source: plugins/base1/se.lu.thep.wenni/trunk/ChangeLog @ 844

$Id: ChangeLog? 844 2008-12-01 16:24:41Z jari $

Copyright (C) 2005, 2006 Jari Häkkinen, Peter Johansson
Copyright (C) 2007 Peter Johansson
Copyright (C) 2008 Jari Häkkinen
This file is part of WeNNI,
http://baseplugins.thep.lu.se/wiki/se.lu.thep.WeNNI
WeNNI is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your
option) any later version.
WeNNI is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
You should have received a copy of the GNU General Public License
along with WeNNI. If not, see <http://www.gnu.org/licenses/>.

version 0.7:

• Added some clarifying details on implementation issues in README.
• Updated plug-in description file, among other changes a reference to the BMC Bioinformatics paper describing WeNNI was added.
• Changed BASE plugin to adhere to the common BASE treatment of A values (log10[int1*int2]) where well defined A values before imputations are kept after transformation (more information in README).
• Included new versions of the matrix and vector class (with support) from theplu C++ tools. NaN entries are treated more gracefully now.
• Added copyright statement to files.
• Added BASE 2 wrapper classes for use of WeNNI in BASE 2 without having to go through the use of BASEfile.
• Three different building modes, stand-alone, base1, and base2.
• Changed default install paths.
• Changed license to GPL3.
• Changed project site URL.
• Added more checks on required build tools.
• Using external abstract class when building Java wrapper.
• Automatic download of required BASE components.

version 0.6 (revision 92):

• Minor changes, basically a maintenence version.
• Added --version option to 'nni' and 'NNIFileConverter'.
• Changed most tests to do numerical tests instead of 'diff's, BASE files are still checked with 'diff'.
• Improved INSTALL document.

version 0.5 (revision 76):

• Added 'make check' that runs test programs.
• Moved wenni source code to BASE plug-ins development site.
• Major changes in the implementation.
• 'nni' accepts SNR values as input as a complement to weights input. Do 'nni -h' for a short description of available command line parameters.
• Non-binary files can be supplied to 'nni' when kNNI is run. A weight cutoff is set with a command line parameter. Do 'nni -h' for a short description of available command line parameters.

version 0.4:

• Added support for imputation starting from ch1 and ch2 intensities (i.e. background subtracted user defined mean/median/... intensities).
• Improved README; Added example usage of the wenni.pl script aswell as examples of using 'raw' and 'derived' type of data.
• Added sample BASE file result file.
• Added WeNNIParams section to input BASE file, used by wenni.pl.

version 0.3:

• Changed test data set to a smaller data set.
• Fixed BASEfile parameter parsing bug in wenni.pl.
• Made M=log2 [I1/I2] and A=log10 sqrt[I1*I2] to behave more coherrently in wenni.pl. Now, A is recalculated with the original value for I2. This will change in future releases such that the orignal A is kept. Imputation of M will change both I1 and I2 in the future, instead of just I1 as it is today.

version 0.2:

• Improved BASE plug-in installation documentation.
• Added a plug-in definition file.

version 0.1:

• First public release of WeNNI