org.forester.phylogeny.data

Class ProteinDomain

java.lang.Object

org.forester.phylogeny.data.ProteinDomain

All Implemented Interfaces:

PhylogenyData

public class ProteinDomain
extends Object
implements PhylogenyData

Field Summary

Fields

Modifier and Type	Field and Description
static double	CONFIDENCE_DEFAULT
static String	IDENTIFIER_DEFAULT

Constructor Summary

Constructors

Constructor and Description
ProteinDomain(String name, int from, int to)
ProteinDomain(String name, int from, int to, double confidence)
ProteinDomain(String name, int from, int to, String id)
ProteinDomain(String name, int from, int to, String id, double confidence)

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.
double	getConfidence()
int	getFrom()
String	getId()
int	getLength()
String	getName()
int	getTo()
boolean	isEqual(PhylogenyData protein_domain) Compares this PhylogenyData to PhylogenyData data.
StringBuffer	toNHX()
void	toPhyloXML(Writer writer, int level, String indentation) Writes a phyloXML representation of this phylogeny data.
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

CONFIDENCE_DEFAULT

public static final double CONFIDENCE_DEFAULT

See Also:

Constant Field Values

IDENTIFIER_DEFAULT

public static final String IDENTIFIER_DEFAULT

See Also:

Constant Field Values

Constructor Detail

ProteinDomain

public ProteinDomain(String name,
                     int from,
                     int to)

ProteinDomain

public ProteinDomain(String name,
                     int from,
                     int to,
                     double confidence)

ProteinDomain

public ProteinDomain(String name,
                     int from,
                     int to,
                     String id)

ProteinDomain

public ProteinDomain(String name,
                     int from,
                     int to,
                     String id,
                     double confidence)

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 double getConfidence()

getFrom

public int getFrom()

getId

public String getId()

getLength

public int getLength()

getName

public String getName()

getTo

public int getTo()

isEqual

public boolean isEqual(PhylogenyData protein_domain)

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

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

toString

public String toString()

Overrides:

toString in class Object