This thesis describes continuing development of new programming language C Plus conceived in earlier Bachelor’s Thesis oriented on enhancing C language with high level constructs with no additional cost. During development, several important languages were compared and C Plus along with its grammar were expanded, advantages of additions were discussed and compared with solutions in other languages. Described enhancements were implemented in the compiler.

Background: The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D) J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D) J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D) J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D) J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results: To help address this problem, we propose a standardized file format for representing V(D) J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D) J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions: The VDJML suite will allow users to streamline their V(D) J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https:// vdjserver. org/ vdjml/. We welcome participation from the community in developing the file format standard, as well as code contributions.

Bibliography: leaves 173-184. This thesis describes Visor++, a tool for visualising programs written in CC++, a task-parallel, object-orientated language derived from C++. Visor++ provides a framework of visualising task-parallel object-orientated programs in the absence of language support for visualisation, i.e. for programs such as CC++ which are written in languages which are not "visualisation-conscious". The development of techniques using a wide selection of language features are described and the effectiveness testified by experimentation.

[pt] Injeção de dependências, uma forma de inversão de controle, é uma forma de estruturar a configuração e composição de componentes de software que traz vários benefícios como um acoplamento reduzido entre componentes. No entanto, um framework genérico de injeção de dependências requer instrospecção em tempo de execução, o que explica por que injeção de dependências é popular em Java mas praticamente inexistente em C Mais Mais. Neste trabalho apresentamos um sistema de introspecção para C Mais Mais 11 e mostramos como ele pode ser usado para melhorar uma implementação de Service Component Architecture (SCA) para C Mais Mais. Usamos vários novas funcionalidades de C Mais Mais 11 como perfect forwarding, variadic templates e lvalue references para melhorar a usabilidade da API de reflexão e minimizar o overhead de execução. / [en] Dependency injection, a form of inversion of control, is a way of structuring the configuration and composition of software components that brings many benefits such as a loose coupling of components. However, a generic dependency injection framework requires runtime type introspection and this is why dependency injection is popular in Java and almost non-existent in C plus plus. In this work we present a introspection system for C plus plus 11 and show how to use it to improve an implementation of the Service Component Architecture (SCA) for C plus plus. It uses several features of C plus plus 11 such as perfect forwarding, variadic templates and lvalue references to improve usability and minimize overhead.