<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
- <classpathentry kind="lib" path="/Users/jprocter/git/jalview/lib/groovy-all-2.4.6.jar"/>
+ <classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
<classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
<classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
--- /dev/null
+uniprot_data_columns
+#
+_group.id
+_group.name
+_group.sort_order
+g1;Quality Measures;3
+g2;Cross References;2
+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_shown_by_default
+_data_column.is_searchable
+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
+#
--- /dev/null
+pdb_data_columns
+#
+_group.id
+_group.name
+_group.sort_order
+g1;Quality Measures;1
+g2;Cross References;2
+g3;Names & Taxonomy;3
+g4;Procedures & Softwares;4
+g5;Date Of;5
+g6;Miscellenous;6
+#
+_data_column.primary_key;pdb_id
+_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_shown_by_default
+_data_column.is_searchable
+PDB Id;pdb_id;String;g2;40;60;45;true;true
+Title;title;String;g6;300;1500;400;true;false
+Molecule;molecule_name;String;g3;50;400;95;false;true
+Molecule Type;molecule_type;String;g3;50;400;95;false;true
+Sequence;molecule_sequence;String;g6;50;400;95;false;false
+PFAM Accession;pfam_accession;String;g2;50;400;95;false;true
+PFAM Name;pfam_name;String;g3;50;400;95;false;true
+InterPro Name;interpro_name;String;g3;50;400;95;false;false
+InterPro Accession;interpro_accession;String;g2;50;400;95;false;false
+UniProt Id;uniprot_id;String;g2;50;400;95;false;true
+UniProt Accession;uniprot_accession;String;g2;50;400;95;false;false
+UniProt Coverage;uniprot_coverage;String;g6;50;400;95;false;false
+Uniprot Features;uniprot_features;String;g6;50;400;95;false;false
+R Factor;r_factor;Double;g1;50;150;85;false;false
+Resolution;resolution;Double;g1;50;150;85;true;false
+Data Quality;data_quality;Double;g1;50;150;85;false;false
+Overall Quality;overall_quality;Double;g1;50;150;85;false;false
+Number of Polymers;number_of_polymers;int;g6;50;400;95;false;false
+Number of Protein Chains;number_of_protein_chains;int;g6;50;400;95;false;false
+Number of Bound Molecule;number_of_bound_molecules;int;g6;50;400;95;false;false
+Number of Polymer Residue;number_of_polymer_residues;int;g6;50;400;95;false;false
+GENUS;genus;String;g3;50;400;95;false;true
+Gene Name;gene_name;String;g3;50;400;95;false;true
+Experimental Method;experimental_method;String;g4;50;400;95;false;false
+GO Id;go_id;String;g2;50;400;95;false;false
+Assembly Id;assembly_id;String;g2;50;400;95;false;false
+Assembly Form;assembly_form;String;g6;50;400;95;false;false
+Assembly Type;assembly_type;String;g6;50;400;95;false;false
+Space Group;spacegroup;String;g6;50;400;95;false;false
+Cath Code;cath_code;String;g2;50;400;95;false;false
+Tax Id;tax_id;String;g2;50;400;95;false;false
+Tax Query;tax_query;String;g2;50;400;95;false;false
+Interacting Entity Id;interacting_entity_id;String;g2;50;400;95;false;false
+Interacting Molecules;interacting_molecules;String;g6;50;400;95;false;false
+Pubmed Id;pubmed_id;int;g2;50;400;95;false;false
+Status;status;String;g6;50;400;95;false;false
+Model Quality;model_quality;Double;g1;50;150;85;false;false
+Pivot Resolution;pivot_resolution;Double;g1;50;150;85;false;false
+Data reduction software;data_reduction_software;String;g4;50;400;95;false;false
+Max observed residues;max_observed_residues;String;g6;50;400;95;false;false
+Organism scientific name;organism_scientific_name;String;g3;50;400;95;false;false
+Super kingdom;superkingdom;String;g3;50;400;95;false;false
+Rank;rank;String;g3;50;400;95;false;false
+Crystallisation Ph;crystallisation_ph;String;g6;50;400;95;false;false
+Biological Function;biological_function;String;g6;50;400;95;false;false
+Biological Process;biological_process;String;g6;50;400;95;false;false
+Biological Cell Component;biological_cell_component;String;g6;50;400;95;false;false
+Compound Name;compound_name;String;g3;50;400;95;false;false
+Compound Id;compound_id;String;g2;50;400;95;false;false
+Compound Weight;compound_weight;String;g6;50;400;95;false;false
+Compound Systematic Name;compound_systematic_name;String;g3;50;400;95;false;false
+Interacting Ligands;interacting_ligands;String;g6;50;400;95;false;false
+Journal;journal;String;g6;50;400;95;false;false
+All Authors;all_authors;String;g6;50;400;95;false;false
+Experiment Data Available;experiment_data_available;String;g6;50;400;95;false;false
+Diffraction Protocol;diffraction_protocol;String;g4;50;400;95;false;false
+Refinement Software;refinement_software;String;g4;50;400;95;false;false
+Structure Determination Method;structure_determination_method;String;g4;50;400;95;false;false
+Synchrotron Site;synchrotron_site;String;g6;50;400;95;false;false
+Sample Preparation Method;sample_preparation_method;String;g4;50;400;95;false;false
+Entry Authors;entry_authors;String;g6;50;400;95;false;false
+Citation Title;citation_title;String;g6;50;400;95;false;false
+Structure Solution Software;structure_solution_software;String;g4;50;400;95;false;false
+Entry Entity;entry_entity;String;g6;50;400;95;false;false
+R Free;r_free;Double;g1;50;150;85;false;false
+Number of Polymer Entities;number_of_polymer_entities;int;g6;50;400;95;false;false
+Number of Bound Entities;number_of_bound_entities;int;g6;50;400;95;false;false
+Crystallisation Reservoir;crystallisation_reservoir;String;g6;50;400;95;false;false
+Data Scalling Software;data_scaling_software;String;g4;50;400;95;false;false
+Detector;detector;String;g6;50;400;95;false;false
+Detector Type;detector_type;String;g6;50;400;95;false;false
+Modified Residue Flag;modified_residue_flag;String;g6;50;400;95;false;false
+Number of Copies;number_of_copies;int;g6;50;400;95;false;false
+Struc Asym Id;struct_asym_id;String;g2;50;400;95;false;false
+Homologus PDB Entity Id;homologus_pdb_entity_id;String;g2;50;400;95;false;false
+Molecule Synonym;molecule_synonym;String;g6;50;400;95;false;false
+Deposition Site;deposition_site;String;g6;50;400;95;false;false
+Synchrotron Beamline;synchrotron_beamline;String;g6;50;400;95;false;false
+Entity Id; entity_id;String;g2;50;400;95;false;false
+Beam Source Name;beam_source_name;String;g3;50;400;95;false;false
+Processing Site;processing_site;String;g6;50;400;95;false;false
+Entity Weight;entity_weight;Double;g6;50;400;95;false;false
+Version;_version_;String;g6;50;400;95;false;false
+ALL;text;String;g6;50;400;95;false;true
+#
--- /dev/null
+uniprot_data_columns
+#
+_group.id
+_group.name
+_group.sort_order
+g1;Quality Measures;3
+g2;Cross References;2
+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_shown_by_default
+_data_column.is_searchable
+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
+#
label.mark_as_representative = Mark as representative
label.open_jabaws_web_page = Open JABAWS web page
label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
-label.pdb_sequence_getcher = PDB Sequence Fetcher
+label.pdb_sequence_fetcher = PDB Sequence Fetcher
label.result = result
label.results = results
label.structure_chooser = Structure Chooser
label.run_groovy = Run Groovy console script
label.run_groovy_tip = Run the script in the Groovy console over this alignment
label.couldnt_run_groovy_script = Failed to run Groovy script
+label.uniprot_sequence_fetcher = UniProt Sequence Fetcher
\ No newline at end of file
--- /dev/null
+/*
+ * 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.api;
+
+/**
+ * This interface provides a model for the summary data;
+ *
+ * @author tcnofoegbu
+ *
+ */
+public interface FTSData
+{
+
+ /**
+ * Return an array of Objects representing the retrieved FTS data
+ *
+ * @return
+ */
+ public Object[] getSummaryData();
+
+ /**
+ * The primary key object for the retrieved FTS data
+ *
+ * @return
+ */
+ public Object getPrimaryKey();
+}
--- /dev/null
+/*
+ * 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.api;
+
+/**
+ * This interface provides a model for the dynamic data column configuration
+ *
+ * @author tcnofoegbu
+ *
+ */
+public interface FTSDataColumnI
+{
+ /**
+ * Returns the name of the data column
+ *
+ * @return the data column's name
+ */
+ public String getName();
+
+ /**
+ * Returns the code of the data column
+ *
+ * @return the data column's code
+ */
+ public String getCode();
+
+ /**
+ * Returns the minimum width of the data column
+ *
+ * @return the data column's minimum width
+ */
+ public int getMinWidth();
+
+ /**
+ * Returns the maximum width of the data column
+ *
+ * @return the data column's maximum width
+ */
+ public int getMaxWidth();
+
+ /**
+ * Returns the preferred width of the data column
+ *
+ * @return the data column's preferred width
+ */
+ public int getPreferredWidth();
+
+ /**
+ * Determines if the data column is the primary key column
+ *
+ * @return true if data column is the primary key column, otherwise false
+ */
+ public boolean isPrimaryKeyColumn();
+
+ /**
+ * Checks if the data column field can be used to perform a search query
+ *
+ * @return true means the data column is searchable
+ */
+ public boolean isSearchable();
+
+ /**
+ * Checks if the data column is displayed by default
+ *
+ * @return true means the data column is shown by default
+ */
+ public boolean isVisibleByDefault();
+
+ /**
+ * Returns the data column's data type class
+ *
+ * @return the Class for the data column's data type
+ */
+ public Class getDataColumnClass();
+
+ /**
+ * Returns the data colum's FTS data column group
+ *
+ * @return the FTSDataColumnGroupI for the column
+ */
+ public FTSDataColumnGroupI getGroup();
+
+ /**
+ * This interface provides a model for the dynamic data column group
+ *
+ */
+ public interface FTSDataColumnGroupI
+ {
+ /**
+ * Returns the Id of the data column's group
+ *
+ * @return the data column's group Id
+ */
+ public String getID();
+
+ /**
+ * Returns the name of the group
+ *
+ * @return the group's name
+ */
+ public String getName();
+
+ /**
+ * Returns the sort order of the group
+ *
+ * @return the group's sort order
+ */
+ public int getSortOrder();
+ }
+}
--- /dev/null
+/*
+ * 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.api;
+
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+
+import java.util.Collection;
+
+/**
+ * Methods for FTS Rest client.
+ *
+ * @author tcnofoegbu
+ */
+public interface FTSRestClientI
+{
+
+ /**
+ * Execute a given FTS request, process the response and return it as an
+ * FTSRestResponse object
+ *
+ * @param ftsRestRequest
+ * the FTS request to execute
+ * @return FTSRestResponse - the response after executing an FTS request
+ * @throws Exception
+ */
+ public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
+ throws Exception;
+
+ /**
+ * Return the resource file path for the data columns configuration file
+ *
+ * @return
+ */
+ public String getColumnDataConfigFileName();
+
+ /**
+ * Fetch FTSDataColumnGroupI by the group's Id
+ *
+ * @param groupId
+ * @return FTSDataColumnGroupI
+ * @throws Exception
+ */
+ public FTSDataColumnGroupI getDataColumnGroupById(String groupId)
+ throws Exception;
+
+ /**
+ * Fetch FTSDataColumnI by name or code
+ *
+ * @param nameOrCode
+ * @return FTSDataColumnI
+ * @throws Exception
+ */
+ public FTSDataColumnI getDataColumnByNameOrCode(String nameOrCode)
+ throws Exception;
+
+
+ /**
+ * Convert collection of FTSDataColumnI objects to a comma delimited string of
+ * the 'code' values
+ *
+ * @param wantedFields
+ * the collection of FTSDataColumnI to process
+ * @return the generated comma delimited string from the supplied
+ * FTSDataColumnI collection
+ */
+ public String getDataColumnsFieldsAsCommaDelimitedString(
+ Collection<FTSDataColumnI> wantedFields);
+
+
+ /**
+ * Fetch index of the primary key column for the dynamic table
+ *
+ * @param wantedFields
+ * the available table columns
+ * @param hasRefSeq
+ * true if the data columns has an additional column for reference
+ * sequence
+ * @return index of the primary key column
+ * @throws Exception
+ */
+ public int getPrimaryKeyColumIndex(
+ Collection<FTSDataColumnI> wantedFields, boolean hasRefSeq)
+ throws Exception;
+
+ /**
+ * Fetch the primary key data column object
+ *
+ * @return the FTSDataColumnI object for the primary key column
+ */
+ public FTSDataColumnI getPrimaryKeyColumn();
+
+ /**
+ * Returns list of FTSDataColumnI objects to be displayed by default
+ *
+ * @return list of columns to display by default
+ */
+ public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns();
+
+ /**
+ * Return list of FTSDataColumnI objects that can be used to perform a search
+ * query
+ *
+ * @return list of searchable FTSDataColumnI object
+ */
+ public Collection<FTSDataColumnI> getSearchableDataColumns();
+
+ /**
+ * Return list of all available FTSDataColumnI object
+ *
+ * @return list of all FTSColumnI objcet
+ */
+ public Collection<FTSDataColumnI> getAllFTSDataColumns();
+
+ /**
+ * Return the default response page limit
+ *
+ * @return the default response page size
+ */
+ public int getDefaultResponsePageSize();
+}
+
--- /dev/null
+/*
+ * 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.api;
+
+import javax.swing.JTable;
+
+/**
+ *
+ * @author tcnofoegbu
+ *
+ */
+public interface GFTSPanelI
+{
+
+ /**
+ * Action performed when a text is entered in the search field.
+ */
+ public void searchAction();
+
+ /**
+ * Action performed when search results are selected and the 'ok' button is
+ * pressed.
