info.bioinfweb.jphyloio.utils

Class SequenceTokensEventManager

java.lang.Object

info.bioinfweb.jphyloio.utils.SequenceTokensEventManager

public class SequenceTokensEventManager
extends java.lang.Object

Class used by implementations of JPhyloIOEventReader to keep track of the current alignment position and replacing match tokens by the according tokens from the first sequence.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
SequenceTokensEventManager(JPhyloIOEventReader owner, java.lang.String matchToken) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
SequenceTokensEvent	createEvent(java.lang.String sequenceID, java.util.List<java.lang.String> tokens) Creates a sequence character event object from the provided data and manages the replacement of match tokens by tokens of the first sequence.
long	getCurrentBlockLength()
long	getCurrentBlockStartPosition()
long	getCurrentPosition()
java.lang.String	getCurrentSequenceName()
java.util.List<java.lang.String>	getFirstSequence()
java.lang.String	getFirstSequenceName()
java.lang.String	getMatchToken()
JPhyloIOEventReader	getOwner() Returns the reader instance using this object.
void	setMatchToken(java.lang.String matchToken)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceTokensEventManager

public SequenceTokensEventManager(JPhyloIOEventReader owner,
                                  java.lang.String matchToken)

Creates a new instance of this class.

Parameters:

owner - the PhyloIO event reader using the returned instance

matchToken - the match token to be replaced in sequences or null if no replacement shall be performed

Throws:

java.lang.NullPointerException - if owner is set to null

Method Detail

getOwner

public JPhyloIOEventReader getOwner()

Returns the reader instance using this object.

Returns:

the reader class (never null)

getMatchToken

public java.lang.String getMatchToken()

setMatchToken

public void setMatchToken(java.lang.String matchToken)

getCurrentPosition

public long getCurrentPosition()

getCurrentBlockStartPosition

public long getCurrentBlockStartPosition()

getCurrentBlockLength

public long getCurrentBlockLength()

getFirstSequenceName

public java.lang.String getFirstSequenceName()

getCurrentSequenceName

public java.lang.String getCurrentSequenceName()

getFirstSequence

public java.util.List<java.lang.String> getFirstSequence()

createEvent

public SequenceTokensEvent createEvent(java.lang.String sequenceID,
                                       java.util.List<java.lang.String> tokens)

Creates a sequence character event object from the provided data and manages the replacement of match tokens by tokens of the first sequence.

This method stores the tokens of the first sequence and the current sequence position. Therefore implementing readers supporting match token replacement must always use this method to create sequence character event objects and never do this directly, otherwise the replacement by this method will not work.

Note that the algorithm for position monitoring will only work for interleaved formats where each sequence part has the same length in each block or for non-interleaved formats (where each sequence only occurs once).

Parameters:

sequenceID - the event ID or another unique name of the sequence to append the tokens to

tokens - the newly read tokens

Returns:

the event object

Throws:

java.lang.NullPointerException - if either sequenceID or tokens is null