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package jalview.gui; |
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import static org.junit.Assert.assertNotEquals; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.Assert.assertFalse; |
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import static org.testng.Assert.assertNotSame; |
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import static org.testng.Assert.assertSame; |
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import static org.testng.Assert.assertTrue; |
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import java.awt.Color; |
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import java.util.Iterator; |
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import org.testng.annotations.AfterMethod; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.BeforeMethod; |
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import org.testng.annotations.Test; |
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import jalview.api.FeatureColourI; |
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import jalview.bin.Cache; |
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import jalview.bin.Jalview; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import jalview.project.Jalview2xmlTests; |
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import jalview.renderer.ResidueShaderI; |
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import jalview.schemes.BuriedColourScheme; |
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import jalview.schemes.FeatureColour; |
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import jalview.schemes.HelixColourScheme; |
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import jalview.schemes.JalviewColourScheme; |
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import jalview.schemes.StrandColourScheme; |
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import jalview.schemes.TurnColourScheme; |
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import jalview.util.MessageManager; |
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| 99.7% |
Uncovered Elements: 1 (292) |
Complexity: 11 |
Complexity Density: 0.04 |
|
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public class AlignFrameTest |
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{ |
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AlignFrame af; |
63 |
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|
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
64 |
1 |
@BeforeClass(alwaysRun = true)... |
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public static void setUpBeforeClass() throws Exception |
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{ |
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setUpJvOptionPane(); |
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69 |
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70 |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
72 |
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Jalview.main(new String[] { "-nonews" }); |
73 |
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} |
74 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
75 |
5 |
@AfterMethod(alwaysRun = true)... |
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public void tearDown() |
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{ |
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Desktop.instance.closeAll_actionPerformed(null); |
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} |
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81 |
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| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
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5 |
@BeforeMethod(alwaysRun = true)... |
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public void setUp() |
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{ |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
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Cache.applicationProperties.setProperty("SHOW_IDENTITY", |
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Boolean.TRUE.toString()); |
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af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa", |
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DataSourceType.FILE); |
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do |
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{ |
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try |
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{ |
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Thread.sleep(50); |
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} catch (InterruptedException x) |
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{ |
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} |
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} while (af.getViewport().getCalcManager().isWorking()); |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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1 |
public static 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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} |
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| 100% |
Uncovered Elements: 0 (39) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
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@Test(groups = "Functional")... |
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public void testHideFeatureColumns() |
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{ |
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SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ"); |
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SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ"); |
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seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null)); |
120 |
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seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f, |
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null)); |
122 |
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seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4, |
