X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=2affde077b5119f404783a20c212df0c59c5fc5d;hb=8337a127bde90beb39c52fb971d0facf6f5b2362;hp=60ca11fc849cfb8c86ad23a6be15ec44af1d5110;hpb=2f9239370a29feee067cf3b992fb4acd859bb728;p=jalview.git diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index 60ca11f..2affde0 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -27,6 +27,14 @@ 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; @@ -39,7 +47,7 @@ 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; @@ -49,20 +57,56 @@ 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() + 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() + { + if (Desktop.instance != null) + 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); @@ -73,13 +117,14 @@ public class AlignFrameTest { 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)); + 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()); @@ -113,18 +158,19 @@ public class AlignFrameTest 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); + 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(); + HiddenColumns hidden = alignFrame.getViewport().getAlignment() + .getHiddenColumns(); assertEquals(hidden.getNumberOfRegions(), 1); Iterator regions = hidden.iterator(); int[] next = regions.next(); @@ -138,8 +184,8 @@ public class AlignFrameTest */ alignFrame.getViewport().showAllHiddenColumns(); assertTrue(alignFrame.hideFeatureColumns("Turn", true)); - regions = alignFrame.getViewport().getAlignment() - .getHiddenColumns().iterator(); + regions = alignFrame.getViewport().getAlignment().getHiddenColumns() + .iterator(); assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() .getNumberOfRegions(), 2); next = regions.next(); @@ -150,58 +196,13 @@ public class AlignFrameTest 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 * @@ -227,8 +228,8 @@ public class AlignFrameTest af.conservationMenuItem_actionPerformed(true); SliderPanel sp = SliderPanel.getSliderPanel(); assertEquals(sp.getTitle(), MessageManager.formatMessage( - "label.conservation_colour_increment", - new String[] { "Background" })); + "label.conservation_colour_increment", new String[] + { "Background" })); assertTrue(sp.isForConservation()); sp.valueChanged(20); assertTrue(av.getResidueShading().conservationApplied()); @@ -241,8 +242,8 @@ public class AlignFrameTest sp = SliderPanel.getSliderPanel(); assertFalse(sp.isForConservation()); assertEquals(sp.getTitle(), MessageManager.formatMessage( - "label.percentage_identity_threshold", - new String[] { "Background" })); + "label.percentage_identity_threshold", new String[] + { "Background" })); sp.valueChanged(10); assertEquals(av.getResidueShading().getThreshold(), 10); assertTrue(av.getResidueShading().conservationApplied()); @@ -260,10 +261,13 @@ 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.changeColour_actionPerformed(JalviewColourScheme.Strand - .toString()); + PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), + null); + popupMenu.changeColour_actionPerformed( + JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); assertEquals(al.getGroups().size(), 1); assertSame(al.getGroups().get(0), sg); @@ -271,8 +275,8 @@ public class AlignFrameTest sp = SliderPanel.getSliderPanel(); assertTrue(sp.isForConservation()); assertEquals(sp.getTitle(), MessageManager.formatMessage( - "label.conservation_colour_increment", - new String[] { sg.getName() })); + "label.conservation_colour_increment", new String[] + { sg.getName() })); sp.valueChanged(30); assertTrue(sg.getGroupColourScheme().conservationApplied()); assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); @@ -284,8 +288,8 @@ public class AlignFrameTest sp = SliderPanel.getSliderPanel(); assertFalse(sp.isForConservation()); assertEquals(sp.getTitle(), MessageManager.formatMessage( - "label.percentage_identity_threshold", - new String[] { sg.getName() })); + "label.percentage_identity_threshold", new String[] + { sg.getName() })); sp.valueChanged(40); assertEquals(sg.getGroupColourScheme().getThreshold(), 40); // conservation threshold is unchanged: @@ -354,7 +358,7 @@ 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"); @@ -373,10 +377,14 @@ 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); @@ -539,9 +547,10 @@ public class AlignFrameTest sg.setStartRes(15); sg.setEndRes(25); av.setSelectionGroup(sg); - PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); - popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand - .toString()); + PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0), + null); + popupMenu.changeColour_actionPerformed( + JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); assertEquals(al.getGroups().size(), 1); assertSame(al.getGroups().get(0), sg); @@ -565,8 +574,8 @@ public class AlignFrameTest sp = SliderPanel.getSliderPanel(); assertTrue(sp.isForConservation()); assertEquals(sp.getTitle(), MessageManager.formatMessage( - "label.conservation_colour_increment", - new String[] { "Background" })); + "label.conservation_colour_increment", new String[] + { "Background" })); /* * make a new View, verify alignment and group colour schemes @@ -595,8 +604,8 @@ public class AlignFrameTest sp = SliderPanel.getSliderPanel(); assertTrue(sp.isForConservation()); assertEquals(sp.getTitle(), MessageManager.formatMessage( - "label.conservation_colour_increment", - new String[] { "View 1" })); + "label.conservation_colour_increment", new String[] + { "View 1" })); sp.valueChanged(22); assertEquals(av2.getResidueShading().getConservationInc(), 22); }