ToC
- Learning Objective
- In this tutorial you will learn how to modify the elements of a container without copying them using SeqAn modifiers. You will learn about the different specializations and how to work with them.
- Difficulty
- Basic
- Duration
- 20 min
- Prerequisites
- :ref:`tutorial-getting-started-first-steps-in-seqan`, :ref:`tutorial-datastructures-sequences`
Modifiers give a different view to other classes. They can be used to change the elements of a container without touching them. For example, someone gave you an algorithm that works on two arbitrary :dox:`String` objects, but you want to use it for the special pair of a string and its reverse (left-to-right mirror). The classical approach would be to make a copy of the one string, where all elements are mirrored from left to right and call the algorithm with both strings. With modifiers, e.g. a :dox:`ModifiedString`, you can create the reverse in \mathcal{O}(1) extra memory without copying the original string. This can be handy if the original sequence is large.
Modifiers implement a certain concept (e.g. :dox:`ContainerConcept`, :dox:`RandomAccessIteratorConcept Iterator`, ...) or class interface (:dox:`String`, ...) and thus can be used as such. The mirror modifier is already part of SeqAn and implements the class interface of :dox:`String` and can be used in every algorithm that works on strings.
The :dox:`ModifiedString ModifiedString` is a modifier that implements the :dox:`String` interface and thus can be used like a :dox:`String`. It has two template parameters. The first one specifies a sequence type (e.g. :dox:`String`, :dox:`Segment`, ...) and the second one specifies the modifiers behavior. That can be :dox:`ModReverseString` for mirroring a string left to right or :dox:`ModViewModifiedString` for applying a function to every single character (like 'C'->'G', 'A'->'T', ...).
We begin with the specialization :dox:`ModReverseString` from the example above. Now we have a given string:
.. includefrags:: demos/tutorial/modifiers/modreverse.cpp :fragment: main
and want to get the reverse.
So we need a :dox:`ModifiedString` specialized with String<char> and :dox:`ModReverseString`.
We create the modifier and link it with myString:
.. includefrags:: demos/tutorial/modifiers/modreverse.cpp :fragment: modifier
The result is:
.. includefrags:: demos/tutorial/modifiers/modreverse.cpp :fragment: output1
.. includefrags:: demos/tutorial/modifiers/modreverse.cpp.stdout :fragment: output1
To verify that we didn't copy myString, we replace an infix of the original string and see that, as a side effect, the modified string has also changed:
.. includefrags:: demos/tutorial/modifiers/modreverse.cpp :fragment: output2
.. includefrags:: demos/tutorial/modifiers/modreverse.cpp.stdout :fragment: output2
Another specialization of the :dox:`ModifiedString` is the :dox:`ModViewModifiedString` modifier.
Assume we need all characters of myString to be in upper case without copying myString.
In SeqAn you first create a functor (a STL unary function) which converts a character to its upper-case character.
.. includefrags:: demos/tutorial/modifiers/modview.cpp :fragment: functor
and then create a :dox:`ModifiedString` specialized with ModView<MyFunctor>:
.. includefrags:: demos/tutorial/modifiers/modview.cpp :fragment: mod_str
The result is:
.. includefrags:: demos/tutorial/modifiers/modview.cpp :fragment: output
.. includefrags:: demos/tutorial/modifiers/modview.cpp.stdout
The upper-case functor and some other predefined functors are part of SeqAn (in seqan/modifier/modifier_functors.h) already.
