X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=e4fa53da00a1e97ea485b5bc6046379c4b3b2cb9;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=1d6b354ed0684417e1f45cc3a93fa8fff356ba3c;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 1d6b354..e4fa53d 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 @@ -171,14 +170,15 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * 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 seqs = alignment.getSequences(); + for (int i = 0, n = seqs.size(); i < n; i++) { - getCrossReferences(seq); + getCrossReferences(seqs.get(i)); } return alignment; @@ -208,10 +208,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ SequenceI genomicSequence = null; EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain()); - EnsemblFeatureType[] features = getFeaturesToFetch(); + EnsemblFeatureType[] features = getFeaturesToFetch(); - Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK); - + // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK); AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId, features); @@ -220,7 +219,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient genomicSequence = geneFeatures.getSequenceAt(0); } - Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK); + // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK); if (genomicSequence != null) { @@ -228,9 +227,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * transfer features to the query sequence */ SequenceI querySeq = alignment.findName(accId, true); - - Platform.timeCheck("ESP.transferfeat", Platform.TIME_MARK); - if (transferFeatures(accId, genomicSequence, querySeq)) { @@ -238,7 +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.addprotein", Platform.TIME_MARK); + // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK); addProteinProduct(querySeq); } } @@ -247,7 +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); } /** @@ -316,7 +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."); } } @@ -342,8 +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) { @@ -361,7 +357,7 @@ 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) @@ -369,7 +365,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient seq = seq.getDatasetSequence(); } - Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK); + // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK); EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(), getEnsemblDataVersion()); @@ -377,7 +373,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient for (int i = 0, n = xrefs.size(); i < n; i++) { - Platform.timeCheck("ESP. getxref + " + (i) + "/" + n, Platform.TIME_MARK); +// 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! @@ -385,22 +381,21 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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); } /** @@ -421,7 +416,7 @@ 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) @@ -488,8 +483,7 @@ 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); + // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK); Map val = (Map) getJSON(null, ids, -1, MODE_MAP, null); if (val == null) return null; @@ -515,7 +509,7 @@ 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; } @@ -695,7 +689,9 @@ 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 @@ -717,6 +713,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (mappedRange != null) { +// Platform.timeCheck(null, Platform.TIME_SET); String group = sf.getFeatureGroup(); if (".".equals(group)) { @@ -724,8 +721,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } 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); /* @@ -761,18 +761,6 @@ 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); - } } /** @@ -830,10 +818,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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()) + " --> " @@ -867,14 +857,23 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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; }