GBrowse
view release on metacpan or search on metacpan
2.10 Tue Jun 15 10:58:32 EDT 2010
* Fully generalized subtrack creation.
2.09 Mon May 24 18:45:48 PDT 2010
* To turn off caching of the config file (which is causing deparse errors for some
callbacks) set the environment variable GBROWSE_NOCACHE to a true value
(like "1" or "yes"). This must be done in the Apache config.
* Fixed various bugs in the processing of SAM and BAM files.
* BAM parser now creates BigWig indexes if library is available.
* Fixed "no overloaded magic in Bio::DAS::Segment" error.
* Made Menus and tabbed section labels larger (if you don't like,
edit htdocs/css/dropdown/default-theme.css).
* Moved track table into its own tabbed section.
* TrackFinder plugin now hilights the matches in the track table.
* New "subtrack table" and "subtrack select" options allow you to create nice
sortable tables of potential subtracks. The old "select" option is still
supported, but deprecated.
* Added "kewl" blinds down effect when changing tabs.
* Greatly improved track configuration.
* From E.O. Stinson: added fixes for embedding GBrowse in other web pages.
* From E.O. Stinson: Added support for regex-style datasources that let you define
conf/plugins/PrimerDesigner.pm view on Meta::CPAN
</script>
JS
}
sub detail_select_menu {
<<DETAILS;
<div id="detailSelectMenu">
<table style="width:100%">
<tr>
<th style="background:lightgrey;cell-padding:5">
SELECTION
<a style="right:0px;position:absolute;color:blue;cursor:pointer"
onclick="oPrimerDesigner.unselectRegion()">
[X]
</a>
</th>
</tr>
docs/pod/CONFIGURE_HOWTO.pod view on Meta::CPAN
Bio::DB::SeqFeature::Store database is a bit smarter about searching,
and will only, by default, search attributes named "Note". You can
expand the search by giving a list of attribute names to the "search
attributes" option.
=item * remote sources
This option allows you to add remote annotation sources to the menu of such
sources at the bottom of the main window. The format is:
remote sources = "Menu Label 1" http://url1.host.com/etc/etc
"Menu Label 2" http://url2.host.com/etc/etc
=item * instructions, search_instructions, navigation_instructions
You may override the default instructions (as defined in the language-specific
configuration files in conf/lang) by setting these options. For example:
instructions = "Type in the name of a contig or clone."
=item * no search
htdocs/css/dropdown/default_theme.css view on Meta::CPAN
@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.
htdocs/css/dropdown/dropdown.css view on Meta::CPAN
@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/
htdocs/js/controller.js view on Meta::CPAN
parameters: {
action: 'render_panels'
},
onSuccess: function(transport) {
$('panels').innerHTML = transport.responseText;
$('panels').innerHTML.evalScripts();
var color = overviewObject.background;
var unit = overviewObject.unit;
var divider = overviewObject.divider;
['overview','region','detail'].each(function(e) {
var m = $(e+'SelectMenu');
if (m) m.remove();
});
this.initialize_page();
set_dragcolors(color);
set_dragunits(unit,divider);
}
});
}, //end render_panels()
htdocs/js/detailSelect.js view on Meta::CPAN
// var help = '<b>Scalebar:</b> Click here to recenter or click and drag left or right to select a region';
// detailBalloon.showTooltip(event,help,0,250);
// }
// i.onmouseover = helpFunction;
// }
// catch(e) {
// i.setAttribute('title','click and drag to select a region');
// }
self.scalebar = i;
self.addSelectMenu('detail');
self.addSelectBox('detail');
detailsObject = self;
}
Details.prototype.startSelection = function(event) {
var self = detailsObject;
var evt = event || window.event;
SelectArea.prototype.startRubber(self,event);
}
htdocs/js/detailSelect.js view on Meta::CPAN
this.padLeft += actualWidth - expectedWidth;
}
// We fetch the left margin again because the controller can change
// the size & position of the section after it is created.
this.left = this.elementLocation($(this.imageId),'x1') - this.elementLocation(this.selectLayer,'x1');
this.pixelStart = this.left + this.padLeft;
}
Details.prototype.formatMenu = function() {
this.menuHTML = this.selectMenu.innerHTML || '\
<table style="width:100%">\
<tr>\
<th style="background:lightgrey;cell-padding:5">\
SELECTION\
<a style="right:0px;position:absolute" href="javascript:SelectArea.prototype.cancelRubber()">\
[X]\
</a>\
</th>\
</tr>\
<tr>\
htdocs/js/login.js view on Meta::CPAN
var LoginScript = '../../gbrowse/';
var Logged = false;
var OpenIDMenu = false;
var ImgLocation, AppName, AppNameLong; // General Information
var Source, CurrentUser, SessionID, LoginPage, EditDetails; // Dynamic Variables
var UsingOpenID, OpenIDCount, SelectedID; // OpenID Variables
////////////////////////////////////////////////////////////////////////////////////
// Logged = true if the user is logged in, false otherwise.
