Annotations

Callplot is a tool for drawing "call-flow" diagrams of the kind common in the telecommunications industry. Input to the tool is in a terse textual notation, and output from the tool can be in several formats, including "ASCII-art", pic format, XML, SVG, and VML. The -pic option produces pic(1)... Platforms: *nix

jZeno is a meta-project that integrates a collection of java open source libraries, to form a ready-to-use web development environment. jZeno is made to allow people to create web applications by using pure java development as much as possible. The main architectural goal of Largely reducing the... Platforms: *nix

ProGuard is a free Java class file shrinker, optimizer, and obfuscator. ProGuard project can detect and remove unused classes, fields, methods, and attributes. It can then optimize bytecode and remove unused instructions. Finally, it can rename the remaining classes, fields, and methods using... Platforms: *nix

Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an... Platforms: *nix

Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #... Platforms: *nix

xpidl project is an XPIDL parser. SYNOPSIS xpidl -m mode [-a] [-w] [-v] [-t version number] [-I path] [-o basename | -e filename.ext] filename.idl OPTIONS -a Emit annotations to typelib. -w Turn on warnings (recommended). -v Display version. -t version number Create a... Platforms: *nix

GO::TermFinder is a Perl module that can identify GO nodes that annotate a group of genes with a significant p-value. This package is intended to provide a method whereby the P-values of a set of GO annotations can be determined for a set of genes, based on the number of genes that exist in the... Platforms: *nix

rpng/rpng2/wpng are the demo programs that accompany OReillys PNG: The Definitive Guide. rpng is a simple file viewer with the ability to set a background color when displaying transparent PNGs. rpng2 is a progressive PNG viewer, designed to work like a web browser (though it contains no... Platforms: *nix

Jodd is a generic purpose open-source Java library bundled with few lightweight frameworks and components: bean manipulation tool, Db for easier database access, Madvoc for web works, Proxetta for building proxies, JDateTime for elegant time handling, Petite as a container. Special attention is... Platforms: *nix

DORM4J (Dynamic Object-Relational Mapping for Java) is an O/R mapping library for Java. DORM4J library uses annotations in JDK 1.5 and dynamic features of the Java language to implement O/R mapping functions without additional XML config files. The development of DORM4J was inspired from the... Platforms: *nix

TECOAS project is an application to interactively browse and discuss a document. It is intended to assist with the co-authoring of papers with remote partners, but is also adapted to small seminars and online discussions. Its main functions are shared browsing of a document, the sharing of... Platforms: *nix

MassSpec::ViewSpectrum is a Perl extension for viewing a mass spectrum. SYNOPSIS use MassSpec::ViewSpectrum; open PNG, ">mygraphic.png" or die "Unable to open output filen"; binmode PNG; my @masses = (1036.4,1133,1437,1480,1502); my @intensities = (0.1,0.15,0.05,0.10,0.2); my... Platforms: *nix

pBeans project is a Object/Relational (O/R) database mapping layer. It is designed to be simple to use and automated. The idea is that you save time and effort by simply focusing on writing Java classes, and not worrying about maintenance of matching SQL scripts, schema evolution, XML based... Platforms: *nix

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;... Platforms: *nix

Bio::DB::GFF::Feature is a relative segment identified by a feature type. Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and... Platforms: *nix

Itadaki is a Japanese language toolset integrated with OpenOffice.org, providing tools intended for students and translators of Japanese. Its features include the automatic addition of furigana (reading annotations) to Japanese text with a high degree of accuracy, and a fast built-in... Platforms: *nix

Panda is a PDF generation API written in C. The Panda PDF Generator is intended to make PDFs on the fly for the Web, but may be used to generate any PDF document you want. Whats New in This Release: - As you may already be aware, the most important change in 0.5.4 is that the library is now... Platforms: *nix

Waffle is a Java web framework that makes the process of developing Java based web applications easier. Waffle Web framework was built to support enterprise level web-based business applications. Waffle is different than the multitude of web frameworks that exist today. - it does NOT have any... Platforms: *nix

Simple is an XML serialization framework for Java. Simple XML Framework goal is to provide an XML framework that enables rapid development of XML configuration and communication systems. This framework aids the development of XML systems with minimal effort and reduced errors. The framework... Platforms: *nix

Access Modifier Eclipse Plug-in allows the user to change the visibility (public, protected, default, private) and other modifiers (final, static, synchronized) of Java classes, interfaces, methods and fields in the workbenchs Outline, Members and Package Explorer views. The plug-in lets you... Platforms: *nix