EPA/600/R-94/034
March 1994
GENETOX MANAGER SYSTEM -
[
PERSONAL COMPUTER SOFTWARE
PROGRAMMER'S GUIDE
Prepared by:
Larry D. Cla,xton, Ph.D. and John Creason, Ph.D.
Health Effects Research Laboratory
U.S. Environmental Protection Agency
Research Triangle Park
North Carolina 27711
and
Joe Nader, Way Poteat, and John Orr
Computer Sciences Corporation
4401 Alexander Drive
Research Triangle Park
North Carolina 27711
Prepared Under
Contract # 68-01-7365
Delivery Order # 220-151
Task Officer: Larry D. Claxton
June 1993
Version 2.21
^ Printed on Recycled Paper
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PREFACE
This programmer's guide is the reference manual for describing software system and
programs used hi constructing personal computer portion of the EPA Genetox Manager System.
GeneTox Manager is a data capture, data management, and statistical analysis program
used for microbial mutagenicity data. Its main purpose is to provide a homogeneous
environment for the collection, organization, and analysis of data generated hi the laboratory
while also supporting a quality assurance program. The complete system consists of both a
personal computer (PC) system and a minicomputer (VAX) system, although the PC system can
be used as a stand-alone system. The system controls the data collection and management
through a user-friendly menu driven system that requests specific information and provides
uniform methods for data and information entry. GeneTox Manager is capable of performing
specialized statistical analysis of the data and creating tabular and graphical summaries. Two
versions of the PC system exist: a stand alone PC only version, and a VAX version. The VAX
version of the system is designed to function with VAX FOCUS databases so that the VAX can
be used for long-term storage, archiving of files, and the analysis of large groups of data. Both
PC versions are described hi this guide.
/ We only make a few REQUESTS OF THE USERS. First, we request that you
provide to the creators of this software proper acknowledgement. [See the title page to the
software and to the User's Guide. Also in the near future, we hope to have references that you
may cite.] Secondly, realizing that the software is provided free of charge, please understand
that we cannot service this software. [Because the source code is available, many consultants
and companies that use Clipper® could provide additional help and programming options for
you.] Follow the installation and distribution instructions very carefully. If you have problems,
first read the section of the User's and Programmer's Guides that deal with problems before
contacting us. Most problems that we have seen are due to either not following installation
instructions completely (especially hi regard to autoexec.bat and config.sys files) or to memory
allocation problems. Most all of the memory allocation problems are due to other "resident
programs" - please see the guides. If you receive and especially if you distribute the software,
be sure to do that in the proper manner. Be sure that you understand the statistics and proper
interpretation of the statistical programs. Also understand that statistics do not replace sound
scientific judgment and that statistics on a single test does not replace replication of an
experiment. Lastly, be sure to read the "readme. 1st" file.
We sincerely hope that this software will be useful to you and will aid you in your
scientific endeavors.
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Acknowledgements
We would like to acknowledge those individuals who used prototype versions of this software
and gave us useful, productive comments. Without their suggestions, this product could have not been done.
In this regard, we give our thanks to Sarah Warren, Erica Perry, Virginia Houk, Sam Schalkowski, Mary Beth
Lawhorn, and Maria Taylor.
We also want to thank those who gave us permission to use the statistical analysis programs that
they developed. These include Dr. L. Berstein, Dr. D. Krewski, and Mr. A. Stead. If you use information from
these statistical programs, we hope that you will give proper acknowledgement to the authors of the statistical
manuscripts.
We also want to thank Mr. Ken Laws for providing administrative support that made this project
possible, and Drs. Lawrence W. Reiter and Michael D. Waters for creating the scientific support that made our
endeavors a joy. Thanks also go to Mr. Ken Mullins, Dr. Davi4 Svendsgaard, and Dr. Bernard Most for review
of this document.
Notice
The software and the user documentation are provided "as is". CSC and EPA make no warranty, express or implied with respect
to the software and/or user documentation and specifically disclaims the implied warranties of merchantability and fitness for a particular purpose.
EPA and CSC do not warrant that the software will be uninterrupted and/or error free. You are solely responsible for the selection of the
software to achieve your intended results and for the results actually obtained.
This document has been reviewed in accordance with U.S. Environmental Protection Agency policy and approved for publication.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.
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Contents
Preface i
Acknowledgements ii
Notice ii
Chapter 1: Introduction 1
Chapter 2: Working With GeneTox Manager 3
System Language 3
Clipper 5.01 and OverLayQ 4
Separate EXEs 4
Additional System EXEs 5
Database Keys 6
GeneTox Load/Install 6
Data Entry 7
Reports 7
Data Status Flags 8
Transfer Files 8
Upload/Download Procedures 8
Data Flow Diagrams 9
Upload/Download Experiment Data 9
Import/Export Experiment Data 10
Archive/Dearchive Experiment Data 11
Transfer Ownership (from Databases) 12
Transfer Ownership (from Local Archives) 13
Transfer Ownership (from Shared Archives) 14
Protocol/Instruction Files 14
Spiral Systems Data 15
Statistical Model Input Format - 16
Procedures and Functions 17
HELP! 17
SNAP! 18
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Chapter 3: Program Maintenance 19
Editing Program Files 19
Compiling Program Files 19
Linking Program Files 20
RMake Facility 20
Error Messages 20
Using dBASE 21
Chapter 4: Program Files 23
Chapter 5: System Default Files 39
Chapter 6: Database Structures 41
Logical Structure 41
Chapter 7: Transfer File Formats 53
Chapter 8: Possible Enhancements 63
Chapter 9: SNAP! Diagrams 69
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CHAPTER 1
INTRODUCTION
The GeneTox Manager System is an U.S. EPA system for the collection, organization,
retrieval, and analysis of microbial mutagenicity data. Although the system was designed
primarily for the Salmonella typhimurium plate incorporation assay, it will accept data and
information for any mutagenicity assay where similar information is obtained.
Microbial assays, especially Salmonella bioassays, are the most common type of
mutation tests. These tests determine whether or not a substance interacts with the DNA of
the organism in such a way as to create permarpt, heritable changes within the DNA. These
tests are important because they can be use! to screen for both mutagens and genotoxic
carcinogens. The Salmonella assay has been reported to have been used by over 2000
laboratories. In comparison to other genotoxicity assays, these microbial assays are relatively
rapid and inexpensive. These |ests, therefore, generate very large databases.
In order to collect, manage, and analyze /nicrobial mutagenicity data in an orderly and
rapid manner, the U.S. EPA (through the services of Computer Sciences Corporation)
developed the GeneTox Manager system. This system enables investigators to use a PC to
collect information and data, to provide short-term storage of the information, and to provide
selected types of statistical analysis. The complex GeneTox Manager system also includes a
VAX FOCUS system that can be used for the/chiving of databases and for the analysis of
large groupings of data. The total system is deigned to achieve compatibility between the PC
and VAX system environments. The GeneTox Manager system is designed to be user friendly
through the availability of a structured menu system, screen entry helps, and other help screens.
Reports are both tabular and graphical in nature, and they can be seen on the computer screen,
sent to a printer, or written to a PC file.
It is the hope of EPA that GeneTox Manager will not only be of benefit to the Agency
but will also be of contractive use to others outside of the EPA.
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CHAPTER 2
WORKING WITH GENETOX MANAGER
The organization of GeneTox Manager is actually fairly simple, though amazingly
intricate in the implementation of this simplicity. Keep in mind that GeneTox Manager is little
more than an overgrown data collection and storage program. When a problem occurs, or
more development is necessary, work from the precept that this is first a data collection system,
then a storage facility, then a data management (Modify) system, a facility to upload
information to the VAX and to report information contained in the databases. Side issues are
the Protocol view, HELP!, Instructions view, and Suggestion boxes. They all happen at once,
and have been coded almost on top of each other at times, but they ARE separate systems:
work on them separately.
The system has 18 databases and 21 indexes, designed to minimize duplication of data,
and hence the size of the running application. This allows the user to maintain much larger
informational reserves with the very limited PC diskspace ceiling. They are designed to look
like and function in a similar fashion to hierarchical databases, but keep in mind that they are
not. This means that there are NO parent/child relationships between the databases (a
particularly important point when attempting data modification or reporting). Eight of these
databases are used for data storage, 3 are temporary (used as interim Enter/Modify databases),
and the remaining 7 are used for principal investigator information, Suggestions and the HELP!
facility. The database structures and indices are explained in detail in Chapter 6.
; The indices and databases are dBASE III+ compatible (DON'T USE dBASE IV - it
creates problems inside the database that are difficult to correct), making for a useful system
manager tool to ensure the integrity of the data.
System Language
GeneTox Manager is written in the Clipper language. Clipper is a compiler that extends
the dBASE III+ language. GeneTox code was originally written under the Summer 87 version
of Clipper, but has not been modified to use Clipper 5.01. Some features specific to Clipper
version 5.01 were use in extending the functionality of GeneTox Manager. The system will
no longer compile'rang the Summer 87 version of Clipper. Clipper 5.01 MUST be used to
produce an executable version of GeneTox Manager from the source code.
All system &ecstables were written in Clipper 5.01 with the exception of the following:
Colony.EXE, the A$£' colony counter interface, was written in C; BernScr.EXE,
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SteadScr.EXE, and HistdSrc.EXE, the statistical modeling code, were written in Fortran.
Programming and maintenance for the statistical modeling code is not covered in the document.
Clipper 5.01 and OverLayQ
Clipper version 5.01 which includes a Virtual Memory Manager (VMM) which allows
large applications to run in a small amount of actual memory. The executable part of the
GeneTox Manager system is G_MENU.EXE, which is started by the GTM.BAT batch file.
The system does, however, make use of several separate executables to provide
statistical modeling, the communications with the VAX databases, and the archiving and
dearchivmg of experimental data. These separate executables are run using a third party library
called OverLayQ. The main use of this library is the OverlayQ function itself, which allows
running large exes from "within" a Clipper program. It does this by swapping Clipper memory
to EMS or disk and thereby freeing memory for use by the called program. After the called
program terminates, Clipper's 'memory is restored and the original Clipper application
continues. The syntax for the OverlayQ call is Overlay("", nMemFree, "", "") where the first parameter is the command line to start
the exe as it would be entered from the DOS prompt, nMemFree is an integer indicating the
number of KBytes to free (0 indicates free as much as possible), the third parameter is the
pathname for creating temporary files if memory must be swapped to disk, and the fourth
parameter is a string of environment variables used to set the environment for the called
program. Other useful OverLayQ library functions include 0_CD() - change directory,
OJMDQ -make directory, O_CurPathQ - return the current path, and O_DirExist() - does a
drive/directory exist.
The linkable OverlayQ library code, contained in OVERCL.LIB, must be present in
order to link compiled system .OBJs into executable code. This library is specific to linkage
using the RTLink linker included with Clipper 5.01.
Separate EXEs
The following separate executables are used by the GeneTox system:
Actual statistical models written in Fortran:
BernScr.EXE
SteadScr.EXE
HistdScr.EXE
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Communication program:
SetHostEXE (DECnet Pathworks connection)
GeneTox.SCR Execute VAX GeneTox Program
UplNew.SCR Upload new data to VAX GeneTox databases
UplMod.SCR Upload modified data to VAX GeneTox databases
DnLoad.SCR Download data from VAX GeneTox databases
Data Compression Utility:
; PKZip.EXE Compress data for archival
PKUnZip.EXE Decompress archived data
Additional System EXEs
i In addition to the G_Menu and GenGTM files, and the separate executables mentioned
above, two files for system distribution exist: GTMLoad, and G_Instal. The GTMLoad
executable compresses the GeneTox system onto floppy disks for distribution. Three
distribution formats are supported according to the type of floppy drives of the recipient.
These are: three 360Kb 5-1/4 diskettes for low density 5-1/4 drives; two 720Kb 3-1/2 diskettes
for low density 3-1/2 drives; and one 1.2Mb 5-1/4 or one 1.44Mb 3-1/2 diskette for high
density 3-1/2 or 5-1/4 drives. GTMLoad will automatically detect the number of free bytes
on the target diskette and determine the format to be used. G_Instal will similarly detect the
number of diskettes used when the installation is run.
I Also, two separate Upgrade programs (G_Upgrd, GTMRest) are provided to upgrade
to version 2.2. For version 2.2 the G_Sample and G_ExSmDt database structures were
changed, and the upgrade program (G_Upgrd) is provided to convert users databases to the
new format. A restoration program (GTMRest) is provided to restore the system to its previous
state should the upgrade be unsuccessful. There is no automated program to generate Upgrade
diskettes. These will have to be hand generated according to the disk format specifications
documented at the beginning of Upgrade.prg.
; G_Instal.EXE and G_Upgrd.EXE are the actual Clipper executables that will preform
the installation or upgrade procedure. The are called from DOS batch files named Install.BAT
and Upgrade.BAT respectively. The batch files set necessary system environment parameters
before executing the Clipper code.
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Database Keys
Numeric key values in the range of 1..999,999,999 are used by the GeneTox Manager
system for tagging and indexing experiment data. Fpur separate database keys exist:
Experiment keys, which are unique to each strain entered for an experiment; sample keys,
which are unique to each sample entered (although samples and sample keys may bridge
several experiments); negative keys, unique to each negative control entered; and positive keys,
unique to each positive control entered. These values are initialized to some value in the
millions range, so that each separate copy of the GeneTox Manager system uses a unique set
of database keys. Each installation of GeneTox Manager then has 999,999 keys it may utilize.
System default files keep track of the next available keys, and these defaults are incremented
as new key values are assigned.
GeneTox Load/Install
The GTMLoad and Install programs were designed for distribution the GeneTox
Manager system to potential users. Running the GTMLgad program will produce a set of
installation diskettes which may be used to install GeneTox on other machines. When
generating a set of installation diskettes, the user is prompted to enter the name of the recipient
of the GeneTox Manager system, the initial distribution key (the millions number at which to
start database key values), and the GeneTox version (PC or VAX). The initial system
password (for access to the protected functions menu) is set to "GENETOX". A database
(GTMDist) is updated for each installation set generated with the recipient's name and; the
distribution key assigned. Distribution keys must be unique. The GTMDist database is also
distributed with the system, so that users will not be able to select distribution keys already
assigned to other users, even when generating additional installation diskettes.
The Install program installs a complete GeneTox Manager system from a set of
installation diskettes generated by GTMLoad. Experiment databases for the installed system
will be empty. System databases, such as suggestion text, investigator lists, and system help
screens will have the same contents as the GeneTox Manager system that generated the
installation diskettes. Once the installation is finished, the initial database keys on the
installation diskettes are incremented by 1 million so that the next installation from these
diskettes will have different starting database key values.
Currently, the distribution scheme automatically distributes the GTMLoad program
when generating the installation diskettes. For some distributions however, you may not wish
to allow potential users to generate more installation diskette sets. In this case, remove the line
"gtmload.exe" from the GTMMisc.TXT file. ( For completeness, you can modify the
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GTMLbad source code so that the GTMDist.DBF and G_DstInd.NTX files are not included
on the distribution diskette. )
Data Entry
The method for adding data to the databases is to use temporary databases until the user
finishes entry and chooses to save the data. This helps simplify removal of data in an abort
situation, since until the last step of data entry nothing has actually been saved to the
permanent databases. It also helps ensure that the proper database keys are used, since these
are set at the time of final submission to the permanent databases.
This is also how the databases are modified: the data for the particular experiment is
copied to temporary holding databases and removed from the permanent ones. Once the
updates are performed the 'new' data is saved to the permanent databases with the old database
keys or if no changes are made the old data is re-saved to the databases.
Temporary databases include: G_TSTRN, which hold the strains entered for the
experiment until they are saved; GJTCNTRL and GJHCNTRL which hold positive and
negative control information; and G_DOSE which holds dose response data for each sample
as it is entered.
