src/jalview/json/binding/v1/AlignmentPojo.java

   1 package jalview.json.binding.v1;
   2
   3 import jalview.schemes.Blosum62ColourScheme;
   4 import jalview.schemes.BuriedColourScheme;
   5 import jalview.schemes.ColourSchemeI;
   6 import jalview.schemes.HelixColourScheme;
   7 import jalview.schemes.HydrophobicColourScheme;
   8 import jalview.schemes.NucleotideColourScheme;
   9 import jalview.schemes.PIDColourScheme;
  10 import jalview.schemes.PurinePyrimidineColourScheme;
  11 import jalview.schemes.RNAInteractionColourScheme;
  12 import jalview.schemes.StrandColourScheme;
  13 import jalview.schemes.TaylorColourScheme;
  14 import jalview.schemes.TurnColourScheme;
  15 import jalview.schemes.ZappoColourScheme;
  16
  17 import java.util.ArrayList;
  18 import java.util.List;
  19
  20 public class AlignmentPojo
  21 {
  22   private String globalColorScheme = "none";
  23
  24   private String jalviewVersion;
  25
  26   private String webStartUrl;
  27
  28   private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
  29
  30   private List<AlignmentAnnotationPojo> alignmentAnnotation = new ArrayList<AlignmentAnnotationPojo>();
  31
  32   private List<SequenceGrpPojo> sequenceGroups = new ArrayList<SequenceGrpPojo>();
  33
  34   public AlignmentPojo()
  35   {
  36
  37   }
  38
  39   public List<SequencePojo> getSeqs()
  40   {
  41     return seqs;
  42   }
  43
  44   public void setSeqs(ArrayList<SequencePojo> seqs)
  45   {
  46     this.seqs = seqs;
  47   }
  48   public String getGlobalColorScheme()
  49   {
  50     return globalColorScheme;
  51   }
  52   public void setGlobalColorScheme(String globalColorScheme)
  53   {
  54     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
  55             .values())
  56     {
  57       if (cs.getJalviewName().equals(globalColorScheme))
  58       {
  59         this.globalColorScheme = cs.getBioJsName();
  60         break;
  61       }
  62     }
  63
  64     // JALVIEW colors not in biojs
  65     // Blosum62
  66     // T-Coffee Scores (almost same with Blosom62
  67     // RNA Interaction type - no color applied
  68     // RNA Helices - missing
  69
  70     // BIOJS Colour not in jalview
  71     // schemes.push name: "Lesk", id: "lesk"
  72     // schemes.push name: "Cinema", id: "cinema"
  73     // schemes.push name: "MAE", id: "mae"
  74     // schemes.push name: "Clustal2", id: "clustal2"
  75
  76   }
  77
  78
  79   public String getJalviewVersion()
  80   {
  81     return jalviewVersion;
  82   }
  83
  84   public void setJalviewVersion(String jalviewVersion)
  85   {
  86     this.jalviewVersion = jalviewVersion;
  87   }
  88
  89   public String getWebStartUrl()
  90   {
  91     return webStartUrl;
  92   }
  93
  94   public void setWebStartUrl(String webStartUrl)
  95   {
  96     this.webStartUrl = webStartUrl;
  97   }
  98
  99   public List<AlignmentAnnotationPojo> getAlignmentAnnotation()
 100   {
 101     return alignmentAnnotation;
 102   }
 103
 104   public void setAlignmentAnnotation(List<AlignmentAnnotationPojo> alignmentAnnotation)
 105   {
 106     this.alignmentAnnotation = alignmentAnnotation;
 107   }
 108
 109   public List<SequenceGrpPojo> getSequenceGroups()
 110   {
 111     return sequenceGroups;
 112   }
 113
 114   public void setSequenceGroups(List<SequenceGrpPojo> sequenceGroups)
 115   {
 116     this.sequenceGroups = sequenceGroups;
 117   }
 118
 119   public enum JalviewBioJsColorSchemeMapper
 120   {
 121     USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
 122             null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
 123             "zappo", new ZappoColourScheme()), TAYLOR(
 124             "Taylor", "taylor", new TaylorColourScheme()), NUCLEOTIDE(
 125             "Nucleotide", "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
 126             "Purine/Pyrimidine", "purine",
 127             new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
 128             "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
 129             "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
 130             "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
 131             "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
 132             "Hydrophobic", "hydro", new HydrophobicColourScheme()),
 133
 134     // The color types below are not yet supported by BioJs MSA viewer
 135     T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores",
 136  null), RNA_INT_TYPE(
 137             "RNA Interaction type", "RNA Interaction type",
 138             new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
 139             "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
 140             "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
 141             "% Identity", "pid",
 142             new PIDColourScheme());
 143
 144     private String jalviewName;
 145     private String bioJsName;
 146
 147     private ColourSchemeI jvColourScheme;
 148
 149     private JalviewBioJsColorSchemeMapper(String jalviewName,
 150             String bioJsName, ColourSchemeI jvColourScheme)
 151     {
 152       this.jalviewName = jalviewName;
 153       this.bioJsName = bioJsName;
 154       this.setJvColourScheme(jvColourScheme);
 155     }
 156
 157     public String getJalviewName()
 158     {
 159       return jalviewName;
 160     }
 161
 162     public String getBioJsName()
 163     {
 164       return bioJsName;
 165     }
 166
 167     public ColourSchemeI getJvColourScheme()
 168     {
 169       return jvColourScheme;
 170     }
 171
 172     public void setJvColourScheme(ColourSchemeI jvColourScheme)
 173     {
 174       this.jvColourScheme = jvColourScheme;
 175     }
 176
 177   }
 178 }