org.utgenome.format.fasta
Class FASTADatabase

java.lang.Object
  org.utgenome.format.fasta.FASTADatabase

public class FASTADatabase
extends Object

Fasta2DB creates a SQLite database file from a given FASTA format file

Author:

leo

Nested Class Summary

static class	FASTADatabase.Config
static class	FASTADatabase.NSeq A holder for retrieving compressed genome sequence
static class	FASTADatabase.TextOutput

Constructor Summary

FASTADatabase()

Method Summary

void	createDB(FASTAPullParser pullParser, org.xerial.db.sql.sqlite.SQLiteAccess db)
void	createDB(Reader fasta, org.xerial.db.sql.sqlite.SQLiteAccess db)
static void	main(String[] args)
static ReferenceSequence	querySequence(File fastaFile, ChrLoc location)
static void	querySequence(File dbFile, ChrLoc location, org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)
static void	querySequence(org.xerial.db.sql.sqlite.SQLiteAccess db, ChrLoc location, org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTADatabase

public FASTADatabase()

Method Detail

createDB

public void createDB(Reader fasta,
                     org.xerial.db.sql.sqlite.SQLiteAccess db)
              throws Exception

Throws:

Exception

createDB

public void createDB(FASTAPullParser pullParser,
                     org.xerial.db.sql.sqlite.SQLiteAccess db)
              throws Exception

Throws:

Exception

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception

querySequence

public static void querySequence(File dbFile,
                                 ChrLoc location,
                                 org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)
                          throws UTGBException

Throws:

UTGBException

querySequence

public static ReferenceSequence querySequence(File fastaFile,
                                              ChrLoc location)
                                       throws UTGBException

Throws:

UTGBException

querySequence

public static void querySequence(org.xerial.db.sql.sqlite.SQLiteAccess db,
                                 ChrLoc location,
                                 org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)
                          throws UTGBException

Throws:

UTGBException