</p>
<p>
Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
- (http://www.cgl.ucsf.edu/chimera/) has been integrated into Jalview
- for interactively viewing structures opened by entries in the <strong>"Structure"</strong>
- submenu in the <a href="../menus/popupMenu.html">sequence id
- pop-up menu</a> (if you can't see this, then you need to <a
- href="viewingpdbs.html"
- >associate a PDB structure</a> with the sequence). Chimera is
- available from the Jalview desktop, provided Chimera has been
- separately installed.
+ (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
+ structures opened via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a>.
</p>
<p>
You can set a default choice of Jmol or Chimera structure viewer in
<a href="preferences.html#structure"> Preferences</a>. You can also
optionally specify the path to the Chimera program here (if it
- differs from the standard paths searched by Jalview).
+ differs from the standard paths searched by Jalview).<br />
+ <strong>Please make sure your version of Chimera is up to
+ date. Jalview requires at least Chimera version 1.11.1</strong>
+ </p>
<p>
If you save your Jalview session as a project file, the state of any
open Chimera windows will also be saved, and can be reopened by
loading the project file on any machine with Chimera installed. <em>Since
Jalview 2.9.</em>
- <!-- <p>The following menu entries are provided for viewing structure data<br>
- <ul>
- <li>The <strong>"Structure→View
- Structure→</strong> submenu allows a single PDB structure to be chosen
- for display from the available structures for a sequence.
- </li>
- <li>The <strong>"Structure→View all <em>N</em>
- structures
- </strong> option will open a new window containing all structures associated
- with the current selection.
- </li>
- <li>The <strong>"Structure→View all <em>N</em>
- representative structures
- </strong> option will open a new window containing exactly one structure per
- currently selected sequence.<br /></li>
- </ul>
- <br>
-</p> -->
<p>
<a name="align"><strong>Superposing structures based on
their aligned sequences</strong></a><br> If several structures are
<!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
</li>
<li>
- <!-- -->
+ <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API
+ </li>
+ <li>
+ <!-- JAL-2049 -->Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
</li>
+ <li><!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot sequences</li>
<li>
<!-- JAL- -->
</li>
<ul>
<li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
<li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
- <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+ <li><!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
<li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
<li><!-- JAL-2067 -->Tidied up links in help file table of contents</li>
<li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
</li>
<li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
<li>
- <!-- JAL- -->
+ <!-- -->
</li>
<li>
<!-- JAL- -->
<li><!-- JAL-2003 -->Export features should only export the currently displayed features for the current selection or view</li>
<li><!-- JAL-2036 -->Enable 'Get Cross-References' in menu after fetching cross-references</li>
<li><!-- JAL-2032 -->Mouseover of a copy of a sequence is not followed in the structure viewer</li>
- <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
+ <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
<li>
<!-- JAL-2145 -->missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
</li>
</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10 ?</strong>
</p>
<p>
Jalview 2.10 is the next major release in the Jalview 2 series. Full
details are in the <a href="releases.html#Jalview.2.10.0">Jalview
2.10 Release Notes</a>, but the highlights are below.
</p>
- <p>
- <strong>Highlights in Jalview 2.10</strong>
<ul>
<li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
transcripts and proteins can be retrieved via Jalview's new <a
<li><strong>Import structures as mmCIF</strong>. Jalview
now downloads data from the EMBL-EBI's PDBe site as <a href="features/mmcif.html">mmCIF</a>.
This allows very large structures to be imported, such as the HIV virus capsid assembly.</li>
+ <li><strong>Chimera users will need to upgrade to
+ 1.11.1.</strong>If you use Chimera to view structures downloaded by
+ Jalview 2.10, you will need to make sure you are running the
+ latest version of <a href="features/chimera.html">Chimera</a>.</li>
</ul></li>
<li><strong>UniProt Free Text Search.</strong> The new search
dialog for UniProt allows you to browse and retrieve sequences
sequence. The reference sequence for alignment views can also be
saved and restored from Jalview projects.</li>
<li><strong>Ensembl and ENA 'show cross-references'
- support.</strong>The Calculations menu's 'Show cross-references' will now
+ support.</strong>The Calculations menu's <strong>'Show cross-references'</strong> will now
offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
mapping data is available for download or display.</li>
+
</ul>
</body>
see ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
see http://www.ebi.ac.uk/ena/submit/data-formats
-->
- <!--
<class name="jalview.datamodel.xdb.embl.EmblFile">
<map-to xml="ROOT"/>
<field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
<bind-xml name="Error"/>
</field>
</class>
- -->
<class name="jalview.datamodel.xdb.embl.EmblEntry">
- <map-to xml="entry"/>
<field name="accession" type="string">
<bind-xml name="accession" node="attribute"/>
</field>
*/
package jalview.datamodel.xdb.embl;
-import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.ws.dbsources.Uniprot;
import java.io.FileReader;
import java.io.PrintWriter;
import java.io.Reader;
-import java.net.URL;
import java.util.Vector;
import org.exolab.castor.mapping.Mapping;
}
/**
- * Parse an Embl XML file into an EmblEntry object
+ * Parse an EmblXML file into an EmblFile object
*
* @param file
* @return parsed EmblXML or null if exceptions were raised
*/
- public static EmblEntry getEmblEntry(File file)
+ public static EmblFile getEmblFile(File file)
{
if (file == null)
{
}
try
{
- return EmblFile.getEntry(new FileReader(file));
+ return EmblFile.getEmblFile(new FileReader(file));
} catch (Exception e)
{
System.err.println("Exception whilst reading EMBLfile from " + file);
return null;
}
- /**
- * Reads the XML response from file and unmarshals into a Java object
- *
- * @param fileReader
- * @return
- */
- public static EmblEntry getEntry(Reader fileReader)
+ public static EmblFile getEmblFile(Reader file)
{
- EmblEntry record = new EmblEntry();
+ EmblFile record = new EmblFile();
try
{
// 1. Load the mapping information from the file
Mapping map = new Mapping(record.getClass().getClassLoader());
- URL url = record.getClass().getResource("/embl_mapping.xml");
+ java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
map.loadMapping(url);
// 2. Unmarshal the data
Unmarshaller unmar = new Unmarshaller(record);
try
{
- if (Cache.getDefault(Cache.CASTORLOGLEVEL,
+ // uncomment to DEBUG EMBLFile reading
+ if (jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL,
"debug").equalsIgnoreCase("DEBUG"))
{
- unmar.setDebug(Cache.log.isDebugEnabled());
- // unmar.setDebug(true);// uncomment to debug unmarshalling
+ unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
}
} catch (Exception e)
{
unmar.setIgnoreExtraAttributes(true);
unmar.setMapping(map);
unmar.setLogWriter(new PrintWriter(System.out));
- record = (EmblEntry) unmar.unmarshal(fileReader);
+ record = (EmblFile) unmar.unmarshal(file);
canonicaliseDbRefs(record);
} catch (Exception e)
* Change blank version to "0" in any DBRefEntry, to ensure consistent
* comparison with other DBRefEntry in Jalview
*
- * @param entry
+ * @param record
* @see Uniprot#getDbVersion
*/
- static void canonicaliseDbRefs(EmblEntry entry)
+ static void canonicaliseDbRefs(EmblFile record)
{
- if (entry == null)
+ for (EmblEntry entry : record.getEntries())
{
- return;
- }
-// for (EmblEntry entry : record.getEntries())
-// {
if (entry.getDbRefs() != null)
{
for (DBRefEntry dbref : entry.getDbRefs())
}
}
- if (entry.getFeatures() != null)
+ if (entry.getFeatures() != null)
{
for (EmblFeature feature : entry.getFeatures())
{
}
}
}
- // }
+ }
}
}
"exception.ebiembl_retrieval_failed_on", new String[] {
emprefx.toLowerCase(), query.trim() }), e);
}
- return getEmblSequenceRecords(emprefx, reply);
+ return getEmblSequenceRecords(emprefx, query, reply);
}
/**
* @param emprefx
* either EMBL or EMBLCDS strings are allowed - anything else will
* not retrieve emblxml
+ * @param query
* @param file
* the EMBL XML file containing the results of a query
* @return
* @throws Exception
*/
- public AlignmentI getEmblSequenceRecords(String emprefx, File reply)
- throws Exception
+ public AlignmentI getEmblSequenceRecords(String emprefx, String query,
+ File reply) throws Exception
{
- EmblEntry entry = null;
+ EmblFile efile = null;
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
if (reply != null && reply.exists())
{
file = reply.getAbsolutePath();
if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
{
- entry = EmblFile.getEmblEntry(reply);
+ efile = EmblFile.getEmblFile(reply);
}
}
- // TODO don't need peptides any more?
