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package jalview.gui; |
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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 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.io.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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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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| 98.9% |
Uncovered Elements: 3 (281) |
Complexity: 10 |
Complexity Density: 0.04 |
|
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public class AlignFrameTest |
60 |
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{ |
61 |
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AlignFrame af; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
63 |
1 |
@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
66 |
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JvOptionPane.setInteractiveMode(false); |
67 |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
68 |
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} |
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| 100% |
Uncovered Elements: 0 (39) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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70 |
1 |
@Test(groups = "Functional")... |
71 |
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public void testHideFeatureColumns() |
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{ |
73 |
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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)); |
76 |
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seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f, |
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null)); |
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seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4, |
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Float.NaN, null)); |
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seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9, |
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Float.NaN, null)); |
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AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); |
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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)); |
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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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assertFalse(alignFrame.hideFeatureColumns("exon", false)); |
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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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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(Color.red, Color.blue, 0f, 10f); |
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fc.setAboveThreshold(true); |
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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)); |
126 |
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HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns(); |
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assertEquals(hidden.getNumberOfRegions(), 1); |
128 |
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Iterator<int[]> regions = hidden.iterator(); |
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int[] next = regions.next(); |
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assertEquals(next[0], 5); |
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assertEquals(next[1], 9); |
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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); |
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next = regions.next(); |
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assertEquals(next[0], 1); |
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assertEquals(next[1], 3); |
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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 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
152 |
1 |
@BeforeClass(alwaysRun = true)... |
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public static void setUpBeforeClass() throws Exception |
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{ |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
159 |
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Jalview.main(new String[] { "-nonews" }); |
160 |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
162 |
4 |
@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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168 |
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169 |
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170 |
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171 |
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| 66.7% |
Uncovered Elements: 3 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
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4 |
@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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183 |
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184 |
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synchronized (this) |
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{ |
186 |
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while (af.getViewport().getConsensusSeq() == null) |
187 |
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{ |
188 |
0 |
try |
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{ |
190 |
0 |
wait(50); |
191 |
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} catch (InterruptedException e) |
192 |
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{ |
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} |
194 |
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} |
195 |
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} |
