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

Description

static final ChangeType

DIGEST

static final String

LANE

Fields inherited from class org.biojava.bio.gui.sequence.MultiLineRenderer
renderers, RENDERERS
Constructor Summary

Constructors

Constructor

Description

AbstractPeptideDigestRenderer()

AbstractPeptideDigestRenderer(FeatureSource source)

AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter)

AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter, int distanceBetweenFeatures)
Method Summary

Modifier and Type

Method

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 Details
- DIGEST
  
  public static final ChangeType DIGEST
- LANE
  
  public static final String LANE
  See Also:
  
  Constant Field Values
Constructor Details
- 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 Details
- 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()

Class AbstractPeptideDigestRenderer

Nested Class Summary

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

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Field Details

DIGEST

LANE

Constructor Details

AbstractPeptideDigestRenderer

AbstractPeptideDigestRenderer

AbstractPeptideDigestRenderer

AbstractPeptideDigestRenderer

Method Details

setFeatureSource

getFeatureSource

getFilter

setFilter

setDistanceBetweenFeatures

getDistanceBetweenFeatures

sortPeptidesIntoLanes

doRefreshRenderers

createRenderer

doSortPeptides