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
tutorial-getting-started-first-steps-in-seqan
,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 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 ModifiedString
, you can create the reverse in 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. ContainerConcept
, RandomAccessIteratorConcept Iterator
, ...) or class interface (String
, ...) and thus can be used as such. The mirror modifier is already part of SeqAn and implements the class interface of String
and can be used in every algorithm that works on strings.
The ModifiedString ModifiedString
is a modifier that implements the String
interface and thus can be used like a String
. It has two template parameters. The first one specifies a sequence type (e.g. String
, Segment
, ...) and the second one specifies the modifiers behavior. That can be ModReverseString
for mirroring a string left to right or ModViewModifiedString
for applying a function to every single character (like 'C'->'G', 'A'->'T', ...).
We begin with the specialization ModReverseString
from the example above. Now we have a given string:
demos/tutorial/modifiers/modreverse.cpp
and want to get the reverse. So we need a ModifiedString
specialized with String<char>
and ModReverseString
. We create the modifier and link it with myString
:
demos/tutorial/modifiers/modreverse.cpp
The result is:
demos/tutorial/modifiers/modreverse.cpp
demos/tutorial/modifiers/modreverse.cpp.stdout
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:
demos/tutorial/modifiers/modreverse.cpp
demos/tutorial/modifiers/modreverse.cpp.stdout
Another specialization of the ModifiedString
is the 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.
demos/tutorial/modifiers/modview.cpp
and then create a ModifiedString
specialized with ModView<MyFunctor>
:
demos/tutorial/modifiers/modview.cpp
The result is:
demos/tutorial/modifiers/modview.cpp
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 ModViewModifiedString
:
FunctorUpcase<TValue>
Converts each character of type
TValue
to its upper-case characterFunctorLowcase<TValue>
Converts each character to type
TValue
to its lower-case characterFunctorComplement<Dna>
Converts each nucleotide to its complementary nucleotide
FunctorComplement<Dna5>
The same for the
Dna5
alphabetFunctorConvert<TInValue,TOutValue>
Converts the type of each character from
TInValue
toTOutValue
So instead of defining your own functor we could have used a predefined one:
demos/tutorial/modifiers/modview.cpp
- 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
ModifiedString
with the specializationModViewModifiedString
using this functor. - Now you can modify both sequences to compare them, treating all 'Cs' as 'Ts'. Print the results.
demos/tutorial/modifiers/assignment1.cpp
- Solution
demos/tutorial/modifiers/assignment1_solution.cpp
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 ModifiedString
can be used to modify strings without touching or copying original data. The same can be done with iterators. The ModifiedIterator
implements the 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 ModifiedIterator
unknowingly in the examples above, as in our cases the ModifiedString
returns a corresponding ModifiedIterator
via the ContainerConcept#Iterator
meta-function. The main work is done in the ModifiedIterator
, whereas the ModifiedString
only overloads the ContainerConcept#begin
and ContainerConcept#end
. Normally, you are going to use the ModifiedString
and maybe the result of its ContainerConcept#Iterator
meta-function instead of a 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 ModifiedString
specialized with ModReverseString
and ModViewModifiedString
can be used. Now we want to combine them to create a modifier for the reverse complement of a DnaString
We begin with the original string:
demos/tutorial/modifiers/nested.cpp
Then we define the modifier that complements a DnaString
:
demos/tutorial/modifiers/nested.cpp
This modifier now should be reversed from left to right:
demos/tutorial/modifiers/nested.cpp
The original string can be given to the constructor.
demos/tutorial/modifiers/nested.cpp
The result is:
demos/tutorial/modifiers/nested.cpp
demos/tutorial/modifiers/nested.cpp.stdout
Using a predefined shortcut, the whole example could be reduced to:
demos/tutorial/modifiers/nested.cpp