X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FSequenceOntologyLite.java;h=7d354e0a039d362e1f0805b6ffdb94a09c8597f6;hb=efb5cfa00ee832a62dfdf59f5fb847a0e16424d9;hp=d2e665448bcf9a434f22cf8d81f04a6d5feb40b8;hpb=71a5df9830e7ea6a5092f1fe2162d93e6341e18c;p=jalview.git
diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index d2e6654..7d354e0 100644
--- a/src/jalview/io/gff/SequenceOntologyLite.java
+++ b/src/jalview/io/gff/SequenceOntologyLite.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io.gff;
import java.util.ArrayList;
@@ -24,7 +44,7 @@ public class SequenceOntologyLite implements SequenceOntologyI
* 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[][] {
@@ -37,6 +57,7 @@ public class SequenceOntologyLite implements SequenceOntologyI
{ "snRNA_gene", "gene" },
{ "miRNA_gene", "gene" },
{ "lincRNA_gene", "gene" },
+ { "rRNA_gene", "gene" },
/*
* transcript sub-types:
@@ -49,19 +70,32 @@ public class SequenceOntologyLite implements SequenceOntologyI
{ "snRNA", "transcript" },
{ "miRNA", "transcript" },
{ "lincRNA", "transcript" },
+ { "lnc_RNA", "transcript" },
+ { "rRNA", "transcript" },
+ { "mRNA", "transcript" },
// 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
@@ -98,8 +132,8 @@ public class SequenceOntologyLite implements SequenceOntologyI
public SequenceOntologyLite()
{
- termsFound = new ArrayList();
- termsNotFound = new ArrayList();
+ termsFound = new ArrayList<>();
+ termsNotFound = new ArrayList<>();
loadStaticData();
}
@@ -108,12 +142,13 @@ public class SequenceOntologyLite implements SequenceOntologyI
*/
private void loadStaticData()
{
- parents = new HashMap>();
- for (String [] pair : TERMS) {
+ parents = new HashMap<>();
+ for (String[] pair : TERMS)
+ {
List p = parents.get(pair[0]);
if (p == null)
{
- p = new ArrayList();
+ p = new ArrayList<>();
parents.put(pair[0], p);
}
p.add(pair[1]);
@@ -178,9 +213,11 @@ public class SequenceOntologyLite implements SequenceOntologyI
{
if (!termsNotFound.contains(term))
{
- System.out.println("SO term " + term
- + " not known - may be invalid, or model if needed in "
- + getClass().getName());
+ // suppress logging here as it reports Uniprot sequence features
+ // (which do not use SO terms) when auto-configuring feature colours
+ // System.out.println("SO term " + term
+ // + " not known - add to model if needed in "
+ // + getClass().getName());
termsNotFound.add(term);
}
}