this plugin adds a checkbox under each track category
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README.md

Hierarchical Checkbox Plugin

Adds a 'select all from category' checkbox to all categories in hierarchical tracklist

When you check/uncheck the box, it applies to all tracks in that category and any subcategories

Install

For JBrowse 1.11.6+ in the JBrowse/plugins folder, type:
git clone https://github.com/bhofmei/jbplugin-hierarchicalcheckbox.git HierarchicalCheckboxPlugin

or

downloaded the latest release version at releases.
Unzip the downloaded folder, place in JBrowse/plugins, and rename the folder HierarchicalCheckboxPlugin

Activate

Add this to jbrowse.conf under [GENERAL]:

[ plugins.HierarchicalCheckboxPlugin ]
location = plugins/HierarchicalCheckboxPlugin

If that doesn't work, add this to jbrowse_conf.json:

"plugins" : {
    "HierarchicalCheckboxPlugin" : { "location" : "plugins/HierarchicalCheckboxPlugin" }
}

Usage

demo image Each category and subcategory will now have a checkbox under the title which says "select all in category". This checkbox can be used to select all or deselect all tracks within that category and subcategories.

When some, but not all, tracks of a category are selected, the checkbox will show an intermediate "check". Clicking this will select all from the category.

There is a known issue where the category check boxes are initially unchecked after page loading.