Biomedical Engineering Reference
In-Depth Information
command-line tool is an optional header containing column labels
followed by a series of labeled vectors (defi ned above) of the same number
of elements. The full list of supported vector and matrix operations can
be found in the User's Manual online (see section 8.8).
8.4 C++ API for developers
Users with basic C++ skills can make use of the genomic_intervals library,
particularly for window-based computations and overlaps. All
implemented classes are fully documented using Doxygen [31] (see
Figure 8.4 for a snapshot). Access to full documentation is provided
along with the source code distribution. In the following sections, we
describe the main classes that are used to represent the genomic data and
perform the various operations.
8.4.1 The GenomicInterval and GenomicRegion
classes
The GenomicInterval class implements the notion of a genomic interval, that
is an interval annotated with chromosome and strand information. The
GenomicRegion class implements the notion of a genomic region (in REG
format), that is a labeled ordered set of genomic intervals, and corresponds
to one single line in the input fi le. The genomic intervals are stored as C++
STL vectors, but there is also an option of C++ STL lists for developers. This
class has a series of constructors, which create genomic regions from an
input fi le (accessed via the FileBuffer class), or from a character array.
The methods of this class are classifi ed into four categories:
■
read & print methods: read and print genomic intervals in various formats;
■
get & set methods: retrieve and set class variables, such as label,
chromosome, etc.;
■
check & compare methods: obtain information about region properties
(sorted, compatible, etc.), and their relationship with other regions
(overlaps, order, etc.);
■
operations: execute operations between or within regions, such as
union, difference, etc.
This GenomicRegion class contains just enough information for the
minimal requirements of the REG format. Most methods described above
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