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[Gmod-gbrowse-cmts] SF.net SVN: gmod:[22157] Generic-Genome-Browser/trunk
|
From: <ls...@us...> - 2009-10-13 01:14:12
|
Revision: 22157
http://gmod.svn.sourceforge.net/gmod/?rev=22157&view=rev
Author: lstein
Date: 2009-10-13 01:13:58 +0000 (Tue, 13 Oct 2009)
Log Message:
-----------
reorganized former menubar into a dropdown menu and a tabbed section
Modified Paths:
--------------
Generic-Genome-Browser/trunk/conf/languages/POSIX.pm
Generic-Genome-Browser/trunk/htdocs/css/gbrowse.css
Generic-Genome-Browser/trunk/htdocs/css/gbrowse_warm.css
Generic-Genome-Browser/trunk/htdocs/js/controller.js
Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm
Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm
Added Paths:
-----------
Generic-Genome-Browser/trunk/htdocs/css/dropdown/
Generic-Genome-Browser/trunk/htdocs/css/dropdown/default_theme.css
Generic-Genome-Browser/trunk/htdocs/css/dropdown/dropdown.css
Generic-Genome-Browser/trunk/htdocs/css/dropdown/helper.css
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/favicon.ico
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/icon.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down-on.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down-open.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left-on.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left-open.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right-on.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right-open.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up-on.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up-open.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern1.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern2.png
Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern3.png
Generic-Genome-Browser/trunk/htdocs/js/tabs.js
Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/generic.pm
Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
Modified: Generic-Genome-Browser/trunk/conf/languages/POSIX.pm
===================================================================
--- Generic-Genome-Browser/trunk/conf/languages/POSIX.pm 2009-10-12 22:19:14 UTC (rev 22156)
+++ Generic-Genome-Browser/trunk/conf/languages/POSIX.pm 2009-10-13 01:13:58 UTC (rev 22157)
@@ -509,4 +509,8 @@
("wiggle" files) and uploaded files can not be shared using DAS.</i>
END
+ MAIN_PAGE => 'Browser',
+ CUSTOM_TRACKS_PAGE => 'Upload and Share Tracks',
+ SETTINGS_PAGE => 'Preferences',
+
};
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/default_theme.css
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/css/dropdown/default_theme.css (rev 0)
+++ Generic-Genome-Browser/trunk/htdocs/css/dropdown/default_theme.css 2009-10-13 01:13:58 UTC (rev 22157)
@@ -0,0 +1,139 @@
+@charset "UTF-8";
+
+/**
+ * Flickr CSS Drop-Down Menu Theme
+ *
+ * @file default.css
+ * @name Flickr
+ * @version beta
+ * @type transitional
+ * @browsers Windows: IE5+, Opera7+, Firefox1+
+ * Mac OS: Safari2+, Firefox2+
+ *
+ * @link http://www.lwis.net/
+ * @copyright 2008 Live Web Institute. All Rights Reserved.
