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.

Method Summary

Modifier and Type	Method	Description
Map<BioSequence,List<BlatResult>>	blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,List<BlatResult>>	blatQuery(Collection<BioSequence> sequences, Taxon taxon)
List<BlatResult>	blatQuery(BioSequence b)	Run a BLAT search using the gfClient.
List<BlatResult>	blatQuery(BioSequence b, Taxon taxon, boolean sensitive)	Run a BLAT search using the gfClient.
void	setBlatScoreThreshold(double blatScoreThreshold)	Set the blat score threshold to use.

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

Method Detail

blatQuery

List<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

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

Throws:

IOException

setBlatScoreThreshold

void setBlatScoreThreshold(double blatScoreThreshold)

Set the blat score threshold to use.

Defaults to DEFAULT_BLAT_SCORE_THRESHOLD.