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} |
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206 |
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|
207 |
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| 100% |
Uncovered Elements: 0 (66) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
208 |
1 |
@Test(groups = "Functional")... |
209 |
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public void testChangeColour_background_groupsAndThresholds() |
210 |
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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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225 |
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af.conservationMenuItem_actionPerformed(true); |
227 |
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SliderPanel sp = SliderPanel.getSliderPanel(); |
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assertEquals(sp.getTitle(), MessageManager.formatMessage( |
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"label.conservation_colour_increment", |
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new String[] { "Background" })); |
231 |
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assertTrue(sp.isForConservation()); |
232 |
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sp.valueChanged(20); |
233 |
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assertTrue(av.getResidueShading().conservationApplied()); |
234 |
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assertEquals(av.getResidueShading().getConservationInc(), 20); |
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236 |
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237 |
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238 |
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239 |
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af.abovePIDThreshold_actionPerformed(true); |
240 |
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sp = SliderPanel.getSliderPanel(); |
241 |
1 |
assertFalse(sp.isForConservation()); |
242 |
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assertEquals(sp.getTitle(), MessageManager.formatMessage( |
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"label.percentage_identity_threshold", |
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new String[] { "Background" })); |
245 |
1 |
sp.valueChanged(10); |
246 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 10); |
247 |
1 |
assertTrue(av.getResidueShading().conservationApplied()); |
248 |
1 |
assertEquals(av.getResidueShading().getConservationInc(), 20); |
249 |
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250 |
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251 |
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252 |
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253 |
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254 |
1 |
SequenceGroup sg = new SequenceGroup(); |
255 |
1 |
sg.addSequence(al.getSequenceAt(0), false); |
256 |
1 |
sg.setStartRes(15); |
257 |
1 |
sg.setEndRes(25); |
258 |
1 |
av.setSelectionGroup(sg); |
259 |
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260 |
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261 |
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262 |
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263 |
1 |
PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); |
264 |
1 |
popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand |
265 |
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.toString()); |
266 |
1 |
assertTrue(sg.getColourScheme() instanceof StrandColourScheme); |
267 |
1 |
assertEquals(al.getGroups().size(), 1); |
268 |
1 |
assertSame(al.getGroups().get(0), sg); |
269 |
1 |
popupMenu.conservationMenuItem_actionPerformed(true); |
270 |
1 |
sp = SliderPanel.getSliderPanel(); |
271 |
1 |
assertTrue(sp.isForConservation()); |
272 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
273 |
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"label.conservation_colour_increment", |
274 |
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new String[] { sg.getName() })); |
275 |
1 |
sp.valueChanged(30); |
276 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
277 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
278 |
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279 |
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|
280 |
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281 |
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282 |
1 |
popupMenu.abovePIDColour_actionPerformed(true); |
283 |
1 |
sp = SliderPanel.getSliderPanel(); |
284 |
1 |
assertFalse(sp.isForConservation()); |
285 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
286 |
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"label.percentage_identity_threshold", |
287 |
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new String[] { sg.getName() })); |
288 |
1 |
sp.valueChanged(40); |
289 |
1 |
assertEquals(sg.getGroupColourScheme().getThreshold(), 40); |
290 |
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|
291 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
292 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
293 |
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294 |
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295 |
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296 |
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297 |
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298 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString()); |
299 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme); |
300 |
1 |
assertTrue(av.getResidueShading().conservationApplied()); |
301 |
1 |
assertEquals(av.getResidueShading().getConservationInc(), 20); |
302 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 10); |
303 |
1 |
assertTrue(sg.getColourScheme() instanceof StrandColourScheme); |
304 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
