| Package | Description |
|---|---|
| info.bioinfweb.jphyloio.exception |
Contains exceptions that are of general use in JPhyloIO.
|
| info.bioinfweb.jphyloio.formats.newick |
Contains classes for reading from and writing to streams/files in Newick tree format.
|
| info.bioinfweb.jphyloio.formats.nexml.elementreader |
Contains implementations of
XMLElementReader used by
NeXMLEventReader. |
| info.bioinfweb.jphyloio.formats.phyloxml |
Contains classes for reading from and writing to streams/files in PhyloXML format.
|
| info.bioinfweb.jphyloio.formats.xml |
Contains classes implementing shared functionality for reading from and writing to streams/files in XML formats.
|
| info.bioinfweb.jphyloio.formats.xml.elementreaders |
Contains general (abstract) implementations of
XMLElementReader used by
readers of XML formats. |
| Modifier and Type | Class and Description |
|---|---|
class |
UnsupportedFormatFeatureException
This exception is thrown by implementations of
JPhyloIOEventReader if a feature of their format is encountered
that is not supported by this reader. |
| Modifier and Type | Method and Description |
|---|---|
void |
HotCommentDataReader.read(java.lang.String comment,
TextReaderStreamDataProvider<?> streamDataProvider,
java.util.Collection<JPhyloIOEvent> eventQueue,
boolean isOnNode)
Reads metadata from the specified hot comment and adds according events to the queue.
|
| Modifier and Type | Method and Description |
|---|---|
protected void |
AbstractNeXMLElementReader.createIntervalEvents(NeXMLReaderStreamDataProvider streamDataProvider,
java.lang.String[] charIDs)
Creates a series of
CharacterSetIntervalEvents from an array of IDs referencing CharacterDefinitionEvents
and adds them to the current event collection. |
protected AbstractNeXMLElementReader.LabeledIDEventInformation |
AbstractNeXMLElementReader.getLabeledIDEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
javax.xml.stream.events.StartElement element)
Obtains information about the ID and label associated with a
StartElement by reading its attributes. |
protected AbstractNeXMLElementReader.OTUorOTUsEventInformation |
AbstractNeXMLElementReader.getOTUorOTUsEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
javax.xml.stream.events.StartElement element)
Obtains information about the ID, label and linked OTU or OTU list associated with a
StartElement by reading its attributes. |
protected abstract void |
AbstractSetElementReader.processIDs(NeXMLReaderStreamDataProvider streamDataProvider,
java.lang.String[] linkedIDs,
javax.xml.namespace.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 java.util.List<java.lang.String> |
AbstractNeXMLElementReader.readSequence(NeXMLReaderStreamDataProvider streamDataProvider,
java.lang.String sequence,
TokenTranslationStrategy translateTokens)
Parses a sequence string to a list of single tokens by using the provided
TokenTranslationStrategy. |
| Modifier and Type | Method and Description |
|---|---|
static javax.xml.namespace.QName |
PhyloXMLEventReader.readDatatypeAttributeValue(java.lang.String datatype,
javax.xml.stream.events.StartElement element) |
| Modifier and Type | Method and Description |
|---|---|
javax.xml.namespace.QName |
AbstractXMLEventReader.parseQName(java.lang.String curie,
javax.xml.stream.events.StartElement element) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
AbstractXMLElementReader.readAttributes(P streamDataProvider,
javax.xml.stream.events.StartElement element,
java.lang.String idPrefix,
AttributeInfo... attributeInformation) |
protected void |
AbstractXMLElementReader.readAttributes(P streamDataProvider,
javax.xml.stream.events.StartElement element,
java.lang.String idPrefix,
java.util.LinkedHashMap<javax.xml.namespace.QName,AttributeInfo> attributeInformationMap) |