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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 LiteralMetadataContentEvents 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 LiteralMetadataContentEvents 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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