From: gmungoc Date: Tue, 30 Jan 2018 16:07:17 +0000 (+0000) Subject: JAL-1793 update spike build to latest incl stop and synonymous variants on peptides X-Git-Tag: Release_2_11_0~62^2~2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=321caefc5a40cd735c93e0bfa450e0e04abc485d;p=jalview.git JAL-1793 update spike build to latest incl stop and synonymous variants on peptides --- diff --git a/RELEASE b/RELEASE index f1faf34..eb9d7cd 100644 --- a/RELEASE +++ b/RELEASE @@ -1,2 +1,2 @@ jalview.release=releases/Release_2_10_3_Branch -jalview.version=2.10.3 +jalview.version=2.10.3b1 diff --git a/benchmarking/README b/benchmarking/README index fac0bf6..ccf53c1 100644 --- a/benchmarking/README +++ b/benchmarking/README @@ -7,16 +7,19 @@ You will need to install Maven: https://maven.apache.org/install.html This builds a jalview.jar file and puts it into dist/ + 2. Make a lib directory in benchmarking/ if not already present and cd into this directory. + 3. Purge any previous maven dependencies: mvn dependency:purge-local-repository -DactTransitively=false -DreResolve=false + 4. Run mvn install:install-file -Dfile=../dist/jalview.jar -DgroupId=jalview.org -DartifactId=jalview -Dversion=1.0 -Dpackaging=jar -DlocalRepositoryPath=lib - to install the jalview.jar file in the local maven repository. The pom.xml in the benchmarking references this installation, so if you change the names the pom.xml file will also need to be updated. + 5. Build and run jmh benchmarking. In the benchmarking directory: mvn clean install java -jar target/benchmarks.jar @@ -24,4 +27,14 @@ to install the jalview.jar file in the local maven repository. The pom.xml in th To get JSON output instead use: java -jar target/benchmarks.jar -rf json - JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/ \ No newline at end of file + JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/ + + To get help use the standard -h option: + java -jar target/benchmarks.jar -h + + More information here: + http://openjdk.java.net/projects/code-tools/jmh/ + http://java-performance.info/jmh/ + + + 6. If you make changes to the Jalview code everything will need to be refreshed, by performing steps 3-5 again. diff --git a/help/help.jhm b/help/help.jhm index 010bca8..732f01b 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -22,7 +22,7 @@ - + diff --git a/help/html/releases.html b/help/html/releases.html index a36e31a..83d2ce4 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -68,22 +68,26 @@ li:before { - +
- 2.10.3b1
5/12/2017 + 2.10.3b1
24/1/2018
- - +
  • Updated Certum Codesigning Certificate + (Valid till 30th November 2018)
+ Desktop
      +
    • Only one structure is loaded when several sequences and structures are selected for viewing/superposing
    • Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
    • Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
    • Helix annotation has 'notches' when scrolled into view if columns are hidden
    • Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
      • -
    • User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
      • -
        +
      • User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
        • +
      • Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes
        • +
      +
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 4bf1cec..6d75f0f 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,14 +24,12 @@

- What's new in Jalview 2.10.3 ? + What's new in Jalview 2.10.3b1 ?

- Version 2.10.3 was released in November 2017. The major focus was to - improve Jalview's sequence features datamodel and the scalability of - the alignment rendering system. The full list of bug fixes and new - features can be found in the 2.10.3 - Release Notes. Key improvements include: + This is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures. + The full list bugs fixed in this release can be found in the 2.10.3b1 + Release Notes. In addition, Jalview 2.10.3 provides:

  • Faster and more responsive UI when importing and working diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 1277a86..0f801eb 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -678,7 +678,8 @@ label.2d_rna_structure_line = 2D RNA {0} (alignment) label.2d_rna_sequence_name = 2D RNA - {0} label.edit_name_and_description_current_group = Edit name and description of current group label.from_file = From File -label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode) +label.enter_pdb_id = Enter PDB Id +label.enter_pdb_id_tip = Enter PDB Id (or pdbid:chaincode) label.text_colour = Text Colour... label.structure = Structure label.show_pdbstruct_dialog = 3D Structure Data... @@ -1345,7 +1346,7 @@ label.score = Score label.colour_by_label = Colour by label label.variable_colour = Variable colour label.select_colour = Select colour -option.enable_disable_autosearch = When ticked, search is performed automatically. +option.enable_disable_autosearch = When ticked, search is performed automatically option.autosearch = Autosearch label.retrieve_ids = Retrieve IDs label.display_settings_for = Display settings for {0} features @@ -1359,3 +1360,10 @@ label.filters_tooltip = Click to set or amend filters label.or = Or label.and = And label.sequence_feature_colours = Sequence Feature Colours +label.best_quality = Best Quality +label.best_resolution = Best Resolution +label.most_protein_chain = Most Protein Chain +label.most_bound_molecules = Most Bound Molecules +label.most_polymer_residues = Most Polymer Residues +label.cached_structures = Cached Structures +label.free_text_search = Free Text Search diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 616cb9d..d035e73 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -337,6 +337,8 @@ label.optimise_order = Optimizar orden label.seq_sort_by_score = Ordenar las secuencias por puntuación label.load_colours = Cargar colores label.save_colours = Guardar colores +label.load_colours_tooltip = Cargar colores y filtros desde fichero +label.save_colours_tooltip = Guardar colores y filtros en fichero label.fetch_das_features = Recuperar funciones DAS label.selected_database_to_fetch_from = Seleccionada {0} Base de datos {1} para buscar de {2} label.database_param = Base de datos: {0} @@ -630,6 +632,7 @@ label.2d_rna_sequence_name = 2D RNA - {0} label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual label.from_file = desde fichero label.enter_pdb_id = Introducir PDB Id +label.enter_pdb_id_tip = Introducir PDB Id (o pdbid:chaincode) label.text_colour = Color de texto... label.structure = Estructura label.create_sequence_details_report_annotation_for = Anotación para {0} @@ -1344,8 +1347,8 @@ label.score = Puntuaci label.colour_by_label = Colorear por texto label.variable_colour = Color variable label.select_colour = Seleccionar color -option.enable_disable_autosearch = Marque para buscar automáticamente -option.autosearch = Búsqueda automática +option.enable_disable_autosearch = Marcar para buscar automáticamente +option.autosearch = Auto búsqueda label.retrieve_ids = Recuperar IDs label.display_settings_for = Visualización de características {0} label.simple = Simple @@ -1356,4 +1359,12 @@ label.by_text_of = Por texto de label.by_range_of = Por rango de label.filters_tooltip = Haga clic para configurar o modificar los filtros label.or = O -label.and = Y \ No newline at end of file +label.and = Y +label.sequence_feature_colours = Colores de características de las secuencias +label.best_quality = Mejor Calidad +label.best_resolution = Mejor Resolución +label.most_protein_chain = Más Cadena de Proteína +label.most_bound_molecules = Más Moléculas Ligadas +label.most_polymer_residues = Más Residuos de Polímeros +label.cached_structures = Estructuras en Caché +label.free_text_search = Búsqueda de texto libre diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index bef667d..bdc5fc1 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -128,7 +128,7 @@ public class AlignmentUtils */ public static AlignmentI expandContext(AlignmentI core, int flankSize) { - List sq = new ArrayList(); + List sq = new ArrayList<>(); int maxoffset = 0; for (SequenceI s : core.getSequences()) { @@ -258,7 +258,7 @@ public class AlignmentUtils public static Map> getSequencesByName( AlignmentI al) { - Map> theMap = new LinkedHashMap>(); + Map> theMap = new LinkedHashMap<>(); for (SequenceI seq : al.getSequences()) { String name = seq.getName(); @@ -267,7 +267,7 @@ public class AlignmentUtils List