TissueInfo API 20130530171129

edu.mssm.crover.tools.tissue
Interface TissueInfo

All Known Implementing Classes:
TissueInfoCacheImpl, TissueInfoJDBCImpl, TissueInfoMemoryImpl, TissueInfoMemoryImpl2

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(String ac, String tissue, String organism, String devStage)
          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(String ac)
          Return the tissue information associated with a sequence accession code.
 String getDevStage(String ac)
          Return the developmental stage information associated with a sequence accession code.
 String getOrganism(String ac)
          Return the organism associated with a sequence accession code.
 String getTissue(String ac)
          Return the tissue information associated with a sequence accession code.
 String[] getTissues(String[] ac)
          Return the tissue information associated with several sequence accession codes.
 

Method Detail

getDetails

TissueDetails getDetails(String ac)
                         throws TissueInfoNotAvailableException
Return the tissue information associated with a sequence accession code.

Parameters:
ac - Accession code of the sequence for which tissue information is requested.
Returns:
the tissue information or null if ac is not found in TissueInfo
Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

getTissue

String getTissue(String ac)
                 throws TissueInfoNotAvailableException
Return the tissue information associated with a sequence accession code.

Parameters:
ac - Accession code of the sequence for which tissue information is requested.
Returns:
the tissue information or null if ac is not found in TissueInfo
Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

getDevStage

String getDevStage(String ac)
                   throws TissueInfoNotAvailableException
Return the developmental stage information associated with a sequence accession code.

Parameters:
ac - Accession code of the sequence for which tissue information is requested.
Returns:
the developmental stage information or null if ac is not found in TissueInfo
Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

getTissues

String[] getTissues(String[] ac)
                    throws TissueInfoNotAvailableException
Return the tissue information associated with several sequence accession codes.

Parameters:
ac - Accession code of the sequence for which tissue information is requested.
Returns:
An array of tissue information or nulls when the corresponding ac is not found in TissueInfo
Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

getOrganism

String getOrganism(String ac)
                   throws TissueInfoNotAvailableException
Return the organism associated with a sequence accession code.

Parameters:
ac - Accession code of the sequence for which tissue information is requested.
Returns:
the organism information or null if ac is not found in TissueInfo
Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

addInfo

void addInfo(String ac,
             String tissue,
             String organism,
             String devStage)
             throws TissueInfoNotAvailableException
Add a new tissue information to TissueInfo. Silently ignores duplicate information.

Parameters:
ac - Accession code of the sequence.
tissue - Tissue in which the sequence has been found to be expressed.
organism - Organism in which the sequence has been found to be expressed.
devStage - The developmental stage in which the sequence has been found
Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

destroy

void destroy()
             throws TissueInfoNotAvailableException
Destroy all TissueInfo data and tables. Subsequent use of methods of this instance will raise TissueInfoNotAvailableException exceptions.

Throws:
TissueInfoNotAvailableException - if we cannot connect to the database or on subsequent uses of this method

empty

void empty()
           throws TissueInfoNotAvailableException
Empty TissueInfo. All data previously stored in TissueInfo is removed. Subsequent use of methods of this instance is allowed.

Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

begin

void begin()
           throws TissueInfoNotAvailableException
Notifies this class that a batch of interaction now begin. Allows specific optimization to be performed.

Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

end

void end()
         throws TissueInfoNotAvailableException
Notifies this class that a batch of interaction now ends. Allows specific optimization to be performed.

Throws:
TissueInfoNotAvailableException - if we cannot connect to the database

TissueInfo API 20130530171129

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