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package jalview.renderer; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertFalse; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.analysis.Conservation; |
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import jalview.datamodel.Profile; |
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import jalview.datamodel.ProfileI; |
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import jalview.datamodel.Profiles; |
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import jalview.datamodel.ProfilesI; |
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import jalview.datamodel.ResidueCount; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.PIDColourScheme; |
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import jalview.schemes.ResidueProperties; |
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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.Collections; |
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import org.testng.annotations.Test; |
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| 89% |
Uncovered Elements: 15 (136) |
Complexity: 17 |
Complexity Density: 0.14 |
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public class ResidueShaderTest |
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{ |
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| 100% |
Uncovered Elements: 0 (27) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
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@Test(groups = "Functional")... |
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public void testAboveThreshold() |
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{ |
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ProfileI[] profiles = new ProfileI[4]; |
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profiles[0] = new Profile(4, 0, 2, "AS"); |
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profiles[1] = new Profile(4, 0, 4, "R"); |
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profiles[2] = new Profile(4, 4, 0, ""); |
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profiles[3] = new Profile(4, 1, 2, "T"); |
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ResidueShader ccs = new ResidueShader(new PIDColourScheme()); |
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ccs.setConsensus(new Profiles(profiles)); |
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ccs.setThreshold(0, true); |
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assertTrue(ccs.aboveThreshold('a', 0)); |
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assertTrue(ccs.aboveThreshold('S', 0)); |
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assertTrue(ccs.aboveThreshold('W', 0)); |
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assertTrue(ccs.aboveThreshold('R', 1)); |
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assertTrue(ccs.aboveThreshold('W', 2)); |
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assertTrue(ccs.aboveThreshold('t', 3)); |
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assertTrue(ccs.aboveThreshold('Q', 3)); |
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ccs.setThreshold(60, false); |
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assertFalse(ccs.aboveThreshold('a', 0)); |
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assertFalse(ccs.aboveThreshold('S', 0)); |
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assertTrue(ccs.aboveThreshold('R', 1)); |
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assertFalse(ccs.aboveThreshold('W', 2)); |
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assertFalse(ccs.aboveThreshold('t', 3)); |
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ccs.setThreshold(60, true); |
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assertFalse(ccs.aboveThreshold('a', 0)); |
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assertFalse(ccs.aboveThreshold('S', 0)); |
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assertTrue(ccs.aboveThreshold('R', 1)); |
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assertFalse(ccs.aboveThreshold('W', 2)); |
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assertTrue(ccs.aboveThreshold('t', 3)); |
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} |
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| 100% |
Uncovered Elements: 0 (49) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
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@Test(groups = "Functional")... |
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public void testApplyConservation() |
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{ |
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ResidueShader ccs = new ResidueShader(new PIDColourScheme()); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 12)); |
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final String consSequence = "0123456789+*-"; |
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Conservation cons = new Conservation(null, |
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Collections.<SequenceI> emptyList(), 0, 0) |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public SequenceI getConsSequence() |
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{ |
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return new Sequence("seq", consSequence); |
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} |
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}; |
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ccs.setConservation(cons); |
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assertEquals(Color.RED, |
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ccs.applyConservation(Color.RED, consSequence.length())); |
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ccs.setConservationInc(100); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 0)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 1)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 2)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 3)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 4)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 5)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 6)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 7)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 8)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 9)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12)); |
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ccs.setConservationInc(0); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 0)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 1)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 2)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 3)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 4)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 5)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 6)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 7)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 8)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 9)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10)); |
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assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11)); |
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assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12)); |
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ccs.setConservationInc(40); |
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Color colour = new Color(155, 105, 55); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 0)); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 1)); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 2)); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 3)); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 4)); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 5)); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 6)); |
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assertEquals(new Color(235, 225, 215), ccs.applyConservation(colour, 7)); |
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assertEquals(new Color(215, 195, 175), ccs.applyConservation(colour, 8)); |
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assertEquals(new Color(195, 165, 135), ccs.applyConservation(colour, 9)); |
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assertEquals(colour, ccs.applyConservation(colour, 10)); |
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assertEquals(colour, ccs.applyConservation(colour, 11)); |
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assertEquals(Color.WHITE, ccs.applyConservation(colour, 12)); |
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} |
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| 100% |
Uncovered Elements: 0 (29) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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@Test(groups = "Functional")... |
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public void testFindColour_gapColour() |
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{ |
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ResidueShader rs = new ResidueShader(new ZappoColourScheme()); |
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assertEquals(Color.white, rs.findColour(' ', 7, null)); |
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Color[] colours = new Color[ResidueProperties.maxProteinIndex + 1]; |
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colours[5] = Color.blue; |
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colours[23] = Color.red; |
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ColourSchemeI cs = new UserColourScheme(colours); |
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rs = new ResidueShader(cs); |
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assertEquals(Color.red, rs.findColour(' ', 7, null)); |
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assertEquals(Color.blue, rs.findColour('Q', 7, null)); |
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final String consSequence = "0123456789+*-"; |
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Conservation cons = new Conservation(null, |
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Collections.<SequenceI> emptyList(), 0, 0) |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public SequenceI getConsSequence() |
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{ |
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return new Sequence("seq", consSequence); |
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} |
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}; |
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rs.setConservation(cons); |
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rs.setConservationInc(0); |
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assertEquals(Color.red, rs.findColour(' ', 7, null)); |
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assertEquals(Color.blue, rs.findColour('Q', 7, null)); |
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rs.setConservationInc(40); |
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assertEquals(Color.red, rs.findColour(' ', 7, null)); |
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assertEquals(Color.red, rs.findColour('-', 7, null)); |
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assertEquals(Color.red, rs.findColour('.', 7, null)); |
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assertEquals(new Color(204, 204, 255), rs.findColour('Q', 7, null)); |
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rs.setConservationApplied(false); |
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ProfilesI consensus = getStubConsensus("Q", 60f); |
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rs.setConsensus(consensus); |
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rs.setThreshold(50, false); |
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assertEquals(Color.blue, rs.findColour('Q', 7, null)); |
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assertEquals(Color.red, rs.findColour('-', 7, null)); |
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rs.setThreshold(70, false); |
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assertEquals(Color.white, rs.findColour('Q', 7, null)); |
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assertEquals(Color.red, rs.findColour('-', 7, null)); |
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} |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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protected ProfilesI getStubConsensus(final String modalResidue,... |
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final float pid) |
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{ |
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ProfilesI consensus = new ProfilesI() { |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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6 |
@Override... |
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public ProfileI get(int i) |
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{ |
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return new ProfileI() { |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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0 |
@Override... |
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public void setCounts(ResidueCount residueCounts) |
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{ |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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6 |
@Override... |
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public float getPercentageIdentity(boolean ignoreGaps) |
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{ |
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return pid; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public ResidueCount getCounts() |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public int getHeight() |
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{ |
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return 0; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public int getGapped() |
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{ |
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return 0; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public int getMaxCount() |
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{ |
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return 0; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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6 |
@Override... |
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public String getModalResidue() |
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{ |
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return modalResidue; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public int getNonGapped() |
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{ |
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return 0; |
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}}; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
318 |
0 |
@Override... |
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public int getStartColumn() |
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{ |
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return 0; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public int getEndColumn() |
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{ |
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return 0; |
328 |
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} |
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}; |
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return consensus; |
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} |
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} |