+ */
+ public void okAction();
+
+ /**
+ * Return the entered text
+ *
+ * @return the entered text
+ */
+ public String getTypedText();
+
+ /**
+ * The JTable for presenting the query result
+ *
+ * @return JTable
+ */
+ public JTable getResultTable();
+
+ /**
+ * Return the title to display on the search interface main panel
+ *
+ * @return String - the title
+ */
+ public String getFTSFrameTitle();
+
+ /**
+ * Return a singleton instance of FTSRestClientI
+ *
+ * @return FTSRestClientI
+ */
+ public FTSRestClientI getFTSRestClient();
+
+ /**
+ * Set error message when one occurs
+ *
+ * @param message
+ * the error message to set
+ */
+ public void setErrorMessage(String message);
+
+ /**
+ * Updates the title displayed on the search interface's main panel
+ *
+ * @param newTitle
+ */
+ public void updateSearchFrameTitle(String newTitle);
+
+ /**
+ * Controls the progress spinner, set to 'true' while search operation is in
+ * progress and 'false' after it completes
+ *
+ * @param isSearchInProgress
+ */
+ public void setSearchInProgress(Boolean isSearchInProgress);
+}
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.jbgui;
+package jalview.fts.core;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField.Group;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.api.FTSRestClientI;
import java.util.ArrayList;
import java.util.Collection;
@SuppressWarnings("serial")
-public class PDBDocFieldPreferences extends JScrollPane
+public class FTSDataColumnPreferences extends JScrollPane
{
- protected JTable tbl_pdbDocFieldConfig = new JTable();
+ protected JTable tbl_FTSDataColumnPrefs = new JTable();
protected JScrollPane scrl_pdbDocFieldConfig = new JScrollPane(
- tbl_pdbDocFieldConfig);
+ tbl_FTSDataColumnPrefs);
- private HashMap<String, PDBDocField> map = new HashMap<String, PDBDocField>();
+ private HashMap<String, FTSDataColumnI> map = new HashMap<String, FTSDataColumnI>();
- private static Collection<PDBDocField> searchSummaryFields = new LinkedHashSet<PDBDocField>();
+ private Collection<FTSDataColumnI> structSummaryColumns = new LinkedHashSet<FTSDataColumnI>();
- private static Collection<PDBDocField> structureSummaryFields = new LinkedHashSet<PDBDocField>();
+ private Collection<FTSDataColumnI> allFTSDataColumns = new LinkedHashSet<FTSDataColumnI>();
public enum PreferenceSource
{
private PreferenceSource currentSource;
- static
- {
- searchSummaryFields.add(PDBDocField.PDB_ID);
- searchSummaryFields.add(PDBDocField.TITLE);
- searchSummaryFields.add(PDBDocField.RESOLUTION);
-
- structureSummaryFields.add(PDBDocField.PDB_ID);
- structureSummaryFields.add(PDBDocField.TITLE);
- structureSummaryFields.add(PDBDocField.RESOLUTION);
- }
+ private FTSRestClientI ftsRestClient;
- public PDBDocFieldPreferences(PreferenceSource source)
+ public FTSDataColumnPreferences(PreferenceSource source,
+ FTSRestClientI ftsRestClient)
{
- tbl_pdbDocFieldConfig.setAutoCreateRowSorter(true);
+ this.ftsRestClient = ftsRestClient;
+ Collection<FTSDataColumnI> defaultCols = ftsRestClient
+ .getAllDefaulDisplayedDataColumns();
+ structSummaryColumns.addAll(defaultCols);
+ allFTSDataColumns.addAll(ftsRestClient.getAllFTSDataColumns());
- this.getViewport().add(tbl_pdbDocFieldConfig);
+ tbl_FTSDataColumnPrefs.setAutoCreateRowSorter(true);
+ this.getViewport().add(tbl_FTSDataColumnPrefs);
this.currentSource = source;
String[] columnNames = null;
break;
}
- Object[][] data = new Object[PDBDocField.values().length - 1][3];
+ Object[][] data = new Object[allFTSDataColumns.size() - 1][3];
+
int x = 0;
- for (PDBDocField field : PDBDocField.values())
+ for (FTSDataColumnI field : allFTSDataColumns)
{
if (field.getName().equalsIgnoreCase("all"))
{
switch (source)
{
case SEARCH_SUMMARY:
- data[x++] = new Object[] { searchSummaryFields.contains(field),
+ data[x++] = new Object[] {
+ ftsRestClient.getAllDefaulDisplayedDataColumns()
+ .contains(field),
field.getName(), field.getGroup() };
break;
case STRUCTURE_CHOOSER:
- data[x++] = new Object[] { structureSummaryFields.contains(field),
+ data[x++] = new Object[] { structSummaryColumns.contains(field),
field.getName(), field.getGroup() };
break;
case PREFERENCES:
data[x++] = new Object[] { field.getName(),
- searchSummaryFields.contains(field),
- structureSummaryFields.contains(field) };
+ ftsRestClient.getAllDefaulDisplayedDataColumns()
+ .contains(field),
+ structSummaryColumns.contains(field) };
break;
default:
break;
map.put(field.getName(), field);
}
- PDBFieldTableModel model = new PDBFieldTableModel(columnNames, data);
- tbl_pdbDocFieldConfig.setModel(model);
+ FTSDataColumnPrefsTableModel model = new FTSDataColumnPrefsTableModel(columnNames, data);
+ tbl_FTSDataColumnPrefs.setModel(model);
switch (source)
{
case SEARCH_SUMMARY:
case STRUCTURE_CHOOSER:
- tbl_pdbDocFieldConfig.getColumnModel().getColumn(0)
+ tbl_FTSDataColumnPrefs.getColumnModel().getColumn(0)
.setPreferredWidth(30);
- tbl_pdbDocFieldConfig.getColumnModel().getColumn(0).setMinWidth(20);
- tbl_pdbDocFieldConfig.getColumnModel().getColumn(0).setMaxWidth(40);
- tbl_pdbDocFieldConfig.getColumnModel().getColumn(1)
+ tbl_FTSDataColumnPrefs.getColumnModel().getColumn(0).setMinWidth(20);
+ tbl_FTSDataColumnPrefs.getColumnModel().getColumn(0).setMaxWidth(40);
+ tbl_FTSDataColumnPrefs.getColumnModel().getColumn(1)
.setPreferredWidth(150);
- tbl_pdbDocFieldConfig.getColumnModel().getColumn(1).setMinWidth(150);
- tbl_pdbDocFieldConfig.getColumnModel().getColumn(2)
+ tbl_FTSDataColumnPrefs.getColumnModel().getColumn(1).setMinWidth(150);
+ tbl_FTSDataColumnPrefs.getColumnModel().getColumn(2)
.setPreferredWidth(150);
- tbl_pdbDocFieldConfig.getColumnModel().getColumn(2)
+ tbl_FTSDataColumnPrefs.getColumnModel().getColumn(2)
.setMinWidth(150);
TableRowSorter<TableModel> sorter = new TableRowSorter<>(
- tbl_pdbDocFieldConfig.getModel());
- tbl_pdbDocFieldConfig.setRowSorter(sorter);
+ tbl_FTSDataColumnPrefs.getModel());
+ tbl_FTSDataColumnPrefs.setRowSorter(sorter);
List<RowSorter.SortKey> sortKeys = new ArrayList<>();
int columnIndexToSort = 2;
sortKeys.add(new RowSorter.SortKey(columnIndexToSort,
sorter.setSortKeys(sortKeys);
sorter.setComparator(
columnIndexToSort,
- new Comparator<jalview.ws.dbsources.PDBRestClient.PDBDocField.Group>()
+ new Comparator<FTSDataColumnGroupI>()
{
@Override
- public int compare(Group o1, Group o2)
+ public int compare(FTSDataColumnGroupI o1,
+ FTSDataColumnGroupI o2)
{
return o1.getSortOrder() - o2.getSortOrder();
}
});
sorter.sort();
- tbl_pdbDocFieldConfig
+ tbl_FTSDataColumnPrefs
.setAutoResizeMode(JTable.AUTO_RESIZE_NEXT_COLUMN);
break;
case PREFERENCES:
}
- public static Collection<PDBDocField> getSearchSummaryFields()
+ public Collection<FTSDataColumnI> getStructureSummaryFields()
{
- return searchSummaryFields;
+ return structSummaryColumns;
}
- public static void setSearchSummaryFields(
- Collection<PDBDocField> searchSummaryFields)
+ class FTSDataColumnPrefsTableModel extends AbstractTableModel
{
- PDBDocFieldPreferences.searchSummaryFields = searchSummaryFields;
- }
-
- public static Collection<PDBDocField> getStructureSummaryFields()
- {
- return structureSummaryFields;
- }
- public static void setStructureSummaryFields(
- Collection<PDBDocField> structureSummaryFields)
- {
- PDBDocFieldPreferences.structureSummaryFields = structureSummaryFields;
- }
-
- class PDBFieldTableModel extends AbstractTableModel
- {
-
- public PDBFieldTableModel(String[] columnNames, Object[][] data)
+ public FTSDataColumnPrefsTableModel(String[] columnNames, Object[][] data)
{
this.data = data;
this.columnNames = columnNames;
{
case SEARCH_SUMMARY:
case STRUCTURE_CHOOSER:
- return (col == 0) && !isPDBID(row, 1);
+ return (col == 0) && !isPrimaryKeyCell(row, 1);
case PREFERENCES:
- return (col == 1 || col == 2) && !isPDBID(row, 0);
+ return (col == 1 || col == 2) && !isPrimaryKeyCell(row, 0);
default:
return false;
}
* @return
*/
- public boolean isPDBID(int row, int col)
+ public boolean isPrimaryKeyCell(int row, int col)
{
- boolean matched = false;
String name = getValueAt(row, col).toString();
- PDBDocField pdbField = map.get(name);
- if (pdbField == PDBDocField.PDB_ID)
- {
- matched = true;
- }
- return matched;
+ FTSDataColumnI pdbField = map.get(name);
+ return pdbField.isPrimaryKeyColumn();
}
/*
}
boolean selected = ((Boolean) value).booleanValue();
- PDBDocField pdbField = map.get(name);
+ FTSDataColumnI ftsDataColumn = map.get(name);
if (currentSource == PreferenceSource.SEARCH_SUMMARY)
{
- updatePrefs(searchSummaryFields, pdbField, selected);
+ updatePrefs(ftsRestClient
+ .getAllDefaulDisplayedDataColumns(), ftsDataColumn,
+ selected);
}
else if (currentSource == PreferenceSource.STRUCTURE_CHOOSER)
{
- updatePrefs(structureSummaryFields, pdbField, selected);
+ updatePrefs(structSummaryColumns, ftsDataColumn, selected);
}
else if (currentSource == PreferenceSource.PREFERENCES)
{
if (col == 1)
{
- updatePrefs(searchSummaryFields, pdbField, selected);
+ updatePrefs(ftsRestClient
+ .getAllDefaulDisplayedDataColumns(), ftsDataColumn,
+ selected);
}
else if (col == 2)
{
- updatePrefs(structureSummaryFields, pdbField, selected);
+ updatePrefs(structSummaryColumns, ftsDataColumn, selected);
}
}
}
- private void updatePrefs(Collection<PDBDocField> prefConfig,
- PDBDocField pdbField, boolean selected)
+ private void updatePrefs(
+ Collection<FTSDataColumnI> prefConfig,
+ FTSDataColumnI dataColumn, boolean selected)
{
- if (prefConfig.contains(pdbField) && !selected)
+ if (prefConfig.contains(dataColumn) && !selected)
{
- prefConfig.remove(pdbField);
+ prefConfig.remove(dataColumn);
}
- if (!prefConfig.contains(pdbField) && selected)
+ if (!prefConfig.contains(dataColumn) && selected)
{
- prefConfig.add(pdbField);
+ prefConfig.add(dataColumn);
}
}
--- /dev/null
+package jalview.fts.core;
+
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.api.FTSRestClientI;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Objects;
+
+/**
+ * Base class providing implementation for common methods defined in
+ * FTSRestClientI
+ *
+ * @author tcnofoegbu
+ *
+ * @note implementations MUST be accessed as a singleton.
+ */
+public abstract class FTSRestClient implements FTSRestClientI
+{
+ protected Collection<FTSDataColumnI> dataColumns = new ArrayList<FTSDataColumnI>();
+
+ protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<FTSDataColumnGroupI>();
+
+ protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<FTSDataColumnI>();
+
+ protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<FTSDataColumnI>();
+
+ protected FTSDataColumnI primaryKeyColumn;
+
+ private String primaryKeyColumnCode = null;
+
+ private int defaultResponsePageSize = 100;
+
+ protected FTSRestClient()
+ {
+
+ }
+
+ public void parseDataColumnsConfigFile()
+ {
+ String fileName = getColumnDataConfigFileName();
+ try (BufferedReader br = new BufferedReader(new FileReader(fileName)))
+ {
+ String line;
+ while ((line = br.readLine()) != null)
+ {
+ final String[] lineData = line.split(";");
+ try
+ {
+ if (lineData.length == 2)
+ {
+ if (lineData[0].equalsIgnoreCase("_data_column.primary_key"))
+ {
+ primaryKeyColumnCode = lineData[1];
+ }
+ if (lineData[0]
+ .equalsIgnoreCase("_data_column.default_response_page_size"))
+ {
+ defaultResponsePageSize = Integer.valueOf(lineData[1]);
+ }
+ }
+ else if (lineData.length == 3)
+ {
+ dataColumnGroups.add(new FTSDataColumnGroupI()
+ {
+ @Override
+ public String getID()
+ {
+ return lineData[0];
+ }
+
+ @Override
+ public String getName()
+ {
+ return lineData[1];
+ }
+
+ @Override
+ public int getSortOrder()
+ {
+ return Integer.valueOf(lineData[2]);
+ }
+
+ @Override
+ public String toString()
+ {
+ return lineData[1];
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(this.getID(), this.getName(),
+ this.getSortOrder());
+ }
+
+ @Override
+ public boolean equals(Object otherObject)
+ {
+ FTSDataColumnGroupI that = (FTSDataColumnGroupI) otherObject;
+ return this.getID().equals(that.getID())
+ && this.getName().equals(that.getName())
+ && this.getSortOrder() == that.getSortOrder();
+ }
+ });
+ }
+ else if (lineData.length > 6)
+ {
+ FTSDataColumnI dataCol = new FTSDataColumnI()
+ {
+ @Override
+ public String toString()
+ {
+ return lineData[0];
+ }
+
+ @Override
+ public String getName()
+ {
+ return lineData[0];
+ }
+
+ @Override
+ public String getCode()
+ {
+ return lineData[1];
+ }
+
+ @Override
+ public Class<?> getDataColumnClass()
+ {
+ String classString = lineData[2];
+ classString = classString.toUpperCase();
+ switch (classString)
+ {
+ case "INT":
+ case "INTEGER":
+ return Integer.class;
+ case "DOUBLE":
+ return Double.class;
+ case "STRING":
+ default:
+ return String.class;
+ }
+ }
+
+ @Override
+ public FTSDataColumnGroupI getGroup()
+ {
+ FTSDataColumnGroupI group = null;
+ try
+ {
+ group = getDataColumnGroupById(lineData[3]);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return group;
+ }
+
+ @Override
+ public int getMinWidth()
+ {
+ return Integer.valueOf(lineData[4]);
+ }
+
+ @Override
+ public int getMaxWidth()
+ {
+ return Integer.valueOf(lineData[5]);
+ }
+
+ @Override
+ public int getPreferredWidth()
+ {
+ return Integer.valueOf(lineData[6]);
+ }
+
+ @Override
+ public boolean isPrimaryKeyColumn()
+ {
+ return getName().equalsIgnoreCase(primaryKeyColumnCode)
+ || getCode().equalsIgnoreCase(primaryKeyColumnCode);
+ }
+
+ @Override
+ public boolean isVisibleByDefault()
+ {
+ return Boolean.valueOf(lineData[7]);
+ }
+
+ @Override
+ public boolean isSearchable()
+ {
+ return Boolean.valueOf(lineData[8]);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(this.getName(), this.getCode(),
+ this.getGroup());
+ }
+
+
+ @Override
+ public boolean equals(Object otherObject)
+ {
+ FTSDataColumnI that = (FTSDataColumnI) otherObject;
+ return this.getCode().equals(that.getCode())
+ && this.getName().equals(that.getName())
+ && this.getGroup().equals(that.getGroup());
+ }
+
+ };
+ dataColumns.add(dataCol);
+
+ if (dataCol.isSearchable())
+ {
+ searchableDataColumns.add(dataCol);
+ }
+
+ if (dataCol.isVisibleByDefault())
+ {
+ defaulDisplayedDataColumns.add(dataCol);
+ }
+
+ }
+ else
+ {
+ continue;
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ try
+ {
+ this.primaryKeyColumn = getDataColumnByNameOrCode(primaryKeyColumnCode);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @Override
+ public int getPrimaryKeyColumIndex(
+ Collection<FTSDataColumnI> wantedFields, boolean hasRefSeq)
+ throws Exception
+ {
+
+ // If a reference sequence is attached then start counting from 1 else
+ // start from zero
+ int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
+
+ for (FTSDataColumnI field : wantedFields)
+ {
+ if (field.isPrimaryKeyColumn())
+ {
+ break; // Once PDB Id index is determined exit iteration
+ }
+ ++pdbFieldIndexCounter;
+ }
+ return pdbFieldIndexCounter;
+ }
+
+ @Override
+ public String getDataColumnsFieldsAsCommaDelimitedString(
+ Collection<FTSDataColumnI> dataColumnFields)
+ {
+ String result = "";
+ if (dataColumnFields != null && !dataColumnFields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (FTSDataColumnI field : dataColumnFields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+ /**
+ * Takes a collection of FTSDataColumnI and converts its 'code' values into a
+ * tab delimited string.
