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.HashMap;
  19 import java.util.List;
  20
  21 public class AlignmentPojo
  22 {
  23   private String svid = "1.0";
  24
  25   private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
  26
  27   private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
  28
  29   private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
  30
  31   private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
  32
  33   HashMap<String, String> appSettings = new HashMap<String, String>();
  34
  35   public AlignmentPojo()
  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
  49   public HashMap<String, String> getAppSettings()
  50   {
  51     return appSettings;
  52   }
  53
  54   public void setAppSettings(HashMap<String, String> appSettings)
  55   {
  56     this.appSettings = appSettings;
  57   }
  58
  59   public List<AlignmentAnnotationPojo> getAlignAnnotation()
  60   {
  61     return alignAnnotation;
  62   }
  63
  64   public void setAlignAnnotation(
  65           List<AlignmentAnnotationPojo> alignAnnotation)
  66   {
  67     this.alignAnnotation = alignAnnotation;
  68   }
  69
  70   public List<SequenceGrpPojo> getSeqGroups()
  71   {
  72     return seqGroups;
  73   }
  74
  75   public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
  76   {
  77     this.seqGroups = seqGroups;
  78   }
  79
  80   public List<SequenceFeaturesPojo> getSeqFeatures()
  81   {
  82     return seqFeatures;
  83   }
  84
  85   public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
  86   {
  87     this.seqFeatures = seqFeatures;
  88   }
  89
  90   public String getSvid()
  91   {
  92     return svid;
  93   }
  94
  95   public void setGlobalColorScheme(String globalColorScheme)
  96   {
  97     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
  98             .values())
  99     {
 100       if (cs.getJalviewName().equals(globalColorScheme))
 101       {
 102         // this.globalColorScheme = cs.getBioJsName();
 103         this.appSettings.put("globalColorScheme", cs.getBioJsName());
 104         break;
 105       }
 106     }
 107   }
 108
 109   public enum JalviewBioJsColorSchemeMapper
 110   {
 111     USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
 112             null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
 113             "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
 114             new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
 115             "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
 116             "Purine/Pyrimidine", "purine",
 117             new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
 118             "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
 119             "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
 120             "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
 121             "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
 122             "Hydrophobic", "hydro", new HydrophobicColourScheme()),
 123
 124     // The color types below are not yet supported by BioJs MSA viewer
 125     T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
 126             "RNA Interaction type", "RNA Interaction type",
 127             new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
 128             "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
 129             "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
 130             "% Identity", "pid", new PIDColourScheme());
 131
 132     private String jalviewName;
 133
 134     private String bioJsName;
 135
 136     private ColourSchemeI jvColourScheme;
 137
 138     private JalviewBioJsColorSchemeMapper(String jalviewName,
 139             String bioJsName, ColourSchemeI jvColourScheme)
 140     {
 141       this.jalviewName = jalviewName;
 142       this.bioJsName = bioJsName;
 143       this.setJvColourScheme(jvColourScheme);
 144     }
 145
 146     public String getJalviewName()
 147     {
 148       return jalviewName;
 149     }
 150
 151     public String getBioJsName()
 152     {
 153       return bioJsName;
 154     }
 155
 156     public ColourSchemeI getJvColourScheme()
 157     {
 158       return jvColourScheme;
 159     }
 160
 161     public void setJvColourScheme(ColourSchemeI jvColourScheme)
 162     {
 163       this.jvColourScheme = jvColourScheme;
 164     }
 165
 166   }
 167
 168 }