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J E P R S
The Journal & Editorial Personal Reference System
User's Guide
Version 2.0
JEPRS(tm) version 2.0
December, 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.
JEPRS User's Guide, page 2
Table of Contents
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . 3
What is JEPRS? . . . . . . . . . . . . . . . . . . . . . . . 3
Features & Requirements . . . . . . . . . . . . . . . . . . 4
Registration & Distribution . . . . . . . . . . . . . . . . 5
Further Help and Questions . . . . . . . . . . . . . . . . . 6
Setting Up JEPRS . . . . . . . . . . . . . . . . . . . . . . . 7
Files on Disk . . . . . . . . . . . . . . . . . . . . . . . 7
Installation . . . . . . . . . . . . . . . . . . . . . . . . 8
Starting JEPRS . . . . . . . . . . . . . . . . . . . . . . . 9
Exiting The Program . . . . . . . . . . . . . . . . . . . . 10
Creating Your Own Database . . . . . . . . . . . . . . . . . 10
The Main Menu . . . . . . . . . . . . . . . . . . . . . . . . 12
Prompts vs. Menus . . . . . . . . . . . . . . . . . . . . . 13
On-Line Help . . . . . . . . . . . . . . . . . . . . . . . . . 15
Global Defaults . . . . . . . . . . . . . . . . . . . . . . . 16
Editing Printer Definitions . . . . . . . . . . . . . . . . 19
Editing Journal Definitions & Format Styles . . . . . . . . 22
List References . . . . . . . . . . . . . . . . . . . . . . . 26
Editing & Updating References . . . . . . . . . . . . . . . 28
Add New References . . . . . . . . . . . . . . . . . . . . . . 29
Suggested Format . . . . . . . . . . . . . . . . . . . . . . 30
Entering Sample References . . . . . . . . . . . . . . . . . 32
Format References . . . . . . . . . . . . . . . . . . . . . . 35
Pre-Defined Settings . . . . . . . . . . . . . . . . . . . . 35
Starting Formatting . . . . . . . . . . . . . . . . . . . . 37
Searching . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Pre-Defined Settings . . . . . . . . . . . . . . . . . . . . 39
Starting a Search . . . . . . . . . . . . . . . . . . . . . 42
Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Importing . . . . . . . . . . . . . . . . . . . . . . . . . 45
Exporting . . . . . . . . . . . . . . . . . . . . . . . . . 47
Compressing the Database . . . . . . . . . . . . . . . . . . 49
JEPRS's Files. . . . . . . . . . . . . . . . . . . . . . . . . 51
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
JEPRS User's Guide, page 3
1 Introduction
1.1 What is JEPRS?
JEPRS (pronounced ``Jeepers!'') stands for the Journal and
Editorial Personal Reference System. It is a program that maintains a
database of references to articles published in journals, books,
and/or magazines. It allows you to add, edit/update, list, search,
import, and export your reference citations. Another feature availabe
in JEPRS is the ability to print your references in virtually any
style imaginable, including underlining, boldface, italics,
superscripts and subscripts.
You may be wondering to yourself, ``Why should I use JEPRS instead
of some other program?''. There are three very good answers to that
question:
** It's inexpensive. At a final cost of only $30, JEPRS is a
great bargain.
** It's very easy to use. JEPRS is a menu-driven program that
lists every single option on the screen--you don't have to memorize
anything. It is run by pull-down menus and pop-up dialog boxes. It
also has most of its defaults pre-defined, so you don't have to wade
through screen after screen of questions. JEPRS prevents you from
entering wrong answers whenever possible. It's very difficult to make
a mistake--you really have to try.
** It's powerful. The combination of importing, exporting,
searching, and formatting capabilities of JEPRS are unequaled in any
other shareware program that I have tried.
***Compatibility with Other Programs***
Other questions you may be asking yourself are: ``What if it
becomes outdated? Will I then have 1000 references that I will have
to type all over again if I switch to another program? Then it really
hasn't saved me any time.'' This is a very reasonable concern. Much
as I hate to admit it, yes, sometime in the future you may want to
switch to a program other than JEPRS. It would be a complete waste of
time to have to manually re-enter every reference in the database into
that new program. One nice feature of JEPRS is the ability to output
references formatted according to the National Library of Medicine's
MedLine format. This is a common format used by most biomedical
reference management systems. For example, PaperChase (an on-line
program that allows you to search the MedLine database) lets you down-
load references in the MedLine format. JEPRS can both read and write
files with this format; any biomedical reference program worth its
salt should be able to do this, also. Therefore, switching between
programs should involve no more work than taking the time to tell
JEPRS to export all the references in the database in MedLine output.
Then just read this text file into the other program. It's that
simple.
JEPRS also has the capability of performing comma-delimited output:
See the chapter in the Tutorial called ``Defining Format Styles''.
Therefore, you will get the benefit of JEPRS now, and be able to
JEPRS User's Guide, page 4
switch to other programs in the future, painlessly.
1.2 Features & Requirements
***New Features of Version 2.0***
Many enhancements to JEPRS 1.1 have occurred with version 2.0.
These have been listed at the end of the file called J200Nw.Doc, but
some of the major points are reiterated here:
** User Interface. JEPRS now has a consistent user interface
system, with pull-down menus and pop-up dialog boxes.
** Configuration File. Now most of the defaults on the menus can
be modified and saved the way you want them to be. In addition, 5
printer definitions and 30 format styles can be stored in this file.
A real benefit is that now these formats can be modified from within
JEPRS--you no longer have to exit the program and use your own text
editor to make changes.
** Searching. Found references are now initially displayed in a
condensed, one line format. You can scroll through this list using
the arrow and [PgUp]/[PgDn] keys. Any displayed reference can be
shown in its entirety by pressing [Enter], and can then be immediately
edited by using [F4]. Groups of references can be Marked by an '*';
these Marked references can be sent to a file or your printer.
** Formatting. References can now be sorted by author and year
before being sent to the output device. 30 different format styles
can be created, and any one of them chosen for output.
** Importing. The Import Menu now supports CL-MedLine and
BRS/Colleague formatted files. In addition, there is now the option
of having references imported one at a time instead of all at once; in
this case, you can discard the reference or edit it before adding it
to your database.
***System Requirements***
JEPRS is made to run under PC/MS-DOS (version 2.0 or higher) on IBM
PC/XT/ATs, PS/2s, and compatibles. In fact, JEPRS was written on a
Zenith PC and so you should not have problems with any reasonable
compatible. JEPRS itself requires only 256 kilobytes of RAM, so any
computer with 320k or more can run the program. Note, however, that
the more references you have, and the more sorting you do (such as on
the Search Menu and Format Menu), the more memory you will need.
Although JEPRS can technically handle up to 64,000 references, it will
quickly run out of computer memory during searches and sorts.
Therefore, if you have more than 10,000 references (which I doubt
anyone does), I would not recommend the use of JEPRS.
A hard disk is not required for proper operation, but searches are
considerably faster on a hard disk compared to floppies. The program
was designed to minimize its use of disk space; therefore, each
reference takes up only as much space as needed--there is no `padding'
of empty spaces. For example, in an average JEPRS database you could
probably store 300 references per 100 kilobytes of disk space (i.e.,
you could probably store 1000 references on a 360k floppy or 2000
references on a 720k diskette).
JEPRS User's Guide, page 5
1.3 Registration & Distribution
***Registering JEPRS***
JEPRS is distributed as ``shareware''; this means that you are free
to try the program for a 30 day evaluation period at no charge. If,
at the end of that time, you decide you like it enough to continue
using it, then you are obligated to pay a registration fee to the
author (me), just like any software you purchase in a store. It is
not public domain, and it is not free. Please see the file called
JOrder.Doc, or the Global Defaults Menu, for ordering information.
The registration fee is ridiculously small considering the amount
of work JEPRS can do. I am currently charging only $30. Registration
has several advantages:
** Unlimited use of the program.
** The latest version of JEPRS will be sent to you (if you do not
already have it).
** Laser-printed documentation will be sent to you (this is a
printed version of the JTutor.Doc and JGuide.Doc files).
** The next major update will be sent free of charge! Later
updates may be purchased for a nominal fee (probably $10). Updates
are planned about every six months to a year, but that is not set in
stone.
** I will answer any questions you have about the program. As you
can tell by the low registration fee, I will not become a millionaire
any time soon; thus I simply cannot afford to answer questions from
unregistered users. If you do not register, the only questions I can
answer are those that have a bearing on whether you decide to purchase
the program, such as questions about compatibility with other
reference management programs.
** Update Notices. Registered users are always kept up-to-date
with reports of minor releases (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.
To order/register use of JEPRS, print out the ``JOrder.Doc'' file
that's included on the disk, and fill out the information requested.
***Shareware Distribution***
If you want to distribute JEPRS to other users (friends and
business acquaintances, for example), you are free to do so as long as
you distribute all the files that you received, in their original
condition (that is, unmodified by you) at no charge. Likewise, JEPRS
may be posted on bulletin boards as long as there is no fee for
downloading the program. If you do so, I would appreciate a note from
you specifying the phone number and name of the bulletin board you
posted it on.
If you charge any fee whatsoever for acquiring JEPRS (for example a
commercial shareware distributor charging $5-10 per disk, or a local
biomedical computing consultant) you must receive an agreement in
writing from me! I do not anticipate denying that right to anyone,
but I would just like to be aware of the distribution channels that
JEPRS is moving through to keep the most current version in
distribution.
JEPRS User's Guide, page 6
1.4 Further Help and Questions
If you have any comments or complaints about JEPRS, I would love to
hear from you. Likewise, if there is a problem with the documentation
or something that is not clear, feel free to write to me at the
address listed on the Opening Screen and I'll write back to you as
soon as possible.
Thank you for your interest and support of JEPRS!
JEPRS User's Guide, page 7
2 Setting Up JEPRS
In this chapter, I will provide information on setting up JEPRS on
your own system. This will entail providing you with a list of all
the files available on the distribution disk (or that you downloaded
from a bulletin board); instructions on installing JEPRS on your own
computer; the very basics in starting and stopping the JEPRS program;
and information on creating your own database.
2.1 Files on Disk
You should find a total of 13 files on this disk. Below is a list
of those files and a short description of their use:
** JReadMe.Doc. This file contains the most basic information for
starting JEPRS.
** JEPRS.Exe. This is the JEPRS program itself; entering JEPRS at
the DOS prompt (C:>) starts the program.
** JTutor.Doc. A tutorial text file that you should read before
doing any extensive work with JEPRS.
** JGuide.Doc. The file you are reading now: The User's Guide to
JEPRS. This contains the most extensive information on JEPRS. It is
not meant to be read sequentially; you should refer to it whenever you
have specific questions about a specific aspect of the program.
** J200Nw.Doc. New features of JEPRS version 2.00 are listed in
this file.
** JOrder.Doc. Printing this file on your printer produces a form
you can use to register your copy of JEPRS, as well as make comments
about the program.
** JEPRS.Hlp. Contains the text for JEPRS's context-sensitive help
screens. If JEPRS can't find this file when it is running, you will
not be able to get help by pressing the [F1] key.
** Ref1.JPR. A sample database file for JEPRS. It contains the
actual text of the database.
** Ref1.JPK. The `key' file that goes along with the Ref1.JPR
database file. You cannot use a database file without a key file!
** JEPRS.Cfg. A sample config (`configuration') file that contains
30 formatting definitions, printer control codes, default directory
and file name information, and user-definable Global Defaults.
** JEPRS.Txt. Sample text file. Since you cannot directly access
the database using the DOS Type command, JEPRS allows you to enter
selected references into an ASCII/DOS text file. You can use DOS's
Type and Print commands on these text files.
** JEPRS.Num. This is a sample ``number'' file. It is really a
normal ASCII/DOS text file, but consists of nothing but numbers of
references. JEPRS can create this file (for example, in a Search) and
then use its contents for input during formatting (on the Format
Menu).
** Procomm.Log. A sample MedLine-formatted file. This can be used
in the Utilities/Import Menu to add a MedLine-formatted file to the
database. (This is probably only of interest to biomedical
researchers who use MedLine-formatted files.)
JEPRS User's Guide, page 8
2.2 Installation
Before installing JEPRS, make a copy of all the files on the
program disk! Never use your original disk to run the program. This
is especially true with a Shareware program like JEPRS, since in order
for the documentation to be correct when you distribute it to other
people (and to prevent major hassles for other users) you must
distribute the software exactly as you received it. If you are
upgrading from version 1.0 or 1.1 to 2.0, please see the chapter in
the Tutorial (JTutor.Doc) on converting Format files to Config files.