+ *
+ */
+
+/* @import "helper.css"; */
+
+
+/*-------------------------------------------------/
+ * @section Base Drop-Down Styling
+ * @structure ul (unordered list)
+ * ul li (list item)
+ * ul li a (links)
+ * /*\.class|(li|a):hover/
+ * @level sep ul
+ */
+
+
+ul.dropdown {
+ padding-bottom: 1px;
+ background: url(images/pattern1.png) 0 100% repeat-x;
+ font: bold 13px/normal Arial, Helvetica, sans-serif;
+}
+
+ ul.dropdown li {
+ padding: 4px 6px;
+ color: #0063dc;
+ }
+
+ ul.dropdown li.divider {
+ border-top: solid 1px #e5e5e5;
+ }
+
+ ul.dropdown li.hover,
+ ul.dropdown li:hover {
+ color: #0063dc;
+ }
+
+ ul.dropdown a:link,
+ ul.dropdown a:visited { color: #0063dc; text-decoration: none; }
+ ul.dropdown a:hover { color: #0063dc; text-decoration: underline; }
+ ul.dropdown a:active { color: #ff0084; }
+
+
+ /* -- level mark -- */
+
+ ul.dropdown ul {
+ width: 150px;
+ padding: 3px 6px;
+ border-style: solid;
+ border-width: 1px;
+ border-color: #f0f0f0 #666 #666 #f0f0f0;
+ background-color: #fff;
+ font-weight: normal;
+ font-size: 11px;
+ }
+
+ ul.dropdown ul li {
+ }
+
+
+
+/*-------------------------------------------------/
+ * @section Support Class `dir`
+ * @level sep ul, .class
+ */
+
+
+ul.dropdown *.dir {
+ padding-right: 25px;
+ background-image: url(images/nav-arrow-down.png);
+ background-position: 95% 50%;
+ background-repeat: no-repeat;
+}
+
+
+/* -- Components override -- */
+
+ul.dropdown-vertical ul {
+ top: 0;
+ left: 100%;
+}
+
+ul.dropdown-vertical-rtl ul {
+ right: 100%;
+}
+
+ul.dropdown-horizontal,
+ul.dropdown-linear,
+ul.dropdown-upward {
+ width: 100%;
+}
+
+ul.dropdown-horizontal ul *.dir {
+ padding-right: 25px;
+ background-image: url(images/nav-arrow-right.png);
+ background-position: 100% 50%;
+ background-repeat: no-repeat;
+}
+
+ul.dropdown-upward *.dir {
+ background-image: url(images/nav-arrow-up.png);
+}
+
+ul.dropdown-vertical *.dir {
+ background-image: url(images/nav-arrow-right.png);
+ background-position: 180px 50%;
+}
+
+ul.dropdown-vertical ul *.dir,
+ul.dropdown-upward ul *.dir {
+ background-image: url(images/nav-arrow-right.png);
+ background-position: 100% 50%;
+}
+
+ul.dropdown-vertical-rtl *.dir {
+ padding-right: 6px;
+ padding-left: 25px;
+ background-image: url(images/nav-arrow-left.png);
+ background-position: 5px 50%;
+}
+
+ul.dropdown-vertical-rtl ul *.dir {
+ padding-right: 0;
+ background-image: url(images/nav-arrow-left.png);
+ background-position: 0 50%;
+}
\ No newline at end of file
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/dropdown.css
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/css/dropdown/dropdown.css (rev 0)
+++ Generic-Genome-Browser/trunk/htdocs/css/dropdown/dropdown.css 2009-10-13 01:13:58 UTC (rev 22157)
@@ -0,0 +1,83 @@
+@charset "UTF-8";
+
+/**
+ * Horizontal CSS Drop-Down Menu Module
+ *
+ * @file dropdown.css
+ * @package Dropdown
+ * @version 0.7.1
+ * @type Transitional
+ * @stacks 597-599
+ * @browsers Windows: IE6+, Opera7+, Firefox1+
+ * Mac OS: Safari2+, Firefox2+
+ *
+ * @link http://www.lwis.net/
+ * @copyright 2006-2008 Live Web Institute. All Rights Reserved.
