JAL-653 JAL-1968 FeaturesFile now handles Jalview or GFF2 or GFF3

[jalview.git] / examples / testdata / simpleGff3.gff

diff --git a/examples/testdata/simplegff3.gff b/examples/testdata/simpleGff3.gff
similarity index 64%
rename from examples/testdata/simplegff3.gff
rename to examples/testdata/simpleGff3.gff
index 2ac5421..0d85293 100644 (file)
--- a/examples/testdata/simplegff3.gff
+++ b/examples/testdata/simpleGff3.gff
@@ -1,15 +1,22 @@
 ##gff-version 2
+# exonerate output in gff2 format; not gff3 because
+#   - 'similarity' is not a Sequence Ontology term
+#   - attributes' name/values are separated by space ' ' not equals '='
 ##source-version exonerate:protein2genome:local 2.2.0
 ##date 2015-01-16
 ##type DNA
 #
-#
+# tab-delimited
 # seqname source feature start end score strand frame attributes
 #
 seq1   exonerate:protein2genome:local  gene    8       11      3652    -       .       gene_id 0 ; sequence seq2 ; gene_orientation .
 seq1   exonerate:protein2genome:local  cds     9       11      .       -       .       
 seq1   exonerate:protein2genome:local  exon    9       11      .       -       .       insertions 3 ; deletions 6
 seq1   exonerate:protein2genome:local  similarity      8       11      3652    -       .       alignment_id 0 ; Query seq2 ; Align 11 1 3
+#
+# appending FASTA sequences is strictly a GFF3 format feature
+# but Jalview is able to handle this mixture of GFF2 / GFF3 :-)
+#
 ##FASTA
 >seq1
 ACTACGACACGACGACGACGACG