jalview.release=releases/Release_2_10_3_Branch
-jalview.version=2.10.3
+jalview.version=2.10.3b1
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
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.
<mapID target="home" url="html/index.html" />
<mapID target="new" url="html/whatsNew.html"/>
- <mapID target="release" url="html/releases.html#Jalview.2.10.3"/>
+ <mapID target="release" url="html/releases.html#Jalview.2.10.3b1"/>
<mapID target="alannotation" url="html/features/annotation.html"/>
<mapID target="keys" url="html/keys.html"/>
<mapID target="newkeys" url="html/features/newkeystrokes.html"/>
</td>
</tr>
<tr>
- <td width=="60" nowrap>
+ <td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>5/12/2017</em></strong>
+ <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
</div>
</td>
<td><div align="left">
- <em></em>
- </td>
+ <ul><li>Updated Certum Codesigning Certificate
+ (Valid till 30th November 2018)</li></ul></div></td>
<td><div align="left">
+ <em>Desktop</em><ul>
<ul>
+ <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
<li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
<li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
<li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
<li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
- <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
- <ul>
+ <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
+ <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
+ </ul>
+ </div>
</td>
</tr>
<tr>
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.3 ?</strong>
+ <strong>What's new in Jalview 2.10.3b1 ?</strong>
</p>
<p>
- 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 <a href="releases.html#Jalview.2.10.3">2.10.3
- Release Notes</a>. 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 <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
+ Release Notes</a>. In addition, Jalview 2.10.3 provides:
</p>
<ul>
<li>Faster and more responsive UI when importing and working
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...
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
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
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}
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}
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
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
*/
public static AlignmentI expandContext(AlignmentI core, int flankSize)
{
- List<SequenceI> sq = new ArrayList<SequenceI>();
+ List<SequenceI> sq = new ArrayList<>();
int maxoffset = 0;
for (SequenceI s : core.getSequences())
{
public static Map<String, List<SequenceI>> getSequencesByName(
AlignmentI al)
{
- Map<String, List<SequenceI>> theMap = new LinkedHashMap<String, List<SequenceI>>();
+ Map<String, List<SequenceI>> theMap = new LinkedHashMap<>();
for (SequenceI seq : al.getSequences())
{
String name = seq.getName();
List<SequenceI> seqs = theMap.get(name);
if (seqs == null)
{
- seqs = new ArrayList<SequenceI>();
+ seqs = new ArrayList<>();
theMap.put(name, seqs);
}
seqs.add(seq);
return false;
}
- Set<SequenceI> mappedDna = new HashSet<SequenceI>();
- Set<SequenceI> mappedProtein = new HashSet<SequenceI>();
+ Set<SequenceI> mappedDna = new HashSet<>();
+ Set<SequenceI> mappedProtein = new HashSet<>();
/*
* First pass - map sequences where cross-references exist. This include
{
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))
{
* 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;
}
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;
}
System.err.println("Wrong alignment type in alignProteinAsDna");
return 0;
}
- List<SequenceI> unmappedProtein = new ArrayList<SequenceI>();
+ List<SequenceI> unmappedProtein = new ArrayList<>();
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = buildCodonColumnsMap(
protein, dna, unmappedProtein);
return alignProteinAs(protein, alignedCodons, unmappedProtein);
* {dnaSequence, {proteinSequence, codonProduct}} at that position. The
* comparator keeps the codon positions ordered.
