Package org.forester.phylogeny.data
Class DomainArchitecture
- java.lang.Object
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- org.forester.phylogeny.data.DomainArchitecture
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- All Implemented Interfaces:
PhylogenyData
- Direct Known Subclasses:
RenderableDomainArchitecture
public class DomainArchitecture extends java.lang.Object implements PhylogenyData
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
NHX_SEPARATOR
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Constructor Summary
Constructors Constructor Description DomainArchitecture()
DomainArchitecture(java.lang.String da_str)
DomainArchitecture(java.util.List<PhylogenyData> domains, int total_length)
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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Field Detail
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NHX_SEPARATOR
public static final java.lang.String NHX_SEPARATOR
- See Also:
- Constant Field Values
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Constructor Detail
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DomainArchitecture
public DomainArchitecture()
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DomainArchitecture
public DomainArchitecture(java.util.List<PhylogenyData> domains, int total_length)
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DomainArchitecture
public DomainArchitecture(java.lang.String da_str)
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Method Detail
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addDomain
public void addDomain(ProteinDomain pd)
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
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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 interfacePhylogenyData
- Returns:
- a ~deep~ copy of this PhylogenyData
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getDomain
public ProteinDomain getDomain(int i)
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getDomains
public java.util.SortedMap<java.math.BigDecimal,ProteinDomain> getDomains()
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getNumberOfDomains
public int getNumberOfDomains()
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getTotalLength
public int getTotalLength()
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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 interfacePhylogenyData
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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setTotalLength
public void setTotalLength(int total_length)
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
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toPhyloXML
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
Description copied from interface:PhylogenyData
Writes a phyloXML representation of this phylogeny data.- Specified by:
toPhyloXML
in interfacePhylogenyData
- Throws:
java.io.IOException
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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