-pdb_data_columns
+uniprot_data_columns
#
_group.id
_group.name
_group.sort_order
-g1;Quality Measures;1
+g1;Quality Measures;3
g2;Cross References;2
-g3;Names & Taxonomy;3
+g3;Names & Taxonomy;1
g4;Procedures & Softwares;4
g5;Date Of;5
g6;Miscellenous;6
+g7;Sequences;7
+g8;Function;8
+g9;Interaction;9
+g10;Expression;10
+g11;Gene Ontology;11
+g12;Pathology & Biotech;12
+g13;Subcellular location;13
+g14;PTM / Processing;14
+g15;Structure;15
+g16;Publications;16
+g17;Date of;17
+g18;Family & Domain;18
+#
+_data_column.primary_key;entry name
+_data_column.default_response_page_size;100
#
_data_column.name
_data_column.code
_data_column.group_id
+_data_column.data_type
_data_column.min_col_width
_data_column.max_col_width
_data_column.preferred_col_width
-_data_column.is_primary_key
_data_column.is_shown_by_default
_data_column.is_searchable
-PDB Id;pdb_id;g2;40;60;45;true;true;true
-Title;title;g6;300;1500;400;false;true;false
-Molecule;molecule_name;g3;50;400;95;false;false;true
-Molecule Type;molecule_type;g3;50;400;95;false;false;true
-Sequence;molecule_sequence;g6;50;400;95;false;false;false
-PFAM Accession;pfam_accession;g2;50;400;95;false;false;true
-PFAM Name;pfam_name;g3;50;400;95;false;false;true
-InterPro Name;interpro_name;g3;50;400;95;false;false;false
-InterPro Accession;interpro_accession;g2;50;400;95;false;false;false
-UniProt Id;uniprot_id;g2;50;400;95;false;false;true
-UniProt Accession;uniprot_accession;g2;50;400;95;false;false;false
-UniProt Coverage;uniprot_coverage;g6;50;400;95;false;false;false
-Uniprot Features;uniprot_features;g6;50;400;95;false;false;false
-R Factor;r_factor;g1;50;150;85;false;false;false
-Resolution;resolution;g1;50;150;85;false;true;false
-Data Quality;data_quality;g1;50;150;85;false;false;false
-Overall Quality;overall_quality;g1;50;150;85;false;false;false
-Number of Polymers;number_of_polymers;g6;50;400;95;false;false;false
-Number of Protein Chains;number_of_protein_chains;g6;50;400;95;false;false;false
-Number of Bound Molecule;number_of_bound_molecules;g6;50;400;95;false;false;false
-Number of Polymer Residue;number_of_polymer_residues;g6;50;400;95;false;false;false
-GENUS;genus;g3;50;400;95;false;false;true
-Gene Name;gene_name;g3;50;400;95;false;false;true
-Experimental Method;experimental_method;g4;50;400;95;false;false;false
-GO Id;go_id;g2;50;400;95;false;false;false
-Assembly Id;assembly_id;g2;50;400;95;false;false;false
-Assembly Form;assembly_form;g6;50;400;95;false;false;false
-Assembly Type;assembly_type;g6;50;400;95;false;false;false
-Space Group;spacegroup;g6;50;400;95;false;false;false
-Cath Code;cath_code;g2;50;400;95;false;false;false
-Tax Id;tax_id;g2;50;400;95;false;false;false
-Tax Query;tax_query;g2;50;400;95;false;false;false
-Interacting Entity Id;interacting_entity_id;g2;50;400;95;false;false;false
-Interacting Molecules;interacting_molecules;g6;50;400;95;false;false;false
-Pubmed Id;pubmed_id;g2;50;400;95;false;false;false
-Status;status;g6;50;400;95;false;false;false
-Model Quality;model_quality;g1;50;150;85;false;false;false
-Pivot Resolution;pivot_resolution;g1;50;150;85;false;false;false
-Data reduction software;data_reduction_software;g4;50;400;95;false;false;false
-Max observed residues;max_observed_residues;g6;50;400;95;false;false;false
-Organism scientific name;organism_scientific_name;g3;50;400;95;false;false;false
-Super kingdom;superkingdom;g3;50;400;95;false;false;false
-Rank;rank;g3;50;400;95;false;false;false
-Crystallisation Ph;crystallisation_ph;g6;50;400;95;false;false;false
-Biological Function;biological_function;g6;50;400;95;false;false;false
-Biological Process;biological_process;g6;50;400;95;false;false;false
-Biological Cell Component;biological_cell_component;g6;50;400;95;false;false;false
-Compound Name;compound_name;g3;50;400;95;false;false;false
-Compound Id;compound_id;g2;50;400;95;false;false;false
-Compound Weight;compound_weight;g6;50;400;95;false;false;false