*/
- Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, AlignedCodon>>(
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<>(
new CodonComparator());
for (SequenceI dnaSeq : dna.getSequences())
// TODO delete this ugly hack once JAL-2022 is resolved
// i.e. we can model startPhase > 0 (incomplete start codon)
- List<SequenceI> sequencesChecked = new ArrayList<SequenceI>();
+ List<SequenceI> sequencesChecked = new ArrayList<>();
AlignedCodon lastCodon = null;
- Map<SequenceI, AlignedCodon> toAdd = new HashMap<SequenceI, AlignedCodon>();
+ Map<SequenceI, AlignedCodon> toAdd = new HashMap<>();
for (Entry<AlignedCodon, Map<SequenceI, AlignedCodon>> entry : alignedCodons
.entrySet())
Map<SequenceI, AlignedCodon> seqProduct = alignedCodons.get(codon);
if (seqProduct == null)
{
- seqProduct = new HashMap<SequenceI, AlignedCodon>();
+ seqProduct = new HashMap<>();
alignedCodons.put(codon, seqProduct);
}
seqProduct.put(protein, codon);
{
continue;
}
- final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ final List<AlignmentAnnotation> result = new ArrayList<>();
for (AlignmentAnnotation dsann : datasetAnnotations)
{
/*
throw new IllegalArgumentException(
"IMPLEMENTATION ERROR: dataset.getDataset() must be null!");
}
- List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
- List<SequenceI> cdsSeqs = new ArrayList<SequenceI>();
+ List<SequenceI> foundSeqs = new ArrayList<>();
+ List<SequenceI> cdsSeqs = new ArrayList<>();
List<AlignedCodonFrame> mappings = dataset.getCodonFrames();
HashSet<SequenceI> productSeqs = null;
if (products != null)
{
- productSeqs = new HashSet<SequenceI>();
+ productSeqs = new HashSet<>();
for (SequenceI seq : products)
{
productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
SequenceI contig, SequenceI proteinProduct, Mapping mapping)
{
// gather direct refs from contig congruent with mapping
- List<DBRefEntry> direct = new ArrayList<DBRefEntry>();
- HashSet<String> directSources = new HashSet<String>();
+ List<DBRefEntry> direct = new ArrayList<>();
+ HashSet<String> directSources = new HashSet<>();
if (contig.getDBRefs() != null)
{
for (DBRefEntry dbr : contig.getDBRefs())
DBRefEntry[] onSource = DBRefUtils.selectRefs(
proteinProduct.getDBRefs(),
directSources.toArray(new String[0]));
- List<DBRefEntry> propagated = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> propagated = new ArrayList<>();
// and generate appropriate mappings
for (DBRefEntry cdsref : direct)
proteinStart++;
proteinLength--;
}
- List<int[]> proteinRange = new ArrayList<int[]>();
+ List<int[]> proteinRange = new ArrayList<>();
/*
* dna length should map to protein (or protein plus stop codon)
*/
protected static List<int[]> findCdsPositions(SequenceI dnaSeq)
{
- List<int[]> result = new ArrayList<int[]>();
+ List<int[]> result = new ArrayList<>();
List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology(
SequenceOntologyI.CDS);
{
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++;
+ }
}
}
}
{
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++;
+ }
}
}
}
{
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++;
+ }
}
}
}
* 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;
}
/**
* 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<Integer, List<DnaVariant>[]> variants = new LinkedHashMap<Integer, List<DnaVariant>[]>();
+ LinkedHashMap<Integer, List<DnaVariant>[]> variants = new LinkedHashMap<>();
List<SequenceFeature> dnaFeatures = dnaSeq.getFeatures()
.getFeaturesByOntology(SequenceOntologyI.SEQUENCE_VARIANT);
if (codonVariants == null)
{
codonVariants = new ArrayList[CODON_LENGTH];
- codonVariants[0] = new ArrayList<DnaVariant>();
- codonVariants[1] = new ArrayList<DnaVariant>();
- codonVariants[2] = new ArrayList<DnaVariant>();
+ codonVariants[0] = new ArrayList<>();
+ codonVariants[1] = new ArrayList<>();
+ codonVariants[2] = new ArrayList<>();
variants.put(peptidePosition, codonVariants);
}
/*
* fancy case - aligning via mappings between sequences
*/
- List<SequenceI> unmapped = new ArrayList<SequenceI>();
+ List<SequenceI> unmapped = new ArrayList<>();
Map<Integer, Map<SequenceI, Character>> columnMap = buildMappedColumnsMap(
unaligned, aligned, unmapped);
int width = columnMap.size();
}
// map from dataset sequence to alignment sequence(s)
- Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<SequenceI, List<SequenceI>>();
+ Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<>();
for (SequenceI seq : aligned.getSequences())
{
SequenceI ds = seq.getDatasetSequence();
* {unalignedSequence, characterPerSequence} at that position.
* TreeMap keeps the entries in ascending column order.
