Java Source Code Research Articles

A novel program synthesis approach in test driven software development

It is a viable alternative to automatically generate Java source code based on the specification provided by the associated unit tests. This possibility may seem far-fetched in the general case, but after considering the most common restrictions, which are applied nowadays as best practice, it turns out that a significant part of the production code can be generated automatically. The goal is to generate viable implementations, which fulfill the requirements imposed by unit tests. According to the presented vision the modern test frameworks, development guidelines and computational capacities make it possible to reach this goal.

High-speed and high-ratio referential genome compression.

The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio. We present a high-performance referential genome compression algorithm named HiRGC. It is based on a 2-bit encoding scheme and an advanced greedy-matching search on a hash table. We compare the performance of HiRGC with four state-of-the-art compression methods on a benchmark dataset of eight human genomes. HiRGC takes <30 min to compress about 21 gigabytes of each set of the seven target genomes into 96-260 megabytes, achieving compression ratios of 217 to 82 times. This performance is at least 1.9 times better than the best competing algorithm on its best case. Our compression speed is also at least 2.9 times faster. HiRGC is stable and robust to deal with different reference genomes. In contrast, the competing methods' performance varies widely on different reference genomes. More experiments on 100 human genomes from the 1000 Genome Project and on genomes of several other species again demonstrate that HiRGC's performance is consistently excellent. The C ++ and Java source codes of our algorithm are freely available for academic and non-commercial use. They can be downloaded from https://github.com/yuansliu/HiRGC. jinyan.li@uts.edu.au. Supplementary data are available at Bioinformatics online.

Agent-oriented model-driven development for JADE with the JADEL programming language

This paper describes, from motivations and main objectives to actual implementation, a novel agent-oriented programming language called JADEL. JADEL is designed to support the effective implementation of JADE agents and multi-agent systems in the scope of real-world model-driven development because it concretely helps developers by natively supporting agent-oriented abstractions, and because it is based on mature industrial-strength technologies. The four core abstractions that JADEL supports, namely agents, behaviours, communication ontologies, and interaction protocols, are presented by gradually introducing the specific syntaxes that the language provides for them. In the last part of the paper, a complete example of a simple JADEL multi-agent system is presented and discussed. Such an example is a well-known example from the official distribution of JADE and many programmers learned the basics of JADE from it. The choice of this example allows comparing JADEL source code with reference Java source code using JADE, and it clearly emphasizes the practical advantages of agent-oriented programming.Section 1 introduces and motivates the presented work. Section 2 surveys major AOP languages and, even if it cannot be considered exhaustive, it highlights the specific features of selected languages that have been relevant for the design of JADEL. Section 3 provides an overview of the features of JADE that are supported by JADEL. Section 4 presents the language in details by discussing main supported abstractions, and by specifying its formal syntax. Section 5 presents the most interesting parts of a complete example of the use of JADEL to develop a simple multi-agent system. Finally, Section 6 concludes the paper with a discussion of the current state of the presented work, and a preliminary assessment of the proposed language.

Fixing Faults in C and Java Source Code

We carried out a family of controlled experiments to investigate whether the use of abbreviated identifier names, with respect to full-word identifier names, affects fault fixing in C and Java source code. This family consists of an original (or baseline) controlled experiment and three replications. We involved 100 participants with different backgrounds and experiences in total. Overall results suggested that there is no difference in terms of effort, effectiveness, and efficiency to fix faults, when source code contains either only abbreviated or only full-word identifier names. We also conducted a qualitative study to understand the values, beliefs, and assumptions that inform and shape fault fixing when identifier names are either abbreviated or full-word. We involved in this qualitative study six professional developers with 1--3 years of work experience. A number of insights emerged from this qualitative study and can be considered a useful complement to the quantitative results from our family of experiments. One of the most interesting insights is that developers, when working on source code with abbreviated identifier names, adopt a more methodical approach to identify and fix faults by extending their focus point and only in a few cases do they expand abbreviated identifiers.

JSEA: A Program Comprehension Tool Adopting LDA-based Topic Modeling

Understanding a large number of source code is a big challenge for software development teams in software maintenance process. Using topic models is a promising way to automatically discover feature and structure from textual software assets, and thus support developers comprehending programs on software maintenance. To explore the application of applying topic modeling to software engineering practice, we proposed JSEA (Java Software Engineers Assistant), an interactive program comprehension tool adopting LDA-based topic modeling, to support developers during performing software maintenance tasks. JSEA utilizes essential information automatically generated from Java source code to establish a project overview and to bring search capability for software engineers. The results of our preliminary experimentation suggest the practicality of JSEA.

