GRAL is a library for creating high quality plots and charts in Java. Many plot types are available like scatter plot, bubble plots, line plots, area plots, pie charts, and bar charts. Additionally, GRAL can exchange and process data (smoothing), and various plug-ins allow the import and export of data and graphics to formats like CSV, JPEG, PNG, EPS, PDF, or SVG.
PDFreactor is a formatting processor to convert HTML and XML to PDF. It uses Cascading Style Sheets (CSS) to define page layout and styles. It allows you to dynamically generate PDF documents such as invoices, delivery notes, shipping documents, or print versions of Web content on-the-fly. Vector graphics (SVG), barcodes, MathML, XSLT, and CMYK colors are supported. All common J2EE application servers are supported. Complete .NET, PHP, Perl, Python, and Ruby APIs are included. Direct integration into automatic build processes using Apache Ant is also possible.
ProteomeCommons.org Java Analysis Framework is a framework for referencing common mass spectrometry data such as atoms and residues. This framework provides a programmer with an easy-to-use library for writing programs that rely on common mass spectrometry data. The framework also contains utilities such as an isotope calculator and a reference for residue abbreviations.
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.
Red-Piranha is a search system that can actually learn what you are looking for. It can be used as a Web page, command line, or XML-WebService, so it will work with most languages, including Java, Perl, C#/.NET, and PHP. It includes learning abilities for the Desktop/Internet search functionality. All feedback from the user is stored in (editable) XML and RDF, and is used by the system to improve the quality of searches.
StelsEngine is a fast in-memory SQL engine (in-memory JDBC) for storing and processing tabular data in Java applications. Using StelsEngine, you can make processing data in your software considerably easier and quicker. It implements the JDBC API standard. It is a JDBC Type 4 driver, supports most keywords of ANSI SQL 92, supports integer, floating point, string, date/time, and Java object data types, supports aggregate, numeric, string, conversion, and user-defined SQL functions, supports data loading from a DBMS, and is platform independent.
StelsCSV is a JDBC driver that allows performing SQL statements and other JDBC operations upon text files (comma separated, tab-separated, fixed length, etc.). Using this driver, users can easily create a simple database consisting of plain text files. The driver can be used for writing data importing programs and migration tools. It supports most keywords of ANSI SQL92, table joins, INSERT, UPDATE, and DELETE statements, data types, aggregate, converting, string, and user-defined SQL functions.