1 package jalview.json.binding.v1;
4 public class AppSettingsPojo
6 // private String globalColorScheme = "none";
10 public AppSettingsPojo()
17 // public void setGlobalColorScheme(String globalColorScheme)
19 // for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
22 // if (cs.getJalviewName().equals(globalColorScheme))
24 // // this.globalColorScheme = cs.getBioJsName();
25 // this.settings.put("globalColorScheme", cs.getBioJsName());
31 // public enum JalviewBioJsColorSchemeMapper
33 // USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
34 // null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
35 // "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
36 // new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
37 // "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
38 // "Purine/Pyrimidine", "purine",
39 // new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
40 // "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
41 // "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
42 // "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
43 // "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
44 // "Hydrophobic", "hydro", new HydrophobicColourScheme()),
46 // // The color types below are not yet supported by BioJs MSA viewer
47 // T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
48 // "RNA Interaction type", "RNA Interaction type",
49 // new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
50 // "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
51 // "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
52 // "% Identity", "pid", new PIDColourScheme());
54 // private String jalviewName;
56 // private String bioJsName;
58 // private ColourSchemeI jvColourScheme;
60 // private JalviewBioJsColorSchemeMapper(String jalviewName,
61 // String bioJsName, ColourSchemeI jvColourScheme)
63 // this.jalviewName = jalviewName;
64 // this.bioJsName = bioJsName;
65 // this.setJvColourScheme(jvColourScheme);
68 // public String getJalviewName()
70 // return jalviewName;
73 // public String getBioJsName()
78 // public ColourSchemeI getJvColourScheme()
80 // return jvColourScheme;
83 // public void setJvColourScheme(ColourSchemeI jvColourScheme)
85 // this.jvColourScheme = jvColourScheme;