305 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
306 |
1 |
assertEquals(sg.getGroupColourScheme().getThreshold(), 40); |
307 |
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308 |
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309 |
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310 |
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311 |
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312 |
1 |
af.applyToAllGroups_actionPerformed(true); |
313 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); |
314 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); |
315 |
1 |
assertTrue(av.getResidueShading().conservationApplied()); |
316 |
1 |
assertEquals(av.getResidueShading().getConservationInc(), 20); |
317 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 10); |
318 |
1 |
assertTrue(sg.getColourScheme() instanceof HelixColourScheme); |
319 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
320 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
321 |
1 |
assertEquals(sg.getGroupColourScheme().getThreshold(), 40); |
322 |
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} |
323 |
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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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332 |
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333 |
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334 |
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335 |
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336 |
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337 |
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338 |
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| 100% |
Uncovered Elements: 0 (91) |
Complexity: 1 |
Complexity Density: 0.01 |
1PASS
|
|
339 |
1 |
@Test(groups = "Functional")... |
340 |
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public void testColourThresholdActions() |
341 |
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{ |
342 |
1 |
AlignViewport av = af.getViewport(); |
343 |
1 |
AlignmentI al = av.getAlignment(); |
344 |
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|
345 |
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346 |
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347 |
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|
348 |
1 |
af.applyToAllGroups_actionPerformed(false); |
349 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); |
350 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); |
351 |
1 |
assertFalse(av.getResidueShading().conservationApplied()); |
352 |
1 |
assertEquals(av.getResidueShading().getThreshold(), 0); |
353 |
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354 |
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355 |
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356 |
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357 |
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|
358 |
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|
359 |
1 |
SequenceI ferCapan = al.findName("FER_CAPAN"); |
360 |
1 |
ResidueShaderI rs = av.getResidueShading(); |
361 |
1 |
Color c = rs.findColour('I', 14, ferCapan); |
362 |
1 |
Color i_original = new Color(138, 117, 138); |
363 |
1 |
assertEquals(c, i_original); |
364 |
1 |
c = rs.findColour('S', 15, ferCapan); |
365 |
1 |
Color s_original = new Color(54, 201, 54); |
366 |
1 |
assertEquals(c, s_original); |
367 |
|
|
368 |
|
|
369 |
|
|
370 |
|
|
371 |
1 |
af.conservationMenuItem_actionPerformed(true); |
372 |
1 |
SliderPanel sp = SliderPanel.getSliderPanel(); |
373 |
1 |
assertTrue(sp.isForConservation()); |
374 |
1 |
assertEquals(sp.getValue(), 30); |
375 |
1 |
sp.valueChanged(10); |
376 |
1 |
assertSame(rs, av.getResidueShading()); |
377 |
1 |
c = rs.findColour('I', 14, ferCapan); |
378 |
1 |
Color i_faded = new Color(196, 186, 196); |
379 |
1 |
assertEquals(c, i_faded); |
380 |
1 |
c = rs.findColour('S', 15, ferCapan); |
381 |
1 |
Color s_faded = new Color(144, 225, 144); |
382 |
1 |
assertEquals(c, s_faded); |
383 |
|
|
384 |
|
|
385 |
|
|
386 |
|
|
387 |
1 |
af.conservationMenuItem_actionPerformed(false); |
388 |
1 |
c = rs.findColour('S', 15, ferCapan); |
389 |
1 |
assertEquals(c, s_original); |
390 |
|
|
391 |
|
|
392 |
|
|
393 |
|
|
394 |
|
|
395 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
396 |
1 |
sp = SliderPanel.getSliderPanel(); |
397 |
1 |
assertFalse(sp.isForConservation()); |
398 |
1 |
assertEquals(sp.getValue(), 0); |
399 |
1 |
c = rs.findColour('I', 14, ferCapan); |
400 |
1 |
assertEquals(c, i_original); |
401 |
1 |
c = rs.findColour('S', 15, ferCapan); |
402 |
1 |
assertEquals(c, s_original); |
403 |
|
|
404 |
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|
405 |
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|
406 |
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|
407 |
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|
408 |
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|
409 |
1 |
sp.valueChanged(1); |
410 |
1 |
c = rs.findColour('I', 14, ferCapan); |
411 |
1 |
assertEquals(c, Color.white); |
412 |
1 |
c = rs.findColour('S', 15, ferCapan); |
413 |
1 |
assertEquals(c, s_original); |
414 |
|
|
415 |
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|
416 |
|
|
417 |
|
|
418 |
1 |
sp.valueChanged(66); |
419 |
1 |
c = rs.findColour('I', 14, ferCapan); |
420 |
1 |
assertEquals(c, Color.white); |
421 |
1 |
c = rs.findColour('S', 15, ferCapan); |
422 |
1 |
assertEquals(c, s_original); |
423 |
|
|
424 |
|
|
425 |
|
|
426 |
|
|
427 |
1 |
sp.valueChanged(67); |
428 |
1 |
c = rs.findColour('I', 14, ferCapan); |
429 |
1 |
assertEquals(c, Color.white); |
430 |
1 |
c = rs.findColour('S', 15, ferCapan); |
431 |
1 |
assertEquals(c, Color.white); |
432 |
|
|
433 |
|
|
434 |
|
|
435 |
|
|
436 |
1 |
af.abovePIDThreshold_actionPerformed(false); |
437 |
1 |
c = rs.findColour('I', 14, ferCapan); |
438 |
1 |
assertEquals(c, i_original); |
