The Code Mini-Map Visualisation - Encoding Conceptual Structures Within Source Code

Modern source code editors typically include a code mini-map visualisation, which provides programmers with an overview of the currently open source code document. This paper proposes to add a layering mechanism to the code mini-map visualisation in order to provide programmers with visual answers to questions related to conceptual structures that are not manifested directly in the code

The Code Mini-Map Visualisation: Encoding Conceptual Structures Within Source Code

Modern source code editors typically include a code mini-map visualisation, which provides programmers with an overview of the currently open source code document. This paper proposes to add a layering mechanism to the code mini- map visualisation in order to provide programmers with visual answers to questions related to conceptual structures that are not manifested directly in the code. Details regarding the design and implementation of this scope information layer, which displays additional encodings that correspond to the scope chain and information related to the scope chain within a source code document, is presented. The scope information layer can be used by programmers to answer questions such as: to which scope does a specific variable belong, and in which scope is the cursor of the source code editor currently located in. Additionally, this paper presents a study that evaluates the effectiveness of adding the scope information layer to a code mini-map visualisation in order to help programmers understand scope relationships within source code. The results of the study show that the incorporating additional layers of information onto the code mini-map visualisation can have a positive effect on code understanding

Scoped: Evaluating A Composite Visualisation Of The Scope Chain Hierarchy Within Source Code

This paper presents two studies that evaluate the effectiveness of a software visualisation tool which uses a com- posite visualisation to encode the scope chain and information related to the scope chain within source code. The first study evaluates the effectiveness of adding the composite visualisation to a source code editor to help programmers understand scope relationships within source code. The second study evaluates the effectiveness of each individual component within the composite visualisation. The composite visualisation is composed of a packed circle tree diagram (overview component) and a list view (detail view component). The packed circle tree functions as an abstract mini-map to provide viewers with a high-level overview of the scope chain hierarchy within a source code document. The list view provides additional information about identifiers (variables, functions, and parameters) that are accessible from the scope within which the cursor is located, in the source code document. Both studies utilise a between-subject design, in which groups of participants were presented with source code fragments and asked to answer a series of code understanding questions. The results of the studies indicate that adding a composite visualisation to a source code editor can have a positive effect on code understanding, especially when the textual representation of the code no longer corresponds to the actual behaviour of the code (as is the case, for example, in languages such as JavaScript that implement variable hoisting)

On Using Tree Visualisation Techniques to Support Source Code Comprehension

This paper presents a design study that investigates the use of compact tree visualisations to provide software de-velopers with an overview of the static structure of a sourcecode document within a code editor in order to facilitate source code understanding and navigation. A prototype is presented which utilises an icicle tree visualisation to encode the control structure hierarchy of a source code document, as well as a circular treemap visualisation to encode the scope hierarchy of a source code document. An overview of the prototype and its functionality is given as well as a detailed discussion on the design rationale behind the tool. Possible applications and future work plans are also discussed

Using Icicle Trees to Encode the Hierarchical Structure of Source Code

This paper presents a study which evaluates the use of a tree visualisation (icicle tree) to encode the hierarchical structure of source code. The tree visualisation was combined with a source code editor in order to function as a compact overview to facilitate the process of comprehending the global structure of a source code document. Results from our study show that pro- viding an overview visualisation led to an increase in accuracy and a decrease in completion time when participants performed counting tasks. However, in locating tasks, the presence of the visualisation led to a decrease in participants’ performance

The Code-Map Metaphor - A Review Of Its Use Within Software Visualisations

Software developers can use software visualisations employing the code-map metaphor to discover and correlate facts spread over a large code base. This work presents an extensive review of the use of the code-map metaphor for software visualisation. The review analyses a set of 29 publications, which together describe 21 software development tools that use visualisations employing the code-map metaphor. The review follows a task oriented framework to guide the analysis of the literature in terms of the task, audience, target, medium, representation, and evidence dimensions based on the code-map metaphor. Although the literature indicates that software visualisations based on the code-map metaphor are perceived by the research community to be helpful across all aspects of the software develop process, the main finding of our review is that there is a lack of quantitative evidence to support this perception. Thus, the effectiveness of visualisations incorporating the code-map metaphor is still unclear. The majority of the software visualisations analysed in this study, however , do provide qualitative observations regarding their usage in various scenarios. These are summarised and presented in this review as we believe the observations can be used as motivation for future empirical evaluations

Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA

While a number of aminoacyl tRNA synthetase (aaRS):tRNA pairs have been engineered to alter or expand the genetic code, only the Methanococcus jannaschii tyrosyl tRNA synthetase and tRNA have been used extensively in bacteria, limiting the types and numbers of unnatural amino acids that can be utilized at any one time to expand the genetic code. In order to expand the number and type of aaRS/tRNA pairs available for engineering bacterial genetic codes, we have developed an orthogonal tryptophanyl tRNA synthetase and tRNA pair, derived from Saccharomyces cerevisiae. In the process of developing an amber suppressor tRNA, we discovered that the Escherichia coli lysyl tRNA synthetase was responsible for misacylating the initial amber suppressor version of the yeast tryptophanyl tRNA. It was discovered that modification of the G:C content of the anticodon stem and therefore reducing the structural flexibility of this stem eliminated misacylation by the E. coli lysyl tRNA synthetase, and led to the development of a functional, orthogonal suppressor pair that should prove useful for the incorporation of bulky, unnatural amino acids into the genetic code. Our results provide insight into the role of tRNA flexibility in molecular recognition and the engineering and evolution of tRNA specificity

Amplitude analysis and branching fraction measurement of B + → D ∗ − D s + π + decays

The decays of the B+ meson to the final state D∗−Ds+π+ are studied in proton-proton collision data collected with the LHCb detector at centre-of-mass energies of 7, 8, and 13 TeV, corresponding to a total integrated luminosity of 9 fb−1. The ratio of branching fractions of the B+→D∗−Ds+π+ and B0→D∗−Ds+ decays is measured to be 0.173 ± 0.006 ± 0.010, where the first uncertainty is statistical and the second is systematic. Using partially reconstructed Ds∗+→Ds+γ and Ds+π0 decays, the ratio of branching fractions between the B+→D∗−Ds∗+π+ and B+→D∗−Ds+π+ decays is determined as 1.31 ± 0.07 ± 0.14. An amplitude analysis of the B+→D∗−Ds+π+ decay is performed for the first time, revealing dominant contributions from known excited charm resonances decaying to the D*−π+ final state. No significant evidence of exotic contributions in the Ds+π+ or D∗−Ds+ channels is found. The fit fraction of the scalar state Tcs¯0∗2900++ observed in the B+→D−Ds+π+ decay is determined to be less than 2.3% at a 90% confidence level

Comprehensive analysis of local and nonlocal amplitudes in the B 0 → K *0 μ + μ − decay

A comprehensive study of the local and nonlocal amplitudes contributing to the decay B0 → K*0(→ K+π−)μ+μ− is performed by analysing the phase-space distribution of the decay products. The analysis is based on pp collision data corresponding to an integrated luminosity of 8.4 fb−1 collected by the LHCb experiment. This measurement employs for the first time a model of both one-particle and two-particle nonlocal amplitudes, and utilises the complete dimuon mass spectrum without any veto regions around the narrow charmonium resonances. In this way it is possible to explicitly isolate the local and nonlocal contributions and capture the interference between them. The results show that interference with nonlocal contributions, although larger than predicted, only has a minor impact on the Wilson Coefficients determined from the fit to the data. For the local contributions, the Wilson Coefficient C9, responsible for vector dimuon currents, exhibits a 2.1σ deviation from the Standard Model expectation. The Wilson Coefficients C10, C9′ and C10′ are all in better agreement than C9 with the Standard Model and the global significance is at the level of 1.5σ. The model used also accounts for nonlocal contributions from B0→ K*0[τ+τ−→ μ+μ−] rescattering, resulting in the first direct measurement of the bsττ vector effective-coupling C9τ

Observation of muonic Dalitz decays of chib mesons and precise spectroscopy of hidden-beauty states

The decays of the χb1(1P), χb2(1P), χb1(2P) and χb2(2P) mesons into the Υ(1S)μ+μ− final state are observed with a high significance using proton-proton collision data collected with the LHCb detector and corresponding to an integrated luminosity of 9 fb−1. The newly observed decays together with the Υ(2S) → Υ(1S)π+π− and Υ(3S) → Υ(2S)π+π− decay modes are used for precision measurements of the mass and mass splittings for the hidden-beauty states