*/
- SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
/*
* record any sequences that have no mapping so can't be realigned
Map<SequenceI, Character> seqsMap = map.get(fromCol);
if (seqsMap == null)
{
- seqsMap = new HashMap<SequenceI, Character>();
+ seqsMap = new HashMap<>();
map.put(fromCol, seqsMap);
}
seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart));
int s;
int sSize = selection.size();
- List<SequenceI> pepseqs = new ArrayList<SequenceI>();
+ List<SequenceI> pepseqs = new ArrayList<>();
for (s = 0; s < sSize; s++)
{
SequenceI newseq = translateCodingRegion(selection.get(s),
if (dnarefs != null)
{
// intersect with pep
- List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> mappedrefs = new ArrayList<>();
DBRefEntry[] refs = dna.getDBRefs();
for (int d = 0; d < refs.length; d++)
{
String seqstring, AlignedCodonFrame acf,
List<SequenceI> proteinSeqs)
{
- List<int[]> skip = new ArrayList<int[]>();
+ List<int[]> skip = new ArrayList<>();
int skipint[] = null;
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
// intervals
skip.add(skipint);
skipint = null;
}
- if (aa.equals("STOP"))
+ if (aa.equals(ResidueProperties.STOP))
{
aa = STOP_ASTERIX;
}
public AlignmentI reverseCdna(boolean complement)
{
int sSize = selection.size();
- List<SequenceI> reversed = new ArrayList<SequenceI>();
+ List<SequenceI> reversed = new ArrayList<>();
for (int s = 0; s < sSize; s++)
{
SequenceI newseq = reverseSequence(selection.get(s).getName(),
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import java.util.HashMap;
-import java.util.Map;
-
import com.stevesoft.pat.Regex;
/**
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
- private static Map<String, String> params = new HashMap<String, String>();
-
- static
- {
- params.put("object_type", "transcript");
- }
-
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
}
/**
- * 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<String, String> getAdditionalParameters()
+ protected String getObjectType()
{
- return params;
+ return OBJECT_TYPE_TRANSCRIPT;
}
}
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
- List<String> queries = new ArrayList<String>();
+ List<String> queries = new ArrayList<>();
queries.add(query);
FileParse fp = getSequenceReader(queries);
if (fp == null || !fp.isValid())
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)
{
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
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)
*/
List<String> getGeneIds(String accessions)
{
- List<String> geneIds = new ArrayList<String>();
+ List<String> geneIds = new ArrayList<>();
for (String acc : accessions.split(getAccessionSeparator()))
{
int transcriptLength = 0;
final char[] geneChars = gene.getSequence();
int offset = gene.getStart(); // to convert to 0-based positions
- List<int[]> mappedFrom = new ArrayList<int[]>();
+ List<int[]> mappedFrom = new ArrayList<>();
for (SequenceFeature sf : splices)
{
* transfer features to the new sequence; we use EnsemblCdna to do this,
* to filter out unwanted features types (see method retainFeature)
*/
- List<int[]> mapTo = new ArrayList<int[]>();
+ List<int[]> mapTo = new ArrayList<>();
mapTo.add(new int[] { 1, transcriptLength });
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
EnsemblCdna cdna = new EnsemblCdna(getDomain());
protected List<SequenceFeature> getTranscriptFeatures(String accId,
SequenceI geneSequence)
{
- List<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> transcriptFeatures = new ArrayList<>();
String parentIdentifier = GENE_PREFIX + accId;
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
- if (parentIdentifier.equals(parent))
+ if (parentIdentifier.equalsIgnoreCase(parent))
{
transcriptFeatures.add(sf);
}
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;
}
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
- if (!(GENE_PREFIX + accessionId).equals(parent))
+ if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
{
return false;
}
{
if (isTranscript(sf.getType()))
{
- String id = (String) sf.getValue(ID);
+ String id = (String) sf.getValue("ID");
if (("transcript:" + accId).equals(id))
{
return true;
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
*/
{
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)
*/
protected URL getUrl(List<String> 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);
}
/**
- * Calls the Ensembl lookup REST endpoint and returns
- * <ul>
- * <li>the 'id' for the identifier if its type is "Gene"</li>
- * <li>the 'Parent' if its type is 'Transcript'</li>
- * <ul>
- * 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));
}
/**
*/
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<BufferedReader, Object> parser)
+ protected JSONObject getResult(String identifier, String objectType)
{
List<String> 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
{
}
/**
- * 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;
}
*/
public GeneLociI getGeneLoci(String geneId)
{
- return (GeneLociI) getResult(geneId, br -> parseGeneLoci(br));
+ return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE));
}
/**
* 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;
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;
}
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
*/
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";
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());
/*
* transfer features to the query sequence
*/
- SequenceI querySeq = alignment.findName(accId);
+ SequenceI querySeq = alignment.findName(accId, true);
if (transferFeatures(accId, genomicSequence, querySeq))
{
urlstring.append("?type=").append(getSourceEnsemblType().getType());
urlstring.append(("&Accept=text/x-fasta"));
- Map<String, String> params = getAdditionalParameters();
- if (params != null)
+ String objectType = getObjectType();
+ if (objectType != null)
{
- for (Entry<String, String> 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());
}
/**
