X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=04d3c1d49ebc910450caf59e351b77cbb2a12fdb;hpb=e861f936ecc297fe636a326db3e04fab182606c8;p=jalview.git
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index 04d3c1d..44aa1c2 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -32,53 +32,55 @@
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" 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.
+ 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.
- Every time a new fetcher is opened, you will need to select the database you want to retrieve
- sequences from the database chooser.
+ Every time a new fetcher is opened, you will need to select
+ the database you want to retrieve sequences from the database
+ chooser.
- The databases are shown as a tree, and ordered alphabetically;
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+
+ 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.
+
+ 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:
- - 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:
-
-
- - Accession based sequence retrieval
-
+
+ - 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:
+
+ - Accession based sequence retrieval
- 
- 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.
-
+
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.
Only retrieving part of a sequence