+ *
+ * @param dataColumnFields
+ * the collection of FTSDataColumnI to process
+ * @return the generated comma delimited string from the supplied
+ * FTSDataColumnI collection
+ */
+ public String getDataColumnsFieldsAsTabDelimitedString(
+ Collection<FTSDataColumnI> dataColumnFields)
+ {
+ String result = "";
+ if (dataColumnFields != null && !dataColumnFields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (FTSDataColumnI field : dataColumnFields)
+ {
+ returnedFields.append("\t").append(field.getName());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+ @Override
+ public Collection<FTSDataColumnI> getAllFTSDataColumns()
+ {
+ if (dataColumns == null || dataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
+ return dataColumns;
+ }
+
+ @Override
+ public Collection<FTSDataColumnI> getSearchableDataColumns()
+ {
+ if (searchableDataColumns == null || searchableDataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
+ return searchableDataColumns;
+ }
+
+ @Override
+ public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns()
+ {
+ if (defaulDisplayedDataColumns == null
+ || defaulDisplayedDataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
+ return defaulDisplayedDataColumns;
+ }
+
+ @Override
+ public FTSDataColumnI getPrimaryKeyColumn()
+ {
+ if (defaulDisplayedDataColumns == null
+ || defaulDisplayedDataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
+ return primaryKeyColumn;
+ }
+
+ @Override
+ public FTSDataColumnI getDataColumnByNameOrCode(String nameOrCode)
+ throws Exception
+ {
+ if (dataColumns == null || dataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
+ for (FTSDataColumnI column : dataColumns)
+ {
+ if (column.getName().equalsIgnoreCase(nameOrCode)
+ || column.getCode().equalsIgnoreCase(nameOrCode))
+ {
+ return column;
+ }
+ }
+ throw new Exception("Couldn't find data column with name : "
+ + nameOrCode);
+ }
+
+ @Override
+ public FTSDataColumnGroupI getDataColumnGroupById(String id)
+ throws Exception
+ {
+ if (dataColumns == null || dataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
+ for (FTSDataColumnGroupI columnGroup : dataColumnGroups)
+ {
+ if (columnGroup.getID().equalsIgnoreCase(id))
+ {
+ return columnGroup;
+ }
+ }
+ throw new Exception("Couldn't find data column group with id : " + id);
+ }
+
+ protected String getResourceFile(String fileName)
+ {
+ String result = "";
+ try
+ {
+ result = getClass().getResource(fileName).getFile();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return result;
+
+ }
+
+ @Override
+ public int getDefaultResponsePageSize()
+ {
+ return defaultResponsePageSize;
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws.uimodel;
+package jalview.fts.core;
import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.fts.api.FTSDataColumnI;
import java.util.Collection;
/**
- * Represents the PDB request to be consumed by the PDBRestClient
+ * Represents the FTS request to be consumed by the FTSRestClient
*
* @author tcnofoegbu
*
*/
-public class PDBRestRequest
+public class FTSRestRequest
{
private String fieldToSearchBy;
private boolean isSortAscending;
- private Collection<PDBDocField> wantedFields;
+ private Collection<FTSDataColumnI> wantedFields;
public String getFieldToSearchBy()
{
this.responseSize = responseSize;
}
- public Collection<PDBDocField> getWantedFields()
+ public Collection<FTSDataColumnI> getWantedFields()
{
return wantedFields;
}
- public void setWantedFields(Collection<PDBDocField> wantedFields)
+ public void setWantedFields(
+ Collection<FTSDataColumnI> wantedFields)
{
this.wantedFields = wantedFields;
}
this.associatedSequence = associatedSequence;
}
- public String getQuery()
- {
- return fieldToSearchBy + searchTerm
- + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]")
- + (isAllowUnpublishedEntries() ? "" : " AND status:REL");
- }
-
- @Override
- public String toString()
- {
- return "Query : " + getQuery() + " sort field: " + fieldToSortBy
- + " isAsc: " + isAscending() + " Associated Seq : "
- + associatedSequence;
- }
-
public boolean isAllowUnpublishedEntries()
{
return allowUnpublishedEntries;
--- /dev/null
+/*
+ * 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.core;
+
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+
+import java.util.Collection;
+
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableModel;
+
+/**
+ * Represents the response model generated by the FTSRestClient upon successful
+ * execution of a given FTS request
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class FTSRestResponse
+{
+ private int numberOfItemsFound;
+
+ private String responseTime;
+
+ private Collection<FTSData> searchSummary;
+
+ public int getNumberOfItemsFound()
+ {
+ return numberOfItemsFound;
+ }
+
+ public void setNumberOfItemsFound(int itemFound)
+ {
+ this.numberOfItemsFound = itemFound;
+ }
+
+ public String getResponseTime()
+ {
+ return responseTime;
+ }
+
+ public void setResponseTime(String responseTime)
+ {
+ this.responseTime = responseTime;
+ }
+
+ public Collection<FTSData> getSearchSummary()
+ {
+ return searchSummary;
+ }
+
+ public void setSearchSummary(Collection<FTSData> searchSummary)
+ {
+ this.searchSummary = searchSummary;
+ }
+
+ /**
+ * Convenience method to obtain a Table model for a given summary List based
+ * on the request parameters
+ *
+ * @param request
+ * the FTSRestRequest object which holds useful information for
+ * creating a table model
+ * @param summariesList
+ * the summary list which contains the data for populating the
+ * table's rows
+ * @return the table model which was dynamically generated
+ */
+ public static DefaultTableModel getTableModel(FTSRestRequest request,
+ Collection<FTSData> summariesList)
+ {
+ final FTSDataColumnI[] cols = request.getWantedFields()
+ .toArray(new FTSDataColumnI[0]);
+ final int colOffset = request.getAssociatedSequence() == null ? 0 : 1;
+ DefaultTableModel tableModel = new DefaultTableModel()
+ {
+ @Override
+ public boolean isCellEditable(int row, int column)
+ {
+ return false;
+ }
+
+ @Override
+ public Class<?> getColumnClass(int columnIndex)
+ {
+ if (colOffset == 1 && columnIndex == 0)
+ {
+ return String.class;
+ }
+ return cols[columnIndex - colOffset].getDataColumnClass();
+ }
+
+ };
+ if (request.getAssociatedSequence() != null)
+ {
+ tableModel.addColumn("Ref Sequence"); // Create sequence column header if
+ // exists in the request
+ }
+ for (FTSDataColumnI field : request
+ .getWantedFields())
+ {
+ tableModel.addColumn(field.getName()); // Create sequence column header if
+ // exists in the request
+ }
+
+ for (FTSData res : summariesList)
+ {
+ tableModel.addRow(res.getSummaryData()); // Populate table rows with
+ // summary list
+ }
+
+ return tableModel;
+ }
+
+ public static void configureTableColumn(JTable tbl_summary,
+ Collection<FTSDataColumnI> wantedFields)
+ {
+ try
+ {
+ // wait for table model initialisation to complete
+ Thread.sleep(1200);
+ } catch (InterruptedException e1)
+ {
+ e1.printStackTrace();
+ }
+ for (FTSDataColumnI wantedField : wantedFields)
+ {
+ try
+ {
+ tbl_summary.getColumn(wantedField.getName()).setMinWidth(
+ wantedField.getMinWidth());
+ tbl_summary.getColumn(wantedField.getName()).setMaxWidth(
+ wantedField.getMaxWidth());
+ tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(
+ wantedField.getPreferredWidth());
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.jbgui;
+package jalview.fts.core;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.GFTSPanelI;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.gui.Desktop;
+import jalview.gui.IProgressIndicator;
import jalview.gui.JvSwingUtils;
-import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
+import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JTabbedPane;
import javax.swing.JTable;
import javax.swing.JTextField;
+import javax.swing.Timer;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
+import javax.swing.table.DefaultTableModel;
/**
- * GUI layout for PDB Fetch Panel
+ * This class provides the swing GUI layout for FTS Panel and implements most of
+ * the contracts defined in GFSPanelI
*
* @author tcnofoegbu
*
*/
+
@SuppressWarnings("serial")
-public abstract class GPDBSearchPanel extends JPanel
+public abstract class GFTSPanel extends JPanel implements GFTSPanelI
{
- protected String frameTitle = MessageManager
- .getString("label.pdb_sequence_getcher");
+ protected JInternalFrame mainFrame = new JInternalFrame(
+ getFTSFrameTitle());
- protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+ protected IProgressIndicator progressIdicator;
- protected JComboBox<PDBDocField> cmb_searchTarget = new JComboBox<PDBDocField>();
+ protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
protected JButton btn_ok = new JButton();
protected JTextField txt_search = new JTextField(20);
- protected JTable tbl_summary = new JTable()
+ protected SequenceFetcher seqFetcher;
+
+ protected Collection<FTSDataColumnI> wantedFields;
+
+ private JTable tbl_summary = new JTable()
{
@Override
public String getToolTipText(MouseEvent evt)
private JTabbedPane tabbedPane = new JTabbedPane();
- private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences(
- PreferenceSource.SEARCH_SUMMARY);
-
private JPanel pnl_actions = new JPanel();
private JPanel pnl_results = new JPanel(new CardLayout());
private BorderLayout mainLayout = new BorderLayout();
- protected PDBDocField[] previousWantedFields;
+ protected Object[] previousWantedFields;
- public GPDBSearchPanel()
+ public GFTSPanel()
{
try
{
case KeyEvent.VK_ENTER: // enter key
if (btn_ok.isEnabled())
{
- btn_ok_ActionPerformed();
+ okAction();
}
evt.consume();
break;
@Override
public void actionPerformed(ActionEvent e)
{
- btn_ok_ActionPerformed();
+ okAction();
}
});
btn_ok.addKeyListener(new KeyAdapter()
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER)
{
- btn_ok_ActionPerformed();
+ okAction();
}
}
});
}
txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
tooltipText));
- txt_search_ActionPerformed();
+ searchAction();
}
});
}
});
- txt_search.getDocument().addDocumentListener(new DocumentListener()
+ final DeferredTextInputListener listener = new DeferredTextInputListener(
+ 500,
+ new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ searchAction();
+ }
+ }, false);
+ txt_search.getDocument().addDocumentListener(listener);
+ txt_search.addFocusListener(new FocusListener()
{
@Override
- public void insertUpdate(DocumentEvent e)
+ public void focusGained(FocusEvent e)
{
- txt_search_ActionPerformed();
+ listener.start();
}
@Override
- public void removeUpdate(DocumentEvent e)
+ public void focusLost(FocusEvent e)
{
- txt_search_ActionPerformed();
- }
-
- @Override
- public void changedUpdate(DocumentEvent e)
- {
- txt_search_ActionPerformed();
+ listener.stop();
}
});
btn_back.setEnabled(false);
btn_cancel.setEnabled(false);
btn_ok.setEnabled(false);
- previousWantedFields = PDBDocFieldPreferences
- .getSearchSummaryFields().toArray(new PDBDocField[0]);
+ previousWantedFields = getFTSRestClient()
+ .getAllDefaulDisplayedDataColumns()
+ .toArray(new Object[0]);
}
if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
{
btn_cancel.setEnabled(true);
if (wantedFieldsUpdated())
{
- txt_search_ActionPerformed();
+ searchAction();
}
else
{
tabbedPane.addChangeListener(changeListener);
tabbedPane.setPreferredSize(new Dimension(500, 300));
tabbedPane.add(searchTabTitle, scrl_searchResult);
- tabbedPane.add(configureCols, pdbDocFieldPrefs);
+ tabbedPane.add(configureCols, new FTSDataColumnPreferences(
+ PreferenceSource.SEARCH_SUMMARY, getFTSRestClient()));
pnl_actions.add(btn_back);
pnl_actions.add(btn_ok);
mainFrame.setVisible(true);
mainFrame.setContentPane(this);
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), 800, 400);
+ }
+
+ public class DeferredTextInputListener implements DocumentListener
+ {
+ private final Timer swingTimer;
+
+ public DeferredTextInputListener(int timeOut, ActionListener listener,
+ boolean repeats)
+ {
+ swingTimer = new Timer(timeOut, listener);
+ swingTimer.setRepeats(repeats);
+ }
+
+ public void start()
+ {
+ swingTimer.start();
+ }
+
+ public void stop()
+ {
+ swingTimer.stop();
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ swingTimer.restart();
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ swingTimer.restart();
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ swingTimer.restart();
+ }
+
}
public boolean wantedFieldsUpdated()
