X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPDBRestClient.java;h=dbdb01deae6b07d97ce1f6aca733f179a1269b56;hb=refs%2Fheads%2Ffeatures%2FJAL-1919_mmCIF-Support;hp=7a5d2412de688c834e812098492012b1800ca6ad;hpb=3c24b4f3503fb8dc9183383369284d7ea0adfd11;p=jalview.git diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index 7a5d241..dbdb01d 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -371,11 +371,12 @@ public class PDBRestClient { PDB_ID("PDB Id", "pdb_id", Group.CROSS_REFS), TITLE( "Title", - "title", Group.MISCELLANEOUS), MOLECULE_NAME("Molecule", + "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.MISCELLANEOUS), PFAM_ACCESSION( + "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( @@ -387,129 +388,143 @@ public class PDBRestClient Group.CROSS_REFS), UNIPROT_COVERAGE( - "UniProt Coverage", "uniprot_coverage", Group.MISCELLANEOUS), UNIPROT_FEATURES( - "Uniprot Features", "uniprot_features", Group.MISCELLANEOUS), R_FACTOR( + "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.MISCELLANEOUS), PROTEIN_CHAIN_COUNT( + "Number of Polymers", "number_of_polymers", Group.MISCELLENOUS), PROTEIN_CHAIN_COUNT( "Number of Protein Chains", "number_of_protein_chains", - Group.MISCELLANEOUS), BOUND_MOLECULE_COUNT( + Group.MISCELLENOUS), BOUND_MOLECULE_COUNT( "Number of Bound Molecule", "number_of_bound_molecules", - Group.MISCELLANEOUS), POLYMER_RESIDUE_COUNT( + Group.MISCELLENOUS), POLYMER_RESIDUE_COUNT( "Number of Polymer Residue", "number_of_polymer_residues", - Group.MISCELLANEOUS), GENUS("GENUS", "genus", + 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.MISCELLANEOUS), ASSEMBLY_TYPE( - "Assembly Type", "assembly_type", Group.MISCELLANEOUS), SPACE_GROUP( - "Space Group", "spacegroup", Group.MISCELLANEOUS), CATH_CODE( + "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.MISCELLANEOUS), PUBMED_ID("Pubmed Id", "pubmed_id", + Group.MISCELLENOUS), PUBMED_ID("Pubmed Id", "pubmed_id", Group.CROSS_REFS), STATUS("Status", "status", - Group.MISCELLANEOUS), MODEL_QUALITY("Model Quality", + 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.MISCELLANEOUS), ORG_SCI_NAME( + "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.MISCELLANEOUS), BIOLOGICAL_FUNCTION( + "crystallisation_ph", Group.MISCELLENOUS), BIOLOGICAL_FUNCTION( "Biological Function", "biological_function", - Group.MISCELLANEOUS), BIOLOGICAL_PROCESS("Biological Process", - "biological_process", Group.MISCELLANEOUS), BIOLOGICAL_CELL_COMPONENT( + Group.MISCELLENOUS), BIOLOGICAL_PROCESS("Biological Process", + "biological_process", Group.MISCELLENOUS), BIOLOGICAL_CELL_COMPONENT( "Biological Cell Component", "biological_cell_component", - Group.MISCELLANEOUS), COMPOUND_NAME("Compound Name", + 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.MISCELLANEOUS), COMPOUND_SYSTEMATIC_NAME( + "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.MISCELLANEOUS), JOURNAL("Journal", - "journal", Group.MISCELLANEOUS), ALL_AUTHORS("All Authors", - "all_authors", Group.MISCELLANEOUS), EXPERIMENTAL_DATA_AVAILABLE( + "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.MISCELLANEOUS), DIFFRACTION_PROTOCOL( + 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.MISCELLANEOUS), SAMPLE_PREP_METHOD( + "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.MISCELLANEOUS), CITATION_TITLE( - "Citation Title", "citation_title", Group.MISCELLANEOUS), STRUCTURE_SOLUTION_SOFTWARE( + "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.MISCELLANEOUS), R_FREE("R Free", "r_free", + "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.MISCELLANEOUS), NO_OF_BOUND_ENTITIES( + Group.MISCELLENOUS), NO_OF_BOUND_ENTITIES( "Number of Bound Entities", "number_of_bound_entities", - Group.MISCELLANEOUS), CRYSTALLISATION_RESERVOIR( + Group.MISCELLENOUS), CRYSTALLISATION_RESERVOIR( "Crystallisation Reservoir", "crystallisation_reservoir", - Group.MISCELLANEOUS), DATA_SCALING_SW("Data Scalling Software", - "data_scaling_software", Group.PROCEDURE_AND_SOFTWARE), DETECTOR( - "Detector", "detector", Group.MISCELLANEOUS), DETECTOR_TYPE( - "Detector Type", "detector_type", Group.MISCELLANEOUS), MODIFIED_RESIDUE_FLAG( + 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.MISCELLANEOUS), NUMBER_OF_COPIES("Number of Copies", - "number_of_copies", Group.MISCELLANEOUS), STRUCT_ASYM_ID( + 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.MISCELLANEOUS), DEPOSITION_SITE( - "Deposition Site", "deposition_site", Group.MISCELLANEOUS), SYNCHROTRON_BEAMLINE( + "molecule_synonym", Group.MISCELLENOUS), DEPOSITION_SITE( + "Deposition Site", "deposition_site", Group.MISCELLENOUS), SYNCHROTRON_BEAMLINE( "Synchrotron Beamline", "synchrotron_beamline", - Group.MISCELLANEOUS), ENTITY_ID("Entity Id", "entity_id", + 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.MISCELLANEOUS), ENTITY_WEIGHT( - "Entity Weight", "entity_weight", Group.MISCELLANEOUS), VERSION( - "Version", "_version_", Group.MISCELLANEOUS), ALL("ALL", "text", - Group.MISCELLANEOUS); + "Processing Site", "processing_site", Group.MISCELLENOUS), ENTITY_WEIGHT( + "Entity Weight", "entity_weight", Group.MISCELLENOUS), VERSION( + "Version", "_version_", Group.MISCELLENOUS), ALL("ALL", "text", + Group.MISCELLENOUS); - private enum Group + public enum Group { - DATE_OF("Date Of"), NAMES_AND_TAXONOMY("Names & Taxonomy"), - MISCELLANEOUS("Miscellaneous"), QUALITY_MEASURES("Quality Measures"), - CROSS_REFS("Cross References"), PROCEDURE_AND_SOFTWARE( - "Procedures & Softwares"); + 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) + 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; @@ -534,9 +549,9 @@ public class PDBRestClient return code; } - public String getGroup() + public Group getGroup() { - return group.getName(); + return group; } @Override