import jalview.exceptions.JalviewException;
import jalview.io.FastaFile;
import jalview.io.FileParse;
+import jalview.io.gff.Gff3Helper;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.Comparison;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
/**
* Base class for Ensembl sequence fetchers
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
- private static final String ALLELES = "alleles";
-
- protected static final String PARENT = "Parent";
-
- protected static final String ID = "ID";
-
protected static final String NAME = "Name";
protected static final String DESCRIPTION = "description";
try
{
/*
- * get 'dummy' genomic sequence with exon, cds and variation features
+ * get 'dummy' genomic sequence with gene, transcript,
+ * exon, cds and variation features
*/
SequenceI genomicSequence = null;
EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
/*
* transfer features to the query sequence
*/
- SequenceI querySeq = alignment.findName(accId);
+ SequenceI querySeq = alignment.findName(accId, true);
if (transferFeatures(accId, genomicSequence, querySeq))
{
urlstring.append("?type=").append(getSourceEnsemblType().getType());
urlstring.append(("&Accept=text/x-fasta"));
- Map<String, String> params = getAdditionalParameters();
- if (params != null)
+ String objectType = getObjectType();
+ if (objectType != null)
{
- for (Entry<String, String> entry : params.entrySet())
- {
- urlstring.append("&").append(entry.getKey()).append("=")
- .append(entry.getValue());
- }
+ urlstring.append("&").append(OBJECT_TYPE).append("=")
+ .append(objectType);
}
URL url = new URL(urlstring.toString());
}
/**
- * Override this method to add any additional x=y URL parameters needed
+ * Override this method to specify object_type request parameter
*
* @return
*/
- protected Map<String, String> getAdditionalParameters()
+ protected String getObjectType()
{
return null;
}
protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
String accId, int start)
{
- // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
List<SequenceFeature> sfs = sourceSequence.getFeatures()
.getPositionalFeatures();
if (sfs.isEmpty())
* generously initial size for number of cds regions
* (worst case titin Q8WZ42 has c. 313 exons)
*/
- List<int[]> regions = new ArrayList<int[]>(100);
+ List<int[]> regions = new ArrayList<>(100);
int mappedLength = 0;
int direction = 1; // forward
boolean directionSet = false;
*/
static void reverseComplementAlleles(SequenceFeature sf)
{
- final String alleles = (String) sf.getValue(ALLELES);
+ final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
if (alleles == null)
{
return;
reverseComplementAllele(complement, allele);
}
String comp = complement.toString();
- sf.setValue(ALLELES, comp);
+ sf.setValue(Gff3Helper.ALLELES, comp);
sf.setDescription(comp);
/*
String atts = sf.getAttributes();
if (atts != null)
{
- atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp);
+ atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
+ Gff3Helper.ALLELES + "=" + comp);
sf.setAttributes(atts);
}
}
return false;
}
- long start = System.currentTimeMillis();
- // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
+// long start = System.currentTimeMillis();
List<SequenceFeature> sfs = sourceSequence.getFeatures()
.getPositionalFeatures();
MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
boolean result = transferFeatures(sfs, targetSequence, mapping,
accessionId);
- System.out.println("transferFeatures (" + (sfs.size()) + " --> "
- + targetSequence.getFeatures().getFeatureCount(true) + ") to "
- + targetSequence.getName() + " took "
- + (System.currentTimeMillis() - start) + "ms");
+// System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+// + targetSequence.getFeatures().getFeatureCount(true) + ") to "
+// + targetSequence.getName() + " took "
+// + (System.currentTimeMillis() - start) + "ms");
return result;
}
{
String parent = (String) sf.getValue(PARENT);
// using contains to allow for prefix "gene:", "transcript:" etc
- if (parent != null && !parent.contains(identifier))
+ if (parent != null
+ && !parent.toUpperCase().contains(identifier.toUpperCase()))
{
// this genomic feature belongs to a different transcript
return false;
protected List<SequenceFeature> findFeatures(SequenceI sequence,
String term, String parentId)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
List<SequenceFeature> sfs = sequence.getFeatures()
.getFeaturesByOntology(term);
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
- if (parent != null && parent.equals(parentId))
+ if (parent != null && parent.equalsIgnoreCase(parentId))
{
result.add(sf);
}