<td>
<div align="left">Add and enable a das server with given
nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments</div>
+ for all alignments<br>
+ Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
+ <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
</td>
</tr>
<tr>
</td>
<td>
<ul>
+ <li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
<li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
</li>
<li>URL links generated from description line for regular-expression based URL links (applet and application)
</td>
<td>
<ul>
+ <li>Better handling of exceptions during sequence retrieval</li>
<li>URL links generated for all feature links (bugfix)</li>
<li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
<li>Added URL embedding instructions to features file documentation.</li>
href="../features/dasfeatures.html">DAS features</a>, and for\r
retrieving sequence cross-references such as the protein products of a\r
DNA sequence.</p>\r
+<p><strong>Initiating reference retrieval</strong><br>\r
+The application provides three ways to access the retrieval function. Either:\r
+<ul><li>select the <strong>Discover PDB IDs</strong> option from the structure submenu of the sequence's popup menu</li>\r
+<li>Select one of the options from the alignment window's <strong>Web Services</strong> menu to fetch references from either the EBI databases plus currently selected DAS sources, or an individual database source</li>\r
+<li>Answer 'Yes' when asked if you wish to retrieve database references for your sequences after initiating a DAS Sequence Feature fetch.</li>\r
+</ul> \r
<p>Jalview discovers references for a sequence by generating a set\r
of ID queries from the ID string of each sequence in the alignment. It\r
-then tries to query all the databases it can access in order to match\r
+then tries to query a subset of all the databases it can access in order to match\r
the alignment sequence to any records retrieved from the database. If a\r
match is found, then the sequence is annotated with that database's\r
reference, and any cross-references that it's records contain.</p>\r
earlier Jalview versions used for Uniprot sequence feature retrieval,\r
and was originally restricted to the identifaction of valid Uniprot\r
accessions.<br>\r
-Essentially, Jalview will try to retrieve records from all the databases\r
+Essentially, Jalview will try to retrieve records from a subset of the databases\r
accessible by the <a href="../features/seqfetch.html">sequence\r
fetcher</a> using each sequence's ID string (or each string in the ID\r
separated by the '∣' symbol).</p>\r
+ "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ "-png FILE\tCreate PNG image FILE from alignment.\n"
+ "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
- + "-eps FILE\tCreate EPS file FILE from alignment."
- + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
- + "-noquestionnaire\tTurn off questionnaire check."
- + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
- + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
- + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)"
- + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ + "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ + "-noquestionnaire\tTurn off questionnaire check.\n"
+ + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+ +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+ +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+ + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
System.exit(0);
}
git://source.jalview.org / jalview.git / commitdiff