X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=949c52e65f01b57b71a49aba3910de4289ee772e;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=e4fa53da00a1e97ea485b5bc6046379c4b3b2cb9;hpb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index e4fa53d..949c52e 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -155,7 +155,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient String msg = "Aborting ID retrieval after " + v + " chunks. Unexpected problem (" + r.getLocalizedMessage() + ")"; - System.err.println(msg); + jalview.bin.Console.errPrintln(msg); r.printStackTrace(); break; } @@ -170,7 +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); } @@ -208,19 +208,19 @@ 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); - + 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) { /* @@ -240,7 +240,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } } catch (IOException e) { - System.err.println( + jalview.bin.Console.errPrintln( "Error transferring Ensembl features: " + e.getMessage()); } // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK); @@ -265,12 +265,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient String accId = querySeq.getName(); try { - System.out.println("Adding protein product for " + accId); + jalview.bin.Console.outPrintln("Adding protein product for " + accId); AlignmentI protein = new EnsemblProtein(getDomain()) .getSequenceRecords(accId); if (protein == null || protein.getHeight() == 0) { - System.out.println("No protein product found for " + accId); + jalview.bin.Console.outPrintln("No protein product found for " + accId); return; } SequenceI proteinSeq = protein.getSequenceAt(0); @@ -295,8 +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) { @@ -356,10 +356,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ protected void getCrossReferences(SequenceI seq) { - + // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK); - while (seq.getDatasetSequence() != null) { seq = seq.getDatasetSequence(); @@ -370,31 +369,33 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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()); + // jalview.bin.Console.outPrintln("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); } @@ -420,7 +421,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient List seqs = parseSequenceJson(ids); if (seqs == null) - return alignment; + return alignment; if (seqs.isEmpty()) { @@ -429,7 +430,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (seqs.size() != ids.size()) { - System.out.println(String.format( + jalview.bin.Console.outPrintln(String.format( "Only retrieved %d sequences for %d query strings", seqs.size(), ids.size())); } @@ -484,9 +485,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * 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); + 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"); @@ -506,7 +508,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient result.add(sequence); } catch (ParseException | IOException e) { - System.err.println("Error processing JSON response: " + e.toString()); + jalview.bin.Console.errPrintln("Error processing JSON response: " + e.toString()); // ignore } // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK); @@ -657,7 +659,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (regions.isEmpty()) { - System.out.println("Failed to identify target sequence for " + accId + jalview.bin.Console.outPrintln("Failed to identify target sequence for " + accId + " from genomic features"); return null; } @@ -689,9 +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 @@ -713,7 +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)) { @@ -721,10 +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); @@ -812,13 +815,13 @@ 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; } @@ -826,10 +829,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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"); + // jalview.bin.Console.outPrintln("transferFeatures (" + (sfs.size()) + " --> " + // + targetSequence.getFeatures().getFeatureCount(true) + ") to " + // + targetSequence.getName() + " took " + // + (System.currentTimeMillis() - start) + "ms"); return result; } @@ -857,14 +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)) @@ -901,8 +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;