// OpenIDMenu = true if the user is viewing the openID login menu.
// OpenIDMenu = true if the user is viewing the openID login menu.
// CurrentUser = holds the value of the currently logged in username.
// SessionID = holds the value of the current session id.
// LoginPage = holds the value of the current login page name.
// EditDetails = holds the value of the current account details page name.
// UsingOpenID = true if the user is logged in with an openID only account.
// OpenIDCount = holds the number of openIDs associated with a given account.
// SelectedID = holds the value of the selected openID which is to be removed.
////////////////////////////////////////////////////////////////////////////////////
//Loads the global variables for the rest of the script
htdocs/js/login.js view on Meta::CPAN
if(username != false) {
Logged = true;
CurrentUser = username;
login_page_change('edit');
edit_details('home');
} else {
CurrentUser = '';
}
//Format the login popup accordingly if it is opened with the openid login screen
if(OpenIDMenu) {login_page_openid(true);}
return;
}
//Shows, hides, and changes the titles of elements for a given page in the login popup
function login_page_change(page) {
LoginPage = page;
login_loading(false);
$('loginPass').value = '';
$('loginPass2').value = '';
$('loginWarning').hide();
htdocs/js/login.js view on Meta::CPAN
$('loginButtons').style.paddingTop = '18px';
} else if(page == 'edit') {
$('loginTable').style.paddingTop = '12px';
$('loginButtons').style.paddingTop = '12px';
} else {
$('loginTable').style.paddingTop = '3px';
$('loginButtons').style.paddingTop = '3px';
}
if (Controller.can_openid) {
if(OpenIDMenu && ((page == 'main') || (page == 'edit'))) {
$('loginDOpenid').show(); $('loginNorm').hide(); $('loginDONew').focus();
} else {
$('loginDOpenid').hide(); $('loginNorm').show();
if(page == 'forgot') {$('loginEmail').focus();}
else {$('loginUser').focus();}
}
}
return;
}
htdocs/js/login.js view on Meta::CPAN
if (table == null) return;
var all = table.select('tr');
all.each(function(a){a.hide()});
rows.each(function(a){$(a).show()});
}
//Switches between a normal username/pass form and an openid form
function login_page_openid(openID) {
$('loginWarning').hide();
if(openID) {
OpenIDMenu = true;
$('loginOpenIDY').hide(); $('loginDOpenid').show();
$('loginOpenIDN').show(); $('loginNorm').hide();
$('loginDONew').focus();
login_openid_html('http://youropenidhere',7,14);
} else {
OpenIDMenu = false;
$('loginOpenIDY').show(); $('loginDOpenid').hide();
$('loginOpenIDN').hide(); $('loginNorm').show();
$('loginUser').focus();
}
}
//Used to disable everything while AJAX requests are being processed
function login_loading(toggle) {
if(toggle) {
$('loginSubmit').disabled = true; $('loginCancel').disabled = true;
htdocs/js/login.js view on Meta::CPAN
break;
case 'new-openid':
if(user==0) {
$('loginWarning').innerHTML = Controller.translate('ALL_FIELDS_REQUIRED') + '<br>' + html;
} else {
add_openid_user(CurrentUser,openid);
return;
}
break;
default:
if(OpenIDMenu) {
if(openid.length==0 || openid=='http://' || openid=='https://' || openid.indexOf('.')==-1) {
$('loginWarning').innerHTML = Controller.translate('TYPE_PROPER_OPENID');
} else {
check_openid(openid);
return;
}
} else {
if(user==0 || pass.length==0) {
$('loginWarning').innerHTML = Controller.translate('ALL_FIELDS_REQUIRED');
} else {
htdocs/js/login.js view on Meta::CPAN
login_get_account(results[0].user,results[0].session,results[0].remember,true);
}
}
});
return;
}
//Handle the different cases and error messages associated with openid accounts
function confirm_openid_error(session,page,logged_in,error,openid,only,email,gecos) {
var event = new fakeEvent();
(only == 0 || logged_in) ? OpenIDMenu = false : OpenIDMenu = true;
load_login_balloon(event,session,false,false);
login_blackout(true,'');
if(only == 1) {UsingOpenID=true;}
if(page == 'openid-add') {login_page_change('edit');}
else {login_page_change(page);}
if(error.indexOf('has not been used before.')!=-1 && LoginPage=='main') {
LoginPage = 'new-openid';
CurrentUser = openid;
htdocs/js/menu.js view on Meta::CPAN
// $Id$
var PopupMenu = Class.create( {
initialize:
function (title,options) {
var d = document.createElement('DIV');
d.innerHTML = title;
d.innerHTML += "<br>item1<br>item2<br>item3";
d.setStyle({position: 'absolute',outline: 'black outset 2px'});
d.hide();
this.contents = d;
},
htdocs/js/overviewSelect.js view on Meta::CPAN
img[n].onclick = nullFunc;
}
}
var p = i.parentNode.parentNode;
i = self.replaceImage(i);
self.selectLayer = $('overview_panels');
self.scalebar = i;
self.addSelectMenu('overview');
self.addSelectBox('overview');
overviewObject = self;
}
Overview.prototype.startSelection = function(event) {
var self = overviewObject;
var evt = event || window.event;
SelectArea.prototype.startRubber(self,event);
}
htdocs/js/overviewSelect.js view on Meta::CPAN
// If the keystyle is left, there may be extra padding
var actualWidth = this.elementLocation(i,'width');
var expectedWidth = parseInt(segment_info.overview_width);
if (actualWidth > expectedWidth) {
this.padLeft += actualWidth - expectedWidth;
}
this.pixelStart = this.padLeft;
}
Overview.prototype.formatMenu = function() {
this.menuHTML = this.selectMenu.innerHTML || '\
<div style="padding:5px;text-align:center">\
<b>SELECTION</b><hr>\
<a href="javascript:SelectArea.prototype.clearAndSubmit()">' + Controller.translate('ZOOM') + '</a>\
| \
<a href="javascript:SelectArea.prototype.cancelRubber()">' + Controller.translate('CANCEL') + '</a>\
</div>';
}
htdocs/js/regionSelect.js view on Meta::CPAN
img[n].onclick = nullFunc;
}
}
var p = i.parentNode.parentNode;
i = self.replaceImage(i);
self.selectLayer = p.parentNode.parentNode;
self.scalebar = i;
self.addSelectMenu('region');
self.addSelectBox('region');
regionObject = self;
}
Region.prototype.startSelection = function(event) {
var self = regionObject;
var evt = event || window.event;
SelectArea.prototype.startRubber(self,event);
}
htdocs/js/regionSelect.js view on Meta::CPAN
// If the keystyle is left, there may been extra padding
var actualWidth = this.elementLocation(i,'width');
var expectedWidth = parseInt(segment_info.overview_width);
if (actualWidth > expectedWidth) {
this.padLeft += actualWidth - expectedWidth;
}
this.pixelStart = this.padLeft;
}
Region.prototype.formatMenu = function() {
this.menuHTML = this.selectMenu.innerHTML || '\
<div style="padding:5px;text-align:center">\
<b>SELECTION</b><hr>\
<a href="javascript:SelectArea.prototype.clearAndSubmit()">' + Controller.translate('ZOOM') + '</a>\
| \
<a href="javascript:SelectArea.prototype.cancelRubber()">' + Controller.translate('CANCEL') + '</a>\
</div>';
}
htdocs/js/rubber.js view on Meta::CPAN
selectAreaIsActive = true;
}
SelectArea.prototype.cancelRubber = function() {
var self = currentSelectArea || new SelectArea;
balloonIsSuppressed = false;
if (!self.selectBox) return false;
self.selectBox.setStyle({visibility:'hidden'});
self.selectMenu.setStyle({visibility:'hidden'});
selectAreaIsActive = false;
if (self.originalLandmark) {
document.searchform.name.value = self.originalLandmark;
}
self.moved = false;
}
SelectArea.prototype.round = function(nearest,num) {
if (num > nearest) {
htdocs/js/rubber.js view on Meta::CPAN
el.onselectstart = function() {
return false;
};
el.unselectable = "on";
el.style.MozUserSelect = "none";
el.style.cursor = "default";
}
// Builds the popup menu that appears when selection is complete
SelectArea.prototype.addSelectMenu = function(view) {
var menu = $(view+'SelectMenu');
if (menu) {
this.autoSubmit = false;
}
else {
menu = this.createAndAppend('div',document.body,view+'SelectMenu');
}
// required style
menu = Element.extend(menu);
menu.setStyle({ position: 'absolute',
display: 'block',
zIndex: '101',