return true;
}
- return Arrays.equals(PDBDocFieldPreferences.getSearchSummaryFields()
- .toArray(new PDBDocField[0]), previousWantedFields) ? false
+ return Arrays.equals(getFTSRestClient()
+ .getAllDefaulDisplayedDataColumns()
+ .toArray(new Object[0]), previousWantedFields) ? false
: true;
}
}
}
- public JComboBox<PDBDocField> getCmbSearchTarget()
+ public JComboBox<FTSDataColumnI> getCmbSearchTarget()
{
return cmb_searchTarget;
}
return mainFrame;
}
- public abstract void transferToSequenceFetcher(String ids);
+ protected void delayAndEnableActionButtons()
+ {
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ Thread.sleep(1500);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ btn_ok.setEnabled(true);
+ btn_back.setEnabled(true);
+ btn_cancel.setEnabled(true);
+ }
+ }.start();
+ }
+
+ protected void checkForErrors()
+ {
+ lbl_warning.setVisible(false);
+ if (errorWarning.length() > 0)
+ {
+ lbl_loading.setVisible(false);
+ lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ errorWarning.toString()));
+ lbl_warning.setVisible(true);
+ }
+ }
+
+ protected void btn_back_ActionPerformed()
+ {
+ mainFrame.dispose();
+ new SequenceFetcher(progressIdicator);
+ }
+
+ protected void disableActionButtons()
+ {
+ btn_ok.setEnabled(false);
+ btn_back.setEnabled(false);
+ btn_cancel.setEnabled(false);
+ }
+
+ protected void btn_cancel_ActionPerformed()
+ {
+ mainFrame.dispose();
+ }
+
+ /**
+ * Populates search target combo-box options
+ */
+ public void populateCmbSearchTargetOptions()
+ {
+ List<FTSDataColumnI> searchableTargets = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ Collection<FTSDataColumnI> foundFTSTargets = getFTSRestClient()
+ .getSearchableDataColumns();
+ searchableTargets.addAll(foundFTSTargets);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ Collections.sort(searchableTargets, new Comparator<FTSDataColumnI>()
+ {
+ @Override
+ public int compare(FTSDataColumnI o1, FTSDataColumnI o2)
+ {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+
+ for (FTSDataColumnI searchTarget : searchableTargets)
+ {
+ cmb_searchTarget.addItem(searchTarget);
+ }
+ }
+
- public abstract void txt_search_ActionPerformed();
+ public void transferToSequenceFetcher(String ids)
+ {
+ // mainFrame.dispose();
+ seqFetcher.getTextArea().setText(ids);
+ Thread worker = new Thread(seqFetcher);
+ worker.start();
+ }
- public abstract void btn_ok_ActionPerformed();
+ @Override
+ public String getTypedText()
+ {
+ return txt_search.getText().trim();
+ }
- public abstract void btn_back_ActionPerformed();
+ @Override
+ public JTable getResultTable()
+ {
+ return tbl_summary;
+ }
- public abstract void btn_cancel_ActionPerformed();
+ public void reset()
+ {
+ lbl_loading.setVisible(false);
+ errorWarning.setLength(0);
+ lbl_warning.setVisible(false);
+ btn_ok.setEnabled(false);
+ mainFrame.setTitle(getFTSFrameTitle());
+ referesh();
+ tbl_summary.setModel(new DefaultTableModel());
+ tbl_summary.setVisible(false);
+ }
+
+ @Override
+ public void setErrorMessage(String message)
+ {
+ errorWarning.append(message);
+ }
+
+ @Override
+ public void updateSearchFrameTitle(String title)
+ {
+ mainFrame.setTitle(title);
+ }
- public abstract void populateCmbSearchTargetOptions();
+ @Override
+ public void setSearchInProgress(Boolean isSearchInProgress)
+ {
+ lbl_loading.setVisible(isSearchInProgress);
+ }
+ public void referesh()
+ {
+ mainFrame.setTitle(getFTSFrameTitle());
+ }
}
--- /dev/null
+/*
+ * 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.pdb;
+
+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 PDBFTSPanel extends GFTSPanel
+{
+ private static String defaultFTSFrameTitle = MessageManager
+ .getString("label.pdb_sequence_fetcher");
+
+ private String ftsFrameTitle = defaultFTSFrameTitle;
+
+ public PDBFTSPanel(SequenceFetcher seqFetcher)
+ {
+ this.seqFetcher = seqFetcher;
+ this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ .getProgressIndicator();
+ }
+
+
+ @Override
+ public void searchAction()
+ {
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ ftsFrameTitle = defaultFTSFrameTitle;
+ reset();
+ boolean allowEmptySequence = false;
+ if (getTypedText().length() > 0)
+ {
+ setSearchInProgress(true);
+ long startTime = System.currentTimeMillis();
+
+ String searchTarget = ((FTSDataColumnI) cmb_searchTarget
+ .getSelectedItem()).getCode();
+ wantedFields = PDBFTSRestClient.getInstance()
+ .getAllDefaulDisplayedDataColumns();
+ String searchTerm = decodeSearchTerm(txt_search.getText(),
+ searchTarget);
+
+ FTSRestRequest request = new FTSRestRequest();
+ request.setAllowEmptySeq(allowEmptySequence);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("(" + searchTarget + ":");
+ request.setSearchTerm(searchTerm + ")");
+ request.setWantedFields(wantedFields);
+ FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(request);
+ } catch (Exception e)
+ {
+ 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();
+ }
+
+ public static String decodeSearchTerm(String enteredText,
+ String targetField)
+ {
+ String foundSearchTerms = enteredText;
+ StringBuilder foundSearchTermsBuilder = new StringBuilder();
+ if (enteredText.contains(";"))
+ {
+ String[] searchTerms = enteredText.split(";");
+ for (String searchTerm : searchTerms)
+ {
+ if (searchTerm.contains(":"))
+ {
+ foundSearchTermsBuilder.append(targetField).append(":")
+ .append(searchTerm.split(":")[0]).append(" OR ");
+ }
+ else
+ {
+ foundSearchTermsBuilder.append(targetField).append(":")
+ .append(searchTerm).append(" OR ");
+ }
+ }
+ int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
+ foundSearchTerms = foundSearchTermsBuilder.toString();
+ if (foundSearchTerms.contains(" OR "))
+ {
+ foundSearchTerms = foundSearchTerms.substring(
+ targetField.length() + 1, endIndex);
+ }
+ }
+ else if (enteredText.contains(":"))
+ {
+ foundSearchTerms = foundSearchTerms.split(":")[0];
+ }
+ return foundSearchTerms;
+ }
+
+ @Override
+ public void okAction()
+ {
+ // mainFrame.dispose();
+ disableActionButtons();
+ StringBuilder selectedIds = new StringBuilder();
+ HashSet<String> selectedIdsSet = new HashSet<String>();
+ int primaryKeyColIndex = 0;
+ try
+ {
+ primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
+ wantedFields,
+ false);
+ } catch (Exception e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ int[] selectedRows = getResultTable().getSelectedRows();
+ for (int summaryRow : selectedRows)
+ {
+ String idStr = getResultTable().getValueAt(summaryRow,
+ primaryKeyColIndex)
+ .toString();
+ String searchTerm = txt_search.getText();
+ selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
+ }
+
+ 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();
+ }
+
+
+ public static String getPDBIdwithSpecifiedChain(String pdbId,
+ String searchTerm)
+ {
+ String pdbIdWithChainCode = "";
+ if (searchTerm.contains(";"))
+ {
+ String[] foundTerms = searchTerm.split(";");
+ for (String foundTerm : foundTerms)
+ {
+ if (foundTerm.contains(pdbId))
+ {
+ pdbIdWithChainCode = foundTerm;
+ }
+ }
+ }
+ else if (searchTerm.contains(pdbId))
+ {
+ pdbIdWithChainCode = searchTerm;
+ }
+ else
+ {
+ pdbIdWithChainCode = pdbId;
+ }
+ return pdbIdWithChainCode;
+ }
+
+
+
+ @Override
+ public FTSRestClientI getFTSRestClient()
+ {
+ return PDBFTSRestClient.getInstance();
+ }
+
+ @Override
+ public String getFTSFrameTitle()
+ {
+ return ftsFrameTitle;
+ }
+
+
+}
--- /dev/null
+/*
+ * 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.pdb;
+
+import jalview.datamodel.SequenceI;
+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 jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Objects;
+
+import javax.ws.rs.core.MediaType;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.ClientConfig;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+
+/**
+ * A rest client for querying the Search endpoint of the PDB API
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBFTSRestClient extends FTSRestClient
+{
+
+ private static FTSRestClientI instance = null;
+
+ public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
+
+ protected PDBFTSRestClient()
+ {
+ }
+
+ /**
+ * Takes a PDBRestRequest object and returns a response upon execution
+ *
+ * @param pdbRestRequest
+ * the PDBRestRequest instance to be processed
+ * @return the pdbResponse object for the given request
+ * @throws Exception
+ */
+ @Override
+ public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
+ throws Exception
+ {
+ try
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ Client client = Client.create(clientConfig);
+
+ String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(pdbRestRequest
+ .getWantedFields());
+ int responseSize = (pdbRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
+ : pdbRestRequest.getResponseSize();
+ String sortParam = null;
+ if (pdbRestRequest.getFieldToSortBy() == null
+ || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
+ {
+ sortParam = "";
+ }
+ else
+ {
+ if (pdbRestRequest.getFieldToSortBy()
+ .equalsIgnoreCase("Resolution"))
+ {
+ sortParam = pdbRestRequest.getFieldToSortBy()
+ + (pdbRestRequest.isAscending() ? " asc" : " desc");
+ }
+ else
+ {
+ sortParam = pdbRestRequest.getFieldToSortBy()
+ + (pdbRestRequest.isAscending() ? " desc" : " asc");
+ }
+ }
+
+ String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest
+ .getFacetPivot().isEmpty()) ? "" : pdbRestRequest
+ .getFacetPivot();
+ String facetPivotMinCount = String.valueOf(pdbRestRequest
+ .getFacetPivotMinCount());
+
+ String query = pdbRestRequest.getFieldToSearchBy()
+ + pdbRestRequest.getSearchTerm()
+ + (pdbRestRequest.isAllowEmptySeq() ? ""
+ : " AND molecule_sequence:['' TO *]")
+ + (pdbRestRequest.isAllowUnpublishedEntries() ? ""
+ : " AND status:REL");
+
+ // Build request parameters for the REST Request
+ WebResource webResource = null;
+ if (pdbRestRequest.isFacet())
+ {
+ webResource = client.resource(PDB_SEARCH_ENDPOINT)
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", String.valueOf(responseSize))
+ .queryParam("q", query)
+ .queryParam("sort", sortParam).queryParam("facet", "true")
+ .queryParam("facet.pivot", facetPivot)
+ .queryParam("facet.pivot.mincount", facetPivotMinCount);
+ }
+ else
+ {
+ webResource = client.resource(PDB_SEARCH_ENDPOINT)
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", String.valueOf(responseSize))
+ .queryParam("q", query)
+ .queryParam("sort", sortParam);
+ }
+ // Execute the REST request
+ ClientResponse clientResponse = webResource.accept(
+ MediaType.APPLICATION_JSON).get(ClientResponse.class);
+
+ // Get the JSON string from the response object
+ String responseString = clientResponse.getEntity(String.class);
+ // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
+
+ // Check the response status and report exception if one occurs
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = "";
+ if (clientResponse.getStatus() == 400)
+ {
+ errorMessage = parseJsonExceptionString(responseString);
+ throw new Exception(errorMessage);
+ }
+ else
+ {
+ errorMessage = getMessageByHTTPStatusCode(clientResponse
+ .getStatus());
+ throw new Exception(errorMessage);
+ }
+ }
+
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ clientResponse = null;
+ client = null;
+
+ // Process the response and return the result to the caller.
+ return parsePDBJsonResponse(responseString, pdbRestRequest);
+ } catch (Exception e)
+ {
+ String exceptionMsg = e.getMessage();
+ if (exceptionMsg.contains("SocketException"))
+ {
+ // No internet connection
+ throw new Exception(
+ MessageManager
+ .getString("exception.unable_to_detect_internet_connection"));
+ }
+ else if (exceptionMsg.contains("UnknownHostException"))
+ {
+ // The server 'www.ebi.ac.uk' is unreachable
+ throw new Exception(
+ MessageManager
+ .getString("exception.pdb_server_unreachable"));
+ }
+ else
+ {
+ throw e;
+ }
+ }
+ }
+
+ public String getMessageByHTTPStatusCode(int code)
+ {
+ String message = "";
+ switch (code)
+ {
+ case 410:
+ message = MessageManager
+ .getString("exception.pdb_rest_service_no_longer_available");
+ break;
+ case 403:
+ case 404:
+ message = MessageManager.getString("exception.resource_not_be_found");
+ break;
+ case 408:
+ case 409:
+ case 500:
+ case 501:
+ case 502:
+ case 503:
+ case 504:
+ case 505:
+ message = MessageManager.getString("exception.pdb_server_error");
+ break;
+
+ default:
+ break;
+ }
+ return message;
+ }
+
+ /**
+ * Process error response from PDB server if/when one occurs.
