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 Object
- implements PhylogenyData
NHX_SEPARATOR
public static final String NHX_SEPARATOR
- See Also:
- Constant Field Values
DomainArchitecture
public DomainArchitecture()
DomainArchitecture
public DomainArchitecture(List<PhylogenyData> domains,
int total_length)
DomainArchitecture
public DomainArchitecture(String da_str)
addDomain
public void addDomain(ProteinDomain pd)
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
getDomain
public ProteinDomain getDomain(int i)
getDomains
public SortedMap<Double,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 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