info.bioinfweb.jphyloio.formats.nexml

Class NeXMLReaderStreamDataProvider

java.lang.Object

info.bioinfweb.jphyloio.ReaderStreamDataProvider<R>

info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider<NeXMLEventReader>

info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider

public class NeXMLReaderStreamDataProvider
extends XMLReaderStreamDataProvider<NeXMLEventReader>

Stores data that shall be shared among different implementations of AbstractNeXMLElementReader reading from the same document.

Author:

Sarah Wiechers

Constructor Summary

Constructors

Constructor and Description
NeXMLReaderStreamDataProvider(NeXMLEventReader nexmlEventReader)

Method Summary

Modifier and Type	Method and Description
void	clearCurrentRowInformation() Method used for reading cell tags that clears the map of buffered cell informations (getCurrentCellsBuffer()) and resets the columns ID iterator used by nextCharID().
URIOrStringIdentifier	getAdditionalResourceMetaRel() Returns a {link URIOrStringIdentifier} if an additional ResourceMetadataEvent is to be created to enclose meta data of elements without a JPhyloIOEvent representation or null if this the enclosing event was already generated.
java.lang.String	getAlternativeStringRepresentation() Returns the value of the content attribute of the current literal meta element to be used as an alternative string representation by a following LiteralMetadataContentEvent.
java.util.List<java.lang.String>	getCharIDs() Returns a list of column IDs obtained from NeXML char elements.
java.util.Map<java.lang.String,java.lang.Integer>	getCharIDToIndexMap() Returns a map linking column indices to column IDs obtained from NeXML char elements.
java.util.Map<java.lang.String,java.lang.String>	getCharIDToStatesMap() Returns a map linking a token set definition ID to a column ID obtained from a NeXML char elements.
java.util.Map<java.lang.String,BufferedEventInfo<SingleSequenceTokenEvent>>	getCurrentCellsBuffer() The returned map is used to buffer SingleTokenDefinitionEvents and their nested events, in cases where the order of cell tags does not match the order of the referenced columns.
java.lang.String	getCurrentExpectedCharID() Returns the column ID that has been the result of the last call of nextCharID().
LiteralContentSequenceType	getCurrentLiteralContentSequenceType() Returns the LiteralContentSequenceType of the content nested under the current literal meta element.
NeXMLSingleTokenDefinitionInformation	getCurrentSingleTokenDefinition() Returns the NeXMLSingleTokenDefinitionInformation instance of the currently read single token definition, e.g to add more constituents.
java.util.EnumMap<EventContentType,java.lang.String>	getElementTypeToCurrentIDMap() Returns a map that links the currently used ID to an EventContentType.
NeXMLEventReader	getEventReader()
java.util.Stack<EventContentType>	getMetaType() Returns a stack of EventContentType that represents the currently encountered nested meta events.
java.util.Map<java.lang.String,java.lang.String>	getOTUIDToLabelMap() Returns a map that links a label to a certain OTU ID.
java.util.Map<java.lang.String,java.lang.String>	getTokenDefinitionIDToSymbolMap() Returns a map that links a symbol (i.e.
java.util.Map<java.lang.String,java.util.List<java.lang.String>>	getTokenSetIDtoColumnsMap() Returns a map that links a symbol (i.e.
java.util.Map<java.lang.String,NeXMLReaderTokenSetInformation>	getTokenSets() Returns a map that links a NeXMLReaderTokenSetInformation to a certain token set ID.
boolean	isAllowLongTokens()
boolean	isCurrentCellBuffered() Determines whether the contents of the current cell tag are buffered or not.
boolean	isCurrentSetSupported() Returns true if the set element that is currently read can be interpreted as a series of JPhyloIOEvents or false if the set and all its contents will be ignored.
java.lang.String	nextCharID() Returns the next NeXML columns ID (ID of a char tag) at the current position of the underlying iterator and stores it in the property getCurrentExpectedCharID().
void	setAdditionalResourceMetaRel(URIOrStringIdentifier additionalResourceMetaRel)
void	setAllowLongTokens(boolean allowLongTokens)
void	setAlternativeStringRepresentation(java.lang.String alternativeStringRepresentation)
void	setCurrentCellBuffered(boolean currentCellBuffered) Allow to specify whether the contents of the current cell tag are buffered or not.
void	setCurrentLiteralContentSequenceType(LiteralContentSequenceType currentLiteralContentSequenceType)
void	setCurrentSetIsSupported(boolean currentSetIsSupported)
void	setCurrentSingleTokenDefinition(NeXMLSingleTokenDefinitionInformation currentSingleTokenDefinition)

