Preferences

From: jprocter Date: Tue, 27 Oct 2009 14:35:38 +0000 (+0000) Subject: synchronized documentation between development and 2.4.0b2 X-Git-Tag: Release_2_5~176 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ddb0a809c051b4e2506aafe9efacbd57868742db;p=jalview.git synchronized documentation between development and 2.4.0b2 --- diff --git a/help/help.jhm b/help/help.jhm index 2e7bec7..3badaaf 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -88,6 +88,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index bd5a9d5..c34a573 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -1,21 +1,21 @@ @@ -116,6 +116,7 @@ + diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 36646d6..2e1cf43 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -1,153 +1,139 @@ -Preferences + +Preferences +

Preferences

There are four tabs in the Preferences dialog box:

The "Visual" Preferences - tab allows you to configure the default display for a new alignment window. -
The "Connections" Preferences - tab allows you to change the links made from Jalview to your default web browser. -
The "Output" Preferences - tab contains settings affecting the export of sequence alignments and EPS - files.
The "Editing" Preferences - tab contains settings affecting the export of sequence alignments and EPS - files.
The "DAS Settings" Preferences - tab allows you to select which DAS sources to use when fetching DAS Features.
The "Visual" + Preferences tab allows you to configure the default display for a new + alignment window.
The "Connections" + Preferences tab allows you to change the links made from Jalview to + your default web browser.
The "Output" + Preferences tab contains settings affecting the export of sequence + alignments and EPS files.
The "Editing" + Preferences tab contains settings affecting the export of sequence + alignments and EPS files.
The "DAS + Settings" Preferences tab allows you to select which DAS sources + to use when fetching DAS Features.

Visual Preferences tab

Maximise Window - If this is selected, a new alignment window will stretch - to fit the available space.

Maximise Window - If this is selected, a new alignment +window will stretch to fit the available space.

Open Overview Window - When this is selected, the alignment overview panel is opened by - default for a new alignment window.

Show Annotations - If this is selected the new window will display an annotation - panel below the sequences. This annotation panel may have several rows describing - the whole alignment. The 3 standard annotations Conservation, Quality and Consensus + href="overview.html">alignment overview panel is opened by default +for a new alignment window.

Show Annotations - If this is selected the new window +will display an annotation panel below the sequences. This annotation +panel may have several rows describing the whole alignment. The 3 +standard annotations Conservation, Quality and Consensus may be shown or hidden by default.

Full Sequence ID - If selected the ID panel will display the name of a sequence - plus the start and end residues in the format name/start-end. If not selected, - the displayed ID will be the name of the sequence.

Right Align IDs - select to align all sequence IDs to the -left-hand edge of the sequence alignment, rather than the left-hand +

Full Sequence ID - If selected the ID panel will display +the name of a sequence plus the start and end residues in the format +name/start-end. If not selected, the displayed ID will be the name of +the sequence.

Right Align IDs - select to align all sequence IDs to +the left-hand edge of the sequence alignment, rather than the left-hand edge of the alignment display window.

Font - The default font name, size and style can be set for a new - alignment window.

Font - The default font name, size and style can be set +for a new alignment window.

Sequence Name Italics - select to apply the italicised vbersion of the font to sequence labels.

Smooth Font - Toggles anti-aliasing on / off for faster rendering - of the alignment.

Wrap Alignment - Select whether to open new alignment windows in wrapped - mode or not.

Gap Symbol - The default gap symbol may be set to either "-" or "."

Colour - The default colour scheme for a new alignment window. If - the chosen option is "User Defined" then the last User Defined Colour - loaded or saved via the User Defined Colours panel will be loaded.

Sort by - When the alignment is loaded in, it will can be sorted by - Id or pairwise identity.

Open file - If this is selected then the default alignment file will - be opened when Jalview is started. You can change the default file by clicking - on file name and either typing in the file path or selecting it from the file - chooser window.

"Connections" Preferences tab

Smooth Font - Toggles anti-aliasing on / off for faster +rendering of the alignment.

Wrap Alignment - Select whether to open new alignment +windows in wrapped mode or not.

Gap Symbol - The default gap symbol may be set to either +"-" or "."

Colour - The default colour scheme for a new alignment +window. If the chosen option is "User Defined" then the last +User Defined Colour loaded or saved via the User Defined Colours panel +will be loaded.

Sort by - When the alignment is loaded in, it will can +be sorted by Id or pairwise identity.

Open file - If this is selected then the default +alignment file will be opened when Jalview is started. You can change +the default file by clicking on file name and either typing in the file +path or selecting it from the file chooser window.

