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.
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.
"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.
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.
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.