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 boolean showSeqFeatures;
  29
  30   private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
  31
  32   private List<AlignmentAnnotationPojo> alignmentAnnotation = new ArrayList<AlignmentAnnotationPojo>();
  33
  34   private List<SequenceGrpPojo> sequenceGroups = new ArrayList<SequenceGrpPojo>();
  35
  36   public AlignmentPojo()
  37   {
  38
  39   }
  40
  41   public List<SequencePojo> getSeqs()
  42   {
  43     return seqs;
  44   }
  45
  46   public void setSeqs(ArrayList<SequencePojo> seqs)
  47   {
  48     this.seqs = seqs;
  49   }
  50   public String getGlobalColorScheme()
  51   {
  52     return globalColorScheme;
  53   }
  54   public void setGlobalColorScheme(String globalColorScheme)
  55   {
  56     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
  57             .values())
  58     {
  59       if (cs.getJalviewName().equals(globalColorScheme))
  60       {
  61         this.globalColorScheme = cs.getBioJsName();
  62         break;
  63       }
  64     }
  65
  66     // JALVIEW colors not in biojs
  67     // Blosum62
  68     // T-Coffee Scores (almost same with Blosom62
  69     // RNA Interaction type - no color applied
  70     // RNA Helices - missing
  71
  72     // BIOJS Colour not in jalview
  73     // schemes.push name: "Lesk", id: "lesk"
  74     // schemes.push name: "Cinema", id: "cinema"
  75     // schemes.push name: "MAE", id: "mae"
  76     // schemes.push name: "Clustal2", id: "clustal2"
  77
  78   }
  79
  80
  81   public String getJalviewVersion()
  82   {
  83     return jalviewVersion;
  84   }
  85
  86   public void setJalviewVersion(String jalviewVersion)
  87   {
  88     this.jalviewVersion = jalviewVersion;
  89   }
  90
  91   public String getWebStartUrl()
  92   {
  93     return webStartUrl;
  94   }
  95
  96   public void setWebStartUrl(String webStartUrl)
  97   {
  98     this.webStartUrl = webStartUrl;
  99   }
 100
 101   public List<AlignmentAnnotationPojo> getAlignmentAnnotation()
 102   {
 103     return alignmentAnnotation;
 104   }
 105
 106   public void setAlignmentAnnotation(List<AlignmentAnnotationPojo> alignmentAnnotation)
 107   {
 108     this.alignmentAnnotation = alignmentAnnotation;
 109   }
 110
 111   public List<SequenceGrpPojo> getSequenceGroups()
 112   {
 113     return sequenceGroups;
 114   }
 115
 116   public void setSequenceGroups(List<SequenceGrpPojo> sequenceGroups)
 117   {
 118     this.sequenceGroups = sequenceGroups;
 119   }
 120
 121   public boolean isShowSeqFeatures()
 122   {
 123     return showSeqFeatures;
 124   }
 125
 126   public void setShowSeqFeatures(boolean showSeqFeatures)
 127   {
 128     this.showSeqFeatures = showSeqFeatures;
 129   }
 130
 131   public enum JalviewBioJsColorSchemeMapper
 132   {
 133     USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
 134             null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
 135             "zappo", new ZappoColourScheme()), TAYLOR(
 136             "Taylor", "taylor", new TaylorColourScheme()), NUCLEOTIDE(
 137             "Nucleotide", "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
 138             "Purine/Pyrimidine", "purine",
 139             new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
 140             "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
 141             "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
 142             "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
 143             "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
 144             "Hydrophobic", "hydro", new HydrophobicColourScheme()),
 145
 146     // The color types below are not yet supported by BioJs MSA viewer
 147     T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores",
 148  null), RNA_INT_TYPE(
 149             "RNA Interaction type", "RNA Interaction type",
 150             new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
 151             "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
 152             "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
 153             "% Identity", "pid",
 154             new PIDColourScheme());
 155
 156     private String jalviewName;
 157     private String bioJsName;
 158
 159     private ColourSchemeI jvColourScheme;
 160
 161     private JalviewBioJsColorSchemeMapper(String jalviewName,
 162             String bioJsName, ColourSchemeI jvColourScheme)
 163     {
 164       this.jalviewName = jalviewName;
 165       this.bioJsName = bioJsName;
 166       this.setJvColourScheme(jvColourScheme);
 167     }
 168
 169     public String getJalviewName()
 170     {
 171       return jalviewName;
 172     }
 173
 174     public String getBioJsName()
 175     {
 176       return bioJsName;
 177     }
 178
 179     public ColourSchemeI getJvColourScheme()
 180     {
 181       return jvColourScheme;
 182     }
 183
 184     public void setJvColourScheme(ColourSchemeI jvColourScheme)
 185     {
 186       this.jvColourScheme = jvColourScheme;
 187     }
 188
 189   }
 190 }