-Compound Systematic Name;compound_systematic_name;g3;50;400;95;false;false;false
-Interacting Ligands;interacting_ligands;g6;50;400;95;false;false;false
-Journal;journal;g6;50;400;95;false;false;false
-All Authors;all_authors;g6;50;400;95;false;false;false
-Experiment Data Available;experiment_data_available;g6;50;400;95;false;false;false
-Diffraction Protocol;diffraction_protocol;g4;50;400;95;false;false;false
-Refinement Software;refinement_software;g4;50;400;95;false;false;false
-Structure Determination Method;structure_determination_method;g4;50;400;95;false;false;false
-Synchrotron Site;synchrotron_site;g6;50;400;95;false;false;false
-Sample Preparation Method;sample_preparation_method;g4;50;400;95;false;false;false
-Entry Authors;entry_authors;g6;50;400;95;false;false;false
-Citation Title;citation_title;g6;50;400;95;false;false;false
-Structure Solution Software;structure_solution_software;g4;50;400;95;false;false;false
-Entry Entity;entry_entity;g6;50;400;95;false;false;false
-R Free;r_free;g1;50;150;85;false;false;false
-Number of Polymer Entities;number_of_polymer_entities;g6;50;400;95;false;false;false
-Number of Bound Entities;number_of_bound_entities;g6;50;400;95;false;false;false
-Crystallisation Reservoir;crystallisation_reservoir;g6;50;400;95;false;false;false
-Data Scalling Software;data_scaling_software;g4;50;400;95 ;false;false;false
-Detector;detector;g6;50;400;95;false;false;false
-Detector Type;detector_type;g6;50;400;95;false;false;false
-Modified Residue Flag;modified_residue_flag;g6;50;400;95;false;false;false
-Number of Copies;number_of_copies;g6;50;400;95;false;false;false
-Struc Asym Id;struct_asym_id;g2;50;400;95;false;false;false
-Homologus PDB Entity Id;homologus_pdb_entity_id;g2;50;400;95;false;false;false
-Molecule Synonym;molecule_synonym;g6;50;400;95;false;false;false
-Deposition Site;deposition_site;g6;50;400;95;false;false;false
-Synchrotron Beamline;synchrotron_beamline;g6;50;400;95;false;false;false
-Entity Id; entity_id;g2;50;400;95;false;false;false
-Beam Source Name;beam_source_name;g3;50;400;95;false;false;false
-Processing Site;processing_site;g6;50;400;95;false;false;false
-Entity Weight;entity_weight;g6;50;400;95;false;false;false
-Version;_version_;g6;50;400;95;false;false;false
-ALL;text;g6;50;400;95;false;false;true
+Entry Name;entry name;String;g3;80;100;85;true;true
+Protein names;protein names;String;g3;300;1500;500;true;true
+Gene Names;genes;String;g3;50;1000;95;true;true
+Organism;organism;String;g3;50;1000;95;true;true
+Organism ID;organism-id;int;g3;60;100;80;false;true
+Proteomes;proteome;String;g3;50;1000;95;false;true
+Taxonomic lineage (ALL);lineage(ALL);String;g3;50;400;95;false;false
+Virus hosts;virus hosts;String;g3;50;1000;95;false;true
+Fragment;fragment;String;g7;50;1000;95;false;true
+Gene encoded by;encodedon;String;g7;50;1000;95;false;true
+Alternative products (isoforms);comment(ALTERNATIVE PRODUCTS);String;g7;50;1000;95;false;false
+Erroneous gene model prediction;comment(ERRONEOUS GENE MODEL PREDICTION);String;g7;50;1000;95;false;false
+Erroneous initiation;comment(ERRONEOUS INITIATION);String;g7;50;1000;95;false;false
+Erroneous translation;comment(ERRONEOUS TRANSLATION);String;g7;50;1000;95;false;false
+Frameshift;comment(FRAMESHIFT);String;g7;50;1000;95;false;false
+Mass spectrometry;comment(MASS SPECTROMETRY);String;g7;50;1000;95;false;false
+Polymorphism;comment(POLYMORPHISM);String;g7;50;1000;95;false;false
+RNA editing;comment(RNA EDITING);String;g7;50;1000;95;false;false
+Sequence caution;comment(SEQUENCE CAUTION);String;g7;50;1000;95;false;false
+Length;length;int;g7;50;100;95;false;true
+Mass;mass;String;g7;50;100;80;false;true
+Sequence;sequence;String;g7;50;1000;95;false;true
+Alternative sequence;feature(ALTERNATIVE SEQUENCE);String;g7;50;1000;95;false;false
+Natural variant;feature(NATURAL VARIANT);String;g7;50;1000;95;false;false
+Non-adjacent residues;feature(NON ADJACENT RESIDUES);String;g7;50;1000;95;false;false
