DAS Features

Execute groovy script in FILE (where diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html deleted file mode 100644 index 1965e70..0000000 --- a/help/html/features/dasfeatures.html +++ /dev/null @@ -1,77 +0,0 @@ - - - -DAS Features - - - -

- DAS Sequence Feature Retrieval -

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 retrieval, then - click the "Fetch DAS Features" button. -
- Cancelling Feature Retrieval
  Press the Cancel - Fetch button to immediately stop feature retrieval. This - will not remove any features already added to the alignment, - but will halt any outstanding DAS requests.The cancel - fetch button is of particular use when one or more DAS - annotation servers are not responding! -
-

- If your DAS source selection contains sources which use UniProt - accession ids, you will be asked whether Jalview should find UniProt - Accession ids for the given sequence names. It is important to - realise that many DAS sources only use UniProt accession ids, rather - than Swissprot/UniProt sequence names.
The database - reference fetcher documentation describes how Jalview discovers - what database references are appropriate for the sequences in the - alignment. -

Note
Please remember to save your - alignment if either the start/end numbering, or the sequence IDs - were updated during the ID retrieval process.

- DAS support was introduced in Jalview Version 2.1. -

-
-

- The DAS registry at http://www.dasregistry.org was - decommissioned early in 2015. An unmaintained mirror is currently - hosted at http://www.ebi.ac.uk/das-srv/registry/. -

- - diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html deleted file mode 100644 index 9600070..0000000 --- a/help/html/features/dassettings.html +++ /dev/null @@ -1,74 +0,0 @@ - - - -DAS Settings - - - -

- DAS Settings -

- Jalview can retrieve sequences and features from many DAS sources. 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. -

- 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. Note that the registry hosted at - http://www.dasregistry.org/das/ was retired at the start of 2015. An - alternative service is currently hosted at - http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this - service, ensure your .jalview_properties file includes the following - line:
DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/ -

- 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. -

- - diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 50f864b..52e88db 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -65,10 +65,6 @@ Preferences tab contains settings affecting the export of sequence alignments and EPS files. -

The "DAS - Settings" Preferences tab allows you to select which DAS - sources to use when fetching DAS Features. -

The "Web Service" Preferences tab allows you to configure the JABAWS diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 3c9d2b8..eeb63f6 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -87,10 +87,7 @@ href="featuresettings.html">Sequence Feature Settings dialog box. Feature colour schemes and display parameters are unique to a particular alignment, so it is possible to colour the same - sequence features differently in different alignment views.
- Since Jalview 2.1, it is possible to add DAS - features to an alignment via the DAS tabbed pane of the feature - settings window. + sequence features differently in different alignment views.

View→Sequence ID Tooltip→Show diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 44aa1c2..e726c49 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -26,19 +26,13 @@

Sequence Fetcher

-
- Jalview can retrieve sequences from certain databases using either - the DBFetch service provided by the EMBL European Bioinformatics - Institute, or, since Jalview 2.4, DAS servers capable of the sequence - command (configured in DAS settings). -
-
The Sequence Fetcher can be opened via the "File" +
Jalview can retrieve sequences from a range of sequence, 3D + structure, genomic and domain family databases provided by EMBL-EBI.
+
The Sequence Fetcher 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. There may be a short delay - when the sequence fetcher is first opened, whilst Jalview compiles - the list of available sequence datasources from the currently - defined DAS server registry.
+ when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.

Every time a new fetcher is opened, you will need to select the database you want to retrieve sequences from the database @@ -51,11 +45,6 @@ tooltips are shown if you mouse over some sources, explaining what the database will retrieve. You can select one by using the up/down arrow keys and hitting return, or by double clicking with the mouse. -
- If you have DAS sources enabled, then you may have several - sources for the same type of sequence identifier, and these will - be grouped together in a sub-branch branch labeled with the - identifier.

Once you have selected a sequence database, its fetcher dialog will open. Jalview provides two types of dialog:
@@ -82,17 +71,6 @@ currently selected database into the retrieval box. Finally, press "OK" to initiate the retrieval.

-
- Only retrieving part of a sequence -
-
- When using DAS sources (indicated by a "(DAS)"), - you can append a range in addition to a sequence ID. For example, to - retrieve 50 residues starting at position 35 in UNIPROT sequence - P73137 using the UNIPROT DAS server, you would enter - "'P73137:35,84'.
Full support for DAS range - queries was introduced in Jalview 2.8 -

If you use the WSDBFetch sequence fetcher services (EMBL, UniProt, PFAM, and RFAM) in work for publication, please cite:
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 00a2ec4..f3ab75d 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -314,9 +314,7 @@ href="../features/featuresettings.html">Sequence Feature Settings...
Opens the Sequence Feature Settings dialog box to control the colour - and display of sequence features on the alignment, and - configure and retrieve features from DAS annotation - servers. + and display of sequence features on the alignment.

