## Uses of Class
info.bioinfweb.jphyloio.exception.JPhyloIOReaderException

- Packages that use JPhyloIOReaderException
  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.

- - ### Uses of JPhyloIOReaderException in info.bioinfweb.jphyloio.exception

    Subclasses of JPhyloIOReaderException in info.bioinfweb.jphyloio.exception
    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.

  - ### Uses of JPhyloIOReaderException in info.bioinfweb.jphyloio.formats.newick

    Methods in info.bioinfweb.jphyloio.formats.newick that throw JPhyloIOReaderException
    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.

  - ### Uses of JPhyloIOReaderException in info.bioinfweb.jphyloio.formats.nexml.elementreader

    Methods in info.bioinfweb.jphyloio.formats.nexml.elementreader that throw JPhyloIOReaderException
    Modifier and Type | Method and Description
    --- | ---
    `protected void` | AbstractNeXMLElementReader.`createIntervalEvents(NeXMLReaderStreamDataProvider streamDataProvider, java.lang.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, 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`.

  - ### Uses of JPhyloIOReaderException in info.bioinfweb.jphyloio.formats.phyloxml

    Methods in info.bioinfweb.jphyloio.formats.phyloxml that throw JPhyloIOReaderException
    Modifier and Type | Method and Description
    --- | ---
    `static javax.xml.namespace.QName` | PhyloXMLEventReader.`readDatatypeAttributeValue(java.lang.String datatype, javax.xml.stream.events.StartElement element)`

  - ### Uses of JPhyloIOReaderException in info.bioinfweb.jphyloio.formats.xml

    Methods in info.bioinfweb.jphyloio.formats.xml that throw JPhyloIOReaderException
    Modifier and Type | Method and Description
    --- | ---
    `javax.xml.namespace.QName` | AbstractXMLEventReader.`parseQName(java.lang.String curie, javax.xml.stream.events.StartElement element)`

  - ### Uses of JPhyloIOReaderException in info.bioinfweb.jphyloio.formats.xml.elementreaders

    Methods in info.bioinfweb.jphyloio.formats.xml.elementreaders that throw JPhyloIOReaderException
    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)`