git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu
[jalview.git]
/
test
/
jalview
/
schemes
/
ResidueColourSchemeTest.java
diff --git
a/test/jalview/schemes/ResidueColourSchemeTest.java
b/test/jalview/schemes/ResidueColourSchemeTest.java
index
4e8ea52
..
e6dc9e6
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));
/*
@@
-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));
@@
-202,7
+207,8
@@
public class ResidueColourSchemeTest
.isApplicableTo(peptide));
assertFalse(new ClustalxColourScheme(nucleotide, null)
.isApplicableTo(nucleotide));
.isApplicableTo(peptide));
assertFalse(new ClustalxColourScheme(nucleotide, null)
.isApplicableTo(nucleotide));
- assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
+ // Blosum requires presence of Conservation annotation
+ assertFalse(new Blosum62ColourScheme().isApplicableTo(peptide));
assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
@@
-219,6
+225,11
@@
public class ResidueColourSchemeTest
assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
+ peptide.addAnnotation(new AlignmentAnnotation("Conservation",
+ "Conservation", new Annotation[1], 0f, 11f,
+ AlignmentAnnotation.BAR_GRAPH));
+ assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
+
/*
* nucleotide-specific colour schemes
*/
/*
* nucleotide-specific colour schemes
*/
@@
-239,8
+250,9
@@
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));
@@
-301,7
+313,7
@@
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
+335,6
@@
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",