- * Override this method to add any additional x=y URL parameters needed
+ * Override this method to specify object_type request parameter
*
* @return
*/
- protected Map<String, String> getAdditionalParameters()
+ protected String getObjectType()
{
return null;
}
protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
String accId, int start)
{
- // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
List<SequenceFeature> sfs = sourceSequence.getFeatures()
.getPositionalFeatures();
if (sfs.isEmpty())
* generously initial size for number of cds regions
* (worst case titin Q8WZ42 has c. 313 exons)
*/
- List<int[]> regions = new ArrayList<int[]>(100);
+ List<int[]> regions = new ArrayList<>(100);
int mappedLength = 0;
int direction = 1; // forward
boolean directionSet = false;
{
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;
protected List<SequenceFeature> findFeatures(SequenceI sequence,
String term, String parentId)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
List<SequenceFeature> 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);
}
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
{
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
*
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))
{
protected JTabbedPane tabs = new JTabbedPane();
protected IProgressIndicator progressIndicator;
- protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
+ protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<>();
protected JButton btn_ok = new JButton();
protected int pageLimit;
- protected HashSet<String> paginatorCart = new HashSet<String>();
+ protected HashSet<String> paginatorCart = new HashSet<>();
private static final int MIN_WIDTH = 670;
private void jbInit() throws Exception
{
- txt_search = new JvCacheableInputBox<String>(getCacheKey());
+ txt_search = new JvCacheableInputBox<>(getCacheKey());
populateCmbSearchTargetOptions();
Integer width = getTempUserPrefs().get("FTSPanel.width") == null ? 800
: getTempUserPrefs().get("FTSPanel.width");
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);
}
*/
public void populateCmbSearchTargetOptions()
{
- List<FTSDataColumnI> searchableTargets = new ArrayList<FTSDataColumnI>();
+ List<FTSDataColumnI> searchableTargets = new ArrayList<>();
try
{
Collection<FTSDataColumnI> foundFTSTargets = getFTSRestClient()
/*
* 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
* structures
*/
protected void populateFilterComboBox(boolean haveData,
- boolean cachedPDBExists)
+ boolean cachedPDBExist)
{
/*
* temporarily suspend the change listener behaviour
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);
// 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";
protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
- protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<FilterOption>();
+ protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
protected AlignmentPanel ap;
protected FTSDataColumnI[] previousWantedFields;
- protected static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ protected static Map<String, Integer> tempUserPrefs = new HashMap<>();
private JTable tbl_summary = new JTable()
{
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()
*/
public class AssciateSeqPanel extends JPanel implements ItemListener
{
- private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<AssociateSeqOptions>();
+ private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
private JLabel lbl_associateSeq = new JLabel();
public static final int[] purinepyrimidineIndex;
- public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
+ public static final Map<String, Integer> aa3Hash = new HashMap<>();
- public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
+ public static final Map<String, String> aa2Triplet = new HashMap<>();
- public static final Map<String, String> nucleotideName = new HashMap<String, String>();
+ public static final Map<String, String> nucleotideName = new HashMap<>();
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
- public static final Map<String, String> modifications = new HashMap<String, String>();
+ public static final Map<String, String> modifications = new HashMap<>();
static
{
* Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
*/
- public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
+ public static String STOP = "STOP";
+
+ public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
public static String START = "ATG";
/**
* Nucleotide Ambiguity Codes
*/
- public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+ public static final Map<String, String[]> ambiguityCodes = new Hashtable<>();
/**
* Codon triplets with additional symbols for unambiguous codons that include
* ambiguity codes
*/
- public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+ public static final Hashtable<String, String> codonHash2 = new Hashtable<>();
/**
* all ambiguity codes for a given base
*/
- public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>();
static
{
List<String> codesfor = _ambiguityCodes.get(r);
if (codesfor == null)
{
- _ambiguityCodes.put(r, codesfor = new ArrayList<String>());
+ _ambiguityCodes.put(r, codesfor = new ArrayList<>());
}
if (!codesfor.contains(acode.getKey()))
{
}
// Stores residue codes/names and colours and other things
- public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
+ public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
- public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> hydrophobic = new Hashtable<>();
- public static Map<String, Integer> polar = new Hashtable<String, Integer>();
+ public static Map<String, Integer> polar = new Hashtable<>();
- public static Map<String, Integer> small = new Hashtable<String, Integer>();
+ public static Map<String, Integer> small = new Hashtable<>();
- public static Map<String, Integer> positive = new Hashtable<String, Integer>();
+ public static Map<String, Integer> positive = new Hashtable<>();
- public static Map<String, Integer> negative = new Hashtable<String, Integer>();
