<mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
<mapID target="features.fileformat" url="html/features/featuresFormat.html"/>
<mapID target="features.featureschemes" url="html/features/featureschemes.html"/>
- <mapID target="das.settings" url="html/features/dassettings.html"/>
- <mapID target="das.viewing" url="html/features/dasfeatures.html"/>
<mapID target="edit" url="html/editing/index.html"/>
<mapID target="jalarchive" url="html/features/jalarchive.html"/>
<mapID target="multipleviews" url="html/features/multipleViews.html"/>
<tocitem text="Feature Colourschemes" target="features.featureschemes" />
<tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
<tocitem text="Editing Sequence Features" target="seqfeatedit" />
- <tocitem text="DAS Feature Retrieval" target="das.viewing" />
- <tocitem text="DAS Feature Settings" target="das.settings" />
<tocitem text="HTML annotation report" target="io.seqreport" />
</tocitem>
<tocitem text="Alignment Conservation Analysis" target="aacon" />
<tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
<tocitem text="Sequence Retrieval" target="seqfetch" />
- <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
- <tocitem text="DAS Feature Retrieval" target="das.viewing" />
+ <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
</tocitem>
<tocitem text="Colour Schemes" target="colours" expand="false">
</tr>
<tr>
<td>
- <div align="center">-dasserver nickname=URL</div>
- <td>
- <div align="left">
- Add and enable a <a href="dassettings.html">DAS server</a>
- with given nickname (alphanumeric or underscores only) for
- retrieval of features 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>
- <div align="center">-fetchfrom nickname</div>
- <td>
- <div align="left">
- Query a <a href="dassettings.html">DAS source</a> called
- nickname for features for the alignments and display them
- </div>
- </td>
- </tr>
- <tr>
- <td>
<div align="center">-groovy FILE/URL</div>
<td>
<div align="left">Execute groovy script in FILE (where
+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>DAS Features</title>
-</head>
-
-<body>
- <p>
- <strong>DAS Sequence Feature Retrieval</strong>
- </p>
- <p>Jalview includes a client for retrieving sequences and their
- features via the Distributed Annotation System.</p>
- <ol>
- <li>Open the Feature Settings panel by selecting "View
- -> Feature Settings..."</li>
- <li>Click on the "<a href="dassettings.html">DAS
- Settings</a>" tabbed pane.
- </li>
- <li>Select the sources to use for DAS feature retrieval, then
- click the "Fetch DAS Features" button.
- <ul>
- <li>Cancelling Feature Retrieval<br> Press the <strong>Cancel
- Fetch</strong> button to immediately stop feature retrieval. This
- will not remove any features already added to the alignment,
- but will halt any outstanding DAS requests.<em>The cancel
- fetch button is of particular use when one or more DAS
- annotation servers are not responding!</em>
- </ul>
- </li>
- </ol>
- <p>
- 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.<br> The <a
- href="../webServices/dbreffetcher.html">database
- reference fetcher</a> documentation describes how Jalview discovers
- what database references are appropriate for the sequences in the
- alignment.
- <ul>
- <li><em>Note</em><br> Please remember to save your
- alignment if either the start/end numbering, or the sequence IDs
- were updated during the ID retrieval process.</li>
- </ul>
- <p>
- <p>
- <em>DAS support was introduced in Jalview Version 2.1.</em>
- </p>
- <br />
- <p>
- <em>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/.</em>
- </p>
- <p>
-</body>
-</html>
+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>DAS Settings</title>
-</head>
-
-<body>
- <p>
- <strong>DAS Settings</strong>
- </p>
- <p>
- Jalview can retrieve sequences and features from many <a
- href="http://biodas.org/">DAS</a> sources. The DAS sources
- that it uses are discovered and selected <em>via</em> the DAS
- settings panel, opened either from the <a
- href="featuresettings.html">View→Feature Settings</a> dialog
- box from the alignment window's menu bar, or the <a
- href="featuresettings.html">Tools→Preferences</a>
- dialog box opened from the Desktop menu bar.
- </p>
- <p>
- <img src="das.gif">
- <p>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.</p>
- <p>You can filter the visible DAS sources by authority, type and
- "label". You should read the DAS documentation to
- understand more about these values.
- <p>
- <strong>Updating the list of sources</strong>
- </p>
- <p>
- When the DAS Settings panel is first opened, and when the <strong>'Refresh
- source'</strong> 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:<br> <b>DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/</b>
- </p>
- <p>
- <strong>Adding your own DAS Sources</strong>
- </p>
- <p>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.
- <p>
-</body>
-</html>
Preferences</a> tab contains settings affecting the export of
sequence alignments and EPS files.
</li>
- <li>The <a href="dassettings.html"><strong>"DAS
- Settings"</strong> Preferences</a> tab allows you to select which DAS
- sources to use when fetching DAS Features.
- </li>
<li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
Service"</strong> Preferences</a> tab allows you to configure the <a
href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
href="featuresettings.html">Sequence Feature Settings</a>
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.<br>
- Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS
- features</a> to an alignment via the DAS tabbed pane of the feature
- settings window.
+ sequence features differently in different alignment views.
</p>
<p>
<strong>View→Sequence ID Tooltip→Show
<p>
<strong>Sequence Fetcher</strong>
</p>
- <p>
- 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 <em>sequence</em>
- command (configured in <a href="dassettings.html">DAS settings</a>).
- </p>
- <p>The Sequence Fetcher can be opened via the "File"
+ <p>Jalview can retrieve sequences from a range of sequence, 3D
+ structure, genomic and domain family databases provided by EMBL-EBI.</p>
+ <p>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.</p>
+ when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.</p>
<p>
Every time a new fetcher is opened, you will need to <strong>select
the database you want to retrieve sequences</strong> from the database
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.
