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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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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