seqs = theMap.get(name); if (seqs == null) { - seqs = new ArrayList(); + seqs = new ArrayList<>(); theMap.put(name, seqs); } seqs.add(seq); @@ -294,8 +294,8 @@ public class AlignmentUtils return false; } - Set mappedDna = new HashSet(); - Set mappedProtein = new HashSet(); + Set mappedDna = new HashSet<>(); + Set mappedProtein = new HashSet<>(); /* * First pass - map sequences where cross-references exist. This include @@ -465,7 +465,7 @@ public class AlignmentUtils { String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(); - for (String stop : ResidueProperties.STOP) + for (String stop : ResidueProperties.STOP_CODONS) { if (lastCodon.equals(stop)) { @@ -536,7 +536,8 @@ public class AlignmentUtils * allow * in protein to match untranslatable in dna */ final char aaRes = aaSeqChars[aaPos]; - if ((translated == null || "STOP".equals(translated)) && aaRes == '*') + if ((translated == null || ResidueProperties.STOP.equals(translated)) + && aaRes == '*') { continue; } @@ -568,7 +569,8 @@ public class AlignmentUtils if (dnaPos == cdnaSeqChars.length - CODON_LENGTH) { String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); - if ("STOP".equals(ResidueProperties.codonTranslate(codon))) + if (ResidueProperties.STOP + .equals(ResidueProperties.codonTranslate(codon))) { return true; } @@ -881,7 +883,7 @@ public class AlignmentUtils System.err.println("Wrong alignment type in alignProteinAsDna"); return 0; } - List unmappedProtein = new ArrayList(); + List unmappedProtein = new ArrayList<>(); Map> alignedCodons = buildCodonColumnsMap( protein, dna, unmappedProtein); return alignProteinAs(protein, alignedCodons, unmappedProtein); @@ -1092,7 +1094,7 @@ public class AlignmentUtils * {dnaSequence, {proteinSequence, codonProduct}} at that position. The * comparator keeps the codon positions ordered. */ - Map> alignedCodons = new TreeMap>( + Map> alignedCodons = new TreeMap<>( new CodonComparator()); for (SequenceI dnaSeq : dna.getSequences()) @@ -1138,9 +1140,9 @@ public class AlignmentUtils // TODO delete this ugly hack once JAL-2022 is resolved // i.e. we can model startPhase > 0 (incomplete start codon) - List sequencesChecked = new ArrayList(); + List sequencesChecked = new ArrayList<>(); AlignedCodon lastCodon = null; - Map toAdd = new HashMap(); + Map toAdd = new HashMap<>(); for (Entry> entry : alignedCodons .entrySet()) @@ -1319,7 +1321,7 @@ public class AlignmentUtils Map seqProduct = alignedCodons.get(codon); if (seqProduct == null) { - seqProduct = new HashMap(); + seqProduct = new HashMap<>(); alignedCodons.put(codon, seqProduct); } seqProduct.put(protein, codon); @@ -1456,7 +1458,7 @@ public class AlignmentUtils { continue; } - final List result = new ArrayList(); + final List result = new ArrayList<>(); for (AlignmentAnnotation dsann : datasetAnnotations) { /* @@ -1638,13 +1640,13 @@ public class AlignmentUtils throw new IllegalArgumentException( "IMPLEMENTATION ERROR: dataset.getDataset() must be null!"); } - List foundSeqs = new ArrayList(); - List cdsSeqs = new ArrayList(); + List foundSeqs = new ArrayList<>(); + List cdsSeqs = new ArrayList<>(); List mappings = dataset.getCodonFrames(); HashSet productSeqs = null; if (products != null) { - productSeqs = new HashSet(); + productSeqs = new HashSet<>(); for (SequenceI seq : products) { productSeqs.add(seq.getDatasetSequence() == null ? seq : seq @@ -2055,8 +2057,8 @@ public class AlignmentUtils SequenceI contig, SequenceI proteinProduct, Mapping mapping) { // gather direct refs from contig congruent with mapping - List direct = new ArrayList(); - HashSet directSources = new HashSet(); + List direct = new ArrayList<>(); + HashSet directSources = new HashSet<>(); if (contig.getDBRefs() != null) { for (DBRefEntry dbr : contig.getDBRefs()) @@ -2076,7 +2078,7 @@ public class AlignmentUtils DBRefEntry[] onSource = DBRefUtils.selectRefs( proteinProduct.getDBRefs(), directSources.toArray(new String[0])); - List propagated = new ArrayList(); + List propagated = new ArrayList<>(); // and generate appropriate mappings for (DBRefEntry cdsref : direct) @@ -2255,7 +2257,7 @@ public class AlignmentUtils proteinStart++; proteinLength--; } - List proteinRange = new ArrayList(); + List proteinRange = new ArrayList<>(); /* * dna length should map to protein (or protein plus stop codon) @@ -2290,7 +2292,7 @@ public class AlignmentUtils */ protected static List findCdsPositions(SequenceI dnaSeq) { - List result = new ArrayList(); + List result = new ArrayList<>(); List sfs = dnaSeq.getFeatures().getFeaturesByOntology( SequenceOntologyI.CDS); @@ -2428,10 +2430,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base + base2 + base3; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base1.equals(base)) { - count++; + String codon = base + base2 + base3; + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon)) + { + count++; + } } } } @@ -2450,10 +2456,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base1 + base + base3; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base2.equals(base)) { - count++; + String codon = base1 + base + base3; + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon)) + { + count++; + } } } } @@ -2472,10 +2482,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base1 + base2 + base; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base3.equals(base)) { - count++; + String codon = base1 + base2 + base; + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon)) + { + count++; + } } } } @@ -2507,57 +2521,71 @@ public class AlignmentUtils * e.g. multibase variants or HGMD_MUTATION etc * are currently ignored here */ - String trans = codon.contains("-") ? "-" + String trans = codon.contains("-") ? null : (codon.length() > CODON_LENGTH ? null : ResidueProperties.codonTranslate(codon)); - if (trans != null && !trans.equals(residue)) + if (trans == null) + { + return false; + } + String desc = codon; + String featureType = ""; + if (trans.equals(residue)) + { + featureType = SequenceOntologyI.SYNONYMOUS_VARIANT; + } + else if (ResidueProperties.STOP.equals(trans)) + { + featureType = SequenceOntologyI.STOP_GAINED; + } + else { String residue3Char = StringUtils .toSentenceCase(ResidueProperties.aa2Triplet.get(residue)); String trans3Char = StringUtils .toSentenceCase(ResidueProperties.aa2Triplet.get(trans)); - String desc = "p." + residue3Char + peptidePos + trans3Char; - SequenceFeature sf = new SequenceFeature( - SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos, - peptidePos, var.getSource()); - StringBuilder attributes = new StringBuilder(32); - String id = (String) var.variant.getValue(ID); - if (id != null) - { - if (id.startsWith(SEQUENCE_VARIANT)) - { - id = id.substring(SEQUENCE_VARIANT.length()); - } - sf.setValue(ID, id); - attributes.append(ID).append("=").append(id); - // TODO handle other species variants JAL-2064 - StringBuilder link = new StringBuilder(32); - try - { - link.append(desc).append(" ").append(id).append( - "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=") - .append(URLEncoder.encode(id, "UTF-8")); - sf.addLink(link.toString()); - } catch (UnsupportedEncodingException e) - { - // as if - } - } - String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE); - if (clinSig != null) + desc = "p." + residue3Char + peptidePos + trans3Char; + featureType = SequenceOntologyI.NONSYNONYMOUS_VARIANT; + } + SequenceFeature sf = new SequenceFeature(featureType, desc, peptidePos, + peptidePos, var.getSource()); + + StringBuilder attributes = new StringBuilder(32); + String id = (String) var.variant.getValue(ID); + if (id != null) + { + if (id.startsWith(SEQUENCE_VARIANT)) { - sf.setValue(CLINICAL_SIGNIFICANCE, clinSig); - attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=") - .append(clinSig); + id = id.substring(SEQUENCE_VARIANT.length()); } - peptide.addSequenceFeature(sf); - if (attributes.length() > 0) + sf.setValue(ID, id); + attributes.append(ID).append("=").append(id); + // TODO handle other species variants JAL-2064 + StringBuilder link = new StringBuilder(32); + try { - sf.setAttributes(attributes.toString()); + link.append(desc).append(" ").append(id).append( + "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=") + .append(URLEncoder.encode(id, "UTF-8")); + sf.addLink(link.toString()); + } catch (UnsupportedEncodingException e) + { + // as if } - return true; } - return false; + String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE); + if (clinSig != null) + { + sf.setValue(CLINICAL_SIGNIFICANCE, clinSig); + attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=") + .append(clinSig); + } + peptide.addSequenceFeature(sf); + if (attributes.length() > 0) + { + sf.setAttributes(attributes.toString()); + } + return true; } /** @@ -2579,7 +2607,7 @@ public class AlignmentUtils * map from peptide position to all variants of the codon which codes for it * LinkedHashMap ensures we keep the peptide features in sequence order */ - LinkedHashMap[]> variants = new LinkedHashMap[]>(); + LinkedHashMap[]> variants = new LinkedHashMap<>(); List dnaFeatures = dnaSeq.getFeatures() .getFeaturesByOntology(SequenceOntologyI.SEQUENCE_VARIANT); @@ -2638,9 +2666,9 @@ public class AlignmentUtils if (codonVariants == null) { codonVariants = new ArrayList[CODON_LENGTH]; - codonVariants[0] = new ArrayList(); - codonVariants[1] = new ArrayList(); - codonVariants[2] = new ArrayList(); + codonVariants[0] = new ArrayList<>(); + codonVariants[1] = new ArrayList<>(); + codonVariants[2] = new ArrayList<>(); variants.put(peptidePosition, codonVariants); } @@ -2764,7 +2792,7 @@ public class AlignmentUtils /* * fancy case - aligning via mappings between sequences */ - List unmapped = new ArrayList(); + List unmapped = new ArrayList<>(); Map> columnMap = buildMappedColumnsMap( unaligned, aligned, unmapped); int width = columnMap.size(); @@ -2839,7 +2867,7 @@ public class AlignmentUtils } // map from dataset sequence to alignment sequence(s) - Map> alignedDatasets = new HashMap>(); + Map> alignedDatasets = new HashMap<>(); for (SequenceI seq : aligned.getSequences()) { SequenceI ds = seq.getDatasetSequence(); @@ -2902,7 +2930,7 @@ public class AlignmentUtils * {unalignedSequence, characterPerSequence} at that position. * TreeMap keeps the entries in ascending column order. */ - SortedMap> map = new TreeMap>(); + SortedMap> map = new TreeMap<>(); /* * record any sequences that have no mapping so can't be realigned @@ -3007,7 +3035,7 @@ public class AlignmentUtils Map seqsMap = map.get(fromCol); if (seqsMap == null) { - seqsMap = new HashMap(); + seqsMap = new HashMap<>(); map.put(fromCol, seqsMap); } seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart)); diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java index f3088ea..ef05a58 100644 --- a/src/jalview/analysis/Dna.java +++ b/src/jalview/analysis/Dna.java @@ -161,7 +161,7 @@ public class Dna int s; int sSize = selection.size(); - List pepseqs = new ArrayList(); + List pepseqs = new ArrayList<>(); for (s = 0; s < sSize; s++) { SequenceI newseq = translateCodingRegion(selection.get(s), @@ -213,7 +213,7 @@ public class Dna if (dnarefs != null) { // intersect with pep - List mappedrefs = new ArrayList(); + List mappedrefs = new ArrayList<>(); DBRefEntry[] refs = dna.getDBRefs(); for (int d = 0; d < refs.length; d++) { @@ -391,7 +391,7 @@ public class Dna String seqstring, AlignedCodonFrame acf, List proteinSeqs) { - List skip = new ArrayList(); + List skip = new ArrayList<>(); int skipint[] = null; ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring // intervals @@ -544,7 +544,7 @@ public class Dna skip.add(skipint); skipint = null; } - if (aa.equals("STOP")) + if (aa.equals(ResidueProperties.STOP)) { aa = STOP_ASTERIX; } @@ -800,7 +800,7 @@ public class Dna public AlignmentI reverseCdna(boolean complement) { int sSize = selection.size(); - List reversed = new ArrayList(); + List reversed = new ArrayList<>(); for (int s = 0; s < sSize; s++) { SequenceI newseq = reverseSequence(selection.get(s).getName(), diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java index 6d031b7..952f01e 100644 --- a/src/jalview/ext/ensembl/EnsemblCdna.java +++ b/src/jalview/ext/ensembl/EnsemblCdna.java @@ -24,9 +24,6 @@ import jalview.datamodel.SequenceFeature; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; -import java.util.HashMap; -import java.util.Map; - import com.stevesoft.pat.Regex; /** @@ -47,13 +44,6 @@ public class EnsemblCdna extends EnsemblSeqProxy private static final Regex ACCESSION_REGEX = new Regex( "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)"); - private static Map params = new HashMap(); - - static - { - params.put("object_type", "transcript"); - } - /* * fetch exon features on genomic sequence (to identify the cdna regions) * and cds and variation features (to retain) @@ -139,13 +129,13 @@ public class EnsemblCdna extends EnsemblSeqProxy } /** - * Parameter object_type=cdna added to ensure cdna and not peptide is returned - * (JAL-2529) + * Parameter object_type=Transcaript added to ensure cdna and not peptide is + * returned (JAL-2529) */ @Override - protected Map getAdditionalParameters() + protected String getObjectType() { - return params; + return OBJECT_TYPE_TRANSCRIPT; } } diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java index 7570822..cb6f548 100644 --- a/src/jalview/ext/ensembl/EnsemblFeatures.java +++ b/src/jalview/ext/ensembl/EnsemblFeatures.java @@ -82,7 +82,7 @@ class EnsemblFeatures extends EnsemblRestClient public AlignmentI getSequenceRecords(String query) throws IOException { // TODO: use a vararg String... for getSequenceRecords instead? - List queries = new ArrayList(); + List queries = new ArrayList<>(); queries.add(query); FileParse fp = getSequenceReader(queries); if (fp == null || !fp.isValid()) @@ -109,9 +109,17 @@ class EnsemblFeatures extends EnsemblRestClient urlstring.append("?content-type=text/x-gff3"); /* + * specify object_type=gene in case is shared by transcript and/or protein; + * currently only fetching features for gene sequences; + * refactor in future if needed to fetch for transcripts + */ + urlstring.append("&").append(OBJECT_TYPE).append("=") + .append(OBJECT_TYPE_GENE); + + /* * specify features to retrieve * @see http://rest.ensembl.org/documentation/info/overlap_id - * could make the list a configurable entry in jalview.properties + * could make the list a configurable entry in .jalview_properties */ for (EnsemblFeatureType feature : featuresWanted) { diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index cdcfa96..7e6f653 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -100,6 +100,12 @@ public class EnsemblGene extends EnsemblSeqProxy return EnsemblSeqType.GENOMIC; } + @Override + protected String getObjectType() + { + return OBJECT_TYPE_GENE; + } + /** * Returns an alignment containing the gene(s) for the given gene or * transcript identifier, or external identifier (e.g. Uniprot id). If given a @@ -149,7 +155,11 @@ public class EnsemblGene extends EnsemblSeqProxy if (geneAlignment.getHeight() == 1) { + // ensure id has 'correct' case for the Ensembl identifier + geneId = geneAlignment.getSequenceAt(0).getName(); + findGeneLoci(geneAlignment.getSequenceAt(0), geneId); + getTranscripts(geneAlignment, geneId); } if (al == null) @@ -235,7 +245,7 @@ public class EnsemblGene extends EnsemblSeqProxy */ List getGeneIds(String accessions) { - List geneIds = new ArrayList(); + List geneIds = new ArrayList<>(); for (String acc : accessions.split(getAccessionSeparator())) { @@ -370,7 +380,7 @@ public class EnsemblGene extends EnsemblSeqProxy int transcriptLength = 0; final char[] geneChars = gene.getSequence(); int offset = gene.getStart(); // to convert to 0-based positions - List mappedFrom = new ArrayList(); + List mappedFrom = new ArrayList<>(); for (SequenceFeature sf : splices) { @@ -412,7 +422,7 @@ public class EnsemblGene extends EnsemblSeqProxy * transfer features to the new sequence; we use EnsemblCdna to do this, * to filter out unwanted features types (see method retainFeature) */ - List mapTo = new ArrayList(); + List mapTo = new ArrayList<>(); mapTo.add(new int[] { 1, transcriptLength }); MapList mapping = new MapList(mappedFrom, mapTo, 1, 1); EnsemblCdna cdna = new EnsemblCdna(getDomain()); @@ -498,7 +508,7 @@ public class EnsemblGene extends EnsemblSeqProxy protected List getTranscriptFeatures(String accId, SequenceI geneSequence) { - List transcriptFeatures = new ArrayList(); + List transcriptFeatures = new ArrayList<>(); String parentIdentifier = GENE_PREFIX + accId; @@ -510,7 +520,7 @@ public class EnsemblGene extends EnsemblSeqProxy for (SequenceFeature sf : sfs) { String parent = (String) sf.getValue(PARENT); - if (parentIdentifier.equals(parent)) + if (parentIdentifier.equalsIgnoreCase(parent)) { transcriptFeatures.add(sf); } @@ -547,8 +557,9 @@ public class EnsemblGene extends EnsemblSeqProxy if (SequenceOntologyFactory.getInstance().isA(sf.getType(), SequenceOntologyI.GENE)) { - String id = (String) sf.getValue(ID); - if ((GENE_PREFIX + accId).equals(id)) + // NB features as gff use 'ID'; rest services return as 'id' + String id = (String) sf.getValue("ID"); + if ((GENE_PREFIX + accId).equalsIgnoreCase(id)) { return true; } @@ -575,7 +586,7 @@ public class EnsemblGene extends EnsemblSeqProxy if (isTranscript(type)) { String parent = (String) sf.getValue(PARENT); - if (!