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Float.NaN, null)); |
124 |
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seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9, |
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Float.NaN, null)); |
126 |
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AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); |
127 |
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AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), |
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al.getHeight()); |
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alignFrame.getFeatureRenderer().findAllFeatures(true); |
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assertFalse(alignFrame.hideFeatureColumns("exon", true)); |
139 |
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assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); |
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141 |
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assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() |
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.getNumberOfRegions(), 0); |
143 |
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assertFalse(alignFrame.hideFeatureColumns("exon", false)); |
145 |
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assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); |
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assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() |
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.getNumberOfRegions(), 0); |
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150 |
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assertFalse(alignFrame.hideFeatureColumns("Metal", true)); |
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assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty()); |
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assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() |
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.getNumberOfRegions(), 0); |
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FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null, |
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0f, 10f); |
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fc.setAboveThreshold(true); |
168 |
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fc.setThreshold(5f); |
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alignFrame.getFeatureRenderer().setColour("Metal", fc); |
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assertTrue(alignFrame.hideFeatureColumns("Metal", true)); |
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1 |
HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns(); |
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assertEquals(hidden.getNumberOfRegions(), 1); |
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Iterator<int[]> regions = hidden.iterator(); |
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1 |
int[] next = regions.next(); |
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assertEquals(next[0], 5); |
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assertEquals(next[1], 9); |
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178 |
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179 |
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180 |
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181 |
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alignFrame.getViewport().showAllHiddenColumns(); |
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assertTrue(alignFrame.hideFeatureColumns("Turn", true)); |
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regions = alignFrame.getViewport().getAlignment() |
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.getHiddenColumns().iterator(); |
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assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns() |
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.getNumberOfRegions(), 2); |
189 |
1 |
next = regions.next(); |
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assertEquals(next[0], 1); |
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1 |
assertEquals(next[1], 3); |
192 |
1 |
next = regions.next(); |
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assertEquals(next[0], 6); |
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assertEquals(next[1], 8); |
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} |
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| 100% |
Uncovered Elements: 0 (66) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
207 |
1 |
@Test(groups = "Functional")... |
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public void testChangeColour_background_groupsAndThresholds() |
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{ |
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AlignViewport av = af.getViewport(); |
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AlignmentI al = av.getAlignment(); |
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af.applyToAllGroups_actionPerformed(false); |
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af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); |
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assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); |
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assertFalse(av.getResidueShading().conservationApplied()); |
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assertEquals(av.getResidueShading().getThreshold(), 0); |
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224 |
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af.conservationMenuItem_actionPerformed(true); |
226 |
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SliderPanel sp = SliderPanel.getSliderPanel(); |
227 |
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assertEquals(sp.getTitle(), MessageManager.formatMessage( |
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"label.conservation_colour_increment", |
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new String[] { "Background" })); |
230 |
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assertTrue(sp.isForConservation()); |
