org.forester.phylogeny.data
Class Sequence

java.lang.Object
  extended by org.forester.phylogeny.data.Sequence
All Implemented Interfaces:
PhylogenyData

public class Sequence
extends Object
implements PhylogenyData


Constructor Summary
Sequence()
           
 
Method Summary
 void addAnnotation(Annotation annotation)
           
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Not a deep copy.
 boolean equals(Object o)
           
 Accession getAccession()
           
 PhylogenyData getAnnotation(int index)
           
 List<PhylogenyData> getAnnotations()
           
 DomainArchitecture getDomainArchitecture()
           
 String getLocation()
           
 String getMolecularSequence()
           
 String getName()
           
 String getSymbol()
           
 String getType()
           
 Uri getUri()
           
 int hashCode()
           
 void init()
           
 boolean isEmpty()
           
 boolean isEqual(PhylogenyData data)
          Compares this PhylogenyData to PhylogenyData data.
 void setAccession(Accession accession)
           
 void setDomainArchitecture(DomainArchitecture ds)
           
 void setLocation(String description)
           
 void setMolecularSequence(String mol_sequence)
           
 void setName(String name)
           
 void setSymbol(String symbol)
           
 void setType(String type)
           
 void setUri(Uri uri)
           
 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, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Sequence

public Sequence()
Method Detail

addAnnotation

public void addAnnotation(Annotation annotation)

asSimpleText

public StringBuffer asSimpleText()
Specified by:
asSimpleText in interface PhylogenyData

asText

public StringBuffer asText()
Specified by:
asText in interface PhylogenyData

copy

public PhylogenyData copy()
Not a deep copy.

Specified by:
copy in interface PhylogenyData
Returns:
a ~deep~ copy of this PhylogenyData

equals

public boolean equals(Object o)
Overrides:
equals in class Object

getAccession

public Accession getAccession()

getAnnotation

public PhylogenyData getAnnotation(int index)

getAnnotations

public List<PhylogenyData> getAnnotations()

getDomainArchitecture

public DomainArchitecture getDomainArchitecture()

getLocation

public String getLocation()

getMolecularSequence

public String getMolecularSequence()

getName

public String getName()

getSymbol

public String getSymbol()

getType

public String getType()

getUri

public Uri getUri()

hashCode

public int hashCode()
Overrides:
hashCode in class Object

init

public void init()

isEmpty

public boolean isEmpty()

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

setAccession

public void setAccession(Accession accession)

setDomainArchitecture

public void setDomainArchitecture(DomainArchitecture ds)

setLocation

public void setLocation(String description)

setMolecularSequence

public void setMolecularSequence(String mol_sequence)

setName

public void setName(String name)

setSymbol

public void setSymbol(String symbol)

setType

public void setType(String type)

setUri

public void setUri(Uri uri)

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