statalign.postprocess.plugins.structalign
Class StructTrace

java.lang.Object
  statalign.postprocess.Postprocess
      statalign.postprocess.plugins.structalign.StructTrace

public class StructTrace
extends Postprocess

Field Summary

int	burninLength
int	MAX_HISTORY_SIZE
int	refreshRate
StructAlign	structAlign

Fields inherited from class statalign.postprocess.Postprocess

active, alignmentType, file, hasToolBar, mcmc, outputable, outputFile, postprocessable, postprocessWrite, rnaAssociated, sampling, screenable, selected, show

Constructor Summary

StructTrace()

Method Summary

void	afterLastSample() This function is called after the MCMC runs.
void	beforeFirstSample(InputData inputData) Called before MCMC start.
int	getCount()
java.lang.String	getFileExtension() Returns default file extension that is to appended to the input file name to get the file this plugin is writing into.
javax.swing.Icon	getIcon()
javax.swing.JPanel	getJPanel()
java.util.List<StructAlignTraceParameters>	getParameterHistory()
java.lang.String	getTabName()
double	getTabOrder() Specifies the order of the tab for this plugin in the GUI.
java.lang.String	getTip() Returns with the tip information (shown when the mouse cursor is moved over the label of the tabulated panel)
void	init(ModelExtManager modelExtMan) Called by PostprocessManager after setting the Postprocess.show field to allow initialisation, possibly involving GUI (toolbar etc.)
void	newPeek(State state) Allows peeking into the Markov chain before actual sampling begins.
void	newSample(State state, int no, int total) This function is called when we sample from the Markov chain.
void	newStep(McmcStep mcmcStep) Called after a new step is made.
static void	printMatrix(double[][] m)
void	setSampling(boolean enabled) This function switches on or off the sampling mode.

Methods inherited from class statalign.postprocess.Postprocess

addTrack, getDependences, getModExtPlugins, getToolBarItems, getTracks, newSample, refToDependences, reloadPanel, setSelected

Methods inherited from class java.lang.Object

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

Field Detail

structAlign

public StructAlign structAlign

burninLength

public int burninLength

MAX_HISTORY_SIZE

public int MAX_HISTORY_SIZE

refreshRate

public int refreshRate

Constructor Detail

StructTrace

public StructTrace()

Method Detail

getParameterHistory

public java.util.List<StructAlignTraceParameters> getParameterHistory()

getCount

public int getCount()

init

public void init(ModelExtManager modelExtMan)

Description copied from class: Postprocess

Called by PostprocessManager after setting the Postprocess.show field to allow initialisation, possibly involving GUI (toolbar etc.)

Overrides:

init in class Postprocess

getTabName

public java.lang.String getTabName()

Specified by:

getTabName in class Postprocess

Returns:

Returns with the name that will appear on the label of the tabulated panel.

getTabOrder

public double getTabOrder()

Description copied from class: Postprocess

Specifies the order of the tab for this plugin in the GUI.

E.g. we probably always want the "sequence input"-tab to appear first and therefore it returns a 1.0d here. The "current alignment"-tab returns 2.0d here and so if we want to make a tab get ordered between the "sequence input" and the "current alignment"-tabs we just make that plugin return 1.5d or something similar here. By default tabs get ordered last.

Overrides:

getTabOrder in class Postprocess

Returns:

the tab order of the tab associated with this plugin, if running in a GUI.

getIcon

public javax.swing.Icon getIcon()

Specified by:

getIcon in class Postprocess

Returns:

Returns with the icon that will appear on the label of the tabulated panel.

getJPanel

public javax.swing.JPanel getJPanel()

Specified by:

getJPanel in class Postprocess

Returns:

Returns with the panel of the GUI

getTip

public java.lang.String getTip()

Description copied from class: Postprocess

Returns with the tip information (shown when the mouse cursor is moved over the label of the tabulated panel)

Specified by:

getTip in class Postprocess

getFileExtension

public java.lang.String getFileExtension()

Description copied from class: Postprocess

Returns default file extension that is to appended to the input file name to get the file this plugin is writing into.

Overrides:

getFileExtension in class Postprocess

setSampling

public void setSampling(boolean enabled)

Description copied from class: Postprocess

This function switches on or off the sampling mode.

Specified by:

setSampling in class Postprocess

Parameters:

enabled - Set it true if you need samples.

beforeFirstSample

public void beforeFirstSample(InputData inputData)

Description copied from class: Postprocess

Called before MCMC start. This is the first time you can use PostprocessManager.mcmc to access internal data structure

Overrides:

beforeFirstSample in class Postprocess

newPeek

public void newPeek(State state)

Description copied from class: Postprocess

Allows peeking into the Markov chain before actual sampling begins. Frequency is determined by the MCMC sampling parameter set by the user, just like for Postprocess.newSample(State, int, int). Unlike that method, this one is called both during and after the burn-in period.

Overrides:

newPeek in class Postprocess

Parameters:

state - A State object representing the current state of the chain

newSample

public void newSample(State state,
                      int no,
                      int total)

Description copied from class: Postprocess

This function is called when we sample from the Markov chain. Frequency is determined by the MCMC sampling parameter set by the user. Unlike Postprocess.newPeek(State state), this method is only called after the burn-in period.

Overrides:

newSample in class Postprocess

Parameters:

state - A State object representing the current state of the chain

no - The number of the current sample

total - The number of the total samples

afterLastSample

public void afterLastSample()

Description copied from class: Postprocess

This function is called after the MCMC runs.

Overrides:

afterLastSample in class Postprocess

printMatrix

public static void printMatrix(double[][] m)

newStep

public void newStep(McmcStep mcmcStep)

Description copied from class: Postprocess

Called after a new step is made. A typical run of MCMC takes hundred thousands of steps, override this function only if it takes a negligible amount of time and does not use too much memory. We use, for example, in drawing the loglikelihood trace.

Overrides:

newStep in class Postprocess