+#*******************************************************************************
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+# Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+#
+# This file is part of Jalview.
+#
+# Jalview is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Jalview is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+# PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+#*******************************************************************************
#!/usr/bin/perl
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+# Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+#
+# This file is part of Jalview.
+#
+# Jalview is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Jalview is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+# PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+
use strict;
use warnings;
=head2 SYNOPSIS
-gff2annot.pl [one or more files containing gff annotation]
+
+ gff2annot.pl [one or more files containing gff annotation]
+
+Generates a nominally usable Jalview Annotation file on B<STDOUT> from arbitrary GFF annotation lines.
=head2 DESCRIPTION
Seq2 blasty significant_hsp 1 5 0.9 + 1 link http://mylink/
Seq2 blastz significant_hsp 1 5 0.9
Seq3 blastx significant_hsp 50 70
- <Control^D>
+ <Control^D/Z>
Produces