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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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static String |
dbName
The name which will be used for the database |
static String |
matchSize
The maximal size for a BLOB match in the database |
static String |
parametersSize
The maximal size for a BLOB parameter match in the database |
Constructor Summary | |
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IdentificationDB(String folder)
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(String key,
UrParameter urParameter)
Deprecated. use match specific mapping instead |
void |
addPeptideMatch(PeptideMatch peptideMatch)
Adds a peptide match to the database |
void |
addPeptideMatchParameter(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(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(String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database |
void |
close()
Closes the db connection |
void |
deleteObject(String tableName,
String objectKey)
Deletes an object from the desired table. |
void |
establishConnection()
Establishes connection to the database |
UrParameter |
getMatchPArameter(String key,
UrParameter urParameter)
Deprecated. use match specific mapping instead |
String |
getParameterTable(UrParameter urParameter)
Deprecated. use match specific mapping instead |
PeptideMatch |
getPeptideMatch(String key)
Returns the desired peptide match |
UrParameter |
getPeptideMatchParameter(String key,
UrParameter urParameter)
Returns the desired peptide match parameter |
String |
getPeptideParameterTable(UrParameter urParameter)
Returns the table name associated to the given peptide parameter |
ProteinMatch |
getProteinMatch(String key)
Returns the desired protein match |
UrParameter |
getProteinMatchPArameter(String key,
UrParameter urParameter)
Returns the desired protein match parameter |
String |
getProteinParameterTable(UrParameter urParameter)
Returns the table name associated to the given protein parameter |
SpectrumMatch |
getSpectrumMatch(String key)
Returns the desired spectrum match |
UrParameter |
getSpectrumMatchParameter(String key,
UrParameter urParameter)
Returns the desired spectrum match parameter. |
String |
getSpectrumMatchTable(String spectrumKey)
Returns the table name associated to the given spectrum key |
String |
getSpectrumParameterTable(String spectrumKey,
UrParameter urParameter)
Returns the table name associated to the given spectrum parameter |
boolean |
inDB(String tableName,
String objectKey)
Indicates whether an object is loaded in the given table |
void |
insertObject(String tableName,
String objectKey,
Object object)
Stores an object in the desired table |
boolean |
peptideMatchInDB(String peptideKey)
Indicates whether a peptide match is loaded |
boolean |
proteinMatchInDB(String proteinKey)
Indicates whether a protein match is loaded |
String |
removeForbiddenCharacters(String tableName)
Removes the characters forbidden in table names and puts a '_' instead |
void |
removeMatch(String key)
Deprecated. it is advised to use the specific psm/peptide/protein method instead |
void |
removePeptideMatch(String key)
Deletes a peptide match from the database |
void |
removeProteinMatch(String key)
Deletes a protein match from the database |
void |
removeSpectrumMatch(String key)
Deletes a spectrum match from the database |
Object |
retrieveObject(String tableName,
String objectKey)
Retrieves an object from the desired table. |
boolean |
spectrumMatchInDB(String spectrumKey)
Indicates whether a spectrum match is loaded |
void |
updateMatch(IdentificationMatch match)
updates a match |
void |
updateObject(String tableName,
String objectKey,
Object object)
Stores an object in the desired table |
void |
updatePeptideMatch(PeptideMatch peptideMatch)
updates a peptide match |
void |
updatePeptideParameter(String key,
UrParameter urParameter)
Updates a peptide match parameter |
void |
updateProteinMatch(ProteinMatch proteinMatch)
updates a protein match |
void |
updateProteinParameter(String key,
UrParameter urParameter)
Updates a protein match parameter |
void |
updateSpectrumMatch(SpectrumMatch spectrumMatch)
updates a spectrum match |
void |
updateSpectrumParameter(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 static final String dbName
public static final String matchSize
public static final String parametersSize
Constructor Detail |
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public IdentificationDB(String folder) throws SQLException
folder
- the folder where to put the database
SQLException
- an exception thrown whenever an error occurred while
creating the databaseMethod Detail |
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public void insertObject(String tableName, String objectKey, Object object) throws SQLException, IOException
tableName
- the name of the tableobjectKey
- the key of the objectobject
- the object to store
SQLException
- exception thrown whenever an error occurred while
storing the object
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic Object retrieveObject(String tableName, String objectKey) throws SQLException, IOException, ClassNotFoundException
tableName
- the name of the tableobjectKey
- the object key
SQLException
- exception thrown whenever an error occurred while
interrogating the database
IOException
- exception thrown whenever an error occurred while
reading the database
ClassNotFoundException
- exception thrown whenever the class of the
object is not found when deserializing it.public boolean inDB(String tableName, String objectKey) throws SQLException
tableName
- the table nameobjectKey
- the object key
SQLException
- exception thrown whenever an exception occurred
while interrogating the databasepublic boolean spectrumMatchInDB(String spectrumKey) throws SQLException
tableName
- the table namespectrumKey
- the spectrumMatch key
SQLException
- exception thrown whenever an exception occurred
while interrogating the databasepublic boolean peptideMatchInDB(String peptideKey) throws SQLException
tableName
- the table namepeptideKey
- the peptide key
SQLException
- exception thrown whenever an exception occurred
while interrogating the databasepublic boolean proteinMatchInDB(String proteinKey) throws SQLException
tableName
- the table nameproteinKey
- the protein key
SQLException
- exception thrown whenever an exception occurred
while interrogating the databasepublic void deleteObject(String tableName, String objectKey) throws SQLException
tableName
- the name of the tableobjectKey
- the object key
SQLException
- exception thrown whenever an error occurred while
interrogating the databasepublic void updateObject(String tableName, String objectKey, Object object) throws SQLException, IOException
tableName
- the name of the tableobjectKey
- the key of the objectobject
- the object to store
SQLException
- exception thrown whenever an error occurred while
storing the object
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateProteinMatch(ProteinMatch proteinMatch) throws SQLException, IOException
proteinMatch
- the protein match
SQLException
- exception thrown whenever an error occurred while
updating a match in the table
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updatePeptideMatch(PeptideMatch peptideMatch) throws SQLException, IOException
peptideMatch
- the peptide match
SQLException
- exception thrown whenever an error occurred while
updating a match in the table
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateSpectrumMatch(SpectrumMatch spectrumMatch) throws SQLException, IOException
spectrumMatch
- the spectrum match
SQLException
- exception thrown whenever an error occurred while
updating a match in the table
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateMatch(IdentificationMatch match) throws SQLException, IOException
match
- the match to update
SQLException
- exception thrown whenever an error occurred while
updating a match in the table
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateProteinParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the key of the protein matchurParameter
- the parameter
SQLException
- exception thrown whenever an error occurred while
updating the parameter in the table
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updatePeptideParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the key of the peptide matchurParameter
- the parameter
SQLException
- exception thrown whenever an error occurred while
updating the parameter in the table
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void updateSpectrumParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the key of the spectrum matchurParameter
- the parameter
SQLException
- exception thrown whenever an error occurred while
updating the parameter in the table
IOException
- exception thrown whenever an error occurred while
writing in the databasepublic void removeProteinMatch(String key) throws SQLException
key
- the key of the match
SQLException
- exception thrown whenever an error occurred while
deleting the matchpublic void removePeptideMatch(String key) throws SQLException
key
- the key of the match
SQLException
- exception thrown whenever an error occurred while
deleting the matchpublic void removeSpectrumMatch(String key) throws SQLException
key
- the key of the match
SQLException
- exception thrown whenever an error occurred while
deleting the matchpublic void removeMatch(String key) throws SQLException
key
- the key of the match
SQLException
- exception thrown whenever an error occurred while
deleting the matchpublic SpectrumMatch getSpectrumMatch(String key) throws SQLException, IOException, ClassNotFoundException
key
- the psm key
SQLException
- exception thrown whenever an error occurred while
loading the object from the database
IOException
- exception thrown whenever an error occurred while
reading the object in the database
ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addSpectrumMatch(SpectrumMatch spectrumMatch) throws SQLException, IOException
spectrumMatch
- the spectrum match to be added
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic PeptideMatch getPeptideMatch(String key) throws SQLException, IOException, ClassNotFoundException
key
- the peptide key
SQLException
- exception thrown whenever an error occurred while
loading the object from the database
IOException
- exception thrown whenever an error occurred while
reading the object in the database
ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addPeptideMatch(PeptideMatch peptideMatch) throws SQLException, IOException
peptideMatch
- the peptide match to be added
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic ProteinMatch getProteinMatch(String key) throws SQLException, IOException, ClassNotFoundException
key
- the protein key
SQLException
- exception thrown whenever an error occurred while
loading the object from the database
IOException
- exception thrown whenever an error occurred while
reading the object in the database
ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addProteinMatch(ProteinMatch proteinMatch) throws SQLException, IOException
proteinMatch
- the protein match to be added
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic void addMatch(IdentificationMatch match) throws SQLException, IOException
match
- the match to be added
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic UrParameter getSpectrumMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, ClassNotFoundException
key
- the psm keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
loading the object from the database
IOException
- exception thrown whenever an error occurred while
reading the object in the database
ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addSpectrumMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the psm keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic UrParameter getPeptideMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, ClassNotFoundException
key
- the peptide keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
loading the object from the database
IOException
- exception thrown whenever an error occurred while
reading the object in the database
ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addPeptideMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the peptide keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic UrParameter getProteinMatchPArameter(String key, UrParameter urParameter) throws SQLException, IOException, ClassNotFoundException
key
- the protein keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
loading the object from the database
IOException
- exception thrown whenever an error occurred while
reading the object in the database
ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addProteinMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the protein keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic UrParameter getMatchPArameter(String key, UrParameter urParameter) throws SQLException, IOException, ClassNotFoundException
key
- the match keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
loading the object from the database
IOException
- exception thrown whenever an error occurred while
reading the object in the database
ClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classpublic void addMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the protein keyurParameter
- the match parameter
SQLException
- exception thrown whenever an error occurred while
adding the object in the database
IOException
- exception thrown whenever an error occurred while
writing the objectpublic String getSpectrumMatchTable(String spectrumKey)
spectrumKey
- the given spectrum key
public String getSpectrumParameterTable(String spectrumKey, UrParameter urParameter)
spectrumKey
- the given spectrum keyurParameter
- the parameter
public String getPeptideParameterTable(UrParameter urParameter)
urParameter
- the parameter
public String getProteinParameterTable(UrParameter urParameter)
urParameter
- the parameter
public String getParameterTable(UrParameter urParameter)
urParameter
- the parameter
public void close() throws SQLException
SQLException
- exception thrown whenever an error occurred while
closing the database connectionpublic void establishConnection() throws SQLException
SQLException
- exception thrown whenever an error occurred while establishing the connectionpublic String removeForbiddenCharacters(String tableName)
tableName
- the table name
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