All data that has been entered by a user for the current sample is saved when they reach
the "Continue" screen and choose to "Continue Entering Dose Response Data", "Change
Sample ID & Description", or "Save Data and Exit". Data is saved to the permanent databases
at the point when all data for the sample has been entered. Strain data is saved when a sample
is analyzed under that particular strain. Strain data will NOT be saved if no samples were
entered for a particular strain even though it was entered on the strains screen. GeneTox
Manager will warn the user if an attempt is made to exit without analyzing the samples under
each strain. ,
Reports
All reports generated by GeneTox Manager are first generated to temporary disk files,
and then directed to the specified output source. This includes Raw Data reports, statistical
models (input to and output from), and database experiment listings (using the EXPLSTP.SCR
report screen file). The output file for the Raw Data report is RawDatDAT; the file for
statistical model input is called Model.DAT; the statistical model output files are
(StatMod
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the printers compressed print mode. GeneTox pauses after generating the model output to
allow users to set their printers to condensed print.
Data Status Flags
All GeneTox Manager data records are tagged with a status marker field (typically
called STATUS in the database). This status marker may have values of "A", "I", "M", "R",
or "V". An "A" status indicates the experiment has been recently added, and has not yet been
uploaded to the VAX Master databases. All entered experiment data will be in "A" status on
a PC version. On VAX versions of GeneTox, you may not run statistical model or archive
data that has not been uploaded. Modifying experiment data that is in "A" status does not
change the status flags. An "I" status indicates that the data has been uploaded to the VAX
(Inactive). Data in "I" status that is modified will have the status reset to "M" for those
records which have been altered. Data that has a status of "R" or "V" is in read-only format
and may not be modified, archived, or uploaded. A status of "R" indicates the data was
imported from another PC; a status of "V" indicates that data was downloaded from the VAX.
Transfer Files
GeneTox Manager has the capability of creating ASCII text files that contain the entire
data set for a particular experiment. This transfer file format (see specifics in Chapter 7) is
used for sharing data between PC copies of GeneTox Manager (import/export), uploading and
downloading data to the VAX Master databases, storing backup copies of experiment data, and
archiving. The GeneTox Manager system contains routines for generating (G_VaxFle) and
reading (GJParse, GJRetDat) data in this transfer file format.
When using the transfer file format for import/export of experiment data, the DOS
filename of the created transfer file will be aaaayynn.nnR where aaaayynnnn is the experiment
name and the letter "R" has been appended to create a 12 character DOS filename (first 8
characters filename, remaining 3 extension). When creating backup files the appended
character will be a "B". When writing data in transfer file format for compression into
GeneTox Manager archives, the appended character will be an "X".
Upload/Download Procedures
GeneTox upload and download procedures also make use of the transfer file format.
The upload routine will generate a transfer file of experiment data which can be transferred to
the VAX and subsequently read into the VAX Master databases (this process is automated for
the HERL laboratory site). This file will contain either a complete set of experiment data, if
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the data has not been previously uploaded, or a subset of data representing the changes to the
data set if the data has already been uploaded. The transfer file generated for uploading is
named iPCFILE.VAX and it is created in the default directory (pointed to by DftStg). The
VAX database is responsible for extracting and generating a transfer file in the appropriate
format if downloading from the VAX is enabled (again this is automated for the HERL site).
I
NOTE! Access to HERL specific upload and download code is simply disabled by
setting ithe G_Version variable to "PC_" in the Version.DFT system default file. To change
the current system version, simply delete the file. When GeneTox Manager is started, it will
not find the default file, and will prompt the user for the version information. Once selected,
GeneTox Manager will create the file and save the user's choice. However, the VAX interface
procedures are specific to the HERL site. It is doubtful if the procedures as they currently
exist would work for other sites, even if the complete VAX version of GeneTox was provided.
Users may have to modify the source code, or at least the communications script files, to match
their systems. If no VAX interaction is desired, the specific code could be removed from the
GeneTox Manager system prior to distribution.
Data Flow Diagrams
Upload/Download Experiment Data
,The VAX databases serve as the "master" copy of the data once the experiment has
been uploaded. There are two upload choices: upload new and upload modified. Users will
use upload new to upload data that has been added to the databases, but which has not been
previously uploaded. This data will have a status of "A" (Active). Users will use upload
modified data to upload data that has been previously uploaded and subsequently modified.
Once data is uploaded, its status flags will be reset to "I" (Inactive).
A second user may choose to download data that has been uploaded to the VAX
databases. The user needs only to know the experiment name to perform the download. The
data is1 downloaded as a Readonly file: its status is set to "V" (VaxDown). Readonly files
may not be modified, archived, or re-uploaded; the user may only run reports on ReadOnly
data.
Some special consideration is given to downloading when the incoming experiment
name matches a current experiment. If the status of the existing experiment is "A", the user
is given the option of renaming the existing experiment (the user could not upload it to the
VAX databases anyway, because all experiment names must be unique). If its status is "M"
or "I", the user is given the option of overwriting the existing data with the download data.
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Up Ioad/Down Ioad Experiment Data
Secondary PC
Down Ioad
VAX t
T
Master^
GeneTox
Data
If its status is "R" or "V" (Readonly), the user is given the option of overwriting the existing
experiment if the download e'xperiment is actually the same experiment (database keys match)
or renaming the download experiment (keys don't match, names just same).
Import/Export Experiment Data
A user may export experiment data in Readonly form for use by another user by
selecting the Export option. The second user retrieves the data into his databases using the
Import option. The imported data is in Readonly form ("R" status flag): it may not be
modified, archived, or re-uploaded. The receiving user may only run reports on the data. To
transfer ownership of the file to another user, users must use the archive/dearchive options (see
below).
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mport/Export Experiment Data
Primary PC
Transfer File
Secondary PC
Special considerations must also be given when importing data if an experiment with
the same experiment name already exists. If the status of the existing experiment is "A", "I",
or "M", the user may not import the experiment if it was originally created on his PC (database
keys match). If it did not come from his PC, he may rename the incoming import experiment
name. If the status of the existing experiment is "R", or "V" (Readonly), the user is given the
choice of overwriting the experiment if it is actually the same experiment (database keys
match), or of renaming the incoming import experiment (keys don't match, names just same).
Archive/Dearchive Experiment Data
Users may elect to archive experiment data to reduce the size of their working databases
and increase the speed of database accesses. Archiving and dearchiving may also be use to
transfer ownership of an experiment to a new user (see below). When archiving data, the data
is first written to a flat file in transfer file format (see Chapter 7). This file has a filename of
the experiment name + "X". This file is then compressed using the PKZip data compression
utility and placed in the designated archive file. The archive filename defaults to
"GTMArchv.ZIP" and the location of the archives defaults to the values using "Locate
Archives" from the Defaults menu. Both location and filename may be specified by the user
when archiving data. The user also selects a password, which must be used to dearchive the
data. Once archived, the data is deleted from the users databases.
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Arch Ive/Dearchlve Experiment Data
Network File Service
Data can be archived to either local archives residing on the PC's hard disk, or to
shared archives residing on a network file service. When data is archived, GeneTox updates
a database of archived experiments residing on the user's PC. The database contains the
experiment name, location, and password for each experiment that has been archived from the
PC. This way, when dearchiving data (use "Dearchive To Databases"), a user does not need
to enter the location information if the location information stored in the archived experiments
database is correct, only the password.
Transfer Ownership (from, Databases)
A second usage of the archive and dearchive functions can be to transfer ownership of
an experiment from one user to another. In this case, it depends on where the archived
experiment is stored, as to how the transfer can be accomplished. If the data is stored in the
original users databases, then a transfer may be accomplished by archiving the data to a floppy
disk rather than the default archive file at the default location. The receiving user may then
retrieve the data by dearchiving the data from the floppy.
