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JAL-2094 first pass with jalview.api.ColorI interface
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
SequenceOntologyLite.java
diff --git
a/src/jalview/io/gff/SequenceOntologyLite.java
b/src/jalview/io/gff/SequenceOntologyLite.java
index
6719ae6
..
b3f8161
100644
(file)
--- a/
src/jalview/io/gff/SequenceOntologyLite.java
+++ b/
src/jalview/io/gff/SequenceOntologyLite.java
@@
-22,6
+22,9
@@
public class SequenceOntologyLite implements SequenceOntologyI
{
/*
* initial selection of types of interest when processing Ensembl features
{
/*
* 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
*/
// @formatter:off
private final String[][] TERMS = new String[][] {
*/
// @formatter:off
private final String[][] TERMS = new String[][] {
@@
-32,15
+35,23
@@
public class SequenceOntologyLite implements SequenceOntologyI
{ "gene", "gene" },
{ "ncRNA_gene", "gene" },
{ "snRNA_gene", "gene" },
{ "gene", "gene" },
{ "ncRNA_gene", "gene" },
{ "snRNA_gene", "gene" },
+ { "miRNA_gene", "gene" },
+ { "lincRNA_gene", "gene" },
+ { "rRNA_gene", "gene" },
/*
* transcript sub-types:
*/
{ "transcript", "transcript" },
{ "mature_transcript", "transcript" },
/*
* transcript sub-types:
*/
{ "transcript", "transcript" },
{ "mature_transcript", "transcript" },
+ { "processed_transcript", "transcript" },
+ { "aberrant_processed_transcript", "transcript" },
{ "ncRNA", "transcript" },
{ "snRNA", "transcript" },
{ "ncRNA", "transcript" },
{ "snRNA", "transcript" },
- { "aberrant_processed_transcript", "transcript" },
+ { "miRNA", "transcript" },
+ { "lincRNA", "transcript" },
+ { "rRNA", "transcript" },
+ // there are many more sub-types of ncRNA...
/*
* sequence_variant sub-types:
/*
* sequence_variant sub-types:
@@
-55,16
+66,20
@@
public class SequenceOntologyLite implements SequenceOntologyI
{ "structural_variant", "sequence_variant" },
/*
{ "structural_variant", "sequence_variant" },
/*
- * no sub-types of exon or CDS yet encountered; add if needed
+ * no sub-types of exon or CDS yet seen in Ensembl
+ * some added here for testing purposes
*/
{ "exon", "exon" },
*/
{ "exon", "exon" },
+ { "coding_exon", "exon" },
{ "CDS", "CDS" },
{ "CDS", "CDS" },
+ { "CDS_predicted", "CDS" },
/*
/*
- * used in exonerate GFF
+ * terms used in exonerate or PASA GFF
*/
{ "protein_match", "protein_match"},
{ "nucleotide_match", "nucleotide_match"},
*/
{ "protein_match", "protein_match"},
{ "nucleotide_match", "nucleotide_match"},
+ { "cDNA_match", "nucleotide_match"},
/*
* used in InterProScan GFF
/*
* used in InterProScan GFF
@@
-166,7
+181,7
@@
public class SequenceOntologyLite implements SequenceOntologyI
if (!termsNotFound.contains(term))
{
System.out.println("SO term " + term
if (!termsNotFound.contains(term))
{
System.out.println("SO term " + term
- + " not known - either invalid or needs modelled in "
+ + " not known - may be invalid, or model if needed in "
+ getClass().getName());
termsNotFound.add(term);
}
+ getClass().getName());
termsNotFound.add(term);
}