+Non-standard residue;feature(NON STANDARD RESIDUE);String;g7;50;1000;95;false;false
+Non-terminal residue;feature(NON TERMINAL RESIDUE);String;g7;50;1000;95;false;false
+Sequence conflict;feature(SEQUENCE CONFLICT);String;g7;50;1000;95;false;false
+Sequence uncertainty;feature(SEQUENCE UNCERTAINTY);String;g7;50;1000;95;false;false
+Version (Sequence);version(sequence);String;g7;50;1000;95;false;false
+EC number;ec;String;g8;50;1000;95;false;true
+Absorption;comment(ABSORPTION);String;g8;50;1000;95;false;false
+Catalytic activity;comment(CATALYTIC ACTIVITY);String;g8;50;1000;95;false;false
+Cofactor;comment(COFACTOR);String;g8;50;1000;95;false;false
+Enzyme regulation;comment(ENZYME REGULATION);String;g8;50;1000;95;false;false
+Function [CC];comment(FUNCTION);String;g8;50;1000;95;false;false
+Kinetics;comment(KINETICS);String;g8;50;1000;95;false;false
+Pathway;comment(PATHWAY);String;g8;50;1000;95;false;false
+Redox potential;comment(REDOX POTENTIAL);String;g8;50;1000;95;false;false
+Temperature dependence;comment(TEMPERATURE DEPENDENCE);String;g8;50;1000;95;false;false
+pH dependence;comment(PH DEPENDENCE);String;g8;50;1000;95;false;false
+Active site;feature(ACTIVE SITE);String;g8;50;1000;95;false;false
+Binding site;feature(BINDING SITE);String;g8;50;1000;95;false;false
+DNA binding;feature(DNA BINDING);String;g8;50;1000;95;false;false
+Metal binding;feature(METAL BINDING);String;g8;50;1000;95;false;false
+Nucleotide binding;feature(NP BIND);String;g8;50;1000;95;false;false
+Site;feature(SITE);String;g8;50;1000;95;false;false
+Annotation;annotation score;String;g6;50;1000;95;false;true
+Features;features;String;g6;50;1000;95;false;true
+Caution;comment(CAUTION);String;g6;50;1000;95;false;false
+Miscellaneous [CC];comment(GENERAL);String;g6;50;1000;95;false;false
+Keywords;keywords;String;g6;50;1000;95;false;true
+Protein existence;existence;String;g6;50;1000;95;false;true
+Status;reviewed;String;g6;50;1000;95;false;true
+ALL;entry name;String;g7;50;1000;95;false;true;
+Subunit structure [CC];comment(SUBUNIT);String;g9;50;1000;95;false;false
+Interacts with;interactor;String;g9;50;1000;95;false;true
+Developmental stage;comment(DEVELOPMENTAL STAGE);String;g10;50;1000;95;false;false
+Induction;comment(INDUCTION);String;g10;50;1000;95;false;false
+Tissue specificity;comment(TISSUE SPECIFICITY);String;g10;50;1000;95;false;false
+Gene ontology (GO);go;String;g11;50;1000;95;false;true
+Gene ontology (biological process);go(biological process);String;g11;50;1000;95;false;false
+Gene ontology (molecular function);go(molecular function);String;g11;50;1000;95;false;false
+Gene ontology (cellular component);go(cellular component);String;g11;50;1000;95;false;false
+Gene ontology IDs;go-id;String;g11;50;1000;95;false;true
+Allergenic properties;comment(ALLERGEN);String;g12;50;1000;95;false;false
+Biotechnological use;comment(BIOTECHNOLOGY);String;g12;50;1000;95;false;false
+Disruption phenotype;comment(DISRUPTION PHENOTYPE);String;g12;50;1000;95;false;false
+Involvement in disease;comment(DISEASE);String;g12;50;1000;95;false;false
+Pharmaceutical use;comment(PHARMACEUTICAL);String;g12;50;1000;95;false;false
+Toxic dose;comment(TOXIC DOSE);String;g12;50;1000;95;false;false
+Subcellular location [CC];comment(SUBCELLULAR LOCATION);String;g13;50;1000;95;false;false
+Intramembrane;feature(INTRAMEMBRANE);String;g13;50;1000;95;false;false
+Topological domain;feature(TOPOLOGICAL DOMAIN);String;g13;50;1000;95;false;false
+Transmembrane;feature(TRANSMEMBRANE);String;g13;50;1000;95;false;false
+Post-translational modification;comment(PTM);String;g14;50;1000;95;false;false
+Chain;feature(CHAIN);String;g14;50;1000;95;false;false
+Cross-link;feature(CROSS LINK);String;g14;50;1000;95;false;false
+Disulfide bond;feature(DISULFIDE BOND);String;g14;50;1000;95;false;false
+Glycosylation;feature(GLYCOSYLATION);String;g14;50;1000;95;false;false
+Initiator methionine;feature(INITIATOR METHIONINE);String;g14;50;1000;95;false;false
