|
\ No newline at end of file
diff --git a/PhyloWidgetPlugin.zip b/PhyloWidgetPlugin.zip
deleted file mode 100644
index a5dfee3..0000000
Binary files a/PhyloWidgetPlugin.zip and /dev/null differ
diff --git a/PhyloWidgetPlugin_installer b/PhyloWidgetPlugin_installer
deleted file mode 100755
index dbd0fd3..0000000
--- a/PhyloWidgetPlugin_installer
+++ /dev/null
@@ -1,174 +0,0 @@
-#!perl
-#
-# Install script for PhyloWidgetPlugin
-#
-# Copyright (C) 2004-2007 Foswiki Contributors. All Rights Reserved.
-# Foswiki Contributors are listed in the AUTHORS file in the root of
-# this distribution. NOTE: Please extend that file, not this notice.
-#
-# This program 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 2
-# of the License, or (at your option) any later version. For
-# more details read LICENSE in the root of this distribution.
-#
-# This program 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.
-#
-# As per the GPL, removal of this notice is prohibited.
-#
-# Author: Crawford Currie http://c-dot.co.uk
-#
-# NOTE TO THE DEVELOPER: THIS FILE IS GENERATED AUTOMATICALLY
-# BY THE BUILD PROCESS DO NOT EDIT IT - IT WILL BE OVERWRITTEN
-#
-use strict;
-use warnings;
-require 5.008;
-
-use File::Spec;
-use Cwd;
-
-=pod
-
----+ PhyloWidgetPlugin_installer
-This is the installer script. The basic function of this script is to
-locate an archive and unpack it.
-
-It will also check the dependencies listed in DEPENDENCIES and assist
-the user in installing any that are missing. The script also automatically
-maintains the revision histories of any files that are being installed by the
-package but already have ,v files on disc (indicating that they are
-revision controlled).
-
-The script also functions as an *uninstaller* by passing the parameter
-=uninstall= on the command-line. Note that uninstallation does *not* revert
-the history of any topic changed during the installation.
-
-The script allows the definition of PREINSTALL and POSTINSTALL scripts.
-These scripts can be used for example to modify the configuration during
-installation, using the functions described below.
-
-Refer to the documentation of =configure=
-
-=cut
-
-# This is all done in package Foswiki so that reading LocalSite.cfg and Foswiki.cfg
-# will put the config vars into the right namespace.
-package Foswiki;
-
-# The root of package URLs
-my $PACKAGES_URL = 'http://foswiki.org/pub/Extensions';
-
-# Extract MANIFEST and DEPENDENCIES from the __DATA__
-undef $/;
-my @DATA = split( /<<<< (.*?) >>>>\s*\n/, );
-shift @DATA; # remove empty first element
-
-# Establish where we are
-my @path = ( 'tools', 'extender.pl' );
-my $wd = Cwd::cwd();
-$wd =~ /^(.*)$/; # untaint
-unshift( @path, $1 ) if $1;
-my $script = File::Spec->catfile(@path);
-
-unless ( my $return = do $script ) {
- my $message = <;
- close(F);
- $data =~ /^(.*)$/s; # untaint
- eval $1;
- if ($@) {
- $message .= "Error when trying to eval the file content: $@\n";
- }
- else {
- print STDERR
- "'do $script failed, but install was able to proceed: $message";
- undef $message;
- }
- }
- else {
- $message .= "Could not open file using open() either: $!\n";
- }
- die $message if $message;
-}
-
-sub preuninstall {
-
- # # No PREUNINSTALL script;
-}
-
-sub postuninstall {
-
- # # No POSTUNINSTALL script;
-}
-
-sub preinstall {
-
- # # No PREINSTALL script;
-}
-
-sub postinstall {
-
- # # No POSTINSTALL script;
-}
-
-Foswiki::Extender::install( $PACKAGES_URL, 'PhyloWidgetPlugin', 'PhyloWidgetPlugin', @DATA );
-
-1;
-
-# MANIFEST and DEPENDENCIES are done this way
-# to make it easy to extract them from this script.
