Les environnements virtuels permettent de représenter des personnes par des humains virtuels ou avatars. Le sentiment de présence virtuelle entre utilisateurs est renforcé lorsque l’avatar ressemble à la personne qu’il représente. L’avatar est alors classiquement un clone de l’utilisateur qui reproduit son apparence et sa voix. Toutefois, la possibilité de cloner l’expressivité des gestes d’une personne a reçu peu d’attention jusqu’ici. Expressivité gestuelle combine le style et l’humeur d’une personne. Des paramètres décrivant l’expressivité ont été proposés dans des travaux antérieurs pour animer les agents conversationnels. Dans ce travail, nous nous intéressons à l’expressivité des mouvements du poignet. Tout d’abord, nous proposons des algorithmes pour estimer trois paramètres d’expressivité à partir des trajectoires dans l’espace du poignet : la répétition, l’étendue spatiale et l’étendue temporelle. Puis, nous avons mené une étude perceptive sur la pertinence de l’expressivité des gestes pour reconnaître des personnes. Nous avons animé un agent virtuel en utilisant l’expressivité estimée de personnes réelles, et évalué si des utilisateurs peuvent reconnaître ces personnes à partir des animations. Nous avons constaté que des gestes répétitifs dans l’animation constituent une caractéristique discriminante pour reconnaître les personnes, tandis que l’absence de répétition est associée à des personnes qui répètent des gestes ou non. Plus important, nous avons trouvé que 75% ou plus des utilisateurs peuvent reconnaître une personne (parmi deux proposée) à partir d’animations virtuelles qui ne diffèrent que par leurs étendues spatiales et temporelles. L’expressivité gestuelle apparaît donc comme un nouvel indice pertinent pour le clonage d’une personne / Virtual environments allow human beings to be represented by virtual humans or avatars. Users can share a sense of virtual presence is the avatar looks like the real human it represents. This classically involves turning the avatar into a clone with the real human’s appearance and voice. However, the possibility of cloning the gesture expressivity of a real person has received little attention so far. Gesture expressivity combines the style and mood of a person. Expressivity parameters have been defined in earlier works for animating embodied conversational agents.In this work, we focus on expressivity in wrist motion. First, we propose algorithms to estimate three expressivity parameters from captured wrist 3D trajectories: repetition, spatial extent and temporal extent. Then, we conducted perceptual study through a user survey the relevance of expressivity for recognizing individual human. We have animated a virtual agent using the expressivity estimated from individual humans, and users have been asked whether they can recognize the individual human behind each animation. We found that, in case gestures are repeated in the animation, this is perceived by users as a discriminative feature to recognize humans, while the absence of repetition would be matched with any human, regardless whether they repeat gesture or not. More importantly, we found that 75 % or more of users could recognize the real human (out of two proposed) from an animated virtual avatar based only on the spatial and temporal extents. Consequently, gesture expressivity is a relevant clue for cloning. It can be used as another element in the development of a virtual clone that represents a person

La problématique de cette thèse repose sur la caractérisation de la qualité des abricots et leur aptitude à la transformation industrielle. Trois axes principaux ont guidé cette étude. Le premier consistait au départ à une caractérisation morphométrique globale des pieds clones des abricots marocains transplantés vers une station expérimentale de l’INRA Marrakech puis suivie par l’analyse de la diversité génétique. 92 accessions, issus de différentes régions géographiques, ont été génotypés en utilisant 21 marqueurs microsatellites. En effet, la collection analysée a été caractérisée par un polymorphisme élevé et une diversité génétique réduite. Au total, 120 allèles ont été identifiés avec une moyenne de 5,71 allèles par locus.Toutes les preuves statistiques (analyse hiérarchique, ACP et analyse de structure) montrent que la structure génétique de l’abricot marocain peut être subdivisée en deux populations :une majeure population constituée de la plupart des accessions de groupes génétiques(population authentique liée notamment à la variété Delpatriarca) et une seconde population moins diversifiée et liée à toutes les variétés de références, y compris la variété Canino. La variabilité observée