+Lipidation;feature(LIPIDATION);String;g14;50;1000;95;false;false
+Modified residue;feature(MODIFIED RESIDUE);String;g14;50;1000;95;false;false
+Peptide;feature(PEPTIDE);String;g14;50;1000;95;false;false
+Propeptide;feature(PROPEPTIDE);String;g14;50;1000;95;false;false
+Signal peptide;feature(SIGNAL);String;g14;50;1000;95;false;false
+Transit peptide;feature(TRANSIT);String;g14;50;1000;95;false;false
+3D;3d;String;g15;50;1000;95;false;false
+Beta strand;feature(BETA STRAND);String;g15;50;1000;95;false;false
+Helix;feature(HELIX);String;g15;50;1000;95;false;false
+Turn;feature(TURN);String;g15;50;1000;95;false;false
+PubMed ID;citation;String;g16;50;1000;95;false;true
+Date of creation;created;String;g17;80;150;100;true;true
+Date of last modification;last-modified;String;g17;80;150;100;true;true
+Date of last sequence modification;sequence-modified;String;g17;80;150;100;false;true
+Version (entry);version(entry);int;g17;80;100;80;false;false
+Domain [CC];comment(DOMAIN);String;g18;80;1000;95;false;false
+Sequence similarities;comment(SIMILARITY);String;g18;50;1000;95;false;false
+Protein families;families;String;g18;50;1000;95;false;true
+Coiled coil;feature(COILED COIL);String;g18;50;1000;95;false;false
+Compositional bias;feature(COMPOSITIONAL BIAS);String;g18;50;1000;95;false;false
+Domain [FT];feature(DOMAIN EXTENT);String;g18;50;1000;95;false;false
+Motif;feature(MOTIF);String;g18;50;1000;95;false;false
+Region;feature(REGION);String;g18;50;1000;95;false;false
+Repeat;feature(REPEAT);String;g18;50;1000;95;false;false
+Zinc finger;feature(ZINC FINGER);String;g18;50;1000;95;false;false
+Cross-reference (EMBL);database(EMBL);String;g2;50;1000;95;false;false
+Cross-reference (PDB);database(PDB);String;g2;50;1000;95;false;false
+Cross-reference (ENSEMBL);database(ENSEMBL);String;g2;50;1000;95;false;false
+Cross-reference (PFAM);database(PFAM);String;g2;50;1000;95;false;false
+Cross-reference (RFAM);database(RFAM);String;g2;50;1000;95;false;false
+Cross-reference (CATH);database(CATH);String;g2;50;1000;95;false;false
+Cross-reference (SCOPE);database(SCOPE);String;g2;50;1000;95;false;false
+Cross-reference (GO);database(GO);String;g2;50;1000;95;false;false
+Cross-reference (INTERPRO);database(INTERPRO);String;g2;50;1000;95;false;false
+Mapped PubMed ID;citationmapping;String;g16;50;1000;95;false;true
#
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.fts.service.uniprot;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+
import javax.ws.rs.core.MediaType;
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
-public class UniProtRestClient extends FTSRestClient
+public class UniProtFTSRestClient extends FTSRestClient
{
private static FTSRestClientI instance = null;
public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
- private static int DEFAULT_RESPONSE_SIZE = 200;
-
@Override
public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
{
ClientConfig clientConfig = new DefaultClientConfig();
Client client = Client.create(clientConfig);
- @SuppressWarnings("unchecked")
- // String wantedFields =
- // getUniProtDocFieldsAsCommaDelimitedString((Collection<UniProtDocField>)
- // uniportRestRequest
- // .getWantedFields());
- int responseSize = (uniportRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
+ .getWantedFields());
+ int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
: uniportRestRequest.getResponseSize();
+ String query = uniportRestRequest.getFieldToSearchBy() + ":"
+ + uniportRestRequest.getSearchTerm();
+ // + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
+ // : " AND status:REL");
+ // System.out.println(">>>>> Query : " + query);
+ // System.out.println(">>>>> Columns : " + wantedFields);
WebResource webResource = null;
-
webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
.queryParam("format", "tab")
- // .queryParam("columns", wantedFields)
+ .queryParam("columns", wantedFields)
.queryParam("limit", String.valueOf(responseSize))
