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;
18 import java.util.List;
20 public class AlignmentPojo
22 private String globalColorScheme = "none";
24 private String jalviewVersion;
26 private String webStartUrl;
28 private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
30 private List<AlignmentAnnotationPojo> alignmentAnnotation = new ArrayList<AlignmentAnnotationPojo>();
32 public AlignmentPojo()
37 public List<SequencePojo> getSeqs()
42 public void setSeqs(ArrayList<SequencePojo> seqs)
46 public String getGlobalColorScheme()
48 return globalColorScheme;
50 public void setGlobalColorScheme(String globalColorScheme)
52 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
55 if (cs.getJalviewName().equals(globalColorScheme))
57 this.globalColorScheme = cs.getBioJsName();
62 // JALVIEW colors not in biojs
64 // T-Coffee Scores (almost same with Blosom62
65 // RNA Interaction type - no color applied
66 // RNA Helices - missing
68 // BIOJS Colour not in jalview
69 // schemes.push name: "Lesk", id: "lesk"
70 // schemes.push name: "Cinema", id: "cinema"
71 // schemes.push name: "MAE", id: "mae"
72 // schemes.push name: "Clustal2", id: "clustal2"
77 public String getJalviewVersion()
79 return jalviewVersion;
82 public void setJalviewVersion(String jalviewVersion)
84 this.jalviewVersion = jalviewVersion;
87 public String getWebStartUrl()
92 public void setWebStartUrl(String webStartUrl)
94 this.webStartUrl = webStartUrl;
97 public List<AlignmentAnnotationPojo> getAlignmentAnnotation()
99 return alignmentAnnotation;
102 public void setAlignmentAnnotation(List<AlignmentAnnotationPojo> alignmentAnnotation)
104 this.alignmentAnnotation = alignmentAnnotation;
107 public enum JalviewBioJsColorSchemeMapper
109 USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
110 null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
111 "zappo", new ZappoColourScheme()), TAYLOR(
112 "Taylor", "taylor", new TaylorColourScheme()), NUCLEOTIDE(
113 "Nucleotide", "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
114 "Purine/Pyrimidine", "purine",
115 new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
116 "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
117 "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
118 "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
119 "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
120 "Hydrophobic", "hydro", new HydrophobicColourScheme()),
122 // The color types below are not yet supported by BioJs MSA viewer
123 T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores",
125 "RNA Interaction type", "RNA Interaction type",
126 new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
127 "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
128 "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
130 new PIDColourScheme());
132 private String jalviewName;
133 private String bioJsName;
135 private ColourSchemeI jvColourScheme;
137 private JalviewBioJsColorSchemeMapper(String jalviewName,
138 String bioJsName, ColourSchemeI jvColourScheme)
140 this.jalviewName = jalviewName;
141 this.bioJsName = bioJsName;
142 this.setJvColourScheme(jvColourScheme);
145 public String getJalviewName()
150 public String getBioJsName()
155 public ColourSchemeI getJvColourScheme()
157 return jvColourScheme;
160 public void setJvColourScheme(ColourSchemeI jvColourScheme)
162 this.jvColourScheme = jvColourScheme;