import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Iterator;
import java.util.List;
* @return
*/
public static String getPDBDocFieldsAsCommaDelimitedString(
- List<PDBDocField> pdbDocfields)
+ Collection<PDBDocField> pdbDocfields)
{
String result = "";
if (pdbDocfields != null && !pdbDocfields.isEmpty())
return result;
}
+ /**
+ * Determines the column index for the pdb id in the summary table. The pdb id
+ * serves as a unique identifier for a given row in the summary table
+ *
+ * @param wantedFeilds
+ * the available table columns in no particular order
+ * @return the pdb id field column index
+ */
+ public static int getPDBIdColumIndex(
+ Collection<PDBDocField> wantedFeilds, boolean hasRefSeq)
+ {
+ int pdbFeildIndex = hasRefSeq ? 1 : 0;
+ for (PDBDocField feild : wantedFeilds)
+ {
+ if (feild.equals(PDBDocField.PDB_ID))
+ {
+ break;
+ }
+ ++pdbFeildIndex;
+ }
+ return pdbFeildIndex;
+ }
/**
* Represents the fields retrievable from a PDB Document response
PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
"Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
"molecule_type"), MOLECULE_SEQUENCE("Sequence",
- "molecule_sequence"), UNIPROT_FEATURES("Uniprot Features",
- "uniprot_features"), PFAM_ACCESSION("PFAM Accession",
- "pfam_accession"), INTERPRO_ACCESSION("InterPro Accession",
- "interpro_accession"), UNIPROT_ACCESSION("UniProt Accession",
- "uniprot_accession"), R_FACTOR("R Factor", "r_factor"), RESOLUTION(
- "Resolution", "resolution"), DATA_QUALITY("Data Quality",
- "data_quality"), OVERALL_QUALITY("Overall Quality",
- "overall_quality"), POLYMER_COUNT("Polymer Count",
- "number_of_polymers"), PROTEIN_CHAIN_COUNT(
- "Protein Chain Count", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
- "Bound Molecule Count", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
- "Polymer Residue Count", "number_of_polymer_residues"), UNIPROT_COVERAGE(
- "UniProt Coverage", "uniprot_coverage"), GENUS("GENUS", "genus"), GENE_NAME(
- "Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
- "Experimental Method", "experimental_method"), ALL("ALL",
+ "molecule_sequence"), PFAM_ACCESSION("PFAM Accession",
+ "pfam_accession"), PFAM_NAME("PFAM Name", "pfam_name"), INTERPRO_NAME(
+ "InterPro Name", "interpro_name"), INTERPRO_ACCESSION(
+ "InterPro Accession", "interpro_accession"), UNIPROT_ID(
+ "UniProt Id", "uniprot_id"), UNIPROT_ACCESSION(
+ "UniProt Accession", "uniprot_accession"), UNIPROT_COVERAGE(
+ "UniProt Coverage", "uniprot_coverage"), UNIPROT_FEATURES(
+ "Uniprot Features", "uniprot_features"), R_FACTOR("R Factor",
+ "r_factor"), RESOLUTION("Resolution", "resolution"), DATA_QUALITY(
+ "Data Quality", "data_quality"), OVERALL_QUALITY(
+ "Overall Quality", "overall_quality"), POLYMER_COUNT(
+ "Number of Polymers", "number_of_polymers"), PROTEIN_CHAIN_COUNT(
+ "Number of Protein Chains", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
+ "Number of Bound Molecule", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
+ "Number of Polymer Residue", "number_of_polymer_residues"), GENUS(
+ "GENUS", "genus"), GENE_NAME("Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
+ "Experimental Method", "experimental_method"), GO_ID("GO Id",
+ "go_id"), ASSEMBLY_ID("Assembly Id", "assembly_form"), ASSEMBLY_FORM(
+ "Assembly Form", "assembly_id"), ASSEMBLY_TYPE("Assembly Type",
