An Integrated Data Analysis Suite and Programming ... - TOBIAS-lib

3.2. A MODULAR SIGNAL-SLOT PROCESSING FRAMEWORK 67
further denes a method dump, which causes all data provided by the incorporated Reader to be
passed to the data signal before triggering the flush signal to nalize processing (line 13).
For cases where application to entire data sets is not the intended use, modules must provide
a means of suspending the ow of processing. Classes implementing the Reader concept may for
example oer congurable standard ltering facilities comprising of multiple cascaded processing
modules. However, while the Reader concept implies that each data set element is retrievable
individually, Pipe elements may produce an arbitrary amount of output in response to input
data processing, which would render such modules unsuitable for this type of reuse. We therefore
introduce the additional module connections freeze and thaw serving to suspend and resume
processing pipeline data ow, respectively (gure 3.2). These connections run anti-parallel to
the data and flush signals. As signal invocation corresponds to a series of nested function
calls transmitted along the connected modules, source and pipe templates are able to directly
detect suspend and resume requests sent by downstream elements. A provided class template
extractor utilizes the implemented suspend facilities to act as a bridge between the Sink and
Reader concepts. Thus, extractor objects may be inserted at the end of a line of processing
modules to retrieve generated output data individually. A complementary template feed provides
bridging between the Writer and Source concepts.
3.2.3 Module Implementation
Encapsulation of subproblems as modules implementing both the Writer and Reader concepts
comes with the disadvantage that all data generated in response to a single invocation of one of
the Writer methods must be kept in an internal buer for subsequent retrieval via the Reader
interface. However, in the context of a processing pipeline each element of output data can in
principle directly be transmitted to downstream modules for further processing, often avoiding
the need to implement internal buering. Direct propagation can be achieved by direct implementation
of the Pipe concept, thus exposing direct access to the module's data and ush
signals. Implementation logic of unbuered, interruptible processing is however more complex
than the buered equivalent. We therefore provide a base class template pipe_facade enforcing
a restricted programming model to support correct implementation of such modules.
The facade template requires distribution of processing implementation across four function
calls prepare, append, next and flush. A function emit is further made accessible to subclasses
to propagate generated output. The template enforces a single-emit rule by which invocation
of the emit base class function is permissible exactly once during each call to either of the four
implementation functions. The purpose of each of the four functions is illustrated by example
(listing 3.3).
Raw sequencing read input data will typically be ordered by an identier specic to the
respective insert, whereas order of the individual reads retrieved from the insert is arbitrary.
For some purposes further ordering of sequencing reads of the same insert by their paired-end
sequencing index may however be convenient. Implementation of an appropriate reordering
module demonstrates the purpose of each of the four facade functions.
The reordering module collects all reads belonging to the same insert in an internal buer,
and subsequently orders them by value of their paired-end index. The prepare method serves as
an initial notication about next element that will be passed to the object's append method. In
the case of the example module, identiers are compared to determine whether further reads are
available for the insert currently being processed. If the next read does not belong to the current
insert, reordering of the reads by paired-end index is triggered. Reads are then transmitted for
downstream processing by invocation of emit on the rst of the collected reads. In concert with