To dearchive data that the user did not originally archive, use "Dearchive To
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Transfer Ownership of Experiment Data
: (from Current Databases])
Primary PC
Hard Disk
Local
Transfer File
CCompressed)
Secondary PC
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Transfer Ownership (from Local Archives)
If a user wishes to transfer ownership of an experiment that has been archived to a local
archive residing on their PC, the following process may be used. Select "Dearchive to Disk"
from the Utilities/PC Functions menu to create a flat file in transfer file format that is
uncompressed. This file can then be brought into a second user's databases using the "Accept
Archived Data From File" option. In this case, the receiving user need only know the name
of the experiment.
Transfer Ownership of Experiment Data
Cfrom Shared Archives}
Network Fi le Service
Secondary PC
Transfer Ownership (from Shared Archives)
If a user wishes to transfer ownership of an experiment that has been archived to a
shared database (that both users can access), the following process may be used. The original
owner of the experiment needs to provide the receiving user with the location and archive
filename and the password under which the experiment was archived. The receiving user may
then use "Dearchive To Disk" to dearchive the data from the shared archives. Because the
receiving user's archives database has no record of the experiment, the user must enter the
location and filename of the archive file, if the default archives were not used.
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Protocol/Instruction Files
I The GeneTox Manager system includes the ability to view protocol files and experiment
instruction files from within a GeneTox Manager session. Protocol files are text files detailing
general methods, procedures, and equipment needed to conduct certain types of experiments.
The protocol information is contained in two levels of text files. The first level file can be
specified by selecting "Protocol File Name" from the Defaults menu (please specify complete
path with filename). The value entered is retained across GeneTox Manager sessions (in the
Proto system default file). The specified file will contain several lines of text in the form of
a table of contents. Appended to the end of each line (starting with column 81, off screen) is
the filename of the text file to display. The second level files are assumed to be in the same
location (drive/directory) as the top level file. Pressing return on a particular line causes the
text contained in the file indicated at the end of that line to be displayed. These files are static
and cannot be modified from within the GeneTox Manager system. There are currently no aids
to assist users in generating their own protocol files, or modifying existing protocol files.
•: Instruction files contain specific instruction for conducting an experiment or set of
experiments and are created and modified from within GeneTox Manager. Instructions specify
the experiment test type, assay modifications, strains, activation conditions, and sample
information for the experiment or set of experiments. The user may select a specific
instruction set from the Instructions-Select menu. That instruction set is in effect until another
instruction set is selected, even after exiting the program (stored in the G_Instr system default
file). The user may choose to append the current instruction set text to the Experimental
Remarks section. The protocol text may be viewed at any point from within GeneTox
Manager by pressing Shift-F5. The instruction set, if selected, may be viewed only when
entering or editing experiment data by pressing Shift-F3.
Spiral Systems Data
A relatively late addition to the GeneTox Manager system has been the ability to read
data collected using the Spiral Systems spiral colony counter and control program. The user
must provide two data files that the spiral program generates: an .ID file and a .PRN file. The
spiral program stores data for each sample analyzed separately under a different filename. The
file containing general sample .and strain information will have an .ID extension. The dose
response data is not stored by the spiral systems program in an ACSII readable format.
However, the spiral program provides an export function for transferring dose response data
to Lotus-123 spreadsheets, which generates a .PRN file containing the control and dose
response data for each strain. Both files must be present for GeneTox to be able to import the
data.
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Imported data is assigned new experiment keys (as if it had been hand entered) and
given a status of "A". Different tests of the same Spiral sample must be saved under different
GeneTox experiment names.
Statistical Model Input Format
The statistical models read a text file generated by GeneTox Manager containing dose
response data for each sample in the following format:
6 Lines of Text, 72 Characters or Less in Length, followed by any number of dose
information lines in the format:
*
where an * (in column 36) indicates a dose line is to be ignored
(positive and additional negative controls would be marked with an *)
and an @EOF (in column 36) marks the end of this sample
is a 2 digit numeric field indicating the pos/neg control.
it is left blank for dose responses
is a 20 character text field describing the pos/neg control.
it is left blank for dose responses
is a numeric field a maximum of 9 characters in length
is a 3 character text field indicating dose amount units
is a numeric field a maximum of 5 characters hi length
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Consider the following example:
.12 3 4-5 6 7 8
123456789012345678901234567890123456789012345678901234567890123456789012345
67890
Sample Id: PARC-91-0017 ResLab..: EHRT Exp Date.: 11/01/91
Samp Desc: 1-Nitrocarbazole
Exp. Name: PARC910044 Lab Tech: MST P Invest.: JL
Strain...: TA98 Str Date: 10/29/91 Act Type.: RLA059
Test Type: 01 - Standard Plate Incorporation Assay Act Level: 0
Time (Hr): 0.0
01 Sodium Azide
control)
Temp C..: 37.0 Input by.: MST
3.000 *ug 344 347 345 (ignore this line, a positive
24
1
0.000
5.000
10.000
25.000
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large when used this way. Originally, GeneTox Manager's HELP! was like this but it was too
large to run. It has been re-written as a general HELP! facility. The original help facility has
been saved as .bak which can be restored at a later date.
SNAP!
At the end of this document are the tree diagrams built by SNAP!, a piece of shareware
that "documents" dBASE and/or Clipper applications. These show the calling order of program
procedures and functions and database files. Each executable file has been documented
separately, since they are indeed segments of one larger system, GeneTox Manager.
To use SNAP! type SNAP at the DOS prompt. The software will ask for the following
information:
System name:
Author:
Copyright holder:
Copyright date:
Top file:
Path for source:
Path for data:
Path for output:
Path for SNAP! files:
GeneTox Manager
Whoever wrote the programs being documented
Person who owns the software
1992
Starting program
Where the .PRG files are located
Where the .DBF files are located
Where the completed files are to go
Where the SNAP! source code is located
Documentation for the SNAP! program can be found on the PC that is being used for
GeneTox Manager.
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CHAPTER 3
PROGRAM MAINTENANCE
, The following sections will explain how to edit, compile and link the files to create the
executable file. It also contains some error messages and how to fix the problems.
Editing Program Files
' To make a change to the GeneTox Manager software, an existing program file must be
edited or a new one created. To make changes to an existing file, first determine which file
has to be edited. If an error message has been received the file will be named hi the message.
If an update is requested, edit the file that performs the function to be modified. If something
new has been requested, a new program file will have to be created. Make sure to name the
new file with a unique name or unexpected results could occur.
Use an editing package that will save the program file in an ASCII format. This is
required because special wordprocessing format characters embedded in the files will cause
error messages during compiling and create other problems.
Certain PRO files contain extended graphics characters used to draw the GeneTox
Manager screens. Some text editors convert these graphics characters to regular text, and will
save the screens in this manner. For this reason, use a text editor that does not destroy the
graphics characters when editing these files.
Compiling the Program Files
Once the necessary changes have been made to a program file, it must be compiled.
This is done using Clipper, so the path must include a call to the Clipper subdirectory or the
CLIPPER.EXE file must be in the same directory as the .PRG files. To compile a program
file with line numbers, type:
CLIPPER filename (without .PRG)
Do this when testing the program as the error messages will include line numbers to
indicate where an error is occurring. However, this option makes the file larger. When testing
is complete, recompile the program file with the following qualifier (a lowercase L):
CLIPPER filename -1
This will compile the program file without line numbers and will reduce the size of the
object file.
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Linking the Program Files
To link the files, use the Clipper "RTLINIC" function. Simply list the names of the
object files be linked. These will in turn create the executable file that will be used to run the
system. The format is:
RTLINK FILE objectfile,objectfile
If the files are not in the current directory, make sure to include the correct paths in the
filenames.
RMake Facility
Clipper 5.01 includes a make facility for automatic executable generation when one of
the source files is modified. To run the Rmake facility set up for GeneTox, type RMAKE
GTM.
