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java.lang.Objectcom.compomics.util.experiment.identification.IdentificationDB
public class IdentificationDB
This class uses a database to manage identification matches.
Field Summary | |
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java.lang.String |
dbName
The name which will be used for the database. |
Constructor Summary | |
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IdentificationDB(java.lang.String folder,
java.lang.String name,
boolean deleteOldDatabase,
ObjectsCache objectCache)
Constructor creating the database and the protein and protein parameters tables. |
Method Summary | |
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void |
addMatch(IdentificationMatch match)
Adds an identification match to the database. |
void |
addMatchParameter(java.lang.String key,
UrParameter urParameter)
Deprecated. use match specific mapping instead |
void |
addPeptideMatch(PeptideMatch peptideMatch)
Adds a peptide match to the database |
void |
addPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a peptide match parameter to the database. |
void |
addProteinMatch(ProteinMatch proteinMatch)
Adds a protein match to the database. |
void |
addProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a protein match parameter to the database. |
void |
addSpectrumMatch(SpectrumMatch spectrumMatch)
Adds a spectrum match to the database. |
void |
addSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database. |
void |
close()
Closes the db connection. |
UrParameter |
getMatchPArameter(java.lang.String key,
UrParameter urParameter)
Deprecated. use match specific mapping instead |
java.lang.String |
getParameterTable(UrParameter urParameter)
Deprecated. use match specific mapping instead |
PeptideMatch |
getPeptideMatch(java.lang.String key)
Returns the desired peptide match. |
UrParameter |
getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired peptide match parameter. |
java.lang.String |
getPeptideParameterTable(UrParameter urParameter)
Returns the table name associated with the given peptide parameter. |
ProteinMatch |
getProteinMatch(java.lang.String key)
Returns the desired protein match. |
UrParameter |
getProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired protein match parameter. |
java.lang.String |
getProteinParameterTable(UrParameter urParameter)
Returns the table name associated with the given protein parameter. |
SpectrumMatch |
getSpectrumMatch(java.lang.String key)
Returns the desired spectrum match. |
UrParameter |
getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired spectrum match parameter. |
java.lang.String |
getSpectrumMatchTable(java.lang.String spectrumKey)
Returns the table name associated with the given spectrum key. |
java.lang.String |
getSpectrumParameterTable(java.lang.String spectrumKey,
UrParameter urParameter)
Returns the table name associated with the given spectrum parameter. |
void |
loadPeptideMatches(java.util.ArrayList<java.lang.String> peptideKeys,
WaitingHandler waitingHandler)
Loads the desired peptide matches of the given type in the cache of the database. |
void |
loadPeptideMatches(WaitingHandler waitingHandler)
Loads all peptide matches in the cache of the database. |
void |
loadPeptideMatchParameters(java.util.ArrayList<java.lang.String> peptideKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads the desired peptide match parameters of the given type in the cache of the database. |
void |
loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all peptide match parameters of the given type in the cache of the database. |
void |
loadProteinMatches(WaitingHandler waitingHandler)
Loads all protein matches in the cache of the database. |
void |
loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all protein match parameters of the given type in the cache of the database. |
void |
loadSpectrumMatches(java.util.ArrayList<java.lang.String> spectrumKeys,
WaitingHandler waitingHandler)
Loads all given spectrum matches in the cache of the database. |
void |
loadSpectrumMatches(java.lang.String fileName,
WaitingHandler waitingHandler)
Loads all spectrum matches of the given file in the cache of the database. |
void |
loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all desired spectrum match parameters in the cache of the database. |
void |
loadSpectrumMatchParameters(java.lang.String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all spectrum match parameters of the given type in the cache of the database. |
boolean |
peptideMatchLoaded(java.lang.String peptideKey)
Indicates whether a peptide match is loaded. |
boolean |
proteinMatchLoaded(java.lang.String proteinKey)
Indicates whether a protein match is loaded. |
void |
removeMatch(java.lang.String key)
Deprecated. it is advised to use the specific psm/peptide/protein method instead |
void |
removePeptideMatch(java.lang.String key)
Deletes a peptide match from the database. |
void |
removeProteinMatch(java.lang.String key)
Deletes a protein match from the database. |
void |
removeSpectrumMatch(java.lang.String key)
Deletes a spectrum match from the database. |
boolean |
spectrumMatchLoaded(java.lang.String spectrumKey)
Indicates whether a spectrum match is loaded. |
void |
updateMatch(IdentificationMatch match)
Updates a match. |
void |
updatePeptideMatch(PeptideMatch peptideMatch)
Updates a peptide match. |
void |
updatePeptideParameter(java.lang.String key,
UrParameter urParameter)
Updates a peptide match parameter. |
void |
updateProteinMatch(ProteinMatch proteinMatch)
Updates a protein match. |
void |
updateProteinParameter(java.lang.String key,
UrParameter urParameter)