439 |
1 |
c = rs.findColour('S', 15, ferCapan); |
440 |
1 |
assertEquals(c, s_original); |
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
|
445 |
|
|
446 |
|
|
447 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
448 |
1 |
sp = SliderPanel.getSliderPanel(); |
449 |
1 |
assertFalse(sp.isForConservation()); |
450 |
1 |
sp.valueChanged(50); |
451 |
1 |
af.conservationMenuItem_actionPerformed(true); |
452 |
1 |
sp = SliderPanel.getSliderPanel(); |
453 |
1 |
assertTrue(sp.isForConservation()); |
454 |
1 |
sp.valueChanged(10); |
455 |
1 |
c = rs.findColour('I', 14, ferCapan); |
456 |
1 |
assertEquals(c, Color.white); |
457 |
1 |
c = rs.findColour('S', 15, ferCapan); |
458 |
1 |
assertEquals(c, s_faded); |
459 |
|
|
460 |
|
|
461 |
|
|
462 |
|
|
463 |
1 |
af.abovePIDThreshold_actionPerformed(false); |
464 |
1 |
c = rs.findColour('I', 14, ferCapan); |
465 |
1 |
assertEquals(c, i_faded); |
466 |
1 |
c = rs.findColour('S', 15, ferCapan); |
467 |
1 |
assertEquals(c, s_faded); |
468 |
|
|
469 |
|
|
470 |
|
|
471 |
|
|
472 |
|
|
473 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
474 |
1 |
SliderPanel.getSliderPanel().valueChanged(50); |
475 |
1 |
c = rs.findColour('I', 14, ferCapan); |
476 |
1 |
assertEquals(c, Color.white); |
477 |
1 |
c = rs.findColour('S', 15, ferCapan); |
478 |
1 |
assertEquals(c, s_faded); |
479 |
|
|
480 |
|
|
481 |
|
|
482 |
|
|
483 |
|
|
484 |
1 |
af.conservationMenuItem_actionPerformed(false); |
485 |
1 |
c = rs.findColour('I', 14, ferCapan); |
486 |
1 |
assertEquals(c, Color.white); |
487 |
1 |
c = rs.findColour('S', 15, ferCapan); |
488 |
1 |
assertEquals(c, s_original); |
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
|
493 |
1 |
af.abovePIDThreshold_actionPerformed(false); |
494 |
1 |
c = rs.findColour('I', 14, ferCapan); |
495 |
1 |
assertEquals(c, i_original); |
496 |
1 |
c = rs.findColour('S', 15, ferCapan); |
497 |
1 |
assertEquals(c, s_original); |
498 |
|
} |
499 |
|
|
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
|
504 |
|
|
505 |
|
|
506 |
|
@see |
507 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (63) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
508 |
1 |
@Test(groups = "Functional")... |
509 |
|
public void testNewView_colourThresholds() |
510 |
|
{ |
511 |
1 |
AlignViewport av = af.getViewport(); |
512 |
1 |
AlignmentI al = av.getAlignment(); |
513 |
|
|
514 |
|
|
515 |
|
|
516 |
|
|
517 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); |
518 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); |
519 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
520 |
1 |
SliderPanel sp = SliderPanel.getSliderPanel(); |
521 |
1 |
assertFalse(sp.isForConservation()); |
522 |
1 |
sp.valueChanged(10); |
523 |
1 |
af.conservationMenuItem_actionPerformed(true); |
524 |
1 |
sp = SliderPanel.getSliderPanel(); |
525 |
1 |
assertTrue(sp.isForConservation()); |
526 |
1 |
sp.valueChanged(20); |
527 |
1 |
ResidueShaderI rs = av.getResidueShading(); |
528 |
1 |
assertEquals(rs.getThreshold(), 10); |
529 |
1 |
assertTrue(rs.conservationApplied()); |
530 |
1 |
assertEquals(rs.getConservationInc(), 20); |
531 |
|
|
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
536 |
1 |
SequenceGroup sg = new SequenceGroup(); |
537 |
1 |
sg.addSequence(al.getSequenceAt(0), false); |
538 |
1 |
sg.setStartRes(15); |
539 |
1 |
sg.setEndRes(25); |
540 |
1 |
av.setSelectionGroup(sg); |
541 |
1 |
PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); |
542 |
1 |
popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand |
543 |
|
.toString()); |
544 |
1 |
assertTrue(sg.getColourScheme() instanceof StrandColourScheme); |
545 |
1 |
assertEquals(al.getGroups().size(), 1); |
546 |
1 |
assertSame(al.getGroups().get(0), sg); |
547 |
1 |
popupMenu.conservationMenuItem_actionPerformed(true); |
548 |
1 |
sp = SliderPanel.getSliderPanel(); |
549 |
1 |
assertTrue(sp.isForConservation()); |
550 |
1 |
sp.valueChanged(30); |
551 |
1 |
popupMenu.abovePIDColour_actionPerformed(true); |
552 |
1 |
sp = SliderPanel.getSliderPanel(); |
553 |
1 |
assertFalse(sp.isForConservation()); |
554 |
1 |
sp.valueChanged(40); |
555 |
1 |
rs = sg.getGroupColourScheme(); |
556 |
1 |
assertTrue(rs.conservationApplied()); |
557 |
1 |
assertEquals(rs.getConservationInc(), 30); |
558 |
1 |
assertEquals(rs.getThreshold(), 40); |
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
1 |
af.conservationMenuItem_actionPerformed(true); |
564 |
1 |
sp = SliderPanel.getSliderPanel(); |
565 |
1 |
assertTrue(sp.isForConservation()); |
566 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
567 |
|
"label.conservation_colour_increment", |
568 |
|
new String[] { "Background" })); |
569 |
|
|
570 |
|
|
571 |
|
|
572 |
|
|
573 |
1 |
af.newView_actionPerformed(null); |
574 |
1 |
assertEquals(af.alignPanel.getViewName(), "View 1"); |
575 |
1 |
AlignViewport av2 = af.getViewport(); |
576 |
1 |
assertNotSame(av, av2); |
577 |
1 |
assertSame(av2, af.alignPanel.av); |
578 |
1 |
rs = av2.getResidueShading(); |
579 |
1 |
assertNotSame(av.getResidueShading(), rs); |
580 |
1 |
assertEquals(rs.getThreshold(), 10); |
581 |
1 |
assertTrue(rs.conservationApplied(), rs.toString()); |
582 |
1 |
assertEquals(rs.getConservationInc(), 20); |
583 |
1 |
assertEquals(av2.getAlignment().getGroups().size(), 1); |
584 |
1 |
sg = av2.getAlignment().getGroups().get(0); |
585 |
1 |
rs = sg.getGroupColourScheme(); |
586 |
1 |
assertTrue(rs.conservationApplied()); |
587 |
1 |
assertEquals(rs.getConservationInc(), 30); |
588 |
1 |
assertEquals(rs.getThreshold(), 40); |
589 |
|
|
590 |
|
|
591 |
|
|
592 |
|
|
593 |
|
|
594 |
1 |
sp = SliderPanel.getSliderPanel(); |
595 |
1 |
assertTrue(sp.isForConservation()); |
596 |
1 |
assertEquals(sp.getTitle(), MessageManager.formatMessage( |
597 |
|
"label.conservation_colour_increment", |
598 |
|
new String[] { "View 1" })); |
599 |
1 |
sp.valueChanged(22); |
600 |
1 |
assertEquals(av2.getResidueShading().getConservationInc(), 22); |
601 |
|
} |
602 |
|
} |