Open Overview Window - When this is selected, the alignment overview panel is opened by default for a new alignment - window. + href="overview.html">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. + panel may have several rows describing the whole alignment. The 4 + standard annotations Conservation, Quality, + Occupancy and Consensus for the alignment may + be shown or hidden by default using the checkboxes adjacent and + below.
Show group: Conservation and Consensus controls the display
@@ -155,9 +158,9 @@
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.
+ path or selecting it from the file chooser window.
Note:
+ The default example alignment is updated periodically to
+ demonstrate new features in Jalview.
"Colours"
@@ -172,9 +175,36 @@
Annotation Shading Default - set the default minimum and
maximum colours used when Colour by Annotation... is selected from the alignment window's
- colours menu.
+ href="../colourSchemes/annotationColouring.html">Colour
+ by Annotation...
+ "Overview" + Preferences tab +
++ Use legacy gap colouring (gaps are white) - when enabled, + Jalview's overview shows gaps as white, and sequences with no + colourscheme applied as grey. +
++ Show Hidden regions when opening overview - default setting + for inclusion of hidden regions. +
++ Gap Colour - When legacy gap colouring is not enabled, this + configures the default colour for gaps in the overview. +
++ Hidden Colour - colour used to highlight regions in the + overview that are hidden in the alignment. +
++ Gap 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.
- 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
+ Default Browser (Unix)
It's 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.
@@ -241,6 +264,37 @@
statement for more information.
+ The "Links" Preferences + tab +
++ This panel shows a table, and two sections - Edit and Filter. + The table shows the available URL link definitions (consisting of a + database, Name, and URL template string), a checkbox In + Menu which indicates if the link is enabled, and Double + Click which marks the link that will be opened if a sequence's ID + is double clicked. The table can be sorted by clicking on the column headers. +
+Edit Links
This section contains three buttons,
+ New, Edit and Delete, which allow you to
+ create, modify and remove user-defined URL links from the Sequence
+ ID's links submenu.
+
+ Filter
The Filter text box allows you to
+ quickly show rows in the table containing a particular text string.
+ The Custom only button limits the entries in the table to
+ just those you have configured yourself via the Edit
+ Links buttons. Press Show all to clear any filters.
+
The links table is prepopulated with persistent URLs for many common + bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from + the identifiers.org website, and the names and URLs are not + user editable. + Read more about configuring + URL links. +
+@@ -248,7 +302,7 @@ allows the user to set a default rendering style for EPS export:
- Sequence//Start-End Numbering
The output tab also
+ 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:
@@ -292,11 +346,10 @@
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. + href="bioJsonFormat.html">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
@@ -309,7 +362,7 @@ and PDB file association (if available). The Jalview id/start-end option is ignored if Modeller output is selected.- Editing Preferences tab + "Editing" Preferences tab
There are currently three options available which can be selected / deselected.