# ##############################################################################
# NLStradamus FOR DISTRIBUTION
# Copyright Alex Nguyen Ba 2008
#
# LICENCE 
#
#    This program 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.

#    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.

# ##############################################################################

CHANGE LOG

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# Version 1.7 2011/04/14 
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- Thanks to Peter Cock from The James Hutton Institute for pointint out the need for the fixes in this patch.
- Now handles zero-length sequences by skipping them.
- Includes a tab delimited flag (-tab) with header and no summary. 
- Quiet mode is now on by default. Tab delimited flag forces quiet mode.
- Order of sequences now retained even with -cpu threading.
- C++ distribution now included. Compile using : g++ NLStradamus.cpp -o NLStradamus.exe -O3
- C++ distribution is not heavily tested and is still in beta. It is still recommended over the perl script.
- Posterior probability of the segment is now displayed instead of the old >threshold


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# Version 1.6 2011/03/18 
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- Fixed CPU flag to actually changing the number of CPU used.

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# Version 1.5 2010/11/04 
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- Thanks to Ron Gejman from Tarakhovsky Lab at the Rockefeller University for pointing out that sequences with amino acids other than the standard 20 caused the predictor to crash.
- NLStradamus now considers the X symbol as any amino acid - B as D or N - Z as E or Q. 
- The model for these non-standard amino acids is the sum of their possibilities. Therefore, the probability of "X" in both the BG and NLS state is 1.
- Other symbols are now completely ignored.
- Added a newline character at the end of the output.
- The default CPU count for multithreading is now set to 1 as opposed to 25. Note that setting the value higher than the CPU count will not cause any weird behavior but may be slower than expected.

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# Version 1.4 2010/10/29 Change log entry date.
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- Allows multithreading with -cpu flag.

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# Version 1.2 2008/11/11
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- Fixed a memory leak. NLStradamus should run much faster now.

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# Version 1.1 2008/10/17
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- Fixed an issue with the Viterbi result display for the four state model.

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# Version 1.0 2008/10/13
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- First release of NLStradamus