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package jalview.renderer; |
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import static org.testng.AssertJUnit.assertEquals; |
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import jalview.bin.Cache; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignViewport; |
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import jalview.gui.JvOptionPane; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.UserColourScheme; |
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import jalview.schemes.ZappoColourScheme; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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| 46.7% |
Uncovered Elements: 56 (105) |
Complexity: 7 |
Complexity Density: 0.07 |
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public class OverviewResColourFinderTest |
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{ |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
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} |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testGetResidueBoxColour_none() |
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{ |
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SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF"); |
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AlignmentI al = new Alignment(new SequenceI[] { seq }); |
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final AlignViewport av = new AlignViewport(al); |
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ResidueColourFinder rcf = new OverviewResColourFinder(); |
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assertEquals(Color.white, rcf.getResidueColour(true, |
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av.getResidueShading(), |
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null, seq, 0, null)); |
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assertEquals(Color.lightGray, rcf |
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.getResidueColour(true, av.getResidueShading(), null, seq, 2, |
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null)); |
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assertEquals(Color.white, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 0, null)); |
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assertEquals(Color.lightGray, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 2, null)); |
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} |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testGetResidueBoxColour_zappo() |
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{ |
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SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); |
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AlignmentI al = new Alignment(new SequenceI[] { seq }); |
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final AlignViewport av = new AlignViewport(al); |
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ResidueColourFinder rcf = new OverviewResColourFinder(); |
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av.setGlobalColourScheme(new ZappoColourScheme()); |
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assertEquals(Color.pink, |
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rcf.getResidueColour(true, av.getResidueShading(), |
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null, seq, 0, null)); |
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assertEquals(Color.green, |
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rcf.getResidueColour(true, av.getResidueShading(), |
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null, seq, 2, null)); |
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assertEquals(Color.magenta, |
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rcf.getResidueColour(true, av.getResidueShading(), |
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null, seq, 5, null)); |
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assertEquals(Color.orange, |
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rcf.getResidueColour(true, av.getResidueShading(), |
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null, seq, 12, null)); |
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assertEquals(Color.lightGray, rcf |
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.getResidueColour(true, av.getResidueShading(), null, seq, 3, |
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null)); |
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assertEquals(Color.pink, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 0, null)); |
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assertEquals(Color.green, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 2, null)); |
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assertEquals(Color.magenta, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 5, null)); |
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assertEquals(Color.orange, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 12, null)); |
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assertEquals(Color.lightGray, rcf |
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.getResidueColour(false, av.getResidueShading(), null, seq, 3, |
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null)); |
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} |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 2 |
Complexity Density: 0.12 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testGetResidueBoxColour_userdef() |
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{ |
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SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); |
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AlignmentI al = new Alignment(new SequenceI[] { seq }); |
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final AlignViewport av = new AlignViewport(al); |
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ResidueColourFinder rcf = new OverviewResColourFinder(); |
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Color[] newColours = new Color[24]; |
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for (int i = 0; i < 24; i++) |
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{ |
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newColours[i] = null; |
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} |
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av.setGlobalColourScheme(new UserColourScheme(newColours)); |
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assertEquals(Color.lightGray, rcf |
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.getResidueColour(true, av.getResidueShading(), null, seq, 3, |
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null)); |
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newColours[23] = Color.pink; |
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av.setGlobalColourScheme(new UserColourScheme(newColours)); |
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assertEquals(Color.pink, rcf.getResidueColour(true, |
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av.getResidueShading(), |
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null, seq, 3, null)); |
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newColours[23] = null; |
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assertEquals(Color.lightGray, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 3, null)); |
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newColours[23] = Color.pink; |
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av.setGlobalColourScheme(new UserColourScheme(newColours)); |
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assertEquals(Color.pink, rcf.getResidueColour(false, |
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av.getResidueShading(), null, seq, 3, null)); |
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} |
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| 0% |
Uncovered Elements: 22 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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@Test... |
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public void testGetResidueBoxColour_group() |
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{ |
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SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF"); |
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AlignmentI al = new Alignment(new SequenceI[] { seq }); |
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ColourSchemeI cs = new ZappoColourScheme(); |
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ArrayList<SequenceI> seqlist = new ArrayList<>(); |
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seqlist.add(seq); |
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SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true, |
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true, true, 5, 9); |
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al.addGroup(sg); |
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SequenceGroup[] groups = new SequenceGroup[1]; |
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groups[0] = sg; |
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final AlignViewport av = new AlignViewport(al); |
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ResidueColourFinder rcf = new OverviewResColourFinder(); |
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assertEquals(Color.magenta, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 7, null)); |
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assertEquals(Color.white, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 0, null)); |
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assertEquals(Color.lightGray, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 2, null)); |
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rcf = new OverviewResColourFinder(true, Color.blue, Color.red); |
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assertEquals(Color.magenta, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 7, null)); |
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assertEquals(Color.lightGray, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 0, null)); |
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assertEquals(Color.white, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 2, null)); |
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rcf = new OverviewResColourFinder(false, Color.blue, Color.red); |
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assertEquals(Color.magenta, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 7, null)); |
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assertEquals(Color.white, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 0, null)); |
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assertEquals(Color.blue, rcf.getResidueColour(false, |
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av.getResidueShading(), groups, seq, 2, null)); |
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} |
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| 0% |
Uncovered Elements: 32 (32) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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@Test... |
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public void testGetBoxColour() |
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{ |
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SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); |
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AlignmentI al = new Alignment(new SequenceI[] { seq }); |
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final AlignViewport av = new AlignViewport(al); |
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ResidueColourFinder rcf = new OverviewResColourFinder(); |
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ResidueShaderI shader = new ResidueShader(); |
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Color c = rcf.getBoxColour(shader, seq, 0); |
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assertEquals(Color.white, c); |
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c = rcf.getBoxColour(shader, seq, 3); |
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assertEquals( |
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jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, |
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c); |
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rcf = new OverviewResColourFinder(true, Color.blue, Color.red); |
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shader = new ResidueShader(); |
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c = rcf.getBoxColour(shader, seq, 0); |
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assertEquals(Color.lightGray, c); |
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c = rcf.getBoxColour(shader, seq, 3); |
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assertEquals(Color.white, c); |
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rcf = new OverviewResColourFinder(); |
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shader = new ResidueShader(); |
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c = rcf.getBoxColour(shader, seq, 0); |
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assertEquals(Color.white, c); |
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c = rcf.getBoxColour(shader, seq, 3); |
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assertEquals( |
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jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, |
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c); |
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rcf = new OverviewResColourFinder(false, Color.blue, Color.red); |
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shader = new ResidueShader(new ZappoColourScheme()); |
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c = rcf.getBoxColour(shader, seq, 0); |
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assertEquals(Color.pink, c); |
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c = rcf.getBoxColour(shader, seq, 3); |
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assertEquals(Color.blue, c); |
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rcf = new OverviewResColourFinder(true, Color.blue, Color.red); |
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c = rcf.getBoxColour(shader, seq, 0); |
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assertEquals(Color.pink, c); |
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c = rcf.getBoxColour(shader, seq, 3); |
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assertEquals(Color.white, c); |
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} |
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} |