public class TaxonXExtractor
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
class |
TaxonXExtractor.MySpecimenOrObservation |
class |
TaxonXExtractor.ReferenceBuilder |
Modifier and Type | Field and Description |
---|---|
protected TaxonXImport |
importer |
protected static java.lang.String |
SPLITTER |
protected TaxonXImportState |
state2 |
Constructor and Description |
---|
TaxonXExtractor() |
Modifier and Type | Method and Description |
---|---|
protected int |
askAddParent(java.lang.String s) |
protected java.lang.String |
askFeatureName(java.lang.String paragraph) |
protected Rank |
askForRank(java.lang.String fullname,
Rank rank,
NomenclaturalCode nomenclaturalCode) |
protected int |
askIfNameContained(java.lang.String fullLineRefName) |
protected boolean |
askIfReuseBestMatchingTaxon(INonViralName taxonname2,
Taxon bestMatchingTaxon,
Reference refMods,
double similarityScore,
double similarityAuthor) |
protected java.lang.String |
askMultiple(org.w3c.dom.Node fullParagraph)
ask user to specify what kind of paragraph the current "multiple" section is
default possibilities are "synonyms","material examined","distribution","image caption","other"
could make sense to replace this list with the CDM-Feature list
if "other" is selected, a second pop-up will be prompted to ask user to specify a new Feature name.
|
protected Taxon |
askParent(Taxon taxon,
Classification classification)
asks for the hierarchical parent, based on the current classification
|
protected int |
askQuestion(java.lang.String question) |
protected java.lang.String |
askRank(java.lang.String s,
java.util.List<java.lang.String> rankListStr) |
protected java.lang.String |
askSetParent(java.lang.String s) |
protected java.lang.String |
askWhichScientificName(java.lang.String fullname,
java.lang.String atomised,
java.lang.String classificationName,
org.w3c.dom.Node fullParagraph) |
protected boolean |
containsDistinctLetters(java.lang.String word) |
protected TaxonXExtractor.MySpecimenOrObservation |
extractSpecimenOrObservation(org.w3c.dom.Node specimenObservationNode,
DerivedUnit derivedUnitBase,
SpecimenOrObservationType defaultAssociation,
TaxonName typifiableName) |
protected java.lang.String |
formatNode(org.w3c.dom.Node node)
Format a XML node for a clean (screen) output with tags
|
protected DerivedUnitFacade |
getFacade(java.lang.String recordBasis,
SpecimenOrObservationType defaultAssoc) |
protected java.lang.String |
getFullReference(java.lang.String name,
java.util.List<ParserProblem> problems) |
protected Rank |
getRank(java.util.Map<java.lang.String,java.lang.String> ato) |
protected Rank |
getRank(java.lang.String r) |
protected Reference |
getReferenceWithType(int reftype) |
protected Feature |
makeFeature(SpecimenOrObservationBase unit) |
protected java.lang.String |
newNameStatus(java.lang.String status)
Tries to match the status string against any new name status
and returns the status if it matches.
|
protected NomenclaturalStatusType |
nomStatusString2NomStatus(java.lang.String nomStatus)
Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
|
protected void |
prepareCollectors(TaxonXImportState state,
IAgentService agentService) |
protected SpecimenTypeDesignationStatus |
typeStatusId2TypeStatus(int typeStatusId) |
protected TaxonXImport importer
protected TaxonXImportState state2
protected static final java.lang.String SPLITTER
protected TaxonXExtractor.MySpecimenOrObservation extractSpecimenOrObservation(org.w3c.dom.Node specimenObservationNode, DerivedUnit derivedUnitBase, SpecimenOrObservationType defaultAssociation, TaxonName typifiableName)
item
- protected DerivedUnitFacade getFacade(java.lang.String recordBasis, SpecimenOrObservationType defaultAssoc)
protected Feature makeFeature(SpecimenOrObservationBase unit)
protected int askQuestion(java.lang.String question)
protected Reference getReferenceWithType(int reftype)
reftype
- protected void prepareCollectors(TaxonXImportState state, IAgentService agentService)
unitsList
- state
- protected java.lang.String getFullReference(java.lang.String name, java.util.List<ParserProblem> problems)
name
- protected java.lang.String askWhichScientificName(java.lang.String fullname, java.lang.String atomised, java.lang.String classificationName, org.w3c.dom.Node fullParagraph) throws javax.xml.transform.TransformerFactoryConfigurationError, javax.xml.transform.TransformerException
name
- javax.xml.transform.TransformerException
javax.xml.transform.TransformerFactoryConfigurationError
protected int askAddParent(java.lang.String s)
protected java.lang.String askSetParent(java.lang.String s)
protected java.lang.String askRank(java.lang.String s, java.util.List<java.lang.String> rankListStr)
protected java.lang.String askFeatureName(java.lang.String paragraph)
name
- javax.xml.transform.TransformerException
javax.xml.transform.TransformerFactoryConfigurationError
protected boolean askIfReuseBestMatchingTaxon(INonViralName taxonname2, Taxon bestMatchingTaxon, Reference refMods, double similarityScore, double similarityAuthor)
taxonname2
- bestMatchingTaxon
- refMods
- similarityAuthor
- protected int askIfNameContained(java.lang.String fullLineRefName)
fullLineRefName
- protected Rank askForRank(java.lang.String fullname, Rank rank, NomenclaturalCode nomenclaturalCode)
name
- protected java.lang.String askMultiple(org.w3c.dom.Node fullParagraph)
fullParagraph
- : the current Nodeprotected Taxon askParent(Taxon taxon, Classification classification)
taxon
- classification
- protected Rank getRank(java.lang.String r)
r:
- the rank as string (with dwc tags)protected Rank getRank(java.util.Map<java.lang.String,java.lang.String> ato)
ato:
- atomised taxon name dataprotected java.lang.String formatNode(org.w3c.dom.Node node) throws javax.xml.transform.TransformerFactoryConfigurationError, javax.xml.transform.TransformerException
Node
- : the node to formatjavax.xml.transform.TransformerFactoryConfigurationError
javax.xml.transform.TransformerException
protected boolean containsDistinctLetters(java.lang.String word)
protected java.lang.String newNameStatus(java.lang.String status)
null
otherwise.status
- protected NomenclaturalStatusType nomStatusString2NomStatus(java.lang.String nomStatus) throws UnknownCdmTypeException
UnknownCdmTypeException
protected SpecimenTypeDesignationStatus typeStatusId2TypeStatus(int typeStatusId) throws UnknownCdmTypeException
UnknownCdmTypeException
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