Trait genomicsqlite::ConnectionMethods

pub trait ConnectionMethods {
    // Required methods
    fn genomicsqlite_version(&self) -> String;
    fn genomicsqlite_attach_sql<P: AsRef<Path>>(
        &self,
        path: P,
        schema_name: &str,
        config: &Object
    ) -> Result<String>;
    fn genomicsqlite_vacuum_into_sql<P: AsRef<Path>>(
        &self,
        path: P,
        config: &Object
    ) -> Result<String>;
    fn create_genomic_range_index_sql(
        &self,
        table_name: &str,
        chromosome: &str,
        begin_pos: &str,
        end_pos: &str
    ) -> Result<String>;
    fn create_genomic_range_index_sql_with_floor(
        &self,
        table_name: &str,
        chromosome: &str,
        begin_pos: &str,
        end_pos: &str,
        floor: i64
    ) -> Result<String>;
    fn put_reference_assembly_sql(&self, assembly: &str) -> Result<String>;
    fn put_reference_assembly_sql_with_schema(
        &self,
        assembly: &str,
        schema: &str
    ) -> Result<String>;
    fn put_reference_sequence_sql(&self, refseq: &RefSeq) -> Result<String>;
    fn put_reference_sequence_sql_with_schema(
        &self,
        refseq: &RefSeq,
        schema: &str
    ) -> Result<String>;
    fn get_reference_sequences_by_rid(&self) -> Result<HashMap<i64, RefSeq>>;
    fn get_reference_sequences_by_rid_with_options(
        &self,
        assembly: Option<&str>,
        schema: Option<&str>
    ) -> Result<HashMap<i64, RefSeq>>;
    fn get_reference_sequences_by_name(&self) -> Result<HashMap<String, RefSeq>>;
    fn get_reference_sequences_by_name_with_options(
        &self,
        assembly: Option<&str>,
        schema: Option<&str>
    ) -> Result<HashMap<String, RefSeq>>;
}

Methods for GenomicSQLite rusqlite::Connections; see Programming Guide for each method’s semantics. The methods can also be invoked on an open rusqlite::Transaction, via its implicit Deref<Target=Connection>.

Required Methods

fn genomicsqlite_version(&self) -> String

Get Genomics Extension version

fn genomicsqlite_attach_sql<P: AsRef<Path>>( &self, path: P, schema_name: &str, config: &Object ) -> Result<String>

Generate SQL command to attach another GenomicSQLite database to an existing connection

fn genomicsqlite_vacuum_into_sql<P: AsRef<Path>>( &self, path: P, config: &Object ) -> Result<String>

Generate SQL command to VACUUM INTO the database into a new file

fn create_genomic_range_index_sql( &self, table_name: &str, chromosome: &str, begin_pos: &str, end_pos: &str ) -> Result<String>

Generate SQL script to create Genomic Range Index for a table

fn create_genomic_range_index_sql_with_floor( &self, table_name: &str, chromosome: &str, begin_pos: &str, end_pos: &str, floor: i64 ) -> Result<String>

fn put_reference_assembly_sql(&self, assembly: &str) -> Result<String>

Generate SQL script to add a reference assembly to the stored metadata

fn put_reference_assembly_sql_with_schema( &self, assembly: &str, schema: &str ) -> Result<String>

fn put_reference_sequence_sql(&self, refseq: &RefSeq) -> Result<String>

Generate SQL script to add one reference sequence to the stored metadata. Set rid: -1 to let the database generate a value.

fn put_reference_sequence_sql_with_schema( &self, refseq: &RefSeq, schema: &str ) -> Result<String>

fn get_reference_sequences_by_rid(&self) -> Result<HashMap<i64, RefSeq>>

Read the stored reference sequence metadata into a lookup table keyed by rid

fn get_reference_sequences_by_rid_with_options( &self, assembly: Option<&str>, schema: Option<&str> ) -> Result<HashMap<i64, RefSeq>>

fn get_reference_sequences_by_name(&self) -> Result<HashMap<String, RefSeq>>

Read the stored reference sequence metadata into a lookup table keyed by name

fn get_reference_sequences_by_name_with_options( &self, assembly: Option<&str>, schema: Option<&str> ) -> Result<HashMap<String, RefSeq>>

Implementations on Foreign Types

impl ConnectionMethods for Connection

fn genomicsqlite_version(&self) -> String

fn genomicsqlite_attach_sql<P: AsRef<Path>>( &self, path: P, schema_name: &str, config: &Object ) -> Result<String>

fn genomicsqlite_vacuum_into_sql<P: AsRef<Path>>( &self, path: P, config: &Object ) -> Result<String>

fn create_genomic_range_index_sql( &self, table_name: &str, chromosome: &str, begin_pos: &str, end_pos: &str ) -> Result<String>

fn create_genomic_range_index_sql_with_floor( &self, table_name: &str, chromosome: &str, begin_pos: &str, end_pos: &str, floor: i64 ) -> Result<String>

fn put_reference_assembly_sql(&self, assembly: &str) -> Result<String>

fn put_reference_assembly_sql_with_schema( &self, assembly: &str, schema: &str ) -> Result<String>

fn put_reference_sequence_sql(&self, refseq: &RefSeq) -> Result<String>

fn put_reference_sequence_sql_with_schema( &self, refseq: &RefSeq, schema: &str ) -> Result<String>

fn get_reference_sequences_by_rid(&self) -> Result<HashMap<i64, RefSeq>>

fn get_reference_sequences_by_rid_with_options( &self, assembly: Option<&str>, schema: Option<&str> ) -> Result<HashMap<i64, RefSeq>>

fn get_reference_sequences_by_name(&self) -> Result<HashMap<String, RefSeq>>

fn get_reference_sequences_by_name_with_options( &self, assembly: Option<&str>, schema: Option<&str> ) -> Result<HashMap<String, RefSeq>>

Implementors