***Floppy Drive Systems***
If you don't have a hard disk, simply use your new copy disk of
JEPRS as your working disk; there's no need for any special
installation procedures. If you are updating a previous version of
JEPRS, copy the following files from your version 2.0 disk onto your
present working disk:
JEPRS.Exe
JEPRS.Hlp
JReadMe.Doc
JTutor.Doc
JGuide.Doc
Note that the only file that is absolutely necessary to copy is
JEPRS.Exe; however, if you want the Help screens to work, you must
also copy JEPRS.Hlp to your work disk. (If you use the version 2.0
JEPRS.Exe file with the version 1.1x Help.JPR file, the Help screens
will give you wrong information!) The last 3 files listed above are
the documentation files (you're reading JGuide.Doc right now) and once
you print them out, there's no need to keep them on your working disk.
Of course, no files should ever be deleted from your original disk!
***Hard Disk Systems***
If you have a hard disk, follow these instructions to install JEPRS
on your hard disk. Once you make a copy of the original disk, insert
the copied disk into one of your floppy drives. Now make sure your
default drive is the hard disk (that is, if your hard disk is drive
C:, then enter C: at the DOS prompt). Now enter the following
commands at the DOS prompt (these commands will create a new directory
called ``JEPRS'', and copy all the files on this disk to that
directory):
C:\> cd \
C:\> md JEPRS
C:\> cd \JEPRS
C:\JEPRS> copy a:*.*
This assumes that your disk is in floppy drive A:. Substitute the
a:*.* above with whatever your floppy drive is (e.g. b:*.* if your
disk is in floppy drive B:).
Now enter dir at the DOS prompt to see if all the files are
there. If not, go through the procedure again just in case you missed
a step or entered something else by mistake.
JEPRS User's Guide, page 9
2.3 Starting JEPRS
You start the program by simply entering the command ``JEPRS'' at
the DOS prompt, like this:
C:\JEPRS> JEPRS
If all goes well, two short messages will scroll onto the bottom of
the screen and the Welcome Screen will appear (which includes the
copyright notice, and to whom the program was provided). Press 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), 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 (see
below for detailed instructions on creating your own database), [F4]
to specify a new name, or [F10] to exit the program.
***Command Line Options***
There are several command line options that you may use when
starting JEPRS. These include 1) Config file name and 2) Screen color
options. The general format for entering these options is:
C:\JEPRS> JEPRS <Config file name> /opt
where <Config file name> is a valid filename for your config file,
including a path if necessary, and /opt is any combination of screen
color options (see below).
** Config File Name. If for some reason you wish to use a
different name for the Config file (in other words, you're not calling
it JEPRS.Cfg or it's not in the current drive and/or directory), then
you can specify its name on the command line, like this:
C:\JEPRS> JEPRS MyRefs.Cfg
This tells JEPRS to use MyRefs.Cfg as the Config file, which must be
in the current directory. If you wish, you may also specify the drive
and/or directory it is in, if this is not the current one. For
example, if you keep MyRefs.Cfg in a directory called C:\PRINTER, then
start JEPRS like this:
C:\JEPRS> JEPRS C:\PRINTER\MyRefs.Cfg
This tells JEPRS not only the name of the file, but also in which
subdirectory it is located.
** Screen Color Options. In addition to Config file names, you can
specify one or more options dealing with the appearance of text on the
screen. The /opt shown in the command line above is any combination
of:
/A --> amber monitor with color video card
/G --> green monitor with color video card
/B --> turns blinking off in formatting
/C --> turns colors off in formatting
Actually /A and /G are the same command, but both options are provided
so that they are somewhat mnemonic. These two commands put the
program into Black and White Mode (see the Global Defaults Menu); that
is, all text is black, white, or gray, so that it can be properly
displayed on any monitor.
The /B option turns off the blinking attribute of italicized text
when displaying output from the Format Menu on the screen.
The /C option turns off the color attributes of boldface and
underlined text when displaying output from the Format Menu on the
JEPRS User's Guide, page 10
screen. Boldface is normally displayed as white on cyan, and
underline is normally blue on black, but both become black on cyan
when this option is invoked.
You can mix and match options in any combination; so if you want to
use your Config file called MyRefs.Cfg (in the subdirectory called
C:\PRINTER); you hate blinking characters; and you are using an amber
monitor with a CGA video adaptor, you could start JEPRS like this:
C:\> JEPRS C:\PRINTER\MyRefs.Cfg /B/A
2.4 Exiting The Program
When you are done with JEPRS, return from wherever you are to the
Main Menu (usually by pressing [Esc]), then exit the program as
follows:
1. Press [E] . . . or . . .
2. Press [Esc] . . . or . . .
3. Use the arrow keys to highlight Exit, then press [Enter].
When you do this, JEPRS will beep (unless you turned off the
``Error/Warning Beep'' on the Global Defaults Menu) and then ask you
if you really want to exit the program; if you do, press [Y]; it you
don't, press [N] (or any other key). If you press [Y], you will be
returned to the PC/MS-DOS operating system (and your screen colors
will return to what they were before JEPRS started). Of course,
the other way of exiting JEPRS is to simply shut off your computer--
but don't do that! If you turn off your computer without exiting
JEPRS, then you may lose data from your data files. So remember,
always exit JEPRS properly before turning off your computer.
2.5 Creating Your Own Database
When using the tutorial, JEPRS automatically uses the sample
Ref1.JPR and Ref1.JPK database files. Now you probably want to create
your own database. You will also probably want to use your own Config
file with your new database files so that it will save all of your
preferences for Global Defaults. In that case copy the Config file to
a new filename. For example, to create your own Config file called
`MyRefs.Cfg', then use the following MS-DOS commands at the DOS
prompt:
C:\JEPRS> Copy JEPRS.Cfg MyRefs.Cfg
Now start JEPRS using your own Config file, as follows:
C:\JEPRS> JEPRS MyRefs.Cfg
Once at the Main Menu, press [F2] to go to the Global Defaults Menu.
Press [F]iles and then [R]eference file; now enter the name that you
want for your database file (for example, MyRefs.JPR) and press
[Enter]. JEPRS will then instantly ask you for the name of the
matching Key file, and it will automatically provide you with a
default name (such as MyRefs.JPK, in this example). You can use the
arrow keys, [Home], [End], [Insert], and [Delete] to edit the name any
way you wish. After you press [Enter], JEPRS will pop up with an
error message--don't worry (be happy!), just press [F6] and JEPRS will
create new Database and Key files with the names you specified.
And now one last thing: save the new Database & Key file names
JEPRS User's Guide, page 11
into your Config file so you won't have to go through this whole
procedure everytime you start JEPRS. Do this now by pressing [Esc] to
return to the Global Defaults Menu; then press [D]efaults, then press
[S]ave defaults + filenames. So from now on when you start JEPRS with
the MyRefs.Cfg Config file, it will automatically look for your new
MyRefs.JPR and MyRefs.JPK files.
***Where To Next?***
Before continuing with this documentation, you should read the file
called JReadMe.Doc and the Tutorial (JTutor.Doc). The JReadMe.Doc
file contains basic information for installing JEPRS and starting the
program up for the first time. The Tutorial then takes you step by
step through some sample JEPRS sessions with the sample database to
give you an idea how to use some of JEPRS's functions. The User's
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 when you have specific
questions or if you want more detailed information on how JEPRS works.
JEPRS User's Guide, page 12
3 The Main Menu
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.
***Screen Design***
Note that the screen is basically divided into 5 sections; since
every menu has this same basic layout, let me describe some background
about it.
** Menu Title. The topmost line on the screen always contains the
menu title. This is meant to give you some idea of where you are in
the program, and what you can do.
** Menu Line. The second line from the top contains a list of the
actual commands you have available to you. When the menu line is
active, the first letter of each command is highlighted and one of the
commands is completely highlighted. This is to let you know that you
can just press the highlighted letter to invoke the command, or if you
just press [Enter] then the command that is completely highlighted is
automatically invoked. You can change the highlighted command by
using the left and right arrow keys.
** Format/Terms/Filename Area. In the middle left of the screen,
one of three lists are displayed: either a list of possible format
styles for formatting, a list of the terms you are using for
searching, or the directory & file names you have programmed into the
Config file. On the Main Menu, for example, the file names are
listed.
** Messages Window. On the bottom left side of the screen, there
is generally a messages window. It has basically two functions: To
provide you with a short description of what you can do, and a list of
the function keys you can press and what their functions are. Note
that now it says you can press [F1] to get help, [F2] to go to the
Global Defaults Menu, or press [Esc] to exit.
** Defaults/Information. The right side of the screen lists the
current local or global defaults, and sometimes some additional
information, such as what you are currently looking at on the Main
Menu.
***System Information***
Notice the information on the right side of the screen labelled
``System Information.'' This provides some useful information to you
regarding the environment that JEPRS is working in. It is also
information that is useful to me if you discover any problems with the
program. If there are any problems, it is very helpful 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:
** Error/Warning Beep. This tells you whether the error beep is
turned on or off. You can change its setting on the Global Defaults
Menu.
** Memory Available. This tells you how much extra space JEPRS has
JEPRS User's Guide, page 13
available to it. The bigger your database, the smaller this number.
Note that this number will vary depending on how many TSR (``Terminate
& Stay Resident'') programs you have in memory, and the number of
successful matches in your last Search. If you have performed a
Search with a large number of matches, this can tie up a lot of
memory; if you plan on sorting formatted output on the Format Menu,
you can free up most of your memory by deliberately performing a
Search that will have only one or a few matches.
** Total Memory (RAM). 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 or use 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, and when you Add or Import
references, it should go up correspondingly.
** Number of relocated references. JEPRS stores your references in
a very compact format. The only disadvantage to this method is that
if you edit any of your references to make them longer, some disk
space is wasted. When this happens, JEPRS increments the number of
relocated references by one. After you have accumulated 20 or so of
these moved references, it starts to take up valuable disk space. To
see how to get rid of these unused references, see the
Utilities/Compress Database Menu.
** Version number. For version 2.01, JEPRS was released to the
public in December 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.
** Original licensee. This is the person or organization to whom
this copy of JEPRS was originally licensed. When you order your own
copy of JEPRS, your name will appear here.
** Disk number. This is the registration number of the disk, and
goes along with the Original Licensee (above).
** 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.)
** Time and date. The current time and date are displayed on the
bottom of the screen. Note that in previous versions this was updated
constantly and automatically; however, that caused certain screen-
blanking routines not to work (such as Borland's SuperKey) so now it
is updated only when you return from a different menu. Of course, if
your computer's internal clock has the wrong time and/or date, then
the time and date displayed here will not be correct.
3.1 Prompts vs. Menus
Note that on the Main Menu you can change the highlighted command
JEPRS User's Guide, page 14
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 the prompt ``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.
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 key you
press must be a non-printing key which must be one of:
[RightArrow]
[LeftArrow]
[Delete]
[Insert]
[Home]
[End]
If you press one of those keys before pressing an alpha-numeric
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 Global
Defaults 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 [End] key and
then press the [LeftArrow] 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.
JEPRS User's Guide, page 15
4 On-Line Help
In order to make your life as simple as possible, JEPRS provides
you with on-line context-sensitive Help screens at the press of a key-
-the [F1] key. At most points within JEPRS (whenever you see
``[F1]=Help'', and sometimes even if you don't), you have the option
of pressing [F1] to get Help. 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.
After pressing [F1], you should see the Help screen on the left
portion of the display (so now you can see your Defaults on the right
side of the screen at the same time). The Help facility provides
context-sensitive help no matter where you are in the program.
***Scrolling Through Help***
Note that after asking for help, several keys are displayed on the
bottom of the Help Screen: [Up Arrow], [Down Arrow], [PgUp], [PgDn],
[Home], [End], and [Esc]. Just like everywhere else in JEPRS,
pressing the [Esc] key will get you out of Help, and back into
whatever you were doing before you pressed [F1].
** Up/Down Arrows. You can scroll through the text on the Help
Screen by pressing the arrow keys. Each key press moves you up or
down one line at a time. JEPRS stops when you have reached the
beginning or end of Help.
** PgUp/PgDn. If more than one page of help text is available, you
can use these keys to page through the text 20 lines at a time.
** Home/End. Pressing these keys will bring you to the very first
or the very last page of the help text, respectively.
** Esc. When you are finished looking at the Help screen, just
press [Esc] to return to where you were in JEPRS before you asked for
Help.
***The Help File***
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.
(where <filename> is the name of the Help file) 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 Global Defaults Menu, then you
should specify its name in the ``Help File name'' on the Global
Defaults 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.
JEPRS User's Guide, page 16
5 Global Defaults
The Global Defaults Menu of JEPRS version 2.0 replaces the Options
Menu of versions 1.0 and 1.1. Its purpose is to allow you to modify
virtually every aspect of JEPRS's working environment, to better suit
it to your personal needs. Everything on this menu can be saved in
your Config file; in this way, once you define your work environment,
JEPRS will act the way you want it to. You won't have to modify these
variables every time you start up JEPRS because it will read them in
from your Config file automatically. Note that this menu is
accessible from the Main Menu, the Search Menu, the Format Menu, and
the Utilities Menu.
On the right side of the screen, you will see all the Defaults that
are accessible from the Defaults choice on this menu. In addition,
``Available space on default drive'' tells you how many bytes of space
are left to use on the current disk drive. 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.
The next few sections of this chapter will explain how to go about
changing, and then saving, the global defaults.
***Files***
This option allows you to change the names of any of the files that
you are using in JEPRS. This prevents you from having to exit the
program just to use a different data file, for example. Note that
when you first start JEPRS, it immediately looks for the Config file
on the current directory with the name ``JEPRS.Cfg'' (unless you
specify a different name on the command line; see the chapter Setting
Up JEPRS, especially the sections Starting JEPRS/Command Line
Options). If JEPRS can't find the Config file, it uses default names
for all of JEPRS's files. The default names are:
Reference File: Ref1.JPR
Ref Key File: Ref1.JPK
Help File: JEPRS.Hlp
Text File: JEPRS.Txt
Number File:JEPRS.Num
Config File: JEPRS.Cfg (or whatever you entered on the command
line)
Import File: ProComm.Log
Export File: JEPRS.Exp
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 JEPRS 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. On the other
hand, when JEPRS creates files (such as Text and Number files) then it
just uses the filename specified (and if no Drive and Directory was
specified, then it uses the current DOS directory).
JEPRS User's Guide, page 17
** Changing a file name. To change a file name, press the first
(highlighted) letter of the file type, or just highlight the file type
using the up and down arrow keys and then press [Enter]. You will be
prompted for the new name of the file in a pop-up dialog box. Note
that the old name is displayed there so that you can edit it (see the
chapter on the Main Menu, especially the subsection called Prompts vs.
Menus, to see how to edit the text at a prompt). Edit the old name or
just type in a completely new name, then press [Enter] when finished.
The filenames you enter here are only temporary; if you want to make
them permanent, you can save them in your Config file. For
instructions, see the section below on [D]efaults/[S]ave
defaults+files.
Note that if you are changing the name of the Reference file or Ref
Key file, you will be prompted for both file names, since they are
specific for each other. JEPRS is smart enough to give the same name
for each file, except for the extension (*.JPR for the Reference file,
and *.JPK for the Ref Key file). You don't have to use *.JPR and
*.JPK as the file extensions, but if you don't then JEPRS will not
automatically use the same file names.
***Defaults***
When you select [D]efaults, a pull-down menu appears. Just like
every other pull-down menu in JEPRS, use the up and down arrow keys
and the [PgUp] and [PgDn] keys to scroll through the choices and press
[Enter] to make a choice (or just press the highlighted letter).
There are a number of items JEPRS lets you configure:
** Error/warning beep. This 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 select [N]o, and JEPRS will never beep at
you.
** Text file formatting. There are several places at which JEPRS
allows you to send formatted output to a Text file. In most cases,
JEPRS will send only your text, and not any printer codes. However,
when you direct Output to a Text file at the Format Menu, JEPRS has
the ability to include the printer codes. That way, you can send your
output to a file, and then use the MS-DOS Print command to print it
later (for example if the printer is already busy, or if you want to
print it on a different machine). If Text file formatting=[Y]es, then
printer codes will be sent to the Text file; if [N]o, then printer
codes will not be sent to the Text file.
** Use printer #. Version 2.0 of JEPRS allows you to define up to
5 printers. This menu option lets you choose which of those printer
definitions to choose. After invoking this command, a menu of your 5
printers is displayed. Use the arrow keys and [PgUp] and [PgDn] to
move among the entries, and then press [Enter]. Or just enter the
number of the printer you want to use. If you press [Esc], then your
previous choice is not changed.
** Save defaults+files. Whenever you change any of the Global
Defaults, they are retained in your computer's memory, but they are
not permanently saved in your Config file. If you would like to save
them, select this command from the menu. When your defaults and files
JEPRS User's Guide, page 18
have been successfully saved, the menu will automatically disappear.
For a list of all the defaults that are saved with this command, see
the chapter on JEPRS's Files, especially the subsection called Config
file.
** Journal Definitions/Format Style Definitions. Your Config file
is capable of storing up to 30 Format Styles (that you use on the
Format Menu). This option lets you change the definitions to anything
you like. For more information on editing these definitions see the
section below called Editing Journal Definitions/Format Styles.
** Printer Definitions. The Config file can store up to 5 Printer
Definitions. This options permits you to edit your definitions to
best suit your printer. For more information on editing your printer
definitions, see the section below called Editing Printer Definitions.
** Colors for screen. In version 1.11 of JEPRS you could specify
screen colors and attributes on the MS-DOS command line (you can still
do this in version 2.0 if you want to). But this series of commands
also allows you to have those choices saved in your Config file. When
you choose this command, a sub-menu appears: you can then choose
[T]ext color/B&W mode, [F]ormatting colors, and [B]linking.
[T]ext color/B&W mode lets you choose either Color mode or Black
and White mode. In color mode, JEPRS uses all the colors available;
in black and white mode, all the screen text is converted to black,
white, and one shade of gray. Here is a brief list of my recommenda-
tions (you may find that a different choice works better on your
particular system):
Video Card: Video Monitor: JEPRS Mode:
CGA, EGA, VGA LCD/Portable B&W
CGA, EGA, MCGA,
or VGA Color Color
CGA, EGA, MCGA Amber, Green,
or White B&W
VGA Amber, Green,
or White Color
MDA/Hercules Amber, Green,
or White B&W
There are some notable exceptions to these general rules. For
example, both Compaq and Zenith have CGA cards that display different
shades of gray on one-color monitors (amber, green, or white). In
that case, the Color mode would probably look best.
[F]ormatting colors affects the look of the screen when you format
references at the Format Menu. If this is set to [C]olors for
formatting, then normal text is displayed as black on cyan, bold text
is white on cyan, and underlined text is represented as cyan on black.
If this is set to [N]o colors for formatting, then all text appears as
cyan on black.
[B]linking is similar to the [F]ormatting colors command, except
that it controls how italic text is represented on the Format Menu.
If this is set to [Y]es, then italic text is represented by blinking
text; if set to [N]o, then blinking is turned off, regardless of
italics.
** Form-feed to printer. Sometimes you may want to eject the last
sheet of paper from your printer. This command allows you to do that
without having to get up and walk over to your printer. Just press
JEPRS User's Guide, page 19
[Y]es to send the form-feed, or any other character to return to the
pull-down menu.
** Ordering information. This choice presents you with details of
how to order the latest version of JEPRS from the author (that's me).
JEPRS is an absolute bargain at $30!
***Go to DOS***
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 may corrupt your data
files! As long as you enter ``exit'' to return to JEPRS, your data
will be completely safe.
An improvement to the [G]o to DOS command in version 2.0 is JEPRS's
use of the COMSPEC specification in your CONFIG.SYS file (note that
this refers to the MS-DOS CONFIG.SYS file and not JEPRS's Config
file!). This change will not affect most users. But if you are a
``power user'' and you use a DOS command processor that is not the
standard COMMAND.COM, then now JEPRS will successfully call this file
via the COMSPEC specification. (In previous versions, JEPRS just
looked for a file called COMMAND.COM in the DOS PATH.)
5.1 Editing Printer Definitions
A variety of printers are supported by JEPRS in the Config file
which comes with the program. If your printer is not one of the pre-
defined ones, or you want to add extra features, then you can easily
modify any or all of the 5 available printer definitions.
ADVANCED TOPIC ADVANCED TOPIC ______________
Why five printer definitions? One easy example is that you
have a laser printer at work and a dot matrix printer at home. By
combining all your formatting and printing commands in one file,
JEPRS prevents you from having to have a new set of Config files
for each printer; you just modify the existing printer definitions
to suit your needs. Another example would be creating files for
word processors. One of the sample printers has commands that are
understood by WordPerfect 4.2, 5.0, and 5.1; but in this case,
instead of sending output to the printer, you would specify a Text
file at the Format Menu. Then you could retrieve your Text file
into WordPerfect. And finally, you could specify one printer
definition for Comma-delimited output. Just like the word
processor printer definition, you would later direct this output
to a Text file rather that your printer.
To edit your printer definition(s), go to the Global Defaults Menu,
choose [D]efaults, and then [P]rinter definitions. A pop-up menu will
appear, listing the five pre-defined printer definitions. Choose one
of the definitions by using the arrow keys and pressing [Enter] or
just entering the number of the printer. Brief help is available by
JEPRS User's Guide, page 20
pressing [F1]. If you want to use the current printer definition,
just press [Esc].
After selecting a printer to edit, you are presented with the
Modify Printer Formats screen. Here is where you can enter all your
printer-specific information. Check your printer manual for the codes
you need to enter for underlining, boldface, etc.
A note about entering printer codes: Many printer codes cannot be
entered directly by the keyboard. For example, if one of your printer
codes was <Esc>, you couldn't just press [Esc] to enter that code,
because JEPRS would interpret that <Esc> as the command to go to the
menu at the top of the screen. To enter a special printer code, first
press ^P; that is, hold down the [Ctrl] key and tap the [P] key once.
Then enter your code. (This is similar to the way WordStar and
SideKick allow you to enter printer codes). Let me give you a quick
example. Let's pretend your printer manual says to enter the
following code to turn underlining on:
<Esc>&d3D
...and the following code to turn underlining off:
<Esc>&d@
You would enter the first code like this:
^P
Esc
&
d
3
D
...and the second code like this:
^P
Esc
&
d
@
...where each line represents a single character (that is, ``^P''
means hold down the [Ctrl] key and press [P], and ``Esc'' means press
the [Esc] key).
You can also enter codes by using the [Alt] key and the number pad
on the right side of the screen. For example, some printer manuals
tell you the printer commands in ``decimal'' format. In this system,
for example, <Esc> is represented by the number 27; this is also the
system used by the ``CHR$'' command in the BASIC computer language
(that is, <Esc> would be ``CHR$(27)''). You can enter these by first
pressing [^P], then while holding down the [Alt] key, pressing [2] and
then [7] on the number pad (note that you cannot press the numbers on
the top row of the keyboard!) and then letting go of the [Alt] key.
Now let me give a brief description of each of the fields listed on
the Modify Printer Formats screen.
** Printer Number. You cannot change this number; it is set by
JEPRS. This number allows you to pick this printer at the [U]se
printer # command on the Global Defaults Menu.
** Printer Name. Enter the name of your printer. This name will
appear next to the printer number on the printer selection menu.
** Printer Initialization Code. You can enter a code here that
will be sent to your printer every time you send output to the printer
JEPRS User's Guide, page 21
at the Format Menu. For example, you may want to specify a certain
font, or character pitch, or otherwise initialize your printer.
** Printer Reset Code. This code will be sent to your printer
every time printer output is finished when you are at the Format Menu.
** Title. This text and/or codes will be sent to the printer as
the title for the first (and only the first) page of output. You may
want to enter something like ``Reference List'' or ``Bibliography'' in
this space.
** Header. This text and/or codes is sent to the printer as the
top line of every page of output. There is also one special code you
can enter: ``\P''. If that code appears anywhere on the line, it
will automatically be replaced with the page number (you can set the
starting page number on the Format Menu). For example, you may want
to enter something like:
JEPRS output for 21 November 1989, page \P
** Left Margin. Enter the number of characters you want JEPRS to
skip to make a left margin. For example, if you enter ``0'', then
JEPRS will start printing at the very left edge of the page; if you
enter ``12'', JEPRS will skip 12 spaces before printing each line.
** Characters per line. This is the number of characters prints on
each line before starting on the next line. Example: You're printing
on 8.5 x 11 inch paper; your printer prints at 10 cpi (characters per
inch); your left margin is 10 characters (= 1 inch); and you want a
right margin of 1 inch. In this case, you should specify ``65'' as
the Characters per line, since there is a total of 85 characters per
line (8.5 inches x 10 char/inch), you have a left margin of 10
characters (1 inch) and you wanted your right margin to be 1 inch (85
- 10 - 10 = 65).
Things get a little tricky if your printer prints a proportionally
spaced font (like a laser printer's Times Roman font). Since each
character's width is different, you'll just have to play around with
the line Length number until you get a number that is large enough so
that it doesn't leave too wide a right margin, yet small enough that
it doesn't chop letters off the right hand side. And if you enter
your Keywords in ALL-CAPITALS remember that these are much wider than
lowercase letters and you'll have to allow for this when printing. If
you want to print keywords in ALL CAPS then I suggest that either you
use a non-proportional (fixed-spacing) font or that you send the
format to a Text file (instead of to the printer) and then import it
into a word processor.
** Pause after each page. For most printers, you would enter
``No'' here. However, for printers in which you have to hand feed
each individual sheet of paper, set this to ``Yes''. When this value
is ``Yes'', then when JEPRS finishes printing one page at the Format
Menu, it will ask you to feed the next sheet of paper and press
[Enter] before it starts printing the next page.
** Top margin. This is the number of spaces to be skipped at the
top of each page. For example, if your printer is set for printing 6
lines per inch and you want to leave a 1-inch top margin, then enter 6
here.
** Lines per page. Enter the number of lines per page, not
including the top margin or header. Let's use the example again of a
printer with 6 lines per vertical inch. On an 11-inch piece of paper,
JEPRS User's Guide, page 22
that's a total of 66 lines. If you set Top margin to 6, then you're
left with 60 lines. But then JEPRS prints the Header and skips 3
lines automatically, so now you're down to 57 lines. If you want to
leave a 1-inch bottom margin (6 lines) then you're down to 51 lines:
this is the number you should enter for Lines per page.
** Form feed last page. If you want JEPRS to eject the final
printed page from your printer, then enter ``Yes'' here.
** Underline/Bold/Italic/Superscript/Subscript On/Off. Enter the
codes your printer requires to start and stop each of these special
features. See the paragraphs at the beginning of this section that
describe how to use the ^P key to enter codes here.
** Comments. This is two lines of text where you can enter any
comments you want. These comments are for your information only;
JEPRS ignores them completely. You might want to enter information
like what your Initialization and Reset codes mean in English!
***Saving Your Definitions***
When finished editing your printer definition, press [Esc] to get
to the menu at the top of the screen. As usual, you may press [H]elp
to get help. Otherwise press [S]ave to save your printer definition,
press [E]dit to modify a different definition (see Advanced Topic,
below), or press [Esc] to return to the Global Defaults Menu.
ADVANCED TOPIC ADVANCED TOPIC ______________
If you don't [S]ave your definition, then it still stays in
your computer's memory, but it will be erased under two
conditions:
1. You exit JEPRS.
2. You choose a printer definition again. Well, sort of! Let
me give an example. Let's say you edited printer definition #2,
and you're now at the menu at the top of the screen. Then you
press [Esc] without [S]aving, so the modified printer definition
#2 is still in memory and the original printer definition #2 is
still in your Config file. If you then access the printer
selection menu (either by pressing [U]se printer #, or by pressing
[P]rinter definitions, at the Global Defaults Menu) and select #2
and press [Enter], then the original #2 is read in from your
Config file and replaces the modified #2 that was in memory. On
the other hand, if you're at the printer selection menu and you
press [Esc] (instead of choosing #2 again) then the modified #2 is
kept in memory and you can edit it (or [S]ave it) again.
5.2 Editing Journal Definitions & Format Styles
You can create up to 30 different Format Styles/Journal Definitions
in JEPRS. These various formats are used for selecting the style of
output at the Format Menu. To edit any of them, go to the Global
Defaults Menu, choose [D]efaults, and then [J]ournal definitions. A
pop-up menu will appear from which you can select any of the 30 Format
styles. To select one, use the up & down arrow keys, [PgUp] & [PgDn],
and [Enter] to select. Or, just enter the number of the style you
wish to edit. If you instead press [Esc], the previously selected
style will be used.
JEPRS User's Guide, page 23
Once you select a Format style to edit, you will be placed at the
Modify Journal Formats screen. Here is where you can directly edit
any aspect of the Format styles/Journal definitions. You can enter
any normal text, any of the codes listed at the bottom of the screen,
or any non-standard character by using the [^P] key (see the previous
section, Editing Printer Definitions for information on entering
special codes with the [^P] key). Here is a brief run-down of each
field.
** Journal Name. Enter the name of the Format style. This name
will be displayed on the pop-up menu that lets you choose among the
thirty Format styles.
** Number. This is the number of the Format style. You cannot
modify this number.
** Sort Reference. If you enter ``Yes'' here, output references
will be sorted by author and year before being sent to the output
device(s) selected at the Format Menu. If ``No'', then no sorting is
done.
** Indent Length. The number of characters each continuation line
is indented beyond the left margin defined in the printer definition.
If this number is zero, then no indenting is done:
1. SA Jones & ME Smith (1989) Fake references
and you, Journal of Irreproducible Results
If this number is set to 5, for example, then five spaces would be
skipped on the 2nd and additional lines:
1. SA Jones & ME Smith (1989) Fake references
and you, Journal of Irreproducible Results
(note that the second line was indented 5 spaces).
** Journal/Abstract/Book. This is where you enter the codes
(listed at the bottom of the screen) that tell JEPRS how to format
your journal, book, and abstract articles. First, here's some basic
information you should know about entering formats:
The first set of characters you enter on a line (before the first
space) will be used to connect the names of the authors if there is
more than one. For example, if you start off the defintion with ``and
'' (don't forget the space), then when multiple authors are listed for
a reference they will be printed as ``WE Wright and LM Miranda''. On
the other hand, if you start off the definition with ``& '', then
multiple authors will be printed like this: ``WE Wright & LM
Miranda''. I can't imagine using anything other than ``and '' or ``&
'' to connect the authors, but if you do, realize that it can't be any
more than 10 characters long and it can't have spaces within it.
Any character that is not a special code will be printed exactly as
is. For example, if your definition is ``and \L (\Y).\/\/'' then a
sample output would be:
WE Wright and LM Miranda (1988).
(yes, that's right; the last two line feed characters (\/\/) create an
extra blank line; also, the year is enclosed in parentheses, just as
you specified in the definition). The best way to understand how
definitions work is to print out sample ones using the Format Menu,
and compare the output to the codes in the Format style definition.
After comparing them carefully, you'll get a better feel for how the
system works.
JEPRS User's Guide, page 24
Here is a complete rundown of what the special codes in the Format
styles are for:
** \F. Place authors in output, first name first (e.g., ``LM
Miranda, VK Lin and WE Wright'').
** \L. Place authors in output, last name first (e.g., ``Miranda,
LM, Lin, VK, and Wright, WE'').
** \1. Place authors in output, last name first for the first
author and first name first for each additional author (e.g.,
``Miranda, LM, VK Lin and WE Wright'').
** \A. Place authors in output without any modifications (that is,
don't add the ``and'' or ``&'' or extra commas). This would likely
only be used for comma-delimited output.
** \T. Place title in output.
** \J. Place journal name in output.
** \N. Place reference number in output. For example, reference
#22 would have a ``22'' in front of it, reference #67 would have a
``67'' in front of it, each regardless of its position in the output.
(See also `\#', below.)
** \C. Place citation type in output (i.e., ``Journal'', ``Book'',
or ``Abstract'').
** \Pa. Place page numbers in output.
** \E. Place editor in output.
** \Pu. Place publisher in output.
** \Y. Place year in output.
** \K. Place keywords in output.
** \#. Number output references sequentially. That is, the first
reference printed (regardless of its number in the database) is
printed with the number `1'; the second reference printed (regardless
of its number in the database) is printed with the number `2'; and so
on. (See also, `\N', above.)
** \/. Start new line. (That's a ``backslash'' followed by a
``forward slash'', not a capital V!)
** \<. Start optional inclusion.
** \>. End optional inclusion. What's an ``optional inclusion''?!
This is used to prevent printing any text that is dependent on one of
the fields being present. Let's say that the rules are that if you
are referencing a book then the title of the chapter has to be in
single quotes. So your definition in JEPRS might look like this:
and \F. `\T' in: \J.
That's fine if every book in your JEPRS database has a chapter title.
A sample would look like this:
WE Wright. `Muscle Cells' in: Cell Development.
But if you had a book that didn't have chapter titles that you could
use, the output would look kind of funny, like the next line:
WE Wright. `' in: Cell Differentiation.
That's not exactly a catastrophe, but it is undesirable. The optional
inclusion codes allow you to get around a situation like this. In
this case, you define your output this way instead (compare it to the
prior definition):
and \F. \<`\T' in: \>\J.
Notice the ``\<'' and ``\>'' optional inclusion codes which surround
```\T' in: ''. What this tells JEPRS is that if the field inside the
JEPRS User's Guide, page 25
optional inclusion characters (in this case ``\T'', or the Title
field) is empty, then don't print any of the characters within the
optional inclusion. Therefore, the two examples above would print
like this:
WE Wright. `Muscle Cells' in: Cell Development.
WE Wright. Cell Differentiation.
And that is much nicer output! More examples are given in the
tutorial for you to study (also look at the examples in the Config
file provided).
The next few codes are ``toggles''. This means that you have to
use them twice: once to turn on the function, and once to turn it
off. You usually have to do the same thing in a word processor, like
entering a command to start boldface, entering the text to be
boldfaced, and then finally entering another code to stop boldface.
** \S. Toggle subscripts.
** \^. Toggle superscripts.
** \~. Toggle italics.
** \B. Toggle boldface.
** \_. Toggle underline.
Note that if you haven't entered the printer-specific sequences for
these codes in your Config file, then they won't print on your
printer.
Once you've spent the time to modify the Format styles to your
specific needs, using JEPRS is an absolute breeze.
** Comments. The last two lines of the screen are where you can
enter any comments you like. These are for your use only; JEPRS will
not try to interpret them or use them for any other function.
***Saving Your Definitions***
When finished editing your journal definition, press [Esc] to get
to the menu at the top of the screen. As usual, you may press [H]elp
to get help. Otherwise press [S]ave to save your Format style
definition, press [E]dit to modify a different definition (see
Advanced Topic, below), or press [Esc] to return to the Global
Defaults Menu.
JEPRS User's Guide, page 26
ADVANCED TOPIC ADVANCED TOPIC ______________
If you don't [S]ave your definition, then it still stays in
your computer's memory, but it will be erased under two
conditions:
1. You exit JEPRS.
2. You choose a Format Style again. Well, sort of! Let me give
an example. Let's say you edited Format Style #2, and you're now
at the menu at the top of the screen. Then you press [Esc]
without [S]aving, so the modified journal definition #2 is still
in memory and the original journal definition #2 is still in your
Config file. If you then access the Format Style selection menu
(by pressing [F]ormat style on the Format Menu, or by pressing
[J]ournal definitions at the Global Defaults Menu) and select #2
and press [Enter], then the original #2 is read in from your
Config file and replaces the modified #2 that was in memory. On
the other hand, if you're at the journal definition selection menu
and you press [Esc] (instead of choosing #2 again) then the
modified #2 is kept in memory and you can edit it (or [S]ave it)
again.
6 List References
Many times you will want to look up just a single reference or two.
There is no need to do a Search through the entire database if you
already know the number of the reference you want to examine or edit.
Just choose [L]ist from the Main Menu to get to the List References
screen. Note: The List References screen can also be called from the
Search Results screen. There are some subtle differences when using
List from the Main Menu and List from the Search Results screen. See
the section below (`List' from `Search Results') for an elaboration of
the differences.
When you first reach the List References screen, JEPRS initially
displays the most recently accessed reference in your database, and
then asks you for a reference number. Enter the number of the
reference you wish to view; the corresponding reference in the
database is subsequently displayed. JEPRS displays your reference in
the standard screen format, allowing 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.
If, by mistake, you enter the number of a reference that is not in
the database (for example, a number larger than the last reference in
the database), JEPRS displays the closest valid reference. You can
use this to your advantage: If you enter a number larger than your
database (such as ``99999''), JEPRS assumes you want to go to the end
of the database, and will display the last reference.
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 #122 then ``122'' will be displayed as the default
value for the next reference; to look at reference #129, just press
JEPRS User's Guide, page 27
[End], then [BackSpace] once, then press [9] and [Enter] and #129 will
be displayed.
***Function Keys***
Note that there are several keys that perform special functions--
these are described on the bottom of the screen. Here is a run-down
of each of those keys and their functions within the program.
** Esc. As you have probably come to expect by now, this key will
end what you're doing and bring you back to the previous menu (which
will be either the Main Menu or the Search Results screen).
** F1. As always, this will give you context-sensitive help,
including a brief description of the function keys available on the
List References screen.
** F4. Edit reference (see separate section, below).
** PgDn. ([Page Down] on 101-key keyboards) displays the next
reference in your database. For example, if you first enter `142',
JEPRS displays reference #142; if you then press [PgDn], reference
number 143 will be displayed.
** PgUp. ([Page Up] on 101-key keyboards) displays the previous
reference, just the opposite of [PgDn].
** F8. Only the number (e.g. ``6'') of the current reference is
sent to a Number File. This Number File can subsequently be used for
input during formatting or exporting.
** F9. The currently displayed reference to be sent to your
printer in the currently defined Format Style (selected on the Format
Menu).
** F10. Sends the current reference to a DOS Text File (again, in
the currently-defined Format Style). Note that the Text File
Formatting on the Global Defaults Menu affects the contents of the
output to this file.
***`List' from `Search Results'***
One of many new features in JEPRS version 2.00 is the ability to
look at your entire reference when at the Search Results screen. When
List References is called from the search module, there are a few
minor changes in the workings of the function keys:
** Esc. This will bring you back to the Search Results screen, not
the Main Menu.
** PgUp. Instead of displaying the previous reference in the
database, the previous found reference is displayed.
** PgDn. Instead of displaying the next reference in the database,
the next found reference is displayed.
The changes in [PgUp]/[PgDn] function may not be intuitive, so let
me provide you with an example:
Let's say you performed a search that found the following
references that matched your search terms:
#3, #6, #88, #122, and #131
You press [Enter] at the Search Results screen while the cursor is on
reference #88; this brings up the List References screen displaying
#88. If you now pressed [PgDn], then instead of #89 being displayed,
#122 would be displayed because it is the next found reference from
the search. Likewise, pressing [PgUp] would display #6, since it was
JEPRS User's Guide, page 28
the previous found reference. Well, what if you really did want to
see reference #87? Don't worry--you can still enter `87' at the
prompt.
6.1 Editing & Updating References
Editing references is essentially identical to adding references.
See the next chapter (`Add New References') for information on the
function keys and menus used for editing/adding references.
Note that since JEPRS does not have a Delete Reference option, Edit
Reference can be used to remove an old reference citation and replace
it with a new one.
JEPRS User's Guide, page 29
7 Add New References
One of the first things you'll want to do after starting your own
database is to add references to it. This part of the program allows
you to enter new references at the keyboard (alternatively, you can
automatically load references in various formats from a file using the
Import Menu).
Notice the standard screen format used for adding, editing, and
listing references. It displays: Title = 3 lines, Authors = 2 lines,
Journal = 2 lines, Volume, Pages, Year, Type, Number, Editor,
Publisher = 2 lines, Keywords = 5 lines. The menu at the top of the
screen is initially inactive. As usual, the function keys are listed
at the bottom of the screen. The cursor is first placed on the Title
field.
***Function Keys***
The function keys used for moving around your text generally
perform the same function they would in a word processor or text
editor:
** Up Arrow. Move the cursor to the previous field.
** Down Arrow. Move the cursor to the next field.
** Right Arrow. Move the cursor one character to the right. When
you reach the end of a field, you are automatically brought back to
the beginning of the same field.
** Left Arrow. Move the cursor one character to the left. When
you reach the beginning of a field, you are automatically brought back
to the end of the same field.
** Enter. Same as the [Down Arrow].
** PgUp. Move the cursor to the first line of the Title.
** PgDn. Move the cursor to the first line of the Keywords.
** Home. Move the cursor to the beginning of the current field.
** End. Move the cursor to the end of the current field.
You just type in text as you want it to appear (but see Suggested
Format below, too). Realize that the cursor wraps around to the
beginning of the same line on multiple-line fields (such as the
Title), so don't forget to press [Enter] when you're near the end of a
line to get to the next line. JEPRS also sports three additional
editing features:
** BackSpace. This deletes the previous character on the line,
just like a typewriter would.
** Del. The deletes the current character over the cursor.
** Ins. This toggles the editor between Insert Mode and Overwrite
Mode. You can tell which mode you are in by looking at the bottom
right corner of the screen; there is a box there that says `Insert' or
`Overwrite'. When in Insert Mode, any characters to the right of the
cursor are pushed over when you type in characters. In Overwrite
Mode, characters to the right of the cursor are written over and
erased by the characters you are entering.
Two more function keys are available that you probably want to know
JEPRS User's Guide, page 30
about.
** F1. As everywhere else in JEPRS, this key will give you context
sensitive help with adding your references.
** Esc. Rather than bring you back to the Main Menu, this key will
activate the menu at the top of the screen.
When you are done adding your reference, press [Esc] to activate
the menu at the top of the screen. Once you do this, you have one of
three choices:
** Save reference. Your reference will be added to the database on
disk.
** Abandon reference. The reference you just edited will be
ignored (it will not be saved to disk) and the screen is cleared.
** Edit. You will be returned to the reference you were just
editing, in order to allow you to continue to modify it.
** Help. This will bring up a help screen.
Once you have chosen [S]ave or [A]bandon above, the next menu will
provide you with two choices:
** Continue. Go back to the Add References screen to add another
references.
** Main Menu. Allows you to return to the Main Menu (pressing
[Esc] here will do the same thing).
7.1 Suggested Format
Most of the time, JEPRS doesn't really care how you enter your
references into the database--the fields are all basically just text
fields, so you can enter anything you want. (The only field it does
care about is the Authors--you should pay close heed to the
suggestions provided below.) However, in order to make the formatted
output as consistent as possible, I have provided a list of
suggestions for how you might enter your references into all of the
fields:
** 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. This is the only field where you must pay strict
attention to the guidelines. Authors are entered last name first,
followed by a space and then the initials. There is no space between
initials (this is crucial), but periods can be used if you like, and
dashes are OK for hyphenated initials. Spaces and dashes are OK
between multiple last names (e.g., `da Vinci' or `Weaver-Jones'). For
multiple authors, place a comma and a space after each author (this is
crucial), 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 Author entries:
Correct: Incorrect: Reason:
Lin VK-I Lin V K-I extra space
Wright WE, Lin V Wright WE & Lin V ampersand
da Vinci L da Vinci, L comma
** Journal. It is generally easier and takes less typing to enter
JEPRS User's Guide, page 31
standard abbreviations for journals, rather than full names, but this
is not required (e.g. ``Mol Cell Biol'' instead of ``Molecular and
Cellular Biology''). When formatting bibliographies/reference lists,
some publications 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 that
publication'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. There are a variety of ways of entering the pages. You
can enter just the first page, or the first page, a dash, and the last
page, or the first page, a dash, and the `significant digits' of the
last page. For example:
134 or 134-139 or 134-9
Note that MedLine does it the last way (134-9), if you want to
maintain consistency with MedLine. See also the note for novices
under Year.
** 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; (2)
it is also required for proper formatting on the Format Menu, 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. Some people prefer entering the full name, some use
just the first initials and full last name; whatever you do, just
maintain consistency. Don't end it with punctuation.
** Publisher. Generally, you would enter the publisher's name and
city. Don't end it with punctuation.
** Keywords. Keywords must be separated by a semicolon (`;').
This is so that when you export your references in the MedLine format,
JEPRS can find a place to break up the keywords into their own fields.
Keywords can be entered either in all capitals or mixed upper- and
lower-case; there is no particular advantage to doing it either way,
since during a Search you can convert them to uppercase for
comparison.
The only disadvantage to using all uppercase 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
JEPRS User's Guide, page 32
of the characters. Look at the following example:
THIS IS A TEST OF FIXED SPACING
This is a test of fixed spacing
THIS IS A TEST OF PROPORTIONAL SPACING
This is a test of proportional spacing
With a fixed-spacing font, both the all-uppercase and the mixed-case
lines take the same amount of space; but with a proportional font, the
all-uppercase 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 uppercase and lowercase) with a very
wide right margin. Of course, if you plan on importing MedLine files,
these have their keywords in all uppercase 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).
7.2 Entering Sample References
In this section, I will present you with suggestions for entering
the three (actually, four) types of references that JEPRS was designed
to deal with.
** Entering a Journal/Magazine Article Reference. These types of
articles generally have: an article title, several authors, a journal
or magazine name, a volume number, page(s) of publication, year of
publication, and any number of keywords you want to add. Let's say
the reference was the article called ``Myogenin, a factor regulating
myogenesis, has a domain homologous to MyoD'' by Woodring E. Wright,
David A. Sassoon, and Victor K. Lin, that appeared in the journal Cell
in 1989, volume 56, pages 607 through 617, and then you wanted to add
some keywords. A sample entry might look like this:
Title:Myogenin, a factor regulating myogenesis, has a
domain homologous to MyoD
Authors:Wright WE, Sassoon DA, Lin VK
Journal:Cell
Volume:56Pages:607-17 Year:1989 Type:Journal #:158
Keywords:Rat;myogenesis;cell differentiation;cell
determination;myogenin;MyoD1;L\S6\S;C\S3\SH10T1/2;
\~myc\~-homology domain;\~myd\~;BUdR/
Bromodeoxyuridine;
Note that some of the keywords above have strange character
doublets like `\S' and `\~'; these are JEPRS's formatting codes for
subscripting and italicizing, respectively. So, when they keywords
are printed on your printer, `C\S3\SH1051/2' will come out as
`C3H10T1/2', and `\~myc\~-homology' will come out as `myc-homology'.
You can enter any of JEPRS's commands for boldfacing, underlining,
italicizing, super-and sub-scripting right into your references;
JEPRS User's Guide, page 33
however, note that this feature is in addition to the Format Menu
formatting options, so don't think you have to italicize every journal
name in your database, because it should be done at the Format Menu.
The formatting commands are described in the Global Defaults chapter
on creating Journal Definitions.
** Entering an Abstract Reference. One of the various types on
entries you may want to make is for a reference to an abstract. In
the biomedical sciences, for example, abstracts of data to be
presented at scientific meetings are published in a softcover book,
generally. The information for an abstract is similar to that of a
book (see below), but quite different from a journal entry. This
example will be from a poster presented at the Cold Spring Harbor
Laboratory meeting in September, 1989:
Title:Developmental regulation of myogenin, a gene
regulating vertebrate myogenesis
Authors:Miranda LM, Wright WE
Journal:Regulation of eukaryotic mRNA transcription
Volume: Pages:150 Year:1989 Type:Abstract #:855
Editor:W Herr, R Tjian, K Yamamoto
Publisher:Cold Spring Harbor Laboratory, Cold
Spring Harbor, NY USA
Keywords:Rat;myogenesis;cell differentiation;
myogenin;MyoD1;L\S6\S;C\S2\SC\S12\S;Promoter
\~myc\~-homology domain;TATA box;transfection;
In this case, note that the `Journal' field becomes the symposium
title, and the `Editor' is actually the organizers of the meeting.
** Entering a Book Reference. The third major category that JEPRS
was designed for is book entries. If you plan on referencing a whole
book as one entity (rather than chapter by chapter), here is a
suggestion:
Title:
Authors:
Journal:Year Book of Developmental Biology
Volume: Pages: Year:1989 Type:Book #:856
Editor:JM Schindler
Publisher:CRC Press, Inc., Boca Raton FL USA
Keywords:cell differentiation;developmental biology;
mini-reviews;cell determination;gene expression;
cell biology;morphogenesis;pattern formation;
Notice that the Title and Authors are blank, the Journal becomes
the book title, the Volume is blank (unless, of course, it is a serial
publication), the Pages are blank, and everything else is as expected.
** Entering a Book Chapter Reference. Sometimes, you will want to
reference a specific chapter of a book, rather than the book as a
whole. This is easily accomplished by a slight modification of the
JEPRS User's Guide, page 34
Book definition above:
Title:Genetics of \~Drosophila\~ embryogenesis
Authors:Mahowald AP, Hardy PA
Journal:Ann Rev Genet
Volume: Pages:149-77 Year:1985 Type:Book #:856
Editor:
Publisher:Annual Reviews, Inc., Palo Alto, CA USA
Keywords:cell differentiation;developmental biology;
cell determination;gene expression;morphogenesis;pattern
formation;\~Drosophila\~;
In this example, the chapter title is entered in the Title field,
the chapter authors in the Author field, the book name in the Journal
field, the `Book' type in the Type field, and the book editors in the
Editor field. Just as in the Journal/Magazine example, JEPRS's
special formatting characters are used, in this case italics for
Drosophila.
JEPRS User's Guide, page 35
8 Format References
Formatting is one of several areas where JEPRS really shines. I
know of no other shareware program that offers anywhere near the
variety of choices that this program offers. Formatted output can be
boldfaced, underlined, italicized, superscripted, and subscripted,
depending upon the capabilities of your printer. You can specify page
length, characters per line, a header, page numbering, and a host of
other parameters. Most of these definitions are defined in the Config
file and are accessed at the Global Defaults Menu under Defaults,
Printer Definitions; and Defaults, Journal Definitions. Once you have
defined these yourself (or use the pre-defined ones), you can format
your references here, at the Format Menu.
The menu at this point contains the commands Go, Format, Input,
Output, Defaults, and Help. As usual, the Help command can be invoked
by pressing [F1], also. Of course, [Esc] brings you back to the Main
Menu. The rest of the commands are described in further detail below.
8.1 Pre-Defined Settings
New in version 2.0 of JEPRS is the ability to have your Input,
Output, Format, and Defaults set to previously determined values. If
you like these values as they are, you can skip over this section and
get right on to formatting. However, if any (or all) of these are not
to your liking, simply modify them as described here.
***Formats***
You can define up to 30 format styles (also known as journal
definitions) in your Config file (see the chapter on Global Defaults
for information on modifying these styles). These format styles
define how the formatted output from JEPRS will look.
When you press [F]ormat while at the Format Menu, you are ready to
pick which format style to use. Use the up and down arrow keys and
the [PgUp] and [PgDn] keys to scroll through the 30 available styles.
When the arrow is next to the format style you wish to use, just press
[Enter]. Or, just enter the number at the ``Format Style:'' prompt.
If you decide you don't want to change the style, just press [Esc].
If there is one format style that you use most often, you can save
its number in your Config file as the default format style. Just go
ahead and choose one of the available styles, then return to the
Format Menu. Now press [F2] to go to the Global Defaults Menu. When
you get to this menu, press [D]efaults, and then [S]ave
defaults+files. Now whenever you use that Config file, the format
style you just saved will be used as the default style.
***Input***
By default, JEPRS uses the keyboard for input. This means that
when you press [G]o to start formatting, you would have to manually
enter the number of each reference that you want formatted at the
keyboard. Sometimes this is not the best way to format your
references. For example, you may want a whole subsection of your
reference file (or the whole thing) formatted, or you may want to use
JEPRS User's Guide, page 36
a Number file as input. Either of these are very easy to do.
When at the Format Menu, press [I]nput. This will bring up a pull-
down menu. Like every other pull-down menu in JEPRS, use the up and
down arrow keys and [PgUp] and [PgDn] keys to move among the choices,
then press [Enter] when the selection you want is highlighted. Or,
just press the highlighted letter of your choice. Notice that when
you make a selection, a yellow arrow appears next to that name on the
right side of the screen. This is a reminder of your choice. Here is
a list of effects of selecting each of the inputs:
** Keyboard input. After pressing [G]o, you will be prompted to
enter the number of every reference that you want formatted.
** Number file input. After pressing [G]o, JEPRS will look for the
Number file, using the name specified on the Global Defaults Menu.
This is just a text file containing numbers of references, with each
number on a separate line. You can create this file yourself with a
text editor or word processor (in the Dos Text/Non-document mode). In
addition, JEPRS can create this file by pressing [F9] when at the List
Menu or the Search Results screen. For more information on the Number
file, see the chapter on JEPRS's Files.
** Reference file input. If you select this item at the pull-down
Input menu, then you are asked at which reference you wish to start
and end. If you want to format the whole database, then just use the
default values (which are the first and last reference in the
database). Otherwise, you can enter any two reference numbers at
which to start and end formatting.
***Output***
When you select [O]utput from the Format Menu, a pull-down menu
pops up to give you a choice of Screen, Printer, or Text File. You
can mix and match any combination of outputs. Check the right side of
the screen under ``Output:'' to see which of the outputs are currently
selected.
** Screen. Once you press [G]o to start, the formatted references
will be displayed on the screen, continuously scrolling from bottom to
top.
** Printer. Your formatted references will be directed to your
printer. The currently defined printer will be used; check the Global
Defaults Menu to see which printer that is.
** Text File. The references will be sent to the currently defined
Text File (see the Global Defaults Menu to view the name of that
file). Note that the global default called Text File Formatting on
the Global Defaults Menu determines how the output references are
formatted, in addition to the current Format Style.
***Defaults***
There are two local defaults on the Format Menu.
** Page Start #. This number tells JEPRS how to number the pages
on your output. JEPRS only numbers the output pages if you include
the ``\P'' code in your header (see Printer definitions on the Global
Defaults Menu). By default, it starts page numbering at page #1, but
you can set this number to anything greater than zero. For example,
if you set it to 23, then the first page of output will be listed as
#23, the second page as #24, the third page as #25, and so on.
JEPRS User's Guide, page 37
** Replace " with.... This default is useful for comma-delimited
output. When you use comma-delimited output as a format style, then
the fields are each enclosed in double quote marks and separated by
commas. For example, if the year was 1989 and the author was Wright
WE in one of your references, then they would appear in comma
delimited output as "Wright WE", "1989". However, there is the
possibility that one of your references might itself contain a double
quote mark. This would seriously interfere with your ability to
import that reference into another database system (the additional
double quote mark would mess it up). The Replace " With... default
allows you to change every occurrence of a double quote mark with some
other character when it is output during formatting. So if you had a
keyword that was:
Open Reading Frame/"ORF"
and you set the Replace " With... default character to a single
backwards quote (`), then JEPRS would send your formatted output like
this:
Open Reading Frame/`ORF`
thereby avoiding the problem of extra double quotes in your output.
8.2 Starting Formatting
Once all the default values are set to your liking, just select
[G]o to start the formatting process. Your screen will vary depending
on the type of input and output you have selected.
** Keyboard Input. If you have selected keyboard input, then the
very last line on the screen will prompt you for a reference number
entry. Type in any number and press [Enter]. The number will
automatically be incremented, so if you want to enter a sequential
series of numbers, just keep pressing enter. Since it is a prompt,
you also have the option of editing the value displayed (see the first
chapter of the User's Guide for more information on prompts).
If you have selected screen output (and any combination of printer
or text file output), then the references will be displayed on the
screen as soon as you enter the number. However, if the particular
format style you have selected has Sort=Yes, then the references are
displayed only after you have entered the last reference number and
then pressed [F3] to start formatting.
If you have not selected screen output, then a pop-up window will
appear. This window will display the number of each reference as
JEPRS is formatting it and sending it to the specified output(s).
** Reference or Number File Input. If you have selected either of
these files as input, then the screen will clear and the following
will appear at the bottom:
[Esc]=Exit [ScrollLock]=Pause
As usual, pressing [Esc] will terminate the current process and bring
you back to the previous menu. Before it does, though, a pop-up
dialog box will first ask you ``Terminate Formatting? (y/n)''; press
[Y] to stop formatting or [N] to continue.
If you have turned screen output on, the formatting references will
scroll by on the screen quite rapidly (much more rapidly than previous
versions of JEPRS). There is, however, an easy way to temporarily
stop the screen: press the [ScrollLock] key on your keyboard (it's
generally at or near the top right corner of your keyboard). If you
JEPRS User's Guide, page 38
do, the screen will pause, and the following message will appear at
the bottom:
Press [ScrollLock] to continue
So, just press the key again to restart the formatting display of your
references.
If you have turned screen output off (and are using text file or
printer output) then a pop-up box will appear displaying the current
reference number being sent to the requested output device(s).
JEPRS User's Guide, page 39
9 Searching
Once your database becomes fairly large, you will often not
remember exactly which references it contains. You would probably
like a system that allows you to search through your database to find
the reference or group of references that you're looking for. JEPRS
is quite flexible in this regard, and allows both very simple and
quite complex searches. This chapter will describe how to go about
searching through your database.
The menu at the top of the screen contains the commands [G]o,
[T]erms, [O]utput, [D]efaults, and [H]elp. As usual, Help can also be
accessed by pressing [F1]. And [Esc] brings you back to the Main
Menu. The rest of the commands are described below.
9.1 Pre-Defined Settings
All you need to do in order to perform a simple search is to
specify one search [T]erm and then press [G]o to start (assuming all
the pre-defined selections listed on the right side of your screen are
to your liking). You cannot start a search without specifying any
Terms; if you try to, you will get an error message.
***Terms***
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 [T]erms.
** Enter ``A'' to search through the author field.
** Enter ``Wright'' to search for this particular text.
Once you press [T]erms, you are asked to ``Enter search:''; this is
where you enter the letters corresponding to the field(s) to be
searched. JEPRS lists the letters and their respective fields at the
bottom of the screen; they are reprinted here for your convenience:
[A]uthors [E]ditor [K]eywords [C]itation type
[T]itle [Y]ear [P]ublisher [J]ournal
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 [A]uthor [+][and] [T]itle, 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.] Thus your screen should look like this:
Enter Search: A+T
JEPRS User's Guide, page 40
Wright
Myogenin
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''; that is, both an
author an a title must be in the same reference.
** ``A/T'' is logically identical to ``T/A''; that is, either an
author or a title must be in the same reference.
** ``A-T'' is very different from ``T-A''. In the first case, the
author must be in a reference and the title must not be in a
reference; in the latter, the title must be in a reference and the
author must not.
** 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 for the second search text enter the name of the
author you don't want to find. This will accomplish the same thing as
``-A''.
** 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) Make Case
Sensitivity=Yes and search for ``Stein''; then ``Frankenstein'' would
not be a match; (2) Use a space, a comma, or other delimiter, for
example ``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 [F4] (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 some of your references
didn't contain both Stein and Steinberg as authors!
***Output***
When you select this option, a pull-down menu appears, allowing you
to select any combination of Screen, Printer, Text file or Number
file. Check the right side of your screen to see which output(s) are
currently selected. The default is Screen=Yes, everything else=No.
If you try to turn all the outputs off, JEPRS will beep and turn the
Screen back on.
** Screen. Once searching begins, successful matches will be
displayed on your screen in a compact, one-line format for each
reference found.
** Printer. Successful matches will be sent to your printer in the
currently-defined format style (see the Format Menu to select the
JEPRS User's Guide, page 41
format style). Note, however, that printer codes will not be sent to
the printer! Also, the margins are predefined and cannot be changed.
If you want to have formatted output (including boldface, etc.) sent
to your printer, you must have output sent to your printer from the
Format Menu, not the Search Menu. You can do this by turning the
Number file on for output at the Search Menu and then using the Number
file as Input at the Format Menu.
** Number File. Only the numbers of the successful matches will be
sent to this DOS text file. This file can then be used as Input on
the Format Menu and the Export Menu. See the chapter on JEPRS's Files
for more information on the Number file.
** Text File. This is identical to having output sent to the
Printer, except that it will be sent to the Text file (see the Global
Defaults Menu for the name of the currently-defined Text file). All
the caveats listed under ``Printer'', above, are also true for the
Text file. In addition, the global default Text File Formatting on
the Global Defaults Menu also affects output to the Text file.
***Defaults***
There are a variety of local defaults that affect how the current
search is executed.
** Begin. Allows 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 references; then you would
specify [B]egin at #600. This would cut down your search time
significantly. The default value is 1 (the first reference in the
database).
** 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 [M]atches 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 total 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. When this is set equal to No, then both your
search text and the references in the database are 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'' for the
search. If you wish to make the comparisons directly without
converting to uppercase, then make [C]ase Sensitivity=Yes. Note that
you can make your choice `permanent' by saving this value in the
Config file. That is, when you press [S]ave defaults+files at the
Global Defaults Menu, the answer you entered here is saved and used
whenever you use your Config file.
JEPRS User's Guide, page 42
** Sort. If this is set to No, then JEPRS displays the references
in the order they were found in the database. If you set [S]ort=Yes,
your matched references 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 sorted by year. Like [C]ase sensitivity, this
value can also be saved in your Config file (see above).
9.2 Starting a Search
Once you press [G]o to start the search, the Messages window on the
bottom of the screen will show you the number of references being
searched as well as how many matches have been found.
You can press [Esc] at any time to stop the search; if you do so,
a pop-up dialog box will ask you to confirm your decision. Press [Y]
to terminate the search, or press any other key to continue. Note
that this terminates the search, it doesn't abandon it. So if any
matches were found before you pressed [Esc], they'd be sent to the
desired output after terminating the search.
** Text file, Number file, & Printer output. If any of these
outputs have been selected, then once the search is completed, a pop-
up box will display the number of each reference as it is being
formatted and sent to the proper output. Again, you can press [Esc]
here to terminate the output.
** Screen Output. If you have selected the screen as output, then
as soon as any matched references are found, the screen switches to
the Search Results window. As each matching reference is found, it is
added to the Search Results in a compact, one-line format. Once the
search is completed, the matches will be displayed in the Search
Results window in the order in which they were found in the database;
unless, of course, sorting was turned on, in which case they will be
sorted before being redisplayed.
***Search Results Screen***
This is a completely new feature of JEPRS 2.0--and one which I
think users will like very much. The idea behind this is that it
presents as many references as possible, with the most useful
information, in the least amount of space. This allows you to scroll
around the matching reference list, select specific references (or
groups of references) you want to send to various outputs, view entire
references, and edit references--all in one place!
The function keys available are described here. Note that the key
used for Modifying the search is different in version 2.0.
** Up Arrow. This moves the cursor up one reference at a time.
The screen is scrolled down one line if necessary.
** Down Arrow. Moves the cursor down one reference at a time. The
screen is scrolled up one line if necessary.
** [PgUp]. Scrolls the screen up one page (if more than one page
of matches has been found).
** [PgDn]. Scrolls the screen down one page (if more than one page
of matches has been found).
** [Enter]. Displays the entire reference. What this actually
does is bring up the List Reference Screen, using the current
reference number. In this way you are not limited to seeing only part
JEPRS User's Guide, page 43
of the matched references--you can see the whole thing. While at the
List Reference Screen, you can press the [F4] key to bring you to the
Edit Reference Screen where you can edit the reference to your heart's
content (see the chapter in this User's Guide on List References for
more information). Note that pressing [PgDn] or [PgUp] while at the
List Reference Screen will display the next or previous found
reference, respectively. In other words, it won't display the next
sequential reference in the database, it will instead display the next
(or previous) reference on the list of matched references on the
Search Results Screen.
** Esc. You will be returned to the Search Menu. At this point
you may 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. Once you return to the
Search Menu, if you decide you want to redisplay your most-recent
search, you can press [F3] to go back to your previous search.
** [F1]: As always, this will give you context-sensitive help.
** [F4]: This allows you to modify your search by bringing you to
the Modify Search Menu. The first time you modify your search, a
short list of instructions is provided. Your previous search terms
are displayed on the top left of the screen. The number of matches
JEPRS has found for the current search is displayed in the upper right
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.
** [*]. Marks the reference that the cursor is sitting on. You
can tell if a reference is Marked because it will have an asterisk
(`*') next to the year. Marking a reference is used for output (see
[F8], [F9], & [F10] below).
** [F5]. Marks all of the matched references. Even if more than
one page of matches has been found, every matched reference on every
page of the Search Results is marked. Marking a reference is used for
output (see [F8], [F9], & [F10] below). Hint: To unMark all the
references, press [F5], then press [F6].
** [F6]. Reverses all the Marks. That is, all Marked references
become unMarked, and all unMarked references become Marked. Let's
say, for example, you have 20 matches and you want to send one subset
to the printer and another subset to a Number file for subsequent
exporting. You would first manually Mark each reference that you want
printed by using the [*] key, and then press [F9] to send them to the
printer. Then you would press [F6] to reverse all the marks, and
press [F8] to send the other subset of references to the Number file.
** [F8]. If no references are Marked, this sends the number of the
JEPRS User's Guide, page 44
current reference (where the cursor is sitting) to the Number file.
If any references are Marked, then only Marked references are sent to
the Number file (regardless of where the cursor is).
** [F9]. If no references are Marked, this sends the entire text
of the current reference (where the cursor is sitting) to the printer.
If any references are Marked, then only Marked references are sent to
the printer (regardless of where the cursor is). Note that the
currently-defined format style (see the Format Menu) is used for
output. Also, the page margins are pre-defined at 65 characters per
line.
** [F10]. If no references are Marked, this sends the entire text
of the current reference (where the cursor is sitting) to the Text
file. If any references are Marked, then only Marked references are
sent to the Text file (regardless of where the cursor is). Note that
the currently-defined format style (see the Format Menu) is used for
output. Also, the page margins are pre-defined at 65 characters per
line. In addition, the global default Text file formatting on the
Global Defaults Menu affects the output.
JEPRS User's Guide, page 45
10 Utilities
The Utilities Menu contains three functions that, while very
useful, are generally used less often than those functions listed at
the Main Menu. Here, JEPRS allows you to import references, export
references, and compress your database.
10.1 Importing
JEPRS has the power to import references in three different formats
from a variety of different sources. These are generally formats used
only by Ph.D.s, M.D.s, and others in biomedical fields. If you know
of a particular format that you think might be useful for JEPRS to
read, let me know and I'll see if I can incorporate it into the
program.
***Formats***
JEPRS supports three different import formats. You can select any
one of them from the ones listed on the screen. The formats and their
potential sources are:
** MedLine. This is a ``standard'' biomedical reference format
defined by the USA's National Library of Medicine. Most commercially
available reference management programs and on-line biomedical
database systems support this type of file. For example, PaperChase
(an on-line system of Harvard University-affiliated Beth Israel
Hospital in Boston) allows you to search through the National Library
of Medicine's main bilbiographic database and download these
references to your own computer. One of the (several) formats they
support is MedLine.
MedLine output is also produced by IBM PC-based programs, such as
ISI's Current Contents on Diskette (CCOD). Just like PaperChase, CCOD
allows you to save files in MedLine format.
** CL-MedLine. This format is slightly different from the standard
MedLine format. It is produced by a program called CL-MedLine from a
company called CLSI, Inc.
** BRS/Colleague. Though this format looks a little like MedLine,
it is really quite different. An on-line database searching system
called BRS/Colleague produces these formatted files.
Note: One good thing to keep in mind is that you can generally
import these files immediately into JEPRS without modifying them at
all. For example, you sometimes get extraneous commands and other
text mixed in with your actual references when you download these
files from the on-line databases. And some other programs actually
make you ``clean-up'' these files before importing them. But not
JEPRS! JEPRS is smart enough to ignore anything that isn't a real
reference.
***Defaults***
Two local defaults are available from the menu:
** Remove subheadings from keywords. MedLine and other files tend
to have a lot of information most people consider superfluous. This
JEPRS User's Guide, page 46
includes keywords for source of grant support (US government vs.
private funding), and subheadings for keywords. Those subheadings can
be useful for PaperChase searches, but tend to be less so in JEPRS.
Therefore, if you set this value to [Y]es, then these terms will be
stripped from your references before being added to your database.
** Edit references before adding to database. In previous version
of JEPRS, once you starting importing, you had an all-or-none
situation: import all the references in a file, or don't import at
all! With version 2.0, you now have the option of importing them one
at a time. If this default is set to [Y]es, then as each reference is
read in from the file, it is displayed on JEPRS's Edit Reference
screen. At this point, you have the option of: discarding the
reference and moving on to the next one; saving the reference as is;
or editing the reference and then saving it. See below for more
details.
***Starting an Import***
After verifying that the Format and Defaults are set to your
liking, you are almost ready to start importing. The one last thing
that must be taken care of is the name of the Import file. There are
two ways to go about this, depending on whether you always import a
file with the same name, or always use different names. If you always
import a file with a standard name (such as ``Medline.txt'') then you
can go to the Global Defaults Menu (by pressing [F2] while at the
Utilities Menu) and specify its name on the Files/Import file
selection. Then go to Defaults/Save defaults+files. In this way, the
name of the Import file will be saved in your Config file, and you
will not have to bother changing it every time you import a file.
The other way of specifying an Import filename is if you have a
different file name every time you perform and Import. In this case,
it would be kind of annoying to have to remember to go to the Global
Defaults Menu and specify the filename for the Import file every time
you performed an Import. What you can do is take advantage of JEPRS's
intelligence: Go to the Global Defaults Menu (by pressing [F2] at the
Utilities Menu) and this time specify a ``fake'' filename at the
Import filename prompt. Choose a name that you know you will never
use, like ``FakeFile.XYZ''. Again, choose Defaults/Save
defaults+filenames to save this filename into your Config file. (Why
are we saving a fake filename?! Read on...) So whenever you are at
the Import File menu and you press [G]o to start importing, a dialog
box will pop-up to tell you there is a file error, since JEPRS can't
find your fake file called ``FakeFile.XYZ''. Then all you have to do
is press [F4], enter the real filename, and press [Enter] and you're
done!
After pressing [G]o to start the Import, JEPRS checks for the
Import file, starts reading from it, and then imports the references
into your database. What you see on the screen depends on how you
asked JEPRS to set the default called ``Edit references before adding
to database?'':
** No editing/Import all at once. The ``Messages'' section of the
screen will clear, and then a horizontal bar graph will appear. As
JEPRS reads in your Import file, the graph will show what percentage
of the file has been read in. If at any point you decide you want to
JEPRS User's Guide, page 47
stop Importing, just press [Esc]; once you do, a pop-up dialog box
will ask you to confirm your decision. Press [Y] to terminate Import
or any other key to continue.
** Edit references/Import one at a time. If this option is
selected, then as each reference is read in from the Import file, you
are presented with the Edit Reference screen. The cursor is placed on
the menu at the top of the screen. If you just press [Enter] or
[S]ave, then the reference is immediately saved into your database.
You can instead press [A]bandon, in which case the current reference
is discarded, or you can press [E]dit, in which case you can edit the
reference before saving it. After you have chosen either [A]bandon or
[S]ave, another menu appears at the top of the screen and a pop-up
window appears. This window tells you the number of references read
in from the Import file, as well as what percentage of the file has
been read in. The menu then allows you to import the next reference
by pressing [I]mport or [Enter], or stop importing by pressing [E]xit.
The two menus are set up to make your life as easy as possible: that
is, if you want to save each reference, you can just press [Enter]
twice (once at the first menu to [S]ave, and once at the second menu
to continue to [I]mport).
Whether or not you have chosen Editing, once 100% of the file is
read in (or you exited Import), the ``Messages'' window will display
the Total number of references read in as well as the Total number of
references saved into the database. You are then prompted to press
any key to return to the Import Menu.
10.2 Exporting
JEPRS has a very rich and powerful Formatting capability, which is
accessed through the Format Menu from the Main Menu. However, there
is one particular type of formatting that JEPRS's format commands
cannot do: the MedLine format. So I have presented you with the
ability to Export in the MedLine format at the Export Menu. Note that
this feature is probably only important to biomedical researchers,
students, and practitioners.
***Input***
By default, JEPRS uses the keyboard for input. This means that
when you press [G]o to start exporting, you would have to manually
enter the number of each reference that you want exported at the
keyboard. Sometimes this is not the best way to export your
references. For example, you may want a whole subsection of your
reference file (or the whole thing) exported, or you may want to use a
Number file as input. Either of these are very easy to do.
When at the Export Menu, press [I]nput. This will bring up a pull-
down menu. Like every other pull-down menu in JEPRS, use the up and
down arrow keys and [PgUp] and [PgDn] keys to move among the choices,
then press [Enter] when the selection you want is highlighted. Or,
just press the highlighted letter of your choice. Notice that when
you make a selection, a yellow arrow appears next to that name on the
right side of the screen. This is a reminder of your choice.
** Keyboard input. After pressing [G]o, you will be prompted to
enter the number of every reference that you want exported.
JEPRS User's Guide, page 48
** Number file input. After pressing [G]o, JEPRS will look for the
Number file, using the name specified on the Global Defaults Menu.
This is just a text file containing numbers of references, with each
number on a separate line. You can create this file yourself with a
text editor or word processor (in the Dos Text/Non-document mode). In
addition, JEPRS can create this file by pressing [F9] when at the List
Menu or the Search Results screen. For more information on the Number
file, see the chapter on the Global Defaults Menu.
** Reference file input. If you select this item at the pull-down
Input menu, then you are asked at which reference you wish to start
and end. If you want to export the whole database, then just use the
default values (which are the first and last reference in the
database). Otherwise, you can enter any two reference numbers at
which to start and end exporting.