231 |
1 |
sp.valueChanged(20); |
232 |
1 |
assertTrue(av.getResidueShading().conservationApplied()); |
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1 |
assertEquals(av.getResidueShading().getConservationInc(), 20); |
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237 |
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238 |
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af.abovePIDThreshold_actionPerformed(true); |
239 |
1 |
sp = SliderPanel.getSliderPanel(); |
240 |
1 |
assertFalse(sp.isForConservation()); |
241 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
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"label.percentage_identity_threshold", |
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new String[] { "Background" })); |
244 |
1 |
sp.valueChanged(10); |
245 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 10); |
246 |
1 |
assertTrue(av.getResidueShading().conservationApplied()); |
247 |
1 |
assertEquals(av.getResidueShading().getConservationInc(), 20); |
248 |
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249 |
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250 |
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251 |
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252 |
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253 |
1 |
SequenceGroup sg = new SequenceGroup(); |
254 |
1 |
sg.addSequence(al.getSequenceAt(0), false); |
255 |
1 |
sg.setStartRes(15); |
256 |
1 |
sg.setEndRes(25); |
257 |
1 |
av.setSelectionGroup(sg); |
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259 |
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260 |
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261 |
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262 |
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263 |
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264 |
1 |
PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), |
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null); |
266 |
1 |
popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand |
267 |
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.toString()); |
268 |
1 |
assertTrue(sg.getColourScheme() instanceof StrandColourScheme); |
269 |
1 |
assertEquals(al.getGroups().size(), 1); |
270 |
1 |
assertSame(al.getGroups().get(0), sg); |
271 |
1 |
popupMenu.conservationMenuItem_actionPerformed(true); |
272 |
1 |
sp = SliderPanel.getSliderPanel(); |
273 |
1 |
assertTrue(sp.isForConservation()); |
274 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
275 |
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"label.conservation_colour_increment", |
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new String[] { sg.getName() })); |
277 |
1 |
sp.valueChanged(30); |
278 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
279 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
280 |
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281 |
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282 |
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283 |
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284 |
1 |
popupMenu.abovePIDColour_actionPerformed(true); |
285 |
1 |
sp = SliderPanel.getSliderPanel(); |
286 |
1 |
assertFalse(sp.isForConservation()); |
287 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
288 |
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"label.percentage_identity_threshold", |
289 |
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new String[] { sg.getName() })); |
290 |
1 |
sp.valueChanged(40); |
291 |
1 |
assertEquals(sg.getGroupColourScheme().getThreshold(), 40); |
292 |
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|
293 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
294 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
295 |
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296 |
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297 |
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298 |
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299 |
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300 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString()); |
301 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme); |
302 |
1 |
assertTrue(av.getResidueShading().conservationApplied()); |
303 |
1 |
assertEquals(av.getResidueShading().getConservationInc(), 20); |
304 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 10); |
305 |
1 |
assertTrue(sg.getColourScheme() instanceof StrandColourScheme); |
306 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
307 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
308 |
1 |
assertEquals(sg.getGroupColourScheme().getThreshold(), 40); |
309 |
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310 |
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311 |
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312 |
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313 |
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314 |
1 |
af.applyToAllGroups_actionPerformed(true); |
315 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); |
316 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); |
317 |
1 |
assertTrue(av.getResidueShading().conservationApplied()); |
318 |
1 |
assertEquals(av.getResidueShading().getConservationInc(), 20); |
319 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 10); |
320 |
1 |
assertTrue(sg.getColourScheme() instanceof HelixColourScheme); |
321 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
322 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
323 |
1 |
assertEquals(sg.getGroupColourScheme().getThreshold(), 40); |
324 |
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} |
325 |
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326 |
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327 |
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328 |
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329 |
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330 |
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331 |
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333 |
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334 |
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336 |
