Azara 2.0 changes from Azara 1.0
0. Notable changes from 22 May 1995 release to 23 Nov 1996 release
0.01 process, combine : fixed reflate bug
The output 'par' structure did not have the reflation (really, deflation) level initialised to zero. On some computers this leads to the key-word 'deflate' or 'reflate' appearing in the output 'par' file.
0.02 plot2, plot1, combine, unblock : checked for deflation
These programs cannot use deflated input files, but this was not checked for.
0.03 plot2, plot1 : cleaned up X code
There were lots of X compiler warnings due to loose function prototyping. Also re-organised some widget routines.0.04 plot1 : fixed polynomial baseline initialisation bug
The initialisation for 'base_poly' had set up the actual processing to use the function for 'base_poly2' by mistake.
0.05 process, plot1 : fixed baseline fitting bug
The baseline fitting was being done even if enough baseline points had not been found.
0.06 plot1 : fixed list initialisation bug
The data object modules were not having the number of data sets being initialised, hence no data sets were being shown. Bug probably introduced in 0.03 above.
0.07 plot2 : fixed list initialisation bug
The position list in the region module was not having the number of saved positions being initialised, hence no positions were being shown. Bug probably introduced in 0.03 above.
0.08 all : tried to make code usable for large (> 1 Gb) data sets
The code was not designed to work on data sets of more than 1 Gb (or so). By changing 'int' to 'long int' in a few appropriate places the code should now work on larger data sets. This has not been tested (not enough disk space!). (PS: there is no difference between 'int' and 'long int'.)
0.09 plot2 : fixed 1D display clipping bug
The code did not clip the axes in the 1D display drawing. This is only relevant to the Postscipt output (the HPGL code does not implement clipping).
0.10 process, plot1 : added new baseline commands
There are three new commands, 'base_points', which allows the user to define the baseline used in the fitting, and 'base_subtract' and 'base_subtract2', which allow the user to subtract an explicitly defined baseline.
0.11 process, plot1 : added normalised Fourier transform commands
The existing Fourier transform commands were not normalised. There are now corresponding normalised (or approximately normalised) routines. For every command *ft there is now a command *ftn.
0.12 plot2 : added baseline correction
As well as phasing, baseline correction of the selected (1-dimensional) slice is now allowed.
0.13 plot2, plot1 : modified objects modules
The default property module and data set property module have been modified so that multiple (instead of single) selections can be made, in order to make the selection process easier.
0.14 plot2 : display modules made iconifiable
The 1D and 2D display modules have been modified so that they are iconifiable separately from the main application. The tracking display module has not been modified, and is not separately iconifiable under the MWM window manager.
0.15 plot1 : display module made iconifiable
The display module has been modified so that it is iconifiable separately from the main application.
0.16 process : added interlace command
A new (effectively multi-dimensional) command has been added which allows the unwrapping of interlaced experiments. The syntax is
interlace <dim>
0.17 plot2, plot1 : allow exit when application iconified
The application could not exit when it was iconfied (at least with the MWM window manager) because the exit question dialogue box would not pop up.
0.18 plot1 : added referencing
Referencing has been added by assuming that the correct reference is that given by the most recent read_par command. Alternatively, an explicit referencing can be set with the command
set_reference <sw> <sf> <refppm> <refpt>
0.19 plot2, plot1 : time and date in output
The time and date are now printed in the lower righthand corner of Postscript and HPGL output.
0.20 plot2 : fixed display destruction bug
The iconifiable displays are destroyed when the display is closed/quit. The code that destroyed these widgets forgot to unregister them from the list of all widgets in the application. This list is used for cursor manipulation, and when the cursor was changed in the timer popup the program tried to access a non-existant widget.
0.21 plot2, plot1 : allow different ticks in x and y directions
There is now allowed a different number of (minor and major) tick marks in the x and y directions. If only one value is specified then it is assumed that the number of tick marks is the same.
0.22 all : work around fseek bug
The system routine fseek (which allows a jump in a disk file) does not seem to work for a negative offset of more than 256*1024*1024 bytes. This has been worked around by breaking the fseek into smaller bits.
0.23 slides : new program
This new program allows the creation of slides using a selection of Postscript files.
0.24 plot2 : script files
Script files are now allowed, which allow, for example, loading up of multiple planes upon start-up.
0.25 plot2_nog : new program
This is a non-graphical (i.e. no Motif, no X) version of plot2, which allows output (e.g. Postscript) to be created just using a script file.
0.26 process : real maxent
Maximum entropy now works on real data as well as complex data.
0.27 process, plot1 : added new convolution commands
In addition to the existing function 'convolve' (now considered obsolote) there are now the commands 'conv_sine' (which is the same as 'convolve' and uses a sine function), 'conv_box' (which uses a box function), 'conv_triangle' (which uses a triangle function), 'conv_gaussian' (which uses a gaussian function) and 'conv_file' (which uses a function specified in a file).
0.28 process, plot1 : added new weight command
There is now a command 'weight_file', which uses a weighting function as specified in a file.
0.29 plot2 : thickness allowed to be an array
The thickness in the extract module is now allowed to be an array instead of a scalar (but it can still be a scalar if desired). This means that the number of planes extracted can be different in the dimensions orthogonal to the plane.
0.30 process, plot1 : modified baseline routine
The routine that finds the baseline points now checks that the first and last baseline points are far enough apart (specifically, at least 0.5 of the number of points).
0.31 process, plot1 : added inverse cosine weighting function
There is now a command 'inv_cosine', which has as 1 / cosine as a weighting function. The syntax is
inv_cosine <frequency> <spectral width>
0.32 all : changed low-level input/output code
The low-level input/output code has been placed in one module. This has been extended to read and write deflated, as well as normal, data. Most programs now allow deflated data as input.
0.33 plot2, plot1, slides : fixed EPS output bug
There were a couple of bugs in the EPS output comments which meant that some programs would not read the files.
0.34 contours : fixed input bug
The change in 0.32 introduced a bug in the initialisation of the input file if a subset of the spectrum was being contoured, in general (a counter was being updated which should not have been). Azara help: CHANGES-2.0-0 / W. Boucher / azara@bioc.cam.ac.uk