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.HashMap;
19 import java.util.List;
21 public class AlignmentPojo
23 private String svid = "1.0";
25 private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
27 private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
29 private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
31 private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
33 HashMap<String, String> appSettings = new HashMap<String, String>();
35 public AlignmentPojo()
39 public List<SequencePojo> getSeqs()
44 public void setSeqs(ArrayList<SequencePojo> seqs)
49 public HashMap<String, String> getAppSettings()
54 public void setAppSettings(HashMap<String, String> appSettings)
56 this.appSettings = appSettings;
59 public List<AlignmentAnnotationPojo> getAlignAnnotation()
61 return alignAnnotation;
64 public void setAlignAnnotation(
65 List<AlignmentAnnotationPojo> alignAnnotation)
67 this.alignAnnotation = alignAnnotation;
70 public List<SequenceGrpPojo> getSeqGroups()
75 public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
77 this.seqGroups = seqGroups;
80 public List<SequenceFeaturesPojo> getSeqFeatures()
85 public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
87 this.seqFeatures = seqFeatures;
90 public String getSvid()
95 public void setGlobalColorScheme(String globalColorScheme)
97 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
100 if (cs.getJalviewName().equals(globalColorScheme))
102 // this.globalColorScheme = cs.getBioJsName();
103 this.appSettings.put("globalColorScheme", cs.getBioJsName());
109 public enum JalviewBioJsColorSchemeMapper
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()),
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());
132 private String jalviewName;
134 private String bioJsName;
136 private ColourSchemeI jvColourScheme;
138 private JalviewBioJsColorSchemeMapper(String jalviewName,
139 String bioJsName, ColourSchemeI jvColourScheme)
141 this.jalviewName = jalviewName;
142 this.bioJsName = bioJsName;
143 this.setJvColourScheme(jvColourScheme);
146 public String getJalviewName()
151 public String getBioJsName()
156 public ColourSchemeI getJvColourScheme()
158 return jvColourScheme;
161 public void setJvColourScheme(ColourSchemeI jvColourScheme)
163 this.jvColourScheme = jvColourScheme;