Package ubic.gemma.core.analysis.sequence

Class ShellDelegatingBlat

java.lang.Object

ubic.gemma.core.analysis.sequence.ShellDelegatingBlat

All Implemented Interfaces:

Blat

public class ShellDelegatingBlat
extends Object
implements Blat

Class to manage the gfServer and run BLAT searches. Delegates to the command-line shell to run blat.

Author:

pavlidis

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ShellDelegatingBlat.BlattableGenome

Field Summary

Fields inherited from interface ubic.gemma.core.analysis.sequence.Blat

DEFAULT_BLAT_SCORE_THRESHOLD, STEPSIZE

Constructor Summary

Constructors

Constructor	Description
ShellDelegatingBlat()	Create a blat object with settings read from the config file.
ShellDelegatingBlat(String host, int humanServerPort, String seqDir)

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()
static ExternalDatabase	getSearchedGenome(Taxon taxon)
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ShellDelegatingBlat

public ShellDelegatingBlat()

Create a blat object with settings read from the config file.

ShellDelegatingBlat

public ShellDelegatingBlat(String host,
                           int humanServerPort,
                           String seqDir)

Method Detail

getSearchedGenome

public static ExternalDatabase getSearchedGenome(Taxon taxon)

blatQuery

public Collection<BlatResult> blatQuery(BioSequence b)
                                 throws IOException

Description copied from interface: Blat

Run a BLAT search using the gfClient.

Specified by:

blatQuery in interface Blat

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

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

Description copied from interface: Blat

Run a BLAT search using the gfClient.

Specified by:

blatQuery in interface Blat

Parameters:

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

taxon - taxon

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

Returns:

Collection of BlatResult objects.

Throws:

IOException - when there are IO problems.

blatQuery

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

Specified by:

blatQuery in interface Blat

Parameters:

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

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

taxon - The taxon whose database will be searched.

Returns:

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

Throws:

IOException - when there are IO problems.

blatQuery

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

Specified by:

blatQuery in interface Blat

Throws:

IOException

getBlatScoreThreshold

public double getBlatScoreThreshold()

Specified by:

getBlatScoreThreshold in interface Blat

Returns:

the blatScoreThreshold

setBlatScoreThreshold

public void setBlatScoreThreshold(double blatScoreThreshold)

Specified by:

setBlatScoreThreshold in interface Blat

Parameters:

blatScoreThreshold - the blatScoreThreshold to set

getGfClientExe

public String getGfClientExe()

Specified by:

getGfClientExe in interface Blat

Returns:

Returns the gfClientExe.

getGfServerExe

public String getGfServerExe()

Specified by:

getGfServerExe in interface Blat

Returns:

Returns the gfServerExe.

getHost

public String getHost()

Specified by:

getHost in interface Blat

Returns:

Returns the host.

getHumanServerPort

public int getHumanServerPort()

Specified by:

getHumanServerPort in interface Blat

Returns:

Returns the humanServerPort.

getMouseServerPort

public int getMouseServerPort()

Specified by:

getMouseServerPort in interface Blat

Returns:

Returns the mouseServerPort.

getRatServerPort

public int getRatServerPort()

Specified by:

getRatServerPort in interface Blat

Returns:

Returns the ratServerPort.

getSeqDir

public String getSeqDir()

Specified by:

getSeqDir in interface Blat

Returns:

Returns the seqDir.

getSeqFiles

public String getSeqFiles(ShellDelegatingBlat.BlattableGenome genome)

Specified by:

getSeqFiles in interface Blat

Parameters:

genome - genome

Returns:

Returns the seqFiles.

processPsl

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

Specified by:

processPsl in interface Blat

Parameters:

inputStream - to the Blat output file in psl format

taxon - taxon

Returns:

processed results.

Throws:

IOException - when there are IO problems.

startServer

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

Description copied from interface: Blat

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

Specified by:

startServer in interface Blat

Parameters:

genome - genome

port - port

Throws:

IOException - when there are IO problems.

stopServer

public void stopServer(int port)

Description copied from interface: Blat

Stop the gfServer, if it was started by this.

Specified by:

stopServer in interface Blat

Parameters:

port - port