1 package jalview.json.binding.v1;
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;
17 import java.util.ArrayList;
19 public class BioJsAlignmentPojo
21 private String globalColorScheme = "none";
23 private String jalviewVersion;
25 private String webStartUrl;
26 private ArrayList<BioJsSeqPojo> seqs = new ArrayList<BioJsSeqPojo>();
28 public BioJsAlignmentPojo()
32 public ArrayList<BioJsSeqPojo> getSeqs()
37 public void setSeqs(ArrayList<BioJsSeqPojo> seqs)
41 public String getGlobalColorScheme()
43 return globalColorScheme;
45 public void setGlobalColorScheme(String globalColorScheme)
47 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
50 if (cs.getJalviewName().equals(globalColorScheme))
52 this.globalColorScheme = cs.getBioJsName();
57 // JALVIEW colors not in biojs
59 // T-Coffee Scores (almost same with Blosom62
60 // RNA Interaction type - no color applied
61 // RNA Helices - missing
63 // BIOJS Colour not in jalview
64 // schemes.push name: "Lesk", id: "lesk"
65 // schemes.push name: "Cinema", id: "cinema"
66 // schemes.push name: "MAE", id: "mae"
67 // schemes.push name: "Clustal2", id: "clustal2"
72 public String getJalviewVersion()
74 return jalviewVersion;
77 public void setJalviewVersion(String jalviewVersion)
79 this.jalviewVersion = jalviewVersion;
82 public String getWebStartUrl()
87 public void setWebStartUrl(String webStartUrl)
89 this.webStartUrl = webStartUrl;
92 public enum JalviewBioJsColorSchemeMapper
94 USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
95 null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
96 "zappo", new ZappoColourScheme()), TAYLOR(
97 "Taylor", "taylor", new TaylorColourScheme()), NUCLEOTIDE(
98 "Nucleotide", "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
99 "Purine/Pyrimidine", "purine",
100 new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
101 "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
102 "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
103 "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
104 "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
105 "Hydrophobic", "hydro", new HydrophobicColourScheme()),
107 // The color types below are not yet supported by BioJs MSA viewer
108 T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores",
110 "RNA Interaction type", "RNA Interaction type",
111 new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
112 "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
113 "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
115 new PIDColourScheme());
117 private String jalviewName;
118 private String bioJsName;
120 private ColourSchemeI jvColourScheme;
122 private JalviewBioJsColorSchemeMapper(String jalviewName,
123 String bioJsName, ColourSchemeI jvColourScheme)
125 this.jalviewName = jalviewName;
126 this.bioJsName = bioJsName;
127 this.setJvColourScheme(jvColourScheme);
130 public String getJalviewName()
135 public String getBioJsName()
140 public ColourSchemeI getJvColourScheme()
142 return jvColourScheme;
145 public void setJvColourScheme(ColourSchemeI jvColourScheme)
147 this.jvColourScheme = jvColourScheme;