org.forester.phylogeny.data
Class Sequence
java.lang.Object
org.forester.phylogeny.data.Sequence
- All Implemented Interfaces:
- PhylogenyData
public class Sequence
- extends Object
- implements PhylogenyData
Sequence
public Sequence()
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