edu.mssm.crover.tools.tissue
Interface TissueInfo

All Known Implementing Classes:

TissueInfo_CacheImpl, TissueInfo_JDBCImpl, TissueInfo_MemoryImpl

public interface 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.

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.
TissueDetails	getDetails(java.lang.String ac) Return the tissue information associated with a sequence accession code.
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 several sequence accession codes.

Method Detail

getDetails

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

Return the tissue information associated with a sequence accession code.

Returns:

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

TissueInfoNotAvailableException

getTissue

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

Return the tissue information associated with a sequence accession code.

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 several sequence accession codes.

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.

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.

TissueInfoNotAvailableException

destroy

public void destroy()
             throws TissueInfoNotAvailableException

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

TissueInfoNotAvailableException

empty

public void empty()
           throws TissueInfoNotAvailableException

Empty TissueInfo. All data previously stored in TissueInfo is removed. Subsequent use of methods of this instance is allowed.

TissueInfoNotAvailableException

begin

public void begin()
           throws TissueInfoNotAvailableException

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

TissueInfoNotAvailableException

end

public void end()
         throws TissueInfoNotAvailableException

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

TissueInfoNotAvailableException