Package ubic.gemma.core.analysis.sequence

Interface Blat

All Known Implementing Classes:

ShellDelegatingBlat

public interface Blat

Field Summary

Fields

Modifier and Type	Field	Description
static double	DEFAULT_BLAT_SCORE_THRESHOLD	This value is basically a threshold fraction of aligned bases in the query.
static double	STEPSIZE

Method Summary

Modifier and Type	Method	Description
Map<BioSequence,Collection<BlatResult>>	blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	blatQuery(Collection<BioSequence> sequences, Taxon taxon)
Collection<BlatResult>	blatQuery(BioSequence b)	Run a BLAT search using the gfClient.
Collection<BlatResult>	blatQuery(BioSequence b, Taxon taxon, boolean sensitive)	Run a BLAT search using the gfClient.
double	getBlatScoreThreshold()
String	getGfClientExe()
String	getGfServerExe()
String	getHost()
int	getHumanServerPort()
int	getMouseServerPort()
int	getRatServerPort()
String	getSeqDir()
String	getSeqFiles(ShellDelegatingBlat.BlattableGenome genome)
Collection<BlatResult>	processPsl(InputStream inputStream, Taxon taxon)
void	setBlatScoreThreshold(double blatScoreThreshold)
void	startServer(ShellDelegatingBlat.BlattableGenome genome, int port)	Start the server, if the port isn't already being used.
void	stopServer(int port)	Stop the gfServer, if it was started by this.

Field Detail

DEFAULT_BLAT_SCORE_THRESHOLD

static final double DEFAULT_BLAT_SCORE_THRESHOLD

This value is basically a threshold fraction of aligned bases in the query. Hits below this score are simply not reported. BlatResult has implementation of score computation.

See Also:

BlatResult, Constant Field Values

STEPSIZE

static final double STEPSIZE

See Also:

Constant Field Values

Method Detail

blatQuery

Collection<BlatResult> blatQuery(BioSequence b)
                          throws IOException

Run a BLAT search using the gfClient.

Parameters:

b - The genome is inferred from the Taxon held by the sequence.

Returns:

Collection of BlatResult objects.

Throws:

IOException - when there are IO problems.

blatQuery

Collection<BlatResult> blatQuery(BioSequence b,
                                 Taxon taxon,
                                 boolean sensitive)
                          throws IOException

Run a BLAT search using the gfClient.

Parameters:

b - The genome is inferred from the Taxon held by the sequence.

sensitive - if true use the more sensitive gfServer, if available.

taxon - taxon

Returns:

Collection of BlatResult objects.

Throws:

IOException - when there are IO problems.

blatQuery

Map<BioSequence,Collection<BlatResult>> blatQuery(Collection<BioSequence> sequences,
                                                        boolean sensitive,
                                                        Taxon taxon)
                                                 throws IOException

Parameters:

sequences - The genome is inferred from the Taxon held by the sequence.

taxon - The taxon whose database will be searched.

sensitive - if true use the more sensitive gfServer, if available.

Returns:

map of the input sequences to a corresponding collection of blat result(s)

Throws:

IOException - when there are IO problems.

blatQuery

Map<BioSequence,Collection<BlatResult>> blatQuery(Collection<BioSequence> sequences,
                                                        Taxon taxon)
                                                 throws IOException

Throws:

IOException

getBlatScoreThreshold

double getBlatScoreThreshold()

Returns:

the blatScoreThreshold

setBlatScoreThreshold

void setBlatScoreThreshold(double blatScoreThreshold)

Parameters:

blatScoreThreshold - the blatScoreThreshold to set

getGfClientExe

String getGfClientExe()

Returns:

Returns the gfClientExe.

getGfServerExe

String getGfServerExe()

Returns:

Returns the gfServerExe.

getHost

String getHost()

Returns:

Returns the host.

getHumanServerPort

int getHumanServerPort()

Returns:

Returns the humanServerPort.

getMouseServerPort

int getMouseServerPort()

Returns:

Returns the mouseServerPort.

getRatServerPort

int getRatServerPort()

Returns:

Returns the ratServerPort.

getSeqDir

String getSeqDir()

Returns:

Returns the seqDir.

getSeqFiles

String getSeqFiles(ShellDelegatingBlat.BlattableGenome genome)

Parameters:

genome - genome

Returns:

Returns the seqFiles.

processPsl

Collection<BlatResult> processPsl(InputStream inputStream,
                                  Taxon taxon)
                           throws IOException

Parameters:

inputStream - to the Blat output file in psl format

taxon - taxon

Returns:

processed results.

Throws:

IOException - when there are IO problems.

startServer

void startServer(ShellDelegatingBlat.BlattableGenome genome,
                 int port)
          throws IOException

Start the server, if the port isn't already being used. If the port is in use, we assume it is a gfServer.

Parameters:

genome - genome

port - port

Throws:

IOException - when there are IO problems.

stopServer

void stopServer(int port)

Stop the gfServer, if it was started by this.

Parameters:

port - port