***Output***
When you select [O]utput from the Export Menu, a pull-down menu
pops up to give you a choice of Screen, Printer, or Text File. You
can mix and match any combination of outputs. Check the right side of
the screen under ``Output:'' to see which of the outputs are currently
selected. New with version 2.0 of JEPRS is the ability to send output
to the screen and/or a printer. Nonetheless, the must useful output
is still a Text file.
** Screen. Once you press [G]o to start, the exported references
will be displayed on the screen, continuously scrolling from bottom to
top.
** Printer. Your exported references will be directed to your
printer.
** Text File. The references will be sent to the currently defined
Text File (see the Global Defaults Menu to view the name of that
file).
***Defaults***
There are two local defaults on the Export Menu.
** Remove printer codes from references. JEPRS is quite powerful
in that in addition to printer codes (for example, underlining,
italics, etc.) in the Format Styles, you can also have printer codes
within your references. However, this can cause a problem during
exporting, since no other program recognizes these codes. Therefore,
if you set this default to [Y]es, then these codes will be removed
before sending your references to the output device(s).
** Convert all keywords to uppercase. JEPRS itself doesn't really
care if you keep your keywords in ALL UPPERCASE, all lowercase, or
miXeD UpPeR ANd LoWerCaSE. However, the standard MedLine format has
its keywords in ALL UPPERCASE. If you want all your keywords
converted to uppercase during export, set this default to [Y]es (note
that this doesn't affect your reference database itself; the keywords
there remain unchanged).
***Starting an Export***
Just press [G]o to start, once you've decided all the defaults are
to your liking. If Screen output is on, then the references will
continuously scroll up the screen. If Screen output is off, a pop-up
JEPRS User's Guide, page 49
box will appear, telling you which references are being sent to the
output device(s). At any time, you can press [Esc] to stop exporting,
and a pop-up dialog box will ask you for confirmation. Press [Y]es to
stop, or any other key to continue.
10.3 Compressing the Database
The file system JEPRS uses for storing your references is very
efficient. It uses much less disk space (and many fewer files) than
most database systems. Nonetheless, it does have one (minor)
inefficiency: When you edit references, it marks the old version as
invalid, and then adds a new version to the end of your database.
This results in some wasted space in your database file. If this ever
becomes a problem (for example if you are running out of disk space),
you can easily correct it.
Note that on the Main Menu and the Compress Database screen, there
is a listing for ``Number of moved references'' or ``Number of
relocated references'' (this is the same thing). This number tells
you how many of your references are (partially) duplicated in your
database. You can now use the Compress Database function to get rid
of these extra references.
The upper left quadrant of the screen displays some useful
information. ``Reference file'' and ``Ref Key file'' refer to the
names of your database files currently in use. The total number of
references in your database, as well as the number of moved
(relocated) references is also listed. Note that if the number of
moved references is zero, there is no point in compressing your
database (but it won't hurt if you do).
** Insufficient Disk Space. JEPRS will tell you whether there is
sufficient disk space to compress your database. That's because JEPRS
needs to create a temporary file that is as big as your current
database. JEPRS is smart enough to check for disk space before
starting the compression. If there is not enough space on the current
default drive, JEPRS will ask you to insert a new disk and/or specify
a new drive name (if you have more than one hard disk or hard disk
partition). Warning!: Do not replace your disk until JEPRS tells you
to. Just enter the one letter drive name and press [Enter] after
replacing your disk. If you do not have sufficient disk space
anywhere, just press [Esc]. If you have a two-floppy drive system,
you can replace your JEPRS program disk with a new floppy; just don't
replace your data disk, because obviously JEPRS will need access to
it! For example, if you have the JEPRS.Exe on drive A: and your
database (Ref1.JPR & Ref1.JPK) on drive B:, then when JEPRS tells you
there's insufficient space, replace your A: disk with a fresh floppy,
then enter [A] when JEPRS asks you for a new disk drive name. (Once
the compression is over, replace your floppy in drive A: with your
JEPRS.Exe disk.)
***Starting File Compression***
Just press [G]o to start the database compression. As JEPRS is
doing its stuff, you'll see ``Number of references processed'' being
incremented for each reference that JEPRS is copying to the fresh
database. You will also see a warning in the ``Messages'' window.
JEPRS User's Guide, page 50
You must obey that message! That is, do not attempt to turn off your
computer while JEPRS is compressing your database. Just like
everywhere else in JEPRS, if you need to abandon program execution,
just press the [Esc] key! If you do press [Esc], then you will be
asked to confirm your decision: press [Y]es to stop compression, or
any other key to continue.
When JEPRS is done with the first part of compression, it will then
display a message saying that it is copying the new database to your
current database's directory. When everything has been completed
successfully, JEPRS will display the following message:
Compression successful.
Press any key to continue.
JEPRS User's Guide, page 51
11 JEPRS's Files.
All of the major file types that JEPRS uses are listed on the top
left quadrant of the Main Menu screen. If you've read through the
tutorial, then you should be at least 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 are 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--otherwise you
will lose all your data!
***Help File***
This file contains all the information displayed in the Help screen
whenever you press [F1] for help in JEPRS; it is provided to you on
the original disk that you received JEPRS.Exe on. Again, do not
modify this file! If you do, the help screens will not display the
proper help, and will become worthless. The default name for this
file is ``JEPRS.Hlp''. Note that each Help File is specific for each
version of JEPRS. If you try to use the Help File from JEPRS Version
2.01 with Version 1.11 of JEPRS.Exe, you will get nonsense help most
of the time.
***Text File***
This is a file that can be created by JEPRS. If you press the
[F10] key when you are displaying the results of a search, or when you
are on the List Reference screen, or if you specify ``Output: Text
File -----> Yes'' on the Search Menu, then the text of the
reference(s) will be sent to this Text file (default name is
``JEPRS.Txt''). Text will also be sent to this file if you specify
File Output on the Format References Menu. Once you create this file
with JEPRS, you are free to edit it in a word processor, or send it to
your printer for printing. JEPRS will never have to get information
from this file; it only sends text to it, so you are free to change it
JEPRS User's Guide, page 52
any way you wish.
Printer codes for underlining, boldface, etc. are sent to this file
only under the following conditions: 1) When you are at the Format
Menu and 2) When the global default called Text file formatting is
set to [Y]es (see the Global Defaults Menu to set this value).
***Number File***
This file (default name is ``JEPRS.Num'') can be created by JEPRS.
If you press the [F8] key when you are displaying the results of a
search, or if you press the [F8] key when you are on the List
Reference screen, or if you specify ``Output: Number File -----> Yes''
on the Search Menu, the number(s) of the reference(s) will be sent to
this file. It is a normal DOS text file, just like the Text File
above, but instead of containing the text of the entire reference, it
only contains the number of the reference, with each number being on a
different line.
You can create a number file yourself with a text editor (or word
processor in DOS Text file/non-document mode). There are a few simple
requirements for a Number File that you must adhere to:
** It must be a normal ASCII text file. You can verify this by
using the MS-DOS Type command at the DOS prompt:
C:\JEPRS> Type JEPRS.Num
If you see any foreign or graphics characters, or if the numbers
aren't lined up on the left side, then it's probably not an ASCII
file.
** Each number must be on its own line. If more than one number
is present, only the first one is used.
** Spaces and/or Tabs are OK before a number, but no other
characters are allowed. If any other characters appear before a
number, that line is treated as a comment.
** Comments can appear by themselves on a line, or after a number.
** Empty lines are treated as comments (they're ignored).
** Invalid numbers (negative numbers or numbers larger than the
database) are ignored.
An example of a legal Number File would be:
34
This line is a comment
55
3 This is another comment (and the "3" is valid)
99
This is also a comment line. The twelve is ignored: 12
Keep in mind that Number files can be quite useful. Recall that
they can be used as Input on both the Format References Menu and the
Export Menu. There is a chapter in the JEPRS Tutorial that explains
some of the advantages of using a Number file.
***Config File***
The Config file (short for ``configuration file'') contains the
Format Styles, Global (and some local) Defaults, default directory and
JEPRS User's Guide, page 53
file names, and Printer Definitions for JEPRS. Its default name is
``JEPRS.Cfg''. New for version 2.0 of JEPRS is the ability to
modify the contents of this file while still in JEPRS; you no longer
have to exit the program and edit it with your text editor (in fact,
now you can't edit it with a text editor!).
** Format Styles. You can define up 30 of your own Format Styles
(also called journal definitions) and keep them in the Config file.
To edit the Format Styles, go to the Global Defaults Menu, choose
[D]efaults, and then [J]ournal definitions. For more information on
editing the Format Styles, see the chapter in this User's Guide on
Global Defaults.
** Printer Definitions. Up to 5 Printer Definitions can also be
stored in the Config file. Follow the instructions above for editing
the Format Styles, except choose [P]rinter definitions. Multiple
printer definitions are useful if, for example, you have a laser
printer at work, and a dot matrix at home. Also, you can define each
printer definition to use different fonts (see your printer
documentation for the codes, and see the chapter on Global Defaults
for information on entering codes into the Printer definitions).
** File/Directory Defaults. The default file names listed on the
Main Menu and the Global Defaults Menu can be changed and permanently
kept in your Config file. For information on changing and saving your
filenames, see the chapter on Global Defaults.
** Global & Local Defaults. In order to customize JEPRS to your
needs, you can save a number of defaults in your Config file.
Here is a list of all the Global and local defaults that JEPRS
saves in the Config file:
Default Name: Menu:
Error Beep Global Defaults
Text File Formatting Global Defaults
Printer # Global Defaults
Format Style # Global Defaults
Color Mode Global Defaults
Colors for Formatting Global Defaults
Blinking on Formatting Global Defaults
Sort References Search Menu
Case Sensitivity Search Menu
Replace " with ... Format Menu
Remove Subheadings Import Menu
Edit During Import Import Menu
Import Format Style Import Menu
Remove Printer Codes Export Menu
Uppercase Keywords Export Menu
Whenever you modify any of the above defaults, and then go to the
Global Defaults Menu and choose [D]efaults and then [S]ave
defaults+files, all of the defaults listed above are saved into your
Config file.
JEPRS User's Guide, page 54
12 Index
Add new references, samples 32
Beep, error/warning 17
BRS/Colleague files
Importing 45
Citation type 31
CL-MedLine
Importing 45
Comma-delimited output 3
Command line options 9
Compressing the Database 49
Computer memory (RAM) 4
COMSPEC (MS-DOS) 19
Config file name 9
CONFIG.SYS file (MS-DOS) 19
Current Contents on Diskette
Importing 45
Database
Creating 10
Defaults
Global 16, 53
Local 53
saving 17, 53
Delete reference 28
Directory, default 16
Disk number 13
Exiting the program 10
Exporting references 47
File names, changing 17
Files 16
Config File 52
Help 15
Help File 51
Number File 52
Ref Key File 51
Reference File 51
Text File 51
Files on disk 7
Format Styles
Default 35
Editing 22
Selecting 35
Formatting codes 24
Go to DOS 19
Help key 15
Importing files 45
Importing references
Editing 46
Indent Length 23
JEPRS User's Guide, page 55
Installation 8
Journal definitions
Editing 22
Journal Name 23
Journal Number 23
Journal/Abstract/Book definitions 23
Main Menu 12
Marking references 43
MedLine files
Exporting 47
Importing 45
Memory
Available 12
Total RAM 13
Menu
Line 12
Title 12
Messages window 12
New Features 4
Optional inclusion 24
Ordering information 5, 19
Original licensee 13
PaperChase
Importing 45
Printer
form-feed 18
initialization code 20
name 20
number 20
reset code 21
selecting 17
Printer codes 20
Printer definitions
editing 19
Saving 22
Printing
attributes (underlining, etc.) 22
characters per line 21
form feed last page 22
header 21
left margin 21
lines per page 21
pause after each page 21
title 21
top margin 21
Printing attributes
codes 25
Prompts vs. Menus 13
Reference type 31
References
Number of in reference file 13
Number of relocated 13
Registering 5
JEPRS User's Guide, page 56
Screen color options 9
Screen colors 18
Screen design 12
Search Results Screen 42
Search terms 39
Searchable fields 39
Searching
Case sensitivity 41
Sorting 42
Shareware 5
Sort references during format 23
Sorting
using Matches to free memory 41
Starting JEPRS 9
System information 12
System Requirements 4
Text file formatting 17
Time and date 13
Version
JEPRS number 13
MS-DOS number 13
Video card 18
Video monitor 18
Welcome Screen 9