4 files changed, 28 insertions, 13 deletions

diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile
index 3e93e8e40b7d..7fff41cc3db4 100644
--- a/biology/p5-AcePerl/Makefile
+++ b/biology/p5-AcePerl/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	AcePerl
-PORTVERSION=	1.75
+PORTVERSION=	1.82
 CATEGORIES=	biology databases perl5
 MASTER_SITES=	${MASTER_SITE_PERL_CPAN}
 MASTER_SITE_SUBDIR=	Ace
@@ -16,11 +16,14 @@ MAINTAINER=	bio@freebsd.net
 
 PERL_CONFIGURE=	yes
 
-MAN3=		Ace.3 Ace::Browser::AceSubs.3 Ace::Graphics::Fk.3 \
+MAN3=		Ace.3 Ace::Browser::AceSubs.3 Ace::Browser::SearchSubs.3 \
+		Ace::Browser::SiteDefs.3 Ace::Graphics::Fk.3 \
 		Ace::Graphics::Glyph.3 Ace::Graphics::Glyph::anchored_arrow.3 \
-		Ace::Graphics::Glyph::arrow.3 Ace::Graphics::Glyph::dot.3 \
-		Ace::Graphics::Glyph::ex.3 Ace::Graphics::Glyph::group.3 \
-		Ace::Graphics::Glyph::line.3 Ace::Graphics::Glyph::primers.3 \
+		Ace::Graphics::Glyph::arrow.3 Ace::Graphics::Glyph::box.3 \
+		Ace::Graphics::Glyph::dot.3 Ace::Graphics::Glyph::ex.3 \
+		Ace::Graphics::Glyph::graded_segments.3 \
+		Ace::Graphics::Glyph::group.3 Ace::Graphics::Glyph::line.3 \
+		Ace::Graphics::Glyph::primers.3 \
 		Ace::Graphics::Glyph::segments.3 Ace::Graphics::Glyph::span.3 \
 		Ace::Graphics::Glyph::toomany.3 \
 		Ace::Graphics::Glyph::transcript.3 \
@@ -29,8 +32,9 @@ MAN3=		Ace.3 Ace::Browser::AceSubs.3 Ace::Graphics::Fk.3 \
 		Ace::Graphics::Track.3 Ace::Iterator.3 Ace::Local.3 \
 		Ace::Model.3 Ace::Object.3 Ace::Sequence.3 \
 		Ace::Sequence::Feature.3 Ace::Sequence::FeatureList.3 \
-		Ace::Sequence::GappedAlignment.3 Ace::Sequence::Homol.3 \
-		Ace::Sequence::Multi.3 Ace::Sequence::Transcript.3
+		Ace::Sequence::GappedAlignment.3 Ace::Sequence::Gene.3 \
+		Ace::Sequence::Homol.3 Ace::Sequence::Multi.3 \
+		Ace::Sequence::Transcript.3
 MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
 
 post-patch:
diff --git a/biology/p5-AcePerl/distinfo b/biology/p5-AcePerl/distinfo
index 3bbe0f036f72..c24be2385f39 100644
--- a/biology/p5-AcePerl/distinfo
+++ b/biology/p5-AcePerl/distinfo
@@ -1 +1 @@
-MD5 (AcePerl-1.75.tar.gz) = a59ce125e8373710bd18191464558cb0
+MD5 (AcePerl-1.82.tar.gz) = e90c1e3d1e28b92ce8bdb95704462a0d
diff --git a/biology/p5-AcePerl/files/patch-ac b/biology/p5-AcePerl/files/patch-ac
index 90194f8b38d7..719769644488 100644
--- a/biology/p5-AcePerl/files/patch-ac
+++ b/biology/p5-AcePerl/files/patch-ac
@@ -1,11 +1,20 @@
---- Makefile.PL.orig	Thu Aug 31 19:02:21 2000
-+++ Makefile.PL	Mon Oct  9 16:43:32 2000
-@@ -1,7 +1,7 @@
- use Config;
+--- Makefile.PL.orig	Fri Sep 28 16:13:04 2001
++++ Makefile.PL	Fri Jan 25 14:11:26 2002
+@@ -2,7 +2,7 @@
  use ExtUtils::MakeMaker qw(prompt WriteMakefile);
+ use File::Path;
  
 -my $choice;
 +my $choice = 3;
  while (!$choice) {
    $reply = prompt(
  		  "\nWhat do you want to build?\n\n" .
+@@ -22,8 +22,6 @@
+ push @extlib,'Freesubs' if $choice >= 2;
+ push @extlib,'RPC'      if $choice >= 3;
+ 
+-print "\n";
+-setup_sitedefs() if prompt("Do you want to install Ace::Browser? ","n") =~ /[yY]/;
+ 
+ my $headers  = "./ace/wh";
+ WriteMakefile(
diff --git a/biology/p5-AcePerl/pkg-plist b/biology/p5-AcePerl/pkg-plist
index d07a2459f6b2..587c387bbf2c 100644
--- a/biology/p5-AcePerl/pkg-plist
+++ b/biology/p5-AcePerl/pkg-plist
@@ -9,9 +9,11 @@ lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Fk.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/anchored_arrow.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/arrow.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/box.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/crossbox.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/dot.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/ex.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/graded_segments.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/group.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/line.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/primers.pm
@@ -33,11 +35,11 @@ lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/GappedAlignment.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Gene.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Transcript.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/SocketServer.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF/Filehandle.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.bs
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.so