com.compomics.util.experiment.identification.matches_iterators

Class PsmIterator

java.lang.Object

com.compomics.util.experiment.identification.matches_iterators.PsmIterator

public class PsmIterator
extends Object

An iterator for spectrum matches.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field and Description
int	defaultBatchSize The default batch size.
double	defaultMargin The default margin to use to start batch loading before the loading index is reached.

Constructor Summary

Constructors

Constructor and Description
PsmIterator(ArrayList<String> spectrumKeys, Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(ArrayList<String> spectrumKeys, Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, ArrayList<String> spectrumKeys, Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, ArrayList<String> spectrumKeys, Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, Identification identification, boolean loadAssumptions, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.

Method Summary

Modifier and Type	Method and Description
boolean	hasNext() Indicates whether the iterator is done iterating.
SpectrumMatch	next() Returns the next match and updates the buffer.
void	setBatchSize(int batchSize) Set the batch size.

Methods inherited from class java.lang.Object

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

Field Detail

defaultBatchSize

public final int defaultBatchSize

The default batch size.

See Also:

Constant Field Values

defaultMargin

public final double defaultMargin

The default margin to use to start batch loading before the loading index is reached.

See Also:

Constant Field Values

Constructor Detail

PsmIterator

public PsmIterator(String spectrumFile,
                   ArrayList<String> spectrumKeys,
                   Identification identification,
                   ArrayList<UrParameter> psmParameters,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

spectrumFile - the spectrum file to iterate

spectrumKeys - the keys to iterate

identification - the identification where to get the matches from

psmParameters - the parameters to load along with the matches

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(ArrayList<String> spectrumKeys,
                   Identification identification,
                   ArrayList<UrParameter> psmParameters,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

spectrumKeys - the keys to iterate

identification - the identification where to get the matches from

psmParameters - the parameters to load along with the matches

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(ArrayList<String> spectrumKeys,
                   Identification identification,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

spectrumKeys - the keys to iterate

identification - the identification where to get the matches from

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(String spectrumFile,
                   ArrayList<String> spectrumKeys,
                   Identification identification,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

spectrumFile - the spectrum file to iterate

spectrumKeys - the keys to iterate

identification - the identification where to get the matches from

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(String spectrumFile,
                   Identification identification,
                   ArrayList<UrParameter> psmParameters,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

spectrumFile - the spectrum file to iterate

identification - the identification where to get the matches from

psmParameters - the parameters to load along with the matches

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(String spectrumFile,
                   Identification identification,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

spectrumFile - the spectrum file to iterate

identification - the identification where to get the matches from

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(String spectrumFile,
                   Identification identification,
                   boolean loadAssumptions,
                   ArrayList<UrParameter> psmParameters,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

spectrumFile - the spectrum file to iterate

identification - the identification where to get the matches from

psmParameters - the parameters to load along with the matches

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(Identification identification,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

identification - the identification where to get the matches from

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

PsmIterator

public PsmIterator(Identification identification,
                   ArrayList<UrParameter> psmParameters,
                   boolean loadAssumptions,
                   WaitingHandler waitingHandler)

Constructor.

Parameters:

identification - the identification where to get the matches from

psmParameters - the parameters to load along with the matches

loadAssumptions - if true the assumptions will be loaded as well

waitingHandler - the waiting handler

Method Detail

hasNext

public boolean hasNext()

Indicates whether the iterator is done iterating. Warning: this method can be wrong when multi threading.

Returns:

false if the iterator is done iterating

next

public SpectrumMatch next()
                   throws SQLException,
                          IOException,
                          ClassNotFoundException,
                          InterruptedException

Returns the next match and updates the buffer. Null if the iterator is done iterating.

Returns:

the next match

Throws:

SQLException - exception thrown whenever an error occurred while interacting with the matches database

IOException - exception thrown whenever an error occurred while interacting with the matches database

ClassNotFoundException - exception thrown whenever an error occurred while deserializing a match from the database

InterruptedException - exception thrown whenever a threading issue occurred while retrieving the match

setBatchSize

public void setBatchSize(int batchSize)

Set the batch size.

Parameters:

batchSize - the batch size