entre les 92 génotypes pourrait être un atout pour améliorer la culture de l’abricot et permettre un développement durable dans l’espace et dans le temps du fruit par la sélection de nouveaux génotypes d’abricots. Finalement, la variabilité génétique observée a été utilisée dans le choix et la sélection de nouveaux clones d’abricots pour une analyse phénotypique. Le deuxième axe s’est intéressé à l’étude des marqueurs biochimiques qui permettent de comprendre et d’évaluer la qualité des abricots sélectionnés, à savoir : le changement des acides organiques et des sucres solubles en relation avec la qualité sensorielle, le développement des pigments et le changement de la couleur, l’’évolution des composés phénoliques en relation avec l’activité antioxydante et la perte de la texture en relation avec la biochimie de la paroi cellulaire. En effet, de bonnes propriétés physicochimiques et biochimiques ont été rapportées pour les dix clones choisis (Valeurs maximales rapportées pour certains composés bioactifs : Vitamine C = 0,15 g/kg ; β-carotène= 149,251 μg/kg ; provitamine A = 0,028 mg/kg), ainsi que des caractères qualitatifs associés à la saison de maturation et au génotype, cela représente certainement une source génétique précieuse pour prolonger la saison des abricots et alimenter les étalages et l’industrie.Le troisième axe était sur l’implication de la texture du fruit dans la transformation industrielle de l’abricot. Nous avons analysé l’aptitude variétale des abricots à la transformation industrielle, par l’analyse de leurs propriétés texturales, avant et après la transformation. Et pour mieux comprendre la variabilité de la texture de l'abricot, nous avons étudié l'impact du traitement thermique en fonction du stade de récolte des fruits sur une large gamme de cultivars français. Au final, cinq variétés d’abricots ont été choisies les plus appropriés pour le processus industriel. / The problematic of this thesis is based on the characterization of the quality of apricotsand their aptitude for industrial processing. Three main axes guided this study. The first oneconsisted initially of a global morphometric characterization of Moroccan apricot clonesmaintened in experimental station of INRA of Marrakech and followed by the analysis ofgenetic diversity. 92 accessions, from different geographical regions, were genotyped using21 microsatellite markers. Indeed, the analyzed collection was characterized by a highpolymorphism and a reduced genetic diversity. A total of 120 alleles were identified with anaverage of 5.71 alleles per locus. All the statistical evidence (hierarchical analysis, PCA andstructural analysis) show that the genetic structure of Moroccan apricot can be subdivided intotwo populations : a major population made up of most accessions of genetic groups (authenticpopulation linked in particular to the Delpatriarca variety) and a second less diversifiedpopulation related to all reference varieties, including the Canino variety. The observedvariability between the 92 genotypes could be an asset to improve the apricot cultivation andto allow a sustainable development in the space and the time of the fruit by the selection ofnew genotypes of apricots. Finally, the observed genetic variability was used in the selectionof new apricot clones for phenotypic analysis. The second axis focused on the study ofbiochemical markers that allow to understand and evaluate the quality of selected apricots,namely : the change of organic acids and soluble sugars in relation to the sensory quality, thedevelopment of pigments and color change, the evolution of phenolic compounds in relationto antioxidant activity and loss of texture according to the cell wall biochemistry. Indeed,good physicochemical and biochemical properties have been reported for the ten chosenclones (Maximum values reported for some bioactif compounds : Vitamin C = 0.15 g / kg, β-carotene = 149.251 μg / kg, provitamin A = 0.028 mg / kg), as well as the qualitative traitsassociated with the maturation season and the genotype, is certainly a valuable genetic sourceto extend the apricot season and to supply stalls and industry. The third axis was on theimplication of the texture of the fruit in the industrial processing of apricot. We analyzed thevarietal ability of apricots for industrial processing by analyzing their textural propertiesbefore and after processing. And to better understand the variability of apricot texture, westudied the impact of heat treatment depending on the stage of fruit harvesting on a widerange of French cultivars. In the end, five apricots varieties were chosen as the mostappropriate for the industrial process.

