*/
package jalview.ext.ensembl;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import org.json.simple.parser.ParseException;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.util.IntRangeComparator;
import jalview.util.MapList;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-import org.json.simple.parser.ParseException;
-
/**
* Base class for Ensembl sequence fetchers
*
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
- protected static final String NAME = "Name";
-
protected static final String DESCRIPTION = "description";
/*
* fetch and transfer genomic sequence features,
* fetch protein product and add as cross-reference
*/
- for (String accId : allIds)
+ for (int i = 0, n = allIds.size(); i < n; i++)
{
- addFeaturesAndProduct(accId, alignment);
+ addFeaturesAndProduct(allIds.get(i), alignment);
}
- for (SequenceI seq : alignment.getSequences())
+ List<SequenceI> seqs = alignment.getSequences();
+ for (int i = 0, n = seqs.size(); i < n; i++)
{
- getCrossReferences(seq);
+ getCrossReferences(seqs.get(i));
}
return alignment;
*/
SequenceI genomicSequence = null;
EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
- EnsemblFeatureType[] features = getFeaturesToFetch();
+ EnsemblFeatureType[] features = getFeaturesToFetch();
+
+ // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);
+
AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
features);
if (geneFeatures != null && geneFeatures.getHeight() > 0)
{
genomicSequence = geneFeatures.getSequenceAt(0);
}
+
+ // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);
+
if (genomicSequence != null)
{
/*
* fetch and map protein product, and add it as a cross-reference
* of the retrieved sequence
*/
+ // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);
addProteinProduct(querySeq);
}
}
System.err.println(
"Error transferring Ensembl features: " + e.getMessage());
}
+ // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
}
/**
String accId = querySeq.getName();
try
{
+ System.out.println("Adding protein product for " + accId);
AlignmentI protein = new EnsemblProtein(getDomain())
.getSequenceRecords(accId);
if (protein == null || protein.getHeight() == 0)
DBRefEntry dbr = new DBRefEntry(getDbSource(),
getEnsemblDataVersion(), proteinSeq.getName(), map);
querySeq.getDatasetSequence().addDBRef(dbr);
- DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
+ List<DBRefEntry> uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
new String[]
{ DBRefSource.UNIPROT });
- DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
+ List<DBRefEntry> upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
new String[]
{ DBRefSource.UNIPROT });
if (uprots != null)
if (upx.size() > 1)
{
- Cache.log.warn(
+ Console.warn(
"Implementation issue - multiple uniprot acc on product sequence.");
}
}
* copy exon features to protein, compute peptide variants from dna
* variants and add as features on the protein sequence ta-da
*/
- AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq,
- mapList);
+ // JAL-3187 render on the fly instead
+ // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList);
}
} catch (Exception e)
{
*/
protected void getCrossReferences(SequenceI seq)
{
+
+ // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);
+
+
while (seq.getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
}
+ // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);
+
EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
getEnsemblDataVersion());
List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
- for (DBRefEntry xref : xrefs)
+
+ for (int i = 0, n = xrefs.size(); i < n; i++)
{
- seq.addDBRef(xref);
+// Platform.timeCheck("ESP. getxref + " + (i) + "/" + n, Platform.TIME_MARK);
+ // BH 2019.01.25 this next method was taking 174 ms PER addition for a 266-reference example.
+ // DBRefUtils.ensurePrimaries(seq)
+ // was at the end of seq.addDBRef, so executed after ever addition!