(GENE_PREFIX + accessionId).equals(parent)) + if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent)) { return false; } diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java index 458a233..bde3c0f 100644 --- a/src/jalview/ext/ensembl/EnsemblGenome.java +++ b/src/jalview/ext/ensembl/EnsemblGenome.java @@ -103,7 +103,7 @@ public class EnsemblGenome extends EnsemblSeqProxy { if (isTranscript(sf.getType())) { - String id = (String) sf.getValue(ID); + String id = (String) sf.getValue("ID"); if (("transcript:" + accId).equals(id)) { return true; diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java index 0d1b554..f6b3a47 100644 --- a/src/jalview/ext/ensembl/EnsemblLookup.java +++ b/src/jalview/ext/ensembl/EnsemblLookup.java @@ -32,14 +32,15 @@ import java.net.URL; import java.util.Arrays; import java.util.Collections; import java.util.List; -import java.util.function.Function; import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; /** - * A client for the Ensembl lookup REST endpoint + * A client for the Ensembl /lookup REST endpoint, used to find the gene + * identifier given a gene, transcript or protein identifier, or to extract the + * species or chromosomal coordinates from the same service response * * @author gmcarstairs */ @@ -47,14 +48,6 @@ public class EnsemblLookup extends EnsemblRestClient { private static final String SPECIES = "species"; - private static final String PARENT = "Parent"; - - private static final String OBJECT_TYPE_TRANSLATION = "Translation"; - private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript"; - private static final String ID = "id"; - private static final String OBJECT_TYPE_GENE = "Gene"; - private static final String OBJECT_TYPE = "object_type"; - /** * Default constructor (to use rest.ensembl.org) */ @@ -89,17 +82,26 @@ public class EnsemblLookup extends EnsemblRestClient protected URL getUrl(List ids) throws MalformedURLException { String identifier = ids.get(0); - return getUrl(identifier); + return getUrl(identifier, null); } /** + * Gets the url for lookup of the given identifier, optionally with objectType + * also specified in the request + * * @param identifier + * @param objectType * @return */ - protected URL getUrl(String identifier) + protected URL getUrl(String identifier, String objectType) { String url = getDomain() + "/lookup/id/" + identifier + CONTENT_TYPE_JSON; + if (objectType != null) + { + url += "&" + OBJECT_TYPE + "=" + objectType; + } + try { return new URL(url); @@ -128,20 +130,15 @@ public class EnsemblLookup extends EnsemblRestClient } /** - * Calls the Ensembl lookup REST endpoint and returns - *
      - *
    • the 'id' for the identifier if its type is "Gene"
      • - *
    • the 'Parent' if its type is 'Transcript'
      • - *
        - * If the type is 'Translation', does a recursive call to this method, passing - * in the 'Parent' (transcript id). + * Returns the gene id related to the given identifier (which may be for a + * gene, transcript or protein) * * @param identifier * @return */ public String getGeneId(String identifier) { - return (String) getResult(identifier, br -> parseGeneId(br)); + return parseGeneId(getResult(identifier, null)); } /** @@ -153,34 +150,45 @@ public class EnsemblLookup extends EnsemblRestClient */ public String getSpecies(String identifier) { - return (String) getResult(identifier, br -> getAttribute(br, SPECIES)); + String species = null; + JSONObject json = getResult(identifier, null); + if (json != null) + { + Object o = json.get(SPECIES); + if (o != null) + { + species = o.toString(); + } + } + return species; } /** - * Calls the /lookup/id rest service and delegates parsing of the JSON - * response to the supplied parser + * Calls the /lookup/id rest service and returns the response as a JSONObject, + * or null if any error * * @param identifier - * @param parser + * @param objectType + * (optional) * @return */ - protected Object getResult(String identifier, - Function parser) + protected JSONObject getResult(String identifier, String objectType) { List ids = Arrays.asList(new String[] { identifier }); BufferedReader br = null; try { - URL url = getUrl(identifier); + URL url = getUrl(identifier, objectType); if (url != null) { br = getHttpResponse(url, ids); } - return br == null ? null : parser.apply(br); - } catch (IOException e) + return br == null ? null : (JSONObject) (new JSONParser().parse(br)); + } catch (IOException | ParseException e) { - // ignore + System.err.println("Error parsing " + identifier + " lookup response " + + e.getMessage()); return null; } finally { @@ -198,74 +206,42 @@ public class EnsemblLookup extends EnsemblRestClient } /** - * Answers the value of 'attribute' from the JSON response, or null if not - * found - * - * @param br - * @param attribute - * @return - */ - protected String getAttribute(BufferedReader br, String attribute) - { - String value = null; - JSONParser jp = new JSONParser(); - try - { - JSONObject val = (JSONObject) jp.parse(br); - value = val.get(attribute).toString(); - } catch (ParseException | NullPointerException | IOException e) - { - // ignore - } - return value; - } - - /** * Parses the JSON response and returns the gene identifier, or null if not * found. If the returned object_type is Gene, returns the id, if Transcript * returns the Parent. If it is Translation (peptide identifier), then the - * Parent is the transcript identifier, so we redo the search with this value. + * Parent is the transcript identifier, so we redo the search with this value, + * specifying that object_type should be Transcript. * - * @param br + * @param jsonObject * @return */ - protected String parseGeneId(BufferedReader br) + protected String parseGeneId(JSONObject json) { + if (json == null) + { + // e.g. lookup failed with 404 not found + return null; + } + String geneId = null; - JSONParser jp = new JSONParser(); - try + String type = json.get(OBJECT_TYPE).toString(); + if (OBJECT_TYPE_GENE.equalsIgnoreCase(type)) { - JSONObject val = (JSONObject) jp.parse(br); - String type = val.get(OBJECT_TYPE).toString(); - if (OBJECT_TYPE_GENE.equalsIgnoreCase(type)) - { - geneId = val.get(ID).toString(); - } - else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type)) - { - geneId = val.get(PARENT).toString(); - } - else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type)) - { - String transcriptId = val.get(PARENT).toString(); - try - { - geneId = getGeneId(transcriptId); - } catch (StackOverflowError e) - { - /* - * unlikely data condition error! - */ - System.err - .println("** Ensembl lookup " - + getUrl(transcriptId).toString() - + " looping on Parent!"); - } - } - } catch (ParseException | IOException e) + // got the gene - just returns its id + geneId = json.get(JSON_ID).toString(); + } + else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type)) + { + // got the transcript - return its (Gene) Parent + geneId = json.get(PARENT).toString(); + } + else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type)) { - // ignore + // got the protein - look up its Parent, restricted to type Transcript + String transcriptId = json.get(PARENT).toString(); + geneId = parseGeneId(getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT)); } + return geneId; } @@ -278,7 +254,7 @@ public class EnsemblLookup extends EnsemblRestClient */ public GeneLociI getGeneLoci(String geneId) { - return (GeneLociI) getResult(geneId, br -> parseGeneLoci(br)); + return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE)); } /** @@ -286,21 +262,24 @@ public class EnsemblLookup extends EnsemblRestClient * seq_region_name, start, end and returns an object that wraps them, or null * if unsuccessful * - * @param br + * @param json * @return */ - GeneLociI parseGeneLoci(BufferedReader br) + GeneLociI parseGeneLoci(JSONObject json) { - JSONParser jp = new JSONParser(); + if (json == null) + { + return null; + } + try { - JSONObject val = (JSONObject) jp.parse(br); - final String species = val.get("species").toString(); - final