Preferences
-The "Visual" tab on the preferences window allows - you to configure the default display for a new alignment window.
-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.
-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.
-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.
-The "Connections" tab allows you to change the links made from Jalview - to your default web browser.
-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.
Preferences
+The preferences panel is opened from the Jalview Desktop’s Tools menu.
+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.
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. +
+"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.
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.
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.
+ +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 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.
++
+ +