PhylogenyData
RenderableDomainArchitecture
public class DomainArchitecture extends java.lang.Object implements PhylogenyData
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
NHX_SEPARATOR |
Constructor | Description |
---|---|
DomainArchitecture() |
|
DomainArchitecture(java.lang.String da_str) |
|
DomainArchitecture(java.util.List<PhylogenyData> domains,
int total_length) |
Modifier and Type | Method | 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() |
public static final java.lang.String NHX_SEPARATOR
public DomainArchitecture()
public DomainArchitecture(java.util.List<PhylogenyData> domains, int total_length)
public DomainArchitecture(java.lang.String da_str)
public void addDomain(ProteinDomain pd)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public PhylogenyData copy()
PhylogenyData
copy
in interface PhylogenyData
public ProteinDomain getDomain(int i)
public java.util.SortedMap<java.math.BigDecimal,ProteinDomain> getDomains()
public int getNumberOfDomains()
public int getTotalLength()
public boolean isEqual(PhylogenyData domain_architecture)
isEqual
in interface PhylogenyData
public void setTotalLength(int total_length)
public java.lang.StringBuffer toNHX()
toNHX
in interface PhylogenyData
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
java.io.IOException
public java.lang.String toString()
toString
in class java.lang.Object