edu.mssm.crover.tools.tissue
Class TissueInfoNullsJDBCImpl

java.lang.Object
  edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl

public final class TissueInfoNullsJDBCImpl
extends Object

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.null.name Name of the tiNull table. tissueinfo.column.length.ac Length of the accession code column in the tissueinfo table. tissueinfo.column.length.rawtissue Length of the tissue column in the tissueinfo table. tissueinfo.column.length.curatedtissue Length of the tissue column in the tissueinfo table. tissueinfo.column.length.organism Length of the organism column in the tissueinfo table.

Field Summary

protected static int	AC_COLNUM The column index for the accession code.
protected static int	CTISSUE_COLNUM The column index for the curated tissue.
protected static int	RTISSUE_COLNUM The column index for the raw tissue.

Method Summary

void	addInfo(String ac, String organism, String rawTissue, String curatedTissue) 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() Clean up.
String	getCuratedTissue(String ac) Return the tissue information associated with a sequence accession code.
String[]	getCuratedTissues(String[] ac) Return the tissue information associated with a set of sequence accession codes.
NullTissueDetails	getDetails(String ac) Return the tissue information associated with a sequence accession code.
static TissueInfoNullsJDBCImpl	getInstance() Gets an instance of this class.
String	getOrganism(String ac) Return the organism associated with a sequence accession code.
String	getRawTissue(String ac) Return the tissue information associated with a sequence accession code.
String[]	getRawTissues(String[] ac) Return the tissue information associated with a set of sequence accession codes.
static void	main(String[] args) Main method.

Methods inherited from class java.lang.Object

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

Field Detail

AC_COLNUM

protected static final int AC_COLNUM

The column index for the accession code.

See Also:

Constant Field Values

RTISSUE_COLNUM

protected static final int RTISSUE_COLNUM

The column index for the raw tissue.

See Also:

Constant Field Values

CTISSUE_COLNUM

protected static final int CTISSUE_COLNUM

The column index for the curated tissue.

See Also:

Constant Field Values

Method Detail

finalize

protected void finalize()
                 throws Throwable

Clean up.

Overrides:

finalize in class Object

Throws:

Throwable - if an Exception occurs.

getInstance

public static TissueInfoNullsJDBCImpl getInstance()
                                           throws TissueInfoNotAvailableException

Gets an instance of this class.

Returns:

the instance

Throws:

TissueInfoNotAvailableException - if the database is unavailable

begin

public void begin()
           throws TissueInfoNotAvailableException

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

Throws:

TissueInfoNotAvailableException - if the database is unavailable

end

public void end()

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

destroy

public void destroy()
             throws TissueInfoNotAvailableException

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

Throws:

TissueInfoNotAvailableException - if the database is unavailable

empty

public void empty()
           throws TissueInfoNotAvailableException

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

Throws:

TissueInfoNotAvailableException - if the database is unavailable

getRawTissue

public String getRawTissue(String ac)
                    throws TissueInfoNotAvailableException

Return the tissue information associated with a sequence accession code.

Parameters:

ac - The accession code

Returns:

the raw tissue information

Throws:

TissueInfoNotAvailableException - if the database is unavailable

getCuratedTissue

public String getCuratedTissue(String ac)
                        throws TissueInfoNotAvailableException

Return the tissue information associated with a sequence accession code.

Parameters:

ac - The accession code

Returns:

the curated tissue information

Throws:

TissueInfoNotAvailableException - if the database is unavailable

getDetails

public NullTissueDetails getDetails(String ac)
                             throws TissueInfoNotAvailableException

Return the tissue information associated with a sequence accession code.

Parameters:

ac - The accession code

Returns:

the tissue details

Throws:

TissueInfoNotAvailableException - if the database is unavailable

getRawTissues

public String[] getRawTissues(String[] ac)
                       throws TissueInfoNotAvailableException

Return the tissue information associated with a set of sequence accession codes.

Parameters:

ac - The accession codes

Returns:

the tissue information

Throws:

TissueInfoNotAvailableException - if the database is unavailable

getCuratedTissues

public String[] getCuratedTissues(String[] ac)
                           throws TissueInfoNotAvailableException

Return the tissue information associated with a set of sequence accession codes.

Parameters:

ac - The accession codes

Returns:

the tissue information

Throws:

TissueInfoNotAvailableException - if the database is unavailable

getOrganism

public String getOrganism(String ac)
                   throws TissueInfoNotAvailableException

Return the organism associated with a sequence accession code.

Parameters:

ac - The accession code

Returns:

the associated organism

Throws:

TissueInfoNotAvailableException - if the database is unavailable

addInfo

public void addInfo(String ac,
                    String organism,
                    String rawTissue,
                    String curatedTissue)
             throws TissueInfoNotAvailableException

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

Parameters:

ac - The accession code

organism - The organism associated with the accession code

rawTissue - The raw tissue associated with the accession code

curatedTissue - The curated tissue associated with the accession code

Throws:

TissueInfoNotAvailableException - if the database is unavailable

main

public static void main(String[] args)

Main method.

Parameters:

args - The command line arguments