From a61c1f7284b94a6db5f5900b6c6dd5844fed8663 Mon Sep 17 00:00:00 2001 From: Olin Blodgett Date: Sun, 26 Jan 2025 09:06:59 -0500 Subject: [PATCH] Format clean up --- .../indexer/indexers/GoIndexer.java | 2 +- .../indexer/indexers/Indexer.java | 8 +- .../interfaces/VocabularyRESTInterface.java | 11 +- .../neo4j/repository/AlleleRepository.java | 223 +++++++----------- 4 files changed, 95 insertions(+), 149 deletions(-) diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/GoIndexer.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/GoIndexer.java index 6fa6c22ef..e6c4a42f1 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/GoIndexer.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/GoIndexer.java @@ -30,7 +30,7 @@ public void index() { log.info("Pulling All Terms Finished"); Iterable docs = goTrans.translateEntities(terms); - for(SearchableItemDocument doc: docs) { + for (SearchableItemDocument doc : docs) { doc.setPopularity(popularityScore.get(doc.getPrimaryKey())); } diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java index d43f8229f..f4f7d590c 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java @@ -1,6 +1,5 @@ package org.alliancegenome.indexer.indexers; - import java.io.IOException; import java.net.URL; import java.nio.file.Files; @@ -41,7 +40,6 @@ import lombok.extern.slf4j.Slf4j; - @Slf4j public abstract class Indexer extends Thread { @@ -99,7 +97,9 @@ public void afterBulk(long executionId, BulkRequest request, Throwable failure) builder.setConcurrentRequests(indexerConfig.getConcurrentRequests()); builder.setBackoffPolicy(BackoffPolicy.exponentialBackoff(TimeValue.timeValueSeconds(1L), 60)); bulkProcessor = builder.build(); - //bulkProcessor = BulkProcessor.builder((request, bulkListener) -> searchClient.bulkAsync(request, RequestOptions.DEFAULT, bulkListener), listener).build(); + // bulkProcessor = BulkProcessor.builder((request, bulkListener) -> + // searchClient.bulkAsync(request, RequestOptions.DEFAULT, bulkListener), + // listener).build(); } @@ -168,7 +168,7 @@ public void indexDocuments(Iterable docs, Class vie } else { json = om.writeValueAsString(doc); } - if(json.length() > 19_000_000) { + if (json.length() > 19_000_000) { log.warn("Document is too large for ES skipping: " + json.length()); continue; } diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/VocabularyRESTInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/VocabularyRESTInterface.java index afe6ecadf..c5ca43bc4 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/VocabularyRESTInterface.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/VocabularyRESTInterface.java @@ -16,16 +16,13 @@ import jakarta.ws.rs.QueryParam; @Path("/vocabularyterm") -@Produces({"application/json"}) -@Consumes({"application/json"}) +@Produces({ "application/json" }) +@Consumes({ "application/json" }) public interface VocabularyRESTInterface { @POST @Path("/find") - @JsonView({View.FieldsAndLists.class}) - SearchResponse find( - @DefaultValue("0") @QueryParam("page") Integer page, - @DefaultValue("10") @QueryParam("limit") Integer limit, - HashMap params); + @JsonView({ View.FieldsAndLists.class }) + SearchResponse find(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); } diff --git a/agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/AlleleRepository.java b/agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/AlleleRepository.java index 9b602a869..9983bae81 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/AlleleRepository.java +++ b/agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/AlleleRepository.java @@ -43,7 +43,7 @@ public class AlleleRepository extends Neo4jRepository { private Map variantSOTermMap; private Map> alleleSynonymMap; private Map> alleleCrossReferenceMap; - + // geneID, chromosome private Map geneChromosomeMap = new HashMap<>(); // allele ID for which disease info exists @@ -54,8 +54,6 @@ public class AlleleRepository extends Neo4jRepository { private static Set allAllelicHgvsGNames; private static Map>> allAllelesMap; - - public AlleleRepository(boolean debug, List testGeneIDs) { super(Allele.class); @@ -145,19 +143,18 @@ public List getAllModelKeys() { public Map getTranscriptWithExonInfo() { String transcriptFileName = "TranscriptWithExonInfoCache.data"; - + if (MapUtils.isNotEmpty(transcriptMap)) { log.info("Transcripts loaded from memory cache"); return transcriptMap; } - - + transcriptMap = readFromCache(transcriptFileName, Map.class); if (transcriptMap != null && transcriptMap.size() > 0) { log.info("Transcripts loaded from file cache"); return transcriptMap; } - + log.info("Transcripts loaded from neo4j"); String query = ""; // get Transcript - Exon relationships @@ -166,13 +163,10 @@ public Map getTranscriptWithExonInfo() { query += " RETURN p1, p2"; Iterable transcriptExonsIter = query(Transcript.class, query); log.info("Number of Transcript/Exon relationships: " + String.format("%,d", (int) StreamSupport.stream(transcriptExonsIter.spliterator(), false).count())); - transcriptMap = StreamSupport.stream(transcriptExonsIter.spliterator(), false) - .collect(Collectors.toSet()) - .stream() - .collect(Collectors.toMap(Transcript::getPrimaryKey, transcript -> transcript)); - + transcriptMap = StreamSupport.stream(transcriptExonsIter.spliterator(), false).collect(Collectors.toSet()).stream().collect(Collectors.toMap(Transcript::getPrimaryKey, transcript -> transcript)); + writeToCache(transcriptFileName, transcriptMap); - + return transcriptMap; } @@ -187,25 +181,23 @@ public Map getGeneChromosomeInfo() { query += " RETURN g.primaryKey, c.primaryKey "; Result map = queryForResult(query); - StreamSupport.stream(map.spliterator(), false) - .forEach(entrySet -> { - final Iterator> iterator = entrySet.entrySet().iterator(); - final Map.Entry entryKey = iterator.next(); - final Map.Entry entryValue = iterator.next(); - geneChromosomeMap.put((String) entryKey.getValue(), (String) entryValue.getValue()); - }); + StreamSupport.stream(map.spliterator(), false).forEach(entrySet -> { + final Iterator> iterator = entrySet.entrySet().iterator(); + final Map.Entry entryKey = iterator.next(); + final Map.Entry entryValue = iterator.next(); + geneChromosomeMap.put((String) entryKey.getValue(), (String) entryValue.getValue()); + }); query = " MATCH p=(g:Gene)"; query += " where not exists ((g)-[:LOCATED_ON]->(:Chromosome)) "; query += " RETURN g.primaryKey "; map = queryForResult(query); - StreamSupport.stream(map.spliterator(), false) - .forEach(entrySet -> { - final Iterator> iterator = entrySet.entrySet().iterator(); - final Map.Entry entryValue = iterator.next(); - geneChromosomeMap.put("", (String) entryValue.getValue()); - }); + StreamSupport.stream(map.spliterator(), false).forEach(entrySet -> { + final Iterator> iterator = entrySet.entrySet().iterator(); + final Map.Entry entryValue = iterator.next(); + geneChromosomeMap.put("", (String) entryValue.getValue()); + }); log.info("Number of Gene/Chromosome relationships: " + String.format("%,d", geneChromosomeMap.size())); return geneChromosomeMap; @@ -220,10 +212,9 @@ public boolean hasAlleleDiseaseInfo(String alleleID) { query += " MATCH (a:Allele)<-[:IS_IMPLICATED_IN]-(doTerm:DOTerm) "; query += " RETURN distinct(a.primaryKey) as ID "; Result result = queryForResult(query); - StreamSupport.stream(result.spliterator(), false) - .forEach(idMap -> { - alleleDiseaseSet.add((String) idMap.get("ID")); - }); + StreamSupport.stream(result.spliterator(), false).forEach(idMap -> { + alleleDiseaseSet.add((String) idMap.get("ID")); + }); log.info("Number of alleles with disease annotations: " + String.format("%,d", alleleDiseaseSet.size())); return alleleDiseaseSet.contains(alleleID); } @@ -237,10 +228,9 @@ public boolean hasAllelePhenoInfo(String alleleID) { query += " MATCH (a:Allele)-[:HAS_PHENOTYPE]->(ph:Phenotype) "; query += " RETURN distinct(a.primaryKey) as ID"; Result result = queryForResult(query); - StreamSupport.stream(result.spliterator(), false) - .forEach(idMap -> { - allelePhenoSet.add((String) idMap.get("ID")); - }); + StreamSupport.stream(result.spliterator(), false).forEach(idMap -> { + allelePhenoSet.add((String) idMap.get("ID")); + }); log.info("Number of alleles with phenotype annotations: " + String.format("%,d", allelePhenoSet.size())); return allelePhenoSet.contains(alleleID); } @@ -271,10 +261,10 @@ public Map>> getAllAllelesCache() { // allele-only (no variants) query += " MATCH p1=(:Species)<-[:FROM_SPECIES]-(a:Allele)-[:IS_ALLELE_OF]->(g:Gene)-[:FROM_SPECIES]-(q:Species) "; query += "where not exists ((a)<-[:VARIATION]-(:Variant)) "; - //query += " AND g.primaryKey = 'WB:WBGene00000913' "; + // query += " AND g.primaryKey = 'WB:WBGene00000913' "; - // query += " AND g.taxonId = 'NCBITaxon:7955' "; - // query += " AND g.primaryKey = 'RGD:9294106' "; + // query += " AND g.taxonId = 'NCBITaxon:7955' "; + // query += " AND g.primaryKey = 'RGD:9294106' "; if (testGeneIDs != null) { StringJoiner joiner = new StringJoiner("','", "'", "'"); testGeneIDs.forEach(joiner::add); @@ -286,15 +276,14 @@ public Map>> getAllAllelesCache() { query += " RETURN p1, p2, crossRef "; Iterable alleles = query(query, new HashMap<>()); - Set allAlleles = StreamSupport.stream(alleles.spliterator(), false) - .collect(Collectors.toSet()); + Set allAlleles = StreamSupport.stream(alleles.spliterator(), false).collect(Collectors.toSet()); log.info("Number of alleles without variants: " + String.format("%,d", allAlleles.size())); // alleles with variant records query = ""; query += " MATCH p1=(g:Gene)<-[:IS_ALLELE_OF]-(a:Allele)<-[:VARIATION]-(variant:Variant)--(:SOTerm) "; query += ", p0=(:Species)<-[:FROM_SPECIES]-(a:Allele) "; - // query += " where g.taxon955' "; + // query += " where g.taxon955' "; if (testGeneIDs != null) { StringJoiner joiner = new StringJoiner("','", "'", "'"); testGeneIDs.forEach(joiner::add); @@ -321,10 +310,7 @@ public Map>> getAllAllelesCache() { // group by taxon ID Map> taxonMap = allAlleleSet.stream().collect(groupingBy(allele -> allele.getGene().getTaxonId())); taxonMap.forEach((taxonID, alleleList) -> { - Set chromosomes = alleleList.stream() - .filter(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey()) != null) - .map(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey())) - .collect(Collectors.toSet()); + Set chromosomes = alleleList.stream().filter(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey()) != null).map(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey())).collect(Collectors.toSet()); // unknown chromosome chromosomes.add(""); @@ -334,10 +320,7 @@ public Map>> getAllAllelesCache() { Set chromosomeAlleles = new HashSet<>(); // all alleles with chromosome info - alleleList.stream() - .filter(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey()) != null) - .filter(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey()).equals(chromosome)) - .forEach(chromosomeAlleles::add); + alleleList.stream().filter(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey()) != null).filter(allele -> getGeneChromosomeInfo().get(allele.getGene().getPrimaryKey()).equals(chromosome)).forEach(chromosomeAlleles::add); chromosomeMap.put(chromosome, chromosomeAlleles); }); allAlleleMap.put(taxonID, chromosomeMap); @@ -365,24 +348,20 @@ public Map>> getAllAllelesCache() { public void fixupAllelesWithVariants(Set allAlleles, Set allelesWithVariants) { getTranscriptWithExonInfo(); - for(Allele allele: allelesWithVariants) { - allele.getVariants().stream() - .filter(Objects::nonNull) - .filter(variant -> variant.getTranscriptList() != null) - .forEach(variant -> - variant.getTranscriptList().forEach(transcript -> { - if (!debug) { - final Transcript transcript1 = transcriptMap.get(transcript.getPrimaryKey()); - if (transcript1 != null) { - if (transcript1.getGenomeLocation() != null) { - transcript.setGenomeLocation(transcript1.getGenomeLocation()); - } - if (transcript1.getExons() != null) { - transcript.setExons(transcript1.getExons()); - } - } + for (Allele allele : allelesWithVariants) { + allele.getVariants().stream().filter(Objects::nonNull).filter(variant -> variant.getTranscriptList() != null).forEach(variant -> variant.getTranscriptList().forEach(transcript -> { + if (!debug) { + final Transcript transcript1 = transcriptMap.get(transcript.getPrimaryKey()); + if (transcript1 != null) { + if (transcript1.getGenomeLocation() != null) { + transcript.setGenomeLocation(transcript1.getGenomeLocation()); + } + if (transcript1.getExons() != null) { + transcript.setExons(transcript1.getExons()); } - })); + } + } + })); } allAlleles.addAll(allelesWithVariants); @@ -396,8 +375,8 @@ public void fixupAllelesWithVariants(Set allAlleles, Set alleles /* * Need to run 3 queries as a union as the where clause is against the gene of - * three typed associations (EXPRESSES, TARGET, IS_REGULATED_BY) against the construct node - * but there might be more genes with the same association + * three typed associations (EXPRESSES, TARGET, IS_REGULATED_BY) against the + * construct node but there might be more genes with the same association */ public List getTransgenicAlleles(String geneID) { HashMap map = new HashMap<>(); @@ -405,14 +384,12 @@ public List getTransgenicAlleles(String geneID) { String query = getCypherQuery("EXPRESSES"); Iterable alleles = query(query, map); - List alleleList = StreamSupport.stream(alleles.spliterator(), false) - .collect(Collectors.toList()); + List alleleList = StreamSupport.stream(alleles.spliterator(), false).collect(Collectors.toList()); query = getCypherQuery("TARGETS"); alleles = query(query, map); - alleleList.addAll(StreamSupport.stream(alleles.spliterator(), false) - .collect(Collectors.toList())); + alleleList.addAll(StreamSupport.stream(alleles.spliterator(), false).collect(Collectors.toList())); alleleList.sort(Comparator.comparing(Allele::getSymbolText)); alleleList.forEach(allele -> { @@ -424,19 +401,16 @@ public List getTransgenicAlleles(String geneID) { public Map> getAllAllelesByTaxonNChromosome(String taxonId, String chr) { - String query = "MATCH p1=(:SOTerm)--(v:Variant)-[:VARIATION]->(a:Allele{taxonId: \"" + taxonId - + "\"})-[:IS_ALLELE_OF]->(g:Gene{taxonId: \"" + taxonId - + "\"})" + "-[r:LOCATED_ON]->(c:Chromosome{primaryKey:\"" + chr + "\"}) "; + String query = "MATCH p1=(:SOTerm)--(v:Variant)-[:VARIATION]->(a:Allele{taxonId: \"" + taxonId + "\"})-[:IS_ALLELE_OF]->(g:Gene{taxonId: \"" + taxonId + "\"})" + "-[r:LOCATED_ON]->(c:Chromosome{primaryKey:\"" + chr + "\"}) "; query += " OPTIONAL MATCH consequence = (t:Transcript)--(:TranscriptLevelConsequence)--(v:Variant)<-[:ASSOCIATION]-(t:Transcript)--(:SOTerm) "; query += " OPTIONAL MATCH loc=(v:Variant)-[:ASSOCIATION]->(:GenomicLocation)"; query += " OPTIONAL MATCH p2=(a:Allele)-[:ALSO_KNOWN_AS]->(synonym:Synonym)"; query += " OPTIONAL MATCH crossRef=(a:Allele)-[:CROSS_REFERENCE]->(c:CrossReference)"; query += " RETURN p1, p2, consequence, loc, crossRef "; - + Iterable allelesWithVariantsIter = query(query, new HashMap<>()); - Set allelesWithVariants = StreamSupport.stream(allelesWithVariantsIter.spliterator(), false) - .collect(Collectors.toSet()); + Set allelesWithVariants = StreamSupport.stream(allelesWithVariantsIter.spliterator(), false).collect(Collectors.toSet()); Map> allelesMap = new HashMap<>(); for (Allele a : allelesWithVariants) { List variants = a.getVariants(); @@ -488,8 +462,7 @@ public Set getAllAlleleVariantInfoOnGene() { query += " RETURN p1, p2, vari, crossRef, loc, consequence, transcript, variantPub, transcriptLocation, transcriptType "; Iterable alleles = query(query, map); - return StreamSupport.stream(alleles.spliterator(), false) - .collect(Collectors.toSet()); + return StreamSupport.stream(alleles.spliterator(), false).collect(Collectors.toSet()); } public Set getAllAllelicHgvsGNameCache() { @@ -497,21 +470,18 @@ public Set getAllAllelicHgvsGNameCache() { String query = "MATCH p1=(variant:Variant)-[:VARIATION]->(a:Allele)-[:IS_ALLELE_OF]->(g:Gene) RETURN variant.hgvsNomenclature as ID"; Result result = queryForResult(query); - allAllelicHgvsGNames = StreamSupport.stream(result.spliterator(), false) - .map(idMap -> (String) idMap.get("ID")) - .collect(Collectors.toSet()); + allAllelicHgvsGNames = StreamSupport.stream(result.spliterator(), false).map(idMap -> (String) idMap.get("ID")).collect(Collectors.toSet()); } return allAllelicHgvsGNames; } - public Map setupVariantToSOTermMap() { if (MapUtils.isNotEmpty(variantSOTermMap)) { return variantSOTermMap; } - + String cacheFileName = "VariantToSOTermMapCache.data"; - + variantSOTermMap = readFromCache(cacheFileName, Map.class); if (variantSOTermMap != null && variantSOTermMap.size() > 0) { log.info("Variant SOTerm Map loaded from file cache"); @@ -523,29 +493,27 @@ public Map setupVariantToSOTermMap() { query += " RETURN p1"; Iterable variantSOTermIter = query(Variant.class, query); - + log.info("Number of Variants: " + String.format("%,d", (int) StreamSupport.stream(variantSOTermIter.spliterator(), false).count())); - + variantSOTermMap = new HashMap<>(); - - for(Variant v: variantSOTermIter) { + + for (Variant v : variantSOTermIter) { variantSOTermMap.put(v.getPrimaryKey(), v.getVariantType()); } - + writeToCache(cacheFileName, variantSOTermMap); - + return variantSOTermMap; } - - - + public Map> setupAlleleSynonymMap() { if (MapUtils.isNotEmpty(alleleSynonymMap)) { return alleleSynonymMap; } String cacheFileName = "AlleleSynonymMapCache.data"; - + alleleSynonymMap = readFromCache(cacheFileName, Map.class); if (alleleSynonymMap != null && alleleSynonymMap.size() > 0) { log.info("Allele Synonym Map loaded from file cache"); @@ -557,28 +525,28 @@ public Map> setupAlleleSynonymMap() { query += " RETURN p1"; Iterable alleleSynonymsIter = query(Allele.class, query); - + log.info("Number of Alleles: " + String.format("%,d", (int) StreamSupport.stream(alleleSynonymsIter.spliterator(), false).count())); - + alleleSynonymMap = new HashMap<>(); - - for(Allele