-
-__DATA__
-<<<< MANIFEST >>>>
-data/System/PhyloWidgetPlugin.txt,0644,
-data/System/PhyloNexusViewer.txt,0644,
-data/System/PhyloWidgetExample.txt,0644,
-data/System/PhyloWidgetViewHelper.txt,0644,
-data/System/VarNEXUSTREES.txt,0644,
-data/System/VarPHYLOWIDGET.txt,0644,
-data/System/ViewTrees.txt,0644,
-lib/Foswiki/Plugins/PhyloWidgetPlugin.pm,0644,
-pub/System/PhyloWidgetExample/Tree.nex,0644,
-pub/System/PhyloWidgetPlugin/bare.html,0644,
-pub/System/PhyloWidgetPlugin/img/pw.ico,0644,
-pub/System/PhyloWidgetPlugin/index.html,0644,
-pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js,0644,
-pub/System/PhyloWidgetPlugin/lib/core.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/freeloader.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/itext.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/loading.gif,0644,
-pub/System/PhyloWidgetPlugin/lib/pdf.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/phylowidget.jar,0644,
-pub/System/PhyloWidgetPlugin/minimal.txt,0644,
-pub/System/PhyloWidgetPlugin/phylotest.html,0644,
-pub/System/PhyloWidgetPlugin/scripts/phylopopup.js,0644,
-pub/System/PhyloWidgetPlugin/scripts/phylowidget.js,0644,
-pub/System/PhyloWidgetPlugin/style.css,0644,
-pub/System/PhyloWidgetPlugin/test.html,0644,
-pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip,0644,
-pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip,0644,
-templates/phylonhx.tmpl,0644,
-
-<<<< DEPENDENCIES >>>>
-Bio::NEXUS,>=0,1,cpan,Required
-Foswiki::Plugins::DBCachePlugin,>=0,1,plugin,Optional, For examples
-
diff --git a/PhyloWidgetPlugin_installer.pl b/PhyloWidgetPlugin_installer.pl
deleted file mode 100644
index dbd0fd3..0000000
--- a/PhyloWidgetPlugin_installer.pl
+++ /dev/null
@@ -1,174 +0,0 @@
-#!perl
-#
-# Install script for PhyloWidgetPlugin
-#
-# Copyright (C) 2004-2007 Foswiki Contributors. All Rights Reserved.
-# Foswiki Contributors are listed in the AUTHORS file in the root of
-# this distribution. NOTE: Please extend that file, not this notice.
-#
-# This program 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 2
-# of the License, or (at your option) any later version. For
-# more details read LICENSE in the root of this distribution.
-#
-# This program 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.
-#
-# As per the GPL, removal of this notice is prohibited.
-#
-# Author: Crawford Currie http://c-dot.co.uk
-#
-# NOTE TO THE DEVELOPER: THIS FILE IS GENERATED AUTOMATICALLY
-# BY THE BUILD PROCESS DO NOT EDIT IT - IT WILL BE OVERWRITTEN
-#
-use strict;
-use warnings;
-require 5.008;
-
-use File::Spec;
-use Cwd;
-
-=pod
-
----+ PhyloWidgetPlugin_installer
-This is the installer script. The basic function of this script is to
-locate an archive and unpack it.
-
-It will also check the dependencies listed in DEPENDENCIES and assist
-the user in installing any that are missing. The script also automatically
-maintains the revision histories of any files that are being installed by the
-package but already have ,v files on disc (indicating that they are
-revision controlled).
-
-The script also functions as an *uninstaller* by passing the parameter
-=uninstall= on the command-line. Note that uninstallation does *not* revert
-the history of any topic changed during the installation.
-
-The script allows the definition of PREINSTALL and POSTINSTALL scripts.
-These scripts can be used for example to modify the configuration during
-installation, using the functions described below.
-
-Refer to the documentation of =configure=
-
-=cut
-
-# This is all done in package Foswiki so that reading LocalSite.cfg and Foswiki.cfg
-# will put the config vars into the right namespace.
-package Foswiki;
-
-# The root of package URLs
-my $PACKAGES_URL = 'http://foswiki.org/pub/Extensions';
-
-# Extract MANIFEST and DEPENDENCIES from the __DATA__
-undef $/;
-my @DATA = split( /<<<< (.*?) >>>>\s*\n/, );
-shift @DATA; # remove empty first element
-
-# Establish where we are
-my @path = ( 'tools', 'extender.pl' );
-my $wd = Cwd::cwd();
-$wd =~ /^(.*)$/; # untaint
-unshift( @path, $1 ) if $1;
-my $script = File::Spec->catfile(@path);
-
-unless ( my $return = do $script ) {
- my $message = <;
- close(F);
- $data =~ /^(.*)$/s; # untaint
- eval $1;
- if ($@) {
- $message .= "Error when trying to eval the file content: $@\n";
- }
- else {
- print STDERR
- "'do $script failed, but install was able to proceed: $message";
- undef $message;
- }
- }
- else {
- $message .= "Could not open file using open() either: $!\n";
- }
- die $message if $message;
-}
-
-sub preuninstall {
-
- # # No PREUNINSTALL script;
-}
-
-sub postuninstall {
-
- # # No POSTUNINSTALL script;
-}
-
-sub preinstall {
-
- # # No PREINSTALL script;
-}
-
-sub postinstall {
-
- # # No POSTINSTALL script;
-}
-
-Foswiki::Extender::install( $PACKAGES_URL, 'PhyloWidgetPlugin', 'PhyloWidgetPlugin', @DATA );
-
-1;
-
-# MANIFEST and DEPENDENCIES are done this way
-# to make it easy to extract them from this script.
