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JEPRS (TM)
User's Guide
JEPRS version 1.10
March, 1989
by Louis M. Miranda
6033 East Northwest Highway, #1106
Dallas, TX 75231-7463 USA
JEPRS is a trademark of Louis M. Miranda;
Copyright 1985-1989 Louis M. Miranda.
Disclaimer of Warranty
This software and documentation are sold "as is" and without
warranties as to performance of merchantability or any other
warranties expressed or implied. Because of the various hardware
and software environments into which this program may be put, no
warranty of fitness for a particular purpose is offered.
Good data processing procedure dictates that any program be
thoroughly tested with non-critical data before relying on it. The
user must assume the entire risk of using this program. Any liability
of the seller will be limited exclusively to product replacement or
refund of purchase price.
1. Introduction.
JEPRS (pronounced "Jeepers!") is a program that maintains a
database of references to articles published in scientific journals
and books. It allows you to add, update, list, search, and format
references in the format required for practically any journal. It is
made to run under PC/MS-DOS (version 2.0 or higher) on IBM PCs and
100% compatibles. JEPRS is distributed as "shareware"; this means
that you may make copies to give to others (at no charge) for test
purposes. If JEPRS is used, then the user is obligated to pay a
shareware fee to the author (me), just like any software you
purchase in a store. It is not public domain! Please see the Options
choice on the Main Menu for ordering information. Registration has
several advantages:
■ I only provide support (i.e., answers to questions) to users
who have registered. If you register, you may write to me and I will
respond as quickly as possible to your question. (If you haven't
registered, you have a much lower priority for answers.)
■ Free update! The next major update is sent free of charge to
registered users. Later updates may be purchased for a nominal fee
(probably $10). Major updates are planned about every six months,
but that is not set in stone.
■ Laser-Printed documentation. The Tutorial and User Guide are
sent to registered users as offset-printed versions of laser-printed
originals.
■ Update Notices. Registered users are always kept up-to-date
with reports of minor updates (to fix bugs or add small numbers of
features). In addition, I anticipate these notices will also include
useful tips for getting the most out of JEPRS.
Before continuing with this documentation, you should have read
the file called ReadMe.JPR and the Tutorial (JPRTutor.JPR). These two
files contain basic information for installing JEPRS and starting the
program up for the first time. The User Guide you are reading now is
meant to provide more in-depth information and is not really meant to
be read from beginning to end in one sitting. Refer to this document
only when you have specific questions or if you want more detailed
information on how JEPRS works.
Creating Your Own Database
When you used the tutorial, JEPRS automatically used the sample
Ref1.JPR and Ref1.JPK database files. Now you probably want to
create your own database. Since JEPRS automatically uses files
named Ref1.JPR and Ref1.JPK, it is easiest to have your database
files use these names. Therefore, before starting up JEPRS the next
time, use the MS-DOS Rename command to rename the sample database
files as follows:
C:\JEPRS> Ren Ref1.JP* Sample.JP*
The command above will rename the sample files to Sample.JPR and
Sample.JPK. If you then start JEPRS as you normally do, that is:
C:\JEPRS> JEPRS
you will get an error message saying that it can't find the database
files. You have the option of quitting the program or creating the
files. Press F6 to create a new database. JEPRS will then create
two new files, called Ref1.JPR and Ref1.JPK, that will be your
database. These files will initially contain no reference citations;
however, they will both be 100 bytes in size because JEPRS keeps
some instructions in them regardless of how many references they
contain.
Of course, you have the option of calling your database files
anything you want: you're not limited to Ref1.JPR and Ref1.JPK. In
order to do this, though, you must edit the Format.JPR file. There is
a section where you can specify the names of the Reference File and
the Ref Key File. Just enter the names of your files there. In
addition, you can call the format file something other than Format.JPR.
See the next section to see how to specify its name on the command
line.
2. Starting JEPRS.
2.1. The Basics.
You start the program by simply entering the command "JEPRS" at
the DOS prompt, like this:
C:\JEPRS> JEPRS
If all goes well, the screen will momentarily clear, some introductory
messages will appear, and finally the Welcome Screen will appear
(which includes the copyright notice, and to whom the program was
provided). Type any key to continue to the Main Menu. If you are
starting JEPRS without a database (for example, when you are creating
a new one, as explained in the previous section), you will get an
error message stating that JEPRS can't find the database files; this
is normal. Just press F6 to create your own database, F4 to specify
a new name, or F10 to exit the program.