A makefile called GTM.RMK has been created which outlines the dependencies between the
source code modules and the procedures for generating a new executable. Only the necessary
files will be recompiled and linked. The makefile will make the G_Menu executable, and the
GTMLoad and Install system distribution utilities. Note however, that the existing makefile
is only valid if existing PRG files are modified. If new files are added to provide additional
functionality, the programmer will also have to update the makefile to describe these new PRG
files and their relationship to the system.
Right now the multitude of PRG procedure and function files have been divided into
categories to group those with similar function together. Data entry/modification files are
compiled into DataEntr.OBJ; Utility functions (PC & VAX) are compiled into Utils.OBJ;
Reporting functions are compiled into Reports. OBJ; System default functions are compiled into
Defaults.OBJ; Data save and storage functions are compiled into DataSave.OBJ; Help functions
are compiled into Help.OBJ. GJFuncts is compiled into its own OBJ. Reports, Defaults,
DataSave, Help, DataEntr, Utils, and G_Functs are linked into G_Menu.EXE.
Error Messages
Most of the error messages will appear on the screen in the following format:
PROC procname LINE lineno, errormsg errobject
where: procname is the procedure where the error occurred, lineno is the program line
number that contains the error (this will be 0 if the file was compiled with the -1
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option), errormsg tells what is wrong, and errobject is the thing (variable name, file,
etc.) that caused the problem.
The following are examples of errors that can occur. The important part is the
errormsg segment to figure out what is wrong.
PROC MCHOICE LINE 0, open error G_ENIND.NDX
Could not open the file G_ENIND.NDX - it could be missing, corrupted, or the
file limit may have been exceeded. Only 15 files may be open at any given
time and with GeneTox Manager, the maximum number of files is open during
the Enter, Modify and Reports options. Reindexing the databases usually will
take care of this error by recreating the index files or making sure only 15
• database or index files are open at one tune.
PROC SETGDEF LINE 1213, unidentified identifier G_VAL1
i
: The variable G_VAL1 was not recognized. Make sure it has been initialized (if
needed) or that the right database file has been called.
An OUT OF MEMORY error will occur if the machine has run out of base memory
because too many other things are running. Make sure no other processes are running
before starting GeneTox Manager to avoid this problem.
Using dBASE
To look at any of the database files, dBASE will have to be used. To invoke dBASE,
type dBASE at the DOS prompt in the subdirectory that contains the dBASE
executable files. Once hi dBASE, there are two ways to look at the data - the Assistant
or dot prompt commands.
The Assistant is an easy-to-use system that guides the user through the process of
looking at a database file, by using pop-up menus and prompts.
Dot prompt commands require a little more knowledge of dBASE. To look at the
data in a database file, type USE filename, where filename is the name of the database
file. Then use the dBASE/ commands to look at the data. A few of the commands are
explained below. To use these commands, just type the word at the dBASE dot
prompt. Then use the and keys to move between records and the
arrow keys and key move between fields. Use the dBASE manual to get a
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more detailed explanation of these commands and other commands that can be used.
EDIT - allows changing the data hi the record.
LIST - lists the records on the screen. Some of the forms of this command are : LIST,
which will list all of the fields for all of the records; LIST FOR fieldname =
"qualifier", which will list all of the fields for all of the records that meet the
condition specified by qualifier; and LIST fieldname, which will list fieldname
for all of the records.
GOTO TOP, GOTO BOTT and GOTO recno - goes to the top of the database, to
the bottom of the database, or to the record number specified by recno.
QUIT - leaves dBASE and returns to the DOS prompt.
Again, see the dBASE manual for more commands.
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CHAPTER 4
PROGRAM FILES
The following is an alphabetical listing of the program files used for the GeneTox
Manager system. The list includes the name of the program and a very brief description of
what the program actually does.
Bbridge.Prg
This routine calls and runs the Bernstein model.
ChkKeys.Prg
Stand alone system utility to report contents of database key default files.
ChkPass.Prg
Stand alone system utility to decrypt and report the current system password.
DSRCH.Prg
This routine searched databases based on selected criteria and sets up the data extraction
to be performed.
G_Accept.Prg
This routine allows the user to receive experiment data that has been dearchived by
another user to a disk file for the purpose of transferring ownership of the experiment.
G_AcInit.Prg
; This routine initializes all variables needed for the Activation System Information
Screen.
G_AcScnr.Prg
This routine draws the initial screen for the Activation System Information Screen.
G_ActSys.Prg
This routine allows the user to enter Activation System Information into temporary
variables.
G_AdSInt.Prg
This routine initializes the necessary variables before calling G_AdSmpl to add new
Samples.
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G_AdSmpl.Prg
This routine allows the user to add new Samples to an existing Experiment.
G_AllRpt.Prg
This routine submits selected data to and runs each statistical model.
G_AMAssc.Prg
This routine draws the Assay Type screen.
G_AMAssy.Prg
This routine allows the user to add or modify the Assay Type for the experiment.
G_Archiv.Prg
This routine allows the user to archive an experiment in compressed format to save disk
space and decrease database size.
G_ArcMnu.Prg
This routine prompts the user to Archive/Dearchive/Accept experiment data.
G_Assay.Prg
This routine allows the user to select the Assay Type for the experiment.
G_AsScnr.Prg
This routine draws the initial screen for the Assay Type Selection Menu.
G_ChkCnt.Prg
This routine provides header information to the VAX UPLOAD option.
G_ChkTpn.Prg
This routine provides header information to the VAX UPLOAD option.
G_ClrSep.Prg
This routine clears the database G_Sep.DBF. The database is used to make sure that
the extended Sample and S9 descriptions are only printed once per RAW DATA output.
This is used to clear that database so that on the next run of a Raw Data report the
EXPKEY will not be found. This is only a quick fix.
G_Colors.Prg
This routine allows the user to change the color settings used in the system.
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G_Commun.Prg
This routine allows the user to select the type of communications procedure to be used.
G_Conmu.Prg
, This routine allows the user to decide what action to take.
G_CurStr.Prg
This routine allows the user to enter the Current Strain, Activation Level and Dose
Units for the current sample.
G_CuScrn.Prg
: This routine draws the screen for the Current Strain and Activation Level Data Entry.
G_DBRInd.Prg
This routine recreates all indexes associated with GeneTox Manager databases.
G_DBZap.Prg
This routine pmnanently deletes all data from GeneTox Manager databases.
G_Dearch.Prg
This routine allows the user to dearchive experiment data which has been stored in
1 compressed format and return it to their databases.
GJDelExp.Prg
This routine permanently deletes an experiment frorn the databases.
G_DelSmp.Prg
This routine allows the user to delete a Sample from an Experiment.
G_DelRV.Prg
This routine deletes an experiment that has been imported from another user or
downloaded from the VAX.
G_DnLoad.Prg
This routine s%ws the user to download experiments stored on the VAX.
G_DpPrnt.Prg
This prints the dose responses if they have been entered into memory variables
previously.
G_DoScrn.Prg
This routine draws the initial screen for the Dose Data Entry.
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GJDose.Prg
This routine will allow the user to enter an unlimited amount of dose data, but presently
only 10 doses are allowed.
G_DoseNu.Prg
This routine draws the correct number of doses to be entered based on NUM_DOSE.
' GJEnFunc.Prg
This routine contains all of the functions used by the enter/modify routines.
G_EnProc.Prg
This routine contains all of the procedures used by the enter/modify routines.
G_Enter.Prg
This routine handles all of the data entry for the GeneTox Manager system.
G_ExInit.Prg
This routine initializes all variables needed for the experiment description screen.
GJExpLod.Prg
This routine allows the user to retrieve backup experiment data should the databases
become corrupted.
G_Expmnt.Prg
This procedure allows the user to enter experiment description data.
G_Export.Prg
This routine allows the user to export experiment data for use by other users. Exported
data is in a "Read Only" status.
G_ExScrn.Prg
This routine draws the screen for experiment data entry.
G_Extrnl.Prg
This routine declares all the data entry routines for execution.
G_Functs
Contains a library of system functions.
G_GenNps.Prg
This routine generates Negative and Positive control data sets for the VAX UPLOAD
option.
