edu.mssm.crover.tools.tissue
Class TissueInfo_JDBCImpl

java.lang.Object
  |
  +--edu.mssm.crover.tools.tissue.TissueInfo_JDBCImpl

All Implemented Interfaces:

TissueInfo

public class TissueInfo_JDBCImpl

extends java.lang.Object

implements TissueInfo

Provides access to tissue information for sequences. This interface is implemented with a JDBC-aware class that connects to a database and retrieves the requested information. The database is loaded with information with DbEstParser, from the dbEst division of genbank. The following properties are obtained through CLI and alter the behaviour of this class: tissueinfo.table.name Name of the tissueinfo table. tissueinfo.column.length.ac Length of the accession code column in the tissueinfo table. tissueinfo.column.length.ac Length of the tissue column in the tissueinfo table. tissueinfo.column.length.ac Length of the organism column in the tissueinfo table.

Field Summary

protected static int	AC_COLNUM
static boolean	DEBUG
java.lang.String	TI_SEQ_TABLENAME Name for table (ac,toKey)
java.lang.String	TI_TO_TABLENAME Name for table (toKey, Tissue, Organism)
java.lang.String	TI_TOKEYID_SEQNAME
protected static int	TISSUE_COLNUM

Method Summary

void	addInfo(java.lang.String ac, java.lang.String tissue, java.lang.String organism) Add a new tissue information to TissueInfo.
void	begin() Notifies this class that a batch of interaction now begin.
void	destroy() Destroy all TissueInfo data and tables.
void	empty() Empty TissueInfo.
void	end() Notifies this class that a batch of interaction now ends.
protected void	finalize()
TissueDetails	getDetails(java.lang.String ac) Return the tissue information associated with a sequence accession code.
static TissueInfo_JDBCImpl	getInstance()
java.lang.String	getOrganism(java.lang.String ac) Return the organism associated with a sequence accession code.
java.lang.String	getTissue(java.lang.String ac) Return the tissue information associated with a sequence accession code.
java.lang.String[]	getTissues(java.lang.String[] ac) Return the tissue information associated with a sequence accession code.
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

DEBUG

public static boolean DEBUG

TI_SEQ_TABLENAME

public final java.lang.String TI_SEQ_TABLENAME

Name for table (ac,toKey)

TI_TO_TABLENAME

public final java.lang.String TI_TO_TABLENAME

Name for table (toKey, Tissue, Organism)

TI_TOKEYID_SEQNAME

public final java.lang.String TI_TOKEYID_SEQNAME

AC_COLNUM

protected static int AC_COLNUM

TISSUE_COLNUM

protected static int TISSUE_COLNUM

Method Detail

finalize

protected void finalize()
                 throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

java.lang.Throwable

getInstance

public static TissueInfo_JDBCImpl getInstance()
                                       throws TissueInfoNotAvailableException

TissueInfoNotAvailableException

begin

public void begin()
           throws TissueInfoNotAvailableException

Notifies this class that a batch of interaction now begin. Allows specific optimization to be performed.

Specified by:

begin in interface TissueInfo

TissueInfoNotAvailableException

end

public void end()
         throws TissueInfoNotAvailableException

Notifies this class that a batch of interaction now ends. Allows specific optimization to be performed.

Specified by:

end in interface TissueInfo

TissueInfoNotAvailableException

destroy

public void destroy()
             throws TissueInfoNotAvailableException

Destroy all TissueInfo data and tables. Subsequent use of methods of this instance will raise TissueInfoNotAvailableException exceptions.

Specified by:

destroy in interface TissueInfo

TissueInfoNotAvailableException

empty

public void empty()
           throws TissueInfoNotAvailableException

Empty TissueInfo. All data previously stored in TissueInfo is removed.

Specified by:

empty in interface TissueInfo

TissueInfoNotAvailableException

getTissue

public java.lang.String getTissue(java.lang.String ac)
                           throws TissueInfoNotAvailableException

Return the tissue information associated with a sequence accession code.

Specified by:

getTissue in interface TissueInfo

Returns:

the tissue information or null if ac is not found in TissueInfo

TissueInfoNotAvailableException

getDetails

public TissueDetails getDetails(java.lang.String ac)
                         throws TissueInfoNotAvailableException

Return the tissue information associated with a sequence accession code.

Specified by:

getDetails in interface TissueInfo

Returns:

the tissue information or null if ac is not found in TissueInfo

TissueInfoNotAvailableException

getTissues

public java.lang.String[] getTissues(java.lang.String[] ac)
                              throws TissueInfoNotAvailableException

Return the tissue information associated with a sequence accession code.

Specified by:

getTissues in interface TissueInfo

Returns:

An array of tissue information or nulls when the corresponding ac is not found in TissueInfo

TissueInfoNotAvailableException

getOrganism

public java.lang.String getOrganism(java.lang.String ac)
                             throws TissueInfoNotAvailableException

Return the organism associated with a sequence accession code.

Specified by:

getOrganism in interface TissueInfo

Returns:

the organism information or null if ac is not found in TissueInfo

TissueInfoNotAvailableException

addInfo

public void addInfo(java.lang.String ac,
                    java.lang.String tissue,
                    java.lang.String organism)
             throws TissueInfoNotAvailableException

Add a new tissue information to TissueInfo. Silently ignores duplicate information.

Specified by:

addInfo in interface TissueInfo

TissueInfoNotAvailableException

main

public static void main(java.lang.String[] args)