Using triple graph grammars to realise incremental round‐trip engineering

Model-driven software engineering is supported with the help of model transformations. At present, the technology for defining and executing uni-directional batch transformations seems to be fairly well developed, while bidirectional and incremental transformations are more difficult to handle. In this study, the authors present a bidirectional and incremental transformation tool for round-trip engineering between class diagrams and Java source code. Unlike other approaches, the tool may work with arbitrary Java code rather than only with source code following specific coding conventions. For its realisation, they selected triple graph grammars (TGGs) because they allow to generate bidirectional incremental transformations from a single set of undirected rules. When applying TGGs, they observed several strengths and weaknesses which are also discussed in this study.

Multiclass cancer classification using a feature subset-based ensemble from microRNA expression profiles

Cancer classification has been a crucial topic of research in cancer treatment. In the last decade, messenger RNA (mRNA) expression profiles have been widely used to classify different types of cancers. With the discovery of a new class of small non-coding RNAs; known as microRNAs (miRNAs), various studies have shown that the expression patterns of miRNA can also accurately classify human cancers. Therefore, there is a great demand for the development of machine learning approaches to accurately classify various types of cancers using miRNA expression data. In this article, we propose a feature subset-based ensemble method in which each model is learned from a different projection of the original feature space to classify multiple cancers. In our method, the feature relevance and redundancy are considered to generate multiple feature subsets, the base classifiers are learned from each independent miRNA subset, and the average posterior probability is used to combine the base classifiers. To test the performance of our method, we used bead-based and sequence-based miRNA expression datasets and conducted 10-fold and leave-one-out cross validations. The experimental results show that the proposed method yields good results and has higher prediction accuracy than popular ensemble methods. The Java program and source code of the proposed method and the datasets in the experiments are freely available at https://sourceforge.net/projects/mirna-ensemble/.

An Advanced Version of CS Unplugged Activity 2

In line with the global trend toward enhancing education on computer programming, Japan has begun to consider making programming a required subject at the elementary-school level. While traditionally some programming education has been conducted starting at the level of secondary education, this policy would introduce it as a required subject at an earlier stage. The authors are involved in programming education at a “Kosen” school, a unique higher education institution of science and technology in Japan that accepts as students junior-high-school graduates. However, since not a few students consider the subject to be difficult, they are in the process of seeking out effective educational methods for beginning learners of programming. As part of this process, we are carrying out research focused mainly on the continuation of CS Unplugged to full-fledged programming. Previously we proposed a Six-Step Method based on CS Unplugged, and we have put it into practice in the classroom. The six steps are as follows: Step 1: CS Unplugged Activity; Step 2: CS Plugged Activity; Step 3: visualization of the processing; Step 4: extraction of elements of the processing; Step 5: writing Java source code; Step 6: validation through table tracing. However, the CS Unplugged Activity was devised originally for children who had no knowledge of computers. In addition, most of the activities prepared have concerned individual topics, with only weak connections among those topics. Focusing on these points, we devised a more advanced version as an activity connected to full-fledged programming and merging the two topics, important to the initial study, of Activity 1 (Binary Numbers) and Activity 2 (Image Representation). This paper reports the results of using this version in classroom practice.

A static technique for detecting input validation vulnerabilities in Android apps

Input validation vulnerabilities are common in Android apps, especially in inter-component communications. Malicious attacks can exploit this kind of vulnerability to bypass Android security mechanism and compromise the integrity, confidentiality and availability of Android devices. However, so far there is not a sound approach at the source code level for app developers aiming to detect input validation vulnerabilities in Android apps. In this paper, we propose a novel approach for detecting input validation flaws in Android apps and we implement a prototype named EasyIVD, which provides practical static analysis of Java source code. EasyIVD leverages backward program slicing to extract transaction and constraint slices from Java source code. Then EasyIVD validates these slices with predefined security rules to detect vulnerabilities in a known pattern. To detect vulnerabilities in an unknown pattern, EasyIVD extracts implicit security specifications as frequent patterns from the duplicated slices and verifies them. Then EasyIVD semi-automatically confirms the suspicious rule violations and reports the confirmed ones as vulnerabilities. We evaluate EasyIVD on four versions of original Android apps spanning from version 2.2 to 5.0. It detects 58 vulnerabilities including confused deputy attacks and denial of service attacks. Our results prove that EasyIVD can provide a practical defensive solution for app developers.

