de.jstacs.motifDiscovery
Class MotifDiscovererToolBox

java.lang.Object
  de.jstacs.motifDiscovery.MotifDiscovererToolBox

Direct Known Subclasses:

MutableMotifDiscovererToolbox

public class MotifDiscovererToolBox
extends Object

This class contains static methods for the MotifDiscoverer.

Author:

Jens Keilwagen

See Also:

MotifDiscoverer

Constructor Summary

MotifDiscovererToolBox()

Method Summary

static ImageResult	plot(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, MotifDiscoverer.KindOfProfile kind) This method creates a simple plot of the profile of scores for a sequence and a start position.
static ImageResult	plotAndAnnotate(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, double yMin, double yMax, double threshold, MotifDiscoverer.KindOfProfile kind) This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot that have a higher score than threshold.

Methods inherited from class java.lang.Object

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

Constructor Detail

MotifDiscovererToolBox

public MotifDiscovererToolBox()

Method Detail

plot

public static ImageResult plot(MotifDiscoverer motifDisc,
                               int component,
                               int motif,
                               Sequence sequence,
                               int startpos,
                               REnvironment r,
                               int width,
                               int height,
                               MotifDiscoverer.KindOfProfile kind)
                        throws Exception

This method creates a simple plot of the profile of scores for a sequence and a start position.

Parameters:

motifDisc - the MotifDiscoverer

component - the index of the component

motif - the index of the motif

sequence - the given sequence

startpos - the start position in the sequence

r - the R environment that is used for drawing the plot

width - the width of the image in pixel

height - the height of the image in pixel

kind - the kind of the score profile

Returns:

an image packed in an ImageResult

Throws:

Exception - if something went wrong

plotAndAnnotate

public static ImageResult plotAndAnnotate(MotifDiscoverer motifDisc,
                                          int component,
                                          int motif,
                                          Sequence sequence,
                                          int startpos,
                                          REnvironment r,
                                          int width,
                                          int height,
                                          double yMin,
                                          double yMax,
                                          double threshold,
                                          MotifDiscoverer.KindOfProfile kind)
                                   throws Exception

This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot that have a higher score than threshold.

Parameters:

motifDisc - the MotifDiscoverer

component - the index of the component

motif - the index of the motif

sequence - the given sequence

startpos - the start position in the sequence

r - the R environment that is used for drawing the plot

width - the width of the image in pixel

height - the height of the image in pixel

yMin - the minimal value of the y-axis

yMax - the maximal value of the y-axis

threshold - the threshold for the annotation

kind - the kind of the score profile

Returns:

an image packed in a result

Throws:

Exception - if some thing went wrong