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337 |
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338 |
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339 |
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340 |
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| 100% |
Uncovered Elements: 0 (95) |
Complexity: 1 |
Complexity Density: 0.01 |
1PASS
|
|
341 |
1 |
@Test(groups = "Functional")... |
342 |
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public void testColourThresholdActions() |
343 |
|
{ |
344 |
1 |
AlignViewport av = af.getViewport(); |
345 |
1 |
AlignmentI al = av.getAlignment(); |
346 |
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|
347 |
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348 |
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349 |
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|
350 |
1 |
af.applyToAllGroups_actionPerformed(false); |
351 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); |
352 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); |
353 |
1 |
assertFalse(av.getResidueShading().conservationApplied()); |
354 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 0); |
355 |
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356 |
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357 |
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358 |
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359 |
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|
360 |
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|
361 |
1 |
SequenceI ferCapan = al.findName("FER_CAPAN"); |
362 |
1 |
ResidueShaderI rs = av.getResidueShading(); |
363 |
1 |
Color c = rs.findColour('I', 14, ferCapan); |
364 |
1 |
Color i_original = new Color(138, 117, 138); |
365 |
1 |
assertEquals(c, i_original); |
366 |
1 |
c = rs.findColour('S', 15, ferCapan); |
367 |
1 |
Color s_original = new Color(54, 201, 54); |
368 |
1 |
assertEquals(c, s_original); |
369 |
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|
370 |
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371 |
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372 |
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|
373 |
1 |
af.conservationMenuItem_actionPerformed(true); |
374 |
1 |
SliderPanel sp = SliderPanel.getSliderPanel(); |
375 |
1 |
assertTrue(sp.isForConservation()); |
376 |
1 |
assertEquals(sp.getValue(), 30); |
377 |
1 |
c = rs.findColour('I', 14, ferCapan); |
378 |
1 |
Color i_faded = new Color(255, 255, 255); |
379 |
1 |
assertEquals(c, i_faded); |
380 |
1 |
sp.valueChanged(10); |
381 |
1 |
assertSame(rs, av.getResidueShading()); |
382 |
1 |
assertEquals(rs.getConservationInc(), 10); |
383 |
1 |
c = rs.findColour('I', 14, ferCapan); |
384 |
1 |
i_faded = new Color(196, 186, 196); |
385 |
1 |
assertEquals(c, i_faded); |
386 |
1 |
c = rs.findColour('S', 15, ferCapan); |
387 |
1 |
Color s_faded = new Color(144, 225, 144); |
388 |
1 |
assertEquals(c, s_faded); |
389 |
|
|
390 |
|
|
391 |
|
|
392 |
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|
393 |
1 |
af.conservationMenuItem_actionPerformed(false); |
394 |
1 |
c = rs.findColour('S', 15, ferCapan); |
395 |
1 |
assertEquals(c, s_original); |
396 |
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|
397 |
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398 |
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|
399 |
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|
400 |
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|
401 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
402 |
1 |
sp = SliderPanel.getSliderPanel(); |
403 |
1 |
assertFalse(sp.isForConservation()); |
404 |
1 |
assertEquals(sp.getValue(), 0); |
405 |
1 |
c = rs.findColour('I', 14, ferCapan); |
406 |
1 |
assertEquals(c, i_original); |
407 |
1 |
c = rs.findColour('S', 15, ferCapan); |
408 |
1 |
assertEquals(c, s_original); |
409 |
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|
410 |
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411 |
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412 |
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413 |
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|
414 |
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|
415 |
1 |
sp.valueChanged(1); |
416 |
1 |
c = rs.findColour('I', 14, ferCapan); |
417 |
1 |
assertEquals(c, Color.white); |
418 |
1 |
c = rs.findColour('S', 15, ferCapan); |
419 |
1 |
assertEquals(c, s_original); |
420 |
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421 |
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422 |
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423 |
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|
424 |
1 |
sp.valueChanged(66); |
425 |
1 |
c = rs.findColour('I', 14, ferCapan); |
426 |
1 |
assertEquals(c, Color.white); |
427 |
1 |
c = rs.findColour('S', 15, ferCapan); |
428 |
1 |
assertEquals(c, s_original); |
429 |
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|
430 |
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|
431 |
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|
432 |
|
|
433 |
1 |
sp.valueChanged(67); |
434 |
1 |
c = rs.findColour('I', 14, ferCapan); |
435 |
1 |
assertEquals(c, Color.white); |
436 |
1 |
c = rs.findColour('S', 15, ferCapan); |
437 |
1 |
assertEquals(c, Color.white); |
438 |
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|
439 |
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|
440 |
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|
441 |
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|
442 |
1 |
af.abovePIDThreshold_actionPerformed(false); |
443 |
1 |
c = rs.findColour('I', 14, ferCapan); |
444 |
1 |
assertEquals(c, i_original); |
445 |
1 |
c = rs.findColour('S', 15, ferCapan); |
446 |
1 |
assertEquals(c, s_original); |
447 |
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|
448 |
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449 |
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450 |
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451 |
|
|
452 |
|
|
453 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
454 |
1 |
sp = SliderPanel.getSliderPanel(); |
455 |
1 |
assertFalse(sp.isForConservation()); |
456 |
1 |
sp.valueChanged(50); |
457 |
1 |