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G_GenRec.Prg
This routine is used by the VAX UPLOAD option.
G_GenTst.Prg
This routine generates Test plate count data for the VAX UPLOAD option.
G_GeScrn.Prg
This is routine draws the main menu screen for the GeneTox Manager system.
G_GetDP.Prg
This routine allows the user to enter a drive and path and verifies their existence.
GJmpExp.Prg
; This routine allows the user to choose Import/Export of experiment data.
G_Import.Prg
This routine allows the user to import experiment data that was exported by another
user. Imported data is in "Read Only" status.
G_InAdd.Prg
This routine allows the user to add instructs to the instruction database.
GJnAScr.Prg
This routine draws the screen for the Instruct add module.
GJnstal.Prg
This routine is part of the Install executable. It loads the GeneTox system onto hard
disk from 2 high density floppies that were created using the GTMLoad exe.
GJnstFV.Prg
This routine allows the user to view instructs that have been saved to disk.
G_Instrc.Prg
This routine allows the user to change the instruction help set.
GJntClr.Prg
This routine defines the default colors to be used with the system.
G_InView.Prg
This routine allows the user to view instructs that have been saved to disk or to modify
the instruction set.
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G_ListEx.Prg
This routine allows the user to view or print the names of the experiments in the
database.
GJLodDatPrg
Contains the routines used for retrieval of data by G_ExpLod, G_Import, and
GJDearch.
G_LstArc.Prg
This routine allows the user to browse the database of archived experiments.
G_MDeflt.Prg
This routine draws the menu for the defaults menu and prompts the user for a selection.
G_MEnter.Prg
This routine draws the Data Entry menu and loads the Screen Array with the necessary
values.
G_Menu.Prg
This routine is the main menu system for the GeneTox Manager system.
G_MoCInt.Prg
This routine initializes the necessary variables before calling G_MoCntl.
G_MoCntl.Prg
This routine allows the user to modify neg/pos control information.
GJModify.Prg
This routine allows the user to modify existing data hi the system.
G_MoDInt.Prg
This routine initializes all of the necessary data for the Dose Data Entry screen.
G_MoDose.Prg
This routine allows the user to modify existing Dose Responses for a given strain, date,
and Act.
GJModSmp.Prg
This routine allows the user to modify Sample data.
G_MoGen.Prg
This routine allows the user to modify general experiment information.
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G_MoGInt.Prg
This routine initializes all necessary data before calling GJMoGen.
G_MoSInt.Prg
This routine initializes all necessary data before calling G_MoSmpl.
G_MoSmpl.Prg
This routine allows the user to modify Experiment Specific Sample Data.
G_MoveDo.Prg
This routine controls the cursor movement for G_Dose.Prg.
G_MQuit.Prg
This routine draws the Quit Menu and accepts user response to Quit/Continue.
G_MSvAct.Prg
This routine saves the modified data for the Activation System Information Screen.
GJVISvAsy.Prg
This routine saves the modified data for the Assay Type Selection Screen.
G_MSvCtl.Prg
; This routine saves the modified data for the Neg/Pos Control Screen.
GJMSvDos.Prg
This routine saves the modified data for the Dose Response Data Entry Screen.
G_MSvExp.Prg
This routine saves the modified data for the Experiment Description Screen.
GJVKvQltPrg
This routine saves the modified data for the Quality Assurance Checks Screen.
G_MSvRmk.Prg
This routine saves the modified data for the Experimental Remarks Screen.
G_MSvSmp.Prg
This routine saves the modified data for the Sample Specific Screen.
G_MSvStn.Prg
This routine saves the modified data for the Final Strain Entry Screen.
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G_NegPos.Prg
This routine allows the user to enter Positive and Negative Controls for a given strain.
G_NeScrn.Prg
This routine draws the initial screen for the Neg/Pos Control Entry Screen.
G_NewPas.Prg
This routine allows the user to enter a new password for the Special Options menu.
GJParse.Prg
This routine parses an input file to make sure all experiment data is in the right format
before saving it to the databases using G_RetDat.
G_PC.Prg
This is the main calling program for the PC Utilities function.
G_PiAdd.Prg
This routine allows the user to enter new Principle Investigators into the List.
G_PMenu.Prg
This routine allows the user to enter, change or delete entries from the Principle
Investigator List.
G_PiMod.Prg
This routine allows the user to change entries hi the Principle Investigator List.
G_PMtr.Prg
This routine allows the user to modify the number of interactive readings from a colony
counter for each plate count.
GJProto.Prg
This routine allows the user to view the Protocol file anytime.
G_Qualty.Prg
This routine allows the user to enter Quality Assurance Checks into the database.
G_QuitAl.Prg
This routine terminates the GeneTox Manager system and returns to DOS.
G_QuScnr.Prg
This routine draws the initial screen for the Quality Assurance Checks Screen.
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G_RawDat.Prg
This routine allows the user to generate a report that includes all data for an
experiment.
G_Remark.Prg
This routine allows the user to enter Experimental Remarks into the database.
G_Replac.Prg
This routine replaces the status variable "A(11)M with 'T(gnore)" following upload to
VAX.
G_Report.Prg
This routine allows for a parameter setup for a data search over all pertinent data
ranges.
G_ReScnr.Prg
This routine draws the initial screen for the Experimental Remarks Screen.
G_RetDat.Prg
This routine saves data in an input file into the databases. It assumes that G_Parse has
been called previously to validate the data.
GJRpPage
;This routine prints the page number information on each report page.
G_RpRaSH.Prg
This procedure prints the Headers for the Sample description and the S9 description.
G_RpRaw9.Prg
This procedure prints S9 Description and information on separate page.
G_RpRawD.Prg
This procedure prints the header for the Dose amounts.
GJRpRawF.Prg
:This procedure prints the Negative control data to the screen or printer if it is the first
time this Strain has been printed.
GJRpRawG.Prg
This procedure prints the general information for the Raw Data Report.
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G_RpRawH.Prg
This procedure prints the header for the Raw data Report.
GJRpRawCXPrg
This procedure prints the Other Control data if it exists.
G_RpRawR.Prg
This procedure prints the Sample Remarks.
G_RpRawS.Prg
This procedure prints the Raw Data separate pages to the screen or the printer. The
separate pages are for the Sample description and the S9 description. The descriptions
are printed once per sample id.
G_RpRawT.Prg
This procedure prints the Dose response data and the plate counts to the screen or the
printer for the current strain.
G_RptChs.Prg
This routine allows the user to select which Report to run.
G_RptOut.Prg
This routine asks the user for the destination of the statistical reports generated.
G_SaveAl.Prg
This routine calls the appropriate modules to save all temporary variables to the
databases.
G_SavExp.Prg
This is routine saves the temporary variables to the G_Expmnt database.
G_SavGen.Prg
This routine save all general data to the G_GenDat database.
G_SavNeg.Prg
This routine saves all negative control information to the GJMegDat database.
G_SavNew.Prg
This routine saves all data for a newly entered experiment.
G_SavNP.Prg
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This routine calls either G_SavNeg or G_SavPos depending on the control code stored
in the temporary controls database. Each positive and negative control will be saved.
NOTE: The first negative control to be used is the control for the statistics model.
GJSavPos.Prg
This routine saves all positive control information to the G_PosDat database.
G_SavSmd.Prg
This routine saves the experiment specific information into the G_Exsmdt database.
G_SavSmp.Prg
This is routine saves all memory variables to the G_Sample database.
G_SavTst.Prg
This routine saves all test data into the G_Test database.
G_SCntrl.Prg
This routine calls the screens as defined by the screen array.
G_SelSug.Prg
This routine sets up the work areas for the suggestion databases.
G_SetFlg.Prg
This routine resets the status flag for a particular experiment to a user specified value.
G_SmpSpc.Prg
This routine allows the user to enter Sample specific data into the system.
G_SmScrn.Prg
This routine draws the initial screen for the Sample Specific Data Entry Screen.
G_SpeQpt.Prg
This routine allows the user to enter special options into the system and is password
protected. The backdoor is "LTC".
