merge from develop

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

diff --git a/src/jalview/json/binding/v1/AlignmentPojo.java b/src/jalview/json/binding/v1/AlignmentPojo.java
deleted file mode 100644 (file)
index 9f129f7..0000000
--- a/src/jalview/json/binding/v1/AlignmentPojo.java
+++ /dev/null
@@ -1,168 +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;
-import java.util.HashMap;
-import java.util.List;
-
-public class AlignmentPojo
-{
-  private String svid = "1.0";
-
-  private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
-
-  private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
-
-  private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
-
-  private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
-
-  HashMap<String, String> appSettings = new HashMap<String, String>();
-
-  public AlignmentPojo()
-  {
-  }
-
-  public List<SequencePojo> getSeqs()
-  {
-    return seqs;
-  }
-
-  public void setSeqs(ArrayList<SequencePojo> seqs)
-  {
-    this.seqs = seqs;
-  }
-
-  public HashMap<String, String> getAppSettings()
-  {
-    return appSettings;
-  }
-
-  public void setAppSettings(HashMap<String, String> appSettings)
-  {
-    this.appSettings = appSettings;
-  }
-
-  public List<AlignmentAnnotationPojo> getAlignAnnotation()
-  {
-    return alignAnnotation;
-  }
-
-  public void setAlignAnnotation(
-          List<AlignmentAnnotationPojo> alignAnnotation)
-  {
-    this.alignAnnotation = alignAnnotation;
-  }
-
-  public List<SequenceGrpPojo> getSeqGroups()
-  {
-    return seqGroups;
-  }
-
-  public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
-  {
-    this.seqGroups = seqGroups;
-  }
-
-  public List<SequenceFeaturesPojo> getSeqFeatures()
-  {
-    return seqFeatures;
-  }
-
-  public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
-  {
-    this.seqFeatures = seqFeatures;
-  }
-
-  public String getSvid()
-  {
-    return svid;
-  }
-
-  public void setGlobalColorScheme(String globalColorScheme)
-  {
-    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-            .values())
-    {
-      if (cs.getJalviewName().equals(globalColorScheme))
-      {
-        // this.globalColorScheme = cs.getBioJsName();
-        this.appSettings.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;
-    }
-
-  }
-
-}