Package | Description |
---|---|
info.bioinfweb.jphyloio.formats.nexml |
Contains classes for reading from and writing to streams/files in NeXML format.
|
info.bioinfweb.jphyloio.formats.nexml.elementreader |
Contains implementations of
XMLElementReader used by
NeXMLEventReader . |
Modifier and Type | Method and Description |
---|---|
protected NeXMLReaderStreamDataProvider |
NeXMLEventReader.createStreamDataProvider() |
protected NeXMLReaderStreamDataProvider |
NeXMLEventReader.createStreamDataProvider() |
Modifier and Type | Method and Description |
---|---|
protected XMLElementReader<NeXMLReaderStreamDataProvider> |
NeXMLEventReader.getElementReader(QName parentTag,
QName elementTag,
int eventType) |
protected XMLElementReader<NeXMLReaderStreamDataProvider> |
NeXMLEventReader.getElementReader(QName parentTag,
QName elementTag,
int eventType) |
Modifier and Type | Method and Description |
---|---|
protected void |
AbstractNeXMLElementReader.createIntervalEvents(NeXMLReaderStreamDataProvider streamDataProvider,
String[] charIDs)
Creates a series of
CharacterSetIntervalEvent s from an array of IDs referencing CharacterDefinitionEvent s
and adds them to the current event collection. |
protected void |
AbstractNeXMLElementReader.createIntervalEvents(NeXMLReaderStreamDataProvider streamDataProvider,
String[] charIDs)
Creates a series of
CharacterSetIntervalEvent s from an array of IDs referencing CharacterDefinitionEvent s
and adds them to the current event collection. |
protected AbstractNeXMLElementReader.LabeledIDEventInformation |
AbstractNeXMLElementReader.getLabeledIDEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
StartElement element)
Obtains information about the ID and label associated with a
StartElement by reading its attributes. |
protected AbstractNeXMLElementReader.LabeledIDEventInformation |
AbstractNeXMLElementReader.getLabeledIDEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
StartElement element)
Obtains information about the ID and label associated with a
StartElement by reading its attributes. |
protected AbstractNeXMLElementReader.OTUorOTUsEventInformation |
AbstractNeXMLElementReader.getOTUorOTUsEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
StartElement element)
Obtains information about the ID, label and linked OTU or OTU list associated with a
StartElement by reading its attributes. |
protected AbstractNeXMLElementReader.OTUorOTUsEventInformation |
AbstractNeXMLElementReader.getOTUorOTUsEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
StartElement element)
Obtains information about the ID, label and linked OTU or OTU list associated with a
StartElement by reading its attributes. |
protected void |
AbstractIDLinkSetElementReader.processIDs(NeXMLReaderStreamDataProvider streamDataProvider,
String[] linkedIDs,
QName attributeName) |
protected abstract void |
AbstractSetElementReader.processIDs(NeXMLReaderStreamDataProvider streamDataProvider,
String[] linkedIDs,
QName attribute)
Method that is called to process a list of IDs that has been found in an according attribute of the tag processed by this
instance.
|
protected abstract void |
AbstractSetElementReader.processIDs(NeXMLReaderStreamDataProvider streamDataProvider,
String[] linkedIDs,
QName attribute)
Method that is called to process a list of IDs that has been found in an according attribute of the tag processed by this
instance.
|
protected void |
AbstractIDLinkSetElementReader.processIDs(NeXMLReaderStreamDataProvider streamDataProvider,
String[] linkedIDs,
QName attributeName) |
void |
AbstractSetElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLMetaEndElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLMetaStartElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLSetEndElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLStartDocumentElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
AbstractSetElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLSetEndElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLStartDocumentElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLMetaEndElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
void |
NeXMLMetaStartElementReader.readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
XMLEvent event) |
protected List<String> |
AbstractNeXMLElementReader.readSequence(NeXMLReaderStreamDataProvider streamDataProvider,
String sequence,
TokenTranslationStrategy translateTokens)
Parses a sequence string to a list of single tokens by using the provided
TokenTranslationStrategy . |
protected List<String> |
AbstractNeXMLElementReader.readSequence(NeXMLReaderStreamDataProvider streamDataProvider,
String sequence,
TokenTranslationStrategy translateTokens)
Parses a sequence string to a list of single tokens by using the provided
TokenTranslationStrategy . |