G_Spiral.Prg
This routine converts data collected from a spiral counter using Spiral Systems data
collection program. Data files .ID and .PRN must be provided
to the conversion routine.
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G_SpMenu.Prg
This routine allows the user to enter options provided by the Special Options. v
G_Strain.Prg
This routine allows the user to enter Strain information into memory variables.
G_StScrn.Prg
This routine draws the initial screen for the Final Strain Entry Screen.
G_SuAct.Prg
This routine allows the user to modify the suggestion box for the Activation System
Information Screen.
;JiJ
G_SuAssy.Prg
This routine allows the user to modify text for the Assay Selection Screen.
G_SuCur.Prg
This routine allows the user to modify the suggestion box for the Current Strain
Selection Screen.
G_SuDose.Prg
This routine allows the user to modify the suggestion box for the Dose Response
Screen.
G_SuExp.Prg
This routine allows the user to modify the suggestion box for the Experiment
Description Screen.
G_SuFinl.Prg
This routine allows the user to modify data for the Suggestion List.
G_Sugges.Prg
This routine allows the user to enter help text or a listing for the suggestion box.
G_SugOff.Prg
This routine turns off the suggestion function keys.
G_SugOn.Prg
This routine sets the suggestion function keys to the routines for the suggestion keys.
G_SuHelp.Prg
This routine allows the user to enter help text for the suggestion box.
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G_SuHMod.Prg
This routine allows the user to modify existing help text in the suggestion box.
GJSuListPrg
This routine fills SUGG 1.DBF with missing information when there is no listing for a
suggestion box.
G_SuLMod.Prg
This routine allows modification of the Suggestion Lists.
G_SuMod.Prg
This routine allows the user to modify the suggestion box for various screens.
G_SuNp.Prg
This routine allows the \iser to modify the suggestion box for the Negative/Positive
^Control Screen.
GJSuQual.Prg
This routine allows the user to modify the suggestion box for the Quality Assurance
Screen.
G_SuRep.Prg
This routine allows the user to modify the suggestion box for the Experiment
.Description Screen.
G_SuRExt.Prg
This routine allows the user to modify the suggestion box for the Reports used hi the
.GeneTox Manager System.
G_SuRmrk.Prg
This routine allows the user to modify the suggestion box for the Experimental
Remarks Screen.
G_SuSamp.Prg
This routine allows the user to modify the suggestion box for the Sample Specific
Screen.
G_SuSel.Prg
This routine allows the user to select which screen to modify the Suggestion text or list
for.
GJTermHe.Prg
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This routine terminates the modify help mode.
G_Util.Prg
This routine allows the user to choose PC/VAX Functions.
G_Vax.Prg
This routine is the mam calling program for the VAX Utilities function.
G_VaxFle.Prg
This routine is the mam calling program for procedures used to create the VAX
UPLOAD file.
G_Vpubl.Prg
This procedure initializes all of the public variables for the GeneTox Manager system.
G_Welcom.Prg
This routine displays a welcome message to the user for 20 seconds or until a key is
pressed.
G_Xtrct.Prg
This is routine prompts the user for the experiment name for which to extract data.
GTMLoad.Prg
Generates a set of installation diskettes from functioning GeneTox Manager system.
GTMRestPrg
Restores GeneTox Manager systems converted to version 2.2 database formats using
the GeneTox Manager Upgrade program to their original condition.
Hbridge.Prg
This routine calls and runs the Histidine model.
Help.Prg
This routine displays the help text on the screen.
HelpTextPrg
Stand Alone system utility to print contents of IVHelp memo fields.
InsLib.Prg
Library routines used by GeneTox Manager install program.
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Version 2.21
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InstalLPrg
: Installation program for GeneTox Manager.
IVFuncts.Prg
Library routines used by GeneTox Manager system.
IVLib.Prg
Library routines used by GeneTox Manager system.
Qbridge.Prg
This routine calls and runs the Quasi-Stead model.
Sbridge.Prg
This routine calls and runs the Stead model.
UpgLib.Prg
Library routines used by GeneTox Manager upgrade program.
Upgrade.Prg
Database upgrade program of upgrading to GeneTox Manager v2.2 database format.
GeneTox Manager PC Programmer's Guide
Version 2.21
Page 37
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CHAPTER 5
SYSTEM DEFAULT FILES
The following default files are used by the GeneTox Manager system. They are
standard Clipper MemVar files 'that have been given a .DFT extension. Most are initialized
by G_VPubl for the duration of the application, although a few are initialized and saved by
individual procedures. They are generally not saved unless the user changes a system default
setting.
MemVar files have .MEM extension and are located in the application directory (directory
where system executables reside).
MemVar File Variable Remarks
DrvPath DftStg GeneTox database location ( < drv > :\ < path > ).
GTMArchv ArchStg Archives location (:\).
Default files have .DFT extension and reside in database directory (specified in the DrvPath.MEM MemVar file).
Default File
ColorHel
ColorsH
ColorsN
Edit_Col
Err_Colo
Exp_Colo
ExpJBdit
Func_Col
G_Array
G_Assays
G Commun
Variables
ColorHelp
Header
Normal
Edit_Color
Err_Color
Exp_Color
Exp_Edit
Func_Color
Inc_Array
Assay 1..26,
AssayEnter,
AssaySave
CommunType
Remarks
Color string used when displaying system help.
Color string used when displaying screen headings.
Color string used for main menu, first level menus, and data entry
screens.
Color string used for second level and lower menus.
Color string used when displaying system error messages using the
Error_Msg() function.
Color string used when displaying expanded suggestion boxes containing
no selectable items.
Color string used when displaying expanded suggestion boxes containing
selectable items.
Color string used to display currently active function keys.
Allow addition of new assays? (T/F)
Contains user entered assay information.
String containing communications link type to VAX databases: "1200" or
"2400" baud modem;
"TERM"inal server; or
"PCSA" DEC Pathworks.
NOTE! This feature not implemented.
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Default File Variables Remarks
G_Coords Win_Coord, Window coordinates and starting position for ACHOICEQ of Win_Pos
assays array.
G_ExpKey T_ExpKeys Contains next available experiment key.
G_Gene Enc_Pas Contains system password for access to Defaults-Set Special Options Menu
(encrypted).
GJtastr InstSelect String containing filename of currently selected instruction set.
G_ItCnt RdCnt Number of times to count each plate when using colony counter interface.
G_Keys S_Key Next available suggestion index key value.
G_ModHel ModHelp Color String used when modify ing system help.
G_NegKey T_NegKey Next available negative control key.
G_PosKey TJPoskey Next available positive control key.
G_SamKey TSampKey Next available sample key.
Proto ProtoNam Drive/Path for Protocol files, top level filename.
Sugg_Col Sugg_Color Color string used when displaying suggestion box text.
Version G_Version String indicating version information ("PC_" or "VAX").
QStead (text file) Presence of this file hi the database directory causes GeneTox Manager
to block execution of the Quasi-Stead model.
GeneTox Manager PC Programmer's Guide
Version 2.21
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CHAPTER 6
DATABASE STRUCTURES
This chapter contains the logical and physical structures of the various databases used with the GeneTox
Manager system.
LOGICAL STRUCTURE
Gen Sample
Exp Samp Ie
ControI PI ate
OneTo-One Relationship
One-To-Many Relationship
Entity
Gen Sample '
*'
Experiment
Strain
Exp Sample
Control
Test Plate
Control Plat
Description
General sample information independent of the experiment(s) hi which the
sample was run (GJSample).
General experiment information (G_GenDat).
Information about each strain used in the experiment (G_Expmnt).
Experiment specific sample information related to the specific strain the sample
was analyzed under (G_ExSmDt).
Positive and negative controls for each strain used in the experiment.
Test plate for a particular dosage, 5 Plates/Dose (G_Test).
Positive or negative control plate, 5 Plates/Dose (G_Neg/PosDat).
