statalign.base
Class MainManager

java.lang.Object
  statalign.base.MainManager

public class MainManager
extends java.lang.Object

This is the central class in the information flow amongst classes. This class also manages the main thread that runs the MCMC.

Author:

miklos, novak

Field Summary

static java.lang.String[]	alignmentTypes Alignment formats in which StatAlign can generate output Implemented formats currently are StatAlign (our own format), Clustal, Fasta, Phylip, Nexus
DataManager	dataMan Data manager that handles all input files.
MainFrame	frame The main window of the program.
java.lang.String	fullPath The full path of the input file from which we read the sequences.
java.lang.String	fullPathWithExtensions After adding on extensions from ModelExtension objects.
InputData	inputData Reference to all input data required to run StatAlign
InputGUI	inputgui The graphical interface of the Input panel
ModelExtManager	modelExtMan Manager for model extension plugins
PostprocessManager	postProcMan This is the postprocess-manager of our program, which handles the postprocesses applied on the MCMC run.
java.lang.Class<? extends SubstitutionModel>[]	substModels Array of substitution model classes that can be selected for an analysis.
MainThread	thread Main (background) calculation thread of the application

Constructor Summary

MainManager(MainFrame frame)
A trivial constructor that only sets MainFrame and substModels.

Method Summary

void	deactivateRNA()
void	finished(int errorCode, java.lang.Exception ex) Called when the MCMC thread terminates, signals end of the process back to MainFrame.
void	init(java.util.ArrayList<java.lang.String> args) Initialises submanagers after the command line has been processed.
void	start() This function starts a new MCMC run.
void	startParallel(int noOfProcesses, int rank)

Methods inherited from class java.lang.Object

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

Field Detail

inputData

public InputData inputData

Reference to all input data required to run StatAlign

postProcMan

public PostprocessManager postProcMan

This is the postprocess-manager of our program, which handles the postprocesses applied on the MCMC run.

dataMan

public DataManager dataMan

Data manager that handles all input files.

modelExtMan

public ModelExtManager modelExtMan

Manager for model extension plugins

substModels

public java.lang.Class<? extends SubstitutionModel>[] substModels

Array of substitution model classes that can be selected for an analysis.

frame

public MainFrame frame

The main window of the program.

inputgui

public InputGUI inputgui

The graphical interface of the Input panel

thread

public MainThread thread

Main (background) calculation thread of the application

fullPath

public java.lang.String fullPath

The full path of the input file from which we read the sequences.

fullPathWithExtensions

public java.lang.String fullPathWithExtensions

After adding on extensions from ModelExtension objects.

alignmentTypes

public static java.lang.String[] alignmentTypes

Alignment formats in which StatAlign can generate output Implemented formats currently are StatAlign (our own format), Clustal, Fasta, Phylip, Nexus

Constructor Detail

MainManager

public MainManager(MainFrame frame)

A trivial constructor that only sets MainFrame and substModels. The MainFrame creates its MainManager, and the MainManager knows who is its owner MainFrame, so it can access GUIs on the MainFrame

Parameters:

frame - The owner of the MainManager, the main window of the graphical interface.

Method Detail

init

public void init(java.util.ArrayList<java.lang.String> args)

Initialises submanagers after the command line has been processed. This is separated from the constructor as some plugins require input from the command line.

Parameters:

params - plugin parameters

start

public void start()

This function starts a new MCMC run. It asks files for writing outputs, and it launches a MainThread that handles the MCMC run.

startParallel

public void startParallel(int noOfProcesses,
                          int rank)

finished

public void finished(int errorCode,
                     java.lang.Exception ex)

Called when the MCMC thread terminates, signals end of the process back to MainFrame.

Parameters:

errorCode - -1: error 0: completed 1: stopped after sampling 2: stopped before sampling

deactivateRNA

public void deactivateRNA()