Fragmentos de código duplicado, ou clones, são inseridos em aplicativos por serem uma maneira simples de reúso, dentre outros motivos. Clones são, portanto, comuns em programas. No entanto, a atividade de manutenção pode ficar custosa se o código do programa analisado possuir muitos clones, principalmente os semânticos, os quais podem possuir códigos distintos, mas realizam tarefas similares. Nesse sentido, a utilização de ferramentas que automatizam a tarefa de detectar clones é desejável. Ferramentas atuais de detecção de clones semânticos são capazes de identificar esses clones com altas taxas de acerto. No entanto, elas não são capazes de identificar clones semânticos considerando também os fluxos dos procedimentos ou funções que são invocados dentro dos fragmentos de código comparados. Essa limitação pode levar as ferramentas a indicarem clones semânticos falso positivos. Este trabalho apresenta uma técnica de detecção de clones semânticos que considera as chamadas de procedimentos presentes nos programas. Essa técnica apresentou uma taxa de acertos 2,5% maior do que técnicas convencionais de acordo com um benchmark, também desenvolvido neste trabalho. Esse benchmark foi criado com base nas classificações de clones fornecidas por programadores da indústria e da academia. A técnica interprocedimental de detecção de clones semânticos pode ser utilizada para evolução, manutenção, refatoração e entendimento de programas. / Fragments of duplicated code, or clones, are embedded in applications as they are a simple way to reuse code, among other reasons. Clones are therefore common in programs. However, the maintenance activity may be costly if the program code has many clones to analyze, specially semantic clones, which are semantically similar but may have different syntax. In this regard, the use of tools that automate the task of detecting clones is desirable. Current tools for detecting semantic clones are able to identify those clones with high hit rates. However, they are not able to detect semantic clones also considering the flow of procedures or functions that are invoked within the compared code fragments. This limitation can lead the tools to indicate false positive semantic clones. This paper presents a technique that takes into account the procedure calls in programs to detect semantic clones. This technique showed a 2.5% higher hit rate than conventional techniques according to a benchmark also developed in this work. This benchmark was created based on evaluations provided by programmers from academic and industrial settings. The interprocedural semantic clone detection technique can be used for evolution, maintenance, refactoring and understanding of programs.

Fragmentos de código duplicado, ou clones, são inseridos em aplicativos por serem uma maneira simples de reúso, dentre outros motivos. Clones são, portanto, comuns em programas. No entanto, a atividade de manutenção pode ficar custosa se o código do programa analisado possuir muitos clones, principalmente os semânticos, os quais podem possuir códigos distintos, mas realizam tarefas similares. Nesse sentido, a utilização de ferramentas que automatizam a tarefa de detectar clones é desejável. Ferramentas atuais de detecção de clones semânticos são capazes de identificar esses clones com altas taxas de acerto. No entanto, elas não são capazes de identificar clones semânticos considerando também os fluxos dos procedimentos ou funções que são invocados dentro dos fragmentos de código comparados. Essa limitação pode levar as ferramentas a indicarem clones semânticos falso positivos. Este trabalho apresenta uma técnica de detecção de clones semânticos que considera as chamadas de procedimentos presentes nos programas. Essa técnica apresentou uma taxa de acertos 2,5% maior do que técnicas convencionais de acordo com um benchmark, também desenvolvido neste trabalho. Esse benchmark foi criado com base nas classificações de clones fornecidas por programadores da indústria e da academia. A técnica interprocedimental de detecção de clones semânticos pode ser utilizada para evolução, manutenção, refatoração e entendimento de programas. / Fragments of duplicated code, or clones, are embedded in applications as they are a simple way to reuse code, among other reasons. Clones are therefore common in programs. However, the maintenance activity may be costly if the program code has many clones to analyze, specially semantic clones, which are semantically similar but may have different syntax. In this regard, the use of tools that automate the task of detecting clones is desirable. Current tools for detecting semantic clones are able to identify those clones with high hit rates. However, they are not able to detect semantic clones also considering the flow of procedures or functions that are invoked within the compared code fragments. This limitation can lead the tools to indicate false positive semantic clones. This paper presents a technique that takes into account the procedure calls in programs to detect semantic clones. This technique showed a 2.5% higher hit rate than conventional techniques according to a benchmark also developed in this work. This benchmark was created based on evaluations provided by programmers from academic and industrial settings. The interprocedural semantic clone detection technique can be used for evolution, maintenance, refactoring and understanding of programs.

