X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FResidueColourSchemeTest.java;fp=test%2Fjalview%2Fschemes%2FResidueColourSchemeTest.java;h=6978ea164feafb9b722e4f0ff42d8ca3e5b245f2;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=b45e0d352fe0b80eb090ebae16cf2167f4cd7cb8;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java
index b45e0d3..6978ea1 100644
--- a/test/jalview/schemes/ResidueColourSchemeTest.java
+++ b/test/jalview/schemes/ResidueColourSchemeTest.java
@@ -92,8 +92,8 @@ public class ResidueColourSchemeTest
     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));
 
@@ -118,8 +118,8 @@ public class ResidueColourSchemeTest
      * 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);
@@ -127,14 +127,15 @@ public class ResidueColourSchemeTest
     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);
@@ -149,7 +150,7 @@ public class ResidueColourSchemeTest
     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
@@ -177,20 +178,25 @@ public class ResidueColourSchemeTest
 
     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",