JAL-1831 added changes to allow auto-generation of BioJSON schema from src code

[jalview.git] / src / jalview / json / binding / biojson / v1 / AppSettingsPojo.java

diff --git a/src/jalview/json/binding/biojson/v1/AppSettingsPojo.java b/src/jalview/json/binding/biojson/v1/AppSettingsPojo.java
new file mode 100644 (file)
index 0000000..3385682
--- /dev/null
+++ b/src/jalview/json/binding/biojson/v1/AppSettingsPojo.java
@@ -0,0 +1,91 @@
+package jalview.json.binding.biojson.v1;
+
+
+public class AppSettingsPojo
+{
+  // private String globalColorScheme = "none";
+
+  
+
+  public AppSettingsPojo()
+  {
+
+  }
+
+  //
+  //
+  // public void setGlobalColorScheme(String globalColorScheme)
+  // {
+  // for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
+  // .values())
+  // {
+  // if (cs.getJalviewName().equals(globalColorScheme))
+  // {
+  // // this.globalColorScheme = cs.getBioJsName();
+  // this.settings.put("globalColorScheme", cs.getBioJsName());
+  // break;
+  // }
+  // }
+  // }
+  //
+  // public enum JalviewBioJsColorSchemeMapper
+  // {
+  // USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
+  // null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
+  // "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
+  // new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
+  // "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
+  // "Purine/Pyrimidine", "purine",
+  // new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
+  // "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
+  // "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
+  // "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
+  // "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
+  // "Hydrophobic", "hydro", new HydrophobicColourScheme()),
+  //
+  // // The color types below are not yet supported by BioJs MSA viewer
+  // T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
+  // "RNA Interaction type", "RNA Interaction type",
+  // new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
+  // "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
+  // "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
+  // "% Identity", "pid", new PIDColourScheme());
+  //
+  // private String jalviewName;
+  //
+  // private String bioJsName;
+  //
+  // private ColourSchemeI jvColourScheme;
+  //
+  // private JalviewBioJsColorSchemeMapper(String jalviewName,
+  // String bioJsName, ColourSchemeI jvColourScheme)
+  // {
+  // this.jalviewName = jalviewName;
+  // this.bioJsName = bioJsName;
+  // this.setJvColourScheme(jvColourScheme);
+  // }
+  //
+  // public String getJalviewName()
+  // {
+  // return jalviewName;
+  // }
+  //
+  // public String getBioJsName()
+  // {
+  // return bioJsName;
+  // }
+  //
+  // public ColourSchemeI getJvColourScheme()
+  // {
+  // return jvColourScheme;
+  // }
+  //
+  // public void setJvColourScheme(ColourSchemeI jvColourScheme)
+  // {
+  // this.jvColourScheme = jvColourScheme;
+  // }
+  //
+  // }
+
+
+}