label.overview = Overview
label.reset_to_defaults = Reset to defaults
label.oview_calc = Recalculating overview...
+label.feature_details = Feature details
+label.matchCondition_contains = Contains
+label.matchCondition_notcontains = Does not contain
+label.matchCondition_matches = Matches
+label.matchCondition_notmatches = Does not match
+label.matchCondition_present = Is present
+label.matchCondition_notpresent = Is not present
+label.matchCondition_eq = =
+label.matchCondition_ne = not =
+label.matchCondition_lt = <
+label.matchCondition_le = <=
+label.matchCondition_gt = >
+label.matchCondition_ge = >=
+label.numeric_required = The value should be numeric
+label.filter = Filter
+label.filters = Filters
+label.join_conditions = Join conditions with
+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
+label.simple = Simple
+label.simple_colour = Simple Colour
+label.colour_by_text = Colour by text
+label.graduated_colour = Graduated Colour
+label.by_text_of = By text of
+label.by_range_of = By range of
+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
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.overview = Resumen
label.reset_to_defaults = Restablecen a los predeterminados
label.oview_calc = Recalculando resumen
+label.feature_details = Detalles de característica
+label.matchCondition_contains = Contiene
+label.matchCondition_notcontains = No contiene
+label.matchCondition_matches = Es igual a
+label.matchCondition_notmatches = No es igual a
+label.matchCondition_present = Está presente
+label.matchCondition_notpresent = No está presente
+label.matchCondition_eq = =
+label.matchCondition_ne = not =
+label.matchCondition_lt = <
+label.matchCondition_le = <=
+label.matchCondition_gt = >
+label.matchCondition_ge = >=
+label.numeric_required = Valor numérico requerido
+label.filter = Filtro
+label.filters = Filtros
+label.join_conditions = Combinar condiciones con
+label.score = Puntuación
+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.simple_colour = Color simple
+label.colour_by_text = Colorear por texto
+label.graduated_colour = Color graduado
+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
++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
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.
++ * 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
*/
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)
*/
}
/**
- * 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
++ * 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 getGeneId(identifier, null);
++ return (String) getResult(identifier, null, br -> parseGeneId(br));
}
/**
* given identifier, or null if not found
*
* @param identifier
+ * @return
+ */
+ public String getSpecies(String identifier)
+ {
- return (String) getResult(identifier, br -> getAttribute(br, SPECIES));
++ return (String) getResult(identifier, null,
++ br -> getAttribute(br, SPECIES));
+ }
+
+ /**
+ * Calls the /lookup/id rest service and delegates parsing of the JSON
+ * response to the supplied parser
+ *
+ * @param identifier
+ * @param objectType
+ * (optional)
+ * @param parser
* @return
*/
- protected Object getResult(String identifier,
- public String getGeneId(String identifier, String objectType)
++ protected Object getResult(String identifier, String objectType,
+ Function<BufferedReader, Object> parser)
{
List<String> ids = Arrays.asList(new String[] { identifier });
* 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
* @return
String type = val.get(OBJECT_TYPE).toString();
if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
{
- geneId = val.get(ID).toString();
+ // got the gene - just returns its id
- geneId = val.get(ID).toString();
++ geneId = val.get(JSON_ID).toString();
}
else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
{
}
else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
{
+ // got the protein - get its Parent, restricted to type Transcript
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!");
- }
- geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
++ geneId = (String) getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT,
++ reader -> parseGeneId(reader));
}
- } catch (ParseException e)
+ } catch (ParseException | IOException e)
{
// ignore
}
return geneId;
}
+ /**
+ * Calls the /lookup/id rest service for the given id, and if successful,
+ * parses and returns the gene's chromosomal coordinates
+ *
+ * @param geneId
+ * @return
+ */
+ public GeneLociI getGeneLoci(String geneId)
+ {
- return (GeneLociI) getResult(geneId, br -> parseGeneLoci(br));
++ return (GeneLociI) getResult(geneId, OBJECT_TYPE_GENE,
++ br -> parseGeneLoci(br));
+ }
+
+ /**
+ * Parses the /lookup/id response for species, asssembly_name,
+ * seq_region_name, start, end and returns an object that wraps them, or null
+ * if unsuccessful
+ *
+ * @param br
+ * @return
+ */
+ GeneLociI parseGeneLoci(BufferedReader br)
+ {
+ JSONParser jp = new JSONParser();
+ 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());
+ int fromEnd = end - start + 1;
+ boolean reverseStrand = "-1".equals(strand);
+ int toStart = reverseStrand ? end : start;
+ int toEnd = reverseStrand ? start : end;
+ List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+ fromEnd });
+ List<int[]> toRange = Collections.singletonList(new int[] { toStart,
+ toEnd });
+ final MapList map = new MapList(fromRange, toRange, 1, 1);
+ return new GeneLociI()
+ {
+
+ @Override
+ public String getSpeciesId()
+ {
+ return species == null ? "" : species;
+ }
+
+ @Override
+ public String getAssemblyId()
+ {
+ return assembly;
+ }
+
+ @Override
+ public String getChromosomeId()
+ {
+ return chromosome;
+ }
+
+ @Override
+ public MapList getMap()
+ {
+ return map;
+ }
+ };
+ } catch (ParseException | NullPointerException | IOException
+ | NumberFormatException | ClassCastException e)
+ {
+ Cache.log.error("Error looking up gene loci: " + e.getMessage());
++ e.printStackTrace();
+ }
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff