ajnexus

Data type AjPNexusTaxa

Alias name(s)

Name
AjSNexusTaxa
AjONexusTaxa

Constructor(s)

Name	Description
nexusTaxaNew	Default constructor

Destructor(s)

Name	Description
nexusTaxaDel	Default destructor

Attributes

Name	Type	Description
TaxLabels	AjPStr*	Taxon names
Ntax	ajuint	Number of taxons
Padding	char[4]	Padding to alignment boundary

Data type AjPNexusCharacters

Alias name(s)

Name
AjSNexusCharacters
AjONexusCharacters

Constructor(s)

Name	Description
nexusCharactersNew	Default constructor

Destructor(s)

Name	Description
nexusCharactersDel	Default destructor

Attributes

Name	Type	Description
NewTaxa	AjBool	New taxa read from data block
Ntax	ajuint	Number of taxons
Nchar	ajuint	Number of characters
RespectCase	AjBool	Respect case if true
DataType	AjPStr	Data type
Symbols	AjPStr	Character symbols
Equate	AjPStr	Character equivalent names
Labels	AjBool	Labels if true
Transpose	AjBool	Transpose data if true
Interleave	AjBool	Interleaved input if true
Tokens	AjBool	If true, tokens set
Items	AjPStr	Character items
StatesFormat	AjPStr	States format string
Eliminate	AjPStr	Eliminate string
CharStateLabels	AjPStr*	Character and state labels
CharLabels	AjPStr*	Character labels
StateLabels	AjPStr*	State labels
Matrix	AjPStr*	Matrix data
Sequences	AjPStr*	Sequence data
Missing	char	Missing character in input data
Gap	char	Gap character in input data
MatchChar	char	Matching character in input
Padding	char[5]	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
AjSNexusUnaligned
AjONexusUnaligned

Constructor(s)

Name	Description
nexusUnalignedNew	Default constructor

Destructor(s)

Name	Description
nexusUnalignedDel	Default destructor

Attributes

Name	Type	Description
NewTaxa	AjBool	New taxa read from data block
Ntax	ajuint	Number of taxons
DataType	AjPStr	Data type
RespectCase	AjBool	Respect case if true
Labels	AjBool	Labels if true
Symbols	AjPStr	Character symbols
Equate	AjPStr	Character equivalent names
Matrix	AjPStr*	Matrix data
Missing	char	Missing character in input data
Padding	char[7]	Padding to alignment boundary

Data type AjPNexusDistances

Alias name(s)

Name
AjSNexusDistances
AjONexusDistances

Constructor(s)

Name	Description
nexusDistancesNew	Default constructor

Destructor(s)

Name	Description
nexusDistancesDel	Default destructor

Attributes

Name	Type	Description
NewTaxa	AjBool	New taxa read from data block
Ntax	ajuint	Number of taxons
Nchar	ajuint	Number of characters
Diagonal	AjBool	If true, expect to read diagonal of matrix
Labels	AjBool	Labels if true
Interleave	AjBool	Interleaved input if true
Triangle	AjPStr	Triangular distances block type
Matrix	AjPStr*	Matrix data
Missing	char	Missing character in input data
Padding	char[7]	Padding to alignment boundary

Data type AjPNexusSets

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

Alias name(s)

Name
AjSNexusSets
AjONexusSets

Constructor(s)

Name	Description
nexusSetsNew	Default constructor

Destructor(s)

Name	Description
nexusSetsDel	Default destructor

Attributes

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

Data type AjPNexusAssumptions

Alias name(s)

Name
AjSNexusAssumptions
AjONexusAssumptions

Constructor(s)

Name	Description
nexusAssumptionsNew	Default constructor

Destructor(s)

Name	Description
nexusAssumptionsDel	Default destructor

Attributes

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

Data type AjPNexusCodons

Alias name(s)

Name
AjSNexusCodons
AjONexusCodons

Constructor(s)

Name	Description
nexusCodonsNew	Default constructor

Destructor(s)

Name	Description
nexusCodonsDel	Default destructor

Attributes

Name	Type	Description
CodonPosSet	AjPStr*	CodonPosSetcommands
GeneticCode	AjPStr*	GeneticCodecommands
CodeSet	AjPStr*	CodeSetcommands

Data type AjPNexusTrees

Alias name(s)

Name
AjSNexusTrees
AjONexusTrees

Constructor(s)

Name	Description
nexusTreesNew	Default constructor

Destructor(s)

Name	Description
nexusTreesDel	Default destructor

Attributes

Name	Type	Description
Translate	AjPStr*	Translate commands
Tree	AjPStr*	Tree commands

Data type AjPNexusNotes

Alias name(s)

Name
AjSNexusNotes
AjONexusNotes

Constructor(s)

Name	Description
nexusNotesNew	Default constructor

Destructor(s)

Name	Description
nexusNotesDel	Default destructor

Attributes

Name	Type	Description
Text	AjPStr*	Text commands
Picture	AjPStr*	Picture commands

Data type AjPNexus

Alias name(s)

Name
AjSNexus
AjONexus

Constructor(s)

Name	Description
ajNexusNew	Default constructor

Destructor(s)

Name	Description
ajNexusDel	Default destructor

Attributes

Name	Type	Description
Taxa	AjPNexusTaxa	Taxa
Characters	AjPNexusCharacters	Characters (or data)
Unaligned	AjPNexusUnaligned	Unaligned
Distances	AjPNexusDistances	Distances
Sets	AjPNexusSets	Sets
Assumptions	AjPNexusAssumptions	Assumptions
Codons	AjPNexusCodons	Codons
Trees	AjPNexusTrees	Trees
Notes	AjPNexusNotes	Notes
Ntax	ajuint	Number of taxa (wherever they were defined)
Padding	char[4]	Padding to alignment boundary