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 description = "An array of Sequences which makes up the Alignment")
21 private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
26 maxItems = 2147483647,
27 exclusiveMaximum = true,
28 description = "Alignment annotations stores symbols and graphs usually rendered </br>below the alignment.")
29 private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
34 maxItems = 2147483647,
35 description = "A sequence group is a region of an alignment which could <br>span across multiple columns and rows. These can be treated as<br> a sub-alignments.")
36 private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
41 maxItems = 2147483647,
42 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).")
43 private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
47 enums = { "None", "User Defined", "Clustal", "Zappo", "Taylor",
48 "Nucleotide", "Pyrimidine", "Purine", "Turn", "Helix", "Strand",
49 "Buried", "Hydro", "T-Coffee Scores", "RNA Interaction type",
50 "Blosum62", "RNA Helices", "% Identity" },
51 description = "The <a href=\"colour_schemes.html\">Colour Scheme</a> applied to the alignment")
52 private String colourScheme;
54 @Attributes(required = true, maxItems = 1, description = "This is an array of key=value pairs for storing custom application <br>specific settings")
55 Map<String, Object> appSettings = new HashMap<String, Object>();
57 public AlignmentPojo()
61 public List<SequencePojo> getSeqs()
66 public void setSeqs(ArrayList<SequencePojo> seqs)
71 public Map<String, Object> getAppSettings()
76 public void setAppSettings(Map<String, Object> appSettings)
78 this.appSettings = appSettings;
81 public List<AlignmentAnnotationPojo> getAlignAnnotation()
83 return alignAnnotation;
86 public void setAlignAnnotation(
87 List<AlignmentAnnotationPojo> alignAnnotation)
89 this.alignAnnotation = alignAnnotation;
92 public List<SequenceGrpPojo> getSeqGroups()
97 public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
99 this.seqGroups = seqGroups;
102 public List<SequenceFeaturesPojo> getSeqFeatures()
107 public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
109 this.seqFeatures = seqFeatures;
112 public String getSvid()
117 public void setGlobalColorScheme(String globalColorScheme)
119 this.appSettings.put("globalColorScheme", globalColorScheme);
122 public String getColourScheme()
127 public void setColourScheme(String colourScheme)
129 this.colourScheme = colourScheme;