1 package jalview.json.binding.biojson.v1;
4 import java.util.ArrayList;
5 import java.util.HashMap;
9 import com.github.reinert.jjschema.Attributes;
11 @Attributes(title="BioJSON", description="A specification for the representation and exchange of bioinformatics data")
12 public class AlignmentPojo
14 @Attributes(required = true, description = "Serial version identifier for <b>BioJSON</b> schema")
15 private String svid = "1.0";
20 maxItems = 2147483647,
21 description = "A sequence group is a bracket of alignment residues spanning <br>across multiple columns and rows. These can be treated as a <br>sub-alignments.")
22 private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
27 maxItems = 2147483647,
28 exclusiveMaximum = true,
29 description = "Alignment annotations stores symbols and graphs usually rendered </br>below the alignment.")
30 private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
35 maxItems = 2147483647,
36 description = "A sequence group is a bracket of alignment residues which <br>could span across multiple columns and/or rows. These can be <br>treated as a sub-alignments.")
37 private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
42 maxItems = 2147483647,
43 description = "Sequence features are associated with sequences rather than <br>alignments. A sequence feature can span across multiple <br>sequences in an alignment. They indicate features generated <br>by the same analysis process or retrieved from the same database <br>(such as Uniprot features).")
44 private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
46 @Attributes(required = false, enums = { "None", "Custom", "Clustal",
47 "Zappo", "Taylor", "Nucleotide", "Pyrimidine", "Purine", "Turn",
48 "Strand", "Buried", "Hydro" })
49 private String colourScheme;
51 @Attributes(required = true, maxItems = 1, description = "This is an array of key=value pairs for storing custom application <br>specific settings")
52 Map<String, Object> appSettings = new HashMap<String, Object>();
54 public AlignmentPojo()
58 public List<SequencePojo> getSeqs()
63 public void setSeqs(ArrayList<SequencePojo> seqs)
68 public Map<String, Object> getAppSettings()
73 public void setAppSettings(Map<String, Object> appSettings)
75 this.appSettings = appSettings;
78 public List<AlignmentAnnotationPojo> getAlignAnnotation()
80 return alignAnnotation;
83 public void setAlignAnnotation(
84 List<AlignmentAnnotationPojo> alignAnnotation)
86 this.alignAnnotation = alignAnnotation;
89 public List<SequenceGrpPojo> getSeqGroups()
94 public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
96 this.seqGroups = seqGroups;
99 public List<SequenceFeaturesPojo> getSeqFeatures()
104 public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
106 this.seqFeatures = seqFeatures;
109 public String getSvid()
114 public void setGlobalColorScheme(String globalColorScheme)
116 this.appSettings.put("globalColorScheme", globalColorScheme);
119 public String getColourScheme()
124 public void setColourScheme(String colourScheme)
126 this.colourScheme = colourScheme;