+ "assembly_type"), SPACE_GROUP("Space Group", "spacegroup"), CATH_CODE(
+ "Cath Code", "cath_code"), TAX_ID("Tax Id", "tax_id"), TAX_QUERY(
+ "Tax Query", "tax_query"), INTERACTING_ENTRY_ID(
+ "Interacting Entry Id", "interacting_entry_id"), INTERACTING_ENTITY_ID(
+ "Interacting Entity Id", "interacting_entity_id"), INTERACTING_MOLECULES(
+ "Interacting Molecules", "interacting_molecules"), PUBMED_ID(
+ "Pubmed Id", "pubmed_id"), STATUS("Status", "status"), MODEL_QUALITY(
+ "Model Quality", "model_quality"), PIVOT_RESOLUTION(
+ "Pivot Resolution", "pivot_resolution"), DATA_REDUCTION_SOFTWARE(
+ "Data reduction software", "data_reduction_software"), MAX_OBSERVED_RES(
+ "Max observed residues", "max_observed_residues"), ORG_SCI_NAME(
+ "Organism scientific name", "organism_scientific_name"), SUPER_KINGDOM(
+ "Super kingdom", "superkingdom"), RANK("Rank", "rank"), CRYSTALLISATION_PH(
+ "Crystallisation Ph", "crystallisation_ph"), BIO_FUNCTION(
+ "Biological Function", "biological_function"), BIO_PROCESS(
+ "Biological Process", "biological_process"), BIO_CELL_COMP(
+ "Biological Cell Component", "biological_cell_component"), COMPOUND_NAME(
+ "Compound Name", "compound_name"), COMPOUND_ID("Compound Id",
+ "compound_id"), COMPOUND_WEIGHT("Compound Weight",
+ "compound_weight"), COMP_SYS_NAME("Compound Systematic Name",
+ "compound_systematic_name"), INTERACTING_LIG(
+ "Interacting Ligands", "interacting_ligands"), JOURNAL(
+ "Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE(
+ "Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL(
+ "Diffraction Protocol", "diffraction_protocol"), REFINEMENT_SOFTWARE(
+ "Refinement Software", "refinement_software"), STRUCTURE_DETERMINATION_METHOD(
+ "Structure Determination Method",
+ "structure_determination_method"), SYNCHROTON_SITE(
+ "Synchrotron Site", "synchrotron_site"), SAMPLE_PREP_METHOD(
+ "Sample Preparation Method", "sample_preparation_method"), ENTRY_AUTHORS(
+ "Entry Authors", "entry_authors"), CITATION_TITLE(
+ "Citation Title", "citation_title"), STRUCTURE_SOLUTION_SOFTWARE(
+ "Structure Solution Software", "structure_solution_software"), ENTRY_ENTITY(
+ "Entry Entity", "entry_entity"), R_FREE("R Free", "r_free"), NO_OF_POLYMER_ENTITIES(
+ "Number of Polymer Entities", "number_of_polymer_entities"), NO_OF_BOUND_ENTITIES(
+ "Number of Bound Entities", "number_of_bound_entities"), CRYSTALLISATION_RESERVOIR(
+ "Crystallisation Reservoir", "crystallisation_reservoir"), DATA_SCALING_SW(
+ "Data Scalling Software", "data_scaling_software"), DETECTOR(
+ "Detector", "detector"), DETECTOR_TYPE("Detector Type",
+ "detector_type"), MODIFIED_RESIDUE_FLAG(
+ "Modified Residue Flag", "modified_residue_flag"), NUMBER_OF_COPIES(
+ "Number of Copies", "number_of_copies"), STRUCT_ASYM_ID(
+ "Struc Asym Id", "struct_asym_id"), HOMOLOGUS_PDB_ENTITY_ID(
+ "Homologus PDB Entity Id", "homologus_pdb_entity_id"), MOLECULE_SYNONYM(
+ "Molecule Synonym", "molecule_synonym"), DEPOSITION_SITE(
+ "Deposition Site", "deposition_site"), SYNCHROTRON_BEAMLINE(
+ "Synchrotron Beamline", "synchrotron_beamline"), ENTITY_ID(
+ "Entity Id", "entity_id"), BEAM_SOURCE_NAME("Beam Source Name",
+ "beam_source_name"), PROCESSING_SITE("Processing Site",
+ "processing_site"), ENTITY_WEIGHT("Entity Weight",
+ "entity_weight"), VERSION("Version", "_version_"), ALL("ALL",
"text");
private String name;
git://source.jalview.org / jalview.git / blobdiff