assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
- assertTrue(new PurinePyrimidineColourScheme()
- .isApplicableTo(nucleotide));
+ assertTrue(
+ new PurinePyrimidineColourScheme().isApplicableTo(nucleotide));
assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
* TCoffee colour requires the presence of TCoffee score annotation
*/
assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
- assertFalse(new TCoffeeColourScheme(nucleotide)
- .isApplicableTo(nucleotide));
+ assertFalse(
+ new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
peptide.addAnnotation(aa);
aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
nucleotide.addAnnotation(aa);
assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
- assertTrue(new TCoffeeColourScheme(nucleotide)
- .isApplicableTo(nucleotide));
+ assertTrue(
+ new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
/*
* RNAHelices requires the presence of rna secondary structure
*/
assertFalse(new RNAHelicesColour(peptide).isApplicableTo(peptide));
- assertFalse(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
+ assertFalse(
+ new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
// add secondary structure (small but perfectly formed)
Annotation[] ss = new Annotation[2];
ss[0] = new Annotation("", "", '{', 0f);
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
SequenceI pep2 = new Sequence("pep2", "AILFQYG");
AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
-
+
/*
* demonstrate that we can 'plug in' a colour scheme with specified
* criteria for applicability; here, that there are more than 2 sequences
assertEquals("Blosum62", new Blosum62ColourScheme().getSchemeName());
assertEquals("Buried Index", new BuriedColourScheme().getSchemeName());
- assertEquals("Helix Propensity", new HelixColourScheme().getSchemeName());
- assertEquals("Hydrophobic", new HydrophobicColourScheme().getSchemeName());
- assertEquals("Strand Propensity", new StrandColourScheme().getSchemeName());
+ assertEquals("Helix Propensity",
+ new HelixColourScheme().getSchemeName());
+ assertEquals("Hydrophobic",
+ new HydrophobicColourScheme().getSchemeName());
+ assertEquals("Strand Propensity",
+ new StrandColourScheme().getSchemeName());
assertEquals("Taylor", new TaylorColourScheme().getSchemeName());
assertEquals("Turn Propensity", new TurnColourScheme().getSchemeName());
assertEquals("Zappo", new ZappoColourScheme().getSchemeName());
- assertEquals("Nucleotide", new NucleotideColourScheme().getSchemeName());
+ assertEquals("Nucleotide",
+ new NucleotideColourScheme().getSchemeName());
assertEquals("Purine/Pyrimidine",
new PurinePyrimidineColourScheme().getSchemeName());
assertEquals("RNA Interaction type",
new RNAInteractionColourScheme().getSchemeName());
assertEquals("User Defined", new UserColourScheme().getSchemeName());
- assertEquals("Score", new ScoreColourScheme(new int[] {},
- new double[] {}, 0, 0d).getSchemeName());
+ assertEquals("Score",
+ new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+ .getSchemeName());
assertEquals("% Identity", new PIDColourScheme().getSchemeName());
assertEquals("Follower", new FollowerColourScheme().getSchemeName());
assertEquals("T-Coffee Scores",