Package ubic.gemma.core.goldenpath

Class GoldenPathQuery

java.lang.Object

ubic.gemma.core.goldenpath.GoldenPath

ubic.gemma.core.goldenpath.GoldenPathQuery

All Implemented Interfaces:

AutoCloseable

public class GoldenPathQuery
extends GoldenPath

Author:

pavlidis

Field Summary

Fields inherited from class ubic.gemma.core.goldenpath.GoldenPath

log

Constructor Summary

Constructors

Constructor	Description
GoldenPathQuery(Taxon taxon)

Method Summary

Modifier and Type	Method	Description
Collection<BlatResult>	findAlignments(String accession)	Locate the alignment for the given sequence, if it exists in the goldenpath database.

Methods inherited from class ubic.gemma.core.goldenpath.GoldenPath

close, getDataSource, getJdbcTemplate, getSearchedDatabase, getTaxon

Methods inherited from class java.lang.Object

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

Constructor Details

GoldenPathQuery

public GoldenPathQuery(Taxon taxon)

Method Details

findAlignments

public Collection<BlatResult> findAlignments(String accession)

Locate the alignment for the given sequence, if it exists in the goldenpath database. Implementation note: This queries the est and mrna tables only.

Parameters:

accession - The genbank accession of the sequence.

Returns:

blat results