+ public static Map<String, Integer> negative = new Hashtable<>();
- public static Map<String, Integer> charged = new Hashtable<String, Integer>();
+ public static Map<String, Integer> charged = new Hashtable<>();
- public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aromatic = new Hashtable<>();
- public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aliphatic = new Hashtable<>();
- public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
+ public static Map<String, Integer> tiny = new Hashtable<>();
- public static Map<String, Integer> proline = new Hashtable<String, Integer>();
+ public static Map<String, Integer> proline = new Hashtable<>();
static
{
String cdn = codonHash2.get(lccodon.toUpperCase());
if ("*".equals(cdn))
{
- return "STOP";
+ return STOP;
}
return cdn;
}
public static Hashtable<String, String> toDssp3State;
static
{
- toDssp3State = new Hashtable<String, String>();
+ toDssp3State = new Hashtable<>();
toDssp3State.put("H", "H");
toDssp3State.put("E", "E");
toDssp3State.put("C", " ");
// / cut here
public static void main(String[] args)
{
- Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
+ Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
System.out.println("my %aa = {");
// invert property hashes
for (String pname : propHash.keySet())
Vector<String> aprops = aaProps.get(rname);
if (aprops == null)
{
- aprops = new Vector<String>();
+ aprops = new Vector<>();
aaProps.put(rname, aprops);
}
Integer hasprop = phash.get(rname);
public static List<String> getResidues(boolean forNucleotide,
boolean includeAmbiguous)
{
- List<String> result = new ArrayList<String>();
+ List<String> result = new ArrayList<>();
if (forNucleotide)
{
for (String nuc : nucleotideName.keySet())
@Test(groups = { "Functional" })
public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> 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<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ List<SequenceI> 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
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
- ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
+ ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
acfs.add(acf);
protein.setCodonFrames(acfs);
public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> 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<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ List<SequenceI> dnaseqs = new ArrayList<>();
// start + SAR:
dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
// = EIQ + stop
@Test(groups = { "Functional" })
public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> 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<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ List<SequenceI> 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
public void testMapProteinAlignmentToCdna_prioritiseXrefs()
throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> 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<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ List<SequenceI> 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
al.addAnnotation(ann4); // Temp for seq1
al.addAnnotation(ann5); // Temp for seq2
al.addAnnotation(ann6); // Temp for no sequence
- List<String> types = new ArrayList<String>();
- List<SequenceI> scope = new ArrayList<SequenceI>();
+ List<String> types = new ArrayList<>();
+ List<SequenceI> scope = new ArrayList<>();
/*
* Set all sequence related Structure to hidden (ann1, ann2)
map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
- ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
+ ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
acfs.add(acf);
protein.setCodonFrames(acfs);
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");
* 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
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<DnaVariant> codon1Variants = new ArrayList<DnaVariant>();
- List<DnaVariant> codon2Variants = new ArrayList<DnaVariant>();
- List<DnaVariant> codon3Variants = new ArrayList<DnaVariant>();
+ 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<DnaVariant> codon1Variants = new ArrayList<>();
+ List<DnaVariant> codon2Variants = new ArrayList<>();
+ List<DnaVariant> codon3Variants = new ArrayList<>();
List<DnaVariant> codonVariants[] = new ArrayList[3];
codonVariants[0] = codon1Variants;
codonVariants[1] = codon2Variants;
*/
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);
/*
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);
/*
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);
* 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<SequenceFeature> 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"));
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"));
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());
}
seq1.createDatasetSequence();
Mapping mapping = new Mapping(seq1, new MapList(
new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
- Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
/*
seq1.createDatasetSequence();
Mapping mapping = new Mapping(seq1, new MapList(
new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
- Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
/*
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));
// 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);
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);
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;
PDBEntry dbRef = new PDBEntry();
dbRef.setId("1tim");
- Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+ Vector<PDBEntry> pdbIds = new Vector<>();
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
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" })
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");
}
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");
}
}
}
List<SequenceFeature> 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");
/*
git://source.jalview.org / jalview.git / commitdiff