org.biojava.bio.gui.sequence
Class AbstractPeptideDigestRenderer

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.gui.sequence.MultiLineRenderer
          extended by 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
static ChangeType DIGEST
           
static String LANE
           
 
Fields inherited from class org.biojava.bio.gui.sequence.MultiLineRenderer
renderers, RENDERERS
 
Constructor Summary
AbstractPeptideDigestRenderer()
           
AbstractPeptideDigestRenderer(FeatureSource source)
           
AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter)
           
AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter, int distanceBetweenFeatures)
           
 
Method Summary
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()