Methods inherited from class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider

getCharacterSetType, getEdgeInfos, getElementName, getIncompleteToken, getNestedMetaNames, getParentName, getSourceNode, getStartDocumentEvent, getXMLReader, hasIncompleteToken, isCreateNodeStart, isCustomXMLStartWritten, isRootedPhylogeny, setCharacterSetType, setCreateNodeStart, setCustomXMLStartWritten, setElementName, setIncompleteToken, setParentName, setRootedPhylogeny, setStartDocumentEvent

Methods inherited from class info.bioinfweb.jphyloio.ReaderStreamDataProvider

eventsUpcoming, getCurrentEventCollection, getIDManager, getParameters, getSequenceTokensEventManager, hasSpecialEventCollection, resetCurrentEventCollection, setCurrentEventCollection

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NeXMLReaderStreamDataProvider

public NeXMLReaderStreamDataProvider(NeXMLEventReader nexmlEventReader)

Method Detail

getEventReader

public NeXMLEventReader getEventReader()

Overrides:

getEventReader in class ReaderStreamDataProvider<NeXMLEventReader>

isAllowLongTokens

public boolean isAllowLongTokens()

setAllowLongTokens

public void setAllowLongTokens(boolean allowLongTokens)

getElementTypeToCurrentIDMap

public java.util.EnumMap<EventContentType,java.lang.String> getElementTypeToCurrentIDMap()

Returns a map that links the currently used ID to an EventContentType. This map is used to determine a the linked ID of a set.

Returns:

the map linking an ID to an EventContentType

getMetaType

public java.util.Stack<EventContentType> getMetaType()

Returns a stack of EventContentType that represents the currently encountered nested meta events.

Returns:

the stack of EventContentType representing the encountered meta events

getCurrentLiteralContentSequenceType

public LiteralContentSequenceType getCurrentLiteralContentSequenceType()

Returns the LiteralContentSequenceType of the content nested under the current literal meta element.

Returns:

the LiteralContentSequenceType of the content nested under the current literal meta element

setCurrentLiteralContentSequenceType

public void setCurrentLiteralContentSequenceType(LiteralContentSequenceType currentLiteralContentSequenceType)

getAlternativeStringRepresentation

public java.lang.String getAlternativeStringRepresentation()

Returns the value of the content attribute of the current literal meta element to be used as an alternative string representation by a following LiteralMetadataContentEvent.

Returns:

the value of the content attribute of the current literal meta element

setAlternativeStringRepresentation

public void setAlternativeStringRepresentation(java.lang.String alternativeStringRepresentation)

getAdditionalResourceMetaRel

public URIOrStringIdentifier getAdditionalResourceMetaRel()

Returns a {link URIOrStringIdentifier} if an additional ResourceMetadataEvent is to be created to enclose meta data of elements without a JPhyloIOEvent representation or null if this the enclosing event was already generated.

Returns:

a {link URIOrStringIdentifier} describing additional metadata or null

setAdditionalResourceMetaRel

public void setAdditionalResourceMetaRel(URIOrStringIdentifier additionalResourceMetaRel)

isCurrentSetSupported

public boolean isCurrentSetSupported()

Returns true if the set element that is currently read can be interpreted as a series of JPhyloIOEvents or false if the set and all its contents will be ignored.

