org.biojava.bio.gui.sequence

Class AbstractPeptideDigestRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.MultiLineRenderer

org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

All Implemented Interfaces:

Serializable, SequenceRenderer, Changeable

Direct Known Subclasses:

PeptideDigestRenderer

public abstract class AbstractPeptideDigestRenderer
extends MultiLineRenderer

A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.

Since:

1.5

Author:

Mark Southern

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderer

SequenceRenderer.RendererForwarder

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	DIGEST
static String	LANE

Fields inherited from class org.biojava.bio.gui.sequence.MultiLineRenderer

renderers, RENDERERS

Constructor Summary

Constructors

Constructor and Description
AbstractPeptideDigestRenderer()
AbstractPeptideDigestRenderer(FeatureSource source)
AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter)
AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter, int distanceBetweenFeatures)

Method Summary

Methods

Modifier and Type	Method and Description
abstract FeatureRenderer	createRenderer(int lane)
protected void	doRefreshRenderers()
protected void	doSortPeptides()
int	getDistanceBetweenFeatures()
FeatureSource	getFeatureSource()
FeatureFilter	getFilter()
void	setDistanceBetweenFeatures(int d)
void	setFeatureSource(FeatureSource source)
void	setFilter(FeatureFilter filter)
void	sortPeptidesIntoLanes()

Methods inherited from class org.biojava.bio.gui.sequence.MultiLineRenderer

_addRenderer, _removeRenderer, addRenderer, clearRenderers, getChangeSupport, getDepth, getMinimumLeader, getMinimumTrailer, paint, processMouseEvent, removeRenderer

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Field Detail

DIGEST

public static final ChangeType DIGEST

LANE

public static final String LANE

See Also:

Constant Field Values

Constructor Detail

AbstractPeptideDigestRenderer

public AbstractPeptideDigestRenderer()

AbstractPeptideDigestRenderer

public AbstractPeptideDigestRenderer(FeatureSource source)

AbstractPeptideDigestRenderer

public AbstractPeptideDigestRenderer(FeatureSource source,
                             FeatureFilter filter)

AbstractPeptideDigestRenderer

public AbstractPeptideDigestRenderer(FeatureSource source,
                             FeatureFilter filter,
                             int distanceBetweenFeatures)

Method Detail

setFeatureSource

public void setFeatureSource(FeatureSource source)

getFeatureSource

public FeatureSource getFeatureSource()

getFilter

public FeatureFilter getFilter()

setFilter

public void setFilter(FeatureFilter filter)

setDistanceBetweenFeatures

public void setDistanceBetweenFeatures(int d)

getDistanceBetweenFeatures

public int getDistanceBetweenFeatures()

sortPeptidesIntoLanes

public void sortPeptidesIntoLanes()
                           throws ChangeVetoException

Throws:

ChangeVetoException

doRefreshRenderers

protected void doRefreshRenderers()
                           throws ChangeVetoException

Throws:

ChangeVetoException

createRenderer

public abstract FeatureRenderer createRenderer(int lane)

doSortPeptides

protected void doSortPeptides()