visibility: 'hidden'
});
// optional style -- check if a custom menu has styles set already
var existingStyle = new String(menu.getAttribute('style'));
if (existingStyle) {
if (!existingStyle.match(/width/i)) menu.setStyle({ width: this.menuWidth||'200px'});
if (!existingStyle.match(/font/i)) menu.setStyle({ font: '12px sans-serif'});
if (!existingStyle.match(/background/i)) menu.setStyle({ background: 'lightyellow'});
if (!existingStyle.match(/border/i)) menu.setStyle({ border: '1px solid #003366'});
}
this.selectMenu = menu;
this.formatMenu();
}
// Initial creation of the select box
SelectArea.prototype.addSelectBox = function(view) {
var supportsTouch = ('createTouch' in document);
if (this.selectBox) return false;
var box = this.createAndAppend('div',this.selectLayer,view+'selectBox');
htdocs/js/rubber.js view on Meta::CPAN
selectAreaIsActive = false;
self.moved = false;
// autoSubmit option will bypass the menu
if (self.autoSubmit && !self.overrideAutoSubmit) {
SelectArea.prototype.cancelRubber();
//document.searchform.submit();
self.submit();
}
else {
self.showMenu(event);
}
}
SelectArea.prototype.showMenu = function(event) {
var self = currentSelectArea;
var menu = self.selectMenu;
menu.innerHTML = self.menuHTML.replace(/SELECTION/g,self.currentSegment);
var pageWidth =
document.viewport.getWidth();
var menuWidth = self.elementLocation(menu,'width');
var menuHeight = self.elementLocation(menu,'height');
var menuYHalf = Math.round(menuHeight/2);
if ('createTouch' in document){
var left = lefttemp+50;
htdocs/js/rubber.js view on Meta::CPAN
// Abort if there is no selection
if (self.selectBox.getStyle('visibility') == 'hidden') {
self.cancelRubber;
return false;
}
menu.setStyle({ visibility: 'visible' });
}
SelectArea.prototype.hideMenu = function() {
var self = currentSelectArea;
self.selectBox.setStyle({ width: 1,
visibility: 'hidden'
});
self.selectMenu.setStyle({visibility: 'hidden'});
}
SelectArea.prototype.clearAndSubmit = function(plugin,action) {
this.hideMenu();
if (plugin) {
action = action || 'Go';
var url = window.location;
url += '?plugin='+plugin+';plugin_do='+action;
document.location = url;
}
else {
this.submit();
}
}
SelectArea.prototype.clearAndRecenter = function() {
this.hideMenu();
var self = currentSelectArea;
self.loadSegmentInfo();
var start = self.detailStart+'';
start = start.replace(/\D+/,'') * 1;
var end = self.detailEnd+'';
end = end.replace(/\D+/,'') * 1;
var half = Math.round(Math.abs((end - start)/2));
var middle = Math.round((self.selectSequenceStart + self.selectSequenceEnd)/2);
var newName = self.ref+':'+(middle-half)+'..'+(middle+half);
self.currentSegment = newName;
lib/Bio/Graphics/Browser2/Render/HTML.pm view on Meta::CPAN
my $val = $self->setting($config_label => $att) || next;
$style{$att} = $val;
}
$style{width} .= 'px';
my $style = join('; ', map {"$_:$style{$_}"} keys %style);
# clean up the HTML just a bit
$menu_html =~ s/\</\n\</g;
return div( { -style => $style,
-id => lc($view).'SelectMenu' },
$menu_html );
}
# Returns the HTML for the page's title, as displayed at the top.
sub render_title {
my $self = shift;
my $title = shift;
my $error = shift;
my $settings = $self->state;
return $settings->{head}
lib/Legacy/Graphics/Browser/Util.pm view on Meta::CPAN
my $val = $CONFIG->setting($config_label => $att) || next;
$style{$att} = $val;
}
$style{width} .= 'px';
my $style = join('; ', map {"$_:$style{$_}"} keys %style);
# clean up the HTML just a bit
$menu_html =~ s/\</\n\</g;
print div( { -style => $style,
-id => lc($view).'SelectMenu' },
$menu_html );
}
sub print_balloon_settings {
my $custom_balloons = $CONFIG->setting('custom balloons');
my $images = $CONFIG->relative_path('images');
my %config_values = $custom_balloons =~ /\[([^]]+)\]([^[]+)/g;
$config_values{'balloon'} ||= <<END;
images = $images/balloons
delayTime = 500
( run in 0.701 second using v1.01-cache-2.11-cpan-49f99fa48dc )