Symbol substitution is one of the most important and useful tools in FELIX. Symbols are used in much the same way as variables in algebra; you can define processing algorithms that incorporate a symbol, and later you can decide on a value for the symbol. You can also store important numbers in symbols so that they may be quickly recalled later.
FELIX symbols are text strings that are evaluated at command execution time. Symbol names may be up to eight characters long and may contain any alphanumeric character. Any single symbol value can contain up to 128 characters.
To display the current symbol definitions and their values, use the list command (lis). The lis command makes use of the wild card character (*). For example:
shows values for only those symbols beginning with the letter h. The result is displayed in the FELIX text-prompt (or parent) window. The output from the above example might look like:
1 hafwid 2
2 hardx0 0
3 hardxs 0
4 hardy0 0
5 hardys 0
6 hardmo 21
7 hilim1 0
8 .... ....
9 harddv temp.plt
To delete or purge one or more of the user symbols, uses the pur command. This command also makes use of the wildcard character (*). For example:
deletes the user symbol count, and:
deletes all user symbols that begin with the letters "loop".
An important subset of the symbols used by FELIX are the reserved symbols. FELIX uses several reserved symbols to hold information about the internal structure of the program and data. Some reserved symbols define the current graphical state of the program, and others remember the current datafile names and display features. By referring to the proper reserved symbols, your macros can find out such things as whether a matrix is open, how large it is, the last contour level drawn, and whether the last macro command was executed successfully.
Reserved symbols generally fall into one of two classes: those that affect a subsequent command, and those that are updated as a result of a command's execution.
An example of reserved symbols that define the graphical state of the program are those symbols that are related to the contour plot command (cp). For each contour plot, certain reserved symbols define how the contour plot appears. These reserved symbols include those that define the contour level (level), the number of levels (nlevel), the contour level mode (clmode). Whenever the contour plot command is executed, FELIX looks at the current values of specific reserved symbols to determine what should be plotted.
Similarly, when you try to read a 1D datafile with the re or rn command, FELIX looks at the values of the symbols datfil and datpfx to determine the current datafile's name and the current data directory.
The values of the reserved symbols described above are usually set within control panels, but they may also be defined with the def command (see below).
The second class of reserved symbol is exemplified by the datsiz symbol. This symbol contains the current data size as a number of points.
Although you can change the value of datsiz using control panels or the def command (see below), the symbol's value is automatically updated to the current data size after reading a datafile or loading a 1D vector from a matrix. Likewise, when FELIX reads a 1D datafile, the reserved symbol datype is changed automatically to reflect the appropriate datatype, whether it is real or complex.
Other reserved symbols of this class include d1size (the size of the current matrix in the D1 dimension) and matfil (the name of the current matrix). These are changed when you open a matrix.
A complete list and definitions of the reserved symbols are given in Appendix B., Symbol reference. In addition, each command in Appendix A., Command reference describes the reserved symbols that affect that command and those symbols that are updated by execution of the command.
You may also define user symbols. In general, user symbols are employed to save specific values so that they may be recalled later. In addition, user symbols are applied to remember the current state of the menu interface. For example, when a toggle or switch value is set, user symbols are included to remember that state or value.
FELIX includes several ways to define symbols and their values.
One method to define symbols and their value is to use the define symbol command (def). For example, to set the value of the symbol filnam to the string "test", enter:
def filnam test
This command is used throughout FELIX macros, especially in the macro routines used for data processing. The def command may also be used to define reserved symbols such as level, which defines the lowest plot level for subsequent 2D plots.
The cdf command (conditional define) lets a macro define a symbol only when that symbol does not yet exist. This gives greater flexibility when writing macros, because you can make sure a symbol exists and has a valid value without changing its previously defined value. Thus, you can make a macro that is executed many times, yet only the needed symbols initialize the first time through, without any special effort.
Another way to define symbols is the eva command. It evaluates arithmetic expressions, mathematical functions, and database functions, and stores the resulting value in a symbol. More information on expressions and functions appears later in this chapter.
Many FELIX commands accept a symbol name as the last parameter on their command line and define that symbol's value to reflect the answer or status of that command's result. For example, the command:
xpk who &pksent -1 whoitm
returns the item number of the cross peak that the user selected with the crosshair cursor. The symbol whoitm gets defined to the value of a cross-peak item number. If no cross peak was selected, whoitm gets the value zero.
Another example shows how to convert a data position in points into ppm:
ppm 0 0 512.0 ppmval
This command calculates the ppm position for datapoint 512 in the current 1D workspace and defines the symbol ppmval as that value.
A third example shows how to extract the reference information for one dimension of a matrix using the rmx command:
rmx -2 rfreq rwid raxis rpnt rval rtext
This command statement extracts the reference information for D2 from the current matrix. It defines six symbols with values corresponding to spectrometer frequency, spectrum width, etc.
