ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
Redet is a tool for developing and executing regular expressions using any of more than 50 search programs, editors, and programming languages, intended both for developing regular expressions for use elsewhere and as a search tool in its own right. For each program in each locale, a palette showing the available constructs is provided. The properties of each program are determined by runtime tests, which guarantees that they will be correct for the program version and locale. Additional features include persistent history, extensive help, a variety of character entry tools, and the ability to change locale while running. Redet is highly configurable and fully supports Unicode.
VTAGS is a command line application that will generate a VI(M) compatible tags file for VHDL source files. This application will read standard VHDL'87 files. It should also parse later VHDL, but it only takes account of the basic parts of the language. It will group items that it finds by architecture, procedure, function, or package. It does this by adding extra information to the extension field of the tags file.
AntFlow builds upon Apache Ant to provide a new approach to simplifying system automation that uses pipelines of hot folders chained together to perform a given task. Using XML, it associates an automated task such as data transfer, encryption, or XML processing with a directory on the local system. Whenever a file is copied or written into the hot folder, the associated task is executed and the file is moved to the next hot folder in the pipeline for further processing.
DiaNa is a Perl framework designed to process a huge amount of data, performing from very easy to very complex tasks in a very efficient, spreadsheet-like, batch fashion. DiaNa also features an interactive Perl/Tk GUI, layered on the top of several batch shell-scripts. The DiaNa syntax is a very small and orthogonal superset of the underlying Perl syntax, which allows, for example, comfortable addressing of file tokens and profitable use of file formats throughout the data processing.
alph implements and analyzes historical and traditional ciphers and codes, such as polyalphabetic, substitutional, and mixed employing human-reconstructable algorithms. It provides a pipe filter interface in order to encrypt and decrypt block text to achieve transparency. The program is meant to be used in conjunction with external programs that transfer data, resulting in transparent encryption or decryption of information. The program can thus be used as a mail filter, IRC filter, IM filter, and so on.