Returns:

true if the set currently read can be interpreted as a series of JPhyloIOEvents

setCurrentSetIsSupported

public void setCurrentSetIsSupported(boolean currentSetIsSupported)

getOTUIDToLabelMap

public java.util.Map<java.lang.String,java.lang.String> getOTUIDToLabelMap()

Returns a map that links a label to a certain OTU ID. This map is used to determine a sequence or node label from the OTU linked to it, in case no sequence or node label could be found.

Returns:

the map linking a label to an OTU ID

getTokenSets

public java.util.Map<java.lang.String,NeXMLReaderTokenSetInformation> getTokenSets()

Returns a map that links a NeXMLReaderTokenSetInformation to a certain token set ID. This is used to buffer information about the token set until the start event is created and to be able to find the right translation map when reading sequences.

Returns:

the map linking a NeXMLReaderTokenSetInformation to an token set ID

getTokenDefinitionIDToSymbolMap

public java.util.Map<java.lang.String,java.lang.String> getTokenDefinitionIDToSymbolMap()

Returns a map that links a symbol (i.e. the name of a token definition like 'A' for Adenin) to a single token definition ID.

Returns:

the map linking a symbol to a single token definition ID

getCurrentSingleTokenDefinition

public NeXMLSingleTokenDefinitionInformation getCurrentSingleTokenDefinition()

Returns the NeXMLSingleTokenDefinitionInformation instance of the currently read single token definition, e.g to add more constituents.

Returns:

the NeXMLSingleTokenDefinitionInformation instance of the currently read single token definition

setCurrentSingleTokenDefinition

public void setCurrentSingleTokenDefinition(NeXMLSingleTokenDefinitionInformation currentSingleTokenDefinition)

getTokenSetIDtoColumnsMap

public java.util.Map<java.lang.String,java.util.List<java.lang.String>> getTokenSetIDtoColumnsMap()

Returns a map that links a symbol (i.e. the name of a token definition like 'A' for Adenin) to a single token definition ID.

Returns:

the map linking a symbol to a single token definition ID

getCharIDs

public java.util.List<java.lang.String> getCharIDs()

Returns a list of column IDs obtained from NeXML char elements.

Returns:

a list of column IDs

getCharIDToIndexMap

public java.util.Map<java.lang.String,java.lang.Integer> getCharIDToIndexMap()

Returns a map linking column indices to column IDs obtained from NeXML char elements.

Returns:

a map linking column indices to column IDs

getCharIDToStatesMap

public java.util.Map<java.lang.String,java.lang.String> getCharIDToStatesMap()

Returns a map linking a token set definition ID to a column ID obtained from a NeXML char elements.

Returns:

a map linking a token set definition ID to a column ID

getCurrentCellsBuffer

public java.util.Map<java.lang.String,BufferedEventInfo<SingleSequenceTokenEvent>> getCurrentCellsBuffer()

The returned map is used to buffer SingleTokenDefinitionEvents and their nested events, in cases where the order of cell tags does not match the order of the referenced columns.

Returns:

the map instance to be used for buffering

clearCurrentRowInformation

public void clearCurrentRowInformation()

Method used for reading cell tags that clears the map of buffered cell informations (getCurrentCellsBuffer()) and resets the columns ID iterator used by nextCharID().

nextCharID

public java.lang.String nextCharID()

Returns the next NeXML columns ID (ID of a char tag) at the current position of the underlying iterator and stores it in the property getCurrentExpectedCharID().

If this method is called the first time after creation of this object or after a call of clearCurrentRowInformation() a new iterator will be created before returning an event.

Returns:

the ID of the next char tag or null if no additional columns are available

getCurrentExpectedCharID

public java.lang.String getCurrentExpectedCharID()

Returns the column ID that has been the result of the last call of nextCharID().

Returns:

the currently expected column ID or null if no more IDs are to come

isCurrentCellBuffered

public boolean isCurrentCellBuffered()

Determines whether the contents of the current cell tag are buffered or not. Buffering becomes necessary, if the order of cell tags differs from the order of column definitions from char tags.

Returns:

true if the current cell is buffered or false otherwise

setCurrentCellBuffered

public void setCurrentCellBuffered(boolean currentCellBuffered)

Allow to specify whether the contents of the current cell tag are buffered or not.