From af933523a5b24cd18b6a54fa2808c8734b9b9ecc Mon Sep 17 00:00:00 2001
From: Sascha Steinbiss <ss34@sanger.ac.uk>
Date: Thu, 6 Feb 2014 11:10:51 +0000
Subject: [PATCH] concatenate 'comment' and 'curation' attributes with blank
---
uk/ac/sanger/artemis/io/GFFStreamFeature.java | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index bfec1da89..f4a0a9b44 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -892,12 +892,29 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
}
};
+ GFF3AttributeAggregator curcomProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ buffer.append(GFF3Encoder.encode(values.elementAt(value_index)));
+ if (value_index < (values.size()) - 1)
+ buffer.append(" ");
+ }
+ }
+ return buffer.toString();
+ }
+ };
+
// map GO -> full_GO
abuf.setMapping("GO", "full_GO");
abuf.setGlue("full_GO", ",");
// merge curation and comment
abuf.setMapping("curation", "comment");
+ abuf.setGlue("comment", " ");
+ abuf.setAggregator("comment", curcomProc);
// also put GOs in Ontology_term
abuf.setClone("full_GO", "Ontology_term");
--
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