+ *
+ */
+
+ul.dropdown,
+ul.dropdown li,
+ul.dropdown ul {
+ list-style: none;
+ margin: 0;
+ padding: 0;
+}
+
+ul.dropdown {
+ position: relative;
+ z-index: 597;
+ float: left;
+}
+
+ul.dropdown li {
+ float: left;
+ line-height: 1.3em;
+ vertical-align: middle;
+ zoom: 1;
+}
+
+ul.dropdown li.hover,
+ul.dropdown li:hover {
+ position: relative;
+ z-index: 599;
+ cursor: default;
+}
+
+ul.dropdown ul {
+ visibility: hidden;
+ position: absolute;
+ top: 100%;
+ left: 0;
+ z-index: 598;
+ width: 100%;
+}
+
+ul.dropdown ul li {
+ float: none;
+}
+
+ul.dropdown ul ul {
+ top: 1px;
+ left: 99%;
+}
+
+ul.dropdown li:hover > ul {
+ visibility: visible;
+}
+
+
+
+
+
+ul.dropdown li.rtl ul {
+ top: 100%;
+ right: 0;
+ left: auto;
+}
+
+ul.dropdown li.rtl ul ul {
+ top: 1px;
+ right: 99%;
+ left: auto;
+}
\ No newline at end of file
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/helper.css
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/css/dropdown/helper.css (rev 0)
+++ Generic-Genome-Browser/trunk/htdocs/css/dropdown/helper.css 2009-10-13 01:13:58 UTC (rev 22157)
@@ -0,0 +1,37 @@
+
+* {
+ margin: 0;
+ padding: 0;
+ outline: none;
+}
+
+body {
+ padding: 50px;
+ background: #fff url(images/pattern3.png) 0 0 repeat-x;
+ font: 14px/normal Tahoma, Arial, Helvetica, sans-serif;
+}
+
+p { margin-bottom: 1em; }
+
+ul.classic {
+ list-style: disc;
+ margin-bottom: 1em;
+ padding-left: 2em;
+}
+
+h1,h2,h3 {
+ margin-bottom: .5em;
+ font-family: Arial, Helvetica, sans-serif;
+}
+
+h1 {
+ border-bottom: solid 1px #d9d9d9;
+ font-weight: normal;
+ font-size: 180%;
+ text-indent: 5px;
+ letter-spacing: -1px;
+}
+
+.dropdown-upward {
+ margin-top: 400px !important;
+}
\ No newline at end of file
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/favicon.ico
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/favicon.ico
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/icon.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/icon.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down-on.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down-on.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down-open.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down-open.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-down.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left-on.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left-on.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left-open.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left-open.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-left.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right-on.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right-on.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right-open.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right-open.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-right.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up-on.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up-on.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up-open.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up-open.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/nav-arrow-up.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern1.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern1.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern2.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern2.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern3.png
===================================================================
(Binary files differ)
Property changes on: Generic-Genome-Browser/trunk/htdocs/css/dropdown/images/pattern3.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: Generic-Genome-Browser/trunk/htdocs/css/gbrowse.css
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/css/gbrowse.css 2009-10-12 22:19:14 UTC (rev 22156)
+++ Generic-Genome-Browser/trunk/htdocs/css/gbrowse.css 2009-10-13 01:13:58 UTC (rev 22157)
@@ -31,6 +31,7 @@
}
DIV { margin: 0 }
H1 { color: navy;
+ font-size: medium;
font-family: sans-serif;
}
H2 { color: navy;
Modified: Generic-Genome-Browser/trunk/htdocs/css/gbrowse_warm.css
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/css/gbrowse_warm.css 2009-10-12 22:19:14 UTC (rev 22156)
+++ Generic-Genome-Browser/trunk/htdocs/css/gbrowse_warm.css 2009-10-13 01:13:58 UTC (rev 22157)
@@ -36,3 +36,46 @@
font-size: small;
margin-left: 1em;
}
+.tabmenu_active { cursor: pointer;
+ color: black;
+ background-color: beige;
+ font-size: 10pt;
+ font-weight: bold;
+ font-family: sans-serif;
+ padding-top: 5px;
+ padding-left: 5px;
+ padding-right: 5px;
+ }
+.tabmenu_inactive { cursor: pointer;
+ color: blue;
+ font-size: 10pt;
+ background-color: transparent;
+ font-weight: bold;
+ font-family: sans-serif;
+ padding-top: 5px;
+ padding-left: 5px;
+ padding-right: 5px;
+ }
+.tabmenu_inactive:hover {
+ text-decoration: underline;
+}
+.tabbed {
+ background-color: beige;
+}
+.tabmenu {
+ background-color: white;
+}
+.menutitle {
+ color: blue;
+ font-size: 10pt;
+ background-color: transparent;
+ font-weight: bold;
+ font-family: sans-serif;
+ cursor: pointer;
+ padding-top: 5px;
+ padding-left: 5px;
+ padding-right: 5px;
+}
+.menutitle:hover {
+ text-decoration: underline;
+}
Modified: Generic-Genome-Browser/trunk/htdocs/js/controller.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/controller.js 2009-10-12 22:19:14 UTC (rev 22156)
+++ Generic-Genome-Browser/trunk/htdocs/js/controller.js 2009-10-13 01:13:58 UTC (rev 22157)
@@ -967,6 +967,9 @@
Details.prototype.initialize();
if ($('autocomplete_choices') != null)
initAutocomplete();
+
+ // These statements initialize the tabbing
+ new TabbedSection(['main_page','custom_tracks_page','settings_page']);
}
// set the colors for the rubberband regions
Added: Generic-Genome-Browser/trunk/htdocs/js/tabs.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/tabs.js (rev 0)
+++ Generic-Genome-Browser/trunk/htdocs/js/tabs.js 2009-10-13 01:13:58 UTC (rev 22157)
@@ -0,0 +1,38 @@
+// $Id$
+
+var TabbedSection = Class.create( {
+
+ initialize:
+ function (tabs,initial) {
+ if (initial==null) initial = 0;
+ this.tab_divs = tabs.map(function(e) { return $(e) });
+ this.tab_menus = tabs.map(function(e) { return $(e+'_select') });
+ for (var i=0;i<tabs.length;i++) {
+ if (i != initial) this.tab_divs[i].hide();
+ Event.observe(this.tab_menus[i],
+ 'click',
+ this.select_tab_event.bindAsEventListener(this));
+ this.tab_menus[i].className =
+ i==initial ? 'tabmenu_active' : 'tabmenu_inactive';
+ }
+ },
+
+ select_tab_event:
+ function(event) {
+ var menu = Event.element(event);
+ var id = menu.id;
+ var whichOne;
+ for (var i=0;i<this.tab_menus.length;i++) {
+ if (this.tab_menus[i].id == id)
+ whichOne=i;
+ }
+ this.tab_menus.each(
+ function(e) {
+ e.className='tabmenu_inactive';
+ });
+ this.tab_divs.each(function(e) {e.hide()});
+ this.tab_menus[whichOne].className='tabmenu_active';
+ this.tab_divs[whichOne].show();
+ }
+
+}); // end Class.create
\ No newline at end of file
Added: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/generic.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/generic.pm (rev 0)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/generic.pm 2009-10-13 01:13:58 UTC (rev 22157)
@@ -0,0 +1,154 @@
+package Bio::Graphics::Browser2::DataLoader::generic;
+
+# $Id$
+use strict;
+use Bio::DB::SeqFeature::Store;
+use Carp 'croak';
+use base 'Bio::Graphics::Browser2::DataLoader';
+
+sub start_load {
+ my $self = shift;
+ my $track_name = $self->track_name;
+ my $data_path = $self->data_path;
+
+ my $db = $self->create_database($data_path);
+ warn "db = $db";
+ my $loader_class = $self->Loader;
+ eval "require $loader_class" unless $loader_class->can('new');
+ my $loader = $loader_class->new(-store=> $db,
+ -fast => 0,
+ -index_subfeatures=>0,
+ );
+ warn "starting load";
+ $loader->start_load();
+ $self->{loader} = $loader;
+ $self->{conflines} = [];
+ $self->state('config');
+}
+
+sub Loader {
+ croak "The Loader() class method must be implemented in a subclass";
+}
+
+sub finish_load {
+ my $self = shift;
+
+ $self->loader->finish_load();
+ my $db = $self->loader->store;
+ my $conf = $self->conf_fh;
+ my $trackname = $self->track_name;
+ my $dsn = $self->dsn;
+ my $backend = $self->backend;
+
+ my $trackno = 0;
+ my $loadid = $self->loadid;
+ $self->set_status('creating configuration');
+
+ print $conf <<END;
+[$loadid:database]
+db_adaptor = Bio::DB::SeqFeature::Store
+db_args = -adaptor $backend
+ -dsn $dsn
+
+END
+
+ if (my @lines = @{$self->{conflines}}) { # good! user has provided some config hints
+ my $in_sub;
+ for my $line (@lines) {
+ if ($line =~ /^\[/) { # overwrite track names to avoid collisions
+ my $trackname = $self->new_track_label;
+ print $conf "[$trackname]\n";
+ print $conf "database = $loadid\n" ;
+ print $conf "category = My Tracks:Uploaded Tracks:",$self->track_name,"\n";
+ } elsif ($line =~ s/(=\s*)(sub .*)/$1 1 # no user subs allowed! $2/) {
+ $in_sub++;
+ print $conf $line;
+ } elsif ($in_sub && $line =~ /^\s+/) { # continuation line
+ $line =~ s/^/# /; # continuation line of
+ print $conf $line;
+ } else {
+ undef $in_sub;
+ print $conf $line;
+ }
+ }
+ } else { # make something up
+ my @types = eval {$db->toplevel_types};
+ @types = $db->types unless @types;
+ my $filename = $self->track_name;
+ for my $t (@types) {
+ my $trackname = $self->new_track_label;
+
+ my ($glyph,$stranded);
+ # start of a big heuristic section
+ if ($t =~ /gene|cds|exon|mRNA|transcript/i) {
+ $glyph = 'gene';
+ $stranded = 0;
+ } else {
+ $glyph = 'segments';
+ $stranded = 1;
+ }
+
+
+ print $conf <<END;
+[$trackname]
+database = $loadid
+feature = $t
+glyph = $glyph
+bgcolor = blue
+label = 1
+stranded = $stranded
+connector = solid
+balloon hover = sub {my \$f=shift;join ' ',\$f->attributes('Note')}
+category = My Tracks:Uploaded Tracks:$filename
+key = $t
+
+END
+ }
+ }
+}
+
+sub loader {shift->{loader}}
+sub state {
+ my $self = shift;
+ my $d = $self->{state};
+ $self->{state} = shift if @_;
+ $d;
+}
+sub load_line {
+ my $self = shift;
+ my $line = shift;
+
+ my $old_state = $self->state;
+ my $state = $self->_state_transition($old_state,$line);
+
+ if ($state eq 'data') {
+ $self->loader->load_line($line);
+ } elsif ($state eq 'config') {
+ push @{$self->{conflines}},$line;
+ }
+ $self->state($state) if $state ne $old_state;
+}
+
+# shamelessly copied from Bio::Graphics:;FeatureFile.
+sub _state_transition {
+ my $self = shift;
+ my ($current_state,$line) = @_;
+
+ if ($current_state eq 'data') {
+ return 'config' if $line =~ m/^\s*\[([^\]]+)\]/; # start of a configuration section
+ }
+
+ elsif ($current_state eq 'config') {
+ return 'data' if $line =~ /^\#\#(\w+)/; # GFF3 meta instruction
+ return 'data' if $line =~ /^reference\s*=/; # feature-file reference sequence directive
+
+ return 'config' if $line =~ /^\s*$/; #empty line
+ return 'config' if $line =~ m/^\[([^\]]+)\]/; # section beginning
+ return 'config' if $line =~ m/^[\w\s]+=/; # arg = value
+ return 'config' if $line =~ m/^\s+(.+)/; # continuation line
+ return 'config' if $line =~ /^\#/; # comment -not a meta
+ return 'data';
+ }
+ return $current_state;
+}
+1;
Added: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/gff3.pm (rev 0)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/DataLoader/gff3.pm 2009-10-13 01:13:58 UTC (rev 22157)
@@ -0,0 +1,12 @@
+package Bio::Graphics::Browser2::DataLoader::gff3;
+
+# $Id$
+use strict;
+use base 'Bio::Graphics::Browser2::DataLoader::generic';
+
+sub Loader {
+ return 'Bio::DB::SeqFeature::Store::GFF3Loader';
+}
+
+
+1;
Modified: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm 2009-10-12 22:19:14 UTC (rev 22156)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm 2009-10-13 01:13:58 UTC (rev 22157)
@@ -37,17 +37,11 @@
my $html = '';
$html .= $self->render_user_header;
- if ($self->setting('login script')) {
- $html .= $self->render_login;
- }
-
$html .= $self->render_title($title,$self->state->{name}
&& @$features == 0);
$html .= $self->html_frag('html1',$self->state);
- $html .= $self->render_instructions;
return $err
- . $self->toggle({nodiv=>1},'banner','',$html)
- . $self->render_links;
+ . $self->toggle({nodiv=>1},'banner','',$html);
}
sub render_error_div {
@@ -71,6 +65,27 @@
);
}
+sub render_tabbed_pages {
+ my $self = shift;
+ my ($main_html,$custom_tracks_html,$settings_html) = @_;
+ my $main_title = $self->tr('MAIN_PAGE');
+ my $custom_tracks_title = $self->tr('CUSTOM_TRACKS_PAGE');
+ my $settings_title = $self->tr('SETTINGS_PAGE');
+
+ my $html = '';
+ $html .= div({-id=>'tabbed_section',-class=>'tabbed'},
+ div({-id=>'tabbed_menu',-class=>'tabmenu'},
+ span({id=>'main_page_select'}, $main_title),
+ span({id=>'custom_tracks_page_select'},$custom_tracks_title),
+ span({id=>'settings_page_select'},$settings_title)
+ ),
+ span({-id=>'main_page'}, $main_html),
+ span({-id=>'custom_tracks_page'},$custom_tracks_html),
+ span({-id=>'settings_page'}, $settings_html)
+ );
+ return $html;
+}
+
sub render_user_head {
my $self = shift;
my $settings = $self->state;
@@ -272,6 +287,7 @@
balloon.config.js
GBox.js
ajax_upload.js
+ tabs.js
controller.js
);
@@ -293,6 +309,8 @@
my $stylesheet = $self->setting('stylesheet')||'/gbrowse/gbrowse.css';
push @stylesheets,{src => $self->globals->resolve_path('css/tracks.css','url')};
push @stylesheets,{src => $self->globals->resolve_path('css/karyotype.css','url')};
+ push @stylesheets,{src => $self->globals->resolve_path('css/dropdown/dropdown.css','url')};
+ push @stylesheets,{src => $self->globals->resolve_path('css/dropdown/default_theme.css','url')};
push @stylesheets,{src => $self->globals->resolve_path($titlebar,'url')};
# colors for "rubberband" selection
@@ -368,6 +386,7 @@
GBox.allowEventHandlers = true;
GBox.opacity = 1;
GBox.fontFamily = 'sans-serif';
+GBox.stemHeight = 0;
END
;
@@ -458,14 +477,14 @@
$html = '';
if ($session->private) {
- $html .= div({-style=>'float:right;font-weight:bold;color:black;'},
+ $html .= span({-style=>'float:right;font-weight:bold;color:black;'},
'Welcome, '.$session->username.'.') . br() .
- div({-style => $style,
- -title => 'Click here to log out from '.$session->username.'',
- -onMouseDown => 'location.href=\'?id=logout\';',
- -onMouseOver => 'this.style.textDecoration=\'underline\'',
- -onMouseOut => 'this.style.textDecoration=\'none\''}, 'Log Out') .
- div({-style=>'float:right;font-weight:bold;color:black;'}, ' ');
+ span({-style => $style,
+ -title => 'Click here to log out from '.$session->username.'',
+ -onMouseDown => 'location.href=\'?id=logout\';',
+ -onMouseOver => 'this.style.textDecoration=\'underline\'',
+ -onMouseOut => 'this.style.textDecoration=\'none\''}, 'Log Out') .
+ span({-style=>'float:right;font-weight:bold;color:black;'}, ' ');
$title = 'Click here to change your account settings';
$text = 'My Account';
@@ -477,12 +496,14 @@
$click .= 'load_login_balloon(event,\''.$session->id.'\',false,false);';
}
- $html .= div({-style => $style, -title => $title, -onMouseDown => $click,
+ $html .= span({-style => $style, -title => $title, -onMouseDown => $click,
-onMouseOver => 'this.style.textDecoration=\'underline\'',
-onMouseOut => 'this.style.textDecoration=\'none\''}, $text);
- my $container = div({-style=>'float:right;'},$html);
+ return $settings->{head} ? $html : '';
+ my $container = span({-style=>'float:right;'},$html);
+
return $settings->{head} ? $container : '';
}
@@ -552,6 +573,72 @@
: '';
}
+# sub render_actionmenu {
+# my $self = shift;
+# my $login = $self->setting('login script') ? $self->render_login : '';
+# my $file_menu = br([qw(one two three four)]);
+# return div({-id=>'actionmenu',
+# -style=>'background-color:lightgray'},
+# $login,
+# span({-class=>'menutitle',
+# -onMouseDown=>"GBox.showTooltip(event,'$file_menu',0)"
+# },'File'),
+# span({-class=>'menutitle'},'Help'));
+# }
+
+sub render_actionmenu {
+ my $self = shift;
+ my $settings = $self->state;
+
+ my $svg_link = HAVE_SVG
+ ? a({-href=>'?make_image=GD::SVG',-target=>'_blank'}, $self->tr('SVG_LINK'))
+ : '';
+
+ my $pdf_link = HAVE_SVG && $self->can_generate_pdf()
+ ? a({-href=>'?make_image=PDF', -target=>'_blank'},$self->tr('PDF_LINK'))
+ : '';
+
+ my $reset_link = a({-href=>'?reset=1',-class=>'reset_button'}, $self->tr('RESET'));
+ my $help_link = a({-href=>$self->general_help(),-target=>'help'},$self->tr('Help'));
+ my $plugin_link = $self->plugin_links($self->plugins);
+ my $galaxy_link = a({-href=>'javascript:'.$self->galaxy_link}, $self->tr('SEND_TO_GALAXY'));
+ my $image_link = a({-href=>'?make_image=GD',-target=>'_blank'}, $self->tr('IMAGE_LINK'));
+ my $rand = substr(md5_hex(rand),0,5);
+
+
+ my @standard_links = ($reset_link);
+
+
+ my @segment_showing_links =(
+ a({-href=>'?action=bookmark'},$self->tr('BOOKMARK')),
+ a({-href => '#',
+ -onMouseDown => "GBox.showTooltip(event,'url:?action=share_track;track=all')"},
+ ($self->tr('SHARE_ALL') || "Share These Tracks" )),
+ $plugin_link,
+ $galaxy_link,
+ $image_link,
+ $svg_link,
+ $pdf_link,
+ );
+
+ my $segment_present = $self->region->feature_count == 1;
+ my @links = $segment_present ? (@segment_showing_links,@standard_links)
+ : @standard_links;
+
+ my $login = $self->setting('login script') ? $self->render_login : '';
+
+ my $file_menu = ul({-id => 'actionmenu',
+ -class => 'dropdown downdown-horizontal'},
+ li({-class=>'dir'},'File',
+ ul(li(\@links))
+ ),
+ li({-class=>'dir'},'About',
+ ul(li($help_link))),
+ );
+ return $file_menu.$login.br({-clear=>'all'});
+}
+
+
sub render_links {
my $self = shift;
my $settings = $self->state;
@@ -1040,34 +1127,40 @@
)
)
) . end_form();
-
- return $self->toggle( 'Display_settings', $content );
+# return $self->toggle( 'Display_settings', $content );
+ return div($content);
}
# This surrounds the external table with a toggle
sub render_toggle_external_table {
my $self = shift;
- return a({-name=>'upload_tracks'},
- $self->toggle('upload_tracks',
- $self->render_external_table()
- )
- );
+ return div($self->render_external_table());
+# return a({-name=>'upload_tracks'},
+# $self->toggle('upload_tracks',
+# $self->render_external_table()
+# )
+# );
}
sub render_toggle_userdata_table {
my $self = shift;
- return $self->toggle('userdata_table',
- $self->render_userdata_table(),
- $self->userdata_upload(),
- );
+ return div($self->render_userdata_table(),
+ $self->userdata_upload());
+# return $self->toggle('userdata_table',
+# $self->render_userdata_table(),
+# $self->userdata_upload(),
+# );
}
sub render_toggle_import_table {
my $self = shift;
