X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=2a768ff6e5942d0f8463e8d3f9368d9e4ffb8216;hb=32a2c42a535d809dfcb48db1e8cc91bb03193f8e;hp=d2284f12593ae4b63b14ee0c15a26c6bcde552e6;hpb=e086b0c30bee5fe084186c65ef1ded42c58560f9;p=jalview.git diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index d2284f1..2a768ff 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; @@ -49,14 +57,6 @@ 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; @@ -79,8 +79,8 @@ public class AlignFrameTest } /** - * configure (read-only) properties for test to ensure Consensus is computed for - * colour Above PID testing + * configure (read-only) properties for test to ensure Consensus is computed + * for colour Above PID testing */ @BeforeMethod(alwaysRun = true) public void setUp() @@ -94,18 +94,15 @@ public class AlignFrameTest /* * wait for Consensus thread to complete */ - synchronized (this) + do { - while (af.getViewport().getConsensusSeq() == null) + try + { + Thread.sleep(50); + } catch (InterruptedException x) { - try - { - wait(50); - } catch (InterruptedException e) - { - } } - } + } while (af.getViewport().getCalcManager().isWorking()); } public static void setUpJvOptionPane() @@ -119,13 +116,14 @@ 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()); @@ -159,7 +157,6 @@ 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 @@ -171,7 +168,8 @@ public class AlignFrameTest 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(); @@ -185,8 +183,8 @@ 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(); @@ -202,7 +200,8 @@ public class AlignFrameTest * @@ -228,8 +227,8 @@ 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()); @@ -242,8 +241,8 @@ 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()); @@ -266,8 +265,8 @@ public class AlignFrameTest */ PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), null); - popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand - .toString()); + popupMenu.changeColour_actionPerformed( + JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); assertEquals(al.getGroups().size(), 1); assertSame(al.getGroups().get(0), sg); @@ -275,8 +274,8 @@ 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); @@ -288,8 +287,8 @@ 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: @@ -358,7 +357,7 @@ 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"); @@ -377,10 +376,14 @@ 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); @@ -545,8 +548,8 @@ public class AlignFrameTest av.setSelectionGroup(sg); PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0), null); - popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand - .toString()); + popupMenu.changeColour_actionPerformed( + JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); assertEquals(al.getGroups().size(), 1); assertSame(al.getGroups().get(0), sg); @@ -570,8 +573,8 @@ 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 @@ -600,8 +603,8 @@ 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); }