Azara 2.8 changes

0. Notable changes from 30 Oct 2002 release to 07 Apr 2010 release

0.01 plot2 : fixed fitting bug

	A couple of bugs in the numerical routines used to do the
	fitting were fixed.

0.02 plot2 : added error estimates for fitting

	If 'sigmas' (giving an estimate of the data noise) in
	addition to 'params' is specified in the par file then
	an estimate of the errors in the fitting parameters is
	given (except in the log linear case).

0.03 plot2 : added output ticks options

	In hardcopy output (PS, EPS and HPGL), ticks used to
	appear always on the inside of the box and always on
	all four borders.  It is now possible to have the ticks
	appear on the outside and also not on all four borders.

0.04 combine : added divide function

	It is now possible to divide two spectra.

0.05 project: fixed boundary bug

	Data files with number of points in the non-projected
	dimensions not a multiple of the block size were being
	summed including the padded points in the last block.
	(In general these contain junk.)

0.06 process: added mask_pm and mask_mp

	Added mask_pm and mask_mp which do what mask_ppmm does
	more generally, so with an arbitrary period.

0.07 contours: fixed large output bug

	Fixed bug which meant that if had too many vertices
	(could happen with as few as 2048 vertices) in one
	contour then program giving incorrect output and could
	even crash.

0.08 process: fixed sigmas bug in par file

	The (optional) sigmas in the input par file were not
	being copied correctly to the output par file.

0.09 plot2: fixed log linear fitting bug

	With log linear fitting routine does not use points
	where y is negative but in those cases it was using
	incorrect x values.

0.10 utility: fixed Felix conversion bug

	The programs mat2par and par2mat were swapping the
	refpt and refppm, and the latter in Felix is in Hz,
	not ppm, so needed to be scaled by sf.

0.11 plot1: fixed gaussian_sw bug

	The option when sw was specified to be 0 was not
	working.  This was supposed to pick up sw from
	the par file but if more than one par file was
	used in the script it was failing.

0.12 all: fixed makefile omission

	Added in (MOTIF_INCLUDE_DIR) into the makefile
	in global for compilation.
	
0.13 connect: added in new residues option

	The residues key can now have extra arguments specifying
	atom names required for a match.  If the last character
	of the name is a * then anything that matches the earlier
	characters is a match.

0.14 process: fixed truncate bug

	The type for the length argument of truncate (used in
	the function truncate_file in files.c) should have been
	off_t, not long.

0.15 contours: added endianess options

	The endianess of the output contour file can now be set
	in the script using either big_endian or little_endian.

0.16 new: added new utility programs

	Added ucsf2azara, azara2ucsf and azara2xeasy.

0.17 process: 2D and 3D non-linear sampling

	Added ability to specify 2D and 3D non-linear sampling
	in maxent routines, using sample2 and sample3 commands.

0.18 new: added Python module for accessing data

	Added Python module in DataRows directory which allows
	pythonic access of blocked data files.

0.19 remove: removed some programs

	Removed components, slides, viewer.

Azara help: CHANGES-2.8-0 / W. Boucher / azara@bioc.cam.ac.uk