TissueInfo API 20130530171129

edu.mssm.crover.tools.tissue
Interface TIWeb

All Known Implementing Classes:
TIWebJDBCImpl

public interface TIWeb

Provides access to tissue information for human mRNA.

This interface is implemented with a JDBC-aware class that connects to a database and retrieves the requested information. The database is loaded with tissue information for the human mRNA.


Method Summary
 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.
 Iterator getAcs(String query)
          Return an iterator of accession numbers.
 String getReport(String accessionNumber)
          Return a report form for the accession number.
 Iterator getTissueList(String organism)
          Return the list of raw tissues associated with an organism.
 String getTS(String sqlProfileQuery)
          Return a string of tissues.
 

Method Detail

getAcs

Iterator getAcs(String query)
                throws TissueInfoNotAvailableException
Return an iterator of accession numbers. Uses a SQL query to query the tiweb database.

Parameters:
query - the keyword to use to query the database
Returns:
an iterator of accession numbers
Throws:
TissueInfoNotAvailableException - if the database is unavailable

getTS

String getTS(String sqlProfileQuery)
             throws TissueInfoNotAvailableException
Return a string of tissues. Uses a SQL query to query the tiweb database.

Parameters:
sqlProfileQuery - the keyword to use to query the database
Returns:
a tissue string
Throws:
TissueInfoNotAvailableException - if the database is unavailable

getReport

String getReport(String accessionNumber)
                 throws TissueInfoNotAvailableException
Return a report form for the accession number. Uses a SQL query to query the tiweb database.

Parameters:
accessionNumber - the keyword to use to query the database
Returns:
the report associated with the accession code
Throws:
TissueInfoNotAvailableException - if the database is unavailable

getTissueList

Iterator getTissueList(String organism)
                       throws TissueInfoNotAvailableException
Return the list of raw tissues associated with an organism. Uses a SQL query to query the tissueinfo database.

Parameters:
organism - the keyword to use to query the database
Returns:
the raw tissues associated with the organism
Throws:
TissueInfoNotAvailableException - if the database is unavailable

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 the database is unavailable

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 the database is unavailable

begin

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

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

Throws:
TissueInfoNotAvailableException - if the database is unavailable

TissueInfo API 20130530171129

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