JAL-3416 remove flat as default for linux

[jalview.git] / utils / gff2annot.pl

diff --git a/utils/gff2annot.pl b/utils/gff2annot.pl
index 0ff1d36..4ee683b 100755 (executable)
--- a/utils/gff2annot.pl
+++ b/utils/gff2annot.pl
@@ -1,4 +1,22 @@
 #!/usr/bin/perl
+##
+# Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+# Copyright (C) $$Year-Rel$$ The Jalview Authors
+# 
+# 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/>.
+# The Jalview Authors are detailed in the 'AUTHORS' file.
+##
 
 use strict;
 use warnings;
@@ -49,7 +67,10 @@ gff2annot.pl
 
 =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
 
@@ -74,7 +95,7 @@ Passing some GFF annotation through STDIN:
   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