b64 is a very small and simple library that provides Base-64 encoding and decoding, according to RFC-1113, in C and C++.

The b64 project is released under the BSD license, which basically means its free for any use, but you cant claim its yours.

Whats New in This Release:

· The code was updated to be fully compatible with STLSoft 1.9.1 (the special version released on Extended STL, volume 1: CD).

shwild provides a platform-independent library for pattern matching.

shwild is a simple, platform-independent library that implements shell-compatible wildcard pattern matching. It is implemented in C/C++, expressing a C API with a C++ wrapper.

Building:

Makefiles for all the main supported compilers are included in the subdirectories of the build directory. For example, the makefile for Borland C/C++ v5.6 is in build/vc6. Since Borland is only supported on Windows, there is a single makefile called makefile.

For compilers that are supported on more than one platform, there are several makefiles located in the build sub-directory.

For example, for GNU C/C++ v3.4 (in /build/gcc34) both makefile.unix and makefile.win32 are provided. Most make tools require that you explicitly specify the makefile name (using -f) to use such makefiles, e.g.

$ make -f makefile.unix.

This will build the shwild library, and the C test programs. It will also attempt to build the C++ test programs. Since the C++ mapping relies on the STLSoft libraries, the makefile will look for the environment variable STLSOFT: it specifies -I%STLSOFT%/include (Windows) / -I$STLSOFT/include (UNIX) to the compiler.

Whats New in This Release:

· fixes to UNIX compilation
· STLSoft 1.9.1 beta 44 or later
· Open-RJ 1.6.1 or later (but only for Test programs)

MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico.

SYNOPSIS

use MassSpec::ViewSpectrum::RealVsHypPeptide;
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
binmode GRAPHIC;

my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
130.1,132.1,147.7,157.1,158.1,159.1,169.1,171.1,175.1,187.1,229.1,246.2,258.1,
266.0,327.2,328.2,345.2,415.2,426.2,432.2,531.2,559.3,623.4,639.3,643.3,644.4,
645.0,647.5,686.4,687.4,689.4);
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
7.7,11.9,9.8,10.1,7.3,10.5,131.0,9.4,50.3,22.7,44.7,16.8,30.4,18.2,53.1,25.5,
15.7,7.7,14.0,46.8,38.4,7.3,11.5,8.7,7.3,8.7,7.3,24.8,194.2);
my $peptide = "RTSVAR";

my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);

my $output = $vs->plot();
print GRAPHIC $output;
close GRAPHIC;

MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.

Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.

PyLUcene SHell (Plush) is an interactive shell to inspect a Lucene store.

Here are some key features of "PyLUcene SHell":

· View store information.
· View indexes definition.
· Search using the Lucene Query Parser Syntax.
· Sort result list.
· Browse by document number.
· Top term occurences for a field, matching a regex.
· Support PyLucene 1.9.1 and 2.0.0.
· Interactive shell emacs like command history and editing features.
· Command line tool and thus scriptable.
· Easy installation, no java required.
· Can load NXLucene analyzers.
· Plush is free software distributed under the GNU GPL.
· Plush is written in python and can be easily customized.

Installation:

You need python 2.4 (2.3 not tested) with the readline support (--enable-readline)

Plush requires PyLucene which is easy to install using binaries.

Here is an example on how to install the latest PyLucene 2.0.0-3 (Lucene 2.0.0-453447) on ubuntu:

cd /tmp
wget http://downloads.osafoundation.org/PyLucene/linux/ubuntu/PyLucene-2.0.0-3.tar.gz
tar xzvf PyLucene-2.0.0-3.tar.gz
cd PyLucene-2.0.0-3/
sudo cp -r python/* /usr/lib/python2.4/site-packages/
sudo cp -r gcj/* /usr/local/lib

Visit the PyLucene site for other pre-built binaries.
Plush is a pure python package that you can get from the Python Cheese Shop

tar xzvf plush-X.Y.Z.tar.gz
cd plush

Install plush either with:

sudo make install

or using the pythonic way:

python setup.py build
sudo python setup.py install

Thats all no .jar nor java required.