JAL-1641 cherry-picked changes into develop compatible branch

[jalview.git] / src / jalview / json / binding / v1 / BioJsAlignmentPojo.java

diff --git a/src/jalview/json/binding/v1/BioJsAlignmentPojo.java b/src/jalview/json/binding/v1/BioJsAlignmentPojo.java
deleted file mode 100644 (file)
index 8e8747f..0000000
--- a/src/jalview/json/binding/v1/BioJsAlignmentPojo.java
+++ /dev/null
@@ -1,151 +0,0 @@
-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;
-    }
-
-  }
-}