| Package | Description |
|---|---|
| info.bioinfweb.jphyloio |
The main package of JPhyloIO.
|
| info.bioinfweb.jphyloio.dataadapters |
Contains adapter interfaces that should be implemented by adapters mediating between the business model of an
application and implementations of
JPhyloIOEventWriter. |
| info.bioinfweb.jphyloio.dataadapters.implementations |
Contains some basic (abstract) implementations of
JPhyloIOEventWriter. |
| info.bioinfweb.jphyloio.dataadapters.implementations.receivers |
Contains some basic (abstract) implementations of
JPhyloIOEventReceiver
to be used by implementations of JPhyloIOEventWriter. |
| info.bioinfweb.jphyloio.dataadapters.implementations.store |
Contains implementations of data adapters that directly store their modeled data in mutable lists or maps instead of delegating to an
application business model.
|
| 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.receivers |
Contains implementations for
JPhyloIOEventReceiver necessary for writing
NeXML. |
| info.bioinfweb.jphyloio.formats.nexus.receivers |
Contains implementations of
JPhyloIOEventReceiver used internally by
NexusEventReader. |
| info.bioinfweb.jphyloio.formats.phyloxml.receivers |
Contains implementations for
JPhyloIOEventReceiver necessary for writing
PhyloXML. |
| info.bioinfweb.jphyloio.formats.text |
Contains classes implementing shared functionality for reading from and writing to streams/files in text formats.
|
| 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.receivers |
Contains general (abstract) implementations for
JPhyloIOEventReceiver necessary for
writing XML formats. |
| info.bioinfweb.jphyloio.formats.xml.stax |
Contains implementations that allow StAX based reading and writing of XML metadata.
|
| info.bioinfweb.jphyloio.utils |
Contains general tool classes of JPhyloIO.
|
| Modifier and Type | Method and Description |
|---|---|
protected void |
AbstractEventWriter.extendSequence(MatrixDataAdapter matrix,
ReadWriteParameterMap parameters,
java.lang.String sequenceID,
long targetLength,
java.lang.String extensionToken,
JPhyloIOEventReceiver receiver) |
| Modifier and Type | Method and Description |
|---|---|
void |
ObjectListDataAdapter.writeContentData(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver,
java.lang.String id)
Writes the nested events in the specified object describing its contents.
|
void |
AnnotatedDataAdapter.writeMetadata(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver)
Writes events describing the metadata associated with the object represented by this instance.
|
void |
MatrixDataAdapter.writeSequencePartContentData(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver,
java.lang.String sequenceID,
long startColumn,
long endColumn)
Implementing classes must write a sequence of events here, that describe the sequence tokens present in
the specified column range.
|
| Modifier and Type | Method and Description |
|---|---|
void |
EmptyObjectListDataAdapter.writeContentData(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver,
java.lang.String id)
Always throws an
IllegalArgumentException, since this default implementation does not contain
any objects. |
void |
UndefinedOTUListDataAdapter.writeContentData(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver,
java.lang.String id) |
void |
EmptyAnnotatedDataAdapter.writeMetadata(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver)
This default implementation does nothing and can be overwritten by inherited classes if necessary.
|
void |
UndefinedOTUListDataAdapter.writeMetadata(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver) |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractSequenceContentReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> |
class |
BasicEventReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>
Most event receivers will be inherited from this class.
|
| Modifier and Type | Method and Description |
|---|---|
void |
StoreOTUListDataAdapter.writeContentData(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver,
java.lang.String id) |
void |
StoreObjectListDataAdapter.writeContentData(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver,
java.lang.String id) |
void |
StoreAnnotatedDataAdapter.writeMetadata(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver) |
void |
StoreMatrixDataAdapter.writeSequencePartContentData(ReadWriteParameterMap parameters,
JPhyloIOEventReceiver receiver,
java.lang.String sequenceID,
long startColumn,
long endColumn) |
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventReceiver |
IllegalEventException.getReceiver() |
| Modifier and Type | Method and Description |
|---|---|
static IllegalEventException |
IllegalEventException.newInstance(JPhyloIOEventReceiver receiver,
JPhyloIOEvent parentEvent,
JPhyloIOEvent invalidEvent)
Tool method that creates a new instance of this class.
