statalign.base
Class InputData

java.lang.Object
  statalign.base.InputData

public class InputData
extends java.lang.Object

Field Summary

java.util.List<DataType>	auxData Non-sequence type auxiliary data that has been loaded, can be used by model extension plugins
int	currentAlignmentType This integer stores the index of the current alignment type, as it is in alignmentTypes
boolean	doReportDuringBurnin If true then logging information is also printed during the burnin.
boolean	isParallel Are we using the parallel version?
SubstitutionModel	model The current substitution model that is used to analyse the sequences.
java.lang.String	outputPath The path where output files will be created.
MCMCPars	pars MCMC parameters such as the number of burn-in cycles, number of steps and sampling rate
RawSequences	seqs The input sequences, optionally aligned
java.lang.String	title The file name (without path) that is chosen to be the base name for all output files, plugins will define their own output file names by adding extensions to this base name.
Tree	tree The initial tree, if given, which is optionally fixed for the whole analysis
int	useAlign Specifies how the alignment of the input sequences in seqs is used.
int	useTree Specifies how the given tree is used.

Constructor Summary

InputData()

Method Summary

void	setBaseFile(java.io.File file) Fills both outputPath and title.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

seqs

public RawSequences seqs

The input sequences, optionally aligned

tree

public Tree tree

The initial tree, if given, which is optionally fixed for the whole analysis

auxData

public java.util.List<DataType> auxData

Non-sequence type auxiliary data that has been loaded, can be used by model extension plugins

pars

public MCMCPars pars

MCMC parameters such as the number of burn-in cycles, number of steps and sampling rate

useAlign

public int useAlign

Specifies how the alignment of the input sequences in seqs is used.

0: it's ignored and sequences are re-aligned from scratch
1: used as the initial alignment and sampled during MCMC
2: fixed throughout the MCMC analysis (currently unsupported)

useTree

public int useTree

Specifies how the given tree is used.

0: unused, the tree is constructed from scratch using NJ
1: it is used as the initial tree and sampled during MCMC
2: the topology is fixed throughout the MCMC analysis, edges are sampled
3: both topology and edge lengths are fixed during the MCMC

isParallel

public boolean isParallel

Are we using the parallel version?

doReportDuringBurnin

public boolean doReportDuringBurnin

If true then logging information is also printed during the burnin.

model

public SubstitutionModel model

The current substitution model that is used to analyse the sequences.

title

public java.lang.String title

The file name (without path) that is chosen to be the base name for all output files, plugins will define their own output file names by adding extensions to this base name. By default, this is the name of the first sequence input file but can be configured by the user.

See Also:

#baseFilePath

outputPath

public java.lang.String outputPath

The path where output files will be created. By default this is the path of the first sequence input file but can be configured by the user.

See Also:

title

currentAlignmentType

public int currentAlignmentType

This integer stores the index of the current alignment type, as it is in alignmentTypes

Constructor Detail

InputData

public InputData()

Method Detail

setBaseFile

public void setBaseFile(java.io.File file)

Fills both outputPath and title.

Parameters:

file - the name and path of the base file