org.geworkbench.bison.datastructure.complex.pattern.matrix
Class CSPositionSpecificAffinityMatrix

java.lang.Object
  extended by org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
All Implemented Interfaces:
java.io.Serializable, DSBioObject, DSPValued, DSPositionSpecificAffintyMatrix, DSDescribable, DSExtendable, DSIdentifiable, DSNamed, DSSequential

public class CSPositionSpecificAffinityMatrix
extends java.lang.Object
implements DSPositionSpecificAffintyMatrix

Version:
$Id: CSPositionSpecificAffinityMatrix.java 10496 2013-05-02 21:33:13Z zji $
Author:
John Watkinson
See Also:
Serialized Form

Constructor Summary
CSPositionSpecificAffinityMatrix()
           
 
Method Summary
 void addNameValuePair(java.lang.String name, java.lang.Object value)
          Adds a new name-value mapping.
 void allowMultipleValues(java.lang.String name)
          Conjugate method for forceUniqueValue.
 void clearName(java.lang.String name)
          Removes all values associated with the given name.
 void forceUniqueValue(java.lang.String name)
          Forces that the name be associated with at most one value.
 long getBonferroni()
           
 double getCoeff()
           
 java.lang.String getConsensusSequence()
           
 java.lang.String getDescription()
          Get the description..
 java.lang.String getExperiment()
           
 java.lang.String getExperimentID()
           
 java.lang.String getID()
          Return the ID of the implementing object.
 java.lang.String getLabel()
          Gets the label for this object.
 double getPValue()
          Get the p-value for this object.
 double[][] getScores()
           
 java.lang.String getSeedSequence()
           
 int getSerial()
          Gets the serial for this object.
 double getTValue()
           
 java.lang.Object[] getValuesForName(java.lang.String name)
          Returns all values mapped to the designated name.
 boolean isTrailingStrand()
           
 boolean isUniqueValue(java.lang.String name)
          Check if forceUniqueValue() is in effect for the designated name.
 void setBonferroni(long bonferroni)
           
 void setCoeff(double F)
           
 void setConsensusSequence(java.lang.String consensusSequence)
           
 void setDescription(java.lang.String description)
          Set new description.
 void setExperiment(java.lang.String experiment)
           
 void setExperimentID(java.lang.String id)
           
 void setID(java.lang.String id)
          Sets the ID of the implementing object.
 void setLabel(java.lang.String label)
          Sets the label for this object.
 void setPValue(double value)
           
 void setScores(double[][] scores)
           
 void setSeedSequence(java.lang.String seedSequence)
           
 void setSerial(int serial)
          Sets the serial for this object
 void setTrailingStrand(boolean trailingStrand)
           
 void setTValue(double t)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

CSPositionSpecificAffinityMatrix

public CSPositionSpecificAffinityMatrix()
Method Detail

isTrailingStrand

public boolean isTrailingStrand()
Specified by:
isTrailingStrand in interface DSPositionSpecificAffintyMatrix

setTrailingStrand

public void setTrailingStrand(boolean trailingStrand)
Specified by:
setTrailingStrand in interface DSPositionSpecificAffintyMatrix

getBonferroni

public long getBonferroni()
Specified by:
getBonferroni in interface DSPositionSpecificAffintyMatrix

setBonferroni

public void setBonferroni(long bonferroni)
Specified by:
setBonferroni in interface DSPositionSpecificAffintyMatrix

getTValue

public double getTValue()
Specified by:
getTValue in interface DSPositionSpecificAffintyMatrix

setTValue

public void setTValue(double t)
Specified by:
setTValue in interface DSPositionSpecificAffintyMatrix

getCoeff

public double getCoeff()
Specified by:
getCoeff in interface DSPositionSpecificAffintyMatrix

setCoeff

public void setCoeff(double F)
Specified by:
setCoeff in interface DSPositionSpecificAffintyMatrix

getExperiment

public java.lang.String getExperiment()
Specified by:
getExperiment in interface DSPositionSpecificAffintyMatrix

getExperimentID

public java.lang.String getExperimentID()
Specified by:
getExperimentID in interface DSPositionSpecificAffintyMatrix

getSeedSequence

public java.lang.String getSeedSequence()
Specified by:
getSeedSequence in interface DSPositionSpecificAffintyMatrix

