Preferences

There are four tabs in the Preferences dialog box:

• The "Visual" Preferences tab allows you to configure the default display for a new alignment window.
• The "Connections" Preferences tab allows you to change the links made from Jalview to your default web browser.
• The "Output" Preferences tab contains settings affecting the export of sequence alignments and EPS files.
• The "Editing" Preferences tab contains settings affecting the export of sequence alignments and EPS f

Visual Preferences tab

Maximise Window - If this is selected, a new alignment window will stretch to fit the available space.

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.

Font - The default font name, size and style can be set for a new alignment window.

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 "."

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.

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.

Output Preferences tab

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

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

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.

Use Modeller Output

This option only applies to PIR format output. Jalview can now read and write PIR files with sequence descriptions compatible with the program Modeller. If this option is selected Jalview will write the sequence description in the following format:

>P1;O80429_MAIZE
sequence:O80429_MAIZE:1:.:140:.:.

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.