X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=7f2fa5985fe885e01a7b8ea778d1215da578628b;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=fb017087fba3f049241eef851dd05fb040016638;hpb=9e5d1bced16aa9975692115a964c661cd7897a7c;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index fb01708..7f2fa59 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -20,9 +20,20 @@ */ 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; @@ -40,18 +51,6 @@ import jalview.util.Comparison; import jalview.util.DBRefUtils; import jalview.util.IntRangeComparator; import jalview.util.MapList; -import jalview.util.Platform; - -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; /** * Base class for Ensembl sequence fetchers @@ -171,7 +170,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * fetch and transfer genomic sequence features, * fetch protein product and add as cross-reference */ - for (int i = 0, n = allIds.size(); i < n; i++) + for (int i = 0, n = allIds.size(); i < n; i++) { addFeaturesAndProduct(allIds.get(i), alignment); } @@ -209,20 +208,19 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ SequenceI genomicSequence = null; EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain()); - EnsemblFeatureType[] features = getFeaturesToFetch(); - - Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK); + 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); - + + // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK); + if (genomicSequence != null) { /* @@ -236,7 +234,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * fetch and map protein product, and add it as a cross-reference * of the retrieved sequence */ - Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK); + // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK); addProteinProduct(querySeq); } } @@ -245,7 +243,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient System.err.println( "Error transferring Ensembl features: " + e.getMessage()); } - Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK); + // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK); } /** @@ -297,8 +295,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient List uprots = DBRefUtils.selectRefs(ds.getDBRefs(), new String[] { DBRefSource.UNIPROT }); - List upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(), - new String[] + List upxrefs = DBRefUtils + .selectRefs(querySeq.getDBRefs(), new String[] { DBRefSource.UNIPROT }); if (uprots != null) { @@ -314,7 +312,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (upx.size() > 1) { - Cache.log.warn( + Console.warn( "Implementation issue - multiple uniprot acc on product sequence."); } } @@ -340,8 +338,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * 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) { @@ -358,47 +356,47 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ protected void getCrossReferences(SequenceI seq) { - - Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK); - + // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK); + while (seq.getDatasetSequence() != null) { seq = seq.getDatasetSequence(); } - Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK); + // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK); EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(), getEnsemblDataVersion()); List xrefs = xrefFetcher.getCrossReferences(seq.getName()); - + for (int i = 0, n = xrefs.size(); i < n; i++) { -// 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() + // 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()); + // System.out.println("primaries are " + seq.getPrimaryDBRefs().toString()); /* * and add a reference to itself */ - -// Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK); + + // 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); + // Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK); seq.addDBRef(self); - - Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK); + // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK); } /** @@ -419,11 +417,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient inProgress = false; throw new JalviewException("ENSEMBL Rest API not available."); } - Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK); + // Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK); List seqs = parseSequenceJson(ids); if (seqs == null) - return alignment; + return alignment; if (seqs.isEmpty()) { @@ -486,11 +484,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * for now, assumes only one sequence returned; refactor if needed * in future to handle a JSONArray with more than one */ - - Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK); - Map val = (Map) getJSON(null, ids, -1, MODE_MAP, null); + // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK); + Map val = (Map) getJSON(null, ids, -1, + MODE_MAP, null); if (val == null) - return null; + return null; Object s = val.get("desc"); String desc = s == null ? null : s.toString(); s = val.get("id"); @@ -513,7 +511,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient System.err.println("Error processing JSON response: " + e.toString()); // ignore } - Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK); + // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK); return result; } @@ -693,9 +691,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ protected abstract List 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 @@ -717,7 +715,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (mappedRange != null) { -// Platform.timeCheck(null, Platform.TIME_SET); + // Platform.timeCheck(null, Platform.TIME_SET); String group = sf.getFeatureGroup(); if (".".equals(group)) { @@ -725,10 +723,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } int newBegin = Math.min(mappedRange[0], mappedRange[1]); int newEnd = Math.max(mappedRange[0], mappedRange[1]); -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); bhtest++; // 280 ms/1000 here: - SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, group, sf.getScore()); + SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, + group, sf.getScore()); // 0.175 ms here: targetSequence.addSequenceFeature(copy); @@ -736,7 +735,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * for sequence_variant on reverse strand, have to convert the allele * values to their complements */ - if (!forwardStrand && SequenceOntologyFactory.getInstance() + if (!forwardStrand && SequenceOntologyFactory.getSequenceOntology() .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT)) { reverseComplementAlleles(copy); @@ -765,18 +764,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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); - } } /** @@ -828,26 +815,24 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return false; } -// long start = System.currentTimeMillis(); + // long start = System.currentTimeMillis(); List sfs = sourceSequence.getFeatures() .getPositionalFeatures(); MapList mapping = getGenomicRangesFromFeatures(sourceSequence, accessionId, targetSequence.getStart()); if (mapping == null) - { + { return false; } - - Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK); - + // Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK); 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; } @@ -875,14 +860,15 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient SequenceFeatures.sortFeatures(sfs, forwardStrand); boolean transferred = false; - + 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); - } + // 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)) @@ -919,8 +905,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected boolean featureMayBelong(SequenceFeature sf, String identifier) { String parent = (String) sf.getValue(PARENT); - if (parent != null - && !parent.equalsIgnoreCase(identifier)) + if (parent != null && !parent.equalsIgnoreCase(identifier)) { // this genomic feature belongs to a different transcript return false; @@ -984,7 +969,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient public static boolean isTranscript(String featureType) { return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType) - || SequenceOntologyFactory.getInstance().isA(featureType, + || SequenceOntologyFactory.getSequenceOntology().isA(featureType, SequenceOntologyI.TRANSCRIPT); } }