-
-__DATA__
-<<<< MANIFEST >>>>
-data/System/PhyloWidgetPlugin.txt,0644,
-data/System/PhyloNexusViewer.txt,0644,
-data/System/PhyloWidgetExample.txt,0644,
-data/System/PhyloWidgetViewHelper.txt,0644,
-data/System/VarNEXUSTREES.txt,0644,
-data/System/VarPHYLOWIDGET.txt,0644,
-data/System/ViewTrees.txt,0644,
-lib/Foswiki/Plugins/PhyloWidgetPlugin.pm,0644,
-pub/System/PhyloWidgetExample/Tree.nex,0644,
-pub/System/PhyloWidgetPlugin/bare.html,0644,
-pub/System/PhyloWidgetPlugin/img/pw.ico,0644,
-pub/System/PhyloWidgetPlugin/index.html,0644,
-pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js,0644,
-pub/System/PhyloWidgetPlugin/lib/core.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/freeloader.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/itext.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/loading.gif,0644,
-pub/System/PhyloWidgetPlugin/lib/pdf.jar,0644,
-pub/System/PhyloWidgetPlugin/lib/phylowidget.jar,0644,
-pub/System/PhyloWidgetPlugin/minimal.txt,0644,
-pub/System/PhyloWidgetPlugin/phylotest.html,0644,
-pub/System/PhyloWidgetPlugin/scripts/phylopopup.js,0644,
-pub/System/PhyloWidgetPlugin/scripts/phylowidget.js,0644,
-pub/System/PhyloWidgetPlugin/style.css,0644,
-pub/System/PhyloWidgetPlugin/test.html,0644,
-pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip,0644,
-pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip,0644,
-templates/phylonhx.tmpl,0644,
-
-<<<< DEPENDENCIES >>>>
-Bio::NEXUS,>=0,1,cpan,Required
-Foswiki::Plugins::DBCachePlugin,>=0,1,plugin,Optional, For examples
-
diff --git a/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST b/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST
index 9123f00..7a1b741 100644
--- a/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST
+++ b/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST
@@ -10,7 +10,6 @@ pub/System/PhyloWidgetExample/Tree.nex 0644
pub/System/PhyloWidgetPlugin/bare.html 0644
pub/System/PhyloWidgetPlugin/img/pw.ico 0644
pub/System/PhyloWidgetPlugin/index.html 0644
-pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js 0644
pub/System/PhyloWidgetPlugin/lib/core.jar 0644
pub/System/PhyloWidgetPlugin/lib/freeloader.jar 0644
pub/System/PhyloWidgetPlugin/lib/itext.jar 0644
@@ -20,7 +19,9 @@ pub/System/PhyloWidgetPlugin/lib/phylowidget.jar 0644
pub/System/PhyloWidgetPlugin/minimal.txt 0644
pub/System/PhyloWidgetPlugin/phylotest.html 0644
pub/System/PhyloWidgetPlugin/scripts/phylopopup.js 0644
+pub/System/PhyloWidgetPlugin/scripts/phylopopup.js.gz 0644
pub/System/PhyloWidgetPlugin/scripts/phylowidget.js 0644
+pub/System/PhyloWidgetPlugin/scripts/phylowidget.js.gz 0644
pub/System/PhyloWidgetPlugin/style.css 0644
pub/System/PhyloWidgetPlugin/test.html 0644
pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip 0644
diff --git a/pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js b/pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js
deleted file mode 100644
index 4985902..0000000
--- a/pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js
+++ /dev/null
@@ -1,3 +0,0 @@
-jQuery(document).ready(function () {
-alert('hi');
-});