List<SequenceI> peptides = new ArrayList<SequenceI>();
- AlignmentI al = null;
- if (entry != null)
+ if (efile != null)
{
- SequenceI seq = entry.getSequence(emprefx, peptides);
- if (seq != null)
+ for (EmblEntry entry : efile.getEntries())
{
- seq.deriveSequence();
- // place DBReferences on dataset and refer
- al = new Alignment(new SequenceI[] { seq });
+ SequenceI seq = entry.getSequence(emprefx, peptides);
+ if (seq != null)
+ {
+ seqs.add(seq.deriveSequence());
+ // place DBReferences on dataset and refer
+ }
}
}
+
+ AlignmentI al = null;
+ if (!seqs.isEmpty())
+ {
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ }
stopQuery();
return al;
}
if (outFile != null)
{
FileOutputStream fio = new FileOutputStream(outFile);
- // fio.write("<?xml version='1.0' encoding='UTF-8'?>\n".getBytes());
byte[] bb = new byte[32 * 1024];
int l;
while ((l = is.read(bb)) > 0)
package jalview.datamodel.xdb.embl;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
// not the whole sequence but enough for this test...
List<SequenceI> peptides = new ArrayList<SequenceI>();
SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
- EmblEntry ef = EmblTestHelper.getEmblFile();
- assertNotNull(ef);
- // assertEquals(1, ef.getEntries().size());
- // EmblEntry testee = ef.getEntries().get(0);
+ EmblFile ef = EmblTestHelper.getEmblFile();
+ assertEquals(1, ef.getEntries().size());
+ EmblEntry testee = ef.getEntries().get(0);
String sourceDb = "EMBL";
- SequenceI dna = ef.makeSequence(sourceDb);
+ SequenceI dna = testee.makeSequence(sourceDb);
/*
* parse three CDS features, with two/one/no Uniprot cross-refs
*/
- for (EmblFeature feature : ef.getFeatures())
+ for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
{
if ("CDS".equals(feature.getName()))
{
- ef.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
+ testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
}
}
package jalview.datamodel.xdb.embl;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.DBRefEntry;
+import java.util.Vector;
+
import org.testng.annotations.Test;
public class EmblFileTest
@Test(groups = { "Functional" })
public void testGetEmblFile()
{
- EmblEntry entry = EmblTestHelper.getEmblFile();
- assertNotNull(entry);
- // assertEquals(1, entries.size());
- // EmblEntry entry = entries.get(0);
+ Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().getEntries();
+ assertEquals(1, entries.size());
+ EmblEntry entry = entries.get(0);
assertEquals("X07547", entry.getAccession());
assertEquals("C. trachomatis plasmid", entry.getDescription());
// adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
// dna and translations truncated for convenience
private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
- // + "<ROOT>"
+ + "<ROOT>"
+ "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
+ " dataClass=\"STD\" taxonomicDivision=\"PRO\""
+ " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
*/
+ "<sequence>GGTATGTCCTCTAGTACAAAC\n"
+ "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
- + "</sequence></entry>";
+ + "</sequence></entry></ROOT>";
- static EmblEntry getEmblFile()
+ static EmblFile getEmblFile()
{
- return EmblFile.getEntry(new StringReader(TESTDATA));
+ return EmblFile.getEmblFile(new StringReader(TESTDATA));
}
}
git://source.jalview.org / jalview.git / commitdiff