DAS Settings

Add and enable a das server with given +

Add and enable a DAS server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments
Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'
@@ -102,7 +102,7 @@

-fetchfrom nickname

Query nickname for features for the alignments +

Query a DAS source called nickname for features for the alignments and display them

diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index 3f2674e..853f6ef 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -6,14 +6,14 @@

DAS Sequence Feature Retrieval

Jalview includes a client for retrieving sequence features via +

Jalview includes a client for retrieving sequences and their features via the Distributed Annotation System.

Open the Feature Settings panel by selecting "View -> Feature Settings..."
Click on the "DAS Settings" tabbed pane.
Select the sources to use for DAS feature retireval, then +
Select the sources to use for DAS feature retrieval, then click the "Fetch DAS Features" button.
- Cancelling Feature Retrieval
  diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html index 30b36b1..2ca2b08 100644 --- a/help/html/features/dassettings.html +++ b/help/html/features/dassettings.html @@ -1,32 +1,38 @@ -DAS Settings + +DAS Settings +
  DAS Settings
  -
  Jalview can retrieve and visualize features from many DAS - sources at once. The DAS sources are discovered and selected via the DAS settings panel.
  +
  Jalview can retrieve sequences or features from many DAS sources at once. The DAS sources that +it uses are discovered and selected via the DAS settings panel, +opened either from the View→Feature +Settings dialog box from the alignment window's menu bar, or the Tools→Preferences dialog box +opened from the Desktop menu bar.
  
  The available sources are listed in the table using each source's Nickname as its identifier. Clicking on a source's entry in the table -reveals more information about that service in the panel to the -right. Select the tickbox in the "Use Source" column for a -source to add it to the set Jalview queries for alignment and sequence -features. -
  -
  You can filter the visible DAS sources by authority, type and "label". - You should read the DAS documentation to understand more about these values. +reveals more information about that service in the panel to the right. +Select the tickbox in the "Use Source" column for a source to +add it to the set Jalview queries for alignment and sequence features.
  +
  You can filter the visible DAS sources by authority, type and +"label". You should read the DAS documentation to understand +more about these values.
  Updating the list of sources
  
  When the DAS Settings panel is first opened, and when the 'Refresh - source' buton is pressed, a list of DAS sources - is retrieved from the DAS registry URL (set by default to the DAS - registration server at - http://das.sanger.ac.uk/registry/das1/sources/).
  +source' buton is pressed, a list of DAS sources is retrieved from the +DAS registry URL (set by default to the DAS registration server at +http://das.sanger.ac.uk/registry/das1/sources/).
  
  Adding your own DAS Sources
  -
  You can add your own DAS source to the list by clicking the "Add Local - Source" button. Enter the URL and nickname of your additional service. - It should be noted that Jalview 2.1 will not query additional sources for more - information, but this will be implemented in future editions. +
  You can add your own DAS source to the list by clicking the +"Add Local Source" button. Enter the URL and nickname of your +additional service. It should be noted that Jalview 2.1 will not query +additional sources for more information, but this will be implemented in +future editions.
  diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 135e4d5..02e9844 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -3,7 +3,7 @@
  Sequence Fetcher
  
  Jalview can retrieve sequences from certain databases using either the -WSDBFetch service provided by the European Bioinformatics Institute, and DAS servers capable of the sequence command (since version 2.4).
  +WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).
  
  The Sequence Fetcher dialog box can be opened via the "File" menu on the main desktop in order to retrieve sequences as a new -- 1.7.10.2