There are six 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 3 standard annotations Conservation, Quality and Consensus for the alignment may be shown or hidden by default using the checkboxes 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.
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 "."
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.
"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.
"Connections" Preferences tab
URL Link From Sequence ID
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.
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:
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.
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:
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.
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.