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O presente estudo foi desenvolvido em dois solos com diferentes fertilidades caracterizados como Podzólico Vermelho Escuro ( P V E ) e Areia Quartzosa Álica (AQ), localizados na região de Lençois Paulista - SP em áreas da DURATEX FLORESTAL S.A. Os dois locais apresentam semelhanças quanto às características climáticas. O estudo objetivou: a) observar a variação genética entre clones de E. grandis propagados por estaquia; b) verificar a interação e clones x solos com diferentes fertilidades; c) comparar o comportamento silvicultural de clones e material propagado por sementes com diferentes graus de melhoria genética; d) avaliar o efeito da competição entre árvores em parcelas monoclonais e misturas de clones. Foram testados 16 tratamentos, distribuídos em blocos ao acaso com três repetições, em parcelas de 36 plantas e espaçamento de 3,0 m x 3,0 m. Os tratamentos estudados foram: - Parcelas monoclonais de oito clones constituídos por plantas propagadas por estaquia (8 tratamentos). Parcelas multiclonais constituídas por plantas dos oito clones, propagados por estaquia. Os oito clones foram distribuídos ao acaso na parcela (3 tratamentos). - Parcelas constituídas por plantas produzidas por sementes de pomar clonal propagado por enxertia (2 tratamentos). - Parcelas constituídas por plantas produzidas por sementes das oito árvores selecionadas (matrizes), de cujas touças retiraram-se as estacas (2 tratamentos).- Parcelas constituídas por plantas originárias de sementes de E. grandis , ex África do Sul, e colhidas em povoamentos comerciais da DURATEX FLORESTAL S.A. em Lençóis Paulista - SP. Os resultados e conclusões da avaliação aos 24 meses foram: a) a produtividade média no PVE (126,29 m3 sólidos /ha), foi 57,32 m3 /ha superior (83%) à media de produtividade da AQ (68,97m3 /ha); b) os materiais propagados via semente apresentaram melhores resultados para pomar clonal, vindo a seguir as sementes de matrizes e por último as sementes comerciais. O material propagado por estaquia não correspondeu à expectativa teórica; c) As parcelas multiclonais apresentaram desenvolvimento superior as parcelas monoclonais, principalmente no PVE, onde a superioridade foi de 8,1% em volume; d) houve variação genética entre clones nos dois solos testados; e) a interação dos dois materiais genéticos com os dois solos mostrou-se pouco expressiva, com comportamento semelhante dos mesmos nos dois solos; f) as estimativas de ganhos genéticos reais foram inferiores as teoricamente esperadas; g) os materiais genéticos mostraram variações nas concentrações de nutrientes em suas folhas / The objectives of this work were: a) to observe the genetic variation among clones of Eucalyptus grandis produced by cutting; b) to verify the interaction of clones x soils with different fertility leveIs; c) to compare the silvicultural performance of clones produced by cutting and trees produced from seeds with different genetic improvement leveIs; and d) to evaluate the compettional effect among trees in monoclonal and multiclonal plots. The trials were established in two soils with different fertility levels and characterized as dark red podzolic (PVE) and aluminous quartzous sand (AQ) under similar climatic conditions in the region of Lençóis Paulista - SP. The trials were set up in a randomized block design with 16 trataments and three replications uti1izing 36 trees in spacings of 3,0 x 3,0 m plots. The treatments were as floows: 1. Eight treatments with different monoclonal plots consisting of trees propagated by cutting; 2. Three treatments with multiclonal plots. Each plot consisted of a misture of the 8 clónes propagated by cutting; 3. Two treatments with plots consisting of trees propagated by seeds from a cIonaI seed orchad established by grafting; 4. Two treatments with plots consisting of trees propagated by seeds from 8 selected trees that gave origin to the 8 clones; 5. One treatment with plots consisting of trees propagated by seeds collected from commercial stands of E. grandis (ex South Afríca) in Lençóis Paulista - SP. The analysis of the results from evaluations made at 24 months of age allowed the following conclusions: a) The mean production for the PVE soil (126,29 m3/ha) was 83% (57,32 m3/ha) higher than that for the QA soil (68,97 m3/ha). b) Trees propagated by seeds showed higher productions than those propagated by cutting. In this case, the highest production was obtained by trees propagated by seeds from the clonal seed orchard, followed by those from selected trees and the last, those from commercial stands; c) The treatments with multiclonal plots showed a higher production than those with monoclonal plots. In the PVE soil, the production in volume for the multiclonal plots was 8,1% higher than that for the monoclonal plots; d) Genetic variations among clones were detected in the two soils tested; e) The interaction of the two types of genetic material (clones and seeds) with the two soils showed little expression with similar performance in both soils; f) The estimates for the observed genetic gains were lower to those theotetically expected; g) The genetic material utilized showed variation in the leaf mineral nutrient content