- return $self->toggle('userimport_table',
- $self->render_userimport_table(),
- $self->userdata_import(),
- );
+ return div(h2('Imported Tracks'),
+ $self->render_userimport_table(),
+ $self->userdata_import());
+# return $self->toggle('userimport_table',
+# $self->render_userimport_table(),
+# $self->userdata_import(),
+# );
}
sub render_external_table {
@@ -1174,8 +1267,8 @@
sub render_userimport_table {
my $self = shift;
my $html = div( { -id => 'userimport_table_div',-class=>'uploadbody' },
- # foo
- );
+ ''
+ );
}
sub list_userdata {
@@ -1317,7 +1410,7 @@
END
;
- return $html;
+ return h2('Upload and Share').$html;
}
sub get_uploaded_file_info {
Modified: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm 2009-10-12 22:19:14 UTC (rev 22156)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm 2009-10-13 01:13:58 UTC (rev 22157)
@@ -634,43 +634,70 @@
my $title = $self->generate_title($features);
- print $self->render_html_start($title);
- print $self->render_top($title,$features);
- print $self->render_navbar($region->seg);
+ my $output;
+ $output .= $self->render_html_start($title);
+ $output .= $self->render_actionmenu;
+ $output .= $self->render_top($title,$features);
+
+# my $main_page = $self->render_instructions;
+# $main_page .= $self->render_links();
+
+ my $main_page .= $self->render_navbar($region->seg);
+
if ($region->feature_count > 1) {
- print $self->render_multiple_choices($features,$self->state->{name});
- print $self->render_toggle_track_table;
- print $self->render_upload_share_section;
+ $main_page .= $self->render_multiple_choices($features,$self->state->{name});
+ $main_page .= $self->render_toggle_track_table;
}
elsif (my $seg = $region->seg) {
- print $self->render_panels($seg,{overview=>1,regionview=>1,detailview=>1});
- print $self->render_toggle_track_table;
- print $self->render_upload_share_section;
- print $self->render_galaxy_form($seg);
+ $main_page .= $self->render_panels($seg,{overview=>1,regionview=>1,detailview=>1});
+ $main_page .= $self->render_toggle_track_table;
+ $main_page .= $self->render_galaxy_form($seg);
}
else {
- print $self->render_toggle_track_table;
- print $self->render_upload_share_section;
+ $main_page .= $self->render_toggle_track_table;
}
- print $self->render_global_config();
- print $self->render_bottom($features);
- if (param('confirm') && param('code') && param('id')) {
- print $self->render_login_account_confirm(param('code'));
- }
+ my $upload_share = $self->render_upload_share_section;
+ my $global_config = $self->render_global_config;
- if (param('openid_confirm') && param('page') && param('s')) {
- print $self->render_login_openid_confirm(param('page'),param('s'));
- }
+ $output .= $self->render_tabbed_pages($main_page,$upload_share,$global_config);
+ $output .= $self->render_bottom($features);
+
+ warn "got here";
+
+ print $output;
}
+sub render_actionmenu {
+ my $self = shift;
+ croak "implement in subclass";
+}
+
+sub render_tabbed_pages {
+ my $self = shift;
+ my ($main,$upload_share,$config) = @_;
+ croak "implement in subclass";
+}
+
+sub render_login_section {
+ my $self = shift;
+ my $output = '';
+
+ if (param('confirm') && param('code') && param('id')) {
+ $output .= $self->render_login_account_confirm(param('code'));
+ }elsif (param('openid_confirm') && param('page') && param('s')) {
+ $output .= $self->render_login_openid_confirm(param('page'),param('s'));
+ }
+ return $output;
+}
+
sub render_upload_share_section {
my $self = shift;
if ($self->setting('activate userdata table')) {
- return $self->render_toggle_userdata_table.
- $self->render_toggle_import_table;
+ return div($self->render_toggle_userdata_table,
+ $self->render_toggle_import_table);
} else {
return $self->render_toggle_external_table;
}
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