edu.mssm.crover.tools.tissue
Class TissueInfo_MemoryImpl

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

All Implemented Interfaces:

TissueInfo

public class TissueInfo_MemoryImpl

extends java.lang.Object

implements TissueInfo

Keeps TissueInfo in memory. This class reads a file representation of TissueInfo and keeps the record in memory.

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.
static TissueInfo_MemoryImpl	getInstance()
static TissueInfo_MemoryImpl	getInstance(java.io.BufferedReader ti_to, java.io.BufferedReader ti_seq, java.lang.String[] organisms)
static TissueInfo_MemoryImpl	getInstance(java.lang.String[] organisms) Obtains the singleton instance.
static TissueInfo_MemoryImpl	getInstance(java.lang.String ti_to, java.lang.String ti_seq) Obtain the singleton instance.
static TissueInfo_MemoryImpl	getInstance(java.lang.String ti_to, java.lang.String ti_seq, java.lang.String[] organisms)
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.
void	loadTiSeq(java.io.BufferedReader ti_seq) Loads a file representation of TissueInfo.
void	loadTiTo(java.io.BufferedReader ti_to) Loads a file representation of TissueInfo.
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static TissueInfo_MemoryImpl getInstance()
                                         throws java.io.IOException,
                                                TissueInfoNotAvailableException

java.io.IOException

TissueInfoNotAvailableException

getInstance

public static TissueInfo_MemoryImpl getInstance(java.lang.String[] organisms)
                                         throws java.io.IOException,
                                                TissueInfoNotAvailableException

Obtains the singleton instance. The filesnames needed to initialize this instance are taken from the properties

tissueinfo.path.ti_to: ti_to file.

tissueinfo.path.ti_seq: ti_seq file.

java.io.IOException

TissueInfoNotAvailableException

getInstance

public static TissueInfo_MemoryImpl getInstance(java.lang.String ti_to,
                                                java.lang.String ti_seq)
                                         throws java.io.IOException,
                                                TissueInfoNotAvailableException

Obtain the singleton instance.

java.io.IOException

TissueInfoNotAvailableException

getInstance

public static TissueInfo_MemoryImpl getInstance(java.lang.String ti_to,
                                                java.lang.String ti_seq,
                                                java.lang.String[] organisms)
                                         throws java.io.IOException,
                                                TissueInfoNotAvailableException

java.io.IOException

TissueInfoNotAvailableException

getInstance

public static TissueInfo_MemoryImpl getInstance(java.io.BufferedReader ti_to,
                                                java.io.BufferedReader ti_seq,
                                                java.lang.String[] organisms)
                                         throws TissueInfoNotAvailableException

TissueInfoNotAvailableException

loadTiTo

public void loadTiTo(java.io.BufferedReader ti_to)
              throws TissueInfoNotAvailableException

Loads a file representation of TissueInfo.

TissueInfoNotAvailableException

loadTiSeq

public void loadTiSeq(java.io.BufferedReader ti_seq)
               throws TissueInfoNotAvailableException

Loads a file representation of 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

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

getTissues

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

Return the tissue information associated with several sequence accession codes.

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

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. Subsequent use of methods of this instance is allowed.

Specified by:

empty in interface TissueInfo

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

main

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