Spec ModCyclicShape ModifiedIterator
Iterates over a string leaving out don't-care-positions defined in CyclicShape.

Extends ModifiedIterator
All Extended ModifiedIterator
All Impl'd BidirectionalIteratorConcept, CopyConstructibleConcept, DefaultConstructibleConcept, EqualityComparableConcept, ForwardIteratorConcept, InputIteratorConcept, IteratorAssociatedTypesConcept, LessThanComparableConcept, RandomAccessIteratorConcept
Defined in <seqan/modifier.h>
Signature template <typename THost, typename TSpec> class ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > >;

Template Parameters

THost The host iterator.
TSpec The specialization of CyclicShape.
TCargo Cargo type of ModCyclicShape
TSize Size type of ModCyclicShape

Member Function Overview

Member Functions Inherited From EqualityComparableConcept

Member Functions Inherited From LessThanComparableConcept

Member Functions Inherited From RandomAccessIteratorConcept

Interface Function Overview

Interface Functions Inherited From BidirectionalIteratorConcept

Interface Functions Inherited From InputIteratorConcept

Interface Functions Inherited From IteratorAssociatedTypesConcept

Interface Functions Inherited From RandomAccessIteratorConcept

Interface Metafunction Overview

Interface Metafunctions Inherited From IteratorAssociatedTypesConcept

Interface Metafunctions Inherited From RandomAccessIteratorConcept

Member Variable Overview

Detailed Description


ModCyclicShape Modifier should only be used to view/read a sequence, never to change the underlying sequence. Some operations will work, e.g. you can use the operator*() of the ModifiedIterator to change a character, but other operations like replace or append are unsafe or even conceptionally wrong.

Using ModCyclicShape you can mask characters at certain positions of a text. A CylcicShape defines these positions (so called don't-care-positions) and the CyclicShape is repeated till the end of the string. The iterator behaves as if the don't-care-positions had been deleted without actually copying the string.

    typedef ModifiedString<CharString, ModCyclicShape<TShape> > TModString;
    typedef Iterator<TModString>::Type TModIter;
    TModIter it = begin(modStr);
    TModIter itBeg = it;
    TModIter itEnd = end(modStr);

    // output iter position and host iter position
    for(; it != itEnd; ++it)
        std::cout << (it - itBeg) << "/" << (host(it) - begin(str)) << ", ";

    //  0/2, 1/3, 2/4, 3/7, 4/9, 5/13, 6/14, 7/15, 8/18, 9/20, 10/24, 11/25, 12/26,

See Also

Member Functions Detail

ModifiedIterator::ModifiedIterator(); ModifiedIterator::ModifiedIterator(host); ModifiedIterator::ModifiedIterator(otherModIter);

The constructor.


host Host iterator to set.
otherModIter ModifiedIterator which may differ in its host type. Copy construction.

The safe way to create this ModifiedIterator is to use the begin and end functions of the ModifiedString or to copy construct. When directly initialized with a host iterator, the CyclicShape is not yet taken into account and you have to set it up yourself, for example a CyclicShape starting with a 01... will have skip the first position. So you would have to reset the host iterator using ++host(myCyclicShape). Use cargo() to assign a shape to the iterator.

Interface Metafunctions Detail

Cargo<ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > >::Type;

Cargo of ModCyclicShape ModCyclicShape Modified Iterator and ModCyclicShape Modified String.

Template Parameters

THost Host iterator of ModifiedIterator.
TSpec Specialization of CyclicShape.


Cargo type of ModCyclicShape Modified Iterator is the CyclicShape itself.

Member Variables Detail

TCargo ModCyclicShapeModifiedIterator::_cargo

Copy of a Cargo object, which is a CyclicShape.

The Cargo is a CyclicShape. This can be very heavy in case of GenericCyclicShape, so prefer the lightweight FixedCyclicShape.

TSize ModCyclicShapeModifiedIterator::_idx

Internal position inside diffs of the CylicShape.