com.compomics.util.experiment.identification.matches_iterators

Class ProteinMatchesIterator

java.lang.Object

com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator

public class ProteinMatchesIterator
extends Object

An iterator of protein 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
ProteinMatchesIterator(ArrayList<String> proteinKeys, Identification identification, ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor.
ProteinMatchesIterator(Identification identification, ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor for an iterator iterating all protein keys.

Method Summary

Modifier and Type	Method and Description
boolean	hasNext() Indicates whether the iterator is done iterating.
ProteinMatch	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

ProteinMatchesIterator

public ProteinMatchesIterator(ArrayList<String> proteinKeys,
                              Identification identification,
                              ArrayList<UrParameter> proteinParameters,
                              boolean loadPeptides,
                              ArrayList<UrParameter> peptideParameters,
                              boolean loadPsms,
                              ArrayList<UrParameter> psmParameters,
                              WaitingHandler waitingHandler)

Constructor.

Parameters:

proteinKeys - the keys of the proteins to iterate

identification - the identification where to get the matches from

proteinParameters - the protein parameters to load along with the matches

loadPeptides - if true the peptides corresponding to these proteins will be batch loaded along with the proteins

peptideParameters - the parameters to load along with the peptide matches

loadPsms - if true the PSMs of the peptides will be batch loaded along with the matches

psmParameters - the parameters to load along with the matches

waitingHandler - the waiting handler

ProteinMatchesIterator

public ProteinMatchesIterator(Identification identification,
                              ArrayList<UrParameter> proteinParameters,
                              boolean loadPeptides,
                              ArrayList<UrParameter> peptideParameters,
                              boolean loadPsms,
                              ArrayList<UrParameter> psmParameters,
                              WaitingHandler waitingHandler)

Constructor for an iterator iterating all protein keys.

Parameters:

identification - the identification where to get the matches from

proteinParameters - the protein parameters to load along with the matches

loadPeptides - if true the peptides corresponding to these proteins will be batch loaded along with the proteins

peptideParameters - the parameters to load along with the peptide matches

loadPsms - if true the PSMs of the peptides will be batch loaded along with the matches

psmParameters - the parameters to load along with the matches

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 ProteinMatch 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