+ *
+ * @param jsonResponse
+ * the JSON string containing error message from the server
+ * @return the processed error message from the JSON string
+ */
+ public static String parseJsonExceptionString(String jsonErrorResponse)
+ {
+ StringBuilder errorMessage = new StringBuilder(
+ "\n============= PDB Rest Client RunTime error =============\n");
+
+ try
+ {
+ JSONParser jsonParser = new JSONParser();
+ JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
+ JSONObject errorResponse = (JSONObject) jsonObj.get("error");
+
+ JSONObject responseHeader = (JSONObject) jsonObj
+ .get("responseHeader");
+ JSONObject paramsObj = (JSONObject) responseHeader.get("params");
+ String status = responseHeader.get("status").toString();
+ String message = errorResponse.get("msg").toString();
+ String query = paramsObj.get("q").toString();
+ String fl = paramsObj.get("fl").toString();
+
+ errorMessage.append("Status: ").append(status).append("\n");
+ errorMessage.append("Message: ").append(message).append("\n");
+ errorMessage.append("query: ").append(query).append("\n");
+ errorMessage.append("fl: ").append(fl).append("\n");
+
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return errorMessage.toString();
+ }
+
+ /**
+ * Parses the JSON response string from PDB REST API. The response is dynamic
+ * hence, only fields specifically requested for in the 'wantedFields'
+ * parameter is fetched/processed
+ *
+ * @param pdbJsonResponseString
+ * the JSON string to be parsed
+ * @param pdbRestRequest
+ * the request object which contains parameters used to process the
+ * JSON string
+ * @return
+ */
+ @SuppressWarnings("unchecked")
+ public static FTSRestResponse parsePDBJsonResponse(
+ String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
+ {
+ FTSRestResponse searchResult = new FTSRestResponse();
+ List<FTSData> result = null;
+ try
+ {
+ JSONParser jsonParser = new JSONParser();
+ JSONObject jsonObj = (JSONObject) jsonParser
+ .parse(pdbJsonResponseString);
+
+ JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
+ String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
+ "QTime").toString();
+ int numFound = Integer
+ .valueOf(pdbResponse.get("numFound").toString());
+ if (numFound > 0)
+ {
+ result = new ArrayList<FTSData>();
+ JSONArray docs = (JSONArray) pdbResponse.get("docs");
+ for (Iterator<JSONObject> docIter = docs.iterator(); docIter
+ .hasNext();)
+ {
+ JSONObject doc = docIter.next();
+ result.add(getFTSData(doc, pdbRestRequest));
+ }
+ searchResult.setNumberOfItemsFound(numFound);
+ searchResult.setResponseTime(queryTime);
+ searchResult.setSearchSummary(result);
+ }
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return searchResult;
+ }
+
+ public static FTSData getFTSData(JSONObject pdbJsonDoc,
+ FTSRestRequest request)
+ {
+
+ String primaryKey = null;
+
+ Object[] summaryRowData;
+
+ SequenceI associatedSequence;
+
+ Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
+ SequenceI associatedSeq = request.getAssociatedSequence();
+ int colCounter = 0;
+ summaryRowData = new Object[(associatedSeq != null) ? diplayFields
+ .size() + 1 : diplayFields.size()];
+ if (associatedSeq != null)
+ {
+ associatedSequence = associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
+
+ for (FTSDataColumnI field : diplayFields)
+ {
+ String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
+ : pdbJsonDoc.get(field.getCode()).toString();
+ 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);
+ }
+ }
+ }
+
+ 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());
+ }
+ };
+ }
+
+ @Override
+ public String getColumnDataConfigFileName()
+ {
+ return getResourceFile("/fts/pdb_data_columns.conf");
+ }
+
+
+ public static FTSRestClientI getInstance()
+ {
+ if (instance == null)
+ {
+ instance = new PDBFTSRestClient();
+ }
+ return instance;
+ }
+}
--- /dev/null
+/*
+ * 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.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.ClientConfig;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+
+public class UniProtFTSRestClient extends FTSRestClient
+{
+ private static FTSRestClientI instance = null;
+
+ public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+
+ @Override
+ public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ Client client = Client.create(clientConfig);
+
+ 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("limit", String.valueOf(responseSize))
+ .queryParam("query", query);
+ // Execute the REST request
+ ClientResponse clientResponse = webResource
+ .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
+ String uniProtTabDelimittedResponseString = clientResponse
+ .getEntity(String.class);
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ clientResponse = null;
+ client = null;
+ // System.out.println(">>>>> response : "
+ // + uniProtTabDelimittedResponseString);
+ return parseUniprotResponse(uniProtTabDelimittedResponseString,
+ uniportRestRequest);
+
+ }
+
+ 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());
+ }
+ };
+ }
+
+
+ public static FTSRestClientI getInstance()
+ {
+ if (instance == null)
+ {
+ instance = new UniProtFTSRestClient();
+ }
+ return instance;
+ }
+
+ @Override
+ public String getColumnDataConfigFileName()
+ {
+ return getResourceFile("/fts/uniprot_data_columns.conf");
+ }
+
+}
--- /dev/null
+/*
+ * 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)
+ {
+ this.seqFetcher = seqFetcher;
+ this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ .getProgressIndicator();
+ }
+
+ @Override
+ public void searchAction()
+ {
+ 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 okAction()
+ {
+ 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 UniProtFTSRestClient.getInstance();
+ }
+
+ @Override
+ public String getFTSFrameTitle()
+ {
+ return ftsFrameTitle;
+ }
+
+}
+++ /dev/null
-/*
- * 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.gui;
-
-import jalview.jbgui.GPDBSearchPanel;
-import jalview.jbgui.PDBDocFieldPreferences;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-
-import javax.swing.table.DefaultTableModel;
-
-@SuppressWarnings("serial")
-public class PDBSearchPanel extends GPDBSearchPanel
-{
- private SequenceFetcher seqFetcher;
-
- private IProgressIndicator progressIdicator;
-
- private Collection<PDBDocField> wantedFields;
-
- public PDBSearchPanel(SequenceFetcher seqFetcher)
- {
- this.seqFetcher = seqFetcher;
- this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
- .getProgressIndicator();
- }
-
- /**
- * Action performed when an input is detected on txt_search field.
- */
- @Override
- public void txt_search_ActionPerformed()
- {
- new Thread()
- {
- @Override
- public void run()
- {
- lbl_loading.setVisible(false);
- errorWarning.setLength(0);
- lbl_warning.setVisible(false);
- btn_ok.setEnabled(false);
- boolean allowEmptySequence = false;
- mainFrame.setTitle(MessageManager
- .getString("label.pdb_sequence_getcher"));
- tbl_summary.setModel(new DefaultTableModel());
- if (txt_search.getText().trim().length() > 0)
- {
- lbl_loading.setVisible(true);
- long startTime = System.currentTimeMillis();
-
- String searchTarget = ((PDBDocField) cmb_searchTarget
- .getSelectedItem()).getCode();
-
- wantedFields = PDBDocFieldPreferences.getSearchSummaryFields();
-
- String searchTerm = decodeSearchTerm(txt_search.getText(),
- searchTarget);
-
- PDBRestRequest request = new PDBRestRequest();
- request.setAllowEmptySeq(allowEmptySequence);
- request.setResponseSize(100);
- request.setFieldToSearchBy("(" + searchTarget + ":");
- request.setSearchTerm(searchTerm + ")");
- request.setWantedFields(wantedFields);
- // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
- PDBRestClient pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(request);
- } catch (Exception e)
- {
- // e.printStackTrace();
- errorWarning.append(e.getMessage());
- checkForErrors();
- return;
- }
-
- if (resultList.getSearchSummary() != null)
- {
- tbl_summary.setModel(PDBRestResponse.getTableModel(request,
- resultList.getSearchSummary()));
- }
-
- PDBRestResponse.configureTableColumn(tbl_summary, wantedFields);
-
- long endTime = System.currentTimeMillis();
- int resultSetCount = resultList.getNumberOfItemsFound();
- String result = (resultSetCount > 1) ? MessageManager
- .getString("label.results") : MessageManager
- .getString("label.result");
- mainFrame.setTitle(frameTitle + " - " + resultSetCount + " "
- + result + " (" + (endTime - startTime) + " milli secs)");
- lbl_loading.setVisible(false);
- }
- }
- }.start();
- }
-
- public static String decodeSearchTerm(String enteredText,
- String targetField)
- {
- String foundSearchTerms = enteredText;
- StringBuilder foundSearchTermsBuilder = new StringBuilder();
- if (enteredText.contains(";"))
- {
- String[] searchTerms = enteredText.split(";");
- for (String searchTerm : searchTerms)
- {
- if (searchTerm.contains(":"))
- {
- foundSearchTermsBuilder.append(targetField).append(":")
- .append(searchTerm.split(":")[0]).append(" OR ");
- }
- else
- {
- foundSearchTermsBuilder.append(targetField).append(":")
- .append(searchTerm).append(" OR ");
- }
- }
- int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
- foundSearchTerms = foundSearchTermsBuilder.toString();
- if (foundSearchTerms.contains(" OR "))
- {
- foundSearchTerms = foundSearchTerms.substring(
- targetField.length() + 1, endIndex);
- }
- }
- else if (enteredText.contains(":"))
- {
- foundSearchTerms = foundSearchTerms.split(":")[0];
- }
- return foundSearchTerms;
- }
-
- @Override
- public void btn_ok_ActionPerformed()
- {
- loadSelectedPDBSequencesToAlignment();
- }
-
- @Override
- public void btn_back_ActionPerformed()
- {
- mainFrame.dispose();
- new SequenceFetcher(progressIdicator);
- }
-
- @Override
- public void btn_cancel_ActionPerformed()
- {
- mainFrame.dispose();
- }
-
- @Override
- public void transferToSequenceFetcher(String ids)
- {
- // mainFrame.dispose();
- seqFetcher.textArea.setText(ids);
- Thread worker = new Thread(seqFetcher);
- worker.start();
- }
-
- /**
- * Add the discovered/selected sequences to a target alignment window
- */
- public void loadSelectedPDBSequencesToAlignment()
- {
- // mainFrame.dispose();
- disableActionButtons();
- StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
- int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
- int[] selectedRows = tbl_summary.getSelectedRows();
- for (int summaryRow : selectedRows)
- {
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
- .toString();
- String searchTerm = txt_search.getText();
- selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
- }
-
- for (String selectedId : selectedIdsSet)
- {
- selectedIds.append(selectedId).append(";");
- }
-
- String ids = selectedIds.toString();
- // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
- seqFetcher.textArea.setText(ids);
- Thread worker = new Thread(seqFetcher);
- worker.start();
- delayAndEnableActionButtons();
-
- }
-
- private void disableActionButtons()
- {
- btn_ok.setEnabled(false);
- btn_back.setEnabled(false);
- btn_cancel.setEnabled(false);
- }
-
- private void delayAndEnableActionButtons()
- {
- new Thread()
- {
- @Override
- public void run()
- {
- try
- {
- Thread.sleep(1500);
- } catch (InterruptedException e)
- {
- e.printStackTrace();
- }
- btn_ok.setEnabled(true);
- btn_back.setEnabled(true);
- btn_cancel.setEnabled(true);
- }
- }.start();
- }
-
- public static String getPDBIdwithSpecifiedChain(String pdbId,
- String searchTerm)
- {
- String pdbIdWithChainCode = "";
- if (searchTerm.contains(";"))
- {
- String[] foundTerms = searchTerm.split(";");
- for (String foundTerm : foundTerms)
- {
- if (foundTerm.contains(pdbId))
- {
- pdbIdWithChainCode = foundTerm;
- }
- }
- }
- else if (searchTerm.contains(pdbId))
- {
- pdbIdWithChainCode = searchTerm;
- }
- else
- {
- pdbIdWithChainCode = pdbId;
- }
- return pdbIdWithChainCode;
- }
-
- /**
- * Populates search target combo-box options
- */
- @Override
- public void populateCmbSearchTargetOptions()
- {
- List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
- searchableTargets.add(PDBDocField.PDB_ID);
- searchableTargets.add(PDBDocField.PFAM_ACCESSION);
- searchableTargets.add(PDBDocField.MOLECULE_TYPE);
- searchableTargets.add(PDBDocField.MOLECULE_NAME);
- searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
- searchableTargets.add(PDBDocField.GENE_NAME);
- searchableTargets.add(PDBDocField.GENUS);
- searchableTargets.add(PDBDocField.ALL);
-
- Collections.sort(searchableTargets, new Comparator<PDBDocField>()
- {
- @Override
- public int compare(PDBDocField o1, PDBDocField o2)
- {
- return o1.getName().compareTo(o2.getName());
- }
- });
-
- for (PDBDocField searchTarget : searchableTargets)
- {
- cmb_searchTarget.addItem(searchTarget);
- }
- }
-
- public void checkForErrors()
- {
- lbl_warning.setVisible(false);
- if (errorWarning.length() > 0)
- {
- lbl_loading.setVisible(false);
- lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
- errorWarning.toString()));
- lbl_warning.setVisible(true);
- }
- }
-}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
int debounceTrap = 0;
+ public JTextArea getTextArea()
+ {
+ return textArea;
+ }
+
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
{
debounceTrap++;
String currentSelection = database.getSelectedItem();
- if (!currentSelection.equalsIgnoreCase("pdb"))
- {
- otherSourceAction();
- }
+
if (currentSelection.equalsIgnoreCase("pdb")
&& (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
{
pdbSourceAction();
}
+ else if (currentSelection.equalsIgnoreCase("uniprot")
+ && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+ {
+ uniprotSourceAction();
+ }
+ else
+ {
+ otherSourceAction();
+ }
database.action = -1;
}
});
private void pdbSourceAction()
{
databaseButt.setText(database.getSelectedItem());
- new PDBSearchPanel(this);
+ new PDBFTSPanel(this);
frame.dispose();
}
+ private void uniprotSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new UniprotFTSPanel(this);
+ frame.dispose();
+ }
private void otherSourceAction()
{
try
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import jalview.ws.sifts.SiftsSettings;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet;
+ private Collection<FTSData> discoveredStructuresSet;
- private PDBRestRequest lastPdbRequest;
+ private FTSRestRequest lastPdbRequest;
- private PDBRestClient pdbRestCleint;
+ private FTSRestClientI pdbRestCleint;
private String selectedPdbFileName;
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
- discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ discoveredStructuresSet = new LinkedHashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setFieldToSearchBy("(");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+ tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode())
+ queryBuilder.append("pdb_id")
.append(":")
.append(entry.getId().toLowerCase())
.append(" OR ");
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