getConsensusSequence

public java.lang.String getConsensusSequence()
Specified by:
getConsensusSequence in interface DSPositionSpecificAffintyMatrix

setExperiment

public void setExperiment(java.lang.String experiment)
Specified by:
setExperiment in interface DSPositionSpecificAffintyMatrix

setExperimentID

public void setExperimentID(java.lang.String id)
Specified by:
setExperimentID in interface DSPositionSpecificAffintyMatrix

setSeedSequence

public void setSeedSequence(java.lang.String seedSequence)
Specified by:
setSeedSequence in interface DSPositionSpecificAffintyMatrix

setConsensusSequence

public void setConsensusSequence(java.lang.String consensusSequence)
Specified by:
setConsensusSequence in interface DSPositionSpecificAffintyMatrix

getScores

public double[][] getScores()
Specified by:
getScores in interface DSPositionSpecificAffintyMatrix

setScores

public void setScores(double[][] scores)
Specified by:
setScores in interface DSPositionSpecificAffintyMatrix

addNameValuePair

public void addNameValuePair(java.lang.String name,
                             java.lang.Object value)
Description copied from interface: DSExtendable
Adds a new name-value mapping.

Specified by:
addNameValuePair in interface DSExtendable

getValuesForName

public java.lang.Object[] getValuesForName(java.lang.String name)
Description copied from interface: DSExtendable
Returns all values mapped to the designated name.

Specified by:
getValuesForName in interface DSExtendable
Returns:
All values associated with the argument name.

forceUniqueValue

public void forceUniqueValue(java.lang.String name)
Description copied from interface: DSExtendable
Forces that the name be associated with at most one value. Attempting to add a name-value pair for a 'name' that already has an associate value, results in old name-value association be replaced by the new one.

Calling this method for an existing 'name' results in all the associated name-value pairs to be cleared.

Specified by:
forceUniqueValue in interface DSExtendable
Parameters:
name - The 'name' upon which uniqueness of value will be enforced.

allowMultipleValues

public void allowMultipleValues(java.lang.String name)
Description copied from interface: DSExtendable
Conjugate method for forceUniqueValue. Enables a 'name' to accept mulptiple name-value asscociations.

Specified by:
allowMultipleValues in interface DSExtendable
Parameters:
name - The 'name' for which multiplicity of value is enabled.

isUniqueValue

public boolean isUniqueValue(java.lang.String name)
Description copied from interface: DSExtendable
Check if forceUniqueValue() is in effect for the designated name.

Specified by:
isUniqueValue in interface DSExtendable
Returns:

clearName

public void clearName(java.lang.String name)
Description copied from interface: DSExtendable
Removes all values associated with the given name.

Specified by:
clearName in interface DSExtendable

setDescription

public void setDescription(java.lang.String description)
Description copied from interface: DSDescribable
Set new description.

Specified by:
setDescription in interface DSDescribable
Parameters:
description - The new description.

getDescription

public java.lang.String getDescription()
Description copied from interface: DSDescribable
Get the description..

Specified by:
getDescription in interface DSDescribable
Returns:
A description.

getID

public java.lang.String getID()
Description copied from interface: DSIdentifiable
Return the ID of the implementing object.

Specified by:
getID in interface DSIdentifiable
Returns:

setID

public void setID(java.lang.String id)
Description copied from interface: DSIdentifiable
Sets the ID of the implementing object.

Specified by:
setID in interface DSIdentifiable

getSerial

public int getSerial()
Description copied from interface: DSSequential
Gets the serial for this object.

Specified by:
getSerial in interface DSSequential
Returns:
the serial index.

setSerial

public void setSerial(int serial)
Description copied from interface: DSSequential
Sets the serial for this object

Specified by:
setSerial in interface DSSequential
Parameters:
serial - the new serial.

getLabel

public java.lang.String getLabel()
Description copied from interface: DSNamed
Gets the label for this object.

Specified by:
getLabel in interface DSNamed
Returns:
the label.

setLabel

public void setLabel(java.lang.String label)
Description copied from interface: DSNamed
Sets the label for this object.

Specified by:
setLabel in interface DSNamed
Parameters:
label - the new label for this object.

getPValue

public double getPValue()
Description copied from interface: DSPValued
Get the p-value for this object.

Specified by:
getPValue in interface DSPValued
Returns:
the p-value (between 0 and 1).

setPValue

public void setPValue(double value)
Specified by:
setPValue in interface DSPValued