- manageLiteralContentMetaNamespaces(XMLWriterStreamDataProvider, ReadWriteParameterMap, LiteralMetadataContentEvent) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
-
- manageLiteralContentMetaNamespaces(XMLWriterStreamDataProvider, ReadWriteParameterMap, LiteralMetadataContentEvent) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
-
- maskReservedLabelCharacters(String) - Method in class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
-
- 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.fasta.FASTAEventWriter
-
- maskReservedLabelCharacters(String) - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter
-
- 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.
- 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_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_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_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
-
- 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.
- 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 - 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
-
- 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
-
- 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.
- 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_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
-
- MEGA_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
-
- 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_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
-
- MEGA_PREDICATE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
-
- MEGAConstants - Interface in info.bioinfweb.jphyloio.formats.mega
-
- MEGAConstants - Interface in info.bioinfweb.jphyloio.formats.mega
-
- MEGAEventReader - Class in info.bioinfweb.jphyloio.formats.mega
-
Event based reader for MEGA alignment files.
- 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.
- 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 - 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
-
- 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_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_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_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_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_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_NUMBER - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
-
- META_TYPE_STRING - 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
-
- MetadataModeling - Class in info.bioinfweb.jphyloio.formatinfo
-
- MetadataModeling(MetadataTopologyType, Set<LiteralContentSequenceType>) - Constructor for class info.bioinfweb.jphyloio.formatinfo.MetadataModeling
-
Creates a new instance of this class.
- 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.
- 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
-
- MetaXMLEventReader - Class in info.bioinfweb.jphyloio.formats.xml.stax
-
- MetaXMLEventReader(XMLReaderStreamDataProvider<?>) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader
-
Creates a new instance of this class.
- 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 - 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.
- 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
-
- MetaXMLStreamReader - Class in info.bioinfweb.jphyloio.formats.xml.stax
-
- MetaXMLStreamReader(XMLReaderStreamDataProvider<?>) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
-
Creates a new instance of this class.
- 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 - 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.
- 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
-
- 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_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
-
- MIXED_DATA_TYPE_VALUE_PATTERN - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader
-