Copying a code fragment and reusing it by pasting with or without minor modifications is a common practice in software development for improved productivity. As a result, software systems often have similar segments of code, called software clones or code clones. Due to many reasons, unintentional clones may also appear in the source code without awareness of the developer. Studies report that significant fractions (5% to 50%) of the code in typical software systems are cloned. Although code cloning may increase initial productivity, it may cause fault propagation, inflate the code base and increase maintenance overhead. Thus, it is believed that code clones should be identified and carefully managed. This Ph.D. thesis contributes in clone management with techniques realized into tools and large-scale in-depth analyses of clones to inform clone management in devising effective techniques and strategies. To support proactive clone management, we have developed a clone detector as a plug-in to the Eclipse IDE. For clone detection, we used a hybrid approach that combines the strength of both parser-based and text-based techniques. To capture clones that are similar but not exact duplicates, we adopted a novel approach that applies a suffix-tree-based k-difference hybrid algorithm, borrowed from the area of computational biology. Instead of targeting all clones from the entire code base, our tool aids clone-aware development by allowing focused search for clones of any code fragment of the developer's interest. A good understanding on the code cloning phenomenon is a prerequisite to devise efficient clone management strategies. The second phase of the thesis includes large-scale empirical studies on the characteristics (e.g., proportion, types of similarity, change patterns) of code clones in evolving software systems. Applying statistical techniques, we also made fairly accurate forecast on the proportion of code clones in the future versions of software projects. The outcome of these studies expose useful insights into the characteristics of evolving clones and their management implications. Upon identification of the code clones, their management often necessitates careful refactoring, which is dealt with at the third phase of the thesis. Given a large number of clones, it is difficult to optimally decide what to refactor and what not, especially when there are dependencies among clones and the objective remains the minimization of refactoring efforts and risks while maximizing benefits. In this regard, we developed a novel clone refactoring scheduler that applies a constraint programming approach. We also introduced a novel effort model for the estimation of efforts needed to refactor clones in source code. We evaluated our clone detector, scheduler and effort model through comparative empirical studies and user studies. Finally, based on our experience and in-depth analysis of the present state of the art, we expose avenues for further research and development towards a versatile clone management system that we envision.

No Brasil e em diversos países têm sido verificados significativos avanços na silvicultura clonal intensiva com diferenças marcantes existentes entre os clones de espécies e de híbridos de Eucalyptus quanto aos parâmetros de crescimento e de desenvolvimento. Ao mesmo tempo, nos últimos tempos, foi introduzido o conceito de uso múltiplo do lenho das árvores com a utilização da madeira como fonte de celulose e papel, madeira sólida e outras aplicações como estratégia de aumento da rentabilidade do empreendimento florestal. Pelo exposto, o presente trabalho de pesquisa teve como objetivo a caracterização da madeira de árvores de 8 anos de clones de Eucalyptus grandis, E. saligna e de E. grandis x urophylla, visando possibilitar a otimização do seu uso. De plantações clonais localizadas no município de São Miguel de Arcanjo-SP da Cia Suzano de Celulose e Papel, foram selecionados os 5 melhores clones de cada espécie e híbrido pelas suas características silviculturais. Para cada clone foram selecionadas e cortadas as 10 melhores árvores (total de 150 árvores) e foram mensurados os parâmetros dendrométricos (DAP, altura total, altura comercial, espessura da casca). Do tronco dessas árvores foram cortados cilindros de madeira, em 5 porcentagens da altura do tronco e no DAP, em um total de 900 amostras. Em condições de laboratório, as amostras de madeira foram preparadas e analisadas com respeito aos parâmetros de qualidade da madeira anatômicos (caracterização da estrutura anatômica, variabilidade radial das dimensões das fibras, vasos, cerne e alburno) e físicos (densidade básica, densidade aparente através de densitometría de raios X, variabilidade radial da densidade) proporcionando a obtenção do índice de unifomidade da madeira. Os resultados possibilitaram a detalhada caracterização dos clones de cada árvore com respeito às variações ao longo do seu tronco e no sentido radial das amostras do DAP, a saber: (i) o teor médio de casca e alburno foi superior nos clones de E.saligna, o de cerne nos de E. grandis, (ii) os valores médios de densidade básica da madeira foram de 0,46; 0,47 e 0,49 g/cm3 para o E. grandis, E. saligna e E. grandis x urophylla; ocorreram variações longitudinais dentro e entre os clones das espécies de Eucalyptus, (iii) foram observadas variações quali e quantitativas dos elementos anatômicos da madeira entre espécies e híbrido de Eucalyptus, (iv) o valor médio da densidade aparente da madeira foi de 0,46; 0,54 e 0,54 g/cm3 nos clones de E. grandis, E. saligna e E. grandis x urophylla, respectivamente, (v) o índice de uniformidade indicou maior homogeneidade da madeira dos clones de E. grandis e E. saligna. A partir dos resultados obtidos foram preconizados alguns usos potenciais da madeira dos clones das duas espécies e híbrido de Eucalyptus. / In Brazil, as in many other countries, it has been verified significant advances in intensive clone silviculture with remarkable differences between clones of species and hybrids of Eucalyptus based on parameters of growth and development. At the same time, during these last years, it has been introduced the concept of multiple uses of trees log, having the wood as cellulose and paper source, solid wood and other applications as strategies for rising rentability of forestry enterprise. For the above, this research was based on wood of 8-year-old clones of Eucalyptus grandis, E. saligna and E. grandis x urophylla, heading to the optimization of its use. The 5 best clones of each specie and hybrid were selected based on their characteristics silviculturais and were chosen from clone cultures of Cia Suzano de Celulose e Papel, located at the district of São Miguel Arcanjo, in SP. For every clone it was selected and sliced the 10 best trees (over 150) and their dendrometrics parameters were measured (DHP, total highness, commercial highness, thicket bark etc). These trees had their log sliced in cylinders of wood, in 5 percentage of highness of the log and DHP, over a total amount of 900 sample. Under laboratory conditions, these wood samples were prepared and analyzed respecting the parameters about the wood quality related to its aspects anatomic (anatomic structure, radial variability of dimensions fibers, vases, heartwood and sapwood) and physics aspects (basic density, density based on densitometry of x-rays, radial variability of parameters about the wood quality related to its aspects anatomic (anatomic structure, radial variability of dimensions fibers, vases, heartwood and sapwood) and physics aspects (basic density, density based on densitometry of x-rays, radial variability of density) to obtain the uniformity index of wood. The results provided a detailed characterization of the clones of each tree related to the variations all over their log and related to the radial direction of DHP samples, as to know: (i) medium content of bark and sapwood was superior in clones of E.saligna, the heartwood in E.grandis, (ii) the medium values of wood basic density were 0,46; 0,47; 0,49 g/cm3 for the E.grandis, E.saligna and E.grandis x urophylla; it has occurred longitudinal variations inside and between clones of eucalyptus species, (iii) it was observed the variations about quality and quantity of anatomic elements of wood between species and hybrid of eucalyptus, (iv) the medium values of density apparent of wood was 0,46; 0,54; 0,55 g/cm3 in clones of E.grandis, E.saligna and E. grandis x urophylla, (v) the uniformity index indicated more homogeneity of wood in clones of E.grandis and E. saligna. Starting from these results, it had been stated some potencial uses of cloned wood for the 2 species and hibryd of Eucalyptus.

