ajnexus

Data type AjPNexusTaxa

Alias name(s)

Name	Description
AjSNexusTaxa
AjONexusTaxa

Constructor(s)

Name	Description
nexusTaxaNew	Default constructor

Destructor(s)

Name	Description
nexusTaxaDel	Default destructor

Attributes

Name	Type	Description
TaxLabels	Taxon names
Ntax	Number of taxons
Padding	Padding to alignment boundary

Data type AjPNexusCharacters

Alias name(s)

Name	Description
AjSNexusCharacters
AjONexusCharacters

Constructor(s)

Name	Description
nexusCharactersNew	Default constructor

Destructor(s)

Name	Description
nexusCharactersDel	Default destructor

Attributes

Name	Type	Description
NewTaxa	New taxa read from data block
Ntax	Number of taxons
Nchar	Number of characters
RespectCase	Respect case if true
DataType	Data type
Symbols	Character symbols
Equate	Character equivalent names
Labels	Labels if true
Transpose	Transpose data if true
Interleave	Interleaved input if true
Tokens	If true, tokens set
Items	Character items
StatesFormat	Statesformat string
Eliminate	Elimioate string
CharStateLabels	Character and state labels
CharLabels	Character labels
StateLabels	State labels
Matrix	Matrix data
Sequences	Sequence data
Missing	Missing character in input data
Gap	Gap character in input data
MatchChar	Matching charater in input
Padding	Padding to alignment boundary

Data type AjPNexusUnaligned

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

Alias name(s)

Name	Description
AjSNexusUnaligned
AjONexusUnaligned

Constructor(s)

Name	Description
nexusUnalignedNew	Default constructor

Destructor(s)

Name	Description
nexusUnalignedDel	Default destructor

Attributes

Name	Type	Description
NewTaxa	New taxa read from data block
Ntax	Number of taxons
DataType	Data type
RespectCase	Respect case if true
Labels	Labels if true
Symbols	Character symbols
Equate	Character equivalent names
Matrix	Matrix data
Missing	Missing character in input data
Padding	Padding to alignment boundary

Data type AjPNexusDistances

Alias name(s)

Name	Description
AjSNexusDistances
AjONexusDistances

Constructor(s)

Name	Description
nexusDistancesNew	Default constructor

Destructor(s)

Name	Description
nexusDistancesDel	Default destructor

Attributes

Name	Type	Description
NewTaxa	New taxa read from data block
Ntax	Number of taxons
Nchar	Number of characters
Diagonal	If true, expect to read diagonal of matrix
Labels	Labels if true
Interleave	Interleaved input if true
Triangle	Triangular distances block type
Matrix	Matrix data
Missing	Missing character in input data
Padding	Padding to alignment boundary

Data type AjPNexusSets

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

Alias name(s)

Name	Description
AjSNexusSets
AjONexusSets

Constructor(s)

Name	Description
nexusSetsNew	Default constructor

Destructor(s)

Name	Description
nexusSetsDel	Default destructor

Attributes

Name	Type	Description
CharSet	Character set commands
StateSet	State set commands
ChangeSet	Change set commands
TaxSet	Taxon set commands
TreeSet	Tree set commands
CharPartition	Character partition statements
TaxPartition	Taxa partition statements
TreePartition	Tree partition statements

Data type AjPNexusAssumptions

Alias name(s)

Name	Description
AjSNexusAssumptions
AjONexusAssumptions

Constructor(s)

Name	Description
nexusAssumptionsNew	Default constructor

Destructor(s)

Name	Description
nexusAssumptionsDel	Default destructor

Attributes

Name	Type	Description
DefType	Options deftype subcommand
PolyTCount	Options polytcount subcommand
GapMode	Options gapmode subcommand
UserType	Usertype commands
TypeSet	Typeset commands
WtSet	Wtset commands
ExSet	Exset commands
AncStates	Ancstates commands

Data type AjPNexusCodons

Alias name(s)

Name	Description
AjSNexusCodons
AjONexusCodons

Constructor(s)

Name	Description
nexusCodonsNew	Default constructor

Destructor(s)

Name	Description
nexusCodonsDel	Default destructor

Attributes

Name	Type	Description
CodonPosSet	CodonPosSetcommands
GeneticCode	GeneticCodecommands
CodeSet	CodeSetcommands

Data type AjPNexusTrees

Alias name(s)

Name	Description
AjSNexusTrees
AjONexusTrees

Constructor(s)

Name	Description
nexusTreesNew	Default constructor

Destructor(s)

Name	Description
nexusTreesDel	Default destructor

Attributes

Name	Type	Description
Translate	Translate commands
Tree	Tree commands

Data type AjPNexusNotes

Alias name(s)

Name	Description
AjSNexusNotes
AjONexusNotes

Constructor(s)

Name	Description
nexusNotesNew	Default constructor

Destructor(s)

Name	Description
nexusNotesDel	Default destructor

Attributes

Name	Type	Description
Text	Text commands
Picture	Picture commands

Data type AjPNexus

Alias name(s)

Name	Description
AjSNexus
AjONexus

Constructor(s)

Name	Description
ajNexusNew	Default constructor

Destructor(s)

Name	Description
ajNexusDel	Default destructor

Attributes

Name	Type	Description
Taxa	Taxa
Characters	Characters (or data)
Unaligned	Unaligned
Distances	Distances
Sets	Sets
Assumptions	Assumptions
Codons	Codons
Trees	Trees
Notes	Notes
Ntax	Number of taxa (wherever they were defined)
Padding	Padding to alignment boundary