - assertEquals(av.getViewportColourScheme().getThreshold(), 10); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); + assertEquals(av.getResidueShading().getThreshold(), 10); + assertTrue(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getConservationInc(), 20); /* * create a group with Strand colouring, 30% Conservation @@ -263,9 +297,9 @@ public class AlignFrameTest */ af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString()); assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); - assertEquals(av.getViewportColourScheme().getThreshold(), 10); + 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); @@ -278,9 +312,9 @@ public class AlignFrameTest af.applyToAllGroups_actionPerformed(true); af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); - assertEquals(av.getViewportColourScheme().getThreshold(), 10); + 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); @@ -314,8 +348,8 @@ public class AlignFrameTest af.applyToAllGroups_actionPerformed(false); af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); - assertFalse(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getThreshold(), 0); + assertFalse(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getThreshold(), 0); /* * inspect the colour of @@ -323,7 +357,7 @@ public class AlignFrameTest * FER_CAPAN.10(SER), column 16 (15 base 0) */ SequenceI ferCapan = al.findName("FER_CAPAN"); - ResidueShaderI rs = av.getViewportColourScheme(); + ResidueShaderI rs = av.getResidueShading(); Color c = rs.findColour('I', 14, ferCapan); Color i_original = new Color(138, 117, 138); assertEquals(c, i_original); @@ -339,7 +373,7 @@ public class AlignFrameTest assertTrue(sp.isForConservation()); assertEquals(sp.getValue(), 30); // initial slider setting sp.valueChanged(10); - assertSame(rs, av.getViewportColourScheme()); + assertSame(rs, av.getResidueShading()); c = rs.findColour('I', 14, ferCapan); Color i_faded = new Color(196, 186, 196); assertEquals(c, i_faded); @@ -490,7 +524,7 @@ public class AlignFrameTest sp = SliderPanel.getSliderPanel(); assertTrue(sp.isForConservation()); sp.valueChanged(20); - ResidueShaderI rs = av.getViewportColourScheme(); + ResidueShaderI rs = av.getResidueShading(); assertEquals(rs.getThreshold(), 10); assertTrue(rs.conservationApplied()); assertEquals(rs.getConservationInc(), 20); @@ -540,10 +574,11 @@ public class AlignFrameTest assertEquals(af.alignPanel.getViewName(), "View 1"); AlignViewport av2 = af.getViewport(); assertNotSame(av, av2); - rs = av2.getViewportColourScheme(); - assertNotSame(av.getViewportColourScheme(), rs); + 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); @@ -562,6 +597,6 @@ public class AlignFrameTest "label.conservation_colour_increment", new String[] { "View 1" })); sp.valueChanged(22); - assertEquals(av2.getViewportColourScheme().getConservationInc(), 22); + assertEquals(av2.getResidueShading().getConservationInc(), 22); } }