X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=877a3b1ed341682a04c3c39893c7d4278d2e56cb;hb=713db61b4724485414159cfc145f9ffa4a24bb6d;hp=e3dc703467bb3fe00acb5d698eb4d253637e5e03;hpb=72f4770815185305bd18aeeb74f829b1f9ed55c8;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index e3dc703..877a3b1 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -4,8 +4,22 @@

Preferences

The "Visual" tab on the preferences window allows you to configure - the default display for a new alignment window.

There are three tabs in the Preferences dialog box: +

The "Visual" + Preferences tab allows + you to configure the default display for a new alignment + window.
The "Connections" + Preferences tab allows you to change the links + made from Jalview to your default web browser. +
The "Output" + Preferences tab contains settings affecting the export of sequence +alignments and EPS files. +

Visual Preferences tab

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 @@ -18,12 +32,63 @@

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.

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
+ Right click a sequence id to see a popup menu with "Link" as one of + the items. By default the item "SRS" is added to this link menu. This + link will show a web page in your default browser with the selected sequence + id as part of the URL.
+ Jalview allows you to add your own custom links to other web pages. Click new + to add a new link. You can name the link, this will be displayed on a new menu + item under the "Link" menu when you right click on a sequence id. +
+ You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen + sequence id when you click on it.

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.

Output Preferences tab

EPS Rendering Style
+This is a selection box which allows the + user to set a default rendering style for EPS export: +

"Lineart"
EPS files will accurately +reproduce the alignment view in Jalview and all characters will be +converted into line art. Files generated in this way are large and are +not easily editable, but have no font table dependencies.
"Text"
EPS files will be a mixture of text and +lineart. This produces compact files that can be edited easily in +programs like Microsoft Word and Adobe Illustrator, but can be +problematic if the fonts available to jalview are not accessible by +the program reading the EPS file. +
"Prompt each time"
Choose this to be asked select between Lineart and Text each time you make an EPS file.

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.