String assembly = val.get("assembly_name").toString(); - final String chromosome = val.get("seq_region_name").toString(); - String strand = val.get("strand").toString(); - int start = Integer.parseInt(val.get("start").toString()); - int end = Integer.parseInt(val.get("end").toString()); + final String species = json.get("species").toString(); + final String assembly = json.get("assembly_name").toString(); + final String chromosome = json.get("seq_region_name").toString(); + String strand = json.get("strand").toString(); + int start = Integer.parseInt(json.get("start").toString()); + int end = Integer.parseInt(json.get("end").toString()); int fromEnd = end - start + 1; boolean reverseStrand = "-1".equals(strand); int toStart = reverseStrand ? end : start; @@ -337,10 +316,10 @@ public class EnsemblLookup extends EnsemblRestClient return map; } }; - } catch (ParseException | NullPointerException | IOException - | NumberFormatException | ClassCastException e) + } catch (NullPointerException | NumberFormatException e) { Cache.log.error("Error looking up gene loci: " + e.getMessage()); + e.printStackTrace(); } return null; } diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 35ceea3..9229379 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -49,8 +49,6 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; -import java.util.Map; -import java.util.Map.Entry; /** * Base class for Ensembl sequence fetchers @@ -60,10 +58,6 @@ import java.util.Map.Entry; */ public abstract class EnsemblSeqProxy extends EnsemblRestClient { - protected static final String PARENT = "Parent"; - - protected static final String ID = "ID"; - protected static final String NAME = "Name"; protected static final String DESCRIPTION = "description"; @@ -208,7 +202,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient try { /* - * get 'dummy' genomic sequence with exon, cds and variation features + * get 'dummy' genomic sequence with gene, transcript, + * exon, cds and variation features */ SequenceI genomicSequence = null; EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain()); @@ -224,7 +219,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient /* * transfer features to the query sequence */ - SequenceI querySeq = alignment.findName(accId); + SequenceI querySeq = alignment.findName(accId, true); if (transferFeatures(accId, genomicSequence, querySeq)) { @@ -471,14 +466,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient urlstring.append("?type=").append(getSourceEnsemblType().getType()); urlstring.append(("&Accept=text/x-fasta")); - Map params = getAdditionalParameters(); - if (params != null) + String objectType = getObjectType(); + if (objectType != null) { - for (Entry entry : params.entrySet()) - { - urlstring.append("&").append(entry.getKey()).append("=") - .append(entry.getValue()); - } + urlstring.append("&").append(OBJECT_TYPE).append("=") + .append(objectType); } URL url = new URL(urlstring.toString()); @@ -486,11 +478,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** - * Override this method to add any additional x=y URL parameters needed + * Override this method to specify object_type request parameter * * @return */ - protected Map getAdditionalParameters() + protected String getObjectType() { return null; } @@ -559,7 +551,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence, String accId, int start) { - // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); List sfs = sourceSequence.getFeatures() .getPositionalFeatures(); if (sfs.isEmpty()) @@ -571,7 +562,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * generously initial size for number of cds regions * (worst case titin Q8WZ42 has c. 313 exons) */ - List regions = new ArrayList(100); + List regions = new ArrayList<>(100); int mappedLength = 0; int direction = 1; // forward boolean directionSet = false; @@ -871,7 +862,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient { String parent = (String) sf.getValue(PARENT); // using contains to allow for prefix "gene:", "transcript:" etc - if (parent != null && !parent.contains(identifier)) + if (parent != null + && !parent.toUpperCase().contains(identifier.toUpperCase())) { // this genomic feature belongs to a different transcript return false; @@ -899,14 +891,14 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected List findFeatures(SequenceI sequence, String term, String parentId) { - List result = new ArrayList(); + List result = new ArrayList<>(); List sfs = sequence.getFeatures() .getFeaturesByOntology(term); for (SequenceFeature sf : sfs) { String parent = (String) sf.getValue(PARENT); - if (parent != null && parent.equals(parentId)) + if (parent != null && parent.equalsIgnoreCase(parentId)) { result.add(sf); } diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java index 598dba1..cfb3c6d 100644 --- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java +++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java @@ -45,6 +45,18 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl protected static final String ENSEMBL_REST = "http://rest.ensembl.org"; + protected static final String OBJECT_TYPE_TRANSLATION = "Translation"; + + protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript"; + + protected static final String OBJECT_TYPE_GENE = "Gene"; + + protected static final String PARENT = "Parent"; + + protected static final String JSON_ID = "id"; + + protected static final String OBJECT_TYPE = "object_type"; + /* * possible values for the 'feature' parameter of the /overlap REST service * @see http://rest.ensembl.org/documentation/info/overlap_id diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java index 65be906..40d6cad 100644 --- a/src/jalview/ext/ensembl/EnsemblSymbol.java +++ b/src/jalview/ext/ensembl/EnsemblSymbol.java @@ -44,8 +44,6 @@ public class EnsemblSymbol extends EnsemblXref { private static final String GENE = "gene"; private static final String TYPE = "type"; - private static final String ID = "id"; - /** * Constructor given the target domain to fetch data from * @@ -77,7 +75,7 @@ public class EnsemblSymbol extends EnsemblXref while (rvals.hasNext()) { JSONObject val = (JSONObject) rvals.next(); - String id = val.get(ID).toString(); + String id = val.get(JSON_ID).toString(); String type = val.get(TYPE).toString(); if (id != null && GENE.equals(type)) { diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java index 9802d4b..86710e1 100644 --- a/src/jalview/fts/core/GFTSPanel.java +++ b/src/jalview/fts/core/GFTSPanel.java @@ -92,7 +92,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI protected JTabbedPane tabs = new JTabbedPane(); protected IProgressIndicator progressIndicator; - protected JComboBox cmb_searchTarget = new JComboBox(); + protected JComboBox cmb_searchTarget = new JComboBox<>(); protected JButton btn_ok = new JButton(); @@ -151,7 +151,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI protected int pageLimit; - protected HashSet paginatorCart = new HashSet(); + protected HashSet paginatorCart = new HashSet<>(); private static final int MIN_WIDTH = 670; @@ -293,7 +293,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI private void jbInit() throws Exception { - txt_search = new JvCacheableInputBox(getCacheKey()); + txt_search = new JvCacheableInputBox<>(getCacheKey()); populateCmbSearchTargetOptions(); Integer width = getTempUserPrefs().get("FTSPanel.width") == null ? 