edu.mssm.crover.mutations.drivers
Interface MutationDriver

All Known Implementing Classes:

MutationDriverCache

public interface MutationDriver

Provides access to mutations in a given mutation database. This interface is independent from the mutation database (source of the mutations).

Method Summary

DriverInformation	getInformation()
Mutant[]	getMutantsFor(java.lang.String origin, java.lang.String accession_code, short pure_type_signature, boolean filter_by_pure_signature, short cumulative_type_signature, boolean filter_by_cumulative_signature, boolean filter_by_exact_cumulative_signature) Obtain a description of the mutants performed on a sequence.
Mutation[][]	getMutationsFor(java.lang.String origin, java.lang.String accession_code, short pure_type_signature, boolean filter_by_pure_signature, short cumulative_type_signature, boolean filter_by_cumulative_signature, boolean filter_by_exact_cumulative_signature) Obtain a description of the mutants performed on a sequence.

Method Detail

getInformation

public DriverInformation getInformation()

getMutationsFor

public Mutation[][] getMutationsFor(java.lang.String origin,
                                    java.lang.String accession_code,
                                    short pure_type_signature,
                                    boolean filter_by_pure_signature,
                                    short cumulative_type_signature,
                                    boolean filter_by_cumulative_signature,
                                    boolean filter_by_exact_cumulative_signature)
                             throws SourceNotAvailable,
                                    ProtocolError,
                                    UnsupportedOrigin

Obtain a description of the mutants performed on a sequence. The mutant information is returned as an array of array of mutations. The elements of the first level encode a mutant. A mutant is represented as a array of Mutation instance.

Parameters:

origin - Orgin of the sequence for which the mutation server is queried.

accession_code - Accession code, relative to the origin, for which the mutation server is queried.

pure_type_signature - Mutants that are returned must have this pure_type_signature.

cumulative_type_signature - Mutants that are returned must have this cumulative_type_signature. The semantic of "have" is defined below.

filter_by_pure_signature - If true, the query results are filtered according to the pure signature, if false the pure signature is ignored.

filter_by_exact_cumulative_signature - If true, the query results are filtered according to the exact cumulative signature (the match can only be accepted when cumulative_type_signature == mutant.cumulative_signature). If false the cumulative signature is ignored.

filter_by_cumulative_signature - If true, the query results are filtered according to the cumulative signature, i.e. (cumulative_type_signature & mutant.cumulative_signature)!=0. If false the cumulative signature is ignored.

SourceNotAvailable

ProtocolError

UnsupportedOrigin

See Also:

Mutant

getMutantsFor

public Mutant[] getMutantsFor(java.lang.String origin,
                              java.lang.String accession_code,
                              short pure_type_signature,
                              boolean filter_by_pure_signature,
                              short cumulative_type_signature,
                              boolean filter_by_cumulative_signature,
                              boolean filter_by_exact_cumulative_signature)
                       throws SourceNotAvailable,
                              ProtocolError,
                              UnsupportedOrigin

Obtain a description of the mutants performed on a sequence. The mutant information is returned as an array of Mutant instances.

Parameters:

origin - Orgin of the sequence for which the mutation server is queried.

accession_code - Accession code, relative to the origin, for which the mutation server is queried.

pure_type_signature - Mutants that are returned must have this pure_type_signature.

cumulative_type_signature - Mutants that are returned must have this cumulative_type_signature. The semantic of "have" is defined below.

filter_by_pure_signature - If true, the query results are filtered according to the pure signature, if false the pure signature is ignored.

filter_by_exact_cumulative_signature - If true, the query results are filtered according to the exact cumulative signature (the match can only be accepted when cumulative_type_signature == mutant.cumulative_signature). If false the cumulative signature is ignored.

filter_by_cumulative_signature - If true, the query results are filtered according to the cumulative signature, i.e. (cumulative_type_signature & mutant.cumulative_signature)!=0. If false the cumulative signature is ignored.

SourceNotAvailable

ProtocolError

UnsupportedOrigin

See Also:

Mutant