Perdas embrionárias e alterações gestacionais são frequentemente observadas em prenhezes de embriões bovinos manipulados in vitro. Sabe-se que tais anormalidades são resultantes de alterações epigenéticas ocasionadas pela manipulação dos gametas e/ou do embrião durante as técnicas de reprodução assistida (ARTs), com destaque para as técnicas de fecundação in vitro (FIV) e da clonagem por transferência nuclear de células somáticas (SCNT). Tais alterações resultam em distúrbios no desenvolvimento do concepto em algum momento crítico entre a fertilização e o parto, fornecendo bons modelos de estudos sobre a fisiopatologia de perdas embrionárias e dos distúrbios de desenvolvimento. Caracterizam-se como momentos críticos após a transferência do embrião (TE) o desenvolvimento embrionário no útero, o reconhecimento materno da gestação, a placentação e o desenvolvimento da placenta e do feto, os quais tem de ser transpassados sem nenhuma falha, permitindo um desenvolvimento normal do concepto até o termo. Sendo assim, o presente trabalho abordou três fases distintas do amplo período gestacional em prenhezes por ARTs. O Estudo 1 foi realizado durante o período peri-reconhecimento materno da gestação e objetivou descrever a abundância de expressão de genes estimulados pelo interferon tau (ISGs) de células mononucleares do sangue periférico (PBMCs) maternas em gestações oriundas de ARTs no primeiro mês de gestação; o Estudo 2 compreendeu os primeiros 35 dias de gestação e objetivou descrever as mudanças morfológicas e vasculares do complexo útero-concepto-ovário e o estímulo à expressão de ISGs em PBMCs em gestações de conceptos clonados por SCNT com diferentes fenótipos de desenvolvimento, sendo esses denominados gestação anembrionada e CL persistente; e o Estudo 3 foi conduzido durante o período pré-parto e objetivou descrever as alterações na produção de esteroides sexuais e corticosteroides em gestações produzidas por ARTs. Três hipóteses foram testadas: (1) Gestações de conceptos clonados por SCNT apresentam uma baixa e mais tardia estimulação de ISGs em PBMCs maternas quando comparadas com gestações de conceptos produzidos por FIV e IA; (2) O concepto clonado por SCNT apresenta um menor estímulo sobre mudanças morfológicas e vasculares do complexo útero-ovário e ISGs em PBMCs maternas durante os primeiros 35 dias de gestação, quando comparado com conceptos oriundos de IA; e (3) Gestações de embriões oriundos de ARTs apresentam alterações na dinâmica esteroidogênica no pré-parto quando comparados com gestações de IA. No estudo 1 foram coletadas amostras de sangue de gestações produzidas por inseminação artificial (IA), FIV e clonagem por SCNT, nos dias 15, 18, 20, 22, 24, 26, 28 e 31 pós-ovulação e foi realizada mensuração da abundância de transcritos de ISGs (OAS1 e ISG15) em PBMCs maternas. No estudo 2, gestações produzidas por IA e clonagem por SCNT, foram submetidas a escaneamentos ultrassonográficos dos ovários, útero e concepto a cada 3 dias do dia 14 ao 35 (dia 0 = ovulação) e amostras de sangue foram coletadas nos dias 15, 18, 20, 22, 24, 26, 28 e 31 para mensuração da abundância de transcritos de ISGs (OAS1 e ISG15) em PBMCs maternas. No estudo 3, foram coletadas amostras de sangue no último mês em gestações naturais, oriundas de FIV e de clonagem por SCNT para análise hormonal de 10 esteroides utilizando o método de espectrometria de massas multi-hormonal de alta resolução LC-MS/MS. O primeiro estudo mostrou semelhanças na expressão de genes estimulados pelo IFNT em gestações oriundas de ARTs e produzidas por IA. Entretanto, a estimulação nas gestações oriundas de ARTs aparentou ser quatro dias mais prolongada, sugerindo uma maior funcionalidade do trofectoderma em conceptos oriundos de ARTs. O segundo estudo demonstrou um aumento na expressão de ISGs em PBMCs maternas tanto em gestações de conceptos normais quanto em anormais, justificando a manutenção da função luteal mesmo na ausência de detecção do concepto por ultrasonografia. No terceiro estudo, demonstrou-se alterações na esteroidogênese nas gestações de embriões FIV e clonados no último mês de gestação, sendo essas compatíveis com a hiperativação da enzima aromatase durante todo o último mês de gestações oriundas de FIV e hiperativação das enzimas P450C11 e P450C21 trinta dias antes do parto em gestações oriundas de clonagem por SCNT. O presente estudo concluiu que conceptos oriundos de FIV e clonagem por SCNT apresentam um prolongamento no estímulo de ISGs pelo IFNT, conceptos clonados anormalos apresentam estímulo de ISGs, o que justifica a manutenção da função luteal, e, por fim, a cascata esteroidonênica que culmina com o parto apresenta-se alterada em gestações oriundas de FIV e clonagem por SCNT. / Pregnancy losses and gestational abnormalities are frequently observed in pregnancies from in vitro produced embryos