Preferences
-There are four tabs in the Preferences dialog box: +
The preferences panel is opened from the Jalview Desktop’s Tools menu.
+There are six tabs in the Preferences dialog box:
Visual Preferences tab
@@ -35,7 +57,13 @@ for a new alignment 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. +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 @@ -45,6 +73,9 @@ 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 @@ -53,16 +84,25 @@ rendering of the 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.
+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. +
+URL Link From Sequence ID
@@ -105,11 +145,15 @@ style for EPS export:
make an EPS file.
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:
-
+sequence positions appended to each sequence id:>ID/1-10 AACDEAAFEA@@ -134,8 +178,6 @@ 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.
- -See DAS Settings