2.2. Advanced Features.
There is one command line option that you may use when starting
JEPRS. If for some reason you wish to use a different name for the
format file (in other words, you're not calling it Format.JPR or it's
not in the current directory), then you can specify its name on the
command line, like this:
C:\JEPRS> JEPRS FormLsr1.JPR
This tells JEPRS to use FormLsr1.JPR as the format file, which must
be in the current directory. If you wish, you may also specify the
directory it is in, if this is not the current one. For example, if you
keep FormLsr1.JPR in a directory called C:\PRINTER, then start JEPRS
like this:
C:\JEPRS> JEPRS C:\PRINTER\FormLsr1.JPR
This tells JEPRS not only the name of the file, but also in which
subdirectory it is located.
3. The Main Menu.
3.1. The Basics.
Once you start JEPRS, and you pass the Welcome Screen, you are
presented with the Main Menu from which you can enter any of JEPRS's
commands. The box on the left side of the screen contains the Main
Menu. Every command listed (Add, Update, List, Format, Search,
Options, Help, and Exit) can be invoked by at least two methods:
■ Use the up and down arrow keys to highlight the command you
want to use, then press Enter to start that command, or
■ Press the key corresponding to the first letter of the command's
name (for example, press H for Help, or O for Options).
Two of the commands have one additional way to invoke them; Help
and Exit can be performed by pressing the function key listed to the
right of the command name (that is, press F1 for Help or Esc for
Exit).
3.2. Advanced Features.
Notice the information on the right side of the screen labelled
"Current System Information." This provides some useful information
to you regarding the environment that JEPRS is working in. It also is
useful to me if you discover any problems with the program. If there
are any problems, it is very helpful to me if you copy down the
information here (or press <Shift><PrtScr> to print it on your printer)
and send it to me along with your problem. Each line is described
briefly here:
■ Version number and date released. For version 1.10, JEPRS was
released to the public in March 1989. Sometimes users don't have the
most current version of JEPRS and a bug you may have discovered may
already have been fixed in a newer release. If you discover a
problem, always let me know what version you are using.
■ MS-DOS version. This tells you which version of PC/-MS-DOS you
are using (e.g., 2.11 or 3.21) to run JEPRS. [My understanding is
that when you run the DOS Compatibility Box in the OS/2 operating
system, the version number will read "10.0"; but I don't have OS/2, so
I don't know for certain that this is true.]
■ Error/Warning Beep. This tells you whether the error beep is
turned on or off. You can change its setting on the Options Menu.
■ System Memory Available. This tells you how much extra space
JEPRS has available to it. The bigger your database, the smaller this
number. Note that this number remains constant no matter how much
memory you have installed in your computer. In future versions, I
may allow JEPRS to take advantage of whatever memory you have
available.
■ Total Computer Memory. This just informs you how much memory
you have installed in your computer. For reasons not evident to me,
some IBM computers display one kilobyte less than they actually have
(e.g., 639kb is displayed even if your computer really has 640kb
installed). JEPRS cannot detect `extended' or `expanded' memory, so if
you have this kind of memory, this program doesn't know it's there and
will not report it.
■ Number of References in Reference File. The total number of
reference citations in your database file is reported here. When you
start a new database, it should say zero.
■ Directory and File Names. These are the names specified in the
format file or, if you haven't specified one, the default names JEPRS
uses. Note that if you specify a different name on the Options Menu,
it will be reflected properly here. A note about the directory name:
this is not necessarily the currently active directory! JEPRS first
searches for files exactly as they are listed; if it can't find them in
the current directory, only then does it look in the directory
specified in Directory Name. See the section of this manual on JEPRS
Files for more information regarding what these files are used for.
■ The current time and date are displayed on the bottom of the
screen. Of course, if your computer's internal clock has the wrong
time and/or date, then this will not be correct.
4. Prompts vs. Menus.
4.1. The Basics.
Note that on the Main Menu you can move the highlight bar around
with the cursor keys, but no matter what alpha-numeric key you
press, it is not actually displayed on the screen. That's because you
are entering input for a Menu. The other type of input is for a
Prompt. An example of a prompt is when you enter search terms on
the Search Menu. The screen shows "Enter Search Terms:" and a
reverse video box is displayed. Often, there is a default value
already present; in that case, just pressing Enter will cause that
default value to be used. Alternatively, you can just start typing
your new entry, and the default one will be replaced by what you
type.
4.2. Advanced Features.
One nice feature about prompts and their default values is that in
addition to either taking them as they are or completely replacing
them, you have the option of editing them. In order to edit text
displayed at a prompt (as oppposed to replacing it), the first
character you press must be a non-printing key which must be one of:
LeftArrow
RightArrow
Delete
If you press one of those keys before pressing a character key, then
you can edit the text displayed after a prompt. For example, let's
say you're entering a file name on the Options Menu and the old file
name is "C:\Lou\Lab\JEPRS\OldFile.JPR". There are two ways to change
the file name to "NewFile.JPR". The first (hard) way is to just start
typing the whole name in: "C:\Lou\Lab\JEPRS\NewFile.JPR". The second
(easier) way is to edit the file name:
1. When the old file name is displayed, press the RightArrow key
until the cursor is under the "O" in "OldFile".
2. Now press Delete 3 times to delete "Old".
3. Just type in "New"; the display should now read
"C:\Lou\Lab\JEPRS\NewFile.JPR".
4. Press Enter to accept your changes.
This saves you a whole lot of unnecessary typing, so keep it in
mind whenever you need to change a default value at a prompt.
5. Help.
5.1. The Basics.
At most points within JEPRS, you have the option of pressing F1 to
get Help. After pressing F1 you should see the Help screen on the
right portion of the display. The Help facility provides context-
sensitive help no matter where you are in the program. If more than
one screen of information is available, the bottom of the screen will
display "Continue or Exit?"; press E to exit and return to what you
were doing before, or press any other key to continue with Help.
Help is generally available throughout the JEPRS program. You will
always know if Help is available, because "F1=Help" will be displayed
on the bottom of the screen if it is. General help is obtained by
pressing F1 while still at the Main Menu. To obtain help with any
command on the Main Menu, invoke that command, and then press the F1
function key.
5.2. Advanced Features.
In order for Help to work, JEPRS must be able to find the file
called "Help.JPR". If JEPRS can't find this file, it displays an error
message:
"<filename> not found. Press any key to continue."
when you try to get Help. If the help file is not in the current
directory, and it is not in the directory specified on the Options
Menu, then you should specify its name in the "Help File name" on the
Options Menu.
Each Help file is specific for each version of JEPRS. Therefore, if
you get an update (for example, you switch from JEPRS version 1.10 to
version 2.00) you must replace the old Help file with the new one
supplied with the update. Otherwise, Help will provide incorrect
information.
6. List References.
6.1. The Basics.
JEPRS asks for the number of the reference you wish to display.
Enter any number; the corresponding reference in the database is
subsequently displayed. JEPRS allows 3 lines for the title, 2 lines
for the author, 2 lines for the journal, space for the volume, pages,
year, and type, one line for the editor (if a book), 2 lines for the
publisher (if a book), and 5 lines for keywords.
JEPRS asks you to enter the number of the next reference to be
displayed. Note, however, that there are several keys that perform
special functions these are described on the bottom of the screen.
Pressing the key marked PgDn (or Page Down on newer keyboards) will
cause the next reference will be displayed. In a similar manner,
pressing PgUp will display the previous reference. Pressing F9 will
cause the currently displayed reference to be sent to the printer in
a standard compact form. Pressing F10 will send the reference to a
DOS Text File (again, in a standard format), while F8 will only send
the number (e.g. "6") to a Number File.
6.2. Advanced Features.
JEPRS is smart enough to know whether you've entered a valid
reference number or not. If you enter a number that's too large, an
error message will be displayed which will tell you both the number
you entered as well as the total number of references in the current
database.
Also, realize that you are entering the numbers at a prompt, so
you can use non-printing keys to edit the value. For example, if you
displayed reference #77 then "77" will be displayed as the default
value for the next reference; just press Delete once and then press
2 and #27 will be displayed.
