Throughout this text, a menu-item will be denoted <item>. A cascaded menu-item by <item>-<sub-item>. A button will be denoted by [button-item]. {entry} denotes an entry field for a specific parameter; Italics denote a value entered by the user in an entry field, or the value of an option such as a radio-button or a check-button.
If samples has been properly installed it can be started at the command line by typing:
samples
The samples interface-window will pop up (see Fig. 1).
Fig. 1: The samples window.
On top is a menu-bar with <File> and <Tools> . There are also several shortcut [buttons] on the righthand side of the menubar. Below the menu-bar is a general window area, that display information about the current file and status and with entry fields for a number of parameters. Below that, a history tab is located. The tab can be closed or opened by clicking on the open/close buttons on the right side. Finally, at the bottom a help bar is present. Moving the mouse over specific items in the samples window, displays a short help text in this bar.
Samples uses text with red fonts for important information relating to the current status. Text with steel-blue fonts is used for giving information, text with green fonts indicates 'action' (usually on buttons). All other text is black. Entry fields can be activated by moving over the appropriate box and clicking the mouse. Sometimes, entry fields contain a cascade pulldown with options to choose from.
A new start can be made by choosing <File>-<New> or by using the [New-File] icon-button in the menu bar.
The program can be quit by choosing <File>-<Quit> or by using the [Quit] icon-button in the menu bar.
Settings can be saved by selecting <File>-<Save>
or by using the [Save-File] icon-button in the menu bar. If the data
were not saved before, you will be prompted for a file name. The suggested
default name is {project}-{sample_id}.
If you want to save an existing file under a different name, choose <File>-<Save
as>.
Data can be restored from file by selecting <File>-<Open>
and clicking the appropriate file or by using the [Open-File] icon-button
in the menu bar. The samples program can also be started by typing the
samples command with the -file fileName argument. FileName will
then be immediatedly loaded, as if selected by <File>-<Open>.
The history tab can be used to enter a logging of the sample and actions. The history can be cleared with <Tools>-<History>-<Clear> . To add a time stamp use <Tools>-<History>-<Append timestamp>.
The <Tools> menu contains miscaleneous menu commands to view directories, view the source code, etc.
The expression editor can be used to calculate any arbitrary expression.
Enter the expression and press return, the result will show next to the entry
field.
Samples is designed to work together with two additional programs (i.e.
procTool and nmrManage) to achieve some simple form of project management.
ProcTool is an nmrPipe interface tool, designed for easy spectral processing
of NMR data. Using predefined and logically ordered fields, parameters can
be entered, modified and nmrPipe conversion and processing scripts can
be generated and executed. Settings, processing scripts, and a history
are stored in a single file, ready for easy reproduction at any stage. The
procTool program can be called from the samples program by choosing button
[Tools]-<Samples> (on the far left in the menubar). Look
here for more details on the procTool program.
The nmrManage program is designed to group sets of related procTool files
and sample files in one place in socalled projects, without actually moving
or copying data. Thus, it is an indirection mechanism (pointer mechamism).
The project name can be selected in the {Project} parameter field.
At startup, samples scans the projects directory to generate a list of options.
You can, however, choose any abitrary name. Using the <File>-<Add
to project> command, the current samples file can be added to the
project. Note that this command will open the nmrManage program.
The nmrManage program can also be called from the samples program by choosing
button [Tools]-<nmrManage> (on the far left in the menubar).
Look here for more details on the nmrManage
program.
There is an internal help facility: button [Help]-<Commands> (on the far right in the menubar) gives an overview of the commands and the parameters, <Help>-<About> shows the about text, <Help>-<Version> shows the version history, and <Help>-<Tutorial> shows the tutorial through your web-browser.
Version 1.5.1: No bugs reported. Undoubtly this will change!
This program and its related software is provided "as is". The author makes no warranties, either express or implied, as to any matter whatsoever with respect to the software. In particular, any and all warranties of merchantability and fitness for any particular purpose are expressly excluded. In no event will the KUN, the Laboratory of Biophysical Chemistry, the NSRIM Center, or the author be liable for any loss of profits, any incidental, special, exemplary, or consequential damages of any nature whatsoever (including without limitation, loss of use or other commercial or research loss) arising out of or relating to the use or performance of the software.
This program may not be distributed without prior permission.
(C) Geerten W. Vuister 1999-2003
Laboratory of Biophysical Chemistry NSRIM Center, University of Nijmegen, The Netherlands Email: vuister@nmr.kun.nl http://www.nmr.kun.nl
Last update: 14 Oct 2003