info.bioinfweb.jphyloio.dataadapters.implementations.store

Class StoreMatrixDataAdapter

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter<LinkedLabeledIDEvent>

info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter

All Implemented Interfaces:

AnnotatedDataAdapter, ElementDataAdapter<LinkedLabeledIDEvent>, MatrixDataAdapter

public class StoreMatrixDataAdapter
extends StoreAnnotatedDataAdapter<LinkedLabeledIDEvent>
implements MatrixDataAdapter

Constructor Summary

Constructors

Constructor and Description
StoreMatrixDataAdapter(LinkedLabeledIDEvent alignmentStartEvent, boolean longTokens, java.util.List<JPhyloIOEvent> annotations)

Method Summary

Modifier and Type	Method and Description
boolean	containsLongTokens(ReadWriteParameterMap parameters) Returns whether tokens longer than one character are contained in the matrix modeled by this instance.
StoreObjectListDataAdapter<CharacterDefinitionEvent>	getCharacterDefinitions(ReadWriteParameterMap parameters) Returns a list of character definitions for the matrix modeled by this instance.
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	getCharacterSets(ReadWriteParameterMap parameters) Returns a list of character sets defined for the matrix modeled by this instance.
long	getColumnCount(ReadWriteParameterMap parameters) Returns the number of columns the modeled matrix has, if it contains aligned data or -1 if it contains unaligned data and each sequence may have a different length.
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	getMatrix()
long	getSequenceCount(ReadWriteParameterMap parameters) Returns the number of sequences contained in this matrix.
java.util.Iterator<java.lang.String>	getSequenceIDIterator(ReadWriteParameterMap parameters) Returns an iterator returning the IDs of all sequences in the represented matrix.
long	getSequenceLength(ReadWriteParameterMap parameters, java.lang.String sequenceID) Returns the length for the specified sequence.
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	getSequenceSets(ReadWriteParameterMap parameters) Returns a list of sequence sets defined for the matrix modeled by this instance.
LinkedLabeledIDEvent	getSequenceStartEvent(ReadWriteParameterMap parameters, java.lang.String sequenceID) Returns an event describing the sequence with the specified ID.
LinkedLabeledIDEvent	getStartEvent(ReadWriteParameterMap parameters) Returns the start event of this data element.
StoreObjectListDataAdapter<TokenSetDefinitionEvent>	getTokenSets(ReadWriteParameterMap parameters) Returns a list of token sets defined for the matrix modeled by this instance.
void	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.

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter

getAnnotations, writeMetadata

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter

writeMetadata

Constructor Detail

StoreMatrixDataAdapter

public StoreMatrixDataAdapter(LinkedLabeledIDEvent alignmentStartEvent,
                              boolean longTokens,
                              java.util.List<JPhyloIOEvent> annotations)

Method Detail

getStartEvent

public LinkedLabeledIDEvent getStartEvent(ReadWriteParameterMap parameters)

Description copied from interface: ElementDataAdapter

Returns the start event of this data element. The returned event can be used to determine the label and ID of the modeled data element or an optionally linked data element.

Specified by:

getStartEvent in interface ElementDataAdapter<LinkedLabeledIDEvent>

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the start event of this data element

getSequenceCount

public long getSequenceCount(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns the number of sequences contained in this matrix.

Specified by:

getSequenceCount in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the number of sequences that will be returned by MatrixDataAdapter.getSequenceIDIterator(ReadWriteParameterMap)

getColumnCount

public long getColumnCount(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns the number of columns the modeled matrix has, if it contains aligned data or -1 if it contains unaligned data and each sequence may have a different length.

For some writers the return value of this method may also determine which type of sequence data is written. (A Nexus writer would e.g. use an UNALIGNED instead of a CHARACTERS block, if -1 is returned.)

Specified by:

getColumnCount in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the number of columns in the matrix or -1 if each sequence may have a different length

containsLongTokens

public boolean containsLongTokens(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns whether tokens longer than one character are contained in the matrix modeled by this instance. Some writers will use this information to determine, whether whitespace needs to be inserted to separate tokens.

Specified by:

containsLongTokens in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

true if tokens longer than one character may occur, or false if all tokens are exactly one character long

getMatrix

public StoreObjectListDataAdapter<LinkedLabeledIDEvent> getMatrix()

getCharacterSets

public StoreObjectListDataAdapter<LinkedLabeledIDEvent> getCharacterSets(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns a list of character sets defined for the matrix modeled by this instance.

