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 public class JalviewSettingsPojo
19 private String globalColorScheme = "none";
21 private String jalviewVersion;
23 private String webStartUrl;
25 private boolean showSeqFeatures;
27 private boolean wrapModeEnabled;
29 public JalviewSettingsPojo()
34 public String getGlobalColorScheme()
36 return globalColorScheme;
39 public void setGlobalColorScheme(String globalColorScheme)
41 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
44 if (cs.getJalviewName().equals(globalColorScheme))
46 this.globalColorScheme = cs.getBioJsName();
52 public String getJalviewVersion()
54 return jalviewVersion;
57 public void setJalviewVersion(String jalviewVersion)
59 this.jalviewVersion = jalviewVersion;
62 public String getWebStartUrl()
67 public void setWebStartUrl(String webStartUrl)
69 this.webStartUrl = webStartUrl;
72 public boolean isShowSeqFeatures()
74 return showSeqFeatures;
77 public void setShowSeqFeatures(boolean showSeqFeatures)
79 this.showSeqFeatures = showSeqFeatures;
82 public boolean isWrapModeEnabled()
84 return wrapModeEnabled;
87 public void setWrapModeEnabled(boolean wrapModeEnabled)
89 this.wrapModeEnabled = wrapModeEnabled;
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("Taylor", "taylor",
97 new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
98 "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", null), RNA_INT_TYPE(
109 "RNA Interaction type", "RNA Interaction type",
110 new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
111 "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
112 "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
113 "% Identity", "pid", new PIDColourScheme());
115 private String jalviewName;
117 private String bioJsName;
119 private ColourSchemeI jvColourScheme;
121 private JalviewBioJsColorSchemeMapper(String jalviewName,
122 String bioJsName, ColourSchemeI jvColourScheme)
124 this.jalviewName = jalviewName;
125 this.bioJsName = bioJsName;
126 this.setJvColourScheme(jvColourScheme);
129 public String getJalviewName()
134 public String getBioJsName()
139 public ColourSchemeI getJvColourScheme()
141 return jvColourScheme;
144 public void setJvColourScheme(ColourSchemeI jvColourScheme)
146 this.jvColourScheme = jvColourScheme;