charite.christo.interfaces
Interface SequenceBlaster

All Superinterfaces:

CacheResult.Cacheable

All Known Implementing Classes:

AbstractBlaster, AbstractBlasterHTTP, Blaster_ebi_ac_uk, Blaster_local_NCBI, Blaster_local_NCBI_gapped_PSI, Blaster_local_Wu

public interface SequenceBlaster
extends CacheResult.Cacheable

A sequence blaster invokes a BLAST search with a given query sequence and returns the result as XML text.

Method Summary

void	compute() Computation is typically very time consuming
String[]	getAvailableDatabases() Names of available databases depend on the type of query (AA or NT)
String[]	getAvailableMatrices()
String	getDatabase()
String	getMatrix()
String	getQuerySequence()
ByteArray	getResultXml()
void	setAAQuerySequence(String s) set the amino acid sequence query
void	setDatabase(String db)
void	setMatrix(String matrix)
void	setNTQuerySequence(String s) the nucleotide sequence query sequence
void	setNumberOfAlignments(int n) Upper Limit of the number of alignments to be shown

Methods inherited from interface charite.christo.CacheResult.Cacheable

getCacheClass, getCacheKey, getCacheSection

Method Detail

setAAQuerySequence

void setAAQuerySequence(String s)

set the amino acid sequence query

setNTQuerySequence

void setNTQuerySequence(String s)

the nucleotide sequence query sequence

getQuerySequence

String getQuerySequence()

setNumberOfAlignments

void setNumberOfAlignments(int n)

Upper Limit of the number of alignments to be shown

setDatabase

void setDatabase(String db)
                 throws IllegalArgumentException

Parameters:

db - db is the name of a database such as "uniprot", "pdb" or "uniref50"

Throws:

IllegalArgumentException

getAvailableDatabases

String[] getAvailableDatabases()

Names of available databases depend on the type of query (AA or NT)

getDatabase

String getDatabase()

setMatrix

void setMatrix(String matrix)
               throws IllegalArgumentException

Parameters:

matrix - matrix is the name of a similarity matrix such as blosum62 which contains a value for each pair of amino acids

Throws:

IllegalArgumentException

getAvailableMatrices

String[] getAvailableMatrices()

getMatrix

String getMatrix()

getResultXml

ByteArray getResultXml()

compute

void compute()

Computation is typically very time consuming