The most common mechanism for defining symbol values in FELIX is from within its control panels. These graphical user interface (GUI) components prompt you for symbol values by using text explanations, switches, toggles, buttons, and scrolling list boxes. FELIX presents all the available choices in a format that simplifies making a selection, while minimizing the possibility of allowing invalid input. Almost every element in a control panel defines a symbol to reflect its state or contents. A more detailed description of defining symbols using control panels is found in Chapter 5., Menus and control panels.
Symbol substitution is one of the most important and useful tools within FELIX. To access and use the value of a symbol, you must precede the symbol name with an ampersand (&). Whenever FELIX encounters an ampersand in a command line, it attempts to perform symbol substitution on the text string that follows the ampersand. For example, if the symbol filnam currently has the value "test", the command line:
is interpreted as:
before it is executed. In this example, FELIX attempts to read a datafile named test.dat. The symbol filnam has been replaced by the text string "test" in the macro.
You can use the value of the reserved symbol datsiz in a command, as follows:
sb &datsiz 0
which applies a zero-degree shifted sinebell function over the number of points specified by the symbol datsiz.
Some applications require more complex symbol substitutions. The following examples illustrate a few of the many possibilities.
First, a symbol can be concatenated with normal text or numbers. For example:
reads a file named test1.dat if the value for the symbol number is equal to the number one. In a macro, the symbol number could be changed at strategic points, allowing you to read a series of datafiles with a single read statement containing a symbol variable. Such use of symbols may be necessary when transforming 3D data, because the initial data in these large matrices may be contained within more than one serial file.
Second, two symbols can be concatenated by placing the symbols adjacent to each other. If the symbol filnam had a value "abc" and the symbol number had a value "001", the command statement:
would be equivalent to ty abc001. In this manner, several symbolic components can be combined into a single string.
Finally, symbol substitution is recursive, as illustrated by the following example. If the symbol filnam had a value of "abc" and the symbol abc had a value of "hello", the following command statement:
would produce "hello". In this case, the sequence of substitution is:
1. Find the string for the symbol &filnam and replace it with its value "abc", thereby leaving "&abc" on the command line
2. Since an ampersand remains on the command line, do another symbol substitution.
In the example, the ""&abc" string is replaced by the value of the symbol abc, namely "hello".
It is also possible to delay symbol substitution until later, by adding an exclamation point (!) to the beginning of a symbol name. For example, the command statement:
def test !&filnam
defines the symbol test to literally be &filnam. The most common use of this symbol-definition method is in combination with the macro put command for building macros from the FELIX command language.
FELIX supports two classes of user symbols: local and global.
Local (user-defined) symbols are used only in the macro in which they are defined and are automatically purged when that macro is finished. In addition, multiple macros can use the same (local) symbol names, without any risk of changing another macro's local symbols.
All local symbols begin with an underscore, "_". This is the only difference between local and global symbols.
Defining and using local symbols is the same as for global symbols. The following example revises the simple macro test1.mac to use a local symbol instead:
2 for _count 1 5
3 ty Count = &_count
5 ex &return
As soon as this macro is finished, the symbol _count becomes undefined.
FELIX supports global user symbols in addition to local reserved symbols and local user symbols (see above). This feature greatly enhances the flexibility of working with multiple connected frame layouts.
By default, the value of a symbol is local to the graphics frame where it is defined. This allows a frame to act independently, without affecting the content or behavior of other frames. To share symbols between frames, it is necessary to explicitly export or import the symbol values to or from another frame.
While this notion of local symbols is good for working with multiple independent frames, it can cause significant problems when working with multiple connected frames all operating on a common dataset.
Global user symbols address this problem. All global user symbols are always known to all frames, and defining the value in any one frame defines that symbol globally in all frames.
To identify a symbol as global rather than local, begin the symbol name with the character string "g_". All symbol names beginning with "g_" are global, and all other symbols are local. There are no global reserved symbols, only global user symbols. All the rules for symbol substitution are exactly the same for global symbols, and a global symbol may be used anywhere a local symbol may be used.
FELIX allows arithmetic expressions to replace any numeric parameter. An arithmetic expression may contain the arithmetic operators plus (+), minus (-), multiply (*), divide (/), and power (^), with left and right parentheses being used to define the order of operations. The syntax for expressions within FELIX is exactly the same as in FORTRAN or BASIC. FELIX also supports the unary (-) operator, which negates the variable, symbol, or expression immediately to its right.
When used for numeric parameters, arithmetic expressions must be enclosed in parentheses without any space between the numbers, operators, and parentheses. This allows FELIX to evaluate the expression before passing the parameter value on; otherwise, the parameter would contain non-numeric characters and be uninterpretable.