in bovines. It is known that these abnormalities are due to epigenetic changes from the manipulation of gametes and/or embryo during the use of assisted reproduction techniques (ARTs), especially for the in vitro fertilization (IFV) and cloning by somatic cells nuclear transfer (SCNT). These changes results in disturbances of conceptus development in any critical stage between the fertilization and parturition, which provides good models for the study of physiopathology of embryo losses and disturbances of development. Critical stages after the embryo transfer (ET) to the uterus are characterized as the maternal recognition of pregnancy, placentation, and fetal-placental development, which needs to be surpassed without failures, in order to develop a normal conceptus until term. Therefore, the present work approached three distinct phases of the wide gestational period in pregnancies from ARTs. The Study 1 was conducted during the maternal peri-recongnition of pregnancy period and aimed to describe the expression of interferon stimulated genes (ISGs) in maternal peripheral blood mononuclear cells (PBMCs) in pregnancies derived of ARTs; the Study 2 comprise the first 35 days of pregnancy and aimed to describe morphological and vascular changes of the complex uterus-ovaries-conceptus, as well as the expression of ISGs in maternal PBMCs in pregnancies of conceptus cloned by SCNT with different phenotypes of development, denominated as anembryonic gestation and persistent CL; the Study 3 was conducted during the pre-partum period and aimed to describe changes in the production of sexual steroids and corticosteroids during the last month of pregnancies derived of ARTs. Three hypothesis were tested: (1) Pregnancies of conceptus cloned by SCNT presented a decrease and delay in the stimulation of ISGs in maternal PBMCs when compared with conceptuses produced by IFV and AI; (2) Stimulus from the conceptus for changes in the morphology and vasculature of the the uterus-ovarian complex, detected by ultrasonography in B and Doppler modes, and the stimulation of ISGs in maternal PBMCs during the first 35 days of pregnancy of conceptus cloned by SCNT are less intense when compared with conceptus derived from AI; and (3) Pregnancies derived of ARTs present changes in the steroidogenic dynamics in the pre-partum, when compared with pregnancies derived from AI. In Study 1 blood samples were collected from pregnancies produced by AI, IVF, and cloning by SCNT, at days 15, 18, 20, 22, 24, 26, 28, and 31 post-ovulation for the measurement of abundance of transcripts of ISGs (OAS1 and ISG15) in maternal PBMCs. In Study 2, pregnancies derived of AI and cloning by SCNT, were submitted to ultrasonographic scans for the evaluation and description of morphological and vascular changes in ovaries, uterus, and conceptus every 3 days from day 14 to 35 (day 0 = ovulation) and blood samples were collected on days 15, 18, 20, 22, 24, 26, 28 e 31 for the measurement of the abundance of transcripts of ISGs (OAS1 and ISG15) in maternal PBMCs. In Study 3, blood samples were collected during the last month of pregnancies naturally conceived, derived of IVF, and cloned by SCNT for the analysis of 10 steroids using the method of mass spectrometry high resolution LC-MS/MS. The first study showed similarities in the ISGs expression stimulation in pregnancies derived of ARTs and AI. However, the stimulation in the ART derived pregnancies was apparently 4 days longer, suggesting a greater placental function in conceptus derived of ARTs. The second study showed an increase in ISG expression in both normal and abnormal conceptus development, which justifies the maintenance of CL in the absence of a conceptus structure detected by ultrasonography. In the third study, was detected changes in the steroidogenesis of pregnancies derived of IFV and cloning by SCNT during the last month of pregnancy, which are compatible with the hyperactivation of the aromatase enzyme during the last month of IFV derived pregnancies, and hyperactivation of the enzymes P450C11 and P450C21 thirty days before parturition in pregnancies derived of cloning by SCNT. The present study concludes that conceptus derived of IFV and cloning by SCNT present a prolonged stimulus of ISGs, cloned conceptus with anomalous development presents a stimulus of ISGs, which justifies the CL function maintenance, and, ultimately, the steroidogenic cascade that culminates with the term is altered in pregnancies derived from IFV and cloning by SCNT.

Bei der Entwicklung von Programmen werden durch Entwickler regelmäßig Code-Clones durch das Kopieren von Quellcode erzeugt. In dieser Arbeit wird ein Ansatz zur automatisierten Messung dieses duplizierten Codes mit Hilfe von Clone-Detection-Tools über mehrere Versionen von verschiedenen Software-Produkten gezeigt. Anhand der Historien von Code-Clones werden Einflüsse auf die Redundanzen dieser Software empirisch gemessen. Damit wird eine Grundlage für den Beweis, dass die Entwicklung von Programmiersprachen zu einem dominanten Teil durch Redundanzreduzierung getrieben wird, geschaffen.:Inhaltsverzeichnis Abstract I Inhaltsverzeichnis II 1 Einleitung 1 1.1 Problemstellung 1 1.2 Zielsetzung 1 1.3 Vorgehensweise 3 2 Vorbetrachtung 5 2.1 Programmierkonzepte 5 2.1.1 Definition 5 2.1.2 Programmierkonzepte in Java 5 2.2 Treiber für die Entwicklung von Programmierkonzepten 8 2.2.1 Arten der Treiber von Programmierkonzepten 9 2.2.2 Reduzierung von Redundanz in Software 10 2.2.2.1 Arten von Redundanz in Software 10 2.2.2.2 Code-Clones 11 2.2.2.3 Folgen von Redundanz in Software 13 2.2.3 Ansätze für den Nachweis von Redundanzreduzierung als Treiber 14 2.3 Auswahl Software Repositories für die Analysen 16 2.3.1 Arten von Software Repositories 16 2.3.2 Anforderung an Software Repositories 17 3 Erhebungsprozess für die Analyse von Software auf Clones 20 3.1 Aufbau des Erhebungsprozesses 20 3.1.1 Lösungsansatz 20 3.1.2 Prozessteuerung 21 3.2 Umgang mit Versionierung 22 3.2.1 Allgemein 22 3.2.2 Commit-Filter 24 3.3 Clone-Detection 25 3.3.1 Arten und Vertreter 25 3.3.2 Eigene Verwendung 28 3.3.2.1 Simian 28 3.3.2.2 CCFinderX 29 3.3.3 Laufzeitproblem und Lösungsansätze 31 3.4 Datenaggregation 32 4 Auswertung der Messungen 35 4.1 Vorgehensweise der Auswertung 35 4.2 Betrachtung von Code-Clone-Historien 35 4.3 Vergleich unterschiedlicher Konfigurationen 41 4.3.1 Vergleich unterschiedlicher Clone-Detection-Tools 41 4.3.2 Vergleich unterschiedlicher Commit-Filter 45 4.3.3 Vergleich unterschiedlicher Schwellwerte für die Erkennung 46 4.4 Untersuchung verschiedener Interessenpunkte 48 5 Nachbetrachtung 53 5.1 Fehlerbetrachtung 53 5.2 Erweiterungsmöglichkeiten 55 5.3 Schlussbemerkung 57 Anhang V Vorgehensweise der Literaturrecherchen V Verwendete Computerkonfiguration IX Beispiele für Dateien X Beispiel für Detailausgabe von Simian X Beispiel für Detailausgabe von CCFinderX XI Beispiel für aggregierte Daten XII Abbildungsverzeichnis XIII Tabellenverzeichnis XIV Programmtextverzeichnis XV Abkürzungsverzeichnis XVI Literaturverzeichnis XVII Eidesstattliche Erklärung XXIII

This report discusses clones with nullary operations and the corresponding relational clones, both defined on arbitrary non-empty sets. The relationship between such clones and clones in the usual sense, i.e. without nullary operations, is investigated, and in particular the latter type of clones is located in the lattice of all clones. By means of two pairs of kernel and closure operators, a framework is developed that allows to transfer statements about usual clones to statements about clones with nullary constants. In this respect, familiar operators and constructions from clone theory, like the operators Pol and Inv, the closure operators belonging to the clone lattices, and the different variants of local closure operators on sets of relations and operations, respectively, are translated from the usual setting to the more general one and vice versa. The applicability of the presented machinery is demonstrated using the example of the theorem characterising Galois closed sets w.r.t. Pol-Inv as local closures of clones and relational clones, respectively.

Code clones are pieces of code that have the same functionality. While some clones may structurally match one another, others may look drastically different. The inclusion of code clones clutters a code base, leading to increased costs through maintenance. Duplicate code is introduced through a variety of means, such as copy-pasting, code generated by tools, or developers unintentionally writing similar pieces of code. While manual clone identification may be more accurate than automated detection, it is infeasible due to the extensive size of many code bases. Software code clone detection methods have differing degree of success based on the analysis performed. This thesis outlines a method of detecting clones using a program dependence graph and subgraph isomorphism to identify similar subgraphs, ultimately illuminating clones. The project imposes few constraints when comparing code segments to potentially reveal more clones.