7. Add New References.
7.1. The Basics.
This part of the program allows you to enter new references at
the keyboard (you can load references in the MedLine format [e.g.
those from PaperChase or Current Contents on Diskette] automatically
using the MedLine File command on the Options Menu). In order to
make the formatted output as consistent as possible, JEPRS has some
very specific expectations in terms of how you add reference
citations:
Title: The first letter of the first word of the title is
capitalized. Do not place a period at the end of the title.
Authors: Authors are entered last name first, followed by a space
and then the initial(s). There is no space or periods between initals
(but dashes are OK for hyphenated names). Spaces and dashes are OK
between long last names (e.g., da Vinci or Weaver-Jones). For
multiple authors, place a comma and a space after each author, except
the last author. Do not place an "and" or "&" before the last
author JEPRS can do this for you when formatting. Here are some
examples of correct and incorrect entries [and the reason why]:
Correct: Incorrect:
Wright WE Wright, W.E. [punctuation]
Lin VK-I Lin V K-I [extra space]
Wright WE, Lin V Wright WE & Lin V [&]
da Vinci L da Vinci, L [comma]
Journal: It is generally easier and takes less typing to enter the
standard abbreviations for journals, rather than the full name, but
this is not required (e.g. "Mol Cell Biol" instead of "Molecular and
Cellular Biology"). When formatting bibliographies/reference lists,
some journals want the full journal name cited, while others want the
abbreviation. JEPRS cannot switch between the two: you must be
consistent and enter one style or the other and leave it up to the
journal's proofers to enter the full text or make the abbreviations!
Volume: If you wish to include the issue number, you may want to
do it the way MedLine does, by enclosing it in parentheses (e.g.,
volume 112, number 8 would be 112(8)) but this is not required. See
note regarding "L"s and "1"s under Year, below.
Pages: No requirements.
Year: No requirements. A note to novice computer users:
although a lowercase L ("l") and a one ("1") and, likewise, an uppercase
o ("O") and a zero ("0") may look very similar to you, they are very
different things to a computer! If, for example, you enter the year
as l988 (using a lowercase "l"), and then use JEPRS's Search option to
find all years equal to 1988 (using a one "1"), JEPRS will not think
that is a match! Keep that in mind when entering the Volume, Pages,
and Year!
Type: You can only enter an A (for abstract), B (for book), or J
(for journal) here. No other input is acceptable. The reference type
is useful for 2 reasons: (1) it allows you to limit your search to,
for example, only books or only journal articles. It is also required
for proper formatting during the Format option, since JEPRS can
format references differently, depending on whether they are an
abstract, book, or journal.
Number (#): This is automatically assigned by JEPRS. Neither you
nor JEPRS can ever change it.
Editor: No requirements (but don't end it with a period).
Publisher: No requirements (but don't end it with a period).
Keywords: Keywords must be separated by a semicolon (";") and a
space. There are two reasons for this. First, the space is
necessary so that, when performing formatted output, JEPRS can find a
space in which to `break' a line if the line is too long. Second, if
you want to output your references in the MedLine format, JEPRS
needs to find the semicolon so that it can place each keyword on its
own line. Keywords can be entered either in all capitals or mixed
upper- and lower-case; there is no particular advantage doing it
either way, since during a Search you can convert them to uppercase
for comparison.
The only disadvantage to using all upper-case is printing formatted
output using a proportionally-spaced font (there is no problem with a
fixed-spacing font). That's because JEPRS determines a line is full of
text based on the number of characters in the line, not the width of
the characters. Look at the following example:
MAMMALIAN MAMMARY GLAND
Mammalian mammary gland
With a fixed-spacing font, both lines take the same amount of space;
but with a proportional font, the top line is much longer. This would
force you to make your line width much smaller, subsequently
displaying the rest of the reference (which would be mixed upper-case
and lower-case) with a very wide right margin. Of course, if you plan
on importing MedLine files, these have their keywords in all upper-
case already, so you'll have to deal with this problem eventually. My
recommendation would be to use a fixed-spacing font when printing out
the keywords (for example, just to get a listing of your entire
database) but you can use a proportional font when printing
bibliographies (because you usually don't print out the keywords for
them anyway).
Notice that a variety of special function keys are displayed on
the bottom of the screen. Many of these perform the same function
they would in a word processor or text editor. The arrow keys move
the cursor in the direction pointed by the arrow. When you go to the
end or beginning or a line, the cursor will wrap around to the other
side. The Enter key is the same as pressing the down arrow key.
