org.forester.phylogeny.data

Class SequenceRelation

java.lang.Object

org.forester.phylogeny.data.SequenceRelation

All Implemented Interfaces:

PhylogenyData

public class SequenceRelation
extends Object
implements PhylogenyData

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SequenceRelation.SEQUENCE_RELATION_TYPE

Field Summary

Fields

Modifier and Type	Field and Description
static String	SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY
static String	SEQUENCE_RELATION_TYPE_ORTHOLOGY
static String	SEQUENCE_RELATION_TYPE_OTHER
static String	SEQUENCE_RELATION_TYPE_PARALOGY
static String	SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY
static String	SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY
static String	SEQUENCE_RELATION_TYPE_UNKNOWN
static String	SEQUENCE_RELATION_TYPE_XENOLOGY
static Map<SequenceRelation.SEQUENCE_RELATION_TYPE,String>	typesToNames

Constructor Summary

Constructors

Constructor and Description
SequenceRelation()

Method Summary

Modifier and Type	Method and Description
StringBuffer	asSimpleText()
StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
Confidence	getConfidence()
Double	getDistance()
static String	getPrintableNameByType(SequenceRelation.SEQUENCE_RELATION_TYPE type)
Sequence	getRef0()
Sequence	getRef1()
SequenceRelation.SEQUENCE_RELATION_TYPE	getType()
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
void	setConfidence(Confidence confidence)
void	setDistance(Double distance)
void	setRef0(Sequence ref0)
void	setRef1(Sequence ref1)
void	setType(SequenceRelation.SEQUENCE_RELATION_TYPE type)
StringBuffer	toNHX()
void	toPhyloXML(Writer writer, int level, String indentation) Writes a phyloXML representation of this phylogeny data.

Methods inherited from class java.lang.Object

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

Field Detail

typesToNames

public static final Map<SequenceRelation.SEQUENCE_RELATION_TYPE,String> typesToNames

SEQUENCE_RELATION_TYPE_ORTHOLOGY

public static final String SEQUENCE_RELATION_TYPE_ORTHOLOGY

See Also:

Constant Field Values

SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY

public static final String SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY

See Also:

Constant Field Values

SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY

public static final String SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY

See Also:

Constant Field Values

SEQUENCE_RELATION_TYPE_PARALOGY

public static final String SEQUENCE_RELATION_TYPE_PARALOGY

See Also:

Constant Field Values

SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY

public static final String SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY

See Also:

Constant Field Values

SEQUENCE_RELATION_TYPE_XENOLOGY

public static final String SEQUENCE_RELATION_TYPE_XENOLOGY

See Also:

Constant Field Values

SEQUENCE_RELATION_TYPE_UNKNOWN

public static final String SEQUENCE_RELATION_TYPE_UNKNOWN

See Also:

Constant Field Values

SEQUENCE_RELATION_TYPE_OTHER

public static final String SEQUENCE_RELATION_TYPE_OTHER

See Also:

Constant Field Values

Constructor Detail

SequenceRelation

public SequenceRelation()

Method Detail

asSimpleText

public StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public StringBuffer asText()

Specified by:

asText in interface PhylogenyData

copy

public PhylogenyData copy()

Description copied from interface: PhylogenyData

Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.

Specified by:

copy in interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

getConfidence

public Confidence getConfidence()

getDistance

public Double getDistance()

getRef0

public Sequence getRef0()

getRef1

public Sequence getRef1()

getType

public SequenceRelation.SEQUENCE_RELATION_TYPE getType()

isEqual

public boolean isEqual(PhylogenyData data)

Description copied from interface: PhylogenyData

Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.

Specified by:

isEqual in interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

setConfidence

public void setConfidence(Confidence confidence)

setDistance

public void setDistance(Double distance)

setRef0

public void setRef0(Sequence ref0)

setRef1

public void setRef1(Sequence ref1)

setType

public void setType(SequenceRelation.SEQUENCE_RELATION_TYPE type)

toNHX

public StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(Writer writer,
                       int level,
                       String indentation)
                throws IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

IOException

getPrintableNameByType

public static String getPrintableNameByType(SequenceRelation.SEQUENCE_RELATION_TYPE type)