queryBuilder
- .append(PDBRestClient.PDBDocField.UNIPROT_ACCESSION
- .getCode()).append(":")
+.append("uniprot_accession").append(":")
.append(getDBRefId(dbRef))
.append(" OR ");
queryBuilder
- .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode())
+.append("uniprot_id")
.append(":")
.append(getDBRefId(dbRef)).append(" OR ");
isUniProtRefsFound = true;
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode())
+ queryBuilder.append("pdb_id")
.append(":").append(getDBRefId(dbRef).toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
public void run()
{
long startTime = System.currentTimeMillis();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
+ Collection<FTSData> filteredResponse = new HashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
{
System.out.println(">>>>>> Filtering with uniprot coverate");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setAssociatedSequence(seq);
}
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
- Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(PDBRestResponse.getTableModel(
+ tbl_summary.setModel(FTSRestResponse.getTableModel(
lastPdbRequest, reorderedStructuresSet));
- PDBRestResponse.configureTableColumn(tbl_summary, wantedFields);
+ FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
if (isStructuresDiscovered())
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
- PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
+ "overall_quality", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
- PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
+ "uniprot_coverage", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Best Resolution",
- PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+ "resolution", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
+ "number_of_protein_chains", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
+ "number_of_bound_molecules", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+ "number_of_polymer_residues", VIEWS_FILTER));
}
cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
VIEWS_ENTER_ID));
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = tbl_summary.getColumn(
- PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+ int pdbIdColIndex = tbl_summary.getColumn("PDB Id")
+ .getModelIndex();
int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
.getModelIndex();
int[] selectedRows = tbl_summary.getSelectedRows();
int[] selectedRows = tbl_local_pdb.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
- int pdbIdColIndex = tbl_local_pdb.getColumn(
- PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+ int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
+ .getModelIndex();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
this.structuresDiscovered = structuresDiscovered;
}
- public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ public Collection<FTSData> getDiscoveredStructuresSet()
{
return discoveredStructuresSet;
}
isValidPBDEntry = false;
if (txt_search.getText().length() > 0)
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.PDB_ID);
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest
.setSearchTerm(txt_search.getText().toLowerCase() + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
*/
package jalview.jbgui;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.JvSwingUtils;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
ypos += lineSpacing;
ypos += lineSpacing;
- PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
- PreferenceSource.PREFERENCES);
+ FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
+ PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
structureTab.add(docFieldPref);
package jalview.jbgui;
import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
-import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.awt.BorderLayout;
import java.awt.CardLayout;
private JTabbedPane pnl_filter = new JTabbedPane();
- private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences(
- PreferenceSource.STRUCTURE_CHOOSER);
+ private FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER, PDBFTSRestClient.getInstance());
- protected PDBDocField[] previousWantedFields;
+ protected FTSDataColumnI[] previousWantedFields;
public GStructureChooser()
{
btn_cancel.setEnabled(false);
btn_view.setVisible(false);
btn_cancel.setVisible(false);
- previousWantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields().toArray(
- new PDBRestClient.PDBDocField[0]);
+ previousWantedFields = PDBFTSRestClient.getInstance()
+ .getAllDefaulDisplayedDataColumns()
+ .toArray(new FTSDataColumnI[0]);
}
if (sourceTabbedPane.getTitleAt(index)
.equals(foundStructureSummary))
return true;
}
- return Arrays.equals(PDBDocFieldPreferences.getStructureSummaryFields()
- .toArray(new PDBRestClient.PDBDocField[0]),
+ return Arrays.equals(
+ PDBFTSRestClient.getInstance()
+ .getAllDefaulDisplayedDataColumns()
+ .toArray(new FTSDataColumnI[0]),
previousWantedFields) ? false : true;
}
+++ /dev/null
-/*
- * 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.ws.dbsources;
-
-import jalview.util.MessageManager;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.List;
-
-import javax.ws.rs.core.MediaType;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-import org.json.simple.parser.ParseException;
-
-import com.sun.jersey.api.client.Client;
-import com.sun.jersey.api.client.ClientResponse;
-import com.sun.jersey.api.client.WebResource;
-import com.sun.jersey.api.client.config.ClientConfig;
-import com.sun.jersey.api.client.config.DefaultClientConfig;
-
-/**
- * A rest client for querying the Search endpoing of the PDB REST API
- *
- * @author tcnofoegbu
- *
- */
-public class PDBRestClient
-{
- public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
-
- private static int DEFAULT_RESPONSE_SIZE = 200;
-
- /**
- * Takes a PDBRestRequest object and returns a response upon execution
- *
- * @param pdbRestRequest
- * the PDBRestRequest instance to be processed
- * @return the pdbResponse object for the given request
- * @throws Exception
- */
- public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
- throws Exception
- {
- try
- {
- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
- String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
- .getWantedFields());
- int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
- : pdbRestRequest.getResponseSize();
- String sortParam = null;
- if (pdbRestRequest.getFieldToSortBy() == null
- || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
- {
- sortParam = "";
- }
- else
- {
- if (pdbRestRequest.getFieldToSortBy()
- .equalsIgnoreCase("Resolution"))
- {
- sortParam = pdbRestRequest.getFieldToSortBy()
- + (pdbRestRequest.isAscending() ? " asc" : " desc");
- }
- else
- {
- sortParam = pdbRestRequest.getFieldToSortBy()
- + (pdbRestRequest.isAscending() ? " desc" : " asc");
- }
- }
-
- String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest
- .getFacetPivot().isEmpty()) ? "" : pdbRestRequest
- .getFacetPivot();
- String facetPivotMinCount = String.valueOf(pdbRestRequest
- .getFacetPivotMinCount());
-
- // Build request parameters for the REST Request
- WebResource webResource = null;
- if (pdbRestRequest.isFacet())
- {
- webResource = client.resource(PDB_SEARCH_ENDPOINT)
- .queryParam("wt", "json").queryParam("fl", wantedFields)
- .queryParam("rows", String.valueOf(responseSize))
- .queryParam("q", pdbRestRequest.getQuery())
- .queryParam("sort", sortParam).queryParam("facet", "true")
- .queryParam("facet.pivot", facetPivot)
- .queryParam("facet.pivot.mincount", facetPivotMinCount);
- }
- else
- {
- webResource = client.resource(PDB_SEARCH_ENDPOINT)
- .queryParam("wt", "json").queryParam("fl", wantedFields)
- .queryParam("rows", String.valueOf(responseSize))
- .queryParam("q", pdbRestRequest.getQuery())
- .queryParam("sort", sortParam);
- }
- // Execute the REST request
- ClientResponse clientResponse = webResource.accept(
- MediaType.APPLICATION_JSON).get(ClientResponse.class);
-
- // Get the JSON string from the response object
- String responseString = clientResponse.getEntity(String.class);
- // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
-
- // Check the response status and report exception if one occurs
- if (clientResponse.getStatus() != 200)
- {
- String errorMessage = "";
- if (clientResponse.getStatus() == 400)
- {
- errorMessage = parseJsonExceptionString(responseString);
- throw new Exception(errorMessage);
- }
- else
- {
- errorMessage = getMessageByHTTPStatusCode(clientResponse
- .getStatus());
- throw new Exception(errorMessage);
- }
- }
-
- // Make redundant objects eligible for garbage collection to conserve
- // memory
- clientResponse = null;
- client = null;
-
- // Process the response and return the result to the caller.
- return parsePDBJsonResponse(responseString, pdbRestRequest);
- } catch (Exception e)
- {
- String exceptionMsg = e.getMessage();
- if (exceptionMsg.contains("SocketException"))
- {
- // No internet connection
- throw new Exception(
- MessageManager
- .getString("exception.unable_to_detect_internet_connection"));
- }
- else if (exceptionMsg.contains("UnknownHostException"))
- {
- // The server 'www.ebi.ac.uk' is unreachable
- throw new Exception(
- MessageManager
- .getString("exception.pdb_server_unreachable"));
- }
- else
- {
- throw e;
- }
- }
- }
-
- public String getMessageByHTTPStatusCode(int code)
- {
- String message = "";
- switch (code)
- {
- case 410:
- message = MessageManager
- .getString("exception.pdb_rest_service_no_longer_available");
- break;
- case 403:
- case 404:
- message = MessageManager.getString("exception.resource_not_be_found");
- break;
- case 408:
- case 409:
- case 500:
- case 501:
- case 502:
- case 503:
- case 504:
- case 505:
- message = MessageManager.getString("exception.pdb_server_error");
- break;
-
- default:
- break;
- }
- return message;
- }
-
- /**
- * Process error response from PDB server if/when one occurs.
- *
- * @param jsonResponse
- * the JSON string containing error message from the server
- * @return the processed error message from the JSON string
- */
- public static String parseJsonExceptionString(String jsonErrorResponse)
- {
- StringBuilder errorMessage = new StringBuilder(
- "\n============= PDB Rest Client RunTime error =============\n");
-
- try
- {
- JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
- JSONObject errorResponse = (JSONObject) jsonObj.get("error");
-
- JSONObject responseHeader = (JSONObject) jsonObj
- .get("responseHeader");
- JSONObject paramsObj = (JSONObject) responseHeader.get("params");
- String status = responseHeader.get("status").toString();
- String message = errorResponse.get("msg").toString();
- String query = paramsObj.get("q").toString();
- String fl = paramsObj.get("fl").toString();
-
- errorMessage.append("Status: ").append(status).append("\n");
- errorMessage.append("Message: ").append(message).append("\n");
- errorMessage.append("query: ").append(query).append("\n");
- errorMessage.append("fl: ").append(fl).append("\n");
-
- } catch (ParseException e)
- {
- e.printStackTrace();
- }
- return errorMessage.toString();
- }
-
- /**
- * Parses the JSON response string from PDB REST API. The response is dynamic
- * hence, only fields specifically requested for in the 'wantedFields'
- * parameter is fetched/processed
- *
- * @param pdbJsonResponseString
- * the JSON string to be parsed
- * @param pdbRestRequest
- * the request object which contains parameters used to process the
- * JSON string
- * @return
- */
- @SuppressWarnings("unchecked")
- public static PDBRestResponse parsePDBJsonResponse(
- String pdbJsonResponseString, PDBRestRequest pdbRestRequest)
- {
- PDBRestResponse searchResult = new PDBRestResponse();
- List<PDBResponseSummary> result = null;
- try
- {
- JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser
- .parse(pdbJsonResponseString);
-
- JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
- String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
- "QTime").toString();
- int numFound = Integer
- .valueOf(pdbResponse.get("numFound").toString());
- if (numFound > 0)
- {
- result = new ArrayList<PDBResponseSummary>();
- JSONArray docs = (JSONArray) pdbResponse.get("docs");
- for (Iterator<JSONObject> docIter = docs.iterator(); docIter
- .hasNext();)
- {
- JSONObject doc = docIter.next();
- result.add(searchResult.new PDBResponseSummary(doc,
- pdbRestRequest));
- }
- searchResult.setNumberOfItemsFound(numFound);
- searchResult.setResponseTime(queryTime);
- searchResult.setSearchSummary(result);
- }
- } catch (ParseException e)
- {
- e.printStackTrace();
- }
- return searchResult;
- }
-
- /**
- * Takes a collection of PDBDocField and converts its 'code' Field values into
- * a comma delimited string.
- *
- * @param pdbDocfields
- * the collection of PDBDocField to process
- * @return the comma delimited string from the pdbDocFields collection
- */
- public static String getPDBDocFieldsAsCommaDelimitedString(
- Collection<PDBDocField> pdbDocfields)
- {
- String result = "";
- if (pdbDocfields != null && !pdbDocfields.isEmpty())
- {
- StringBuilder returnedFields = new StringBuilder();
- for (PDBDocField field : pdbDocfields)
- {
- returnedFields.append(",").append(field.getCode());
- }
- returnedFields.deleteCharAt(0);
- result = returnedFields.toString();
- }
- return result;
- }
-
- /**
- * Determines the column index for 'PDB Id' Fields in the dynamic summary
- * table. The PDB Id serves as a unique identifier for a given row in the
- * summary table
- *
- * @param wantedFields
- * the available table columns in no particular order
- * @return the pdb id field column index
- */
- public static int getPDBIdColumIndex(
- Collection<PDBDocField> wantedFields, boolean hasRefSeq)
- {
-
- // If a reference sequence is attached then start counting from 1 else
- // start from zero
- int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
-
- for (PDBDocField field : wantedFields)
- {
- if (field.equals(PDBDocField.PDB_ID))
- {
- break; // Once PDB Id index is determined exit iteration
- }
- ++pdbFieldIndexCounter;
- }
- return pdbFieldIndexCounter;
- }
-
- public static PDBDocField getPDBDocFieldByCode(String fieldCode)
- throws Exception
- {
- for (PDBDocField curPDBDocField : PDBDocField.values())
- {
- if (curPDBDocField.getCode().equalsIgnoreCase(fieldCode))
- {
- return curPDBDocField;
- }
- }
- throw new Exception("PDB doc Field not found!");
- }
-
- /**
- * This enum represents the fields available in the PDB JSON response
- *
- */
- public enum PDBDocField
- {
- PDB_ID("PDB Id", "pdb_id", Group.CROSS_REFS), TITLE(
- "Title",
- "title", Group.MISCELLENOUS),
- MOLECULE_NAME("Molecule",
- "molecule_name",
- Group.NAMES_AND_TAXONOMY), MOLECULE_TYPE(
- "Molecule Type", "molecule_type", Group.NAMES_AND_TAXONOMY), MOLECULE_SEQUENCE(
- "Sequence", "molecule_sequence", Group.MISCELLENOUS), PFAM_ACCESSION(
- "PFAM Accession", "pfam_accession",