PgUp will move you to the first line of the Title; PgDn will move you
to the first line of Keywords. Home moves you to the first
character of the line your are on; End moves you to the end.
BackSpace deletes the previous character, while Del deletes the
current one. Ins toggles the Insert/Overwrite mode. Check the box in
the lower right portion of the screen to see which mode you are in.
In Insert mode, characters to he right of the cursor are pushed ahead
when new charcters are typed; in Overwrite mode, characters to the
right of the cursor are overwritten when new characters are typed.
F1 will give you help (just like it always does).
Pressing Esc will bring you to the one-line menu at the top of the
screen. Since this is a menu, use the arrow keys to highlight a
command and then press enter, or just press the first character of
the command. Use Save to save this reference; use Abandon if you
made a mistake or change your mind and decide not to save this
reference citation; use Return to Edit to go back to this reference
and continue editing it; use Help (or F1) to get Help. At the next
menu, use Continue to add another reference or use Main Menu (or
press Esc) to return to the Main Menu.
8. Update References.
8.1. The Basics.
Updating references is essentially identical to adding references.
The only difference is that you are specifically asked which reference
you wish to edit. Since this is a prompt, you can enter a new number
or edit the default value; you also have the option of pressing PgDn
to edit the next reference or PgUp to edit the previous one.
8.2. Advanced Features.
Note that since JEPRS does not have a Delete Reference option,
the Update Reference option can be used to remove an old reference
citation and replace it with a new one.
9. Format References.
9.1. The Basics.
JEPRS's most powerful utility is its ability to format references in
the style of almost any journal. Your first choice will be where you
want the output generated by this part of the program to be sent:
printer, screen, text file, or various combinations thereof. Note that
an "s" appears at the cursor; this means that if you just press Enter
here, the screen is the default output. The next screen asks you
what format you want to use. Note that you have the ability to
define any 10 formats you wish (format number 11 [MedLine format] is
predefined by JEPRS). If the Format file wasn't found by JEPRS when
it started up, then no titles will be listed; otherwise, the titles
present in the Format file are listed from 1-10. Enter any number
from 1 to 11. JEPRS then informs you that it is reading data from
the Format file (unless it is using the pre-defined MedLine format);
these are the actual formatting instructions used.
The final question is to determine what will be the source of the
numbers of the references to be formatted. Again, a letter appears
at the cursor position (this time "k") to signal a default value will be
chosen if you just press Enter. If you press K, then you will be
queried to enter the reference numbers at the keyboard. If you
press N, then JEPRS will look for a Number File which is a text file
that contains just numbers of references in the order you want them
formatted. If JEPRS can't find the number file, it will let you know,
and then ask for a new name. At this point you can either enter a
new file name or press F9 to go back to the Main Menu.
If you press R, then all the references in the data file will be
formatted automatically (note that if you have a large data file, this
may take a long time).
In the case of file input (either reference or number files), you
are additionally asked: "Do you wish to pause after ever 20 lines?".
If you press Y, the screen will display 20 lines of text, then pause
and wait for you to press any key to continue. Then it will display
the next 20 lines of text and pause again; in this manner, text will
not scroll off the screen before you get a chance to look at it. If
you press N, the screen will to continue to scroll without stopping
(you can press Ctrl-NumLock to pause the screen display). In either
case, pressing Esc will bring you back to the Main Menu after the
next full reference has been displayed.
If you press K to list the references specified by keyboard input,
you are then prompted for the number of the reference to be
formatted. After pressing Enter, the program will read in the number
you specified, and then display it according to the formatting
instructions in the format file corresponding to the choice you made
previously. If you enter an invalid number, it will be ignored (don't
worry, the system won't crash). Pressing Esc will bring you back to
the Main Menu.
9.2. Advanced Features.
The Format References section is by far the oldest module of
JEPRS, and this is reflected in its rather antiquated user interface.
I am very well aware of this limitation and, in fact, the next major
update (due out probably in September 1989 or so) will sport a
completely rewritten user interface here; I plan on making it look
very much like the Search Menu (which is the newest module). I would
also like to provide the user (you) with the ability to modify the
Format File from within JEPRS (without having to exit the program and
use your own editor) but this is a large undertaking and may not make
it into the next version, but should be done by the version after
that (March 1990?). If you have any suggestions on how to improve
JEPRS's user interface, please let me know and I'll see if I can
incorporate them into the next release.
