From: Jim Procter Date: Fri, 16 Sep 2016 16:05:04 +0000 (+0100) Subject: JAL-2089 tidied docs for sequence fetcher
 X-Git-Tag: Release_2_10_0~20^2~42 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e861f936ecc297fe636a326db3e04fab182606c8;p=jalview.git JAL-2089 tidied docs for sequence fetcher
 --- diff --git a/help/html/features/selectfetchdb.gif b/help/html/features/selectfetchdb.gif index 6e1ce10..de0a7e6 100644 Binary files a/help/html/features/selectfetchdb.gif and b/help/html/features/selectfetchdb.gif differ diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index ff5c1b0..04d3c1d 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -32,10 +32,7 @@ Institute, or, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).

- The Jalview Sequence Fetcher Dialog Box -

The Sequence Fetcher dialog box can be opened via the +

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 @@ -43,47 +40,56 @@ whilst Jalview compiles the list of available sequence datasources from the currently defined DAS server registry.

- First, select the database you want to retrieve - sequences from by clicking the button labeled 'Select database - retrieval source'. If a database source is already selected, then - the button's label will change to show the currently selected - database. + Every time a new fetcher is opened, you will need to select the database you want to retrieve + sequences from the database chooser.

- Database selection dialog for fetching sequences (introduced in Jalview 2.8) -

Since Jalview 2.8, the available databases are shown as a tree - in a popup dialog box. The databases are ordered alphabetically, and - if there are many sources for the same type of sequence identifier, - they will be grouped together in a sub-branch branch labeled with - the identifier.

-

- Once you have selected the sequence database using the popup dialog - box, enter one or more accession ids (as a - semi-colon separated list), or press the "Example" button - to paste the example accession for the currently selected database - into the retrieval box. Finally, press "OK" to initiate - the retrieval. -

-

- Fetching from The PDB with the EMBL-EBI PDBe Search - Interface -

-

- Since Jalview 2.9, selecting PDB as the sequence database will open - the PDB Sequence Fetcher for - discovering and retrieving structures. -

+

The databases are shown as a tree, and ordered alphabetically; + 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:

+
  1. The Free-text Search Interface + +
    Free-text search clients are provided for PDB (Since 2.9), and + UniProt (Since 2.10). They provide access to each database's own + query system, enabling you to retrieve data by accession, free text + description, or any other type of supported field. For full details, + see each client's help page: + +
    2. +
  2. Accession based sequence retrieval +
    + + The Jalview Sequence Fetcher Dialog Box
    + To retrieve sequences, simply enter one or more accession ids (as a semi-colon + separated list), or press the "Example" button to paste the + example accession for the currently selected database into the + retrieval box. Finally, press "OK" to initiate the + retrieval. +
    3. +

Only retrieving part of a sequence

- DAS sources (indicated by a "(DAS)") allow a - range to be specified in addition to a sequence ID. 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 + 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,