Specified by:

getCharacterSets in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

a (possibly empty) list of character sets

getTokenSets

public StoreObjectListDataAdapter<TokenSetDefinitionEvent> getTokenSets(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns a list of token sets defined for the matrix modeled by this instance.

Specified by:

getTokenSets in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

a (possibly empty) list of token sets

getSequenceIDIterator

public java.util.Iterator<java.lang.String> getSequenceIDIterator(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns an iterator returning the IDs of all sequences in the represented matrix.

Note that the returned iterator will be in ongoing use while other methods (e.g. #writeSequencePartContent(JPhyloIOEventReceiver, String, long, long)) are called. Therefore implementing classes should make sure, that the source of the iterator is not modified while a JPhyloIO writer is in use. (The iterator should not throw a ConcurrentModificationException before writing the target document is finished.)

Specified by:

getSequenceIDIterator in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

an iterator returning the edge IDs (Must return at least one element.)

getSequenceStartEvent

public LinkedLabeledIDEvent getSequenceStartEvent(ReadWriteParameterMap parameters,
                                                  java.lang.String sequenceID)
                                           throws java.lang.IllegalArgumentException

Description copied from interface: MatrixDataAdapter

Returns an event describing the sequence with the specified ID.

Specified by:

getSequenceStartEvent in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

sequenceID - the ID of the sequence to be described

Returns:

an linked OTU event describing the specified sequence

Throws:

java.lang.IllegalArgumentException

getSequenceLength

public long getSequenceLength(ReadWriteParameterMap parameters,
                              java.lang.String sequenceID)
                       throws java.lang.IllegalArgumentException

Description copied from interface: MatrixDataAdapter

Returns the length for the specified sequence. If MatrixDataAdapter.getColumnCount(ReadWriteParameterMap) returns does not return -1, this method should return the same value as MatrixDataAdapter.getColumnCount(ReadWriteParameterMap) for each sequence. Otherwise it may return different values for each sequence.

Specified by:

getSequenceLength in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

sequenceID - the ID of the sequence which defined the length

Returns:

the length of the according sequence

Throws:

java.lang.IllegalArgumentException - if an unknown sequence ID was specified

writeSequencePartContentData

public void writeSequencePartContentData(ReadWriteParameterMap parameters,
                                         JPhyloIOEventReceiver receiver,
                                         java.lang.String sequenceID,
                                         long startColumn,
                                         long endColumn)
                                  throws java.io.IOException,
                                         java.lang.IllegalArgumentException

Description copied from interface: MatrixDataAdapter

Implementing classes must write a sequence of events here, that describe the sequence tokens present in the specified column range. A valid event sequence corresponds to the grammar node SequencePartContent in the documentation of JPhyloIOEventReader.

Note that (according to the grammar definition) metadata related to the sequence as a whole can also be passed to the receiver in this method. In most cases it makes sense to pass the respective metaevents at the beginning of this sequence, i.e., if this method is called with startColumn = 0 the first events written should be the metaevents for the whole sequence. (Note that the grammar in principle allows such metaevents also between sequence token events, but not all formats (not all writers) support metadata at such a position.) The same applies to comment events. (See the documentation of the single writers for further details on supported data.)

Note that column indices in JPhyloIO start with 0.

Specified by:

writeSequencePartContentData in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

receiver - the receiver to write the events to

sequenceID - the ID of the sequence from which a part shall be written

startColumn - the first column of the sequence part to be written (inclusive)

endColumn - the last column of the sequence part to be written (exclusive)

Throws:

java.io.IOException - if a I/O error occurs while writing the data

java.lang.IllegalArgumentException - if an unknown sequence ID was specified

getCharacterDefinitions

public StoreObjectListDataAdapter<CharacterDefinitionEvent> getCharacterDefinitions(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns a list of character definitions for the matrix modeled by this instance.

Specified by:

getCharacterDefinitions in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

a (possibly empty) list of character definitions

getSequenceSets

public StoreObjectListDataAdapter<LinkedLabeledIDEvent> getSequenceSets(ReadWriteParameterMap parameters)

Description copied from interface: MatrixDataAdapter

Returns a list of sequence sets defined for the matrix modeled by this instance.

Specified by:

getSequenceSets in interface MatrixDataAdapter

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

a (possibly empty) list of sequence sets