develop merge

diff --cc resources/lang/Messages.properties
index 15724d3,8aa072c..05505a4
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -1285,4 -1291,3 +1290,5 @@@ label.mapping_method = Sequence \u27f7 
  status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file.
  status.cancelled_image_export_operation = Cancelled {0} export operation.
  info.error_creating_file = Error creating {0} file.
- exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File
++exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File
++info.error_creating_file = Error creating {0} file.

diff --cc src/MCview/PDBChain.java
Simple merge

diff --cc src/jalview/datamodel/DBRefSource.java
Simple merge

diff --cc src/jalview/datamodel/Sequence.java
Simple merge

diff --cc src/jalview/io/AppletFormatAdapter.java
index 285a953,e34093d..65fd72f
--- 1/src/jalview/io/AppletFormatAdapter.java
--- 2/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@@ -87,7 -86,7 +87,7 @@@ public class AppletFormatAdapte
    public static final String[] READABLE_FORMATS = new String[] { "BLC",
        "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
        "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
-       IdentifyFile.GFF3File, "HTML", "mmCIF" };
 -      IdentifyFile.FeaturesFile, "HTML" };
++      IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
  
    /**
     * List of readable format file extensions by application in order
@@@ -104,8 -103,8 +104,8 @@@
     */
    public static final String[] READABLE_FNAMES = new String[] { "Fasta",
        "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
-       PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+       PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
 -      "Jalview", HtmlFile.FILE_DESC };
 +      "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
  
    /**
     * List of valid format strings for use by callers of the formatSequences
@@@ -328,9 -306,9 +328,9 @@@
        {
          alignFile = new RnamlFile(inFile, type);
        }
-       else if (format.equals(IdentifyFile.GFF3File))
+       else if (format.equals(IdentifyFile.FeaturesFile))
        {
-         alignFile = new Gff3File(inFile, type);
 -        alignFile = new FeaturesFile(true, inFile, type);
++        alignFile = new FeaturesFile(inFile, type);
        }
        return buildAlignmentFrom(alignFile);
      } catch (Exception e)
@@@ -468,9 -426,10 +468,9 @@@
        {
          alignFile = new PhylipFile(source);
        }
-       else if (format.equals(IdentifyFile.GFF3File))
+       else if (format.equals(IdentifyFile.FeaturesFile))
        {
-         alignFile = new Gff3File(inFile, type);
 -        // enforce 'parseImmediately' here:
 -        alignFile = new FeaturesFile(true, inFile, type);
++        alignFile = new FeaturesFile(inFile, type);
        }
        else if (format.equals(JSONFile.FILE_DESC))
        {

