model
Class UDMObject

java.lang.Object
  extended by model.UDMObject

public class UDMObject
extends java.lang.Object

This class represents a user defined method (UDM) object, which should be generic for a any file which gives position, amino acid and score.


Constructor Summary
UDMObject()
           
 
Method Summary
 double getCurrentScoreCutoff()
           
 java.lang.String getFilename()
          Returns the name of the file.
 double getMaxValue()
           
 java.lang.String getMethodName()
           
 double getMinValue()
           
 java.util.HashMap<java.lang.Integer,ResidueImpl> getPos2ResMap()
          Returns the Position-To-Residue HashMap.
 ResidueImpl[] getResidues()
          Returns the residues as an array.
 int getResNumber()
          Returns the residue number.
 double getScoreCutoff()
          Returns the score cutoff.
 boolean isIncreasingScore()
           
 void setCurrentScoreCutoff(double currentScoreCutoff)
           
 void setFilename(java.lang.String filename)
          Sets the name of the file.
 void setIncreasingScore(boolean isIncreasingScore)
           
 void setMethodName(java.lang.String methodName)
           
 void setPos2ResMap(java.util.HashMap<java.lang.Integer,ResidueImpl> pos2ResMap)
          Sets the Position-To-Residue HashMap.
 void setResidues(ResidueImpl[] residues)
          Sets the functional residues array.
 void setResNumber(int resNumber)
          Set the residues number.
 void setScoreCutoff(double scoreCutoff)
          Sets the score cutoff.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

UDMObject

public UDMObject()
Method Detail

getFilename

public java.lang.String getFilename()
Returns the name of the file.

Returns:
String filename

setFilename

public void setFilename(java.lang.String filename)
Sets the name of the file.

Parameters:
filename -

getResidues

public ResidueImpl[] getResidues()
Returns the residues as an array.

Returns:
ResidueImpl residues

setResidues

public void setResidues(ResidueImpl[] residues)
Sets the functional residues array.

Parameters:
residues -

getResNumber

public int getResNumber()
Returns the residue number.

Returns:
resNumber Integer

setResNumber

public void setResNumber(int resNumber)
Set the residues number.

Parameters:
resNumber -

getPos2ResMap

public java.util.HashMap<java.lang.Integer,ResidueImpl> getPos2ResMap()
Returns the Position-To-Residue HashMap.

Returns:
HashMap pos2Resmap

setPos2ResMap

public void setPos2ResMap(java.util.HashMap<java.lang.Integer,ResidueImpl> pos2ResMap)
Sets the Position-To-Residue HashMap.

Parameters:
pos2ResMap -

getScoreCutoff

public double getScoreCutoff()
Returns the score cutoff.

Returns:
scoreCutoff double

setScoreCutoff

public void setScoreCutoff(double scoreCutoff)
Sets the score cutoff.

Parameters:
scoreCutoff - double

getCurrentScoreCutoff

public double getCurrentScoreCutoff()
Returns:
the currentScoreCutoff

setCurrentScoreCutoff

public void setCurrentScoreCutoff(double currentScoreCutoff)
Parameters:
currentScoreCutoff - the currentScoreCutoff to set

getMethodName

public java.lang.String getMethodName()
Returns:
the methodName

setMethodName

public void setMethodName(java.lang.String methodName)
Parameters:
methodName - the methodName to set

getMaxValue

public double getMaxValue()
Returns:
the highest score

getMinValue

public double getMinValue()
Returns:
the lowest score

isIncreasingScore

public boolean isIncreasingScore()
Returns:
the increasingScore

setIncreasingScore

public void setIncreasingScore(boolean isIncreasingScore)
Parameters:
isIncreasingScore - the increasingScore to set