10. Options.
10.1. The Basics.
This menu allows you to change the names of any of the files that
you are using in JEPRS, so you don't have to exit the program just to
use a different data file, for example. In addition, you can enter a
drive and directory name. If you do so, then anytime JEPRS goes
looking for a file (for example, the Help file), it will first look in the
directory specified in the Help file name; if none were specified, then
it looks in the current default directory. If JEPRS doesn't find it
there, then it looks in the directory specified in the Drive and
directory name.
Changing a file name. To change a file name, press the first letter
of the file type, or just highlight the file type and name using the up
and down arrow keys and press Enter. At the bottom of the screen,
you will be prompted for the new name of the file. Note that the old
name is displayed there so that you can edit it (see the section in
this manual on Prompts vs. Menus to see how). Edit the old name or
just type in a completely new name, then press Enter when finished.
Note that if you are changing the name of the reference file or
reference key file, you will be prompted for both file names, since
they are specific for each other.
Further down on the list are a few additional commands:
Error/warning beep, Ordering information, MedLine format file, and Go
to DOS. To invoke any command, do the same thing you did on the Main
Menu: either use the arrow keys to highlight the command you want
and then press Enter, or just type the first letter of the command
(e.g., O for Ordering information).
■ Error/warning beep allows you to turn JEPRS's beeping on or off.
Whenever you type an incorrect command, or at various other times
when JEPRS wants your attention, it will beep at you. If for some
reason you wish JEPRS wouldn't do that (you're working late at night
for example), just type "off" after invoking this command, and JEPRS
will never beep at you.
■ Ordering information will present you with details of how to
order the latest version of JEPRS from the author (that's me). JEPRS
is an absolute bargain at $25!
■ MedLine format file allows you to add references formatted
according to the National Library of Medicine's standard MedLine
format. Most reference management programs can format files this
way (including such things as PaperChase, an online access system to
MedLine, and Current Contents on Diskette), so it's an easy way to
interchange files between programs. For example, if you use
PaperChase (or Current Contents on Diskette) to search for any
papers published on a particular subject, PaperChase allows you to
save them in the National Library of Medicine (NLM) format. You can
then download those references to a file on your computer. Then
start up JEPRS and invoke the MedLine format file command, specify
the name of that file when it asks you for the name of the MedLine
format file, and JEPRS will automatically add those references to
your database! Isn't that easy?
■ Go to DOS allows you to temporarily exit JEPRS and return to
the PC/MS-DOS operating system. This would be useful, for example,
to get a directory listing without having to exit from JEPRS.
Whenever you use this command, however, don't forget to type
"Exit" and then press Enter to return to JEPRS! If you use this
command, but forget to enter "exit" and then run JEPRS again, you will
permanently mess up your datafiles! As long as you enter "exit" to
return to JEPRS, your data will be completely safe.
10.2. Advanced Features.
On your right, you will see "Additional System Information." The
first four pieces of information (MS-DOS and JEPRS version numbers,
Disk #, and Licensee) are more for my use in case you are having a
problem with the program. "Number of references in reference file"
tells you how big your database is; it should say zero when you first
create a new database, and should grow as you add more reference
citations.
"Number of relocated references" isn't much use to you now, but it
will be in the future. In order for JEPRS to make the database as
compact as possible, it stores references exactly as you enter
them they are in "variable length" fields. The only problem a
programmer (that's me) runs into is if the user (that's you) decides to
modify one of the references and make it longer than it used to be.
In order to cope with this possiblity (so you, the user, do not have
to worry about it) JEPRS marks the old (shorter) reference as invalid
and then adds the modified one to the end of the file: this is a
"relocated" reference. If a significant number of references are
"relocated" then a lot of disk space is wasted. What I plan on doing
in the future is to create a command to get rid of these garbage
references. In the meantime, they are harmlessly sitting in your
database.
"Available space on default drive" tells you how many bytes of
space are left to use. If you're getting low on space, you might want
to keep track of this number to make sure you don't try to add
references if there is no space left on your disk. "Total disk space
on default drive" tells you how many total bytes your drive is
capable of holding.