- .queryParam("query", "name:filaggrin");
+ .queryParam("query", query);
// Execute the REST request
ClientResponse clientResponse = webResource
.accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
- String responseString = clientResponse.getEntity(String.class);
- String[] results = responseString.split("\n");
- for (String result : results)
- {
- String[] columns = result.split("\t");
- System.out.println("Entry : " + columns[0]);
- System.out.println("Entry name : " + columns[1]);
- System.out.println("Status : " + columns[2]);
- System.out.println("Protein names : " + columns[3]);
- System.out.println("Gene name : " + columns[4]);
- System.out.println("Organism : " + columns[5]);
- System.out.println("Lenght : " + columns[6]);
- System.out.println("");
- }
-
+ String uniProtTabDelimittedResponseString = clientResponse
+ .getEntity(String.class);
// Make redundant objects eligible for garbage collection to conserve
// memory
clientResponse = null;
client = null;
- return null;
+ // System.out.println(">>>>> response : "
+ // + uniProtTabDelimittedResponseString);
+ return parseUniprotResponse(uniProtTabDelimittedResponseString,
+ uniportRestRequest);
- // Process the response and return the result to the caller.
- // return parsePDBJsonResponse(responseString, pdbRestRequest);
- // System.out.println(">>>>> " + responseString);
+ }
+ public FTSRestResponse parseUniprotResponse(
+ String uniProtTabDelimittedResponseString,
+ FTSRestRequest uniprotRestRequest)
+ {
+ FTSRestResponse searchResult = new FTSRestResponse();
+ List<FTSData> result = null;
+ String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
+ if (foundDataRow != null && foundDataRow.length > 0)
+ {
+ result = new ArrayList<FTSData>();
+ String titleRow = getDataColumnsFieldsAsTabDelimitedString(uniprotRestRequest
+ .getWantedFields());
+ // System.out.println(">>>>Title row : " + titleRow);
+ for (String dataRow : foundDataRow)
+ {
+ if (dataRow.equalsIgnoreCase(titleRow))
+ {
+ // System.out.println(">>>>>>>>>> matched!!!");
+ continue;
+ }
+ // System.out.println(dataRow);
+ result.add(getFTSData(dataRow, uniprotRestRequest));
+ }
+ searchResult.setNumberOfItemsFound(result.size());
+ searchResult.setSearchSummary(result);
+ }
+ return searchResult;
+ }
+
+ public static FTSData getFTSData(String tabDelimittedDataStr,
+ FTSRestRequest request)
+ {
+ String primaryKey = null;
+
+ Object[] summaryRowData;
+
+ Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
+ int colCounter = 0;
+ summaryRowData = new Object[diplayFields.size()];
+ String[] columns = tabDelimittedDataStr.split("\t");
+ for (FTSDataColumnI field : diplayFields)
+ {
+ try
+ {
+ String fieldData = columns[colCounter];
+ if (field.isPrimaryKeyColumn())
+ {
+ primaryKey = fieldData;
+ summaryRowData[colCounter++] = primaryKey;
+ }
+ else if (fieldData == null || fieldData.isEmpty())
+ {
+ summaryRowData[colCounter++] = null;
+ }
+ else
+ {
+ try
+ {
+ summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
+ .valueOf(fieldData)
+ : (field.getDataColumnClass() == Double.class) ? Double
+ .valueOf(fieldData) : fieldData;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.out.println("offending value:" + fieldData);
+ }
+ }
+ } catch (Exception e)
+ {
+ // e.printStackTrace();
+ }
+ }
+
+ final String primaryKey1 = primaryKey;
+
+ final Object[] summaryRowData1 = summaryRowData;
+ return new FTSData()
+ {
+ @Override
+ public Object[] getSummaryData()
+ {
+ return summaryRowData1;
+ }
+
+ @Override
+ public Object getPrimaryKey()
+ {
+ return primaryKey1;
+ }
+
+ /**
+ * Returns a string representation of this object;
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder summaryFieldValues = new StringBuilder();
+ for (Object summaryField : summaryRowData1)
+ {
+ summaryFieldValues.append(
+ summaryField == null ? " " : summaryField.toString())
+ .append("\t");
+ }
+ return summaryFieldValues.toString();
+ }
+
+ /**
+ * Returns hash code value for this object
