info.bioinfweb.jphyloio.dataadapters.implementations

Class UndefinedOTUListDataAdapter

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter

All Implemented Interfaces:

AnnotatedDataAdapter, ElementDataAdapter<LabeledIDEvent>, ObjectListDataAdapter<LabeledIDEvent>, OTUListDataAdapter, NeXMLConstants

public class UndefinedOTUListDataAdapter
extends java.lang.Object
implements OTUListDataAdapter, NeXMLConstants

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

ATTR_ABOUT, ATTR_CELL_SET_LINKED_IDS, ATTR_CHAR_SET_LINKED_IDS, ATTR_CODON_POSITION, ATTR_CONTENT, ATTR_DATATYPE, ATTR_GENERATOR, ATTR_HREF, ATTR_ID, ATTR_LABEL, ATTR_LENGTH, ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS, ATTR_NODE_EDGE_SET_LINKED_NODE_IDS, ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS, ATTR_OTU_SET_LINKED_IDS, ATTR_OTUS, ATTR_PROPERTY, ATTR_REL, ATTR_ROOT, ATTR_SEQUENCE_SET_LINKED_IDS, ATTR_SINGLE_CHAR_LINK, ATTR_SINGLE_OTU_LINK, ATTR_SINGLE_STATE_LINK, ATTR_SOURCE, ATTR_STATE_SET_LINKED_IDS, ATTR_STATES, ATTR_SYMBOL, ATTR_TARGET, ATTR_TOKENS, ATTR_TREE_SET_LINKED_NETWORK_IDS, ATTR_TREE_SET_LINKED_TREE_IDS, ATTR_VERSION, ATTR_XSI_TYPE, DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX, NEXML_DEFAULT_NAMESPACE_PREFIX, NEXML_FORMAT_NAME, NEXML_NAMESPACE, NEXML_NAMESPACE_PREFIX, NEXML_PREDICATE_NAMESPACE, NEXML_VERSION, PREDICATE_CHAR_ATTR_CODON_POSITION, PREDICATE_CHAR_ATTR_TOKENS, PREDICATE_FORMAT, PREDICATE_MATRIX, PREDICATE_ORIGINAL_LABEL, PREDICATE_ORIGINAL_TOKEN_NAME, TAG_CELL, TAG_CHAR, TAG_CHARACTERS, TAG_EDGE, TAG_FORMAT, TAG_MATRIX, TAG_MEMBER, TAG_META, TAG_NETWORK, TAG_NODE, TAG_OTU, TAG_OTUS, TAG_POLYMORPHIC, TAG_ROOT, TAG_ROOTEDGE, TAG_ROW, TAG_SEQ, TAG_SET, TAG_STATE, TAG_STATES, TAG_TREE, TAG_TREES, TAG_UNCERTAIN, TYPE_CONTIN_CELLS, TYPE_CONTIN_SEQ, TYPE_DNA_CELLS, TYPE_DNA_SEQS, TYPE_FLOAT_NETWORK, TYPE_FLOAT_TREE, TYPE_INT_NETWORK, TYPE_INT_TREE, TYPE_LITERAL_META, TYPE_PROTEIN_CELLS, TYPE_PROTEIN_SEQS, TYPE_RESOURCE_META, TYPE_RESTRICTION_CELLS, TYPE_RESTRICTION_SEQS, TYPE_RNA_CELLS, TYPE_RNA_SEQS, TYPE_STANDARD_CELLS, TYPE_STANDARD_SEQ, UNDEFINED_OTU_ID_PREFIX, UNDEFINED_OTU_LABEL, UNDEFINED_OTUS_ID_PREFIX, UNDEFINED_OTUS_LABEL

Constructor Summary

Constructors

Constructor and Description
UndefinedOTUListDataAdapter(java.lang.String undefinedOTUsID, java.lang.String undefinedOTUID)

