From: kiramt Date: Tue, 13 Dec 2016 08:58:26 +0000 (+0000) Subject: JAL-2316 Documentation update X-Git-Tag: Release_2_10_3b1~346^2~15 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e390c310cb1391beba4b0238645120f772a99b98;p=jalview.git JAL-2316 Documentation update --- diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index 1a1f0d0..7ac76c1 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -27,7 +27,9 @@ Opening URLs from Jalview
Both the applet and the desktop application are able to open URLs as 'popups' in your web browser.
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 "Connections" tab of the Jalview desktop + preferences. This is by default the EMBL-EBI site, but you can easily configure your own sequence URL links.

@@ -43,14 +45,39 @@ href="../features/preferences.html">Jalview desktop preferences, or specified as applet - parameters.
By default the item "EMBL-EBI Search" 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.
- In the preferences dialog box, click new to add a + parameters.

+

+ By default, the list of available links in the preferences dialog box + contains the item "EMBL-EBI Search", + 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. +
+ Also by default, the list of available links contains persistent URLs for many common + bioinformatics databases. These links are downloaded by Jalview from + the identifiers.org website, and the names and URLs are not user editable. +
+ 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 + "Custom Only" button, which displays only user-defined links. +

+

+ In the preferences dialog box, the links which appear in the Links menu + can be configured by selecting or deselecting links in the "In Menu" + column. The names of selected links will be displayed + on new menu items under the "Link" menu when you right + click on a sequence id.
+ You can configure which link is used when double-clicking on a sequence + by selecting or deselecting links in the "On Click" 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 + "$SEQUENCE_ID$" token (see below for details of the "$SEQUENCE_ID$" + and other tokens).

+

+ Additionally you can click new to add a new link, and edit to modify an existing link, or delete - to remove it.
You can name the link, this will be displayed - on a new menu item under the "Link" menu when you right - click on a sequence id.
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 "$SEQUENCE_ID$", which will be replaced by the chosen sequence id when you click on it. diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 477b3d6..bee4809 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1285,5 +1285,5 @@ label.inmenu = In Menu label.id = ID label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option label.edit_sequence_url_link = Edit sequence URL link -warn.name_cannot_be_duplicate = URL names must be unique +warn.name_cannot_be_duplicate = URL names must be unique and cannot be MIRIAM ids label.invalid_name = Invalid Name ! \ No newline at end of file diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index d2d04a9..99aeed5 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -1286,5 +1286,5 @@ label.inmenu = In Menu label.id = ID label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option label.edit_sequence_url_link = Edit sequence URL link -warn.name_cannot_be_duplicate = URL names must be unique +warn.name_cannot_be_duplicate = URL names must be unique and cannot be MIRIAM ids label.invalid_name = Invalid Name ! \ No newline at end of file