af.conservationMenuItem_actionPerformed(true); |
458 |
1 |
sp = SliderPanel.getSliderPanel(); |
459 |
1 |
assertTrue(sp.isForConservation()); |
460 |
1 |
sp.valueChanged(10); |
461 |
1 |
c = rs.findColour('I', 14, ferCapan); |
462 |
1 |
assertEquals(c, Color.white); |
463 |
1 |
c = rs.findColour('S', 15, ferCapan); |
464 |
1 |
assertEquals(c, s_faded); |
465 |
|
|
466 |
|
|
467 |
|
|
468 |
|
|
469 |
1 |
af.abovePIDThreshold_actionPerformed(false); |
470 |
1 |
c = rs.findColour('I', 14, ferCapan); |
471 |
1 |
assertEquals(c, i_faded); |
472 |
1 |
c = rs.findColour('S', 15, ferCapan); |
473 |
1 |
assertEquals(c, s_faded); |
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
|
|
479 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
480 |
1 |
SliderPanel.getSliderPanel().valueChanged(50); |
481 |
1 |
c = rs.findColour('I', 14, ferCapan); |
482 |
1 |
assertEquals(c, Color.white); |
483 |
1 |
c = rs.findColour('S', 15, ferCapan); |
484 |
1 |
assertEquals(c, s_faded); |
485 |
|
|
486 |
|
|
487 |
|
|
488 |
|
|
489 |
|
|
490 |
1 |
af.conservationMenuItem_actionPerformed(false); |
491 |
1 |
c = rs.findColour('I', 14, ferCapan); |
492 |
1 |
assertEquals(c, Color.white); |
493 |
1 |
c = rs.findColour('S', 15, ferCapan); |
494 |
1 |
assertEquals(c, s_original); |
495 |
|
|
496 |
|
|
497 |
|
|
498 |
|
|
499 |
1 |
af.abovePIDThreshold_actionPerformed(false); |
500 |
1 |
c = rs.findColour('I', 14, ferCapan); |
501 |
1 |
assertEquals(c, i_original); |
502 |
1 |
c = rs.findColour('S', 15, ferCapan); |
503 |
1 |
assertEquals(c, s_original); |
504 |
|
} |
505 |
|
|
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
@see |
513 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (63) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
514 |
1 |
@Test(groups = "Functional")... |
515 |
|
public void testNewView_colourThresholds() |
516 |
|
{ |
517 |
1 |
AlignViewport av = af.getViewport(); |
518 |
1 |
AlignmentI al = av.getAlignment(); |
519 |
|
|
520 |
|
|
521 |
|
|
522 |
|
|
523 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); |
524 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); |
525 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
526 |
1 |
SliderPanel sp = SliderPanel.getSliderPanel(); |
527 |
1 |
assertFalse(sp.isForConservation()); |
528 |
1 |
sp.valueChanged(10); |
529 |
1 |
af.conservationMenuItem_actionPerformed(true); |
530 |
1 |
sp = SliderPanel.getSliderPanel(); |
531 |
1 |
assertTrue(sp.isForConservation()); |
532 |
1 |
sp.valueChanged(20); |
533 |
1 |
ResidueShaderI rs = av.getResidueShading(); |
534 |
1 |
assertEquals(rs.getThreshold(), 10); |
535 |
1 |
assertTrue(rs.conservationApplied()); |
536 |
1 |
assertEquals(rs.getConservationInc(), 20); |
537 |
|
|
538 |
|
|
539 |
|
|
540 |
|
|
541 |
|
|
542 |
1 |
SequenceGroup sg = new SequenceGroup(); |
543 |
1 |
sg.addSequence(al.getSequenceAt(0), false); |
544 |
1 |
sg.setStartRes(15); |
545 |
1 |
sg.setEndRes(25); |
546 |
1 |
av.setSelectionGroup(sg); |
547 |
1 |
PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0), |
548 |
|
null); |
549 |
1 |
popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand |
550 |
|
.toString()); |
551 |
1 |
assertTrue(sg.getColourScheme() instanceof StrandColourScheme); |
552 |
1 |
assertEquals(al.getGroups().size(), 1); |
553 |
1 |
assertSame(al.getGroups().get(0), sg); |
554 |
1 |
popupMenu.conservationMenuItem_actionPerformed(true); |
555 |
1 |
sp = SliderPanel.getSliderPanel(); |
556 |
1 |
assertTrue(sp.isForConservation()); |
557 |
1 |
sp.valueChanged(30); |
558 |
1 |
popupMenu.abovePIDColour_actionPerformed(true); |
559 |
1 |
sp = SliderPanel.getSliderPanel(); |
560 |
1 |
assertFalse(sp.isForConservation()); |
561 |
1 |
sp.valueChanged(40); |
562 |
1 |
rs = sg.getGroupColourScheme(); |
563 |
1 |
assertTrue(rs.conservationApplied()); |
564 |
1 |
assertEquals(rs.getConservationInc(), 30); |
565 |
1 |
assertEquals(rs.getThreshold(), 40); |
566 |
|
|
567 |
|
|
568 |
|
|
569 |
|
|
570 |
1 |
af.conservationMenuItem_actionPerformed(true); |
571 |
1 |
sp = SliderPanel.getSliderPanel(); |
572 |
1 |
assertTrue(sp.isForConservation()); |
573 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
574 |
|
"label.conservation_colour_increment", |
575 |
|
new String[] { "Background" })); |
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
1 |
af.newView_actionPerformed(null); |
581 |
1 |
assertEquals(af.alignPanel.getViewName(), "View 1"); |
582 |
1 |
AlignViewport av2 = af.getViewport(); |
583 |
1 |
assertNotSame(av, av2); |
584 |
1 |
assertSame(av2, af.alignPanel.av); |
585 |
1 |
rs = av2.getResidueShading(); |
586 |
1 |
assertNotSame(av.getResidueShading(), rs); |
587 |
1 |
assertEquals(rs.getThreshold(), 10); |
588 |
1 |
assertTrue(rs.conservationApplied(), rs.toString()); |
589 |
1 |
assertEquals(rs.getConservationInc(), 20); |
590 |
1 |
assertEquals(av2.getAlignment().getGroups().size(), 1); |
591 |
1 |
sg = av2.getAlignment().getGroups().get(0); |
592 |
1 |
rs = sg.getGroupColourScheme(); |
593 |
1 |
assertTrue(rs.conservationApplied()); |
594 |
1 |
assertEquals(rs.getConservationInc(), 30); |
595 |
1 |
assertEquals(rs.getThreshold(), 40); |
596 |
|
|
597 |
|
|
598 |
|
|
599 |
|
|
600 |
|
|
601 |
1 |
sp = SliderPanel.getSliderPanel(); |
602 |
1 |
assertTrue(sp.isForConservation()); |
603 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
604 |
|
"label.conservation_colour_increment", |
605 |
|
new String[] { "View 1" })); |
606 |
1 |
sp.valueChanged(22); |
607 |
1 |
assertEquals(av2.getResidueShading().getConservationInc(), 22); |
608 |
|
} |
609 |
|
|
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
|
615 |
|
|
616 |
|
@see |
617 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
|
|
618 |
1 |
@Test(groups = "Functional")... |
619 |
|
public void testNewView_dsRefPreserved() |
620 |
|
{ |
621 |
1 |
AlignViewport av = af.getViewport(); |
622 |
1 |
AlignmentI al = av.getAlignment(); |
623 |
1 |
AlignmentI original_ds = al.getDataset(); |
624 |
1 |
af.newView_actionPerformed(null); |
625 |
1 |
assertNotEquals("New view didn't select the a new panel", av, |
626 |
|
af.getViewport()); |
627 |
1 |
org.testng.Assert.assertEquals(original_ds, |
628 |
|
af.getViewport().getAlignment().getDataset(), |
629 |
|
"Dataset was not preserved in new view"); |
630 |
|
} |
631 |
|
} |