The determination of semantic equivalence is an undecidable problem; however, this dissertation shows that a reasonable approximation can be obtained using a combination of static and dynamic analysis. This study investigates the detection of functional duplicates, referred to as semantic method clones (SMCs), in Java code. My algorithm extends the input-output notion of observable behavior, used in related work [1, 2], to include the effects of the method. The latter property refers to the persistent changes to the heap, brought about by the execution of the method. To differentiate this from the typical input-output behavior used by other researchers, I have coined the term method IOE-Behavior; which means its input-output and effects behavior [3]. Two methods are defined as semantic method clones, if they have identical IOE-Behavior; that is, for the same inputs (actual parameters and initial heap state), they produce the same output (that is result- for non-void methods, an final heap state). The detection process consists of two static pre-filters used to identify candidate clone sets. This is followed by dynamic tests that actually run the candidate methods, to determine semantic equivalence. The first filter groups the methods by type. The second filter refines the output of the first, grouping methods by their effects. This algorithm is implemented in my tool JSCTracker, used to automate the SMC detection process. The algorithm and tool are validated using a case study comprising of 12 open source Java projects, from different application domains and ranging in size from 2 KLOC (thousand lines of code) to 300 KLOC. The objectives of the case study are posed as 4 research questions: 1. Can method IOE-Behavior be used in SMC detection? 2. What is the impact of the use of the pre-filters on the efficiency of the algorithm? 3. How does the performance of method IOE-Behavior compare to using only inputoutput for identifying SMCs? 4. How reliable are the results obtained when method IOE-Behavior is used in SMC detection? Responses to these questions are obtained by checking each software sample with JSCTracker and analyzing the results. The number of SMCs detected range from 0-45 with an average execution time of 8.5 seconds. The use of the two pre-filters reduces the number of methods that reach the dynamic test phase, by an average of 34%. The IOE-Behavior approach takes an average of 0.010 seconds per method while the input-output approach takes an average of 0.015 seconds. The former also identifies an average of 32% false positives, while the SMCs identified using input-output, have an average of 92% false positives. In terms of reliability, the IOE-Behavior method produces results with precision values of an average of 68% and recall value of 76% on average. These reliability values represent an improvement of over 37% (for precision) and 30% (for recall) of the values in related work [4, 5]. Thus, it is my conclusion that IOE-Behavior can be used to detect SMCs in Java code with reasonable reliability.

Current software engineering topics such as clone detection and service selection need to improve the capability of detection process and selection process. The clone detection is the process of finding duplicated code through the system for several purposes such as removal of repeated portions as maintenance part of legacy system. Service selection is the process of finding the appropriate web service which meets the consumer’s request. Both problems can be converted into a matching problem. Matching process forms an essential part of software engineering activities. In this research, a well-known mathematical algorithm Stable Marriage Problem (SMP) and its variations are investigated to fulfil the purposes of matching processes in software engineering area. We aim to provide a competitive matching algorithm that can help to detect cloned software accurately and ensure high scalability, precision and recall. We also aim to apply matching algorithm on incoming request and service profile to deal with the web service as a clever independent object so that we can allow the services to accept or decline requests (equal opportunity) rather than the current state of service selection (search-based), in which service lacks of interacting as an independent candidate. In order to meet the above aims, the traditional SMP algorithm has been extended to achieve the cardinality of many-to-many. This adaptation is achieved by defining the selective strategy which is the main engine of the new adaptations. Two adaptations, Dual-Proposed and Dual-Multi-Allocation, have been proposed to both service selection and clone detection process. The proposed approach (SMP-based) shows very competitive results compare to existing software clone approaches, especially in identifying type 3 (copy with further modifications such update, add and delete statements) of cloned software. It performs the detection process with a relatively high precision and recall compare to the CloneDR tool and shows good scalability on a middle sized program. For service selection, the proposed approach has several advantages such as service protection and service quality. The services gain equal opportunity against the incoming requests. Therefore, the intelligent service interaction is achieved, and both stability and satisfaction of the candidates are ensured. This dissertation contributes to several contributions firstly, the new extended SMP algorithm by introducing selective strategy to accommodate many-to-many matching problems, to improve overall features. Secondly, a new SMP-based clone detection approach to detect cloned software accurately and ensures high precision and recall. Ultimately, a new SMPbased service selection approach allows equal opportunity between services and requests. This led to improve service protection and service quality. Case studies are carried out for experiments with the proposed approach, which show that the new adaptations can be applied effectively to clone detection and service selection processes with several features (e.g. accuracy). It can be concluded that the match based approach is feasible and promising in software engineering domain.