Preferences
-There are four 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 "."
-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
-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:
-
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:
++ 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 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. +
++ 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. +
++ "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. +
+ "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.
--
+
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. +
++