org.utgenome.format.keyword
Class KeywordDB

java.lang.Object
  extended by 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


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