org.utgenome.format.keyword
Class KeywordDB

java.lang.Object
  org.utgenome.format.keyword.KeywordDB

public class KeywordDB
extends Object

Keyword database generator/query interface

Author:

leo

Constructor Summary

KeywordDB(File dbPath)

KeywordDB(org.xerial.db.sql.sqlite.SQLiteAccess db)

KeywordDB(String dbPath)

Method Summary

void	add(GenomeKeywordEntry.KeywordAlias alias)
void	add(GenomeKeywordEntry entry)
void	close()
void	importFromBAM(String ref, InputStream samOrBamInput)
void	importFromBED(String ref, Reader bed)
void	importFromFASTAIndex(String ref, Reader fastaIndexFile)
void	importFromTAB(String ref, Reader tabFileReader)
void	importKeywordAliasFile(Reader keywordAliasFile)
void	initDB()
KeywordSearchResult	query(String ref, String keyword, int page, int pageSize)
static String	sanitize(String text)
static String	splitAndAddStar(String keyword)

Methods inherited from class java.lang.Object

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

Constructor Detail

KeywordDB

public KeywordDB(File dbPath)
          throws org.xerial.db.DBException

Throws:

org.xerial.db.DBException

KeywordDB

public KeywordDB(String dbPath)
          throws org.xerial.db.DBException,
                 UTGBException

Throws:

org.xerial.db.DBException

UTGBException

KeywordDB

public KeywordDB(org.xerial.db.sql.sqlite.SQLiteAccess db)
          throws org.xerial.db.DBException

Throws:

org.xerial.db.DBException

Method Detail

initDB

public void initDB()
            throws org.xerial.db.DBException

Throws:

org.xerial.db.DBException

query

public KeywordSearchResult query(String ref,
                                 String keyword,
                                 int page,
                                 int pageSize)
                          throws Exception

Throws:

Exception

splitAndAddStar

public static String splitAndAddStar(String keyword)

sanitize

public static String sanitize(String text)

add

public void add(GenomeKeywordEntry entry)
         throws org.xerial.db.DBException

Throws:

org.xerial.db.DBException

add

public void add(GenomeKeywordEntry.KeywordAlias alias)
         throws org.xerial.db.DBException

Throws:

org.xerial.db.DBException

importKeywordAliasFile

public void importKeywordAliasFile(Reader keywordAliasFile)
                            throws UTGBException

Throws:

UTGBException

importFromFASTAIndex

public void importFromFASTAIndex(String ref,
                                 Reader fastaIndexFile)
                          throws UTGBException

Throws:

UTGBException

importFromTAB

public void importFromTAB(String ref,
                          Reader tabFileReader)
                   throws UTGBException

Throws:

UTGBException

importFromBED

public void importFromBED(String ref,
                          Reader bed)
                   throws UTGBException

Throws:

UTGBException

importFromBAM

public void importFromBAM(String ref,
                          InputStream samOrBamInput)
                   throws UTGBException

Throws:

UTGBException

close

public void close()
           throws org.xerial.db.DBException

Throws:

org.xerial.db.DBException