Package org.forester.phylogeny.data
Class Taxonomy
- java.lang.Object
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- org.forester.phylogeny.data.Taxonomy
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- All Implemented Interfaces:
java.lang.Comparable<Taxonomy>
,MultipleUris
,PhylogenyData
public class Taxonomy extends java.lang.Object implements PhylogenyData, MultipleUris, java.lang.Comparable<Taxonomy>
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Constructor Summary
Constructors Constructor Description Taxonomy()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addUri(Uri uri)
java.lang.StringBuffer
asSimpleText()
java.lang.StringBuffer
asText()
int
compareTo(Taxonomy o)
PhylogenyData
copy()
Creates a new PhylogenyData object with identical values as this PhylogenyData.boolean
equals(java.lang.Object o)
java.lang.String
getAuthority()
java.lang.String
getCommonName()
Identifier
getIdentifier()
java.util.List<java.lang.String>
getLineage()
java.lang.String
getRank()
java.lang.String
getScientificName()
java.util.List<java.lang.String>
getSynonyms()
java.lang.String
getTaxonomyCode()
Uri
getUri(int index)
java.util.List<Uri>
getUris()
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(java.lang.String authority)
void
setCommonName(java.lang.String common_name)
void
setIdentifier(Identifier identifier)
void
setLineage(java.util.List<java.lang.String> lineage)
void
setRank(java.lang.String rank)
void
setScientificName(java.lang.String scientific_name)
void
setTaxonomyCode(java.lang.String taxonomy_code)
void
setUris(java.util.List<Uri> uris)
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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Method Detail
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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getUri
public Uri getUri(int index)
- Specified by:
getUri
in interfaceMultipleUris
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addUri
public void addUri(Uri uri)
- Specified by:
addUri
in interfaceMultipleUris
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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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equals
public boolean equals(java.lang.Object o)
- Overrides:
equals
in classjava.lang.Object
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getAuthority
public java.lang.String getAuthority()
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getCommonName
public java.lang.String getCommonName()
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getIdentifier
public Identifier getIdentifier()
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getRank
public java.lang.String getRank()
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getScientificName
public java.lang.String getScientificName()
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getSynonyms
public java.util.List<java.lang.String> getSynonyms()
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getTaxonomyCode
public java.lang.String getTaxonomyCode()
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getUris
public java.util.List<Uri> getUris()
- Specified by:
getUris
in interfaceMultipleUris
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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init
public void init()
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isEmpty
public boolean isEmpty()
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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 interfacePhylogenyData
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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setAuthority
public void setAuthority(java.lang.String authority)
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setCommonName
public void setCommonName(java.lang.String common_name)
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setIdentifier
public void setIdentifier(Identifier identifier)
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setRank
public void setRank(java.lang.String rank) throws PhyloXmlDataFormatException
- Throws:
PhyloXmlDataFormatException
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setScientificName
public void setScientificName(java.lang.String scientific_name)
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setTaxonomyCode
public void setTaxonomyCode(java.lang.String taxonomy_code) throws PhyloXmlDataFormatException
- Throws:
PhyloXmlDataFormatException
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setUris
public void setUris(java.util.List<Uri> uris)
- Specified by:
setUris
in interfaceMultipleUris
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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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compareTo
public int compareTo(Taxonomy o)
- Specified by:
compareTo
in interfacejava.lang.Comparable<Taxonomy>
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setLineage
public void setLineage(java.util.List<java.lang.String> lineage)
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getLineage
public java.util.List<java.lang.String> getLineage()
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