Method Summary

Modifier and Type	Method and Description
long	getCount(ReadWriteParameterMap parameters) Returns the number of objects to be returned by ObjectListDataAdapter.getIDIterator(ReadWriteParameterMap).
java.util.Iterator<java.lang.String>	getIDIterator(ReadWriteParameterMap parameters) Returns an iterator returning the IDs of all objects contained in the list modeled by this instance.
LabeledIDEvent	getObjectStartEvent(ReadWriteParameterMap parameters, java.lang.String id) Returns the start event of an object determined by the specified object ID.
ObjectListDataAdapter<LinkedLabeledIDEvent>	getOTUSets(ReadWriteParameterMap parameters) Returns a list of OTU sets defined for the OTU list modeled by this instance.
LabeledIDEvent	getStartEvent(ReadWriteParameterMap parameters) Returns the start event of this data element.
java.lang.String	getUndefinedOtuID()
void	writeContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String id) Writes the nested events in the specified object describing its contents.
void	writeMetadata(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver) Writes events describing the metadata associated with the object represented by this instance.

Methods inherited from class java.lang.Object

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

Constructor Detail

UndefinedOTUListDataAdapter

public UndefinedOTUListDataAdapter(java.lang.String undefinedOTUsID,
                                   java.lang.String undefinedOTUID)

Method Detail

getObjectStartEvent

public LabeledIDEvent getObjectStartEvent(ReadWriteParameterMap parameters,
                                          java.lang.String id)
                                   throws java.lang.IllegalArgumentException

Description copied from interface: ObjectListDataAdapter

Returns the start event of an object determined by the specified object ID.

Specified by:

getObjectStartEvent in interface ObjectListDataAdapter<LabeledIDEvent>

Parameters:

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

id - the ID of the requested object

Returns:

an instance of a labeled ID event that describes the specified object

Throws:

java.lang.IllegalArgumentException - if no to object for the specified ID is present

getCount

public long getCount(ReadWriteParameterMap parameters)

Description copied from interface: ObjectListDataAdapter

Returns the number of objects to be returned by ObjectListDataAdapter.getIDIterator(ReadWriteParameterMap).

Specified by:

getCount in interface ObjectListDataAdapter<LabeledIDEvent>

Parameters:

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

Returns:

the number of objects in the list modeled by this instance

getIDIterator

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

Description copied from interface: ObjectListDataAdapter

Returns an iterator returning the IDs of all objects contained in the list modeled by this instance.

Specified by:

getIDIterator in interface ObjectListDataAdapter<LabeledIDEvent>

Parameters:

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

Returns:

an iterator returning the IDs (Depending in the usage of this object, the returned iterator must return at least one element or can be empty, but it may never be null.)

getUndefinedOtuID

public java.lang.String getUndefinedOtuID()

writeContentData

public void writeContentData(ReadWriteParameterMap parameters,
                             JPhyloIOEventReceiver receiver,
                             java.lang.String id)
                      throws java.io.IOException,
                             java.lang.IllegalArgumentException

Description copied from interface: ObjectListDataAdapter

Writes the nested events in the specified object describing its contents.

Specified by:

writeContentData in interface ObjectListDataAdapter<LabeledIDEvent>

Parameters:

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

receiver - the receiver for the events

Throws:

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

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

writeMetadata

public void writeMetadata(ReadWriteParameterMap parameters,
                          JPhyloIOEventReceiver receiver)
                   throws java.io.IOException

Description copied from interface: AnnotatedDataAdapter

Writes events describing the metadata associated with the object represented by this instance.

Specified by:

writeMetadata in interface AnnotatedDataAdapter

Parameters:

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

receiver - the writer accepting the events

Throws:

java.io.IOException

getStartEvent

public LabeledIDEvent 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<LabeledIDEvent>

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

getOTUSets

public ObjectListDataAdapter<LinkedLabeledIDEvent> getOTUSets(ReadWriteParameterMap parameters)

Description copied from interface: OTUListDataAdapter

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

Specified by:

getOTUSets in interface OTUListDataAdapter

Parameters:

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

Returns:

a (possibly empty) list of OTU sets