The following functors can be used as an argument of :dox:`ModViewModifiedString`:
FunctorUpcase<TValue>- Converts each character of type
TValueto its upper-case character FunctorLowcase<TValue>- Converts each character to type
TValueto its lower-case character FunctorComplement<Dna>- Converts each nucleotide to its complementary nucleotide
FunctorComplement<Dna5>- The same for the :dox:`Dna5` alphabet
FunctorConvert<TInValue,TOutValue>- Converts the type of each character from
TInValuetoTOutValue
So instead of defining your own functor we could have used a predefined one:
.. includefrags:: demos/tutorial/modifiers/modview.cpp :fragment: predefined
- Type
- Review
- Objective
In this assignment you will create a modifier using your own functor. Assume you have given two Dna sequences as strings as given in the code example below. Let's assume you know that in one of your Dna sequences a few 'C' nucleotides are converted into 'T' nucleotides, but you still want to compare the sequence. Extend the code example as follows:
- Write a functor which converts all 'C' nucleotides to 'T' nucleotides.
- Define a :dox:`ModifiedString` with the specialization :dox:`ModViewModifiedString` using this functor.
- Now you can modify both sequences to compare them, treating all 'Cs' as 'Ts'. Print the results.
.. includefrags:: demos/tutorial/modifiers/assignment1.cpp
- Solution
.. includefrags:: demos/tutorial/modifiers/assignment1_solution.cpp
.. includefrags:: demos/tutorial/modifiers/assignment1_solution.cpp.stdout
For some commonly used modifiers you can use the following shortcuts:
| Shortcut | Substitution |
|---|---|
ModComplementDna |
ModView<FunctorComplement<Dna> > |
ModComplementDna5 |
ModView<FunctorComplement<Dna5> > |
DnaStringComplement |
ModifiedString<DnaString, ModComplementDna> |
Dna5StringComplement |
ModifiedString<Dna5String, ModComplementDna5> |
DnaStringReverse |
ModifiedString<DnaString, ModReverse> |
Dna5StringReverse |
ModifiedString<Dna5String, ModReverse> |
DnaStringReverseComplement |
ModifiedString<ModifiedString<DnaString, ModComplementDna>, ModReverse> |
Dna5StringReverseComplement |
ModifiedString<ModifiedString<Dna5String, ModComplementDna5>, ModReverse> |
We have seen how a :dox:`ModifiedString` can be used to modify strings without touching or copying original data. The same can be done with iterators. The :dox:`ModifiedIterator` implements the :dox:`RandomAccessIteratorConcept Iterator` concept and thus can be used in every algorithm or data structure that expects an iterator. In fact, we have already used the :dox:`ModifiedIterator` unknowingly in the examples above, as in our cases the :dox:`ModifiedString` returns a corresponding :dox:`ModifiedIterator` via the :dox:`ContainerConcept#Iterator` meta-function. The main work is done in the :dox:`ModifiedIterator`, whereas the :dox:`ModifiedString` only overloads the :dox:`ContainerConcept#begin` and :dox:`ContainerConcept#end`. Normally, you are going to use the :dox:`ModifiedString` and maybe the result of its :dox:`ContainerConcept#Iterator` meta-function instead of a :dox:`ModifiedIterator` directly.
As modifiers implement a certain concept and depend on classes of this concept, two modifiers can be chained to create a new modifier. We have seen how the :dox:`ModifiedString` specialized with :dox:`ModReverseString` and :dox:`ModViewModifiedString` can be used. Now we want to combine them to create a modifier for the reverse complement of a :dox:`DnaString` We begin with the original string:
.. includefrags:: demos/tutorial/modifiers/nested.cpp :fragment: string
Then we define the modifier that complements a :dox:`DnaString`:
.. includefrags:: demos/tutorial/modifiers/nested.cpp :fragment: complement
This modifier now should be reversed from left to right:
.. includefrags:: demos/tutorial/modifiers/nested.cpp :fragment: reverse
The original string can be given to the constructor.
.. includefrags:: demos/tutorial/modifiers/nested.cpp :fragment: constructor
The result is:
.. includefrags:: demos/tutorial/modifiers/nested.cpp :fragment: output
.. includefrags:: demos/tutorial/modifiers/nested.cpp.stdout
:fragment: output
Using a predefined shortcut, the whole example could be reduced to:
.. includefrags:: demos/tutorial/modifiers/nested.cpp :fragment: alternative