org.forester.phylogeny.data
Class Taxonomy

java.lang.Object
  extended by org.forester.phylogeny.data.Taxonomy
All Implemented Interfaces:
PhylogenyData

public class Taxonomy
extends Object
implements PhylogenyData


Constructor Summary
Taxonomy()
           
 
Method Summary
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 boolean equals(Object o)
           
 String getAuthority()
           
 String getCommonName()
           
 Identifier getIdentifier()
           
 String getRank()
           
 String getScientificName()
           
 List<String> getSynonyms()
           
 String getTaxonomyCode()
           
 Uri getUri()
           
 int hashCode()
           
 void init()
           
 boolean isEmpty()
           
 boolean isEqual(PhylogenyData data)
          If this and taxonomy 'data' has an identifier, comparison will be based on that.
 void setAuthority(String authority)
           
 void setCommonName(String common_name)
           
 void setIdentifier(Identifier identifier)
           
 void setRank(String rank)
           
 void setScientificName(String scientific_name)
           
 void setTaxonomyCode(String taxonomy_code)
           
 void setUri(Uri uri)
           
 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, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Taxonomy

public Taxonomy()
Method Detail

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

equals

public boolean equals(Object o)
Overrides:
equals in class Object

getAuthority

public String getAuthority()

getCommonName

public String getCommonName()

getIdentifier

public Identifier getIdentifier()

getRank

public String getRank()

getScientificName

public String getScientificName()

getSynonyms

public List<String> getSynonyms()

getTaxonomyCode

public String getTaxonomyCode()

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)
If this and taxonomy 'data' has an identifier, comparison will be based on that. Otherwise, if this and taxonomy 'data' has a code, comparison will be based on that. Otherwise, if Taxonomy 'data' has a scientific name, comparison will be based on that (case insensitive!). Otherwise, if Taxonomy 'data' has a common name, comparison will be based on that (case insensitive!). (Note. This is important and should not be change without a very good reason.)

Specified by:
isEqual in interface PhylogenyData
Returns:
in general, true if and only if all fiels are exactly identical, false otherwise

setAuthority

public void setAuthority(String authority)

setCommonName

public void setCommonName(String common_name)

setIdentifier

public void setIdentifier(Identifier identifier)

setRank

public void setRank(String rank)

setScientificName

public void setScientificName(String scientific_name)

setTaxonomyCode

public void setTaxonomyCode(String taxonomy_code)

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