O objetivo do experimento foi estudar o efeito de várias fontes de nitrogênio na multiplicação e desenvolvimento dos clones de Eucalyptus grandis Hill ex Maiden GO269, GO694 e GO246, os quais vinham sendo mantidos ”in vitro” por cerca de 2 anos em meio contendo a proporção 3 : 1 de NOa- / NH4+, outros sais, vitaminas e adição 0,2mg/l de BA (benziladenina). Os tratamentos realizados constituíram alteração na fonte de nitrogênio e não na quantidade deste, com exceção dos tratamentos com aminoácidos onde adicionou-se 60 mg/l Glu; 30 mg/l Cys; 60mg/l Glu + 30mg/l Cys ao meio MG2. Como outras formas de nitrogênio utilizou-se uréia (100 mg/l; 200 mg/l e 300 mg/l), cloreto de amônio (800 mg/l, 1000 mg/l, 1200 mg/l) havendo sempre um balanceamento das formas iônicas, mantendo-se o teor total de nitrogênio. Os resultados mostraram que o meio MG2 pode ser melhorado com adição de uréia (300mg/l) onde ocorreu maior alongamento dos clones (principalmente GO694) e enraizamento dos clone GO269. Os tratamentos com cloreto de amônio não tiveram um efeito positivo, na multiplicação de gemas, enquanto que a adição de aminoácidos provocaram uma melhoria nesta, especialmente para p clone GO269. Quando foi adicionada somente Cys ao meio MG2, os resultados foram negativos em relação a todos os parâmetros fisiológicos analisados / The objective of this experiment was o study the influence of different sources of nitrogen in the multiplication and development of clones of EucaLyptus grandis. Hill ex Maiden GO269, GO694 and GO246 which were maintaned ”in vitro" for 2 years in medium containing 3: 1 NO3 / NH4+ ratio, other salts, vitamins and the addition of 0.2 mg/l of BA. The treatments were an alteration in the source of nitrogen and not in its quantity, with the except of the treatments in which the following amino acids were added to MG2 medium: Glu (60 mg/l); Cys (30 mg/l); Glu (60 mg/l) + Cys (30 mg/l) (no alteration in the salts was made). Other forms of nitrogen were utilized such as: urea (100 mg/l, 200 mg/l and 300 mg/l) and ammonium chloride (800 mg/l; 1000 mg/l and 1200 mg/l) , with adjustment in the total content of the nitrogen salts. The results showed that the MG2 medium can be improved with the addition of urea (specially 300 mg/l) in terms of shoot ellongation (mainly in the clone G0694) and rooting of clone G0269. The treatments with ammonium chloride did not show a positive effect shoot multiplication, whereas the addition of amino promoted an improvement specially in the clone GO269. Addition of Cys as nitrogen was negative relative to all physiological parameters analysed

Student Number : 0115350V - MSc dissertation - School of Plant, Animal and Environmental Science - Faculty of Science / The effect of between-tree competition in separate even aged stands of a Eucalyptus grandis seedling and a single Eucalyptus grandis x Eucalyptus urophylla hybrid clone was assessed. This was done by comparing treatments within an experiment, that was designed to test the effect planting density and genotype had on timber production and stand dynamics through time. This experiment is located on an escarpment in the Summer rainfall region of South Africa, approximately 7 km North West of Albert Falls dam in the Kwa-Zulu Natal Midlands. The terrain is flat with deep apedal soils, and the site has an estimated mean annual precipitation of 1143 mm. The simplest method of evaluating competition effects in plantation stands is through the use of spacing trials. Spacing trials create stands/plots in which all silvicultural and climatic variables are constant. Differences between treatments can then be attributed to competition alone. The planting densities tested were 6667 stems.ha-1, 3333 stems.ha-1, 2222 stems.ha-1, 1587 stems.ha-1 and 1111 stems.ha-1 respectively. Competition was measured at three levels, namely; (i)individual tree, (ii)size-class and (iii)stand level. Vigour and its distribution within the population were used to explain competition processes. Basal area was chosen as the size variable for which vigour would be analysed. Relative Growth Rate (RGR) and Relative Production Rate (RPR) were chosen as the measures of vigour for analysis. Morphological changes in the trees as a result of competition were also used to understand the competitive mechanisms. It was found that resources are not shared amongst individuals in proportion to their size, but rather the larger individuals use disproportionately more of the resources than the smaller individuals, and therefore competition is asymmetrical. The dominant form of competition was found to be resource pre-emption where larger individuals passively prevent solar resources from reaching smaller competitors. Using RPR as the measure of vigour, competition was found to be one-sided, meaning that smaller individuals do not reduce the vigour of larger ones. If RGR is accepted as the measure of vigour then competition is two-sided meaning that the smaller individuals do reduce the vigour of the larger ones to a certain extent. There was no difference in the degree to which the smaller competitors in the clonal and seedling treatments reduced the growth of the larger individuals. The self-thinning rate in the seedling treatments was significantly higher than in the clonal treatments. Increases in mean tree size and production per hectare were accompanied by increases in mortality in the seedling treatments. In the clonal treatments it was found that even once the mean tree size approached the self thinning line, very few or no trees died, however there was also very little or no increase in mean tree size. When the relationship between number of live trees and production per hectare was analysed it was found that the clone could increase production per hectare without any change in survivorship, which is contrary to popular theory. As time progressed the skewness of the population progressed from negative to positive. This increase was the most pronounced in the higher planting density treatments, and the clonal treatments. The size variability in the population first decreased, then steadily increased. This increase was more pronounced in the high planting density treatments, and the clonal treatments. Clones and seedlings react in very different ways to competition. The large differences in population dynamics observed, indicate that we cannot just apply knowledge built up over the years regarding the management of Eucalyptus grandis and other plantation species to Eucalyptus hybrid clones.