Updates a protein match parameter. |
void |
updateSpectrumMatch(SpectrumMatch spectrumMatch)
Updates a spectrum match. |
void |
updateSpectrumParameter(java.lang.String key,
UrParameter urParameter)
Updates a spectrum match parameter. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public java.lang.String dbName
Constructor Detail |
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public IdentificationDB(java.lang.String folder, java.lang.String name, boolean deleteOldDatabase, ObjectsCache objectCache) throws java.sql.SQLException
folder
- the folder where to put the databasename
- deleteOldDatabase
- if true, tries to delete the old databaseobjectCache
-
java.sql.SQLException
- an exception thrown whenever an error occurred while
creating the databaseMethod Detail |
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public boolean spectrumMatchLoaded(java.lang.String spectrumKey) throws java.sql.SQLException
spectrumKey
- the spectrumMatch key
java.sql.SQLException
- exception thrown whenever an exception occurred
while interrogating the databasepublic boolean peptideMatchLoaded(java.lang.String peptideKey) throws java.sql.SQLException
peptideKey
- the peptide key
java.sql.SQLException
- exception thrown whenever an exception occurred
while interrogating the databasepublic boolean proteinMatchLoaded(java.lang.String proteinKey) throws java.sql.SQLException
proteinKey
- the protein key
java.sql.SQLException
- exception thrown whenever an exception occurred
while interrogating the databasepublic void updateProteinMatch(ProteinMatch proteinMatch) throws java.sql.SQLException, java.io.IOException
proteinMatch
- the protein match
java.sql.SQLException
- exception thrown whenever an error occurred while
updating a match in the table
java.io.IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updatePeptideMatch(PeptideMatch peptideMatch) throws java.sql.SQLException, java.io.IOException
peptideMatch
- the peptide match
java.sql.SQLException
- exception thrown whenever an error occurred while
updating a match in the table
java.io.IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateSpectrumMatch(SpectrumMatch spectrumMatch) throws java.sql.SQLException, java.io.IOException
spectrumMatch
- the spectrum match
java.sql.SQLException
- exception thrown whenever an error occurred while
updating a match in the table
java.io.IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateMatch(IdentificationMatch match) throws java.sql.SQLException, java.io.IOException
match
- the match to update
java.sql.SQLException
- exception thrown whenever an error occurred while
updating a match in the table
java.io.IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateProteinParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException
key
- the key of the protein matchurParameter
- the parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
updating the parameter in the table
java.io.IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updatePeptideParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException
key
- the key of the peptide matchurParameter
- the parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
updating the parameter in the table
java.io.IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateSpectrumParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException
key
- the key of the spectrum matchurParameter
- the parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
updating the parameter in the table
java.io.IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void removeProteinMatch(java.lang.String key) throws java.sql.SQLException, java.io.IOException
key
- the key of the match
java.sql.SQLException
- exception thrown whenever an error occurred while
deleting the match
java.io.IOException
public void removePeptideMatch(java.lang.String key) throws java.sql.SQLException, java.io.IOException
key
- the key of the match
java.sql.SQLException
- exception thrown whenever an error occurred while
deleting the match
java.io.IOException
public void removeSpectrumMatch(java.lang.String key) throws java.sql.SQLException, java.io.IOException
key
- the key of the match
java.sql.SQLException
- exception thrown whenever an error occurred while
deleting the match
java.io.IOException
public void removeMatch(java.lang.String key) throws java.sql.SQLException, java.io.IOException
key
- the key of the match
java.sql.SQLException
- exception thrown whenever an error occurred while
deleting the match
java.io.IOException
public SpectrumMatch getSpectrumMatch(java.lang.String key) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
key
- the psm key
java.sql.SQLException
- exception thrown whenever an error occurred while
loading the object from the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the object in the database
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addSpectrumMatch(SpectrumMatch spectrumMatch) throws java.sql.SQLException, java.io.IOException
spectrumMatch
- the spectrum match to be added
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic PeptideMatch getPeptideMatch(java.lang.String key) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
key
- the peptide key
java.sql.SQLException
- exception thrown whenever an error occurred while
loading the object from the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the object in the database
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addPeptideMatch(PeptideMatch peptideMatch) throws java.sql.SQLException, java.io.IOException
peptideMatch
- the peptide match to be added
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic ProteinMatch getProteinMatch(java.lang.String key) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
