Uses of Interface
info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

Packages that use MatrixDataAdapter

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.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.formats.fasta	Contains classes for reading from and writing to streams/files in FASTA format.
info.bioinfweb.jphyloio.formats.phylip	Contains classes for reading from and writing to streams/files in Phylip format.

Uses of MatrixDataAdapter in info.bioinfweb.jphyloio

Methods in info.bioinfweb.jphyloio with parameters of type MatrixDataAdapter

Modifier and Type	Method and Description
static long	AbstractEventWriter.determineMaxSequenceLength(MatrixDataAdapter matrix, ReadWriteParameterMap parameters) Calculates the maximum sequence length in matrix with unequal lengths.
protected void	AbstractEventWriter.extendSequence(MatrixDataAdapter matrix, ReadWriteParameterMap parameters, java.lang.String sequenceID, long targetLength, java.lang.String extensionToken, JPhyloIOEventReceiver receiver)
protected abstract void	AbstractSingleMatrixEventWriter.writeSingleMatrix(DocumentDataAdapter document, MatrixDataAdapter matrix, java.util.Iterator<java.lang.String> sequenceIDIterator, ReadWriteParameterMap parameters) Implementations of this method should write a single matrix to their target format.

Uses of MatrixDataAdapter in info.bioinfweb.jphyloio.dataadapters

Methods in info.bioinfweb.jphyloio.dataadapters that return types with arguments of type MatrixDataAdapter

Modifier and Type	Method and Description
java.util.Iterator<MatrixDataAdapter>	DocumentDataAdapter.getMatrixIterator(ReadWriteParameterMap parameters) Returns an iterator providing access to all matrices contained in the document to be written.

Uses of MatrixDataAdapter in info.bioinfweb.jphyloio.dataadapters.implementations

Classes in info.bioinfweb.jphyloio.dataadapters.implementations that implement MatrixDataAdapter

Modifier and Type

Class and Description

class

NoCharDefsNoSetsMatrixDataAdapter Abstract implementation of MatrixDataAdapter, which returns empty object list adapters for NoCharDefsNoSetsMatrixDataAdapter.getCharacterDefinitions(ReadWriteParameterMap), NoCharDefsNoSetsMatrixDataAdapter.getTokenSets(ReadWriteParameterMap), NoCharDefsNoSetsMatrixDataAdapter.getSequenceSets(ReadWriteParameterMap), NoCharDefsNoSetsMatrixDataAdapter.getCharacterSets(ReadWriteParameterMap).

Methods in info.bioinfweb.jphyloio.dataadapters.implementations that return types with arguments of type MatrixDataAdapter

Modifier and Type	Method and Description
java.util.List<MatrixDataAdapter>	ListBasedDocumentDataAdapter.getMatrices()
java.util.Iterator<MatrixDataAdapter>	EmptyDocumentDataAdapter.getMatrixIterator(ReadWriteParameterMap parameters)
java.util.Iterator<MatrixDataAdapter>	ListBasedDocumentDataAdapter.getMatrixIterator(ReadWriteParameterMap parameters)

Constructor parameters in info.bioinfweb.jphyloio.dataadapters.implementations with type arguments of type MatrixDataAdapter

Constructor and Description
ListBasedDocumentDataAdapter(org.apache.commons.collections4.map.ListOrderedMap<java.lang.String,OTUListDataAdapter> otusMap, java.util.List<MatrixDataAdapter> matrices, java.util.List<TreeNetworkGroupDataAdapter> treeNetworkGroups) Creates a new instance of this class using the specified lists.

Uses of MatrixDataAdapter in info.bioinfweb.jphyloio.dataadapters.implementations.store

Classes in info.bioinfweb.jphyloio.dataadapters.implementations.store that implement MatrixDataAdapter

Modifier and Type	Class and Description
class	StoreMatrixDataAdapter

Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store that return types with arguments of type MatrixDataAdapter

Modifier and Type	Method and Description
java.util.List<MatrixDataAdapter>	StoreDocumentDataAdapter.getMatrices()
java.util.Iterator<MatrixDataAdapter>	StoreDocumentDataAdapter.getMatrixIterator(ReadWriteParameterMap parameters)

Constructor parameters in info.bioinfweb.jphyloio.dataadapters.implementations.store with type arguments of type MatrixDataAdapter

Constructor and Description
StoreDocumentDataAdapter(java.util.List<JPhyloIOEvent> annotations, org.apache.commons.collections4.OrderedMap<java.lang.String,OTUListDataAdapter> otusMap, java.util.List<MatrixDataAdapter> matrices, java.util.List<TreeNetworkGroupDataAdapter> treeNetworkGroups)

Uses of MatrixDataAdapter in info.bioinfweb.jphyloio.formats.fasta

Methods in info.bioinfweb.jphyloio.formats.fasta with parameters of type MatrixDataAdapter

Modifier and Type	Method and Description
protected void	FASTAEventWriter.writeSingleMatrix(DocumentDataAdapter document, MatrixDataAdapter matrix, java.util.Iterator<java.lang.String> sequenceIDIterator, ReadWriteParameterMap parameters)

Uses of MatrixDataAdapter in info.bioinfweb.jphyloio.formats.phylip

Methods in info.bioinfweb.jphyloio.formats.phylip with parameters of type MatrixDataAdapter

Modifier and Type	Method and Description
protected void	PhylipEventWriter.writeSingleMatrix(DocumentDataAdapter document, MatrixDataAdapter matrix, java.util.Iterator<java.lang.String> sequenceIDIterator, ReadWriteParameterMap parameters)