Package com.compomics.util.experiment.identification.matches_iterators

Class MatchesIterator

java.lang.Object

com.compomics.util.experiment.identification.matches_iterators.MatchesIterator

Direct Known Subclasses:

PeptideMatchesIterator, ProteinMatchesIterator, SpectrumMatchesIterator

public abstract class MatchesIterator
extends Object

An abstract iterator class to iterate identification matches. Note: multiple threads are synchronized using semaphores. Should a thread be interrupted, the exception will be sent as RunTimeException. This is because our tools recover from these exceptions similarly as for other unchecked exceptions. Please contact us if you need another/better exception handling.

Author:

Dominik Kopczynski, Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor	Description
MatchesIterator(long[] keys, Class className, Identification identification, WaitingHandler waitingHandler, boolean displayProgress, String filters)	Constructor.
MatchesIterator(Class className, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.

Method Summary

Modifier and Type	Method	Description
Object	nextObject()	Returns the next match and updates the buffer.

Methods inherited from class java.lang.Object

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

Constructor Details

MatchesIterator

public MatchesIterator(Class className,
 Identification identification,
 WaitingHandler waitingHandler,
 boolean displayProgress)

Constructor.

Parameters:

className - the class name

identification - the identification where to get the matches from

waitingHandler - the waiting handler allowing displaying progress and canceling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on the waiting handler

MatchesIterator

public MatchesIterator(long[] keys,
 Class className,
 Identification identification,
 WaitingHandler waitingHandler,
 boolean displayProgress,
 String filters)

Constructor.

Parameters:

keys - the keys of the objects

className - the className

identification - the identification where to get the matchesloadPs from

waitingHandler - the waiting handler allowing displaying progress and canceling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on the waiting handler

filters - filters for the class

Method Details

nextObject

public Object nextObject()

Returns the next match and updates the buffer. Null if the iterator is done iterating or the iteration has been cancelled.

Returns:

the next match