Yan, J; (2014) Mass spectrometric studies of proteins and protein complexes involved in bacterial secretion and regulatory systems. Doctoral thesis , UCL (University College London).

Abstract

This paper presents the results of a large scale empirical study of coherent dependence clusters. All statements in a coherent dependence cluster depend upon the same set of statements and affect the same set of statements; a coherent cluster's statements have ‘coherent’ shared backward and forward dependence. We introduce an approximation to efficiently locate coherent clusters and show that it has a minimum precision of 97.76%. Our empirical study also finds that, despite their tight coherence constraints, coherent dependence clusters are in abundance: 23 of the 30 programs studied have coherent clusters that contain at least 10% of the whole program. Studying patterns of clustering in these programs reveals that most programs contain multiple substantial coherent clusters. A series of subsequent case studies uncover that all clusters of significant size map to a logical functionality and correspond to a program structure. For example, we show that for the program acct, the top five coherent clusters all map to specific, yet otherwise non-obvious, functionality. Cluster visualization also brings out subtle deficiencies in program structure and identifies potential refactoring candidates. A study of inter-cluster dependence is used to highlight how coherent clusters are connected to each other, revealing higher-level structures, which can be used in reverse engineering. Finally, studies are presented to illustrate how clusters are not correlated with program faults as they remain stable during most system evolution.

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