Class ProfileChar
Alphabet type for profiles over another alphabet.

Defined in <seqan/basic.h>
Signature template <typename TValue[, typename TCount[, typename TSpec]]> class ProfileChar;

Template Parameters

TValue The underlying alphabet type.
TCount The type to use for counting, default: unsigned int.
TSpec Specialization tag, default: void

Interface Function Overview

Interface Metafunction Overview

Member Variable Overview

Interface Functions Detail

bool empty(c);

Check whether there are only gaps in the representation of the ProfileChar.

Parameters

c ProfileChar to query.

Returns

bool Whether or not the ProfileChar only contains gaps.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TSize getMaxIndex(c);

Return number of dominating entry in ProfileChar.

Parameters

c ProfileChar to query for its dominating entry.

Returns

TSize index (with the ordValue) of the dominating character in c

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TCount totalCount(c);

Return sum of counts in ProfileChar.

Parameters

c ProfileChar to query.

Returns

TCount Total number of characters represented by c.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Interface Metafunctions Detail

SourceValue<T>::Type

Returns underlying value for ProfileChar.

Template Parameters

T Type to query.

Returns

Type The type of the underlying character.

Examples

typedef ProfileChar<Dna5>               TProfileChar;
typedef SourceValue<TProfileChar>::Type TType;  // Is Dna.

ValueSize<T>::VALUE;

Number of different values a value type object can have.

Template Parameters

T The type to query.

Returns

VALUE Number of different values T can have.

Member Variables Detail

VariableType ProfileChar::count[]

Array of ValueSize elements, giving counts in profile.