X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2Fgff%2FSequenceOntologyLite.java;h=1e77f788ec7b105d589d1867409c98d398dcde2a;hb=1ef93cb2817f75699773f049b8d25e5b509c2830;hp=2c972ad7c40ec0f47cae2e74d039362b4e4d7944;hpb=9e5253dce9d7547e3191d596ed10f73e4af0cc1d;p=jalview.git

diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index 2c972ad..1e77f78 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 <http://www.gnu.org/licenses/>.
+ * 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[][] {
@@ -50,21 +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
@@ -101,8 +132,8 @@ public class SequenceOntologyLite implements SequenceOntologyI
 
   public SequenceOntologyLite()
   {
-    termsFound = new ArrayList<String>();
-    termsNotFound = new ArrayList<String>();
+    termsFound = new ArrayList<>();
+    termsNotFound = new ArrayList<>();
     loadStaticData();
   }
 
@@ -111,12 +142,13 @@ public class SequenceOntologyLite implements SequenceOntologyI
    */
   private void loadStaticData()
   {
-    parents = new HashMap<String, List<String>>();
-    for (String [] pair : TERMS) {
+    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]);
@@ -181,9 +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
+        // jalview.bin.Console.outPrintln("SO term " + term
+        // + " not known - add to model if needed in "
+        // + getClass().getName());
         termsNotFound.add(term);
       }
     }