Your theme can add JavaScript files in two ways:
1. To add a JavaScript file to all pages on your website, edit your sub-theme's
.info file and add a line like this one:
scripts[] = js/my-jquery-script.js
2. To add a JavaScript file depending on a certain condition, you can add it
using some PHP code in a preprocess function:
drupal_add_js(drupal_get_path('theme', 'THEME_NAME') . '/js/my-jquery-script.js', array('group' => JS_THEME));
For the full documentation of drupal_add_js(), see:
http://api.drupal.org/api/function/drupal_add_js
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