X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FSequenceOntologyLite.java;h=f989f7b78a53e98a33ee170fe4b9ec335ffc284f;hb=0a1556c9d4503b4832d0ca83346c4394b8539016;hp=61b34ad499af18a4f94600c15d955ae0e51e945a;hpb=af091f745fcb56de68e6bfbe8b3320ab92a448d7;p=jalview.git
diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index 61b34ad..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;
@@ -112,7 +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)
{
@@ -181,9 +202,11 @@ public class SequenceOntologyLite implements SequenceOntologyI
{
if (!termsNotFound.contains(term))
{
- System.out.println("SO term " + term
- + " not known - add to 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);
}
}