Clones are a matter of great concern to the software engineering community because of their dual but contradictory impact on software maintenance. While there is strong empirical evidence of the harmful impact of clones on maintenance, a number of studies have also identified positive sides of code cloning during maintenance. Recently, to help determine if clones are beneficial or not during software maintenance, software researchers have been conducting studies that measure source code stability (the likelihood that code will be modified) of cloned code compared to non-cloned code. If the presence of clones in program artifacts (files, classes, methods, variables) causes the artifacts to be more frequently changed (i.e., cloned code is more unstable than non-cloned code), clones are considered harmful. Unfortunately, existing stability studies have resulted in contradictory results and even now there is no concrete answer to the research question "Is cloned or non-cloned code more stable during software maintenance?" The possible reasons behind the contradictory results of the existing studies are that they were conducted on different sets of subject systems with different experimental setups involving different clone detection tools investigating different stability metrics. Also, there are four major types of clones (Type 1: exact; Type 2: syntactically similar; Type 3: with some added, deleted or modified lines; and, Type 4: semantically similar) and none of these studies compared the instability of different types of clones. Focusing on these issues we perform an empirical study implementing seven methodologies that calculate eight stability-related metrics on the same experimental setup to compare the instability of cloned and non-cloned code in the maintenance phase. We investigated the instability of three major types of clones (Type 1, Type 2, and Type 3) from different dimensions. We excluded Type 4 clones from our investigation, because the existing clone detection tools cannot detect Type 4 clones well. According to our in-depth investigation on hundreds of revisions of 16 subject systems covering four different programming languages (Java, C, C#, and Python) using two clone detection tools (NiCad and CCFinder) we found that clones generally exhibit higher instability in the maintenance phase compared to non-cloned code. Specifically, Type 1 and Type 3 clones are more unstable as well as more harmful compared to Type 2 clones. However, although clones are generally more unstable sometimes they exhibit higher stability than non-cloned code. We further investigated the effect of clones on another important aspect of stability: method co-changeability (the degree methods change together). Intuitively, higher method co-changeability is an indication of higher instability of software systems. We found that clones do not have any negative effect on method co-changeability; rather, cloning can be a possible way of minimizing method co-changeability when clones are likely to evolve independently. Thus, clones have both positive and negative effects on software stability. Our empirical studies demonstrate how we can effectively use the positive sides of clones by minimizing their negative impacts.

The cloning of code is controversial as a development practice. Empirical studies on the long-term effects of cloning on software quality and maintainability have produced mixed results. Some studies have found that cloning has a negative impact on code readability, bug propagation, and the presence of cloning may indicate wider problems in software design and management. At the same time, other studies have found that cloned code is less likely to have defects, and thus is arguably more stable, better designed, and better maintained. These results suggest that the effect of cloning on software quality and maintainability may be determinable only on a case-by-case basis, and this only aggravates the challenge of establishing a principled framework of clone management and understanding. This thesis aims to improve the understanding and management of clones within software systems. There are two main contributions. First, we have conducted an empirical study on cloning in one of the major device drivers families of the Linux kernel. Different from many previous empirical studies on cloning, we incorporate the knowledge about the development style, and the architecture of the subject system into our study; our findings address the evolution of clones; we have also found that the presence of cloning is a strong predictor (87\% accuracy) of one aspect of underlying hardware similarity when compared to a vendor-based model (55\% accuracy) and a randomly chosen model (9\% accuracy). The effectiveness of using the presence of cloning to infer high-level similarity suggests a new perspective of using cloning information to assist program comprehension, aspect mining, and software product-line engineering. Second, we have devised a triage-oriented taxonomy of clones to aid developers in prioritizing which kinds of clones are most likely to be problematic and require attention; a preliminary validation of the utility of this taxonomy has been performed against a large open source system. The cloning-based software quality assurance (QA) framework based on our taxonomy adds a new dimension to traditional software QA processes; by exploiting the clone detection results within a guided framework, the developer is able to evaluate which instances of cloning are most likely to require urgent attention.