+ // This method was moved to seq.getPrimaryDBRefs()
+ seq.addDBRef(xrefs.get(i));
}
+// System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
/*
* and add a reference to itself
*/
+
+// Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);
+
DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
- seq.getName());
+ seq.getName());
+
+// Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);
+
seq.addDBRef(self);
+
+ // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);
}
/**
inProgress = false;
throw new JalviewException("ENSEMBL Rest API not available.");
}
- BufferedReader br = getSequenceReader(ids);
- if (br == null)
- {
- return alignment;
- }
+ // Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
- List<SequenceI> seqs = parseSequenceJson(br);
+ List<SequenceI> seqs = parseSequenceJson(ids);
+ if (seqs == null)
+ return alignment;
if (seqs.isEmpty())
{
}
/**
- * Parses a JSON response into a list of sequences
+ * Parses a JSON response for a single sequence ID query
*
* @param br
- * @return
+ * @return a single jalview.datamodel.Sequence
* @see http://rest.ensembl.org/documentation/info/sequence_id
*/
- protected List<SequenceI> parseSequenceJson(BufferedReader br)
+ @SuppressWarnings("unchecked")
+ protected List<SequenceI> parseSequenceJson(List<String> ids)
{
- JSONParser jp = new JSONParser();
List<SequenceI> result = new ArrayList<>();
try
{
* for now, assumes only one sequence returned; refactor if needed
* in future to handle a JSONArray with more than one
*/
- final JSONObject val = (JSONObject) jp.parse(br);
+ // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
+ Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
+ if (val == null)
+ return null;
Object s = val.get("desc");
String desc = s == null ? null : s.toString();
s = val.get("id");
System.err.println("Error processing JSON response: " + e.toString());
// ignore
}
+ // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
return result;
}
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
urlstring.append("?type=").append(getSourceEnsemblType().getType());
urlstring.append(("&Accept=application/json"));
- urlstring.append(("&Content-Type=application/json"));
+ urlstring.append(("&content-type=application/json"));
String objectType = getObjectType();
if (objectType != null)
*/
protected abstract List<SequenceFeature> getIdentifyingFeatures(
SequenceI seq, String accId);
-
+
+ int bhtest = 0;
+
/**
* Transfers the sequence feature to the target sequence, locating its start
* and end range based on the mapping. Features which do not overlap the
if (mappedRange != null)
{
+// Platform.timeCheck(null, Platform.TIME_SET);
String group = sf.getFeatureGroup();
if (".".equals(group))
{
}
int newBegin = Math.min(mappedRange[0], mappedRange[1]);
int newEnd = Math.max(mappedRange[0], mappedRange[1]);
- SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
- group, sf.getScore());
+// Platform.timeCheck(null, Platform.TIME_MARK);
+ bhtest++;
+ // 280 ms/1000 here:
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, group, sf.getScore());
+ // 0.175 ms here:
targetSequence.addSequenceFeature(copy);
/*
String comp = complement.toString();
sf.setValue(Gff3Helper.ALLELES, comp);
sf.setDescription(comp);
-
- /*
- * replace value of "alleles=" in sf.ATTRIBUTES as well
- * so 'output as GFF' shows reverse complement alleles
- */
- String atts = sf.getAttributes();
- if (atts != null)
- {
- atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
- Gff3Helper.ALLELES + "=" + comp);
- sf.setAttributes(atts);
- }
}
/**
MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
accessionId, targetSequence.getStart());
if (mapping == null)
- {
+ {
return false;
}
+ // Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);
+
boolean result = transferFeatures(sfs, targetSequence, mapping,
accessionId);
// System.out.println("transferFeatures (" + (sfs.size()) + " --> "
SequenceFeatures.sortFeatures(sfs, forwardStrand);
boolean transferred = false;
- for (SequenceFeature sf : sfs)
+
+ for (int i = 0, n = sfs.size(); i < n; i++)
{
+
+// if ((i%1000) == 0) {
+//// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
+// Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);
+// }
+
+ SequenceFeature sf = sfs.get(i);
if (retainFeature(sf, parentId))
{
transferFeature(sf, targetSequence, mapping, forwardStrand);
transferred = true;
}
}
+
return transferred;
}
protected boolean featureMayBelong(SequenceFeature sf, String identifier)
{
String parent = (String) sf.getValue(PARENT);
- // using contains to allow for prefix "gene:", "transcript:" etc
if (parent != null
- && !parent.toUpperCase().contains(identifier.toUpperCase()))
+ && !parent.equalsIgnoreCase(identifier))
{
// this genomic feature belongs to a different transcript
return false;
return true;
}
+ /**
+ * Answers a short description of the sequence fetcher
+ */
@Override
public String getDescription()
{
/**
* Answers true if the feature type is either 'NMD_transcript_variant' or
- * 'transcript' or one of its sub-types in the Sequence Ontology. This is
- * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl
+ * 'transcript' (or one of its sub-types in the Sequence Ontology). This is
+ * because NMD_transcript_variant behaves like 'transcript' in Ensembl
* although strictly speaking it is not (it is a sub-type of
* sequence_variant).
+ * <p>
+ * (This test was needed when fetching transcript features as GFF. As we are
+ * now fetching as JSON, all features have type 'transcript' so the check for
+ * NMD_transcript_variant is redundant. Left in for any future case arising.)
*
* @param featureType
* @return
git://source.jalview.org / jalview.git / blobdiff