11. Search.
11.1. The Basics.
All you need to do in order to perform a simple search is to
specify one search term and then press Go to start. Search terms
specify the fields to be searched as well as the text that you want
to match. To search for all papers by an author named "Wright", you
would:
■ Press Terms.
■ Enter "A" to search the author field.
■ Enter "Wright" to search for this text.
Once you press Terms, you are asked to "Enter search:"; this is
where you enter the letter(s) corresponding to the fields to be
searched. JEPRS lists the letters and fields at the bottom of the
screen; they are reprinted here for your convenience:
Authors Editor Keywords Citation type
Title Year Publisher Journal
You can perform mulitple searches by connecting the field names
with operators. An operator is one of:
+ = AND - = NOT / = OR
These are the Boolean logical operators. So if you want to search
for papers by Author "Wright" AND Title "Myogenin" then you would
enter "A+T" for Author +[and] Title, then enter "Wright", then enter
"Myogenin". [When you're entering the text, you must enter it in the
same order as the field names; that is, you couldn't enter "Myogenin"
first and "Wright" second, otherwise it would look for "Myogenin" in
the authors and "Wright" in the titles, giving you a nonsense answer.
In order to help you along, JEPRS will make the current field letter
blink while you are entering the search text for it.]
Because the logical operators are not always intuitive, let me give
a brief explanation of each. If your search is "A+T" then both the
author and the title you specify must be in the same reference
citation in order for it to be considered a match. If your search is
"A-T" then the author must be in the reference citation and the title
must not be in that same reference to be a match. If your search is
"A/T" then either that author or that title must be in the reference
in order to be a match. Here are some additional tidbits to ponder:
■ "A+T" is logically identical to "T+A".
■ "A/T" is logically identical to "T/A".
■ "A-T" is very different from "T-A".
■ JEPRS doesn't allow you to do a search like "-A" (in other
words, find all references except those with a certain author).
You can get around this by doing something like "A-A"; when
asked for the first search text just press Enter (this will
match all references) and then enter the name of the author you
don't want to find. This will accomplish the same thing as "-A".
Once you press Go to start the search, the Messages window on the
bottom of the screen will show you the number of the references
being searched as well as how many matches have been found. You can
press Esc at any time to stop the search and display the results
found at that point.
If Text File, Number File, or Printer Output is on, then when
searching is done the Messages window will show which references are
being sent to the designated output. If Screen Output is on, then
the screen will clear and the Search Display will be shown. The first
reference found (or the first one alphabetically, if Sort in on) is
displayed and function key assignments are shown on the bottom of
the screen. These are described here:
■ Esc: You will be returned to the Main Menu.
■ F3: You will be returned to the Search Menu. At this point you
may then start a completely new search, or you can modify any aspect
of the previous search. The latter is possible because JEPRS saves
the search terms and default values from your last search. JEPRS
will even save them if you go off to some other part of the program
and then come back to search later. Of course, once you exit the
program your search terms and defaults are lost.
■ F1: As always, this will give you help.
■ F5: This allows you to modify your search by bringing you to
the Modify Search Menu. The first time you modify your search, two
or three lines of instructions are provided (with "Instructions" in red
letters on color monitors). Your previous search terms are displayed
on the top right of the screen. The number of matches JEPRS has
found for the current search is displayed in the upper left corner.
When you are specifying terms for Modify Search, think of it as being
added to your original terms. For example, if your original search
was "A+A" but you found too many matches, you could modify your
search with "-K" which would be equivalent to an original search of
"A+A-K". Notice that searching by Modify Search is usually very
quick; that's because it doesn't search the entire database it only
searches those references that have already yielded a match (and
that's the reason you can't use the OR (/) operator, because then it
would have to search the entire database). You can modify a search
up to a total of 3 times.
■ F8: Sends the number of the most-recently displayed reference
to the Number File (see description of files near the end of this
guide).
■ F9: Sends the entire text of the most-recently displayed
reference to your printer. It uses a compact format pre-defined by
JEPRS which includes boldfacing and underlining. However, if you have
not properly defined those attributes in the Format File then it will
not print correctly on your printer.
■ F10: Sends the entire text of the most-recently displayed
reference to a Text File. Note that it includes printer formatting
codes (underlining and boldface) so that you can still print it on your
printer. However, if you import it into a word processor, you will
see all of those weird codes mixed in with your text. If you want to
create a Text File without codes, then create a Format File without
codes for a printer and use that one in JEPRS before creating a Text
File.
