ajnexus


Data type AjPNexusTaxa

Ajax nexus data taxa block object.

Alias name(s)

Name
AjSNexusTaxa
AjONexusTaxa

Constructor(s)

NameDescription
nexusTaxaNewDefault constructor

Destructor(s)

NameDescription
nexusTaxaDelDefault destructor

Attributes

NameTypeDescription
TaxLabelsAjPStr*Taxon names
NtaxajuintNumber of taxons
Paddingchar[4]Padding to alignment boundary


Data type AjPNexusCharacters

Ajax nexus data characters block object.

Alias name(s)

Name
AjSNexusCharacters
AjONexusCharacters

Constructor(s)

NameDescription
nexusCharactersNewDefault constructor

Destructor(s)

NameDescription
nexusCharactersDelDefault destructor

Attributes

NameTypeDescription
NewTaxaAjBoolNew taxa read from data block
NtaxajuintNumber of taxons
NcharajuintNumber of characters
RespectCaseAjBoolRespect case if true
DataTypeAjPStrData type
SymbolsAjPStrCharacter symbols
EquateAjPStrCharacter equivalent names
LabelsAjBoolLabels if true
TransposeAjBoolTranspose data if true
InterleaveAjBoolInterleaved input if true
TokensAjBoolIf true, tokens set
ItemsAjPStrCharacter items
StatesFormatAjPStrStates format string
EliminateAjPStrEliminate string
CharStateLabelsAjPStr*Character and state labels
CharLabelsAjPStr*Character labels
StateLabelsAjPStr*State labels
MatrixAjPStr*Matrix data
SequencesAjPStr*Sequence data
MissingcharMissing character in input data
GapcharGap character in input data
MatchCharcharMatching character in input
Paddingchar[5]Padding to alignment boundary


Data type AjPNexusUnaligned

Ajax nexus data unaligned block object.

Very similar to a character block and will be merged with AjPNexusCharacter in the near future

Alias name(s)

Name
AjSNexusUnaligned
AjONexusUnaligned

Constructor(s)

NameDescription
nexusUnalignedNewDefault constructor

Destructor(s)

NameDescription
nexusUnalignedDelDefault destructor

Attributes

NameTypeDescription
NewTaxaAjBoolNew taxa read from data block
NtaxajuintNumber of taxons
DataTypeAjPStrData type
RespectCaseAjBoolRespect case if true
LabelsAjBoolLabels if true
SymbolsAjPStrCharacter symbols
EquateAjPStrCharacter equivalent names
MatrixAjPStr*Matrix data
MissingcharMissing character in input data
Paddingchar[7]Padding to alignment boundary


Data type AjPNexusDistances

Ajax nexus data distances block object.

Alias name(s)

Name
AjSNexusDistances
AjONexusDistances

Constructor(s)

NameDescription
nexusDistancesNewDefault constructor

Destructor(s)

NameDescription
nexusDistancesDelDefault destructor

Attributes

NameTypeDescription
NewTaxaAjBoolNew taxa read from data block
NtaxajuintNumber of taxons
NcharajuintNumber of characters
DiagonalAjBoolIf true, expect to read diagonal of matrix
LabelsAjBoolLabels if true
InterleaveAjBoolInterleaved input if true
TriangleAjPStrTriangular distances block type
MatrixAjPStr*Matrix data
MissingcharMissing character in input data
Paddingchar[7]Padding to alignment boundary


Data type AjPNexusSets

Ajax nexus data sets block object.

The data is generally the NEXUS command strings as in the original file.

Alias name(s)

Name
AjSNexusSets
AjONexusSets

Constructor(s)

NameDescription
nexusSetsNewDefault constructor

Destructor(s)

NameDescription
nexusSetsDelDefault destructor

Attributes

NameTypeDescription
CharSetAjPStr*Character set commands
StateSetAjPStr*State set commands
ChangeSetAjPStr*Change set commands
TaxSetAjPStr*Taxon set commands
TreeSetAjPStr*Tree set commands
CharPartitionAjPStr*Character partition statements
TaxPartitionAjPStr*Taxa partition statements
TreePartitionAjPStr*Tree partition statements


Data type AjPNexusAssumptions

Ajax nexus data assumptions block object.

Alias name(s)

Name
AjSNexusAssumptions
AjONexusAssumptions

Constructor(s)

NameDescription
nexusAssumptionsNewDefault constructor

Destructor(s)

NameDescription
nexusAssumptionsDelDefault destructor

Attributes

NameTypeDescription
DefTypeAjPStrOptions deftype subcommand
PolyTCountAjPStrOptions polytcount subcommand
GapModeAjPStrOptions gapmode subcommand
UserTypeAjPStr*Usertype commands
TypeSetAjPStr*Typeset commands
WtSetAjPStr*Wtset commands
ExSetAjPStr*Exset commands
AncStatesAjPStr*Ancstates commands


Data type AjPNexusCodons

Ajax nexus data codons block object.

Alias name(s)

Name
AjSNexusCodons
AjONexusCodons

Constructor(s)

NameDescription
nexusCodonsNewDefault constructor

Destructor(s)

NameDescription
nexusCodonsDelDefault destructor

Attributes

NameTypeDescription
CodonPosSetAjPStr*CodonPosSetcommands
GeneticCodeAjPStr*GeneticCodecommands
CodeSetAjPStr*CodeSetcommands


Data type AjPNexusTrees

Ajax nexus data trees block object.

Alias name(s)

Name
AjSNexusTrees
AjONexusTrees

Constructor(s)

NameDescription
nexusTreesNewDefault constructor

Destructor(s)

NameDescription
nexusTreesDelDefault destructor

Attributes

NameTypeDescription
TranslateAjPStr*Translate commands
TreeAjPStr*Tree commands


Data type AjPNexusNotes

Ajax nexus data notes block object.

Alias name(s)

Name
AjSNexusNotes
AjONexusNotes

Constructor(s)

NameDescription
nexusNotesNewDefault constructor

Destructor(s)

NameDescription
nexusNotesDelDefault destructor

Attributes

NameTypeDescription
TextAjPStr*Text commands
PictureAjPStr*Picture commands


Data type AjPNexus

Ajax nexus data object.

Alias name(s)

Name
AjSNexus
AjONexus

Constructor(s)

NameDescription
ajNexusNewDefault constructor

Destructor(s)

NameDescription
ajNexusDelDefault destructor

Attributes

NameTypeDescription
TaxaAjPNexusTaxaTaxa
CharactersAjPNexusCharactersCharacters (or data)
UnalignedAjPNexusUnalignedUnaligned
DistancesAjPNexusDistancesDistances
SetsAjPNexusSetsSets
AssumptionsAjPNexusAssumptionsAssumptions
CodonsAjPNexusCodonsCodons
TreesAjPNexusTreesTrees
NotesAjPNexusNotesNotes
NtaxajuintNumber of taxa (wherever they were defined)
Paddingchar[4]Padding to alignment boundary