*/
package jalview.ws.dbsources;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
+
import jalview.analysis.SequenceIdMatcher;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.util.DnaUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.xml.binding.embl.EntryType;
import jalview.xml.binding.embl.EntryType.Feature;
import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.embl.ROOT;
import jalview.xml.binding.embl.XrefType;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.regex.Pattern;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
+ private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
+
/*
* JAL-1856 Embl returns this text for query not found
*/
private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
- private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
-
public EmblXmlSource()
{
super();
try
{
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
- "xml");
+ emprefx.toLowerCase(Locale.ROOT) + ":" + query.trim(),
+ "display=xml", "xml");
} catch (Exception e)
{
stopQuery();
- throw new Exception(MessageManager.formatMessage(
- "exception.ebiembl_retrieval_failed_on", new String[]
- { emprefx.toLowerCase(), query.trim() }), e);
+ throw new Exception(
+ String.format("EBI EMBL XML retrieval failed for %s:%s",
+ emprefx.toLowerCase(Locale.ROOT), query.trim()),
+ e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(is);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- jalview.xml.binding.embl.ROOT root = (jalview.xml.binding.embl.ROOT) um
- .unmarshal(streamReader);
+ JAXBElement<ROOT> rootElement = um.unmarshal(streamReader,
+ ROOT.class);
+ ROOT root = rootElement.getValue();
/*
* document root contains either "entry" or "entrySet"
else
{
// final product length truncation check
- int[] cdsRanges = adjustForProteinLength(translationLength,
- exons);
- dnaToProteinMapping = new Mapping(product, cdsRanges,
+ int[] exons2 = adjustForProteinLength(translationLength, exons);
+ dnaToProteinMapping = new Mapping(product, exons2,
new int[]
{ 1, translationLength }, 3, 1);
if (product != null)
proteinSeq = new Sequence(proteinSeqName,
product.getSequenceAsString());
matcher.add(proteinSeq);
+ proteinSeq.setDescription(product.getDescription());
peptides.add(proteinSeq);
}
dnaToProteinMapping.setTo(proteinSeq);
&& dnaToProteinMapping.getTo() != null)
{
DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, sequenceVersion,
- proteinId);
+ DBRefSource.EMBLCDSProduct, sequenceVersion, proteinId);
dnaToEmblProteinRef.setMap(dnaToProteinMapping);
dnaToProteinMapping.setMappedFromId(proteinId);
dna.addDBRef(dnaToEmblProteinRef);
{
return new int[] {};
}
-
+
try
{
List<int[]> ranges = DnaUtils.parseLocation(location);
return listToArray(ranges);
} catch (ParseException e)
{
- Cache.log.warn(
+ Console.warn(
String.format("Not parsing inexact CDS location %s in ENA %s",
location, accession));
return new int[] {};
SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
if (!vals.isEmpty())
{
- StringBuilder sb = new StringBuilder();
- boolean first = true;
for (Entry<String, String> val : vals.entrySet())
{
- if (!first)
- {
- sb.append(";");
- }
- sb.append(val.getKey()).append("=").append(val.getValue());
- first = false;
sf.setValue(val.getKey(), val.getValue());
}
- sf.setAttributes(sb.toString());
}
return sf;
}
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return ACCESSION_REGEX;
+ }
+
+ @Override
+ public String getDbVersion()
+ {
+ return "0";
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ if (accession == null || accession.length() < 2)
+ {
+ return false;
+ }
+ return getAccessionValidator().search(accession);
+ }
+
/**
* Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
+ * the protein (including truncation for stop codon included in exon)
*
* @param proteinLength
* @param exon
}
int expectedCdsLength = proteinLength * 3;
int exonLength = MappingUtils.getLength(Arrays.asList(exon));
-
+
/*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
+ * if exon length matches protein, or is shorter, then leave it unchanged
*/
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
+ if (expectedCdsLength >= exonLength)
{
return exon;
}
-
+
int origxon[];
int sxpos = -1;
int endxon = 0;
// .println("Truncating final exon interval on region by "
// + (cdspos - cdslength));
}
-
+
/*
* shrink the final exon - reduce end position if forward
* strand, increase it if reverse
break;
}
}
-
+
if (sxpos != -1)
{
// and trim the exon interval set if necessary
git://source.jalview.org / jalview.git / blobdiff