a: alleleSynonymsIter) { + + for (Allele a : alleleSynonymsIter) { alleleSynonymMap.put(a.getPrimaryKey(), a.getSynonyms()); } - + writeToCache(cacheFileName, alleleSynonymMap); - + return alleleSynonymMap; } - + public Map> setupAlleleCrossReferenceMap() { if (MapUtils.isNotEmpty(alleleCrossReferenceMap)) { return alleleCrossReferenceMap; } - + String cacheFileName = "AlleleCrossReferenceMapCache.data"; - + alleleCrossReferenceMap = readFromCache(cacheFileName, Map.class); if (alleleCrossReferenceMap != null && alleleCrossReferenceMap.size() > 0) { log.info("Allele CrossReference Map loaded from file cache"); @@ -590,36 +558,19 @@ public Map> setupAlleleCrossReferenceMap() { query += " RETURN p1"; Iterable alleleCrossReferenceIter = query(Allele.class, query); - + log.info("Number of Alleles: " + String.format("%,d", (int) StreamSupport.stream(alleleCrossReferenceIter.spliterator(), false).count())); - + alleleCrossReferenceMap = new HashMap<>(); - - for(Allele a: alleleCrossReferenceIter) { + + for (Allele a : alleleCrossReferenceIter) { alleleCrossReferenceMap.put(a.getPrimaryKey(), a.getCrossReferences()); } - + writeToCache(cacheFileName, alleleCrossReferenceMap); - + return alleleCrossReferenceMap; } - - - - - - - - - - - - - - - - - public Map getAllAlleleVariants() { @@ -627,7 +578,7 @@ public Map getAllAlleleVariants() { setupAlleleSynonymMap(); setupAlleleCrossReferenceMap(); getTranscriptWithExonInfo(); - + String query = "MATCH path1=(:Species)<-[:FROM_SPECIES]-(a:Allele)"; // 26s query += " OPTIONAL MATCH path2=(a:Allele)-[:IS_ALLELE_OF]-(g:Gene)"; // +7 query += " OPTIONAL MATCH path3=(a:Allele)<-[:VARIATION]-(variant:Variant)"; // +5 @@ -641,22 +592,21 @@ public Map getAllAlleleVariants() { Iterable allelesWithVariantsIter = query(query, new HashMap<>()); log.info("Query to pull Alleles is finished"); - Set allelesWithVariants = StreamSupport.stream(allelesWithVariantsIter.spliterator(), false).collect(Collectors.toSet()); Map alleleVariantsMap = new HashMap<>(); ProcessDisplayHelper ph = new ProcessDisplayHelper(10000); ph.startProcess("Pulling Allele's from Neo", allelesWithVariants.size()); for (Allele a : allelesWithVariants) { - if(alleleSynonymMap.containsKey(a.getPrimaryKey())) { + if (alleleSynonymMap.containsKey(a.getPrimaryKey())) { a.setSynonyms(alleleSynonymMap.get(a.getPrimaryKey())); } - if(alleleCrossReferenceMap.containsKey(a.getPrimaryKey())) { + if (alleleCrossReferenceMap.containsKey(a.getPrimaryKey())) { a.setCrossReferences(alleleCrossReferenceMap.get(a.getPrimaryKey())); } - + if (a.getVariants() != null && a.getVariants().size() > 0) { for (Variant v : a.getVariants()) { - if(variantSOTermMap.containsKey(v.getPrimaryKey())) { + if (variantSOTermMap.containsKey(v.getPrimaryKey())) { v.setVariantType(variantSOTermMap.get(v.getPrimaryKey())); } if (v.getTranscriptLevelConsequence() != null && v.getTranscriptLevelConsequence().size() > 0) { @@ -667,7 +617,7 @@ public Map getAllAlleleVariants() { t.setExons(transcript.getExons()); // System.out.println("EXONS SIZE: "+ transcript.getExons().size()); } - + } } } @@ -676,12 +626,12 @@ public Map getAllAlleleVariants() { alleleVariantsMap.put(a.getPrimaryKey(), a); } ph.finishProcess(); - + log.info("Number of alleles with variants: " + String.format("%,d", allelesWithVariants.size())); return alleleVariantsMap; } - + protected E readFromCache(String fileName, Class clazz) { try { ObjectFileStorage storage = new ObjectFileStorage<>(); @@ -703,6 +653,5 @@ protected void writeToCache(String fileName, E object) { e.printStackTrace(); } } - }