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.
- - + + + +Preferences
+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.
+ +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:
+
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.
++
+ +