X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FSequenceOntologyLite.java;h=f989f7b78a53e98a33ee170fe4b9ec335ffc284f;hb=ba2312aee832027b7dcf53d7b2cc1325948b2821;hp=b3f81611d761880e2941186d622688d0a0625118;hpb=b223b8f0879291e998b0e197e3901805837e6cf0;p=jalview.git
diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index b3f8161..f989f7b 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;
@@ -51,6 +71,7 @@ public class SequenceOntologyLite implements SequenceOntologyI
{ "miRNA", "transcript" },
{ "lincRNA", "transcript" },
{ "rRNA", "transcript" },
+ { "mRNA", "transcript" },
// there are many more sub-types of ncRNA...
/*
@@ -111,7 +132,8 @@ public class SequenceOntologyLite implements SequenceOntologyI
private void loadStaticData()
{
parents = new HashMap>();
- for (String [] pair : TERMS) {
+ for (String[] pair : TERMS)
+ {
List p = parents.get(pair[0]);
if (p == null)
{
@@ -180,9 +202,11 @@ 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);
}
}