* initial selection of types of interest when processing Ensembl features
* NB unlike the full SequenceOntology we don't traverse indirect
* child-parent relationships here so e.g. need to list every sub-type
- * of gene (direct or indirect) that is of interest
+ * (direct or indirect) that is of interest
*/
// @formatter:off
private final String[][] TERMS = new String[][] {
// there are many more sub-types of ncRNA...
/*
- * sequence_variant sub-types:
+ * sequence_variant sub-types
*/
{ "sequence_variant", "sequence_variant" },
+ { "structural_variant", "sequence_variant" },
{ "feature_variant", "sequence_variant" },
{ "gene_variant", "sequence_variant" },
+ { "transcript_variant", "sequence_variant" },
// NB Ensembl uses NMD_transcript_variant as if a 'transcript'
// but we model it here correctly as per the SO
{ "NMD_transcript_variant", "sequence_variant" },
- { "transcript_variant", "sequence_variant" },
- { "structural_variant", "sequence_variant" },
+ { "missense_variant", "sequence_variant" },
+ { "synonymous_variant", "sequence_variant" },
+ { "frameshift_variant", "sequence_variant" },
+ { "5_prime_UTR_variant", "sequence_variant" },
+ { "3_prime_UTR_variant", "sequence_variant" },
+ { "stop_gained", "sequence_variant" },
+ { "stop_lost", "sequence_variant" },
+ { "inframe_deletion", "sequence_variant" },
+ { "inframe_insertion", "sequence_variant" },
+ { "splice_region_variant", "sequence_variant" },
/*
* no sub-types of exon or CDS yet seen in Ensembl
public SequenceOntologyLite()
{
- termsFound = new ArrayList<String>();
- termsNotFound = new ArrayList<String>();
+ termsFound = new ArrayList<>();
+ termsNotFound = new ArrayList<>();
loadStaticData();
}
*/
private void loadStaticData()
{
- parents = new HashMap<String, List<String>>();
+ parents = new HashMap<>();
for (String[] pair : TERMS)
{
List<String> p = parents.get(pair[0]);
if (p == null)
{
- p = new ArrayList<String>();
+ p = new ArrayList<>();
parents.put(pair[0], p);
}
p.add(pair[1]);