X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=259b0f4366ca051de793822f508438e819d54b09;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=03b4993d2ae0765a985a2138485acce02bc93858;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 03b4993..259b0f4 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -1,20 +1,21 @@ Preferences @@ -22,11 +23,15 @@

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

@@ -78,16 +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.
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. +

+
+

"Connections" Preferences tab

URL Link From Sequence ID
@@ -130,6 +145,11 @@ 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