- <br />
- <em>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.</em>
</p>
<p>Once you have selected a sequence database, its fetcher dialog
will open. Jalview provides two types of dialog:</p>
currently selected database into the retrieval box. Finally, press
"OK" to initiate the retrieval.</li>
</ol>
- <p>
- <strong>Only retrieving part of a sequence</strong>
- </p>
- <p>
- When using DAS sources (indicated by a "<em>(DAS)</em>"),
- 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'.<br /> <em>Full support for DAS range
- queries was introduced in Jalview 2.8</em>
- </p>
<p>If you use the WSDBFetch sequence fetcher services (EMBL,
UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
href="../features/featuresettings.html">Sequence
Feature Settings...</a> </strong><br> <em>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.</em></li>
+ and display of sequence features on the alignment.</em></li>
<li><strong>Sequence ID Tooltip</strong><em>
(application only) <br>This submenu's options allow the
inclusion or exclusion of non-positional sequence features
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
<ul>
- <li><strong>Fetch DB References</strong><br> <em>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.
- <ul>
- <li>'Trim Retrieved Sequences' - when checked, Jalview
- will discard any additional sequence data for accessions
- associated with sequences in the alignment. <br> <strong>Note:
- Disabling this could cause out of memory errors when
- working with genomic sequence records !</strong><br> <strong>Added
- in Jalview 2.8.1</strong>
- </li>
- <li>'Standard Databases' will check sequences against
- the EBI databases plus any active DAS sequence sources</li>
- </ul> Other sub-menus allow you to pick a specific source to query
- - sources are listed alphabetically according to their
- nickname.
- </em><br></li>
- </ul>
+ <li><strong>Fetch DB References</strong><br> <em>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.
+ <ul>
+ <li>'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated
+ with sequences in the alignment. <br> <strong>Note:
+ Disabling this could cause out of memory errors when working
+ with genomic sequence records !</strong><br> <strong>Added
+ in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the
+ EBI databases.</li>
+ </ul> Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em><br></li>
+ </ul>
<p>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
<li><strong><a href="../features/featuresettings.html">Sequence
Feature Settings...</a></strong><em><br> 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.</em></li>
+ sequence features on the alignment.</em></li>
<li><strong>Sequence ID Tooltip</strong><em> (application
only) <br>This submenu's options allow the inclusion or
exclusion of non-positional sequence features or database cross
dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
<ul>
- <li><strong>Fetch DB References</strong><br> <em>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.
- <ul>
+ <li><strong>Fetch DB References</strong><br> <em>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.
+ <ul>
<li>'Retrieve full Sequence' - when checked, Jalview will
retrieve the full sequence for any accessions associated
with sequences in the alignment. <br> <strong>Note:
in Jalview 2.8.1</strong>
</li>
<li>'Standard Databases' will check sequences against the
- EBI databases plus any active DAS sequence sources<</li>
+ EBI databases</li>
</ul> Other submenus allow you to pick a specific source to query -
sources are listed alphabetically according to their nickname.
</em></li>
ID, and can be viewed in full via the
<a href="../io/exportseqreport.html">Sequence Details</a> window. .
Jalview also uses references for the retrieval of
- <a href="../features/viewingpdbs.html">PDB structures</a> and <a
- href="../features/dasfeatures.html">DAS features</a>, and for
+ <a href="../features/viewingpdbs.html">PDB structures</a>, and for
retrieving sequence cross-references such as the protein products of a
DNA sequence.
</p>
application provides three ways to access the retrieval function.
Either:
<ul>
- <li>select the <strong>Discover PDB IDs</strong> option from the
- structure submenu of the sequence's popup menu
- </li>
- <li>Choose one of the options from the 'Fetch DB Refs' submenu in
+ <li>select the <strong>Structure Chooser...</strong> option from
+ the Sequence ID popup menu.
+ </li>
+ <li>Choose one of the options from the 'Fetch DB Refs' submenu in
the alignment window's <strong>Web Services</strong> menu:
<ul>
- <li><em>Standard Databases</em> will fetch references from
- the EBI databases plus currently selected DAS sources</li>
- <li>The other entries submenus leading to lists of individual
+ <li><em>Standard Databases</em> will fetch references from EBI
+ databases appropriate for the sequence type (Nucleotide or Protein)</li>
+ <li>The other entries submenus leading to lists of individual
database sources that Jalview can access.</li>
</ul>
</li>
- <li>Answer 'Yes' when asked if you wish to retrieve database
- references for your sequences after initiating a DAS Sequence
- Feature fetch.</li>
</ul>
<p>Jalview discovers references for a sequence by generating a set
of ID queries from the ID string of each sequence in the alignment. It
Institute (EBI) and Distributed Annotation System servers that are
capable of serving sequences.
</li>
- <li>The <a href="../features/dasfeatures.html">DAS Feature
- Fetcher</a> enables the retrieval and visualization of features from
- DAS annotation sources
- </li>
- <li>The <a href="dbreffetcher.html">Database Reference
- Fetcher</a> transfers database references from records available
- from DAS or the public sequence databases.
- </li>
- <li>The <strong>Web Services</strong> menu in each alignment
+ <li>The <a href="dbreffetcher.html">Database Reference
+ Fetcher</a> transfers database references and annotation from the public
+ sequence databases.
+ </li>
+ <li>The <strong>Web Services</strong> menu in each alignment
window also provides access to the following:
<ul>
<li>Programs for <a href="msaclient.html">multiple
git://source.jalview.org / jalview.git / commitdiff