JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...

[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 72e906c..1e77f78 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyLite.java
+++ b/src/jalview/io/gff/SequenceOntologyLite.java
@@ -70,6 +70,7 @@ 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...
@@ -214,7 +215,7 @@ public class SequenceOntologyLite implements SequenceOntologyI
       {
         // 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
+        // jalview.bin.Console.outPrintln("SO term " + term
         // + " not known - add to model if needed in "
         // + getClass().getName());
         termsNotFound.add(term);