diff --git a/data/System/PhyloNexusViewer.txt b/data/System/PhyloNexusViewer.txt index 229c2c7..d1d8f98 100644 --- a/data/System/PhyloNexusViewer.txt +++ b/data/System/PhyloNexusViewer.txt @@ -4,14 +4,15 @@ * Set ATOPIC=%URLPARAM{"qTopic" default="%topic%"}% * Set AATTACH=%URLPARAM{"qAttachment" default="%attachment%"}% --> -
+ +
%PHYLOWIDGET{width="420" height="495" useBranchLengths="true"}%
-
+
%NEXUSTREES{"%URLPARAM{"qWeb" default="%web%"}%/%URLPARAM{"qTopic" default="%topic%"}%" attachment="%URLPARAM{"qAttachment" default="%attachment%"}%" header="

Tree List

$n" format = " * $treeName" separator="$n"}%
- + %ADDTOZONE{ "script" text="" + # "" + "" + #."" + #."" + ."" ."" + #."" + #."" + #."" + #."" + #."" + #."" ); +# my $restUrlPath = Foswiki::Func::getScriptUrl(undef,undef,'rest'); +# Foswiki::Func::addToZone( +# "script", +# "phyloOverlayCode", +# "" +# ."" +# ."", +# 'JQUERYPLUGIN' +# ); + # # # here # my $str = join(',',@str); # my $theurl = Foswiki::Func::getViewUrl($webname,$url); -my $height = $params->{'height'}+6; -my $width = $params->{'width'}+6; + +# add the function that will interface with processClade rest handler + my $mobbs = '%INCLUDE{"System.VarPHYLOWIDGET" section="jscode"}%'; + $mobbs = Foswiki::Func::expandCommonVariables($mobbs); + Foswiki::Func::addToZone('script','jscode','','JQUERY'); + +# add a form to the returned text + my $form = '%INCLUDE{"System.VarPHYLOWIDGET" section="cladeform"}%'; +# $form = Foswiki::Func::addToZone('','',''); + + my $height = $params->{'height'}+6; + my $width = $params->{'width'}+6; my $param = join ',', @tree; - return "
"; + return "
$form
"; +# style='width: $width; height: $height; border: 2px solid; padding: 3px;display:inline-table' # return "
WEB: $theweb url: $thetopic created url: $createdurl
"; # return "

Phylowidget! :)

" . Dumper($params) . '
'; diff --git a/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST b/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST index 35515ab..72bb8f4 100644 --- a/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST +++ b/lib/Foswiki/Plugins/PhyloWidgetPlugin/MANIFEST @@ -5,6 +5,7 @@ data/System/PhyloWidgetViewHelper.txt 0644 data/System/VarNEXUSTREES.txt 0644 data/System/VarPHYLOWIDGET.txt 0644 data/System/PhyloViewTrees.txt 0644 +data/System/PhyloWidgetError.txt 0644 lib/Foswiki/Plugins/PhyloWidgetPlugin.pm 0644 pub/System/PhyloWidgetExample/Tree.nex 0644 pub/System/PhyloWidgetPlugin/bare.html 0644 @@ -26,4 +27,5 @@ 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 +pub/System/PhyloWidgetPlugin/loading.gif 0644 templates/phylonhx.tmpl 0644 diff --git a/pub/System/PhyloWidgetPlugin/lib/core.jar b/pub/System/PhyloWidgetPlugin/lib/core.jar index 1066fb2..10ba410 100644 Binary files a/pub/System/PhyloWidgetPlugin/lib/core.jar and b/pub/System/PhyloWidgetPlugin/lib/core.jar differ diff --git a/pub/System/PhyloWidgetPlugin/lib/freeloader.jar b/pub/System/PhyloWidgetPlugin/lib/freeloader.jar index 7372ecb..ea91f03 100644 Binary files a/pub/System/PhyloWidgetPlugin/lib/freeloader.jar and b/pub/System/PhyloWidgetPlugin/lib/freeloader.jar differ diff --git a/pub/System/PhyloWidgetPlugin/lib/itext.jar b/pub/System/PhyloWidgetPlugin/lib/itext.jar index 0c75c6c..2c45c63 100644 Binary files a/pub/System/PhyloWidgetPlugin/lib/itext.jar and b/pub/System/PhyloWidgetPlugin/lib/itext.jar differ diff --git a/pub/System/PhyloWidgetPlugin/lib/pdf.jar b/pub/System/PhyloWidgetPlugin/lib/pdf.jar index 403ac72..c5b11ad 100644 Binary files a/pub/System/PhyloWidgetPlugin/lib/pdf.jar and b/pub/System/PhyloWidgetPlugin/lib/pdf.jar differ diff --git a/pub/System/PhyloWidgetPlugin/lib/phylowidget.jar b/pub/System/PhyloWidgetPlugin/lib/phylowidget.jar index 822d706..9e66ac5 100644 Binary files a/pub/System/PhyloWidgetPlugin/lib/phylowidget.jar and b/pub/System/PhyloWidgetPlugin/lib/phylowidget.jar differ diff --git a/pub/System/PhyloWidgetPlugin/phylotest.html b/pub/System/PhyloWidgetPlugin/phylotest.html index 8e13451..57ca529 100644 --- a/pub/System/PhyloWidgetPlugin/phylotest.html +++ b/pub/System/PhyloWidgetPlugin/phylotest.html @@ -1,8 +1,8 @@ - + - + diff --git a/pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip b/pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip index 0b13833..783e0ff 100644 Binary files a/pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip and b/pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip differ diff --git a/pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip b/pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip index 9c345a0..ada1aaf 100644 Binary files a/pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip and b/pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip differ