Spec SimpleScore
Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.

Extends Score
All Extended Score
Defined in <seqan/score.h>
Signature template <typename TValue> class Score<TValue, Simple>;

Template Parameters

TValue The score value to use.

Member Function Overview

Interface Function Overview

Interface Functions Inherited From Score

Interface Metafunction Overview

Interface Metafunctions Inherited From Score

Member Functions Detail

Score::Score(); Score::Score(score); Score::Score(match, mismatch, gap[, gapOpen]);

Constructor

Parameters

score Other SimpleScore object to copy from.
match Match score value, type TValue, default 0.
msmatch Mismatch score value, type TValue, default -1.
gap Gap extension value, type TValue, default -1.
gapOpen Gap open value (defaults to gap), type TValue.

Data Races

Thread safety unknown!

Interface Functions Detail

TValue scoreGap(score);

Set gap score.

Parameters

score The SimpleScore to query for its gap score.

Returns

TValue The gap score.

Data Races

Thread safety unknown!

TValue scoreGapExtend(score);

Set gap extension score.

Parameters

score The SimpleScore to query for its gap extension score.

Returns

TValue The gap extension score.

Data Races

Thread safety unknown!

TValue scoreGapOpen(score);

Set gap open score.

Parameters

score The SimpleScore to query for its gap open score.

Returns

TValue The gap open score.

Data Races

Thread safety unknown!

TValue scoreMatch(score);

Match score

Parameters

score The SimpleScore scoring scheme.

Returns

TValue The match score.

Data Races

Thread safety unknown!

TValue scoreMismatch(score);

Set mismatch score.

Parameters

score The SimpleScore to query for its mismatch score.

Returns

TValue The mismatch score.

Data Races

Thread safety unknown!

void setScoreGap(score, value);

Set gap score.

Parameters

score The SimpleScore scoring scheme to set the gap value for.
value The value to set the gap score to.

Data Races

Thread safety unknown!

void setScoreGapExtend(score, value);

Set gap extend score.

Parameters

score The SimpleScore scoring scheme to set the gap extend value for.
value The value to set the gap open score to.

Data Races

Thread safety unknown!

void setScoreGapOpen(score, value);

Set gap open score.

Parameters

score The SimpleScore scoring scheme to set the gap open value for.
value The value to set the gap open score to.

Data Races

Thread safety unknown!

void setScoreMatch(score, value);

Set match score.

Parameters

score The SimpleScore scoring scheme to set the value for.
value The value to set the match score to.

Data Races

Thread safety unknown!

void setScoreMismatch(score, value);

Set mismatch score.

Parameters

score The SimpleScore scoring scheme to set the mismatch value for.
value The value to set the mismatch score to.

Data Races

Thread safety unknown!