info.bioinfweb.libralign.model.implementations

Class AbstractSequenceIDIterator<P extends AlignmentModel>

java.lang.Object

info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator<P>

Type Parameters:

P - the implementing class of AlignmentModel which will return the iterator inherited from this class

All Implemented Interfaces:

java.util.Iterator<java.lang.String>

public abstract class AbstractSequenceIDIterator<P extends AlignmentModel>
extends java.lang.Object
implements java.util.Iterator<java.lang.String>

Abstract implementation of an iterator returning the IDs of all sequences provided by an implementation of AlignmentModel.

Besides the sequence provider this class needs another iterator as a constructor parameter which is responsible for returning new IDs in the correct order. This class implements a remove method which throws an UnsupportedOperationException if the underlying data source does not allow writing sequences and calls the remove methods of the specified iterator. Additionally it offers an abstract method doRemove() that allows the implementations of AlignmentModel to perform additional specific removal operations. When overwriting this method the ID that is currently removed can be obtained by getCurrentID().

Since:

0.1.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
AbstractSequenceIDIterator(P model, java.util.Iterator<java.lang.String> iterator) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected abstract void	doRemove() Overwrite this method to perform implementation specific remove operations.
protected java.lang.String	getCurrentID() The ID that has been returned by this iterator by the last call of next().
protected java.util.Iterator<java.lang.String>	getIterator() Returns the underlying iterator object.
protected P	getModel() Returns the sequence data provider that returned this iterator.
boolean	hasNext()
java.lang.String	next()
void	remove() Removes the current ID from the underlying iterator and calls doRemove().

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

AbstractSequenceIDIterator

public AbstractSequenceIDIterator(P model,
                                  java.util.Iterator<java.lang.String> iterator)

Creates a new instance of this class.

Parameters:

model - the provider that is going to return this iterator with one of its methods

iterator - the underlying iterator that returns the sequence IDs in the correct order

Method Detail

getModel

protected P getModel()

Returns the sequence data provider that returned this iterator.

Returns:

the provider instance specified in the constructor of this class.

getIterator

protected java.util.Iterator<java.lang.String> getIterator()

Returns the underlying iterator object.

Returns:

the iterator instance specifying the ID order

getCurrentID

protected java.lang.String getCurrentID()

The ID that has been returned by this iterator by the last call of next().

Returns:

the current ID or null if next() has never been called until now

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<java.lang.String>

next

public java.lang.String next()

Specified by:

next in interface java.util.Iterator<java.lang.String>

doRemove

protected abstract void doRemove()

Overwrite this method to perform implementation specific remove operations.

This method is called by remove() if the underlying data source in writable for sequences. The remove() method of the underlying iterator has already been called before the call of this method, therefore this method will not be executed, if an exception was thrown by getIterator().remove().

remove

public void remove()

Removes the current ID from the underlying iterator and calls doRemove().

Specified by:

remove in interface java.util.Iterator<java.lang.String>

Throws:

java.lang.UnsupportedOperationException - if next() has not yet been called or the underlying data source is not writable for sequences or the underlying iterator does not support this operation

See Also:

Iterator.remove()