- Group.CROSS_REFS), PFAM_NAME(
- "PFAM Name", "pfam_name", Group.NAMES_AND_TAXONOMY), INTERPRO_NAME(
- "InterPro Name", "interpro_name", Group.NAMES_AND_TAXONOMY), INTERPRO_ACCESSION(
- "InterPro Accession", "interpro_accession",
- Group.CROSS_REFS), UNIPROT_ID("UniProt Id",
- "uniprot_id", Group.CROSS_REFS), UNIPROT_ACCESSION(
- "UniProt Accession", "uniprot_accession",
- Group.CROSS_REFS),
-
- UNIPROT_COVERAGE(
- "UniProt Coverage", "uniprot_coverage", Group.MISCELLENOUS), UNIPROT_FEATURES(
- "Uniprot Features", "uniprot_features", Group.MISCELLENOUS), R_FACTOR(
-"R Factor",
- "r_factor", Group.QUALITY_MEASURES), RESOLUTION("Resolution",
- "resolution", Group.QUALITY_MEASURES), DATA_QUALITY(
- "Data Quality", "data_quality", Group.QUALITY_MEASURES), OVERALL_QUALITY(
- "Overall Quality", "overall_quality", Group.QUALITY_MEASURES), POLYMER_COUNT(
- "Number of Polymers", "number_of_polymers", Group.MISCELLENOUS), PROTEIN_CHAIN_COUNT(
- "Number of Protein Chains", "number_of_protein_chains",
- Group.MISCELLENOUS), BOUND_MOLECULE_COUNT(
- "Number of Bound Molecule", "number_of_bound_molecules",
- Group.MISCELLENOUS), POLYMER_RESIDUE_COUNT(
- "Number of Polymer Residue", "number_of_polymer_residues",
- Group.MISCELLENOUS), GENUS("GENUS", "genus",
- Group.NAMES_AND_TAXONOMY), GENE_NAME("Gene Name", "gene_name",
- Group.NAMES_AND_TAXONOMY), EXPERIMENTAL_METHOD(
- "Experimental Method", "experimental_method",
- Group.PROCEDURE_AND_SOFTWARE), GO_ID("GO Id", "go_id",
- Group.CROSS_REFS), ASSEMBLY_ID("Assembly Id",
- "assembly_id", Group.CROSS_REFS), ASSEMBLY_FORM(
- "Assembly Form", "assembly_form", Group.MISCELLENOUS), ASSEMBLY_TYPE(
- "Assembly Type", "assembly_type", Group.MISCELLENOUS), SPACE_GROUP(
- "Space Group", "spacegroup", Group.MISCELLENOUS), CATH_CODE(
- "Cath Code", "cath_code", Group.CROSS_REFS), TAX_ID(
- "Tax Id", "tax_id", Group.CROSS_REFS), TAX_QUERY(
- "Tax Query", "tax_query", Group.CROSS_REFS), INTERACTING_ENTITY_ID(
- "Interacting Entity Id", "interacting_entity_id",
- Group.CROSS_REFS), INTERACTING_MOLECULES(
- "Interacting Molecules", "interacting_molecules",
- Group.MISCELLENOUS), PUBMED_ID("Pubmed Id", "pubmed_id",
- Group.CROSS_REFS), STATUS("Status", "status",
- Group.MISCELLENOUS), MODEL_QUALITY("Model Quality",
- "model_quality", Group.QUALITY_MEASURES), PIVOT_RESOLUTION(
- "Pivot Resolution", "pivot_resolution", Group.QUALITY_MEASURES), DATA_REDUCTION_SOFTWARE(
- "Data reduction software", "data_reduction_software",
- Group.PROCEDURE_AND_SOFTWARE), MAX_OBSERVED_RES(
- "Max observed residues",
- "max_observed_residues", Group.MISCELLENOUS), ORG_SCI_NAME(
- "Organism scientific name", "organism_scientific_name",
- Group.NAMES_AND_TAXONOMY), SUPER_KINGDOM("Super kingdom",
- "superkingdom", Group.NAMES_AND_TAXONOMY), RANK("Rank", "rank",
- Group.NAMES_AND_TAXONOMY), CRYSTALLISATION_PH(
- "Crystallisation Ph",
- "crystallisation_ph", Group.MISCELLENOUS), BIOLOGICAL_FUNCTION(
- "Biological Function", "biological_function",
- Group.MISCELLENOUS), BIOLOGICAL_PROCESS("Biological Process",
- "biological_process", Group.MISCELLENOUS), BIOLOGICAL_CELL_COMPONENT(
- "Biological Cell Component", "biological_cell_component",
- Group.MISCELLENOUS), COMPOUND_NAME("Compound Name",
- "compound_name", Group.NAMES_AND_TAXONOMY), COMPOUND_ID(
- "Compound Id", "compound_id", Group.CROSS_REFS), COMPOUND_WEIGHT(
- "Compound Weight", "compound_weight", Group.MISCELLENOUS), COMPOUND_SYSTEMATIC_NAME(
- "Compound Systematic Name", "compound_systematic_name",
- Group.NAMES_AND_TAXONOMY), INTERACTING_LIG(
- "Interacting Ligands",
- "interacting_ligands", Group.MISCELLENOUS), JOURNAL("Journal",
- "journal", Group.MISCELLENOUS), ALL_AUTHORS("All Authors",
- "all_authors", Group.MISCELLENOUS), EXPERIMENTAL_DATA_AVAILABLE(
- "Experiment Data Available", "experiment_data_available",
- Group.MISCELLENOUS), DIFFRACTION_PROTOCOL(
- "Diffraction Protocol", "diffraction_protocol",
- Group.PROCEDURE_AND_SOFTWARE), REFINEMENT_SOFTWARE(
- "Refinement Software", "refinement_software",
- Group.PROCEDURE_AND_SOFTWARE), STRUCTURE_DETERMINATION_METHOD(
- "Structure Determination Method",
- "structure_determination_method", Group.PROCEDURE_AND_SOFTWARE), SYNCHROTON_SITE(
- "Synchrotron Site", "synchrotron_site", Group.MISCELLENOUS), SAMPLE_PREP_METHOD(
- "Sample Preparation Method", "sample_preparation_method",
- Group.PROCEDURE_AND_SOFTWARE), ENTRY_AUTHORS("Entry Authors",
- "entry_authors", Group.MISCELLENOUS), CITATION_TITLE(
- "Citation Title", "citation_title", Group.MISCELLENOUS), STRUCTURE_SOLUTION_SOFTWARE(
- "Structure Solution Software", "structure_solution_software",
- Group.PROCEDURE_AND_SOFTWARE), ENTRY_ENTITY("Entry Entity",
- "entry_entity", Group.MISCELLENOUS), R_FREE("R Free", "r_free",
- Group.QUALITY_MEASURES), NO_OF_POLYMER_ENTITIES(
- "Number of Polymer Entities", "number_of_polymer_entities",
- Group.MISCELLENOUS), NO_OF_BOUND_ENTITIES(
- "Number of Bound Entities", "number_of_bound_entities",
- Group.MISCELLENOUS), CRYSTALLISATION_RESERVOIR(
- "Crystallisation Reservoir", "crystallisation_reservoir",
- Group.MISCELLENOUS), DATA_SCALING_SW("Data Scalling Software",
- "data_scaling_software", Group.PROCEDURE_AND_SOFTWARE), DETECTOR(
- "Detector", "detector", Group.MISCELLENOUS), DETECTOR_TYPE(
- "Detector Type", "detector_type", Group.MISCELLENOUS), MODIFIED_RESIDUE_FLAG(
- "Modified Residue Flag", "modified_residue_flag",
- Group.MISCELLENOUS), NUMBER_OF_COPIES("Number of Copies",
- "number_of_copies", Group.MISCELLENOUS), STRUCT_ASYM_ID(
- "Struc Asym Id", "struct_asym_id",
- Group.CROSS_REFS), HOMOLOGUS_PDB_ENTITY_ID(
- "Homologus PDB Entity Id", "homologus_pdb_entity_id",
- Group.CROSS_REFS), MOLECULE_SYNONYM(
- "Molecule Synonym",
- "molecule_synonym", Group.MISCELLENOUS), DEPOSITION_SITE(
- "Deposition Site", "deposition_site", Group.MISCELLENOUS), SYNCHROTRON_BEAMLINE(
- "Synchrotron Beamline", "synchrotron_beamline",
- Group.MISCELLENOUS), ENTITY_ID("Entity Id", "entity_id",
- Group.CROSS_REFS), BEAM_SOURCE_NAME(
- "Beam Source Name",
- "beam_source_name",
- Group.NAMES_AND_TAXONOMY), PROCESSING_SITE(
- "Processing Site", "processing_site", Group.MISCELLENOUS), ENTITY_WEIGHT(
- "Entity Weight", "entity_weight", Group.MISCELLENOUS), VERSION(
- "Version", "_version_", Group.MISCELLENOUS), ALL("ALL", "text",
- Group.MISCELLENOUS);
-
- public enum Group
- {
- DATE_OF("Date Of", 5), NAMES_AND_TAXONOMY("Names & Taxonomy", 3),
- MISCELLENOUS("Miscellenous", 6), QUALITY_MEASURES("Quality Measures",
- 1), CROSS_REFS("Cross References", 2),
- PROCEDURE_AND_SOFTWARE("Procedures & Softwares", 4);
-
- Group(String name, int sortOrder)
- {
- this.name = name;
- this.sortOrder = sortOrder;
- }
-
- private String name;
-
- private int sortOrder;
-
- public String getName()
- {
- return this.name;
- }
-
- public int getSortOrder()
- {
- return sortOrder;
- }
-
- @Override
- public String toString()
- {
- return this.name;
- }
- };
- private String name;
-
- private String code;
-
- private Group group;
-
- PDBDocField(String name, String code, Group group)
- {
- this.name = name;
- this.code = code;
- this.group = group;
- }
-
- public String getName()
- {
- return name;
- }
-
- public String getCode()
- {
- return code;
- }
-
- public Group getGroup()
- {
- return group;
- }
-
- @Override
- public String toString()
- {
- return name;
- }
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.ws.uimodel;
-
-import jalview.datamodel.SequenceI;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField.Group;
-
-import java.util.Collection;
-import java.util.Objects;
-
-import javax.swing.JTable;
-import javax.swing.table.DefaultTableModel;
-
-import org.json.simple.JSONObject;
-
-/**
- * Represents the response model produced by the PDBRestClient upon successful
- * execution of a given request
- *
- * @author tcnofoegbu
- *
- */
-public class PDBRestResponse
-{
- private int numberOfItemsFound;
-
- private String responseTime;
-
- private Collection<PDBResponseSummary> searchSummary;
-
- public int getNumberOfItemsFound()
- {
- return numberOfItemsFound;
- }
-
- public void setNumberOfItemsFound(int itemFound)
- {
- this.numberOfItemsFound = itemFound;
- }
-
- public String getResponseTime()
- {
- return responseTime;
- }
-
- public void setResponseTime(String responseTime)
- {
- this.responseTime = responseTime;
- }
-
- public Collection<PDBResponseSummary> getSearchSummary()
- {
- return searchSummary;
- }
-
- public void setSearchSummary(Collection<PDBResponseSummary> searchSummary)
- {
- this.searchSummary = searchSummary;
- }
-
- /**
- * Convenience method to obtain a Table model for a given summary List based
- * on the request parameters
- *
- * @param request
- * the PDBRestRequest object which holds useful information for
- * creating a table model
- * @param summariesList
- * the summary list which contains the data for populating the
- * table's rows
- * @return the table model which was dynamically generated
- */
- public static DefaultTableModel getTableModel(PDBRestRequest request,
- Collection<PDBResponseSummary> summariesList)
- {
- final PDBDocField[] cols = request.getWantedFields().toArray(
- new PDBDocField[0]);
- final int colOffset = request.getAssociatedSequence() == null ? 0 : 1;
- DefaultTableModel tableModel = new DefaultTableModel()
- {
- @Override
- public boolean isCellEditable(int row, int column)
- {
- return false;
- }
-
- @Override
- public Class<?> getColumnClass(int columnIndex)
- {
- if (colOffset == 1 && columnIndex == 0)
- {
- return String.class;
- }
- if (cols[columnIndex - colOffset].getGroup().getName()
- .equalsIgnoreCase(Group.QUALITY_MEASURES.getName()))
- {
- return Double.class;
- }
- return String.class;
- }
-
- };
- if (request.getAssociatedSequence() != null)
- {
- tableModel.addColumn("Ref Sequence"); // Create sequence column header if
- // exists in the request
- }
- for (PDBDocField field : request.getWantedFields())
- {
- tableModel.addColumn(field.getName()); // Create sequence column header if
- // exists in the request
- }
-
- for (PDBResponseSummary res : summariesList)
- {
- tableModel.addRow(res.getSummaryData()); // Populate table rows with
- // summary list
- }
-
- return tableModel;
- }
-
- /**
- * Model for a unique response summary
- *
- */
- public class PDBResponseSummary
- {
- private String pdbId;
-
- private Object[] summaryRowData;
-
- private SequenceI associatedSequence;
-
- public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
- {
- Collection<PDBDocField> diplayFields = request.getWantedFields();
- SequenceI associatedSeq = request.getAssociatedSequence();
- int colCounter = 0;
- summaryRowData = new Object[(associatedSeq != null) ? diplayFields
- .size() + 1 : diplayFields.size()];
- if (associatedSeq != null)
- {
- this.associatedSequence = associatedSeq;
- summaryRowData[0] = associatedSequence;
- colCounter = 1;
- }
-
- for (PDBDocField field : diplayFields)
- {
- String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
- : pdbJsonDoc.get(field.getCode()).toString();
- if (field.equals(PDBDocField.PDB_ID))
- {
- this.pdbId = fieldData;
- summaryRowData[colCounter++] = this.pdbId;
- }
- else
- {
- if (field.getGroup().getName()
- .equals(Group.QUALITY_MEASURES.getName()))
- {
- try
- {
- if (fieldData == null || fieldData.isEmpty())
- {
- summaryRowData[colCounter++] = null;
- }
- else
- {
- Double value = Double.valueOf(fieldData);
- summaryRowData[colCounter++] = value;
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- System.out.println("offending value:" + fieldData);
- summaryRowData[colCounter++] = 0.0;
- }
- }else{
- summaryRowData[colCounter++] = (fieldData == null || fieldData
- .isEmpty()) ? null : fieldData;
- }
- }
- }
- }
-
- public Object getPdbId()
- {
- return pdbId;
- }
-
- public void setPdbId(String pdbId)
- {
- this.pdbId = pdbId;
- }
-
- public Object[] getSummaryData()
- {
- return summaryRowData;
- }
-
- public void setSummaryData(Object[] summaryData)
- {
- this.summaryRowData = summaryData;
- }
-
- /**
- * Returns a string representation of this object;
- */
- @Override
- public String toString()
- {
- StringBuilder summaryFieldValues = new StringBuilder();
- for (Object summaryField : summaryRowData)
- {
- 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(this.pdbId, this.toString());
- }
-
- /**
- * Indicates whether some object is equal to this one
- */
- @Override
- public boolean equals(Object that)
- {
- if (!(that instanceof PDBResponseSummary))
- {
- return false;
- }
- PDBResponseSummary another = (PDBResponseSummary) that;
- return this.toString().equals(another.toString());
- }
-
- }
-
- public static void configureTableColumn(JTable tbl_summary,
- Collection<PDBDocField> wantedFields)
- {
- try
- {
- // wait for table model initialisation to complete
- Thread.sleep(1200);
- } catch (InterruptedException e1)
- {
- e1.printStackTrace();
- }
- for (PDBDocField wantedField : wantedFields)
- {
- try
- {
- if (wantedField.equals(PDBDocField.PDB_ID))
- {
- tbl_summary.getColumn(wantedField.getName()).setMinWidth(40);
- tbl_summary.getColumn(wantedField.getName()).setMaxWidth(60);
- tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(45);
- }
- else if (wantedField.equals(PDBDocField.TITLE))
- {
- tbl_summary.getColumn(wantedField.getName()).setMinWidth(300);
- tbl_summary.getColumn(wantedField.getName()).setMaxWidth(1000);
- tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(400);
- }
- else if (wantedField.getGroup() == Group.QUALITY_MEASURES)
- {
- tbl_summary.getColumn(wantedField.getName()).setMinWidth(50);
- tbl_summary.getColumn(wantedField.getName()).setMaxWidth(150);
- tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(85);
- }
- else
- {
- tbl_summary.getColumn(wantedField.getName()).setMinWidth(50);
- tbl_summary.getColumn(wantedField.getName()).setMaxWidth(400);
- tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(95);
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- }
- }
-}
--- /dev/null
+package jalview.fts.core;
+
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class FTSRestClientTest
+{
+ private FTSRestClient ftsRestClient;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setup()
+ {
+ ftsRestClient = new FTSRestClient()
+ {
+
+ @Override
+ public String getColumnDataConfigFileName()
+ {
+ return "examples/testdata/test_fts_data_columns.conf";
+ }
+
+ @Override
+ public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
+ throws Exception
+ {
+ return null;
+ }
+ };
+ }
+
+ @Test(groups = { "Functional" })
+ public void getPrimaryKeyColumIndexTest()
+ {
+ Collection<FTSDataColumnI> wantedFields = ftsRestClient
+ .getAllDefaulDisplayedDataColumns();
+ int foundIndex = -1;
+ try
+ {
+ Assert.assertEquals(foundIndex, -1);
+ foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
+ false);
+ Assert.assertEquals(foundIndex, 0);
+ foundIndex = ftsRestClient