UPC BARCODE APPS FOR DRUG REGISTERED VERIFICATION

In pharmacology, drug is used to prevent and cure diseases and to improve the physical or mental well-being. All medicinal products must be registered with Drug Control Authority (DCA) of Malaysia before being marketed. However, there are still numerous unregistered products being sold in night markets and grocery stalls that contained unknown materials that could harm our bodies. As nowadays most people own smartphones, thus it will be great if the smartphone is being utilized to become a mobile apps that can prevent consumers from buying unregistered products. This study described the process of creating a barcode reader application for drug registered verification. The application is created using Android Studio software, Java programming language and source code from GitHub, which is then synchronized with the database of some medicinal products. The barcode scanner is then tested to read the UPC barcode on the products and the result of registration confirmation will be shown on the screen of the smartphone. Thus, it will aware the user from buying the unregistered products.

Piracy Detection App of Android Applications

increase of Smartphone users worldwide has moved developers attention towards Mobile platform to create applications for Smartphone. Android is one such major mobile platform and also an open source operating system. With the rapid increase in the android applications some undesirable apps begin to show up. Two kinds of such apps are pirated and malware. This focuses on piracy of application in android market, because one developer pirates the other developer's work. Two type of piracy present in android application, first copied java source code and other is graphical asset. This paper discusses on how to identify pirated application both graphical and java source code piracy. Androguard tool analyze similarity of bytecode in applications. With this tool, add extra feature to Combined Graphical asset comparison in Androguard. Finally, experimented result shows within 50sec can compare 20 Mb application graphical similarities and 120sec for source code comparison using Androsim (Snappy compressor).

Round-trip Engineering UML Class Models and Java Models

Model transformations constitute the key technology for model-driven software development, a software engineering discipline which became more and more important during the last decade. While tool support for unidirectional batch transformations is rather mature, bidirectional and incremental transformations are only weakly investigated. Nevertheless, several usage scenarios demand for incremental and bidirectional transformations, like round-trip engineering between UML class models and Java source code. This paper presents a bidirectional transformation between UML class models and a Java model which is obtained from Java source code. The transformation is written in QVT Relations, a declarative model transformation language provided by the OMG. While the case study demonstrates that it is possible to specify bidirectional transformations between heterogeneous metamodels in a single relational specification, it also reveals some inherent limitations of the language and the corresponding tool support.

Coupling Measures and its Impact on Object-Oriented Software Quality

Metrics measurement is an important means to access the quality of software systems. Software metrics measurement helps in quick and accurate analysis of software quality. Coupling metrics is a kind of software metrics having a significant impact on several qualities attributes of the object-oriented software. In literature, coupling metrics is used to access the software quality attributes like reliability, efficiency, integrity, maintainability, flexibility, portability, reusability and interoperability, etc. of object-oriented software. However, the threshold values for software coupling measures are still not fully defined. This paper investigates the values of seven coupling metrics and explores the impact of coupling metrics values on different quality attributes of the object-oriented software. The Java source code is analyzed to find coupling between different modules of java code. The coupling values of twenty five Java projects are measured to find behavior of coupling values. Using the resulting coupling values of the twenty five projects, percentage threshold values of seven coupling measures are defined. Also the behavior of coupling metrics is plotted using graph. It is found from the results that the percentage threshold value of parameter coupling is in between 24 to 34. Similarly, the threshold percentage of inheritance coupling is between 3 to 13, global coupling is 0 to 7, data abstraction coupling is 9 to 19, import coupling is 18 to 28, export coupling is 19 to 29 and external coupling is 0 to 5. It means parameter coupling, import and export coupling has higher range of values. Inheritance and data abstraction coupling has a medium range of values and global and external coupling have a least range of values. It is also found that the coupling measures have an impact on various quality attributes of the object-oriented software. If the developer could control the values of few important metrics like parameter, inheritance and data abstraction coupling, it will result in improving the overall quality of object-oriented software. Applications: This work is useful for software professionals to maintain level of coupling while developing software. The data set used in this work is totally new and unique.

Integration of the Java Image Science Toolkit with E-Science Platform

Medical image analyses rely on diverse software packages assembled into a “pipeline”. The Java Image Science Toolkit (JIST) has served as a standalone plugin into the Medical Image Processing Analysis and Visualization (MIPAV). We addressed shortcomings that previously prevented deeper integration of JIST with other E-science platforms. First, we developed an interface for integrating externally compiled packages (similar to the interfaces in NiPy) such that the application can become a “draggable module” in the module tree. This allows for connection of inputs and outputs to other JIST modules while maintaining external processing and monitoring. Second, we develop an integration interface with the Neuroimaging Informatics Tools and Resources Clearinghouse Cloud Environment (NITRC-CE). User can launch and terminate pre-configured nodes to utilize computational resources of the Amazon cloud. Finally, we define a new external data source, which can connect to the eXtensible Neuroimaging Archive Toolkit (XNAT) to query and retrieve remote data using XNAT’s REST API. Specifically, we define dataflow for files that can readily be converted into volumes and collections of volumes to interface with any JIST module that expects volumetric image data as an input. Users now have the ability to run their pipelines from a well-defined external data source and no longer are required to already have data on the disk. With these upgrades we have extended JIST’s capabilities outside of complied java source code and enhanced capabilities to seamlessly interface with E-science platforms.