key
- the protein key
java.sql.SQLException
- exception thrown whenever an error occurred while
loading the object from the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the object in the database
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addProteinMatch(ProteinMatch proteinMatch) throws java.sql.SQLException, java.io.IOException
proteinMatch
- the protein match to be added
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic void addMatch(IdentificationMatch match) throws java.sql.SQLException, java.io.IOException
match
- the match to be added
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic void loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
urParameter
- the parameter typewaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadPeptideMatchParameters(java.util.ArrayList<java.lang.String> peptideKeys, UrParameter urParameter, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
peptideKeys
- the list of peptide keys of the parameters to loadurParameter
- the parameter typewaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadPeptideMatches(java.util.ArrayList<java.lang.String> peptideKeys, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
peptideKeys
- the list of peptide keys to loadwaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
urParameter
- the parameter typewaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadProteinMatches(WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
waitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadPeptideMatches(WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
waitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadSpectrumMatches(java.lang.String fileName, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
fileName
- the file namewaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadSpectrumMatches(java.util.ArrayList<java.lang.String> spectrumKeys, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
spectrumKeys
- the key of the spectrum matches to be loadedwaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadSpectrumMatchParameters(java.lang.String fileName, UrParameter urParameter, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
fileName
- the file nameurParameter
- the parameter typewaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public void loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
spectrumKeys
- the key of the spectrum match of the parameters to be
loadedurParameter
- the parameter typewaitingHandler
- the waiting handler
java.sql.SQLException
- exception thrown whenever an error occurred while
interrogating the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public UrParameter getSpectrumMatchParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
key
- the psm keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
loading the object from the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the object in the database
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addSpectrumMatchParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException
key
- the psm keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic UrParameter getPeptideMatchParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
key
- the peptide keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
loading the object from the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the object in the database
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addPeptideMatchParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException
key
- the peptide keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic UrParameter getProteinMatchParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
key
- the protein keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
loading the object from the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the object in the database
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addProteinMatchParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException
key
- the protein keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic UrParameter getMatchPArameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
key
- the match keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
loading the object from the database
java.io.IOException
- exception thrown whenever an error occurred while
reading the object in the database
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addMatchParameter(java.lang.String key, UrParameter urParameter) throws java.sql.SQLException, java.io.IOException
key
- the protein keyurParameter
- the match parameter
java.sql.SQLException
- exception thrown whenever an error occurred while
adding the object in the database
java.io.IOException
- exception thrown whenever an error occurred while
writing the objectpublic java.lang.String getSpectrumMatchTable(java.lang.String spectrumKey)
spectrumKey
- the given spectrum key
public java.lang.String getSpectrumParameterTable(java.lang.String spectrumKey, UrParameter urParameter)
spectrumKey
- the given spectrum keyurParameter
- the parameter
public java.lang.String getPeptideParameterTable(UrParameter urParameter)
urParameter
- the parameter
public java.lang.String getProteinParameterTable(UrParameter urParameter)
urParameter
- the parameter
public java.lang.String getParameterTable(UrParameter urParameter)
urParameter
- the parameter
public void close() throws java.sql.SQLException
java.sql.SQLException
- exception thrown whenever an error occurred while
closing the database connection
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