| 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.events |
Contains implementations of JPhyloIO events, triggered during event based parsing.
|
| info.bioinfweb.jphyloio.events.meta |
Contains event classes that model metadata, as well as related implementations.
|
| info.bioinfweb.jphyloio.exception |
Contains exceptions that are of general use in JPhyloIO.
|
| info.bioinfweb.jphyloio.formats |
The subpackages of this package contain implementations of JPhyloIO readers and writers for different formats.
|
| info.bioinfweb.jphyloio.formats.newick |
Contains classes for reading from and writing to streams/files in Newick tree format.
|
| info.bioinfweb.jphyloio.formats.nexml |
Contains classes for reading from and writing to streams/files in NeXML format.
|
| info.bioinfweb.jphyloio.formats.nexml.receivers |
Contains implementations for
JPhyloIOEventReceiver necessary for writing
NeXML. |
| info.bioinfweb.jphyloio.formats.nexus |
Contains classes for reading from and writing to streams/files in Nexus format.
|
| info.bioinfweb.jphyloio.formats.nexus.commandreaders |
Contains general classes for reading Nexus commands.
|
| 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.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.push |
Contains classes that allow push-parsing.
|
| info.bioinfweb.jphyloio.utils |
Contains general tool classes of JPhyloIO.
|
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| Class and Description |
|---|
| CharacterDefinitionEvent
Event that indicates a defined character (alignment column).
|
| EdgeEvent
Event indicating an edge in a tree or network.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| NodeEvent
Event indicating a node in a tree or network.
|
| TokenSetDefinitionEvent
Event that indicates that a (predefined) definition of a character state set was found in the parsed file.
|
| Class and Description |
|---|
| CharacterDefinitionEvent
Event that indicates a defined character (alignment column).
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| TokenSetDefinitionEvent
Event that indicates that a (predefined) definition of a character state set was found in the parsed file.
|
| Class and Description |
|---|
| CommentEvent
Event that indicates that a comment has been parsed at the current position or within the data the last
non-comment event has been parsed from.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| CharacterDefinitionEvent
Event that indicates a defined character (alignment column).
|
| EdgeEvent
Event indicating an edge in a tree or network.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| NodeEvent
Event indicating a node in a tree or network.
|
| TokenSetDefinitionEvent
Event that indicates that a (predefined) definition of a character state set was found in the parsed file.
|
| Class and Description |
|---|
| CharacterDefinitionEvent
Event that indicates a defined character (alignment column).
|
| CharacterSetIntervalEvent
Event that indicates that new information on a character set has been read.
|
| CommentEvent
Event that indicates that a comment has been parsed at the current position or within the data the last
non-comment event has been parsed from.
|
| ConcreteJPhyloIOEvent
Implements basic functionality for
JPhyloIOEvents. |
| ContinuedEvent
Base class for events that have a content that may be split across separate subsequent events, if it is large.
|
| EdgeEvent
Event indicating an edge in a tree or network.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LabeledEvent |
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| LinkedIDEvent
Interface to be implemented by event objects that can link previous events by their ID.
|
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| NodeEvent
Event indicating a node in a tree or network.
|
| PartEndEvent
Indicates the end of a part of a sequence or character set definition.
|
| SequenceTokensEvent
Indicates that one or more sequence tokens have been read from an alignment.
|
| SetElementEvent
Event object that models an ID-based link to an object that is contained in set.
|
| SingleSequenceTokenEvent |
| SingleTokenDefinitionEvent
Event that indicates the definition of a single new valid token that could be contained in a sequence
of the current alignment.
|
| TokenSetDefinitionEvent
Event that indicates that a (predefined) definition of a character state set was found in the parsed file.
|
| UnknownCommandEvent
Event to be fired, if an unknown command was found (e.g.
|
| Class and Description |
|---|
| ConcreteJPhyloIOEvent
Implements basic functionality for
JPhyloIOEvents. |
| ContinuedEvent
Base class for events that have a content that may be split across separate subsequent events, if it is large.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LabeledEvent |
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| CommentEvent
Event that indicates that a comment has been parsed at the current position or within the data the last
non-comment event has been parsed from.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| SingleSequenceTokenEvent |
| Class and Description |
|---|
| CommentEvent
Event that indicates that a comment has been parsed at the current position or within the data the last
non-comment event has been parsed from.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| LinkedLabeledIDEvent
Instances of this class model data elements with an ID and an optional label, that link another data
element in a phylogenetic document.
|
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| CharacterSetIntervalEvent
Event that indicates that new information on a character set has been read.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| SetElementEvent
Event object that models an ID-based link to an object that is contained in set.
|
| Class and Description |
|---|
| CommentEvent
Event that indicates that a comment has been parsed at the current position or within the data the last
non-comment event has been parsed from.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| CommentEvent
Event that indicates that a comment has been parsed at the current position or within the data the last
non-comment event has been parsed from.
|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| CommentEvent
Event that indicates that a comment has been parsed at the current position or within the data the last
non-comment event has been parsed from.
|
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| Class and Description |
|---|
| JPhyloIOEvent
This interface is implemented by all events generated by implementations of
JPhyloIOEventReader. |
| LabeledIDEvent
Event that indicate data objects that carry an unique ID and a label.
|
| SequenceTokensEvent
Indicates that one or more sequence tokens have been read from an alignment.
|