org.forester.phylogeny.data
Class DomainArchitecture

java.lang.Object
  extended by org.forester.phylogeny.data.DomainArchitecture
All Implemented Interfaces:
PhylogenyData
Direct Known Subclasses:
RenderableDomainArchitecture

public class DomainArchitecture
extends Object
implements PhylogenyData


Field Summary
static String NHX_SEPARATOR
           
 
Constructor Summary
DomainArchitecture()
           
DomainArchitecture(List<PhylogenyData> domains, int total_length)
           
DomainArchitecture(String da_str)
           
 
Method Summary
 void addDomain(ProteinDomain pd)
           
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 ProteinDomain getDomain(int i)
           
 SortedMap<Double,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)
           
 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

NHX_SEPARATOR

public static final String NHX_SEPARATOR
See Also:
Constant Field Values
Constructor Detail

DomainArchitecture

public DomainArchitecture()

DomainArchitecture

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

DomainArchitecture

public DomainArchitecture(String da_str)
Method Detail

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