800 : getTempUserPrefs().get("FTSPanel.width"); @@ -681,7 +681,8 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI if (tabs != null) { tabs.setOpaque(true); - tabs.insertTab("Free Text Search", null, this, "", 0); + tabs.insertTab(MessageManager.getString("label.free_text_search"), + null, this, "", 0); mainFrame.setContentPane(tabs); tabs.setVisible(true); } @@ -871,7 +872,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI */ public void populateCmbSearchTargetOptions() { - List searchableTargets = new ArrayList(); + List searchableTargets = new ArrayList<>(); try { Collection foundFTSTargets = getFTSRestClient() diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java index 285e574..85f2498 100644 --- a/src/jalview/gui/CrossRefAction.java +++ b/src/jalview/gui/CrossRefAction.java @@ -176,10 +176,14 @@ public class CrossRefAction implements Runnable /* * copy feature rendering settings to split frame */ - newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(myFeatureStyling); - copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(myFeatureStyling); + FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer(); + fr1.transferSettings(myFeatureStyling); + fr1.findAllFeatures(true); + FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer(); + fr2.transferSettings(myFeatureStyling); + fr2.findAllFeatures(true); /* * apply 'database source' feature configuration diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 7c386f1..217f653 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -525,7 +525,7 @@ public class StructureChooser extends GStructureChooser * structures */ protected void populateFilterComboBox(boolean haveData, - boolean cachedPDBExists) + boolean cachedPDBExist) { /* * temporarily suspend the change listener behaviour @@ -535,25 +535,33 @@ public class StructureChooser extends GStructureChooser cmb_filterOption.removeAllItems(); if (haveData) { - cmb_filterOption.addItem(new FilterOption("Best Quality", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_quality"), "overall_quality", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Best Resolution", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_resolution"), "resolution", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Most Protein Chain", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_protein_chain"), "number_of_protein_chains", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_bound_molecules"), "number_of_bound_molecules", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_polymer_residues"), "number_of_polymer_residues", VIEWS_FILTER, true)); } cmb_filterOption.addItem( - new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false)); + new FilterOption(MessageManager.getString("label.enter_pdb_id"), + "-", VIEWS_ENTER_ID, false)); cmb_filterOption.addItem( - new FilterOption("From File", "-", VIEWS_FROM_FILE, false)); + new FilterOption(MessageManager.getString("label.from_file"), + "-", VIEWS_FROM_FILE, false)); - if (cachedPDBExists) + if (cachedPDBExist) { - FilterOption cachedOption = new FilterOption("Cached Structures", + FilterOption cachedOption = new FilterOption( + MessageManager.getString("label.cached_structures"), "-", VIEWS_LOCAL_PDB, false); cmb_filterOption.addItem(cachedOption); cmb_filterOption.setSelectedItem(cachedOption); diff --git a/src/jalview/io/gff/SequenceOntologyI.java b/src/jalview/io/gff/SequenceOntologyI.java index c0570e0..307e1d1 100644 --- a/src/jalview/io/gff/SequenceOntologyI.java +++ b/src/jalview/io/gff/SequenceOntologyI.java @@ -42,6 +42,15 @@ public interface SequenceOntologyI // SO:0001060 public static final String SEQUENCE_VARIANT = "sequence_variant"; + // SO:0001819 + public static final String SYNONYMOUS_VARIANT = "synonymous_variant"; + + // SO:0001992 + public static final String NONSYNONYMOUS_VARIANT = "nonsynonymous_variant"; + + // SO:0001587 + public static final String STOP_GAINED = "stop_gained"; + // SO:0000147 public static final String EXON = "exon"; diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java index 7c4672a..9bcaa5a 100644 --- a/src/jalview/jbgui/GStructureChooser.java +++ b/src/jalview/jbgui/GStructureChooser.java @@ -91,7 +91,7 @@ public abstract class GStructureChooser extends JPanel protected JInternalFrame mainFrame = new JInternalFrame(frameTitle); - protected JComboBox cmb_filterOption = new JComboBox(); + protected JComboBox cmb_filterOption = new JComboBox<>(); protected AlignmentPanel ap; @@ -182,7 +182,7 @@ public abstract class GStructureChooser extends JPanel protected FTSDataColumnI[] previousWantedFields; - protected static Map tempUserPrefs = new HashMap(); + protected static Map tempUserPrefs = new HashMap<>(); private JTable tbl_summary = new JTable() { @@ -474,7 +474,7 @@ public abstract class GStructureChooser extends JPanel chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12)); chk_rememberSettings.setVisible(false); txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.enter_pdb_id"))); + MessageManager.getString("label.enter_pdb_id_tip"))); cmb_filterOption.setToolTipText( MessageManager.getString("info.select_filter_option")); txt_search.getDocument().addDocumentListener(new DocumentListener() @@ -803,7 +803,7 @@ public abstract class GStructureChooser extends JPanel */ public class AssciateSeqPanel extends JPanel implements ItemListener { - private JComboBox cmb_assSeq = new JComboBox(); + private JComboBox cmb_assSeq = new JComboBox<>(); private JLabel lbl_associateSeq = new JLabel(); diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 55df1d1..a4e6480 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -39,14 +39,14 @@ public class ResidueProperties public static final int[] purinepyrimidineIndex; - public static final Map aa3Hash = new HashMap(); + public static final Map aa3Hash = new HashMap<>(); - public static final Map aa2Triplet = new HashMap(); + public static final Map aa2Triplet = new HashMap<>(); - public static final Map nucleotideName = new HashMap(); + public static final Map nucleotideName = new HashMap<>(); // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET) - public static final Map modifications = new HashMap(); + public static final Map modifications = new HashMap<>(); static { @@ -496,25 +496,27 @@ public class ResidueProperties * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap */ - public static List STOP = Arrays.asList("TGA", "TAA", "TAG"); + public static String STOP = "STOP"; + + public static List STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG"); public static String START = "ATG"; /** * Nucleotide Ambiguity Codes */ - public static final Map ambiguityCodes = new Hashtable(); + public static final Map ambiguityCodes = new Hashtable<>(); /** * Codon triplets with additional symbols for unambiguous codons that include * ambiguity codes */ - public static final Hashtable codonHash2 = new Hashtable(); + public static final Hashtable codonHash2 = new Hashtable<>(); /** * all ambiguity codes for a given base */ - public final static Hashtable> _ambiguityCodes = new Hashtable>(); + public final static Hashtable> _ambiguityCodes = new Hashtable<>(); static { @@ -638,7 +640,7 @@ public class ResidueProperties List codesfor = _ambiguityCodes.get(r); if (codesfor == null) { - _ambiguityCodes.put(r, codesfor = new ArrayList()); + _ambiguityCodes.put(r, codesfor = new ArrayList<>()); } if (!codesfor.contains(acode.getKey())) { @@ -755,27 +757,27 @@ public class ResidueProperties } // Stores residue codes/names and colours and other things - public static Map> propHash = new Hashtable>(); + public static Map> propHash = new Hashtable<>(); - public static Map hydrophobic = new Hashtable(); + public static Map hydrophobic = new Hashtable<>(); - public static Map polar = new Hashtable(); + public static Map polar = new Hashtable<>(); - public static Map small = new Hashtable(); + public static Map small = new Hashtable<>(); - public static Map positive = new Hashtable(); + public static Map positive = new Hashtable<>(); - public static Map negative = new Hashtable(); + public static Map negative = new Hashtable<>(); - public static Map charged = new Hashtable(); + public static Map charged = new Hashtable<>(); - public static Map aromatic = new Hashtable(); + public static Map aromatic = new Hashtable<>(); - public static Map aliphatic = new Hashtable(); + public static Map aliphatic = new Hashtable<>(); - public static Map tiny = new Hashtable(); + public static Map tiny = new Hashtable<>(); - public static Map proline = new Hashtable(); + public static Map proline = new Hashtable<>(); static { @@ -1149,7 +1151,7 @@ public class ResidueProperties String cdn = codonHash2.get(lccodon.toUpperCase()); if ("*".equals(cdn)) { - return "STOP"; + return STOP; } return cdn; } @@ -1157,7 +1159,7 @@ public class ResidueProperties public static Hashtable toDssp3State; static { - toDssp3State = new Hashtable(); + toDssp3State = new Hashtable<>(); toDssp3State.put("H", "H"); toDssp3State.put("E", "E"); toDssp3State.put("C", " "); @@ -2525,7 +2527,7 @@ public class ResidueProperties // / cut here public static void main(String[] args) { - Hashtable> aaProps = new Hashtable>(); + Hashtable> aaProps = new Hashtable<>(); System.out.println("my %aa = {"); // invert property hashes for (String pname : propHash.keySet()) @@ -2536,7 +2538,7 @@ public class ResidueProperties Vector aprops = aaProps.get(rname); if (aprops == null) { - aprops = new Vector(); + aprops = new Vector<>(); aaProps.put(rname, aprops); } Integer