charite.christo.strap.extensions
Class AbstractAlignAndCompare

java.lang.Object
  charite.christo.strap.extensions.AbstractAlignAndCompare

All Implemented Interfaces:

Disposable, HasControlPanel, HasProtein, HasSharedControlPanel, NeedsSharedInstance, ProteinProteinValue, StrapListener, ValueOfProtein

Direct Known Subclasses:

AlignmentScore, IndividualSequenceDisSimilarity, RmsdValue, SequenceDisSimilarityAsAligned

public class AbstractAlignAndCompare
extends Object
implements NeedsSharedInstance, ProteinProteinValue, HasSharedControlPanel, HasControlPanel, Disposable, StrapListener

Constructor Summary

AbstractAlignAndCompare()

Method Summary

ChCombo	comboClass()
void	compute() When it is time consuming then do the calculation in the compute method.
void	dispose()
Container	getControlPanel()
int	getModificationCount()
Object	getOtherClass()
StrapProtein	getOtherProtein()
StrapProtein	getProtein()
Container	getSharedControlPanel()
Object	getSharedInstance()
double	getValue() please store and reuse values if appropriate return NaN when not calculated yet
void	handleEvent(StrapEvent ev)
void	setColumnRange(int f, int t) the values may depend on the range of alignment positions
void	setOtherClass(Object o)
void	setOtherProtein(StrapProtein prot1)
boolean	setProtein(Protein prot0)
void	setSharedInstance(Object i)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractAlignAndCompare

public AbstractAlignAndCompare()

Method Detail

setProtein

public boolean setProtein(Protein prot0)

Specified by:

setProtein in interface ValueOfProtein

setOtherProtein

public void setOtherProtein(StrapProtein prot1)

Specified by:

setOtherProtein in interface ProteinProteinValue

getProtein

public StrapProtein getProtein()

Specified by:

getProtein in interface HasProtein

getOtherProtein

public StrapProtein getOtherProtein()

Specified by:

getOtherProtein in interface ProteinProteinValue

comboClass

public ChCombo comboClass()

getOtherClass

public Object getOtherClass()

setOtherClass

public void setOtherClass(Object o)

setSharedInstance

public void setSharedInstance(Object i)

Specified by:

setSharedInstance in interface NeedsSharedInstance

getSharedInstance

public Object getSharedInstance()

Specified by:

getSharedInstance in interface NeedsSharedInstance

getSharedControlPanel

public Container getSharedControlPanel()

Specified by:

getSharedControlPanel in interface HasSharedControlPanel

getControlPanel

public Container getControlPanel()

Specified by:

getControlPanel in interface HasControlPanel

setColumnRange

public void setColumnRange(int f,
                           int t)

Description copied from interface: ProteinProteinValue

the values may depend on the range of alignment positions

Specified by:

setColumnRange in interface ProteinProteinValue

getValue

public double getValue()

Description copied from interface: ProteinProteinValue

please store and reuse values if appropriate return NaN when not calculated yet

Specified by:

getValue in interface ProteinProteinValue

Specified by:

getValue in interface ValueOfProtein

compute

public void compute()

Description copied from interface: ProteinProteinValue

When it is time consuming then do the calculation in the compute method. Non time intensive calculations can be performed in getValue();

Specified by:

compute in interface ProteinProteinValue

Specified by:

compute in interface ValueOfProtein

getModificationCount

public int getModificationCount()

Specified by:

getModificationCount in interface ProteinProteinValue

Specified by:

getModificationCount in interface ValueOfProtein

dispose

public void dispose()

Specified by:

dispose in interface Disposable

handleEvent

public void handleEvent(StrapEvent ev)

Specified by:

handleEvent in interface StrapListener