Preferences

The preferences panel is opened from the Jalview Desktop’s Tools menu.

There are eight tabs in the Preferences dialog box:

- The "Visual" Preferences tab allows you to configure the default display for a new alignment window.
- The "Colours" Preferences tab allows you to configure default colourschemes for a new alignment window.
- The "Overview" Preferences tab configures defaults for the overview window.
- The "Structure" Preferences tab allows you to configure options for obtaining and displaying structure information.
- The "Connections" Preferences tab allows you to configure Jalview's internet settings.
- 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 sequence alignments and EPS files.
- The "Editing" Preferences tab contains settings affecting behaviour when editing alignments.
- The "Startup" Preferences tab allows you to adjust how much memory is allocated to Jalview when it is launched.
- The "Web Service" Preferences tab allows you to configure the JABAWS servers that Jalview uses, and change the layout of the alignment's Web Services menu.

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.

"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.

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.
Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.

Default structure viewer - choose Jmol, CHIMERA, CHIMERAX or PYMOL for viewing 3D structures.

Path to Chimera/X/Pymol program - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have installed the chosen viewer in a non-standard location, you can specify it here, by entering the full path to its executable.
For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also double-click this field to open a file chooser dialog.

Sequence <-> Structure Mapping Method - This setting controls whether Jalview attempts to retrieve mappings between Uniprot protein sequences and 3D structures in the PDBe with SIFTS, or constructs a mapping by conservative alignment between the sequences and chains in the 3D structure data using the Needleman and Wunsch algorithm. SIFTS is enabled by default.

PDB Fields shown in Search and Structure Summaries - ticks in this table indicate fields shown by default when browsing results of a free text search via the PDB sequence fetcher, or 3D structures offered by the 3D Structure Chooser.

"Connections" Preferences tab

Default Browser (Unix)
It's 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
There are three settings to choose from:

- No proxy servers will configure Jalview to use a direct internet connection.
- System proxy servers will configure Jalview to use the proxy server passed to it by your system at startup.
- Use these proxy servers: allows you to set a custom proxy server.

If you normally use a proxy server for using the internet, you must choose one of System proxy servers, or if these have not been passed correctly you should set your own proxy servers to use by selecting Use these proxy servers. You will then need to enter the host and port details as necessary. Web Services will not work if you are using a proxy server and do not choose the system proxy or enter your own settings here.
There are separate host and port settings for HTTP and HTTPS proxies. Often these are the same but you should enter the host and port into both rows.
You can also check the Authentication required box if your proxy requires username and password authentication. You can enter both the Username and Password but only the Username will be stored in Jalview's preferences file, the password will only be stored until the end of the current Jalview session.
This means that if the proxy settings are still valid, Jalview will ask for the password when it starts the next session.

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 "Backups" Preferences Tab

Since Jalview 2.11.0, overwriting an existing file when saving or exporting data will by default trigger a backup file to be created. Several options are provided to control how backup files are named, and how many old versions will be kept.

Schemes - select from three default schemes Single Backup, Keep All Versions, and Rolled Backup Files, or choose Custom to enable a previously defined custom scheme.

Custom - Check this box to adjust the parameters of the currently selected scheme. Once OK is selected these parameters will be saved as the Custom scheme in your user preferences. To revert changes hit Cancel.

Scheme Examples - shows how backup files will appear according to the currently selected scheme and parameters.

Deleting Old Backup Files - these settings control how many backups are kept.

Backup filename strategy - specify the naming convention for numbered backups and how they are ordered.

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 prepopulated 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.

Output Preferences tab

EPS Rendering Style
This is a selection box which allows the user to set a default rendering style for EPS export:

- "Prompt each time"
  Choose this to be asked to select between Lineart and Text each time you make an EPS file.
- "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.

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.

"Editing" Preferences tab

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.

Startup

When Jalview is launched it by default examines the available memory and requests up to 90% to be allocated to the application, or 32G, which ever is smaller. The Startup tab allows you to adjust the maximum percentage and hard limits for Jalview memory allocation stored in your .jalview_properties file.

Web Services Preferences - documentation for this tab is given in the Web Services Preferences section.