"Connections" +Preferences tab

URL Link From Sequence ID
- Right click a sequence id to see a popup menu with "Link" as one of - the items. By default the item "SRS" 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.
- Jalview allows you to add your own custom links to other web pages. Click new - to add a new link. 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. -
- You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen - sequence id when you click on it.

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 $SEQUENCE_ID$ string will be replaced with - the accession string for the database cross-reference, rather than the - sequence ID for the sequence (since Jalview 2.4). -
- Regular Expression Substitution
- A url may contain a string of the form $SEQUENCE_ID=/regular expression/=$. In this case, the regular expression will be applied to the full sequence ID string and the resulting match will be inserted into the URL. - Groups of parentheseses 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-parentheseses 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 Brand of the Free University of Amsterdam for testing this new regular-expression expansion feature! -

-
+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 - browser application.
+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 browser application.

Proxy Server
- If you normally use a proxy server for using the internet, you must tick the - box "Use a Proxy Server" and enter the address and port details as - necessary. Web Services will not work if you are using a proxy server and do - not enter the settings here.
+If you normally use a proxy server for using the internet, you must tick +the box "Use a Proxy Server" and enter the address and port +details as necessary. Web Services will not work if you are using a +proxy server and do not enter the settings here.
+
Usage statistics, Questionnaire and Version checks
+Uncheck these options to prevent Jalview from submitting usage +statistics to google analytics, checking for jalview questionnaires or +retrieving details of the latest release version (at www.jalview.org). +See the user privacy statement for more +information.

Output Preferences tab

EPS Rendering Style
-This is a selection box which allows the - user to set a default rendering style for EPS export: -
"Lineart"
EPS files will accurately -reproduce the alignment view in Jalview and all characters will be -converted into line art. Files generated in this way are large and are -not easily editable, but have no font table dependencies.
-
"Text"
EPS files will be a mixture of text and -lineart. This produces compact files that can be edited easily in -programs like Microsoft Word and Adobe Illustrator, but can be -problematic if the fonts available to jalview are not accessible by -the program reading the EPS file. -
"Prompt each time"
Choose this to be asked select between Lineart and Text each time you make an EPS file.
+This is a selection box which allows the user to set a default rendering +style for EPS export: +
+
"Lineart"
+ EPS files will accurately reproduce the alignment view in Jalview and + all characters will be converted into line art. Files generated in this + way are large and are not easily editable, but have no font table + dependencies.
+
"Text"
+ EPS files will be a mixture of text and lineart. This produces compact + files that can be edited easily in programs like Microsoft Word and + Adobe Illustrator, but can be problematic if the fonts available to + jalview are not accessible by the program reading the EPS file. +
"Prompt each time"
+ Choose this to be asked select between Lineart and Text each time you + make an EPS file.

Sequence//Start-End Numbering
- The output tab also has a group of checkboxes for each file format. If these - are ticked, then Jalview will write files with the start and end sequence positions - appended to each sequence id: +The output tab also has a group of checkboxes for each file format. If +these are ticked, then Jalview will write files with the start and end +sequence positions appended to each sequence id:
>ID/1-10 AACDEAAFEA
-
If the boxes are left unchecked for a particular format, the sequence limits - will not be appended to the sequence id.
+
If the boxes are left unchecked for a particular format, the +sequence limits will not be appended to the sequence id.

Use Modeller Output

This option only applies to PIR format output. Jalview - automatically reads PIR files with sequence descriptions compatible - with the program Modeller. - If this option is selected Jalview will write Modeller style PIR - files with correct start/end numbering and PDB file association (if - available). The Jalview id/start-end option is ignored if Modeller output is selected. +automatically reads PIR files with sequence descriptions compatible with +the program Modeller. If this +option is selected Jalview will +write Modeller style PIR files with correct start/end numbering and PDB +file association (if available). The Jalview id/start-end option is +ignored if Modeller output is selected.
Editing Preferences tab
-
There are currently 2 options available which can be selected / deselected. -
-
AutoCalculate Consensus - For large alignments it can be useful to - deselect "Autocalculate Consensus" when editing. This prevents lengthy - calculations which are performed after each sequence edit. New alignment windows - will have their "Autocalculate Consensus" option set according to - this setting.
-
Pad gaps when editing - New alignment windows will "Pad Gaps" - according to this setting.
+
There are currently 2 options available which can be selected / +deselected.
+
AutoCalculate Consensus - For large alignments it can be +useful to deselect "Autocalculate Consensus" when editing. +This prevents lengthy calculations which are performed after each +sequence edit. New alignment windows will have their "Autocalculate +Consensus" option set according to this setting.
+
Pad gaps when editing - New alignment windows will +"Pad Gaps" according to this setting.