+ */
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(primaryKey1, this.toString());
+ }
+ };
}
{
if (instance == null)
{
- instance = new UniProtRestClient();
+ instance = new UniProtFTSRestClient();
}
return instance;
}
@Override
- public String getColumnDataConfigFile()
+ public String getColumnDataConfigFileName()
{
- return "fts/uniprot_data_columns.conf";
+ return getResourceFile("fts/uniprot_data_columns.conf");
}
}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.fts.service.uniprot;
+import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
+import java.util.HashSet;
+
@SuppressWarnings("serial")
public class UniprotFTSPanel extends GFTSPanel
{
+ private static String defaultFTSFrameTitle = MessageManager
+ .getString("label.uniprot_sequence_fetcher");
+
+ private String ftsFrameTitle = defaultFTSFrameTitle;
public UniprotFTSPanel(SequenceFetcher seqFetcher)
{
}
@Override
- public void txt_search_ActionPerformed()
+ public void searchAction()
{
- // TODO Auto-generated method stub
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ ftsFrameTitle = defaultFTSFrameTitle;
+ reset();
+ if (getTypedText().length() > 0)
+ {
+ setSearchInProgress(true);
+ long startTime = System.currentTimeMillis();
+
+ String searchTarget = ((FTSDataColumnI) cmb_searchTarget
+ .getSelectedItem()).getCode();
+
+ wantedFields = UniProtFTSRestClient.getInstance()
+ .getAllDefaulDisplayedDataColumns();
+ String searchTerm = txt_search.getText();
+
+ FTSRestRequest request = new FTSRestRequest();
+ request.setFieldToSearchBy(searchTarget);
+ request.setSearchTerm(searchTerm);
+ request.setWantedFields(wantedFields);
+ FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
+ .getInstance();
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = uniProtRestCleint.executeRequest(request);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ setErrorMessage(e.getMessage());
+ checkForErrors();
+ return;
+ }
+
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ getResultTable().setModel(
+ FTSRestResponse.getTableModel(request,
+ resultList.getSearchSummary()));
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields);
+ getResultTable().setVisible(true);
+ }
+
+ long endTime = System.currentTimeMillis();
+ int resultSetCount = resultList.getNumberOfItemsFound();
+ String result = (resultSetCount > 1) ? MessageManager
+ .getString("label.results") : MessageManager
+ .getString("label.result");
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+ + resultSetCount + " " + result + " ("
+ + (endTime - startTime) + " milli secs)");
+ setSearchInProgress(false);
+ }
+ }
+ }.start();
}
@Override
- public void btn_ok_ActionPerformed()
+ public void okAction()
{
- // TODO Auto-generated method stub
+ disableActionButtons();
+ StringBuilder selectedIds = new StringBuilder();
+ HashSet<String> selectedIdsSet = new HashSet<String>();
+ int primaryKeyColIndex = 0;
+ try
+ {
+ primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
+ wantedFields, false);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ int[] selectedRows = getResultTable().getSelectedRows();
+ for (int summaryRow : selectedRows)
+ {
+ String idStr = getResultTable().getValueAt(summaryRow,
+ primaryKeyColIndex).toString();
+ selectedIdsSet.add(idStr);
+ }
- }
+ for (String selectedId : selectedIdsSet)
+ {
+ selectedIds.append(selectedId).append(";");
+ }
+ String ids = selectedIds.toString();
+ // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
+ seqFetcher.getTextArea().setText(ids);
+ Thread worker = new Thread(seqFetcher);
+ worker.start();
+ delayAndEnableActionButtons();
+ }
@Override
public FTSRestClientI getFTSRestClient()
{
- return UniProtRestClient.getInstance();
+ return UniProtFTSRestClient.getInstance();
}
@Override
public String getFTSFrameTitle()
{
- return MessageManager.getString("label.uniprot_sequence_fetcher");
+ return ftsFrameTitle;
}
}
git://source.jalview.org / jalview.git / commitdiff