X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Furllinks.html;h=d99633a6bf3aba2fd704c9c75d782413b5c2b6d5;hb=0fcc08f1f633aa9eae854ebe0c78b5fb75471898;hp=088a5398aabaf90acca304e88852dce3ee7efaf4;hpb=2da3a29ae39b692964b85456353985d388aa3858;p=jalview.git

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index 088a539..d99633a 100644
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -27,7 +27,9 @@
     <strong>Opening URLs from Jalview</strong><br> Both the applet
     and the desktop application are able to open URLs as 'popups' in
     your web browser. <br> Double-clicking on the ID of a sequence
-    will open the first URL that can be generated from its sequence ID.
+    will open the URL designated for 'popups' in the &quot;Connections&quot; tab of the <a
+    href="../features/preferences.html">Jalview desktop
+    preferences</a>.
     This is by default the EMBL-EBI site, but you can easily configure your own <a
       href="#urllinks">sequence URL links</a>.
   </p>
@@ -43,14 +45,39 @@
     href="../features/preferences.html">Jalview desktop
     preferences</a>, or specified as <a
     href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
-    parameters</a>. <br> By default the item &quot;EMBL-EBI Search&quot; is added
-    to this link menu. This link will show a web page in your default
-    browser with the selected sequence id as part of the URL.<br>
-    In the preferences dialog box, click <strong>new</strong> to add a
+    parameters</a>.</p>
+    <p> 
+    By default, the list of available links in the preferences dialog box 
+    contains the item &quot;EMBL-EBI Search&quot;, 
+    which is set as the URL which opens on double-clicking on a sequence ID, and as a 
+    menu item in the Links menu. This link will show a web page in your default
+    browser with the selected sequence id as part of the URL.
+    <br>
+    Also by default, the list of available links contains persistent URLs for many common 
+    bioinformatics databases. These links are downloaded by Jalview from
+    the <em>identifiers.org</em> website, and the names and URLs are not user editable.
+    <br>
+    The list of links is sortable, by clicking on the headers of the table. The list
+    can be filtered using the free text search box below the table, or the 
+    &quot;Custom Only&quot; button, which displays only user-defined links.
+    </p> 
+    <p>
+    In the preferences dialog box, the links which appear in the Links menu 
+    can be configured by selecting or deselecting links in the &quot;In Menu&quot; 
+    column. The names of selected links will be displayed
+    on new menu items under the &quot;Link&quot; menu when you right
+    click on a sequence id.<br> 
+    You can configure which link is used when double-clicking on a sequence
+    by selecting or deselecting links in the &quot;On Click&quot; column. Exactly one
+    link must be configured for double-clicking. Since the link uses the sequence id
+    to construct the URL to open, the selected link must contain the 
+    &quot;$SEQUENCE_ID$&quot; token (see below for details of the &quot;$SEQUENCE_ID$&quot;
+    and other tokens).</p>
+    <p>
+    Additionally you can click <strong>new</strong> to add a
     new link, and <strong>edit</strong> to modify an existing link, or <strong>delete</strong>
-    to remove it.<br> You can name the link, this will be displayed
-    on a new menu item under the &quot;Link&quot; menu when you right
-    click on a sequence id. <br> The URL string must contain a
+    to remove it. Only URLs entered by the user (or the default EMBL-EBI link) may
+    be edited or deleted. When adding or editing a link, the URL string must contain a
     token that can be replaced with a sequence ID or DB accession ID. The simplest token is
     &quot;$SEQUENCE_ID$&quot;, which will be replaced by the chosen
     sequence id when you click on it.