org.forester.phylogeny.data

Class DomainArchitecture

java.lang.Object

org.forester.phylogeny.data.DomainArchitecture

All Implemented Interfaces:

PhylogenyData

Direct Known Subclasses:

RenderableDomainArchitecture

public class DomainArchitecture
extends java.lang.Object
implements PhylogenyData

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	NHX_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
DomainArchitecture()
DomainArchitecture(java.util.List<PhylogenyData> domains, int total_length)
DomainArchitecture(java.lang.String da_str)

Method Summary

Methods

Modifier and Type	Method and Description
void	addDomain(ProteinDomain pd)
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
ProteinDomain	getDomain(int i)
java.util.SortedMap<java.math.BigDecimal,ProteinDomain>	getDomains()
int	getNumberOfDomains()
int	getTotalLength()
boolean	isEqual(PhylogenyData domain_architecture) Returns true if the names and the order of the domains match (domain and linker lengths are ignored).
void	setTotalLength(int total_length)
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) Writes a phyloXML representation of this phylogeny data.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

NHX_SEPARATOR

public static final java.lang.String NHX_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

DomainArchitecture

public DomainArchitecture()

DomainArchitecture

public DomainArchitecture(java.util.List<PhylogenyData> domains,
                  int total_length)

DomainArchitecture

public DomainArchitecture(java.lang.String da_str)

Method Detail

addDomain

public void addDomain(ProteinDomain pd)

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.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

getDomain

public ProteinDomain getDomain(int i)

getDomains

public java.util.SortedMap<java.math.BigDecimal,ProteinDomain> getDomains()

getNumberOfDomains

public int getNumberOfDomains()

getTotalLength

public int getTotalLength()

isEqual

public boolean isEqual(PhylogenyData domain_architecture)

Returns true if the names and the order of the domains match (domain and linker lengths are ignored).

Specified by:

isEqual in interface PhylogenyData

Returns:

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

setTotalLength

public void setTotalLength(int total_length)

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(java.io.Writer writer,
              int level,
              java.lang.String indentation)
                throws java.io.IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object