X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=2a768ff6e5942d0f8463e8d3f9368d9e4ffb8216;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=af9c045f993e8e20c45e18f4e1cdb814a8dbaf8b;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index af9c045..2a768ff 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -20,108 +20,51 @@ */ 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() - { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); - } - - @Test(groups = "Functional") - public void testHideFeatureColumns() - { - 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("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()); - - /* - * hiding a feature not present does nothing - */ - assertFalse(alignFrame.hideFeatureColumns("exon", true)); - assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); - assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns() - .getHiddenColumnsCopy() - .isEmpty()); - assertFalse(alignFrame.hideFeatureColumns("exon", false)); - assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); - assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns() - .getHiddenColumnsCopy() - .isEmpty()); - - /* - * hiding a feature in all columns does nothing - */ - assertFalse(alignFrame.hideFeatureColumns("Metal", true)); - assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); - List hidden = alignFrame.getViewport().getAlignment() - .getHiddenColumns() - .getHiddenColumnsCopy(); - 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() - .getHiddenColumnsCopy(); - 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); - } - - @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { + setUpJvOptionPane(); /* * use read-only test properties file */ @@ -151,18 +94,105 @@ 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() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + @Test(groups = "Functional") + public void testHideFeatureColumns() + { + 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)); + AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); + 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()); + + assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() + .getNumberOfRegions(), 0); + + assertFalse(alignFrame.hideFeatureColumns("exon", false)); + assertTrue(alignFrame.getViewport().getColumnSelection().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()); + + 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)); + 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); } /** @@ -170,7 +200,8 @@ public class AlignFrameTest * @@ -196,8 +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()); @@ -210,8 +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()); @@ -229,10 +260,13 @@ 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); @@ -240,8 +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); @@ -253,8 +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: @@ -323,7 +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"); @@ -342,10 +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); @@ -508,9 +546,10 @@ 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); @@ -534,8 +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 @@ -564,9 +603,31 @@ 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); } + + /** + * 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"); + } }