X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=e4fa53da00a1e97ea485b5bc6046379c4b3b2cb9;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;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..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 @@ -211,8 +210,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain()); EnsemblFeatureType[] features = getFeaturesToFetch(); - Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK); - + // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK); AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId, features); @@ -221,7 +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) { @@ -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); } /** @@ -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) { @@ -359,7 +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) @@ -367,7 +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()); @@ -397,8 +395,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient seq.addDBRef(self); - Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK); - + // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK); } /** @@ -419,7 +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) @@ -486,8 +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; @@ -513,7 +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; } @@ -765,18 +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); - } } /** @@ -838,9 +822,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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); @@ -879,10 +861,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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))