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## M

manageLiteralContentMetaNamespaces(XMLWriterStreamDataProvider, ReadWriteParameterMap, LiteralMetadataContentEvent) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
  This method manages namespaces used or declared in any custom XML events depending on the parameter `ReadWriteParameterNames.KEY_CUSTOM_XML_NAMESPACE_HANDLING`.
maskReservedLabelCharacters(String) - Method in class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
maskReservedLabelCharacters(String) - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter
maskReservedLabelCharacters(String) - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter
maskReservedPhylipLabelCharacters(String) - Static method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter
  Replaces characters that may not occur in Phylip labels according to this definition.
MATRIX_POLYMORPHIC_TOKEN_END - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
MATRIX_POLYMORPHIC_TOKEN_START - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
MATRIX_UNCERTAINS_TOKEN_END - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
MATRIX_UNCERTAINS_TOKEN_START - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
MatrixDataAdapter - Interface in info.bioinfweb.jphyloio.dataadapters
  Adapter interface used to provide any type of character matrix data to instances of `JPhyloIOEventWriter`, including token and character set definitions related to this matrix.
MatrixReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
  Parser for the `MATRIX` command in a `CHARACTERS`, `UNALIGNED` or `DATA` block.
MatrixReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.MatrixReader
MAX_STRING_REPRESENTATION_LENGTH - Static variable in class info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator
MAXIMUM_EXPECTED_DIGITS_OR_WHITESPACE - Static variable in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
  Defines the maximum number of digits in a column or line count definition of a Phylip file.
MEGA_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
MEGA_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
MEGA_NAMESPACE_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
MEGA_PREDICATE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
MEGAConstants - Interface in info.bioinfweb.jphyloio.formats.mega
MEGAEventReader - Class in info.bioinfweb.jphyloio.formats.mega
  Event based reader for MEGA alignment files.
MEGAEventReader(BufferedReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.mega.MEGAEventReader
  Creates a new instance of this class.
MEGAEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.mega.MEGAEventReader
  Creates a new instance of this class.
MEGAEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.mega.MEGAEventReader
  Creates a new instance of this class.
MEGAEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.mega.MEGAEventReader
  Creates a new instance of this class.
MEGAFactory - Class in info.bioinfweb.jphyloio.formats.mega
  Reader and writer factory for the MEGA format.
MEGAFactory() - Constructor for class info.bioinfweb.jphyloio.formats.mega.MEGAFactory
META_ID_ACCESS_NUMBER - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
META_ID_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
META_ID_LINKED_FILE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
META_ID_SEQUENCE_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
META_TYPE_FILE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
META_TYPE_NUMBER - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
META_TYPE_STRING - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
MetadataModeling - Class in info.bioinfweb.jphyloio.formatinfo
  Instances of this class describe which metadata can be nested under a certain content type in a certain format and are returned by `JPhyloIOFormatInfo.getMetadataModeling(info.bioinfweb.jphyloio.events.type.EventContentType, boolean)`.
MetadataModeling(MetadataTopologyType, Set<LiteralContentSequenceType>) - Constructor for class info.bioinfweb.jphyloio.formatinfo.MetadataModeling
  Creates a new instance of this class.
MetadataTopologyType - Enum in info.bioinfweb.jphyloio.formatinfo
  Enumerates possible combinations of meta events to be nested between start and end events of other content types.
MetaXMLEventReader - Class in info.bioinfweb.jphyloio.formats.xml.stax
  Adapter class that allows reading a sequence of `LiteralMetadataContentEvent`s using an `XMLEventReader`.
MetaXMLEventReader(XMLReaderStreamDataProvider<?>) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader
  Creates a new instance of this class.
MetaXMLEventWriter - Class in info.bioinfweb.jphyloio.formats.xml.stax
  This writer can be used by applications already implementing iterator-based StAX-writing of metadata as an adapter to a `JPhyloIOEventWriter`.
MetaXMLEventWriter(JPhyloIOEventReceiver, XMLStreamWriter) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
  Creates a new instance of this class.
MetaXMLStreamReader - Class in info.bioinfweb.jphyloio.formats.xml.stax
  Adapter class that allows reading a sequence of `LiteralMetadataContentEvent`s using an `XMLStreamReader`.
MetaXMLStreamReader(XMLReaderStreamDataProvider<?>) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
  Creates a new instance of this class.
MetaXMLStreamWriter - Class in info.bioinfweb.jphyloio.formats.xml.stax
  This writer can be used by applications already implementing cursor-based StAX-writing of metadata as an adapter to a `JPhyloIOEventWriter`.
MetaXMLStreamWriter(JPhyloIOEventReceiver, XMLStreamWriter) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
  Creates a new instance of this class.
MILLIMETERS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
MIXED_DATA_TYPE_SINGLE_SET_PATTERN - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader
MIXED_DATA_TYPE_VALUE_PATTERN - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

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