Sequence ID Tooltip (application only)
This submenu's options allow the inclusion or exclusion of non-positional sequence features @@ -579,28 +577,26 @@ is dynamic, and may contain user-defined web service entries in addition to any of the following ones:

Fetch DB References
This - submenu contains options for accessing any of the database - services that Jalview is aware of (e.g. DAS sequence servers - and the WSDBFetch service provided by the EBI) to verify - sequence start/end positions and retrieve all database cross - references and PDB ids associated with all or just the - selected sequences in the alignment. -
-
'Trim Retrieved Sequences' - when checked, Jalview - will discard any additional sequence data for accessions - associated with sequences in the alignment.
Note: - Disabling this could cause out of memory errors when - working with genomic sequence records !
Added - in Jalview 2.8.1 -
-
'Standard Databases' will check sequences against - the EBI databases plus any active DAS sequence sources
-
Other sub-menus allow you to pick a specific source to query - - sources are listed alphabetically according to their - nickname. -

Fetch DB References
This + submenu contains options for accessing any of the database + services that Jalview is aware of (e.g. those provided by + EMBL-EBI) to verify sequence start/end positions and retrieve all + database cross references and PDB ids associated with all or just + the selected sequences in the alignment. +
+
'Trim Retrieved Sequences' - when checked, Jalview will + discard any additional sequence data for accessions associated + with sequences in the alignment.
Note: + Disabling this could cause out of memory errors when working + with genomic sequence records !
Added + in Jalview 2.8.1 +
+
'Standard Databases' will check sequences against the + EBI databases.
+
Other sub-menus allow you to pick a specific source to query - + sources are listed alphabetically according to their nickname. +

Selecting items from the following submenus will start a remote service on compute facilities at the University of Dundee, or elsewhere. You need a continuous network connection in order to diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 2028304..33ec77f 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -53,8 +53,7 @@

Sequence Feature Settings...
Opens the Sequence Feature Settings dialog box to control the colour and display of - sequence features on the alignment, and configure and retrieve - features from DAS annotation servers.

+ sequence features on the alignment.

Sequence ID Tooltip (application only)
This submenu's options allow the inclusion or exclusion of non-positional sequence features or database cross diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index b71bc1a..b8b357e 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -29,14 +29,13 @@ dynamic, and may contain user-defined web service entries in addition to any of the following ones:

Fetch DB References
This - submenu contains options for accessing any of the database - services that Jalview is aware of (e.g. DAS sequence servers and - the WSDBFetch service provided by the EBI) to verify sequence - start/end positions and retrieve all database cross references - and PDB ids associated with all or just the selected sequences - in the alignment. -
+
Fetch DB References
This submenu + contains options for accessing any of the database services that + Jalview is aware of (e.g services provided by the EBI) to verify + sequence start/end positions and retrieve all database cross + references and PDB ids associated with all or just the selected + sequences in the alignment. +

'Retrieve full Sequence' - when checked, Jalview will retrieve the full sequence for any accessions associated with sequences in the alignment.
Note: @@ -45,7 +44,7 @@ in Jalview 2.8.1

'Standard Databases' will check sequences against the - EBI databases plus any active DAS sequence sources<
+ EBI databases
Other submenus allow you to pick a specific source to query - sources are listed alphabetically according to their nickname.
diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html index 83c80ba..1f61dea 100644 --- a/help/html/webServices/dbreffetcher.html +++ b/help/html/webServices/dbreffetcher.html @@ -30,8 +30,7 @@ ID, and can be viewed in full via the Sequence Details window. . Jalview also uses references for the retrieval of - PDB structures and DAS features, and for + PDB structures, and for retrieving sequence cross-references such as the protein products of a DNA sequence.
@@ -40,21 +39,18 @@ application provides three ways to access the retrieval function. Either:
-
select the Discover PDB IDs option from the - structure submenu of the sequence's popup menu -
-
Choose one of the options from the 'Fetch DB Refs' submenu in +
select the Structure Chooser... option from + the Sequence ID popup menu. +
+
Choose one of the options from the 'Fetch DB Refs' submenu in the alignment window's Web Services menu:
-
Standard Databases will fetch references from - the EBI databases plus currently selected DAS sources
-
The other entries submenus leading to lists of individual +
Standard Databases will fetch references from EBI + databases appropriate for the sequence type (Nucleotide or Protein)
+
The other entries submenus leading to lists of individual database sources that Jalview can access.

-
Answer 'Yes' when asked if you wish to retrieve database - references for your sequences after initiating a DAS Sequence - Feature fetch.

Jalview discovers references for a sequence by generating a set of ID queries from the ID string of each sequence in the alignment. It diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index d0b497c..8f36013 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -36,15 +36,11 @@ Institute (EBI) and Distributed Annotation System servers that are capable of serving sequences. -
The DAS Feature - Fetcher enables the retrieval and visualization of features from - DAS annotation sources -
-
The Database Reference - Fetcher transfers database references from records available - from DAS or the public sequence databases. -
-
The Web Services menu in each alignment +
The Database Reference + Fetcher transfers database references and annotation from the public + sequence databases. +
+
The Web Services menu in each alignment window also provides access to the following:

Programs for multiple -- 1.7.10.2