charite.christo.blast
Interface SequenceBlaster

All Known Implementing Classes:

AbstractBlaster, Blaster_local_NCBI, Blaster_local_NCBI_gapped_PSI, Blaster_local_Wu, Blaster_SOAP_ebi

public interface SequenceBlaster

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

Field Summary

static int	DATABASES_FULL_LIST Names of available databases depend on the type of query (AA or NT)
static int	DATABASES_NUCLEOTIDES Names of available databases depend on the type of query (AA or NT)

Method Summary

void	cachedResultsNotOlderThanSec(int time) Use cached results only when new
void	compute() Computation is typically very time consuming
java.lang.String[]	getAvailableDatabases(int opt)
java.lang.String[]	getAvailableMatrices()
java.lang.String	getDatabase()
java.lang.String	getMatrix()
BA	getResultXml()
void	setAAQuerySequence(java.lang.String s) set the amino acid sequence query
void	setDatabase(java.lang.String db)
void	setMatrix(java.lang.String matrix)
void	setNTQuerySequence(java.lang.String s) the nucleotide sequence query sequence
void	setNumberOfAlignments(int n) Upper Limit of the number of alignments to be shown
void	setSensitivity(int n)

Field Detail

DATABASES_NUCLEOTIDES

static final int DATABASES_NUCLEOTIDES

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

See Also:

Constant Field Values

DATABASES_FULL_LIST

static final int DATABASES_FULL_LIST

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

See Also:

Constant Field Values

Method Detail

setAAQuerySequence

void setAAQuerySequence(java.lang.String s)

set the amino acid sequence query

setNTQuerySequence

void setNTQuerySequence(java.lang.String s)

the nucleotide sequence query sequence

setSensitivity

void setSensitivity(int n)

setNumberOfAlignments

void setNumberOfAlignments(int n)

Upper Limit of the number of alignments to be shown

setDatabase

void setDatabase(java.lang.String db)
                 throws java.lang.IllegalArgumentException

Parameters:

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

Throws:

java.lang.IllegalArgumentException

getAvailableDatabases

java.lang.String[] getAvailableDatabases(int opt)

getDatabase

java.lang.String getDatabase()

setMatrix

void setMatrix(java.lang.String matrix)
               throws java.lang.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:

java.lang.IllegalArgumentException

getAvailableMatrices

java.lang.String[] getAvailableMatrices()

getMatrix

java.lang.String getMatrix()

getResultXml

BA getResultXml()

compute

void compute()

Computation is typically very time consuming

cachedResultsNotOlderThanSec

void cachedResultsNotOlderThanSec(int time)

Use cached results only when new