diff --cc src/jalview/io/IdentifyFile.java
Simple merge

diff --cc src/jalview/structure/StructureSelectionManager.java
Simple merge

diff --cc src/jalview/ws/dbsources/PDBRestClient.java
index 05dab95,ebe18f7..7a5d241
--- 1/src/jalview/ws/dbsources/PDBRestClient.java
--- 2/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@@ -352,81 -369,148 +369,148 @@@ public class PDBRestClien
     */
    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.MISCELLENOUS), MOLECULE_NAME("Molecule",
++            "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.MISCELLENOUS), PFAM_ACCESSION(
++            "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.MISCELLENOUS), UNIPROT_FEATURES(
 -            "Uniprot Features", "uniprot_features", Group.MISCELLENOUS), R_FACTOR(
++            "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.MISCELLENOUS), PROTEIN_CHAIN_COUNT(
++            "Number of Polymers", "number_of_polymers", Group.MISCELLANEOUS), PROTEIN_CHAIN_COUNT(
+             "Number of Protein Chains", "number_of_protein_chains",
 -            Group.MISCELLENOUS), BOUND_MOLECULE_COUNT(
++            Group.MISCELLANEOUS), BOUND_MOLECULE_COUNT(
+             "Number of Bound Molecule", "number_of_bound_molecules",
 -            Group.MISCELLENOUS), POLYMER_RESIDUE_COUNT(
++            Group.MISCELLANEOUS), POLYMER_RESIDUE_COUNT(
+             "Number of Polymer Residue", "number_of_polymer_residues",
 -            Group.MISCELLENOUS), GENUS("GENUS", "genus",
++            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.MISCELLENOUS), ASSEMBLY_TYPE(
 -            "Assembly Type", "assembly_type", Group.MISCELLENOUS), SPACE_GROUP(
 -            "Space Group", "spacegroup", Group.MISCELLENOUS), CATH_CODE(
++            "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.MISCELLENOUS), PUBMED_ID("Pubmed Id", "pubmed_id",
++            Group.MISCELLANEOUS), PUBMED_ID("Pubmed Id", "pubmed_id",
+             Group.CROSS_REFS), STATUS("Status", "status",
 -            Group.MISCELLENOUS), MODEL_QUALITY("Model Quality",
++            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.MISCELLENOUS), ORG_SCI_NAME(
++            "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.MISCELLENOUS), BIOLOGICAL_FUNCTION(
++            "crystallisation_ph", Group.MISCELLANEOUS), BIOLOGICAL_FUNCTION(
+             "Biological Function", "biological_function",
 -            Group.MISCELLENOUS), BIOLOGICAL_PROCESS("Biological Process",
 -            "biological_process", Group.MISCELLENOUS), BIOLOGICAL_CELL_COMPONENT(
++            Group.MISCELLANEOUS), BIOLOGICAL_PROCESS("Biological Process",
++            "biological_process", Group.MISCELLANEOUS), BIOLOGICAL_CELL_COMPONENT(
+             "Biological Cell Component", "biological_cell_component",
 -            Group.MISCELLENOUS), COMPOUND_NAME("Compound Name",
++            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.MISCELLENOUS), COMPOUND_SYSTEMATIC_NAME(
++            "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.MISCELLENOUS), JOURNAL("Journal",
 -            "journal", Group.MISCELLENOUS), ALL_AUTHORS("All Authors",
 -            "all_authors", Group.MISCELLENOUS), EXPERIMENTAL_DATA_AVAILABLE(
++            "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.MISCELLENOUS), DIFFRACTION_PROTOCOL(
++            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.MISCELLENOUS), SAMPLE_PREP_METHOD(
++            "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.MISCELLENOUS), CITATION_TITLE(
 -            "Citation Title", "citation_title", Group.MISCELLENOUS), STRUCTURE_SOLUTION_SOFTWARE(
++            "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.MISCELLENOUS), R_FREE("R Free", "r_free",
++            "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.MISCELLENOUS), NO_OF_BOUND_ENTITIES(
++            Group.MISCELLANEOUS), NO_OF_BOUND_ENTITIES(
+             "Number of Bound Entities", "number_of_bound_entities",
 -            Group.MISCELLENOUS), CRYSTALLISATION_RESERVOIR(
++            Group.MISCELLANEOUS), CRYSTALLISATION_RESERVOIR(
+             "Crystallisation Reservoir", "crystallisation_reservoir",
 -            Group.MISCELLENOUS), DATA_SCALING_SW("Data Scalling Software",
++            Group.MISCELLANEOUS), 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(
++            "Detector", "detector", Group.MISCELLANEOUS), DETECTOR_TYPE(
++            "Detector Type", "detector_type", Group.MISCELLANEOUS), 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(
++            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.MISCELLENOUS), DEPOSITION_SITE(
 -            "Deposition Site", "deposition_site", Group.MISCELLENOUS), SYNCHROTRON_BEAMLINE(
++            "molecule_synonym", Group.MISCELLANEOUS), DEPOSITION_SITE(
++            "Deposition Site", "deposition_site", Group.MISCELLANEOUS), SYNCHROTRON_BEAMLINE(
+             "Synchrotron Beamline", "synchrotron_beamline",
 -            Group.MISCELLENOUS), ENTITY_ID("Entity Id", "entity_id",
++            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.MISCELLENOUS), ENTITY_WEIGHT(
 -            "Entity Weight", "entity_weight", Group.MISCELLENOUS), VERSION(
 -            "Version", "_version_", Group.MISCELLENOUS), ALL("ALL", "text",
 -            Group.MISCELLENOUS);
++            "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"), MISCELLENOUS(
 -              "Miscellenous"), QUALITY_MEASURES("Quality Measures"), CROSS_REFS(
 -              "Cross References"), PROCEDURE_AND_SOFTWARE(
++      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;

diff --cc test/jalview/io/IdentifyFileTest.java
index 1b1bfac,60f2e48..b1efb7a
--- 1/test/jalview/io/IdentifyFileTest.java
--- 2/test/jalview/io/IdentifyFileTest.java
+++ b/test/jalview/io/IdentifyFileTest.java
@@@ -54,9 -79,9 +79,10 @@@ public class IdentifyFileTes
          { "examples/testdata/test.html", "HTML" },
          { "examples/testdata/test.pileup", "PileUp" },
          { "examples/testdata/test.blc", "BLC" },
-         { "examples/testdata/simplegff3.gff", "GFF v2 or v3" },
+         { "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
+         { "examples/testdata/simpleGff3.gff", IdentifyFile.FeaturesFile },
          { "examples/testdata/test.jvp", "Jalview" },
 +        { "examples/testdata/test.cif", "mmCIF" },
          {
              "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
              "FASTA" },