From ddb0a809c051b4e2506aafe9efacbd57868742db Mon Sep 17 00:00:00 2001
From: jprocter Preferences There are four tabs in the Preferences dialog box:
-
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.
- +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:
-
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.
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.
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.
EPS Rendering Style
-This is a selection box which allows the
- user to set a default rendering style for EPS export:
-
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.
-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.
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 @@ + +
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:
+
+ 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
+
+
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:
+
+ \ No newline at end of file -- 1.7.10.2