statalign.postprocess.plugins.structalign
Class RmsdTrace

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

public class RmsdTrace
extends Postprocess

Field Summary

double[][]	distanceMatrix
java.lang.String[]	fullAlign
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

RmsdTrace()

Method Summary

void	afterLastSample() This function is called after the MCMC runs.
void	beforeFirstSample(InputData inputData) Called before MCMC start.
double[]	calcGyration()
double[][]	calcMSD()
double[][]	calcSeqID()
java.lang.String[]	getDependences() Override this and return an array of full-qualified class names of the plugins this plugin depends on.
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.lang.String	getTabName()
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.
static void	printMatrix(double[][] m)
void	refToDependences(Postprocess[] plugins) Override this to get access to instances of the plugins your plugin depends on.
void	setSampling(boolean enabled) This function switches on or off the sampling mode.
double	sqDistance(double[] x, double[] y)
void	updateTracks(java.lang.String[] align)

Methods inherited from class statalign.postprocess.Postprocess

addTrack, getModExtPlugins, getTabOrder, getToolBarItems, getTracks, newSample, newStep, reloadPanel, setSelected

Methods inherited from class java.lang.Object

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

Field Detail

structAlign

public StructAlign structAlign

distanceMatrix

public double[][] distanceMatrix

fullAlign

public java.lang.String[] fullAlign

Constructor Detail

RmsdTrace

public RmsdTrace()

Method Detail

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.

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

getDependences

public java.lang.String[] getDependences()

Description copied from class: Postprocess

Override this and return an array of full-qualified class names of the plugins this plugin depends on.

Overrides:

getDependences in class Postprocess

refToDependences

public void refToDependences(Postprocess[] plugins)

Description copied from class: Postprocess

Override this to get access to instances of the plugins your plugin depends on. This function will be called by the PostprocessManager during its initialisation.

Overrides:

refToDependences in class Postprocess

Parameters:

plugins - reference to Postprocess objects in the order they are specified in getDependences() or null if it returns null

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)

calcMSD

public double[][] calcMSD()

updateTracks

public void updateTracks(java.lang.String[] align)

sqDistance

public double sqDistance(double[] x,
                         double[] y)

calcGyration

public double[] calcGyration()

calcSeqID

public double[][] calcSeqID()

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.

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