jspp
Class SearchMatrix

java.lang.Object
  |
  +--jspp.SearchMatrix

All Implemented Interfaces:

java.io.Serializable

public class SearchMatrix

extends java.lang.Object

implements java.io.Serializable

See Also:

Serialized Form

Constructor Summary

SearchMatrix(int sequencelength, int cleavageposition)
constructs an empty SearchMatrix

SearchMatrix(java.lang.String[] alignedsequences, int cleavageposition)
constructs a new SearchMatrix

Method Summary

void	addSearchMatrix(SearchMatrix matrix) Adds a complete SearchMatrix object to this SearchMatrixThe length of both SearchMatrix must be the same, otherwise a SequenceLengthException will be thrown
void	addSequence(java.lang.String sequence) Adds new sequences to the SearchMatrix.
int	getCleavagePosition() Returns the cleavage position.
double	getCutOffScore() Returns the cutoff score
double	getInformation(int position) Returns the information contents of the specified position
int[][]	getMatrix() Returns the alignment matrix
double	getRawScore(java.lang.String sequence) Returns the raw score
double	getScore(java.lang.String sequence) Returns the normalized score.
int	getSequenceLength()
double	raw2normalizedScore(double rawscore) Transfers a raw score to a normalized score
void	removeSequence(java.lang.String sequence) Removes a sequence from the SearchMatrix The sequence length must be the same as the initial weight matrix size, otherwise a SequenceLengthException will be thrown
void	setFrequencyMatrix(SearchMatrix sequences) Method for considering the amino acid background
void	setFrequencyMatrix(java.lang.String[] sequences) Method for considering the amino acid background
void	setLimits(double cutoff, double uppercutoff) Sets the limits for score normalization.
void	writeMatrix(java.io.File file) Writes the content of this object as tabulator seperated values in a file

Methods inherited from class java.lang.Object

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

Constructor Detail

SearchMatrix

public SearchMatrix(java.lang.String[] alignedsequences,
                    int cleavageposition)

constructs a new SearchMatrix

Parameters:

alignedsequences - String-Array of aligned sequences

cleavageposition - cleavage position inside the aligned sequences

SearchMatrix

public SearchMatrix(int sequencelength,
                    int cleavageposition)

constructs an empty SearchMatrix

Parameters:

sequencelength - length of sequences (signalpeptide+mature protein)

cleavageposition - cleavageposition, normally the same length as signalpeptide

Method Detail

getSequenceLength

public int getSequenceLength()

Returns:

the sequence length of the aligned sequences

addSequence

public void addSequence(java.lang.String sequence)
                 throws jspp.SequenceLengthException

Adds new sequences to the SearchMatrix.

The sequence length must be the same as the initial weight matrix size, otherwise a SequenceLengthException will be thrown

Parameters:

sequence - the sequence to add to the matrix

Throws:

jspp.SequenceLengthException

addSearchMatrix

public void addSearchMatrix(SearchMatrix matrix)
                     throws jspp.SequenceLengthException

Adds a complete SearchMatrix object to this SearchMatrix

The length of both SearchMatrix must be the same, otherwise a SequenceLengthException will be thrown

Parameters:

matrix - SearchMatrix to add to this SearchMatrix

Throws:

jspp.SequenceLengthException

removeSequence

public void removeSequence(java.lang.String sequence)
                    throws jspp.SequenceLengthException

Removes a sequence from the SearchMatrix

The sequence length must be the same as the initial weight matrix size, otherwise a SequenceLengthException will be thrown

Parameters:

sequence - Sequence to remove from the SearchMatrix

Throws:

jspp.SequenceLengthException

getCleavagePosition

public int getCleavagePosition()

Returns the cleavage position.

Returns:

the cleavage position.

setLimits

public void setLimits(double cutoff,
                      double uppercutoff)

Sets the limits for score normalization.

Scores are normalized in a linear manner, where cutoff is normalized to 0.5 and uppercuttoff is normalized to 1.0.

Parameters:

cutoff - cutoff-score will be normalized to 0.5.

uppercutoff - upper-limit will be normalized to 1.0.

getScore

public double getScore(java.lang.String sequence)
                throws jspp.SequenceLengthException

Returns the normalized score.

Method setLimits() should be called before.

Parameters:

sequence - sequence for score calculation

Returns:

a normalized score for sequence

Throws:

jspp.SequenceLengthException

getRawScore

public double getRawScore(java.lang.String sequence)
                   throws jspp.SequenceLengthException

Returns the raw score

Parameters:

sequence - sequence for score calculation

Returns:

the raw score

Throws:

jspp.SequenceLengthException

getCutOffScore

public double getCutOffScore()

Returns the cutoff score

Returns:

the cutoff score

raw2normalizedScore

public double raw2normalizedScore(double rawscore)

Transfers a raw score to a normalized score

Parameters:

rawscore - the raw score

Returns:

the normalized score

getInformation

public double getInformation(int position)
                      throws jspp.SequenceLengthException

Returns the information contents of the specified position

Parameters:

position - the weight matrix position

Returns:

the information content of specified weight matrix position

Throws:

jspp.SequenceLengthException

getMatrix

public int[][] getMatrix()

Returns the alignment matrix

Returns:

the alignment matrix

setFrequencyMatrix

public void setFrequencyMatrix(java.lang.String[] sequences)

Method for considering the amino acid background

Parameters:

sequences - array of Strings containing sequences of dependent organism / group

setFrequencyMatrix

public void setFrequencyMatrix(SearchMatrix sequences)

Method for considering the amino acid background

Parameters:

sequences - sequences stored in a SearchMatrix object

writeMatrix

public void writeMatrix(java.io.File file)
                 throws java.io.IOException

Writes the content of this object as tabulator seperated values in a file

Parameters:

file - the output file

Throws:

java.io.IOException