Public Member Functions
	SmithWatermanAlignment (String seq)

	SmithWatermanAlignment (String seq, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty)

jaligner.Alignment	align (String seq)

Static Public Member Functions
static jaligner.Alignment	align (String seq1, String seq2, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty)

static String	getFullPrintableAlignment (jaligner.Alignment alignment)

static int	ungappedMatchStartOnFirstSequence (String seq1, String seq2, float matchScore, float mismatchScore, float minPctIdentity)

static int	matchStartOnFirstSequence (String seq1, String seq2, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty, float minPctIdentity)

static boolean	containsFullLengthUngappedMatch (String seq1, String seq2, int seq1start, int maxMismatches)

static boolean	containsFullLengthUngappedMatch (String seq1, String seq2, int seq1start, float matchScore, float mismatchScore, int maxMismatches)

static boolean	containsFullLengthUngappedMatch (String seq1, String seq2, int maxMismatches)

static boolean	containsFullLengthUngappedMatch (String seq1, String seq2, float matchScore, float mismatchScore, int maxMismatches)

Static Public Attributes
static float	DEFAULT_MATCH_SCORE = 5

static float	DEFAULT_MISMATCH_SCORE = -4

static float	DEFAULT_GAP_OPEN_PENALTY = 8

static float	DEFAULT_GAP_EXTEND_PENALTY = 2

Constructor & Destructor Documentation

umms.core.alignment.SmithWatermanAlignment.SmithWatermanAlignment ( String seq )

umms.core.alignment.SmithWatermanAlignment.SmithWatermanAlignment	(	String	seq,
		float	matchScore,
		float	mismatchScore,
		float	gapOpenPenalty,
		float	gapExtendPenalty
	)

Member Function Documentation

jaligner.Alignment umms.core.alignment.SmithWatermanAlignment.align ( String seq )

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static jaligner.Alignment umms.core.alignment.SmithWatermanAlignment.align	(	String	seq1,
		String	seq2,
		float	matchScore,
		float	mismatchScore,
		float	gapOpenPenalty,
		float	gapExtendPenalty
	)

static

static boolean umms.core.alignment.SmithWatermanAlignment.containsFullLengthUngappedMatch	(	String	seq1,
		String	seq2,
		int	seq1start,
		int	maxMismatches
	)

static

Whether there is a full length ungapped match of sequence 2 to sequence 1, starting at specified position of sequence 1, allowing mismatches Uses default match and mismatch scores

Parameters

seq1	Sequence 1
seq2	Sequence 2
seq1start	Required start position of match on sequence 1

Returns: Whether the best ungapped alignment is full length and has at most the max number of mismatches

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static boolean umms.core.alignment.SmithWatermanAlignment.containsFullLengthUngappedMatch	(	String	seq1,
		String	seq2,
		int	seq1start,
		float	matchScore,
		float	mismatchScore,
		int	maxMismatches
	)

static

Whether there is a full length ungapped match of sequence 2 to sequence 1, starting at specified position of sequence 1, allowing mismatches

Parameters

seq1	Sequence 1
seq2	Sequence 2
seq1start	Required start position of match on sequence 1
matchScore	Match score
mismatchScore	Mismatch score
maxMismatches	Max allowable number of mismatches

Returns: Whether the best ungapped alignment is full length and has at most the max number of mismatches

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static boolean umms.core.alignment.SmithWatermanAlignment.containsFullLengthUngappedMatch	(	String	seq1,
		String	seq2,
		int	maxMismatches
	)

static

Whether there is a full length ungapped match of the shorter sequence to the longer sequence, allowing mismatches Uses default match and mismatch scores

Parameters

seq1	Sequence 1
seq2	Sequence 2
maxMismatches	Max allowable number of mismatches

Returns: Whether the best ungapped alignment is full length and has at most the max number of mismatches

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static boolean umms.core.alignment.SmithWatermanAlignment.containsFullLengthUngappedMatch	(	String	seq1,
		String	seq2,
		float	matchScore,
		float	mismatchScore,
		int	maxMismatches
	)

static

Whether there is a full length ungapped match of the shorter sequence to the longer sequence, allowing mismatches

Parameters

seq1	Sequence 1
seq2	Sequence 2
matchScore	Match score
mismatchScore	Mismatch score
maxMismatches	Max allowable number of mismatches

Returns: Whether the best ungapped alignment is full length and has at most the max number of mismatches

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static String umms.core.alignment.SmithWatermanAlignment.getFullPrintableAlignment ( jaligner.Alignment alignment )

static

static int umms.core.alignment.SmithWatermanAlignment.matchStartOnFirstSequence	(	String	seq1,
		String	seq2,
		float	matchScore,
		float	mismatchScore,
		float	gapOpenPenalty,
		float	gapExtendPenalty,
		float	minPctIdentity
	)

static

Get start position on first sequence of the Smith-Waterman alignment

Parameters

seq1	First sequence
seq2	Second sequence
matchScore	Match score
mismatchScore	Mismatch score
gapOpenPenalty	Gap open penalty
gapExtendPenalty	Gap extend penalty
minPctIdentity	Min percent identity for alignment

Returns: Start position of alignment on first sequence, or -1 if no suitable alignment exists

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static int umms.core.alignment.SmithWatermanAlignment.ungappedMatchStartOnFirstSequence	(	String	seq1,
		String	seq2,
		float	matchScore,
		float	mismatchScore,
		float	minPctIdentity
	)

static

Get start position on first sequence of an ungapped Smith-Waterman alignment First sequence must be at least as long as second sequence

Parameters

seq1	Longer sequence
seq2	Shorter sequence
matchScore	Match score
mismatchScore	Mismatch score
gapOpenPenalty	Gap open penalty
gapExtendPenalty	Gap extend penalty
minPctIdentity	Min percent identity for alignment

Returns: Start position of alignment on first sequence, or -1 if no suitable alignment exists

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Member Data Documentation

float umms.core.alignment.SmithWatermanAlignment.DEFAULT_GAP_EXTEND_PENALTY = 2

static

Default gap extend penalty for Smith Waterman

float umms.core.alignment.SmithWatermanAlignment.DEFAULT_GAP_OPEN_PENALTY = 8

static

Default gap open penalty for Smith Waterman

float umms.core.alignment.SmithWatermanAlignment.DEFAULT_MATCH_SCORE = 5

static

Default match score for Smith Waterman

float umms.core.alignment.SmithWatermanAlignment.DEFAULT_MISMATCH_SCORE = -4

static

Default mismatch score for Smith Waterman

The documentation for this class was generated from the following file:

java/umms/core/alignment/SmithWatermanAlignment.java

Public Member Functions

Static Public Member Functions

Static Public Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation