package jalview.json.binding.v1;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAInteractionColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
import java.util.ArrayList;
public class BioJsAlignmentPojo
{
+ private String globalColorScheme = "none";
private ArrayList<BioJsSeqPojo> seqs = new ArrayList<BioJsSeqPojo>();
public BioJsAlignmentPojo()
{
this.seqs = seqs;
}
+ public String getGlobalColorScheme()
+ {
+ return globalColorScheme;
+ }
+ public void setGlobalColorScheme(String globalColorScheme)
+ {
+ for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
+ .values())
+ {
+ if (cs.getJalviewName().equals(globalColorScheme))
+ {
+ this.globalColorScheme = cs.getBioJsName();
+ break;
+ }
+ }
+
+ // JALVIEW colors not in biojs
+ // Blosum62
+ // T-Coffee Scores (almost same with Blosom62
+ // RNA Interaction type - no color applied
+ // RNA Helices - missing
+
+ // BIOJS Colour not in jalview
+ // schemes.push name: "Lesk", id: "lesk"
+ // schemes.push name: "Cinema", id: "cinema"
+ // schemes.push name: "MAE", id: "mae"
+ // schemes.push name: "Clustal2", id: "clustal2"
+
+ }
+
+
+ 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;
+ }
+
+ }
}