- Preferences -
-- The preferences panel is opened from the Jalview Desktop’s Tools - menu. -
-There are eight 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. -
-- 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 4 - standard annotations Conservation, Quality, - Occupancy and Consensus for the alignment may - be shown or hidden by default using the checkboxes adjacent and - below. -
-- Show group: Conservation and Consensus controls the display - of per-group automatic annotation. -
-- Consensus: Histogram and Logo checkboxes control the - display of the consensus histogram and sequence logo for consensus - annotation rows. -
-- 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. -
-- Sequence ID Tooltip: Control the display of Database - References and Non-positional annotation in the tooltip displayed - when the mouse is over a sequence's ID. -
-- Show Unconserved - When this is selected, all consensus - sequence symbols will be rendered as a '.', highlighting mutations - in highly conserved alignments. -
-- Sequence Name Italics - select to apply the italicised - version of the font to sequence labels. -
-- Smooth Font - Toggles anti-aliasing on / off for faster - rendering of the alignment. -
-- Gap Symbol - The default gap symbol may be set to either - "-" or "." -
-- Wrap Alignment - Select whether to open new alignment - windows in wrapped mode or not. -
-- Sort alignment by - When the alignment is loaded in, it can - be ordered as read (No sort), or sorted by Id or pairwise identity. -
-- Sort annotations by - Annotations can be unsorted, sorted - by the order of the related sequences in the alignment, or by label. - Autocalculated annotations (e.g. Consensus) can be shown either last - (below sequence annotations) or first (above sequence annotations). - Since Jalview 2.8.2. -
-
- 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.
Note:
- The default example alignment is updated periodically to
- demonstrate new features in Jalview.
-
- "Colours" - Preferences tab -
-- Alignment 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. -
-- Annotation Shading Default - set the default minimum and - maximum colours used when Colour - by Annotation... is selected from the alignment window's colours - menu. -
-- "Overview" - Preferences tab -
-- Use legacy gap colouring (gaps are white) - when enabled, - Jalview's overview shows gaps as white, and sequences with no - colourscheme applied as grey. -
-- Show Hidden regions when opening overview - default setting - for inclusion of hidden regions. -
-- Gap Colour - When legacy gap colouring is not enabled, this - configures the default colour for gaps in the overview. -
-- Hidden Colour - colour used to highlight regions in the - overview that are hidden in the alignment. -
-- Gap 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. -
-- "Structure" - Preferences tab added in Jalview 2.8.2 -
-- Process secondary structure from PDB - if selected, then - structure information read from PDB will be processed and annotation - added to associated sequences. -
- Use RNAView for secondary structure - if selected, the - pyRNA RNAView service (https://github.com/fjossinet/PyRNA) - will be called to derive secondary structure information for RNA - chains. -
- Add secondary structure annotation to alignment - if - selected, Jmol's - implementation DSSP will be used to add annotation to polypeptide - chains in the structure. -
- Add Temperature Factor annotation to alignment - if - selected, values extracted from the Temperature Factor column for - the backbone atoms in the PDB file will be extracted as annotation - lines shown on the alignment. -
- Default structure viewer - choose JMOL or CHIMERA for - viewing 3D structures. -
- Path to Chimera program - Optional, as Jalview will search - standard installation paths for Windows, Linux or MacOS. If you have - installed Chimera in a non-standard location, you can specify it - here, by entering the full path to the Chimera executable program. - Double-click this field to open a file chooser dialog. -
- "Connections" - Preferences tab -
-
- 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.
-
- 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.
-
The links table is prepoulated with persistent URLs for many common - bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from - the identifiers.org website, and the names and URLs are not - user editable. - Read more about configuring - URL links. -
- -
- EPS Rendering Style
This is a selection box which
- allows the user to set a default rendering style for EPS export:
-
- Automatically set ID width
When enabled, the
- column containing sequence and annotation labels at the left hand
- side of an exported figure will be made large enough to display each
- sequence ID and annotation label in its own line. Enable this if you
- have particularly long sequence IDs and need to generate EPS or PNG
- figures or web pages.
-
- Figure ID column width
Manually specify the width
- of the left hand column where sequence IDs and annotation labels
- will be rendered in exported alignment figures. This setting will be
- ignored if "Automatically set ID width" is set.
-
- 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:
-
- >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.
-- Embed BioJSON to HTML export -
-- When this option is enabled, Jalview embeds BioJSON data within HTML files - exported from Jalview at generation time. This enables the exported - HTML files to be extracted and imported back into the Jalview - desktop application at a later time. -
- 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. -
-There are currently three 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. -
-- Sort with New Tree - When selected, any trees calculated or - loaded onto the alignment will automatically sort the alignment. -
--
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