|
| Constructor and Description |
|---|
IllegalEventException(java.lang.String message,
JPhyloIOEventReceiver receiver,
JPhyloIOEvent parentEvent,
JPhyloIOEvent invalidEvent) |
| Modifier and Type | Class and Description |
|---|---|
class |
NewickNodeEdgeEventReceiver<E extends JPhyloIOEvent> |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractNeXMLDataReceiver
Implements basic functionality for event receivers writing NeXML.
|
class |
NeXMLAttributeMetadataReceiver
Receiver that is used to store the contents of metadata events with certain predicates in a map to be written
as attribute/value pairs later on.
|
class |
NeXMLCharacterSetEventReceiver
Receiver that ensures no other events than character set intervals are contained in a character set.
|
class |
NeXMLCollectCharSetDataReceiver
Receiver that collects the IDs of character set elements.
|
class |
NeXMLCollectNamespaceReceiver
Receiver that collects namespace definitions occurring in document metadata by calling the according methods of
the
AbstractNeXMLDataReceiverMixin. |
class |
NeXMLCollectSequenceDataReceiver
Receiver that collects information about the sequence tokens contained in a document.
|
class |
NeXMLCollectSetMetadataReceiver
Receiver that collects information about sets contained in a document.
|
class |
NeXMLCollectTokenSetDefinitionDataReceiver
Receiver that is used to check the contents of a token set.
|
class |
NeXMLHandleSequenceDataReceiver
General implementation of a receiver that processes sequence tokens.
|
class |
NeXMLIgnoreCertainMetadataReceiver
Receiver that is able to ignore metadata events with certain predicates, e.g.
|
class |
NeXMLMetaDataReceiver
This receiver should be used if no other elements than meta are expected under an element.
|
class |
NeXMLMolecularDataTokenDefinitionReceiver
Receiver that writes token definitions for molecular data, such as DNA, RNA or protein sequences.
|
class |
NeXMLOnlyWriteMetaDataReceiver
Receiver that writes meta data but ignores other events that were processed previously.
|
class |
NeXMLPredicateMetaReceiver
General implementation of a receiver that allows to process metadata events with certain predicates in a special way.
|
class |
NeXMLSequenceTokensReceiver
Receiver that is used to write sequence tokens.
|
class |
NeXMLTokenSetEventReceiver
Receiver that is used to write token sets.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractNexusEventReceiver
Implements basic functionality for event receivers writing Nexus.
|
class |
AbstractNexusSetsEventReceiver
General implementation for event receivers writing Nexus set commands.
|
class |
CharacterSetEventReceiver |
class |
ReferenceOnlySetReceiver |
class |
TokenSetEventReceiver |
| Modifier and Type | Class and Description |
|---|---|
class |
PhyloXMLCollectMetadataDataReceiver
Receiver that is used to collect information from meta events (e.g.
|
class |
PhyloXMLMetaDataReceiver
Receiver that implements a general strategy of writing metadata to a PhyloXML document.
|
class |
PhyloXMLOnlyCustomXMLDataReceiver
Receiver, that writes only custom XML, e.g nested under
document. |
class |
PhyloXMLPropertyMetadataReceiver
This receiver is used to write the contents of meta events to a document, if their predicates indicate
that they contain information about a PhyloXML
property tag. |
class |
PhyloXMLSpecificPredicatesDataReceiver
Receiver that is used to translate between meta events with certain predicates indicating
they contain information about a PhyloXML tag and the actual tag.
|
| Modifier and Type | Class and Description |
|---|---|
class |
BasicTextCommentEventReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>
Basic event receiver implementation that writes comments to text formats that are delimited by a start and an end string.
|
class |
TextSequenceContentReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>
Receiver that writes all encountered sequence tokens and comments to the current line and ignores all metadata.
