Index A | B | C | D | F | G | L | M | N | O | P | R | S | T | U | V | W A Alignment (class in cogent3.core.alignment) Alphabet (class in cogent3.core.alphabet) ArrayAlignment (class in cogent3.core.alignment) available_apps() (in module cogent3.__init__) available_codes() (in module cogent3.__init__) available_models() (in module cogent3.__init__) available_moltypes() (in module cogent3.__init__) B BasicAnnotationDb (class in cogent3.core.annotation_db) C close() (DataStoreSqlite method) cogent.app cogent.db.ensembl cogent.db.eutils cogent.maths.unifrac cogent.motif cogent.seqsim cogent.struct cogent3.util.misc Columns (class in cogent3.util.table) completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) completed members D data store data_store (DataMember property) DataMember (class in cogent3.app.data_store) DataStoreDirectory (class in cogent3.app.data_store) DataStoreSqlite (class in cogent3.app.sqlite_data_store) db (DataStoreSqlite property) define_app() (in module cogent3.app.composable) describe (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) deserialise_object() (in module cogent3.util.deserialise) DnaSequence (class in cogent3.core.sequence) drop_not_completed() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) F Feature (class in cogent3.core.annotation) FilteringParser (class in cogent3.parse.table) G GenbankAnnotationDb (class in cogent3.core.annotation_db) GeneticCode (class in cogent3.core.genetic_code) get_code() (in module cogent3.__init__) get_model() (in module cogent3.__init__) get_moltype() (in module cogent3.__init__) GffAnnotationDb (class in cogent3.core.annotation_db) L limit (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) load_aligned_seqs() (in module cogent3.__init__) load_annotations() (in module cogent3.__init__) load_delimited() (in module cogent3.__init__) load_seq() (in module cogent3.__init__) load_table() (in module cogent3.__init__) load_tree() (in module cogent3.__init__) load_unaligned_seqs() (in module cogent3.__init__) lock() (DataStoreSqlite method) locked (DataStoreSqlite property) logs (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) M make_aligned_seqs() (in module cogent3.__init__) make_seq() (in module cogent3.__init__) make_table() (in module cogent3.__init__) make_tree() (in module cogent3.__init__) make_unaligned_seqs() (in module cogent3.__init__) md5 (DataMember property) md5() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) members (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) mode (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) MolType (class in cogent3.core.moltype) N not_completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) O open_() (in module cogent3.__init__) open_data_store() (in module cogent3.__init__) P PhyloNode (class in cogent3.core.tree) ProteinSequence (class in cogent3.core.sequence) R read() (DataMember method) (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) ReadOnlyDataStoreZipped (class in cogent3.app.data_store) record_type (DataStoreSqlite property) register_datastore_reader() (in module cogent3.app.io) register_deserialiser (class in cogent3.util.deserialise) RnaSequence (class in cogent3.core.sequence) S SequenceCollection (class in cogent3.core.alignment) source (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) store_suffix (DataStoreSqlite attribute) summary_logs (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) summary_not_completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) T Table (class in cogent3.util.table) U unique_id (DataMember property) unlock() (DataStoreSqlite method) V validate() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) W write() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) write_log() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) write_not_completed() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method)