From 3c2ee3e1b9c507c7dfa550bc8546a43ff305f85a Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 8 Feb 2017 16:33:35 +0000 Subject: [PATCH] JAL-2316 tidied up documentation for Links tab --- help/help.jhm | 3 + help/helpTOC.xml | 3 + help/html/features/preferences.html | 43 ++++++++++++--- help/html/webServices/urllinks.html | 104 +++++++++++++++-------------------- 4 files changed, 83 insertions(+), 70 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index f69ed00..984c2d1 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -150,6 +150,9 @@ + + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 54abd53..482ccdf 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -131,6 +131,9 @@ + + + diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 6a8c86c..fb21836 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -46,8 +46,13 @@ and displaying structure information.

The "Connections" - Preferences tab allows you to change the links made from Jalview - to your default web browser. + Preferences tab allows you to configure Jalview's internet + settings and specify your default web browser. +

The "Links" + Preferences tab shows the currently configured URL + Links shown in the Link submenu in the Sequence + ID popup menu.

The "Output" Preferences tab contains settings affecting the export of @@ -212,13 +217,6 @@ Preferences tab

- URL Link From Sequence ID
These definitions are - used to generate URLs from a sequence's ID or database cross - references. Read more about configuring - URL links here. -

Default Browser (Unix)
Its difficult in Java to detect the default web browser for Unix users. If Jalview can't find your default web browser, enter the name or full path to your web @@ -240,6 +238,33 @@ statement for more information.

+ The "Links" Preferences + tab +

+ This panel shows a table, and two sections - Edit and Filter. + The table shows the available URL link definitions (consisting of a + database, Name, and URL template string), a checkbox In + Menu which indicates if the link is enabled, and Double + Click which marks the link that will be opened if a sequence's ID + is double clicked. The table can be sorted by clicking on the column headers. +

Edit Links
This section contains three buttons, + New, Edit and Delete, which allow you to + create, modify and remove user-defined URL links from the Sequence + ID's links submenu. +

+ Filter
The Filter text box allows you to + quickly show rows in the table containing a particular text string. + The Custom only button limits the entries in the table to + just those you have configured yourself via the Edit + Links buttons. Press Show all to clear any filters. +

Output Preferences tab

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index 0da8a4d..da5d7dd 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -23,12 +23,12 @@

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 whichever URL is selected for 'popups' in the "Links" tab of the Jalview desktop + your web browser.

Double-clicking on the ID of a sequence + will open whichever URL is selected for 'popups' in the "Links" tab of the Jalview desktop preferences. This is by default the EMBL-EBI site, but you can easily configure your own sequence URL links. @@ -41,51 +41,37 @@

Configuring URL Links
URL - links are defined in the "Connections" tab of the Jalview desktop + links are defined in the "Links" tab of the Jalview desktop preferences, or specified as applet parameters.

- By default, the list of available links in the preferences dialog box - contains the item "EMBL-EBI Search". - This link is initially configured so that it is the URL which opens on double-clicking on a sequence ID. It is also a - menu item in the "Link" menu. When clicked, 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 in the preferences dialog box contains persistent URLs for many common +

+ Default Link Settings
The "EMBL-EBI Search" + link is the default link shown in the "Link" submenu, and + opened when double-clicking on a sequence ID. When clicked, this + link will show a web page in your default browser with the selected + sequence ID as part of the URL. +

+ Adding additional links
You can configure your own + links via the Jalview Preferences + dialog. Jalview also provides 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 can be sorted 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 "Link" menu - can be configured by selecting or deselecting links in the "In Menu" - column. The names of selected links will be displayed - as 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. 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. + the identifiers.org website, and the names and URLs are not + user editable.

- eg.
UniRef100 = - http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
- Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$

+ Creating your own URL link URL links are specified as a + template containing special tokens that Jalview will replace with + the Sequence ID or Database Accession of the sequence when you + double click on its ID or open it's Link submenu. + Link URL templates must contain at least one token. +

+ eg.

 UniRef100 =
+    http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100

+    Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$

Links will also be made for any database cross references associated with the sequence where the database name exactly matches a URL link name. In this case, the $DB_ACCESSION$ string will be replaced with @@ -110,33 +96,29 @@

Regular Expression Substitution
A url may contain a string of the form $SEQUENCE_ID=/regular - expression/=$ or $DB_ACCESSION=/regular expression/=$. - In this case, the regular expression will be - applied to the full sequence ID or DB accession ID string and the resulting match will + expression/=$ or $DB_ACCESSION=/regular expression/=$. In + this case, the regular expression will be applied to the full + sequence ID or DB accession ID string and the resulting match will be inserted into the URL. Groups of parentheses can be used to specify which regions of the regular expression will be used to generate the URL: +

Each top level parenthesis will yield a URL containing the text matched within that parenthesis.
Regions matching sub-parentheses within a top-level parenthesis will be concatenated to form the text inserted into the URL for the top-level parenthesis.

Please Note: -
-
The regular expressions supported by Jalview are those - provided by the Stevesoft - javaregex package. -
-
Some characters must be escaped when specifying them as - a match within a regular expression.
-

Many Thanks to Bernd Brandt of the Free University of - Amsterdam for testing this new regular-expression expansion - feature! -

-
-
+ Please Note: +
+
The regular expressions supported by Jalview are those + provided by the Stevesoft + javaregex package. +
+
Some characters must be escaped when specifying them as a + match within a regular expression.
+

Many Thanks to Bernd Brandt of the Free University of + Amsterdam for testing the regular-expression expansion feature! -- 1.7.10.2