Detecting Android Malware Using Clone Detection

Android is currently one of the most popular smartphone operating systems. However, Android has the largest share of global mobile malware and significant public attention has been brought to the security issues of Android. In this paper, we investigate the use of a clone detector to identify known Android malware. We collect a set of Android applications known to contain malware and a set of benign applications. We extract the Java source code from the binary code of the applications and use NiCad, a near-miss clone detector, to find the classes of clones in a small subset of the malicious applications. We then use these clone classes as a signature to find similar source files in the rest of the malicious applications. The benign collection is used as a control group. In our evaluation, we successfully decompile more than 1 000 malicious apps in 19 malware families. Our results show that using a small portion of malicious applications as a training set can detect 95% of previously known malware with very low false positives and high accuracy at 96.88%. Our method can effectively and reliably pinpoint malicious applications that belong to certain malware families.

SPOON: A library for implementing analyses and transformations of Java source code

This paper presents SPOON, a library for the analysis and transformation of Java source code. SPOON enables Java developers to write a large range of domain-specific analyses and transformations in an easy and concise manner. SPOON analyses and transformations are written in plain Java. With SPOON, developers do not need to dive into parsing, to hack a compiler infrastructure, or to master a new formalism. Copyright © 2015 John Wiley & Sons, Ltd.

MULTILANGUAGE SOURCE CODE GENERATOR FOR DATABASE ORIENTED APPLICATION USING JSP

The goal of automated software engineering is to increase by order of magnitude both the quality and productivity factor. To date most successful approach is producing a special-purpose code generator, such as screen generator, report generator, swing builder, Meta programming etc., these software tools is produce source code for specific language. This study provides mechanism to make a generalized system of Multi-Language Source Code Generation (MLSCG). It takes database structure of metadata as input and produce source code in Java, Java script, JSP, PHP and ASP. We utilize the target output code for both web and pc-based application.

GroupTracker: Video tracking system for multiple animals under severe occlusion

Quantitative analysis of behaviors shown by interacting multiple animals can provide a key for revealing high-order functions of their nervous systems. To resolve these complex behaviors, a video tracking system that preserves individual identity even under severe overlap in positions, i.e., occlusion, is needed. We developed GroupTracker, a multiple animal tracking system that accurately tracks individuals even under severe occlusion. As maximum likelihood estimation of Gaussian mixture model whose components can severely overlap is theoretically an ill-posed problem, we devised an expectation–maximization scheme with additional constraints on the eigenvalues of the covariance matrix of the mixture components. Our system was shown to accurately track multiple medaka (Oryzias latipes) which freely swim around in three dimensions and frequently overlap each other. As an accurate multiple animal tracking system, GroupTracker will contribute to revealing unexplored structures and patterns behind animal interactions. The Java source code of GroupTracker is available at https://sites.google.com/site/fukunagatsu/software/group-tracker.

A proposal for teaching programming through the Five-Step Method

We have proposed a new method of advancing from CS Unplugged through the new process of CS Plugged to fullfledged computer programming languages, as a means of deepening understanding in computer programming education. We also have proposed a new Five-Step Method consisting of the following steps: Step 1, A CS Unplugged activity; Step 2, A CS Plugged activity; Step 3, A trace table, Step 4, Preparing pseudocode; and Step 5, Writing Java source code.

Certifying a java type resolution function using program transformation, annotation, and reflection

In Java, type resolution is a function that takes a reference to a type occurring in a given context as input and returns the canonical name of that type. This information is fundamental to static analysis--a "must have" function underlying virtually all forms of semantic-based analysis. In the case of Java, this function is also complex and it is quite common to encounter tools where it is implemented incorrectly. This paper presents a novel approach for certifying the correctness of a given type resolution function with respect to an arbitrary Java source code base. The approach uses program transformation to instrument a subject code base in such a way that reflection can then be used to certify the correctness of the type resolution function against the function used by the Java compiler. In this form of certification, the type resolution function of the Java compiler serves as the test oracle.