11.2. Advanced Features.
One important thing you should realize about searches is that
JEPRS doesn't necessarily search for whole words. So if you specify
a search for authors named "STEIN" it will also find "STEINBERG" and
"FRANKENSTEIN" because they both have "STEIN" in them. There are
three ways to try to get around this: (1) Turn Case Sensitivity on
and search for "Stein"; then "Frankenstein" would not be a match; (2)
Use a space or other delimiter such as "Stein,"; then "Steinberg" would
not be a match; and finally (3) if after performing your search you
find that there are one or two common `contaminants', you can use F5
(Modify Search) to specifically exclude them (e.g., "-A" "Steinberg"
would get rid of all matches that had "Steinberg" in them). Of course
in this case you would have to be careful to make sure that one of
your references didn't contain both Stein and Steinberg as authors!
There are a number of options (displayed on the right side of the
Search Screen) that can modify your basic search strategy:
■ Begin. When at the Search Menu, pressing Begin will allow you to
specify at which reference number the search will start. An example
of its use would be if you had a database of 900 references and you
knew that the paper you were looking for was in the last 300 or so;
then you would specify Begin at #600. This would cut down your
search time significantly. The default value is 1.
■ End. This is just like Begin, but at the other end of the
spectrum; just specify at what reference number you want searching
to stop. The default value is the last reference in the database.
■ Matches. This tells JEPRS to stop the search after this many
number of matches have been found. Let's say that you know that a
certain search, like keywords for "DNA" will yield a lot of matches,
but you only want to see the first 15 of them. Press Matches and
enter "15". Then when you start the search, as soon as the 15th
match is found, searching automatically stops. If fewer than 15
matches are found it will just search to the end of the database and
then stop. The default value is the number of references in the
database. (If you have a very large database and you wish to sort
it before displaying it, it is a good idea to use a Match number
smaller than the database; this frees up memory for the sorting.)
■ Case Sensitivity. Normally when JEPRS does a search this option
is Off. That means that both your search text and the references in
the database are both converted to uppercase before being compared.
That way you don't have to worry about entering "DNA-binding protein"
or "dna-Binding Protein", since they will both be converted to "DNA-
BINDING PROTEIN". If you wish to make the comparisons directly
without converting to uppercase, then turn Case Sensitivity "On". The
default is "off".
■ Output. JEPRS lets you specify any combination of output to
Screen, Printer, Text File, and/or Number File. When you press Output,
the cursor moves next to Screen and lets you enter "on" or "off";
then press Enter and "on" or "off" for the printer; and so on until
you specify values for each output. Any combination is allowed
except turning them all off; if you do so, JEPRS will beep and then
turn on the Screen for you. The default is Screen on, everything
else off.
■ Sort. By default, JEPRS displays the references in the order
they were found in the database. Optionally, you can turn Sort On, in
which case they will be displayed alphabetically by the first author's
last name. If there is more than one paper by the first author, they
will be displayed together, but in no particular order. I am thinking
about adding the ability to sort first by author and then by year if
the first author is the same. If you think this is a good idea, or if
you have any better ideas, let me know.
12. JEPRS's Files.
12.1. The Basics.
All of the major file types that JEPRS uses are listed on the right
side of the screen of the Main Menu. If you've read through the
tutorial, then you should be vaguely familiar with the names of each
of these files. Here is a complete description of their functions and
uses.
■ Reference File: The reference file is the main database file
that JEPRS uses to store the references you enter using the
program. This file (which has a default name of "Ref1.JPR") is
maintained completely by JEPRS. You should never try to modify this
file using any other program! For example, if you tried to look at
this file using a word processor, you would probably only see 3 words
on the screen: "JEPRS Reference File" (the same is true if you try to
use MS-DOS's Type command to view the file), but all the data is still
there. However, if you then saved this file with your word
processor, you would delete all the references that JEPRS had saved!
Therefore, let me repeat: Never modify the Reference file with
any program other than JEPRS!
■ Ref Key File: This is a matching file for the main database
(Reference file) that JEPRS uses for keeping track of where the
references are in the main file. You cannot access the main
Reference file without this Key file. The Key file's default name
is "Ref1.JPK". Again, do not try to modify this file with any program
other than JEPRS