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

Description

static enum

SequenceRelation.SEQUENCE_RELATION_TYPE
Field Summary

Fields

Modifier and Type

Field

Description

static final String

SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY

static final String

SEQUENCE_RELATION_TYPE_ORTHOLOGY

static final String

SEQUENCE_RELATION_TYPE_OTHER

static final String

SEQUENCE_RELATION_TYPE_PARALOGY

static final String

SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY

static final String

SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY

static final String

SEQUENCE_RELATION_TYPE_UNKNOWN

static final String

SEQUENCE_RELATION_TYPE_XENOLOGY

static final Map<SequenceRelation.SEQUENCE_RELATION_TYPE,String>

typesToNames
Constructor Summary

Constructors

Constructor

Description

SequenceRelation()
Method Summary

Modifier and Type

Method

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 Details
- 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 Details
- SequenceRelation
  
  public SequenceRelation()
Method Details
- 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)

Class SequenceRelation

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

typesToNames

SEQUENCE_RELATION_TYPE_ORTHOLOGY

SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY

SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY

SEQUENCE_RELATION_TYPE_PARALOGY

SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY

SEQUENCE_RELATION_TYPE_XENOLOGY

SEQUENCE_RELATION_TYPE_UNKNOWN

SEQUENCE_RELATION_TYPE_OTHER

Constructor Details

SequenceRelation

Method Details

asSimpleText

asText

copy

getConfidence

getDistance

getRef0

getRef1

getType

isEqual

setConfidence

setDistance

setRef0

setRef1

setType

toNHX

toPhyloXML

getPrintableNameByType