hasprop = phash.get(rname); @@ -2578,7 +2580,7 @@ public class ResidueProperties public static List getResidues(boolean forNucleotide, boolean includeAmbiguous) { - List result = new ArrayList(); + List result = new ArrayList<>(); if (forNucleotide) { for (String nuc : nucleotideName.keySet()) diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 1bff8bf..be6ba60 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -263,14 +263,14 @@ public class AlignmentUtilsTests @Test(groups = { "Functional" }) public void testMapProteinAlignmentToCdna_noXrefs() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + List dnaseqs = new ArrayList<>(); dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ @@ -507,7 +507,7 @@ public class AlignmentUtilsTests acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map); acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map); acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map); - ArrayList acfs = new ArrayList(); + ArrayList acfs = new ArrayList<>(); acfs.add(acf); protein.setCodonFrames(acfs); @@ -605,14 +605,14 @@ public class AlignmentUtilsTests public void testMapProteinAlignmentToCdna_withStartAndStopCodons() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + List dnaseqs = new ArrayList<>(); // start + SAR: dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC")); // = EIQ + stop @@ -697,14 +697,14 @@ public class AlignmentUtilsTests @Test(groups = { "Functional" }) public void testMapProteinAlignmentToCdna_withXrefs() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + List dnaseqs = new ArrayList<>(); dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ @@ -774,14 +774,14 @@ public class AlignmentUtilsTests public void testMapProteinAlignmentToCdna_prioritiseXrefs() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); AlignmentI protein = new Alignment( protseqs.toArray(new SequenceI[protseqs.size()])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + List dnaseqs = new ArrayList<>(); dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs @@ -848,8 +848,8 @@ public class AlignmentUtilsTests al.addAnnotation(ann4); // Temp for seq1 al.addAnnotation(ann5); // Temp for seq2 al.addAnnotation(ann6); // Temp for no sequence - List types = new ArrayList(); - List scope = new ArrayList(); + List types = new ArrayList<>(); + List scope = new ArrayList<>(); /* * Set all sequence related Structure to hidden (ann1, ann2) @@ -1783,7 +1783,7 @@ public class AlignmentUtilsTests map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1); acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map); - ArrayList acfs = new ArrayList(); + ArrayList acfs = new ArrayList<>(); acfs.add(acf); protein.setCodonFrames(acfs); @@ -1932,6 +1932,7 @@ public class AlignmentUtilsTests sf6.setValue("alleles", "g, a"); // should force to upper-case sf6.setValue("ID", "sequence_variant:rs758803216"); dna.addSequenceFeature(sf6); + SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 15, 15, 0f, null); sf7.setValue("alleles", "A, T"); @@ -2021,6 +2022,7 @@ public class AlignmentUtilsTests * variants: * GAA -> E source: Ensembl * CAA -> Q source: dbSNP + * TAA -> STOP source: dnSNP * AAG synonymous source: COSMIC * AAT -> N source: Ensembl * ...TTC synonymous source: dbSNP @@ -2036,39 +2038,50 @@ public class AlignmentUtilsTests String ensembl = "Ensembl"; String dbSnp = "dbSNP"; String cosmic = "COSMIC"; + SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1, 0f, ensembl); - sf1.setValue("alleles", "A,G"); // GAA -> E + sf1.setValue("alleles", "A,G"); // AAA -> GAA -> K/E sf1.setValue("ID", "var1.125A>G"); + SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1, 0f, dbSnp); - sf2.setValue("alleles", "A,C"); // CAA -> Q + sf2.setValue("alleles", "A,C"); // AAA -> CAA -> K/Q sf2.setValue("ID", "var2"); sf2.setValue("clinical_significance", "Dodgy"); - SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3, - 0f, cosmic); - sf3.setValue("alleles", "A,G"); // synonymous + + SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 1, 1, + 0f, dbSnp); + sf3.setValue("alleles", "A,T"); // AAA -> TAA -> stop codon sf3.setValue("ID", "var3"); - sf3.setValue("clinical_significance", "None"); + sf3.setValue("clinical_significance", "Bad"); + SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3, + 0f, cosmic); + sf4.setValue("alleles", "A,G"); // AAA -> AAG synonymous + sf4.setValue("ID", "var4"); + sf4.setValue("clinical_significance", "None"); + + SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 3, 3, 0f, ensembl); - sf4.setValue("alleles", "A,T"); // AAT -> N - sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off - sf4.setValue("clinical_significance", "Benign"); - SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6, + sf5.setValue("alleles", "A,T"); // AAA -> AAT -> K/N + sf5.setValue("ID", "sequence_variant:var5"); // prefix gets stripped off + sf5.setValue("clinical_significance", "Benign"); + + SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 6, 6, 0f, dbSnp); - sf5.setValue("alleles", "T,C"); // synonymous - sf5.setValue("ID", "var5"); - sf5.setValue("clinical_significance", "Bad"); - SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8, - 0f, cosmic); - sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R + sf6.setValue("alleles", "T,C"); // TTT -> TTC synonymous sf6.setValue("ID", "var6"); - sf6.setValue("clinical_significance", "Good"); - List codon1Variants = new ArrayList(); - List codon2Variants = new ArrayList(); - List codon3Variants = new ArrayList(); + SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 8, 8, + 0f, cosmic); + sf7.setValue("alleles", "C,A,G"); // CCC -> CAC,CGC -> P/H/R + sf7.setValue("ID", "var7"); + sf7.setValue("clinical_significance", "Good"); + + List codon1Variants = new ArrayList<>(); + List codon2Variants = new ArrayList<>(); + List codon3Variants = new ArrayList<>(); List codonVariants[] = new ArrayList[3]; codonVariants[0] = codon1Variants; codonVariants[1] = codon2Variants; @@ -2079,10 +2092,11 @@ public class AlignmentUtilsTests */ codon1Variants.add(new DnaVariant("A", sf1)); codon1Variants.add(new DnaVariant("A", sf2)); + codon1Variants.add(new DnaVariant("A", sf3)); codon2Variants.add(new DnaVariant("A")); - codon2Variants.add(new DnaVariant("A")); - codon3Variants.add(new DnaVariant("A", sf3)); + // codon2Variants.add(new DnaVariant("A")); codon3Variants.add(new DnaVariant("A", sf4)); + codon3Variants.add(new DnaVariant("A", sf5)); AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants); /* @@ -2093,7 +2107,7 @@ public class AlignmentUtilsTests codon3Variants.clear(); codon1Variants.add(new DnaVariant("T")); codon2Variants.add(new DnaVariant("T")); - codon3Variants.add(new DnaVariant("T", sf5)); + codon3Variants.add(new DnaVariant("T", sf6)); AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants); /* @@ -2103,7 +2117,7 @@ public class AlignmentUtilsTests codon2Variants.clear(); codon3Variants.clear(); codon1Variants.add(new DnaVariant("C")); - codon2Variants.add(new DnaVariant("C", sf6)); + codon2Variants.add(new DnaVariant("C", sf7)); codon3Variants.add(new DnaVariant("C")); AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants); @@ -2111,35 +2125,43 @@ public class AlignmentUtilsTests * verify added sequence features for * var1 K -> E Ensembl * var2 K -> Q dbSNP - * var4 K -> N Ensembl - * var6 P -> H COSMIC - * var6 P -> R COSMIC + * var3 K -> stop + * var4 synonymous + * var5 K -> N Ensembl + * var6 synonymous + * var7 P -> H COSMIC + * var8 P -> R COSMIC */ List sfs = peptide.getSequenceFeatures(); SequenceFeatures.sortFeatures(sfs, true); - assertEquals(5, sfs.size()); + assertEquals(8, sfs.size()); /* * features are sorted by start position ascending, but in no * particular order where start positions match; asserts here * simply match the data returned (the order is not important) */ + // AAA -> AAT -> K/N SequenceFeature sf = sfs.get(0); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Asn", sf.getDescription()); - assertEquals("var4", sf.getValue("ID")); + assertEquals("var5", sf.getValue("ID")); assertEquals("Benign", sf.getValue("clinical_significance")); - assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes()); + assertEquals("ID=var5;clinical_significance=Benign", + sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( - "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", + "p.Lys1Asn