X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPDBRestClient.java;h=7a5d2412de688c834e812098492012b1800ca6ad;hb=4da7d6ec8ef5ff030c6d06d37a099da2d92d7246;hp=05dab95c83187fbacbb57209c1f0f3c738085c8d;hpb=43ee8686fab13cd6952335ade1382adf3226f7a1;p=jalview.git

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 05dab95..7a5d241 100644
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -75,10 +75,27 @@ public class PDBRestClient
               .getWantedFields());
       int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
               : pdbRestRequest.getResponseSize();
-      String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
-              .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
-              .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
-              : " desc"));
+      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();
@@ -352,89 +369,159 @@ public class PDBRestClient
    */
   public enum PDBDocField
   {
-    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"), 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"), BIOLOGICAL_FUNCTION(
-            "Biological Function", "biological_function"), BIOLOGICAL_PROCESS(
-            "Biological Process", "biological_process"), BIOLOGICAL_CELL_COMPONENT(
-            "Biological Cell Component", "biological_cell_component"), COMPOUND_NAME(
-            "Compound Name", "compound_name"), COMPOUND_ID("Compound Id",
-            "compound_id"), COMPOUND_WEIGHT("Compound Weight",
-            "compound_weight"), COMPOUND_SYSTEMATIC_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(
+    PDB_ID("PDB Id", "pdb_id", Group.CROSS_REFS), TITLE(
+            "Title",
+            "title", Group.MISCELLANEOUS), 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(
+            "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.MISCELLANEOUS), UNIPROT_FEATURES(
+            "Uniprot Features", "uniprot_features", Group.MISCELLANEOUS), 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 Protein Chains", "number_of_protein_chains",
+            Group.MISCELLANEOUS), BOUND_MOLECULE_COUNT(
+            "Number of Bound Molecule", "number_of_bound_molecules",
+            Group.MISCELLANEOUS), POLYMER_RESIDUE_COUNT(
+            "Number of Polymer Residue", "number_of_polymer_residues",
+            Group.MISCELLANEOUS), 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(
+            "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.CROSS_REFS), STATUS("Status", "status",
+            Group.MISCELLANEOUS), 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(
+            "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(
+            "Biological Function", "biological_function",
+            Group.MISCELLANEOUS), BIOLOGICAL_PROCESS("Biological Process",
+            "biological_process", Group.MISCELLANEOUS), BIOLOGICAL_CELL_COMPONENT(
+            "Biological Cell Component", "biological_cell_component",
+            Group.MISCELLANEOUS), 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 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(
+            "Experiment Data Available", "experiment_data_available",
+            Group.MISCELLANEOUS), 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"), 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");
+            "structure_determination_method", Group.PROCEDURE_AND_SOFTWARE), SYNCHROTON_SITE(
+            "Synchrotron Site", "synchrotron_site", Group.MISCELLANEOUS), 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(
+            "Structure Solution Software", "structure_solution_software",
+            Group.PROCEDURE_AND_SOFTWARE), ENTRY_ENTITY("Entry Entity",
+            "entry_entity", Group.MISCELLANEOUS), 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(
+            "Number of Bound Entities", "number_of_bound_entities",
+            Group.MISCELLANEOUS), 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(
+            "Modified Residue Flag", "modified_residue_flag",
+            Group.MISCELLANEOUS), NUMBER_OF_COPIES("Number of Copies",
+            "number_of_copies", Group.MISCELLANEOUS), 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(
+            "Synchrotron Beamline", "synchrotron_beamline",
+            Group.MISCELLANEOUS), 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);
+
+    private 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");
+
+      Group(String name)
+      {
+        this.name = name;
+      }
+
+      private String name;
 
+      public String getName()
+      {
+        return this.name;
+      }
+    };
     private String name;
 
     private String code;
 
-    PDBDocField(String name, String code)
+    private Group group;
+
+    PDBDocField(String name, String code, Group group)
     {
       this.name = name;
       this.code = code;
+      this.group = group;
     }
 
     public String getName()
@@ -447,6 +534,11 @@ public class PDBRestClient
       return code;
     }
 
+    public String getGroup()
+    {
+      return group.getName();
+    }
+
     @Override
     public String toString()
     {