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java.lang.Object | +--jspp.SearchMatrix
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 |
public SearchMatrix(java.lang.String[] alignedsequences, int cleavageposition)
alignedsequences
- String-Array of aligned sequencescleavageposition
- cleavage position inside the aligned sequencespublic SearchMatrix(int sequencelength, int cleavageposition)
sequencelength
- length of sequences (signalpeptide+mature protein)cleavageposition
- cleavageposition, normally the same length as signalpeptideMethod Detail |
public int getSequenceLength()
public void addSequence(java.lang.String sequence) throws jspp.SequenceLengthException
The sequence length must be the same as the initial weight matrix size, otherwise a SequenceLengthException
will be thrown
sequence
- the sequence to add to the matrix
jspp.SequenceLengthException
public void addSearchMatrix(SearchMatrix matrix) throws jspp.SequenceLengthException
The length of both SearchMatrix must be the same, otherwise a SequenceLengthException
will be thrown
matrix
- SearchMatrix to add to this SearchMatrix
jspp.SequenceLengthException
public void removeSequence(java.lang.String sequence) throws jspp.SequenceLengthException
The sequence length must be the same as the initial weight matrix size, otherwise a SequenceLengthException
will be thrown
sequence
- Sequence to remove from the SearchMatrix
jspp.SequenceLengthException
public int getCleavagePosition()
public void setLimits(double cutoff, double uppercutoff)
Scores are normalized in a linear manner, where cutoff is normalized to 0.5 and uppercuttoff is normalized to 1.0.
cutoff
- cutoff-score will be normalized to 0.5.uppercutoff
- upper-limit will be normalized to 1.0.public double getScore(java.lang.String sequence) throws jspp.SequenceLengthException
Method setLimits()
should be called before.
sequence
- sequence for score calculation
sequence
jspp.SequenceLengthException
public double getRawScore(java.lang.String sequence) throws jspp.SequenceLengthException
sequence
- sequence for score calculation
jspp.SequenceLengthException
public double getCutOffScore()
public double raw2normalizedScore(double rawscore)
rawscore
- the raw score
public double getInformation(int position) throws jspp.SequenceLengthException
position
- the weight matrix position
jspp.SequenceLengthException
public int[][] getMatrix()
public void setFrequencyMatrix(java.lang.String[] sequences)
sequences
- array of Strings containing sequences of dependent organism / grouppublic void setFrequencyMatrix(SearchMatrix sequences)
sequences
- sequences stored in a SearchMatrix objectpublic void writeMatrix(java.io.File file) throws java.io.IOException
file
- the output file
java.io.IOException
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