From 5326cbb4462396e84cdbbc178040f42b436c9146 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 5 Oct 2016 15:12:01 +0100 Subject: [PATCH] JAL-1191 revert to using SequenceOntologyLite due to downstream dependencies --- src/jalview/bin/Jalview.java | 5 +++-- src/jalview/io/gff/SequenceOntologyLite.java | 8 +++++--- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index ce29f01..763b10b 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -291,9 +291,10 @@ public class Jalview } /* - * configure 'full' SO model unless preferences say not to + * configure 'full' SO model if preferences say to, + * else use the default (SO Lite) */ - if (!Cache.getDefault("USE_SO_LITE", false)) + if (Cache.getDefault("USE_FULL_SO", false)) { SequenceOntologyFactory.setInstance(new SequenceOntology()); } diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java index 61b34ad..d46dcbe 100644 --- a/src/jalview/io/gff/SequenceOntologyLite.java +++ b/src/jalview/io/gff/SequenceOntologyLite.java @@ -181,9 +181,11 @@ 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); } } -- 1.7.10.2