DAS Settings

See DAS Settings

diff --git a/help/html/privacy.html b/help/html/privacy.html new file mode 100644 index 0000000..febd44e --- /dev/null +++ b/help/html/privacy.html @@ -0,0 +1,29 @@ + + Jalview Privacy Statement +
Privacy for Jalview Users
+ The Jalview Desktop application available from the www.jalview.org site does not contain code that is designed to collate any personal or private information without your consent. + + However, the application does contain routines which contact a variety of web services, and some of these are specifically designed to assess who is using Jalview. + + We collect usage statistics in the following ways: +
HTTP logs on the Jalview website
+ We record IP addresses of machines which access the web site, either via the browser when downloading the application, or when the Jalview Desktop user interface is launched. +
The JNLP file at www.jalview.org/webstart/jalview.jnlp is retrieved to determine if you are running the latest version of Jalview.
+
The questionnaire web service at www.jalview.org/cgi-bin/questionnaire.pl is checked and a unique cookie for the current questionnaire is stored in the Jalview properties file.
+
The Jalview web services stack is contacted to retrieve the currently available web services. All interactions with the public jalview web services are logged, but we delete all job data (input data and results) after about two weeks.
+
+
Google Analytics
+ Since jalview 2.4.0b2, the Jalview Desktop records usage data with Google Analytics via the JGoogleAnalytics class.
The Google Analytics logs for Jalview version 2.4 only record the fact that the application was started, but in the future, we will use this mechanism to improve the Desktop user interface, by tracking which parts of the user interface are being used most often.
+
+
+ Stopping Jalview from calling home + If you run Jalview in 'headless mode' via the command line, then the program shouldn't try to contact any of the web servers mentioned above (if it does, then its a bug!). You can also specify some command line options to disable the questionnaire and usage statistics check. Finally, the Connections Tab of the jalview preferences contains options for controlling the submission of usage statistics. + Other Web Clients in Jalview
+ The Jalview desktop is intended to make it easier to interact with web-based bioinformatics resources, but we cannot vouch for the integrity of any of the services you might access via the program. + + You can turn this off + your machine to the outside world. + You may voluntarily submit query text +
+ + \ No newline at end of file diff --git a/help/html/releases.html b/help/html/releases.html index f26f8b1..00d99e5 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -50,7 +50,6 @@
URL links generated for all feature links (bugfix)

Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)

Added URL embedding instructions to features file documentation.
-
Sequences are now validated against EMBL database (broken in Version 2.4.0)

Codons containing ambiguous nucleotides translated as 'X' in peptide product

Sequence description lines properly shared via VAMSAS

Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.
@@ -62,34 +61,33 @@
2.4.0.b2
- 2/6/2009
+ 28/10/2009 -
Experimental support for google analytics usage tracking.
+
Experimental support for google analytics usage tracking.
+
Jalview privacy settings (user preferences and docs).

-
Fixed race condition in applet preventing startup in jre1.6.0u12+.
-
+
Race condition in applet preventing startup in jre1.6.0u12+.
+
Exception when feature created from selection beyond length of sequence.
+
Allow synthetic PDB files to be imported gracefully
+
Sequence associated annotation rows associate with all sequences with a given id
+
Find function matches case-insensitively for sequence ID string searches
+
Application Issues
+
Sequences are now validated against EMBL database
+
Sequence fetcher fetches multiple records for all data sources
+
+ InstallAnywhere Issues +
+
Dock icon works for Mac OS X java (Mac 1.6 update issue with installAnywhere mechanism)
+
Command line launching of JARs from InstallAnywhere version (java class versioning error fixed)

-
2.4 bugfixes
- 12/11/2008
- - - - -
-
Sequences are now validated against EMBL database
-
Sequence fetcher fetches multiple records for all data sources
-
- - - - +
2.4
27/8/2008
diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html new file mode 100644 index 0000000..32111e4 --- /dev/null +++ b/help/html/webServices/urllinks.html @@ -0,0 +1,72 @@ + + +Opening URLs from Jalview + + +
+
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. This is often the SRS site, but you +can easily configure your own Configuring URL Links +
URL links are defined in the "Connections" tab of the Jalview desktop preferences, or +specified as applet +parameters.
+By default the item "SRS" 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 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 token that can be replaced with a sequence +ID. The simplest token is "$SEQUENCE_ID$", which will be +replaced by the chosen sequence id when you click on it.
+
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 $SEQUENCE_ID$ string will be replaced with the +accession string for the database cross-reference, rather than the +sequence ID for the sequence (since Jalview 2.4).
+
Regular Expression Substitution
+A url may contain a string of the form $SEQUENCE_ID=/regular +expression/=$. In this case, the regular expression will be applied to +the full sequence 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! + +
+
+
+ \ No newline at end of file