## 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)`