From: jprocter 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:
+
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 @@ -27,8 +41,7 @@ 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.
-The "Connections" tab allows you to change the links - made from Jalview to your default web browser.
+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
@@ -49,19 +62,31 @@
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.
The "Output" tab has a selection box allowing the
- user to set a default rendering style for EPS export. "Lineart" will
- produce an accurate representation of the visible alignment in Jalview, all
- the characters will be graphics objects. "Text" will produce a much
- smaller file and will rely on the software you use to view the EPS file, such
- as Adobe Illustrator, having the same font as the file was created with. You
- will only be able to edit text in an EPS file if you select the "Text"
- option.
- Choose "Prompt each time" to select between Lineart and Text each
- time you make an EPS file.
The output tab also has a group of checkboxes for each file format. If these +
+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. If the boxes are left unchecked for a paritcular
+ appended to each sequence id:
+
+ >ID//1-10 + AACDEAAFEA ++
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 02ff94e..2833770 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -2,13 +2,21 @@
Sequence Fetcher
-The Sequence Fetcher can be started from the main desktop "File" - menu or from a particular alignment window.
-Select which database to fetch your sequence from and enter the sequence id. - If you are retrieving sequences from PDB database and you know which chain you - would like to retrieve, append the chain id after colon to the PDB id. eg 1GAQ:A
-The Sequence Fetcher uses WSDBFetch provided by the European Bioinformatics - Institute. If you use this service please quote:
+Jalview can retrieve sequences from certain databases via the +WSDBFetch service provided by the European Bioinformatics Institute.
+A Sequence Fetcher dialog box can be opened via the "File" + menu on the main desktop in order to retrieve sequences as a new + alignment, or opened via the "File" menu of an existing alignment + to import additional sequences. +
+Select the database you want to retrieve sequences from, and enter a + the database id (or a semi-colon separated list of several ids) in + the text box. Finally, press OK to initiate the retrieval.
+
+ If you are retrieving sequences from the PDB, you can retrieve
+ specific chains by appending a colon and the chain id to the PDB
+ id. For example :
1GAQ:A+
If you use the sequence fetcher in work for publication, then please cite:
Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
SOAP-based services provided by the European Bioinformatics Institute.