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Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
[jalview.git]
/
test
/
jalview
/
schemes
/
ResidueColourSchemeTest.java
diff --git
a/test/jalview/schemes/ResidueColourSchemeTest.java
b/test/jalview/schemes/ResidueColourSchemeTest.java
index
809dce3
..
c3ea385
100644
(file)
--- a/
test/jalview/schemes/ResidueColourSchemeTest.java
+++ b/
test/jalview/schemes/ResidueColourSchemeTest.java
@@
-44,6
+44,11
@@
import org.testng.annotations.Test;
public class ResidueColourSchemeTest
{
public class ResidueColourSchemeTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+
+ }
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
@@
-67,7
+72,7
@@
public class ResidueColourSchemeTest
profiles[1] = new Profile(4, 0, 4, "R");
profiles[2] = new Profile(4, 4, 0, "");
profiles[3] = new Profile(4, 1, 2, "T");
profiles[1] = new Profile(4, 0, 4, "R");
profiles[2] = new Profile(4, 4, 0, "");
profiles[3] = new Profile(4, 1, 2, "T");
- ResidueColourScheme rcs = new ResidueColourScheme();
+ ResidueColourScheme rcs = new PIDColourScheme();
rcs.setConsensus(new Profiles(profiles));
/*
rcs.setConsensus(new Profiles(profiles));
/*
@@
-76,11
+81,11
@@
public class ResidueColourSchemeTest
rcs.setThreshold(0, true);
assertTrue(rcs.aboveThreshold('a', 0));
assertTrue(rcs.aboveThreshold('S', 0));
rcs.setThreshold(0, true);
assertTrue(rcs.aboveThreshold('a', 0));
assertTrue(rcs.aboveThreshold('S', 0));
- assertFalse(rcs.aboveThreshold('W', 0));
+ assertTrue(rcs.aboveThreshold('W', 0));
assertTrue(rcs.aboveThreshold('R', 1));
assertTrue(rcs.aboveThreshold('R', 1));
- assertFalse(rcs.aboveThreshold('W', 2));
+ assertTrue(rcs.aboveThreshold('W', 2));
assertTrue(rcs.aboveThreshold('t', 3));
assertTrue(rcs.aboveThreshold('t', 3));
- assertFalse(rcs.aboveThreshold('Q', 3));
+ assertTrue(rcs.aboveThreshold('Q', 3));
/*
* with threshold, include gaps
/*
* with threshold, include gaps
@@
-110,7
+115,7
@@
public class ResidueColourSchemeTest
@Test(groups = "Functional")
public void testApplyConservation()
{
@Test(groups = "Functional")
public void testApplyConservation()
{
- ResidueColourScheme rcs = new ResidueColourScheme();
+ ResidueColourScheme rcs = new PIDColourScheme();
// no conservation present - no fading
assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
// no conservation present - no fading
assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
@@
-185,7
+190,7
@@
public class ResidueColourSchemeTest
assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
}
assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
}
- @Test
+ @Test(groups = "Functional")
public void testIsApplicableTo()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
public void testIsApplicableTo()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
@@
-239,8
+244,9
@@
public class ResidueColourSchemeTest
.isApplicableTo(peptide));
assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
.isApplicableTo(nucleotide));
.isApplicableTo(peptide));
assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
.isApplicableTo(nucleotide));
- assertTrue(new ResidueColourScheme().isApplicableTo(peptide));
- assertTrue(new ResidueColourScheme().isApplicableTo(nucleotide));
+ ResidueColourScheme rcs = new PIDColourScheme();
+ assertTrue(rcs.isApplicableTo(peptide));
+ assertTrue(rcs.isApplicableTo(nucleotide));
assertTrue(new PIDColourScheme().isApplicableTo(peptide));
assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
assertTrue(new PIDColourScheme().isApplicableTo(peptide));
assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
@@
-275,7
+281,7
@@
public class ResidueColourSchemeTest
assertTrue(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
}
assertTrue(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
}
- @Test
+ @Test(groups = "Functional")
public void testIsApplicableTo_dynamicColourScheme()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
public void testIsApplicableTo_dynamicColourScheme()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
@@
-301,7
+307,7
@@
public class ResidueColourSchemeTest
assertTrue(cs.isApplicableTo(peptide));
}
assertTrue(cs.isApplicableTo(peptide));
}
- @Test
+ @Test(groups = "Functional")
public void testGetName()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
public void testGetName()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
@@
-323,7
+329,6
@@
public class ResidueColourSchemeTest
assertEquals("User Defined", new UserColourScheme().getSchemeName());
assertEquals("Score", new ScoreColourScheme(new int[] {},
new double[] {}, 0, 0d).getSchemeName());
assertEquals("User Defined", new UserColourScheme().getSchemeName());
assertEquals("Score", new ScoreColourScheme(new int[] {},
new double[] {}, 0, 0d).getSchemeName());
- assertEquals("Residue", new ResidueColourScheme().getSchemeName());
assertEquals("% Identity", new PIDColourScheme().getSchemeName());
assertEquals("Follower", new FollowerColourScheme().getSchemeName());
assertEquals("T-Coffee Scores",
assertEquals("% Identity", new PIDColourScheme().getSchemeName());
assertEquals("Follower", new FollowerColourScheme().getSchemeName());
assertEquals("T-Coffee Scores",