|
| Modifier and Type | Method and Description |
|---|---|
javax.xml.stream.XMLEventWriter |
AbstractXMLEventWriter.createMetaXMLEventWriter(JPhyloIOEventReceiver receiver) |
javax.xml.stream.XMLEventWriter |
JPhyloIOXMLEventWriter.createMetaXMLEventWriter(JPhyloIOEventReceiver receiver)
Creates a new
XMLEventWriter that allows to write events of XML content of literal metadata to this
JPhyloIO event writer instance through that interface. |
javax.xml.stream.XMLStreamWriter |
AbstractXMLEventWriter.createMetaXMLStreamWriter(JPhyloIOEventReceiver receiver) |
javax.xml.stream.XMLStreamWriter |
JPhyloIOXMLEventWriter.createMetaXMLStreamWriter(JPhyloIOEventReceiver receiver)
Creates a new
XMLStreamWriter that allows to write events of XML content of literal metadata to this
JPhyloIO event writer instance through that interface. |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractXMLDataReceiver<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>>
Abstract implementation of a data receiver that can be used to write XML formats.
|
| Modifier and Type | Method and Description |
|---|---|
protected JPhyloIOEventReceiver |
AbstractMetaXMLWriter.getReceiver() |
| Constructor and Description |
|---|
AbstractMetaXMLWriter(JPhyloIOEventReceiver receiver,
javax.xml.stream.XMLStreamWriter underlyingXMLWriter) |
MetaXMLEventWriter(JPhyloIOEventReceiver receiver,
javax.xml.stream.XMLStreamWriter underlyingXMLWriter)
Creates a new instance of this class.
|
MetaXMLStreamWriter(JPhyloIOEventReceiver receiver,
javax.xml.stream.XMLStreamWriter underlyingXMLWriter)
Creates a new instance of this class.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
JPhyloIOWritingUtils.writeCharSequencePartContent(JPhyloIOEventReceiver receiver,
long startColumn,
long endColumn,
java.lang.CharSequence source) |
static void |
JPhyloIOWritingUtils.writeListSequencePartContent(JPhyloIOEventReceiver receiver,
long startColumn,
long endColumn,
java.util.List<?> source) |
static void |
JPhyloIOWritingUtils.writeSimpleLiteralMetadata(JPhyloIOEventReceiver receiver,
java.lang.String id,
java.lang.String label,
javax.xml.namespace.QName predicate,
javax.xml.namespace.QName originalType,
java.lang.Object objectValue)
Writes an event subsequence modeling a literal metadata annotation with a simple value.
|
static void |
JPhyloIOWritingUtils.writeSimpleLiteralMetadata(JPhyloIOEventReceiver receiver,
java.lang.String id,
java.lang.String label,
javax.xml.namespace.QName predicate,
javax.xml.namespace.QName originalType,
java.lang.Object objectValue,
java.lang.String stringRepresentation)
Writes an event subsequence modeling a literal metadata annotation with a simple value.
|
static void |
JPhyloIOWritingUtils.writeSimpleLiteralMetadata(JPhyloIOEventReceiver receiver,
java.lang.String id,
java.lang.String label,
URIOrStringIdentifier predicate,
URIOrStringIdentifier originalType,
java.lang.Object objectValue,
java.lang.String stringRepresentation)
Writes an event subsequence modeling a literal metadata annotation with a simple value.
|
static void |
JPhyloIOWritingUtils.writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver,
java.lang.String id,
java.lang.String label,
javax.xml.namespace.QName rel,
java.net.URI hRef)
Writes a
ResourceMetadataEvent and its respective end event to the specified receiver. |
static void |
JPhyloIOWritingUtils.writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver,
java.lang.String id,
java.lang.String label,
javax.xml.namespace.QName rel,
java.net.URI hRef,
java.lang.String about)
Writes a
ResourceMetadataEvent and its respective end event to the specified receiver. |
static void |
JPhyloIOWritingUtils.writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver,
java.lang.String id,
java.lang.String label,
URIOrStringIdentifier rel,
java.net.URI hRef)
Writes a
ResourceMetadataEvent and its respective end event to the specified receiver. |
static void |
JPhyloIOWritingUtils.writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver,
java.lang.String id,
java.lang.String label,
URIOrStringIdentifier rel,
java.net.URI hRef,
java.lang.String about)
Writes a
ResourceMetadataEvent and its respective end event to the specified receiver. |