+ .getPrimaryKeyColumIndex(wantedFields, true);
+ Assert.assertEquals(foundIndex, 1);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getAllDefaulDisplayedDataColumns()
+ {
+ Assert.assertNotNull(ftsRestClient.getAllDefaulDisplayedDataColumns());
+ Assert.assertTrue(!ftsRestClient.getAllDefaulDisplayedDataColumns()
+ .isEmpty());
+ Assert.assertEquals(ftsRestClient.getAllDefaulDisplayedDataColumns()
+ .size(), 6);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnsFieldsAsCommaDelimitedString()
+ {
+ Collection<FTSDataColumnI> wantedFields = ftsRestClient
+ .getAllDefaulDisplayedDataColumns();
+ String actual = ftsRestClient
+ .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
+ Assert.assertEquals(actual,
+ "entry name,protein names,genes,organism,created,last-modified");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnsFieldsAsTabDelimitedString()
+ {
+ Collection<FTSDataColumnI> wantedFields = ftsRestClient
+ .getAllDefaulDisplayedDataColumns();
+ String actual = ftsRestClient
+ .getDataColumnsFieldsAsTabDelimitedString(wantedFields);
+ Assert.assertEquals(actual,
+ "Entry Name\tProtein names\tGene Names\tOrganism\tDate of creation\tDate of last modification");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getAllFTSDataColumns()
+ {
+ Collection<FTSDataColumnI> allFields = ftsRestClient
+ .getAllFTSDataColumns();
+ Assert.assertNotNull(allFields);
+ Assert.assertEquals(allFields.size(), 116);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getSearchableDataColumns()
+ {
+ Collection<FTSDataColumnI> searchalbeFields = ftsRestClient
+ .getSearchableDataColumns();
+ Assert.assertNotNull(searchalbeFields);
+ Assert.assertEquals(searchalbeFields.size(), 28);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getPrimaryKeyColumn()
+ {
+ FTSDataColumnI expectedPKColumn;
+ try
+ {
+ expectedPKColumn = ftsRestClient
+ .getDataColumnByNameOrCode("Entry Name");
+ Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
+ Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
+ expectedPKColumn);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnByNameOrCode()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("genes");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getName(), "Gene Names");
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnGroupById()
+ {
+ FTSDataColumnGroupI foundDataColGroup;
+ try
+ {
+ foundDataColGroup = ftsRestClient.getDataColumnGroupById("g3");
+ Assert.assertNotNull(foundDataColGroup);
+ Assert.assertEquals(foundDataColGroup.getName(), "Names & Taxonomy");
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDefaultResponsePageSize()
+ {
+ int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
+ Assert.assertEquals(defaultResSize, 100);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getColumnMinWidthTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("Protein names");
+ Assert.assertNotNull(foundDataCol);
+ int actualColMinWidth = foundDataCol.getMinWidth();
+ Assert.assertEquals(actualColMinWidth, 300);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getColumnMaxWidthTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("Protein names");
+ Assert.assertNotNull(foundDataCol);
+ int actualColMinWidth = foundDataCol.getMaxWidth();
+ Assert.assertEquals(actualColMinWidth, 1500);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getColumnPreferredWidthTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("Protein names");
+ Assert.assertNotNull(foundDataCol);
+ int actualColMinWidth = foundDataCol.getPreferredWidth();
+ Assert.assertEquals(actualColMinWidth, 500);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getColumnClassTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("Protein names");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getDataColumnClass(), String.class);
+ foundDataCol = ftsRestClient.getDataColumnByNameOrCode("length");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getDataColumnClass(), Integer.class);
+ // foundDataCol = ftsRestClient.getDataColumnByNameOrCode("length");
+ // Assert.assertNotNull(foundDataCol);
+ // Assert.assertEquals(foundDataCol.getDataColumnClass(), Double.class);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void coverageForEqualsAndHashFunction()
+ {
+ Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
+ Collection<FTSDataColumnI> searchableCols = ftsRestClient
+ .getSearchableDataColumns();
+ for (FTSDataColumnI foundCol : searchableCols)
+ {
+ uniqueSet.add(foundCol);
+ uniqueSet.add(foundCol);
+ }
+ Assert.assertTrue(!uniqueSet.isEmpty());
+ Assert.assertEquals(uniqueSet.size(), 28);
+ }
+
+ @Test(groups = { "Functional" })
+ public void coverageForMiscellaneousBranches()
+ {
+ String actual = ftsRestClient.getPrimaryKeyColumn().toString();
+ Assert.assertEquals(actual, "Entry Name");
+
+ String actualGroupStr;
+ try
+ {
+ actualGroupStr = ftsRestClient.getDataColumnGroupById("g4")
+ .toString();
+ Assert.assertEquals(actualGroupStr, "Procedures & Softwares");
+ actualGroupStr = ftsRestClient.getDataColumnGroupById(
+ "unavailable group").toString();
+ } catch (Exception e)
+ {
+ Assert.assertTrue(true);
+ }
+
+ String actualResourseFile = ftsRestClient
+ .getResourceFile("fts/uniprot_data_columns.conf");
+ Assert.assertNotNull(actualResourseFile);
+ Assert.assertTrue(actualResourseFile.length() > 31);
+ }
+
+ @Test(groups = { "Functional" }, expectedExceptions = Exception.class)
+ public void coverageForExceptionBranches() throws Exception
+ {
+ try
+ {
+ ftsRestClient.getDataColumnByNameOrCode("unavailable column");
+ } catch (Exception e)
+ {
+ System.out.println(e.getMessage());
+ String expectedMessage = "Couldn't find data column with name : unavailable column";
+ Assert.assertEquals(e.getMessage(), expectedMessage);
+ }
+ try
+ {
+ ftsRestClient.getDataColumnGroupById("unavailable column group Id");
+ } catch (Exception e)
+ {
+ System.out.println(e.getMessage());
+ String expectedMessage = "Couldn't find data column group with id : unavailable column group Id";
+ Assert.assertEquals(e.getMessage(), expectedMessage);
+ }
+
+ ftsRestClient.getDataColumnByNameOrCode("unavailable column");
+
+ ftsRestClient.getResourceFile("unavailable resource file");
+
+ }
+
+}
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.gui;
+package jalview.fts.service.pdb;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.fts.service.pdb.PDBFTSPanel;
+
import javax.swing.JInternalFrame;
import javax.swing.JTextField;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-public class PDBSearchPanelTest
+public class PDBFTSPanelTest
{
@BeforeMethod(alwaysRun = true)
@Test(groups = { "Functional" })
public void populateCmbSearchTargetOptionsTest()
{
- PDBSearchPanel searchPanel = new PDBSearchPanel(null);
+ PDBFTSPanel searchPanel = new PDBFTSPanel(null);
assertTrue(searchPanel.getCmbSearchTarget().getItemCount() > 0);
searchPanel.populateCmbSearchTargetOptions();
}
public void testDecodeSearchTerm()
{
String expectedString = "1xyz OR text:2xyz OR text:3xyz";
- String outcome = PDBSearchPanel.decodeSearchTerm("1xyz:A;2xyz;3xyz",
+ String outcome = PDBFTSPanel.decodeSearchTerm("1xyz:A;2xyz;3xyz",
"text");
// System.out.println("1 >>>>>>>>>>> " + outcome);
assertEquals(expectedString, outcome);
expectedString = "1xyz";
- outcome = PDBSearchPanel.decodeSearchTerm("1xyz", "text");
+ outcome = PDBFTSPanel.decodeSearchTerm("1xyz", "text");
// System.out.println("2 >>>>>>>>>>> " + outcome);
assertEquals(expectedString, outcome);
}
{
String expectedString = "1xyz:A";
- String outcome = PDBSearchPanel.getPDBIdwithSpecifiedChain("1xyz",
+ String outcome = PDBFTSPanel.getPDBIdwithSpecifiedChain("1xyz",
"2xyz;3xyz;1xyz:A");
System.out.println("1 >>>>>>>>>>> " + outcome);
assertEquals(expectedString, outcome);
expectedString = "2xyz";
- outcome = PDBSearchPanel.getPDBIdwithSpecifiedChain("2xyz",
+ outcome = PDBFTSPanel.getPDBIdwithSpecifiedChain("2xyz",
"1xyz:A;2xyz;3xyz");
System.out.println("2 >>>>>>>>>>> " + outcome);
assertEquals(expectedString, outcome);
expectedString = "2xyz:A";
- outcome = PDBSearchPanel.getPDBIdwithSpecifiedChain("2xyz", "2xyz:A");
+ outcome = PDBFTSPanel.getPDBIdwithSpecifiedChain("2xyz", "2xyz:A");
System.out.println("3 >>>>>>>>>>> " + outcome);
assertEquals(expectedString, outcome);
}
@Test(groups = { "Network", "External" }, timeOut = 7000)
public void txt_search_ActionPerformedTest()
{
- PDBSearchPanel searchPanel = new PDBSearchPanel(null);
+ PDBFTSPanel searchPanel = new PDBFTSPanel(null);
JInternalFrame mainFrame = searchPanel.getMainFrame();
JTextField txt_search = searchPanel.getTxtSearch();
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws.dbsources;
+package jalview.fts.service.pdb;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
import java.io.BufferedReader;
import java.io.FileReader;
import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
-public class PDBRestClientTest
+public class PDBFTSRestClientTest
{
@BeforeMethod(alwaysRun = true)
@Test(groups = { "External", "Network" })
public void executeRequestTest()
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
-
- PDBRestRequest request = new PDBRestRequest();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("molecule_type"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("pdb_id"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("genus"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("gene_name"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("title"));
+ } catch (Exception e1)
+ {
+ e1.printStackTrace();
+ }
+
+ FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
request.setResponseSize(100);
request.setFieldToSearchBy("text:");
request.setSearchTerm("abc");
request.setWantedFields(wantedFields);
- PDBRestResponse response;
+ FTSRestResponse response;
try
{
- response = new PDBRestClient().executeRequest(request);
+ response = PDBFTSRestClient.getInstance().executeRequest(request);
} catch (Exception e)
{
e.printStackTrace();
@Test(groups = { "Functional" })
public void getPDBDocFieldsAsCommaDelimitedStringTest()
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("molecule_type"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("pdb_id"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("genus"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("gene_name"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("title"));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
String expectedResult = "molecule_type,pdb_id,genus,gene_name,title";
- String actualResult = PDBRestClient
- .getPDBDocFieldsAsCommaDelimitedString(wantedFields);
+ String actualResult = PDBFTSRestClient.getInstance()
+ .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
assertEquals("", expectedResult, actualResult);
}
@Test(groups = { "External, Network" })
public void parsePDBJsonExceptionStringTest()
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
-
- PDBRestRequest request = new PDBRestRequest();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("molecule_type"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("pdb_id"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("genus"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("gene_name"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("title"));
+ } catch (Exception e1)
+ {
+ e1.printStackTrace();
+ }
+
+ FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
request.setResponseSize(100);
request.setFieldToSearchBy("text:");
e.printStackTrace();
}
- String parsedErrorResponse = PDBRestClient
+ String parsedErrorResponse = PDBFTSRestClient
.parseJsonExceptionString(jsonErrorResponse);
String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
expectedExceptions = Exception.class)
public void testForExpectedRuntimeException() throws Exception
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.PDB_ID);
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("pdb_id"));
- PDBRestRequest request = new PDBRestRequest();
+ FTSRestRequest request = new FTSRestRequest();
request.setFieldToSearchBy("text:");
request.setSearchTerm("abc OR text:go:abc");
request.setWantedFields(wantedFields);
- new PDBRestClient().executeRequest(request);
+ PDBFTSRestClient.getInstance().executeRequest(request);
}
@Test(groups = { "External" })
public void parsePDBJsonResponseTest()
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
-
- PDBRestRequest request = new PDBRestRequest();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("molecule_type"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("pdb_id"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("genus"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("gene_name"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("title"));
+ } catch (Exception e1)
+ {
+ e1.printStackTrace();
+ }
+
+ FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
request.setWantedFields(wantedFields);
{
e.printStackTrace();
}
- PDBRestResponse response = PDBRestClient.parsePDBJsonResponse(
+ FTSRestResponse response = PDBFTSRestClient.parsePDBJsonResponse(
jsonString, request);
assertTrue(response.getSearchSummary() != null);
assertTrue(response.getNumberOfItemsFound() == 931);
@Test(groups = { "Functional" })
public void getPDBIdColumIndexTest()
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
- wantedFields.add(PDBDocField.PDB_ID);
- assertEquals(5, PDBRestClient.getPDBIdColumIndex(wantedFields, true));
- assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("molecule_type"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("genus"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("gene_name"));
+ wantedFields.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("title"));
+ wantedFields
+.add(PDBFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("pdb_id"));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ try
+ {
+ assertEquals(5,
+ PDBFTSRestClient.getInstance()
+ .getPrimaryKeyColumIndex(wantedFields, true));
+ assertEquals(4,
+ PDBFTSRestClient.getInstance()
+ .getPrimaryKeyColumIndex(wantedFields, false));
+ } catch (Exception e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
@Test(groups = { "External" })
// Build request parameters for the REST Request
WebResource webResource = client
- .resource(PDBRestClient.PDB_SEARCH_ENDPOINT)
+ .resource(PDBFTSRestClient.PDB_SEARCH_ENDPOINT)
.queryParam("wt", "json").queryParam("rows", String.valueOf(1))
.queryParam("q", "text:abc AND molecule_sequence:['' TO *]");
JSONObject pdbJsonDoc = docIter.next();
- for (PDBDocField field : PDBDocField.values())
+ for (FTSDataColumnI field : PDBFTSRestClient.getInstance()
+ .getAllFTSDataColumns())
{
- if (field == PDBDocField.ALL)
+ if (field.getName().equalsIgnoreCase("ALL"))
{
continue;
}
sc.populateFilterComboBox();
try
{
- Thread.sleep(1000);
+ Thread.sleep(2000);
} catch (InterruptedException e)
{
e.printStackTrace();
git://source.jalview.org / jalview.git / commitdiff