Sometimes you may want to force evaluation of an arithmetic expression: the eva (evaluate) command is useful for doing this. For example:
eva temp (4*3+1)
forces the value of the symbol temp to be 13.
Expressions are even more powerful when they are combined with user-defined symbols. For example:
eva temp (4*3+&shift)
determines a number for the symbol temp, whose value depends on the current value of the symbol shift. The ability to evaluate arithmetic expressions in combination with symbols provides a very powerful method of data manipulation.
Expressions are most often used within FELIX for determining data characteristics. For example, to determine the number of points currently displayed on the screen, the following expression can be used:
eva scnsiz (&last-&first+1)
The value for the symbol scnsiz is the difference between the symbols last (the last-displayed datapoint) and first (the first-displayed datapoint). After the above expression, your macro would usually contain a sequence of commands using the value of scnsiz.
A slightly more complex expression finds the value of the midpoint displayed on the screen:
eva midpt ((&first+&last)/2)
Another use for expression evaluation is to manipulate values found in the database. For instance, specific elements can be loaded into symbols, with the resulting symbols being evaluated via expressions.
A simple example is to find the separation between two resonances found in a 1D spectrum. First, load the first two resonance positions into the symbols cen1 and cen2 using the standard database-access methodology:
dba element load pic:1d_picks.1.cenpnt cen1
dba element load pic:1d_picks.2.cenpnt cen2
Next, evaluate their separation, using symbol evaluation:
eva separ (&cen2-&cen1)
To view the resulting symbol for the separation, use the lis command:
Or within a macro, use the ty command to print comments along with symbol values to the parent window:
ty Separation between item 1 and 2 is: &separ
In a macro, you may also check to ensure that the resultant value is a positive number, and if it's not, take its absolute magnitude:
if &separ lt 0 then
eva separ (abs(&separ))
A more complicated example of expression evaluation makes use of an exponential or power evaluation. The example shown below uses NOESY cross-peak volumes to measure distance constraints. This example is used for measuring proton-proton distances from an NOE volume at a single mixing time by using the sixth-power dependence ratio as it relates to a fixed distance (dissum) and volume (volsum):
dba element load &volent.10.vol1 volum1
eva dist ((((&dissum)^6.0)*&volsum/&voluml)^(1.0/6.0))
The distance may be further modified to reflect upper and lower bounds:
eva lower (&dist-(&dist*0.1))
eva upper (&dist+(&dist*0.1))
ty Lower bound is: &lower
ty Upper bound is: &upper
FELIX supports both integer and floating-point arithmetic expressions. Several algorithms require integer division.
When any of the operands in the expression has a decimal point, then the expression is evaluated as real and the result is real. If no decimal points are present in the operands, then the expression is evaluated as integer and the result is integer. Thus there is a difference between the following two values:
eva int (17/2)
eva real (17.0/2.0)
The value of int is 8, and the value of real is 8.5.
FELIX allows some arithmetic functions to be evaluated and saved as symbols. These mathematical functions can appear anywhere that simple expressions may be used. The arithmetic functions currently supported are:
abs - absolute value
acos - arccosine
asin - arcsine
atan - arctangent
cos - cosine
exp - exponential
float - turn integer to real
int - truncate real to integer
log - natural logarithm
log10 - logarithm base 10
nint - round real to nearest integer
ran - random number generator
sqrt - square root
sin - sine
tan - tangent
The trigonometric functions require all angles to be in degrees. These functions are combined using the standard evaluation nomenclature to calculate resultant values.
The ran function returns a random value between zero and the value of its argument. For example, ran(1.0) returns a value between zero and one, and ran(500.0) returns a value between zero and five hundred. It may be used in any arithmetic expressions and in the eva command:
eva value (ran(1.0)
Working with the example above for finding the absolute value of a negative peak separation, we can use the following sequence of commands in a macro:
if &separ lt 0 then
eva separ (abs(&separ))
In other words, the above "if/then/else" sequence could be replaced by the absolute value calculation, since only positive values are acceptable in this instance.
Another example is used to ensure that each dimension of a new matrix has a size of root 2:
2 eva n2size (log(&d2size) / log (2.0))
3 eva n2int (nint(&n2size))
4 if &n2size eq &n2int onward
Again, examples such as these may be added to your own macros.
FELIX supports one other class of functions that evaluate the state of database components.
These functions are only valid in the eva command and cannot be combined on the same command line with other functions or expressions. The form of all database functions is db$nnnn(arg), where nnnn is the function name and arg is the argument passed to the function. More information can be found in Chapter 6., Database and tables.
eva open db$open()
determines whether a database is open. The symbol open is set to zero (not open) or one (open).
eva exist db$entity(xpk:peaks)
determines if an entity with the name xpk:peaks exists in the current database. The symbol exist is set to zero if no entity with that name exists and to non-zero if the entity does exist.
The complete list of database functions is shown below: