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 String jalviewVersion;

  private String webStartUrl;
  private ArrayList<BioJsSeqPojo> seqs = new ArrayList<BioJsSeqPojo>();

  public BioJsAlignmentPojo()
  {

  }
  public ArrayList<BioJsSeqPojo> getSeqs()
  {
    return seqs;
  }

  public void setSeqs(ArrayList<BioJsSeqPojo> seqs)
  {
    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 String getJalviewVersion()
  {
    return jalviewVersion;
  }

  public void setJalviewVersion(String jalviewVersion)
  {
    this.jalviewVersion = jalviewVersion;
  }

  public String getWebStartUrl()
  {
    return webStartUrl;
  }

  public void setWebStartUrl(String webStartUrl)
  {
    this.webStartUrl = webStartUrl;
  }

  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;
    }

  }
}