Structured Review of Code Clone Literature

This report presents the results of a structured review of code clone literature. The aim of the review is to assemble a conceptual model of clone-related concepts which helps us to reason about clones. This conceptual model unifies clone concepts from a wide range of literature, so that findings about clones can be compared with each other

Clone Detection and Elimination for Haskell

Duplicated code is a well known problem in software maintenance and refactoring. Code clones tend to increase program size and several studies have shown that duplicated code makes maintenance and code understanding more complex and time consuming. This paper presents a new technique for the detection and removal of duplicated Haskell code. The system is implemented within the refactoring framework of the Haskell Refactorer (HaRe), and uses an Abstract Syntax Tree (AST) based approach. Detection of duplicate code is automatic, while elimination is semi-automatic, with the user managing the clone removal. After presenting the system, an example is given to show how it works in practice

Stack Overflow: A Code Laundering Platform?

Developers use Question and Answer (Q&A) websites to exchange knowledge and expertise. Stack Overflow is a popular Q&A website where developers discuss coding problems and share code examples. Although all Stack Overflow posts are free to access, code examples on Stack Overflow are governed by the Creative Commons Attribute-ShareAlike 3.0 Unported license that developers should obey when reusing code from Stack Overflow or posting code to Stack Overflow. In this paper, we conduct a case study with 399 Android apps, to investigate whether developers respect license terms when reusing code from Stack Overflow posts (and the other way around). We found 232 code snippets in 62 Android apps from our dataset that were potentially reused from Stack Overflow, and 1,226 Stack Overflow posts containing code examples that are clones of code released in 68 Android apps, suggesting that developers may have copied the code of these apps to answer Stack Overflow questions. We investigated the licenses of these pieces of code and observed 1,279 cases of potential license violations (related to code posting to Stack overflow or code reuse from Stack overflow). This paper aims to raise the awareness of the software engineering community about potential unethical code reuse activities taking place on Q&A websites like Stack Overflow.Comment: In proceedings of the 24th IEEE International Conference on Software Analysis, Evolution, and Reengineering (SANER

Mycobiome of the Bat White Nose Syndrome (WNS) Affected Caves and Mines reveals High Diversity of Fungi and Local Adaptation by the Fungal Pathogen Pseudogymnoascus (Geomyces) destructans

The investigations of the bat White Nose Syndrome (WNS) have yet to provide answers as to how the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) first appeared in the Northeast and how a single clone has spread rapidly in the US and Canada. We aimed to catalogue Pd and all other fungi (mycobiome) by the culture-dependent (CD) and culture-independent (CI) methods in four Mines and two Caves from the epicenter of WNS zoonotic. Six hundred sixty-five fungal isolates were obtained by CD method including the live recovery of Pd. Seven hundred three nucleotide sequences that met the definition of operational taxonomic units (OTUs) were recovered by CI methods. Most OTUs belonged to unidentified clones deposited in the databases as environmental nucleic acid sequences (ENAS). The core mycobiome of WNS affected sites comprised of 46 species of fungi from 31 genera recovered in culture, and 17 fungal genera and 31 ENAS identified from clone libraries. Fungi such as Arthroderma spp., Geomyces spp., Kernia spp., Mortierella spp., Penicillium spp., and Verticillium spp. were predominant in culture while Ganoderma spp., Geomyces spp., Mortierella spp., Penicillium spp. and Trichosporon spp. were abundant is clone libraries. Alpha diversity analyses from CI data revealed that fungal community structure was highly diverse. However, the true species diversity remains undetermined due to under sampling. The frequent recovery of Pd indicated that the pathogen has adapted to WNS-afflicted habitats. Further, this study supports the hypothesis that Pd is an introduced species. These findings underscore the need for integrated WNS control measures that target both bats and the fungal pathogen.Comment: 59 pages, 7figure

A new reference genome assembly for the microcrustacean Daphnia pulex

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with similar to 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome

Visualization and analysis of software clones

Code clones are identical or similar fragments of code in a software system. Simple copy-paste programming practices of developers, reusing existing code fragments instead of implementing from the scratch, limitations of both programming languages and developers are the primary reasons behind code cloning. Despite the maintenance implications of clones, it is not possible to conclude that cloning is harmful because there are also benefits in using them (e.g. faster and independent development). As a result, researchers at least agree that clones need to be analyzed before aggressively refactoring them. Although a large number of state-of-the-art clone detectors are available today, handling raw clone data is challenging due to the textual nature and large volume. To address this issue, we propose a framework for large-scale clone analysis and develop a maintenance support environment based on the framework called VisCad. To manage the large volume of clone data, VisCad employs the Visual Information Seeking Mantra: overview first, zoom and filter, then provide details-on-demand. With VisCad users can analyze and identify distinctive code clones through a set of visualization techniques, metrics covering different clone relations and data filtering operations. The loosely coupled architecture of VisCad allows users to work with any clone detection tool that reports source-coordinates of the found clones. This yields the opportunity to work with the clone detectors of choice, which is important because each clone detector has its own strengths and weaknesses. In addition, we extend the support for clone evolution analysis, which is important to understand the cause and effect of changes at the clone level during the evolution of a software system. Such information can be used to make software maintenance decisions like when to refactor clones. We propose and implement a set of visualizations that can allow users to analyze the evolution of clones from a coarse grain to a fine grain level. Finally, we use VisCad to extract both spatial and temporal clone data to predict changes to clones in a future release/revision of the software, which can be used to rank clone classes as another means of handling a large volume of clone data. We believe that VisCad makes clone comprehension easier and it can be used as a test-bed to further explore code cloning, necessary in building a successful clone management system