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 private List<SequenceGrpPojo> sequenceGroups = new ArrayList<SequenceGrpPojo>();
34 public AlignmentPojo()
39 public List<SequencePojo> getSeqs()
44 public void setSeqs(ArrayList<SequencePojo> seqs)
48 public String getGlobalColorScheme()
50 return globalColorScheme;
52 public void setGlobalColorScheme(String globalColorScheme)
54 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
57 if (cs.getJalviewName().equals(globalColorScheme))
59 this.globalColorScheme = cs.getBioJsName();
64 // JALVIEW colors not in biojs
66 // T-Coffee Scores (almost same with Blosom62
67 // RNA Interaction type - no color applied
68 // RNA Helices - missing
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"
79 public String getJalviewVersion()
81 return jalviewVersion;
84 public void setJalviewVersion(String jalviewVersion)
86 this.jalviewVersion = jalviewVersion;
89 public String getWebStartUrl()
94 public void setWebStartUrl(String webStartUrl)
96 this.webStartUrl = webStartUrl;
99 public List<AlignmentAnnotationPojo> getAlignmentAnnotation()
101 return alignmentAnnotation;
104 public void setAlignmentAnnotation(List<AlignmentAnnotationPojo> alignmentAnnotation)
106 this.alignmentAnnotation = alignmentAnnotation;
109 public List<SequenceGrpPojo> getSequenceGroups()
111 return sequenceGroups;
114 public void setSequenceGroups(List<SequenceGrpPojo> sequenceGroups)
116 this.sequenceGroups = sequenceGroups;
119 public enum JalviewBioJsColorSchemeMapper
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()),
134 // The color types below are not yet supported by BioJs MSA viewer
135 T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores",
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(
142 new PIDColourScheme());
144 private String jalviewName;
145 private String bioJsName;
147 private ColourSchemeI jvColourScheme;
149 private JalviewBioJsColorSchemeMapper(String jalviewName,
150 String bioJsName, ColourSchemeI jvColourScheme)
152 this.jalviewName = jalviewName;
153 this.bioJsName = bioJsName;
154 this.setJvColourScheme(jvColourScheme);
157 public String getJalviewName()
162 public String getBioJsName()
167 public ColourSchemeI getJvColourScheme()
169 return jvColourScheme;
172 public void setJvColourScheme(ColourSchemeI jvColourScheme)
174 this.jvColourScheme = jvColourScheme;