From 96b4831c8077728623cb84cfd6940ac5b37df2c4 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sat, 6 Jun 2015 18:00:53 +0100 Subject: [PATCH] JAL-653 make sure dummy sequences created during GFF parsing are actually resolved and annotated --- src/jalview/io/FeaturesFile.java | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 4085fc1..d6c3c21 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -1082,6 +1082,16 @@ public class FeaturesFile extends AlignFile else { match = align.findName(seqId, true); + if (match == null && newseqs != null) + { + for (SequenceI m : newseqs) + { + if (seqId.equals(m.getName())) + { + return m; + } + } + } } if (match==null && newseqs!=null) @@ -1092,6 +1102,8 @@ public class FeaturesFile extends AlignFile matcher.addAll(Arrays.asList(new SequenceI[] { match })); } + // add dummy sequence to the newseqs list + newseqs.add(match); } return match; } -- 1.7.10.2