-<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\r
-<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
--->\r
-<html xmlns="http://www.w3.org/1999/xhtml">\r
-<head>\r
-Database Reference Fetching\r
-</head>\r
-<p>\r
-<p><strong>Discovering Database References for Sequences</strong><br>\r
-Database references are associated with a sequence are displayed as a\r
-list in the tooltip shown when mousing over its sequence ID. Jalview\r
-uses references for the retrieval of <a\r
- href="../features/viewingpdbs.html">PDB structures</a> and <a\r
- 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>Choose one of the options from the 'Fetch DB Refs' submenu in the alignment window's <strong>Web Services</strong> menu:<ul>\r
-<li><em>Standard Databases</em> will fetch references from the EBI databases plus currently selected DAS sources</li>\r
-<li>The other entries submenus leading to lists of individual database sources that Jalview can access.</li></ul></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 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
-<p><strong>The Sequence Identification Process</strong><br>\r
-The method of accession id discovery is derived from the method which\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 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
-<p>If a record (or set of records) is retrieved by any query derived\r
-from the ID string of a sequence, then the sequence is aligned to the\r
-ones retrieved to determine the correct start and end residue positions\r
-(which are displayed when the 'Show Full Sequence ID' option). This is\r
-important for the correct display of the location of any features\r
-associated with that database.</p>\r
-<p>If the alignment reveals differences between the sequence in the\r
-alignment and the one in the record, then Jalview will assume that the\r
-aligned sequence is not the one in the retrieved record.</p>\r
-<p>In some cases, the ID used to retrieve records may be out\r
-of date and a dialog box will be opened indicating that a 100% match\r
-between the sequence and the record was identified, but the\r
-sequence name is different. In this case, the can be manually\r
-changed (by right clicking on the sequence ID and selecting <strong>Sequence→Edit\r
-Name</strong>).\r
-<ul>\r
- <li><em>Note</em><br>\r
- Please remember to save your alignment if either the start/end\r
- numbering, or the sequence IDs were updated during the ID\r
- retrieval process.</li>\r
-</ul>\r
-<body></body>\r
-</html>\r
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ -->
+<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>Database Reference Fetching
+</head>
+<p>
+<p>
+ <strong>Discovering Database References for Sequences</strong><br>
+ Database references are associated with a sequence are displayed as a
+ list in the tooltip shown when mousing over its sequence ID. Jalview
+ 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 retrieving sequence cross-references such as the
+ protein products of a DNA sequence.
+</p>
+<p>
+ <strong>Initiating reference retrieval</strong><br> The
+ 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
+ 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
+ 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
+ then tries to query a subset of all the databases it can access in
+ order to match the alignment sequence to any records retrieved from
+ the database. If a match is found, then the sequence is annotated with
+ that database's reference, and any cross-references that its records
+ contain.</p>
+<p>
+ <strong>The Sequence Identification Process</strong><br> The
+ method of accession id discovery is derived from the method which
+ earlier Jalview versions used for Uniprot sequence feature retrieval,
+ and was originally restricted to the identification of valid Uniprot
+ accessions.<br> Essentially, Jalview will try to retrieve records
+ from a subset of the databases accessible by the <a
+ href="../features/seqfetch.html"
+ >sequence fetcher</a> using each sequence's ID string (or each string in
+ the ID separated by the '∣' symbol).
+</p>
+<p>If a record (or set of records) is retrieved by any query derived
+ from the ID string of a sequence, then the sequence is aligned to the
+ ones retrieved to determine the correct start and end residue
+ positions (which are displayed when the 'Show Full Sequence ID'
+ option). This is important for the correct display of the location of
+ any features associated with that database.</p>
+<p>If the alignment reveals differences between the sequence in the
+ alignment and the one in the record, then Jalview will assume that the
+ aligned sequence is not the one in the retrieved record.</p>
+<p>
+ In some cases, the ID used to retrieve records may be out of date and
+ a dialog box will be opened indicating that a 100% match between the
+ sequence and the record was identified, but the sequence name is
+ different. In this case, the can be manually changed (by right
+ clicking on the sequence ID and selecting <strong>Sequence→Edit
+ Name</strong>).
+<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>
+<body></body>
+</html>
git://source.jalview.org / jalview.git / blobdiff