var5|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var5", sf.links.get(0)); assertEquals(ensembl, sf.getFeatureGroup()); + // AAA -> CAA -> K/Q sf = sfs.get(1); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Gln", sf.getDescription()); assertEquals("var2", sf.getValue("ID")); assertEquals("Dodgy", sf.getValue("clinical_significance")); @@ -2150,9 +2172,11 @@ public class AlignmentUtilsTests sf.links.get(0)); assertEquals(dbSnp, sf.getFeatureGroup()); + // AAA -> GAA -> K/E sf = sfs.get(2); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Glu", sf.getDescription()); assertEquals("var1.125A>G", sf.getValue("ID")); assertNull(sf.getValue("clinical_significance")); @@ -2164,30 +2188,79 @@ public class AlignmentUtilsTests sf.links.get(0)); assertEquals(ensembl, sf.getFeatureGroup()); + // AAA -> TAA -> stop codon sf = sfs.get(3); + assertEquals(1, sf.getBegin()); + assertEquals(1, sf.getEnd()); + assertEquals("stop_gained", sf.getType()); + assertEquals("TAA", sf.getDescription()); + assertEquals("var3", sf.getValue("ID")); + assertEquals("Bad", sf.getValue("clinical_significance")); + assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( + "TAA var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3", + sf.links.get(0)); + assertEquals(dbSnp, sf.getFeatureGroup()); + + // AAA -> AAG synonymous + sf = sfs.get(4); + assertEquals(1, sf.getBegin()); + assertEquals(1, sf.getEnd()); + assertEquals("synonymous_variant", sf.getType()); + assertEquals("AAG", sf.getDescription()); + assertEquals("var4", sf.getValue("ID")); + assertEquals("None", sf.getValue("clinical_significance")); + assertEquals("ID=var4;clinical_significance=None", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( + "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", + sf.links.get(0)); + assertEquals(cosmic, sf.getFeatureGroup()); + + // TTT -> TTC synonymous + sf = sfs.get(5); + assertEquals(2, sf.getBegin()); + assertEquals(2, sf.getEnd()); + assertEquals("synonymous_variant", sf.getType()); + assertEquals("TTC", sf.getDescription()); + assertEquals("var6", sf.getValue("ID")); + assertNull(sf.getValue("clinical_significance")); + assertEquals("ID=var6", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( + "TTC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", + sf.links.get(0)); + assertEquals(dbSnp, sf.getFeatureGroup()); + + // var7 generates two distinct protein variant features (two alleles) + // CCC -> CGC -> P/R + sf = sfs.get(6); assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Pro3Arg", sf.getDescription()); - assertEquals("var6", sf.getValue("ID")); + assertEquals("var7", sf.getValue("ID")); assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes()); + assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( - "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", + "p.Pro3Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7", sf.links.get(0)); assertEquals(cosmic, sf.getFeatureGroup()); - // var5 generates two distinct protein variant features - sf = sfs.get(4); + // CCC -> CAC -> P/H + sf = sfs.get(7); assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Pro3His", sf.getDescription()); - assertEquals("var6", sf.getValue("ID")); + assertEquals("var7", sf.getValue("ID")); assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes()); + assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( - "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", + "p.Pro3His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7", sf.links.get(0)); assertEquals(cosmic, sf.getFeatureGroup()); } @@ -2308,7 +2381,7 @@ public class AlignmentUtilsTests seq1.createDatasetSequence(); Mapping mapping = new Mapping(seq1, new MapList( new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1)); - Map> map = new TreeMap>(); + Map> map = new TreeMap<>(); AlignmentUtils.addMappedPositions(seq1, from, mapping, map); /* @@ -2340,7 +2413,7 @@ public class AlignmentUtilsTests seq1.createDatasetSequence(); Mapping mapping = new Mapping(seq1, new MapList( new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1)); - Map> map = new TreeMap>(); + Map> map = new TreeMap<>(); AlignmentUtils.addMappedPositions(seq1, from, mapping, map); /* diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java index 6611e05..779962c 100644 --- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java +++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java @@ -228,6 +228,9 @@ public class EnsemblCdnaTest sf.setValue("Parent", "transcript:" + accId); assertTrue(testee.retainFeature(sf, accId)); + // test is not case-sensitive + assertTrue(testee.retainFeature(sf, accId.toLowerCase())); + // feature with wrong parent is not retained sf.setValue("Parent", "transcript:XYZ"); assertFalse(testee.retainFeature(sf, accId)); diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java index 5920b89..1b1a2b4 100644 --- a/test/jalview/ext/ensembl/EnsemblGeneTest.java +++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java @@ -173,7 +173,8 @@ public class EnsemblGeneTest // NMD_transcript_variant treated like transcript in Ensembl SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "", 22000, 22500, 0f, null); - sf3.setValue("Parent", "gene:" + geneId); + // id matching should not be case-sensitive + sf3.setValue("Parent", "gene:" + geneId.toLowerCase()); sf3.setValue("transcript_id", "transcript3"); genomic.addSequenceFeature(sf3); @@ -259,6 +260,9 @@ public class EnsemblGeneTest sf.setValue("ID", "gene:" + accId); assertTrue(testee.identifiesSequence(sf, accId)); + // test is not case-sensitive + assertTrue(testee.identifiesSequence(sf, accId.toLowerCase())); + // transcript not valid: sf = new SequenceFeature("transcript", "", 1, 2, 0f, null); sf.setValue("ID", "gene:" + accId); diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java index e2af26b..42afa82 100644 --- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java +++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java @@ -21,9 +21,7 @@ package jalview.ext.ensembl; import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertSame; -import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.Alignment; import jalview.datamodel.SequenceFeature; diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index 4535c93..91fe602 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -65,7 +65,7 @@ public class StructureChooserTest PDBEntry dbRef = new PDBEntry(); dbRef.setId("1tim"); - Vector pdbIds = new Vector(); + Vector pdbIds = new Vector<>(); pdbIds.add(dbRef); seq.setPDBId(pdbIds); @@ -133,7 +133,7 @@ public class StructureChooserTest assertTrue(sc.getCmbFilterOption().getSelectedItem() != null); FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption() .getSelectedItem(); - assertEquals("Cached PDB Entries", filterOpt.getName()); + assertEquals("Cached Structures", filterOpt.getName()); } @Test(groups = { "Network" }) diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java index a02cc5a..7099282 100644 --- a/test/jalview/io/vcf/VCFLoaderTest.java +++ b/test/jalview/io/vcf/VCFLoaderTest.java @@ -170,7 +170,7 @@ public class VCFLoaderTest assertEquals(sf.getFeatureGroup(), "VCF"); assertEquals(sf.getBegin(), 1); assertEquals(sf.getEnd(), 1); - assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); + assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); assertEquals(sf.getDescription(), "p.Ser1Thr"); } @@ -425,7 +425,7 @@ public class VCFLoaderTest assertEquals(sf.getFeatureGroup(), "VCF"); assertEquals(sf.getBegin(), 6); assertEquals(sf.getEnd(), 6); - assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); + assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); assertEquals(sf.getDescription(), "p.Ala6Gly"); } @@ -570,12 +570,19 @@ public class VCFLoaderTest } } List proteinFeatures = peptide.getSequenceFeatures(); - assertEquals(proteinFeatures.size(), 1); + SequenceFeatures.sortFeatures(proteinFeatures, true); + assertEquals(proteinFeatures.size(), 2); sf = proteinFeatures.get(0); assertEquals(sf.getFeatureGroup(), "VCF"); + assertEquals(sf.getBegin(), 1); + assertEquals(sf.getEnd(), 1); + assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT); + assertEquals(sf.getDescription(), "AGT"); + sf = proteinFeatures.get(1); + assertEquals(sf.getFeatureGroup(), "VCF"); assertEquals(sf.getBegin(), 4); assertEquals(sf.getEnd(), 4); - assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); + assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); assertEquals(sf.getDescription(), "p.Glu4Gly"); /*