1 package jalview.json.binding.biojson.v1;
3 import jalview.schemes.Blosum62ColourScheme;
4 import jalview.schemes.BuriedColourScheme;
5 import jalview.schemes.ColourSchemeI;
6 import jalview.schemes.HelixColourScheme;
7 import jalview.schemes.HydrophobicColourScheme;
8 import jalview.schemes.NucleotideColourScheme;
9 import jalview.schemes.PIDColourScheme;
10 import jalview.schemes.PurinePyrimidineColourScheme;
11 import jalview.schemes.RNAInteractionColourScheme;
12 import jalview.schemes.StrandColourScheme;
13 import jalview.schemes.TaylorColourScheme;
14 import jalview.schemes.TurnColourScheme;
15 import jalview.schemes.ZappoColourScheme;
17 public enum JalviewBioJsColorSchemeMapper
20 USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
21 null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
22 "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
23 new TaylorColourScheme()), NUCLEOTIDE("Nucleotide", "nucleotide",
24 new NucleotideColourScheme()), PURINE_PYRIMIDINE(
25 "Purine/Pyrimidine", "purine", new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
26 "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
27 "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
28 "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
29 "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
30 "Hydrophobic", "hydro", new HydrophobicColourScheme()),
32 // The color types below are not yet supported by BioJs MSA viewer
33 T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
34 "RNA Interaction type", "RNA Interaction type",
35 new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
36 "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
37 "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
38 "% Identity", "pid", new PIDColourScheme());
40 private String jalviewName;
42 private String bioJsName;
44 private ColourSchemeI jvColourScheme;
46 private JalviewBioJsColorSchemeMapper(String jalviewName,
47 String bioJsName, ColourSchemeI jvColourScheme)
49 this.jalviewName = jalviewName;
50 this.bioJsName = bioJsName;
51 this.setJvColourScheme(jvColourScheme);
54 public String getJalviewName()
59 public String getBioJsName()
64 public ColourSchemeI getJvColourScheme()
66 return jvColourScheme;
69 public void setJvColourScheme(ColourSchemeI jvColourScheme)
71 this.jvColourScheme = jvColourScheme;