InvalidAlignmentInputException
extends InvalidArgumentException
in package
Class InvalidAlignmentInputException
Tags
Table of Contents
Methods
- emptyAlignedSequence() : InvalidAlignmentInputException
- Builds the exception raised when a PairwiseAlignmentResult is given an empty aligned sequence.
- mismatchedAlignedLength() : InvalidAlignmentInputException
- Builds the exception raised when a PairwiseAlignmentResult is given two aligned sequences of different lengths, which breaks the one-to-one column correspondence an alignment requires.
- mismatchedMoleculeTypes() : InvalidAlignmentInputException
- Builds the exception raised when the two sequences to align are not the same molecule.
- nonNegativeGapPenalty() : InvalidAlignmentInputException
- Builds the exception raised when a gap penalty is not strictly negative, which would make the dynamic programming matrix prefer inserting gaps without bound instead of penalizing them.
- noScoreForSymbolPair() : InvalidAlignmentInputException
- Builds the exception raised when a substitution matrix (e.g. PAM250) has no entry for a pair of symbols, typically an ambiguous or stop-codon symbol the matrix was never defined for.
- scoringNotMadeForMolecule() : InvalidAlignmentInputException
- Builds the exception raised when the scoring is made for another molecule than the sequences.
Methods
emptyAlignedSequence()
Builds the exception raised when a PairwiseAlignmentResult is given an empty aligned sequence.
public
static emptyAlignedSequence() : InvalidAlignmentInputException
Return values
InvalidAlignmentInputExceptionmismatchedAlignedLength()
Builds the exception raised when a PairwiseAlignmentResult is given two aligned sequences of different lengths, which breaks the one-to-one column correspondence an alignment requires.
public
static mismatchedAlignedLength(int $iFirstLength, int $iSecondLength) : InvalidAlignmentInputException
Parameters
- $iFirstLength : int
- $iSecondLength : int
Return values
InvalidAlignmentInputExceptionmismatchedMoleculeTypes()
Builds the exception raised when the two sequences to align are not the same molecule.
public
static mismatchedMoleculeTypes(string $sFirstMolType, string $sSecondMolType) : InvalidAlignmentInputException
Parameters
- $sFirstMolType : string
- $sSecondMolType : string
Return values
InvalidAlignmentInputExceptionnonNegativeGapPenalty()
Builds the exception raised when a gap penalty is not strictly negative, which would make the dynamic programming matrix prefer inserting gaps without bound instead of penalizing them.
public
static nonNegativeGapPenalty(int $iGapPenalty) : InvalidAlignmentInputException
Parameters
- $iGapPenalty : int
-
The rejected gap penalty
Return values
InvalidAlignmentInputExceptionnoScoreForSymbolPair()
Builds the exception raised when a substitution matrix (e.g. PAM250) has no entry for a pair of symbols, typically an ambiguous or stop-codon symbol the matrix was never defined for.
public
static noScoreForSymbolPair(string $sFirstSymbol, string $sSecondSymbol) : InvalidAlignmentInputException
Parameters
- $sFirstSymbol : string
- $sSecondSymbol : string
Return values
InvalidAlignmentInputExceptionscoringNotMadeForMolecule()
Builds the exception raised when the scoring is made for another molecule than the sequences.
public
static scoringNotMadeForMolecule(string $sScoringClass, string $sMolType) : InvalidAlignmentInputException
Parameters
- $sScoringClass : string
- $sMolType : string