Magnum One

home *** CD-ROM | disk | FTP | other *** search

/ Magnum One / Magnum One (Mid-American Digital) (Disc Manufacturing).iso / d3 / j203doc.arc / JGUIDE.DOC < prev next >

Wrap

Text File | 1990-01-21 | 164.9 KB | 3,697 lines

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