"GeneTox Manager PC Programmer's Guide
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The following sections contain the name, alias, and indices used with each database, as well as the name
type, width, number of decimal places and contents of each field hi the database.
Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15 .
16
17
18
19
20
21
22
23
24
G GENDAT.DBF - general experiment information
GENERAL
ExpNam
G GENIND (ExpNam)
STORAGE
field name
EXPNAM
STATUS
RESLABID
EXPDATE
TESTYPCOD
S9TYPLOT
LABTECH
TESTYPDES
TIMEMI
TIMEHR
TEMPERATRC
TEMPERATRF
LABBOOK
ASYMODF
ENTERDATE
ENTRYTECH
P INVEST
S9_DESC
S9STRB
S9STRA
S9LEVEL1
S9LEVEL2
S9UNITS1
S9UNITS2
Type
Character
Character
Character
Date
Numeric
Character
Character
Character
Numeric
Numeric
Numeric
Numeric
Character
Character
Date
Character
Character
Memo
Numeric
Numeric
Character
Character
Character
Character
Width
10
1
4
8
2
. 6
4
35
3
6
6
6
25
35
8
4
4
10
1
1
6
6
4
4
Dec
1
1
1
Contents
Experiment name
Upload status flag
Research lab ID
Date conducted
Type of test conducted
S9 type and lot number
Person conducting exp
Test type description
Minutes
Hours
Temperature Celsius
Temperature Fahrenheit
Labbook number
Assay modification.
Date data entered
Person entering data
Principal Investigator
S9 description
Sterility before
Sterility after
Activation level
Activation level
Units of measurement
Units of measurement
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Name:
Alias:
Keys:
Index:
G SAMPLE.DBF - sample specific data
SAMPLE
SampKey
G SAKIND (Str(SampKey,9))
G SAMIND (Samplabid+Str(GbbSmplyr,2)+Str(GbbSmpln,4)
Type:
Field
1
2
3
4
5
6
7
8
9
10
11
Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
7
STORAGE
Field name Type Width Dec
SAMPKEY Numeric 9
SM STATUS Character 1
RESLABID Character 4
SAMPLABID Character 4
GBBSMPLYR Numeric 2
GBBSMPLN Numeric 4
DS STATUS Character 1
SAMPDESC Memo 10
GS STATUS Character 1
SC BAT LOT Character 51
CAS_NUM Character 15
G EXPMNT.DBF - experiment information
EXPMNT
Contents
Sample key
Sample upload status
Research lab ID
Sample lab ID
Year info recorded
Sample ID
Dose upload status
Sample description
Overall upload status
Sample source/ batch/lot
Sample CAS number
ExpKeys, ExpNam
G EXPIND(Expnam+StraiaAbr+Dtoc(StmDate)+Str(ActLevel,l))
G EXKIND (ExpKeys)
STORAGE
Field name Type Width Dec
EXPKEYS Numeric 9
STATUS Character 1
EXPNAM Character 10
STRAINABR Character 6
! STRNDATE Date 8
ACTLEVEL Numeric 1
CULTDNSY Character 10
Contents
Experiment key
Upload status flag
Experiment name
Strain abbreviation
Strain date
Activation level
Culture density
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Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
7
8
9
10
11
12
13
Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
7
G EXSMDT.DBF - experiment specific data
EXSPECBFIC
ExpKeys, SampKey
G EXSIND (Str(ExpKeys,9)+Str(SampKey,9))
G ESSIND (Str(SampKey,9))
STORAGE
Fieldname Type Width Dec
EXPKEYS Numeric 9
SAMPKEY Numeric 9
STATUS Character 1
PHENOCOD Numeric 1
SMPLSTRB Numeric 1
SMPLSTRA Numeric 1
DOSUNITS Character 24
REMARK Memo 10
OLD EXPKEY Numeric 9
SOLV DESC Character 25
SOLV AMTPT Numeric 4
SOLV UNITS Character 3
INCUBATJHR Numeric 6 2
G TSTRN.DBF
TSTRAIN
GJTSKIND (G_SKey)
G TSTIND (G Strain+Dtoc(G StrDate)+Str(G ActLevel
TEMPORARY
Field name Tjpe Width Dec
G_STRAIN Character 6
G STRDATE Date 8
G ACTLEVEL Numeric 1
G DENSITY Character 10
G EXPMNT Character 1
G EXSMDT Character 1
G SKEY Numeric 9
Contents
Experiment key
Sample key
Upload status flag
Pheno code check
Sterility before
Sterility after
Units for dose
Remark field
Trash field
Solvent description
Solvent amount
Units of measure
Hours of incubation
,D)
Contents
Strain used
Date
Activation level
Culture density
Experiment name
Experiment date
Sample key
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Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
Name:
Alias:
Keys:
Index:
G HCNTRL.DBF
HCONTROL
G Key, NPKey
G HCNIND (G Key)
G HCCIND (Str(G Code,2)+Str(G Amnt,9)+G_Unit)
TEMPORARY
Field name
G KEY
G NPKEY
G STATUS
G CODE
G NAME
G AMNT
G UNIT
G MEAN
G STD
G PLATE1
G BKGRND1
G PLATE2
G BKGRND2
G PLATE3
G BKGRND3
G PLATE4
G BKGRND4
G PLATES
G_BKGRND5
G TCNTRL.DB?
TCONTROL
G Key, G NPKif
Type
Numeric
Numeric
Character
Numeric
Character
Numeric
Character
Numeric
Numeric
Numeric
Character
Numeric
Character
Numeric
Character
Numeric
Character
Numeric
Character
Width
9
9
1
2
20
6
3
10
9
5
1
5
1
5
1
5
1
5
1
Dec
2
4
4
G TCNIND/£Key)
G_TCCIND|tt(G_Code,2)+Str(G_Amnt,9)+G_Unit)
Type:
Field
1
2
3
4
5
6
7
8
9
10
11
12
TEMPORARY
Field name
G KEY ^
G NPKEY I
G STATUS
G CODE
G NAME I ^
G AMNT y"'
G UNIT P
G MEAN I
G STD
G PLATE1
G BKGRNDi
G PLATE2"
Type
Numeric
Numeric
Character
Numeric
Character
Numeric
Character
Numeric
Numeric
Numeric
Character
Numeric
Width
9
9
1
2
20
6
3
10
9
5
1
5
Dec
2
4
4
Contents
Experiment key
Neg/Pos control key
Upload status flag
Neg/Pos control code
Name of control
Amount used
Unit of measurement
Calculated mean
Calculated standard dev
Temp plate counts
Temp background code
Temp plate counts
Temp background code
Temp plate counts
Temp background code
Temp plate counts
Temp background code
Temp plate counts
Temp background code
Contents
Experiment key
Neg/Pos control key
Upload status flag
Neg/Pos control code
Name of control
Amount used
Units of measurement
Calculated mean
Calculated standard dev
Temp plate counts
Temp background code
Temp plate counts
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Reid
13
14
15
16
17
18
19
Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
Field name
G BKGRND2
G PLATES
G BKGRND3
G PLATE4
G BKGRND4
G PLATES
G_BKGRND5
G NEGDAT.DBF
NEGATIVE
ExpKeys, NegKey
Type Width
Character
Numeric
Character
Numeric
Character
Numeric
Character
- negative control
1
5
1
5
1
5
1
data
G NEGIND (Str(ExpKeys,9)+Str(NegKey,9))
STORAGE
Field name
EXPKEYS
NEGKEY
STATUS
NEGCODE
NEGCTRLNA
NEGAMT
NEGUNT
NEGMEAN
NEGSTDEV
NEGPLTCNT1
NEGBKGRND1
NEGPLTCNT2
NEGBKGRND2
NEGPLTCNT3
NEGBKGRND3
NEGPLTCNT4
NEGBKGRND4
NEGPLTCNT5
NEGBKGRND5
Type Width
Numeric
Numeric
Character
Numeric
Character
Numeric
Character
Numeric
Numeric
Numeric
Character
Numeric
Character
Numeric
Character
Numeric
Character
Numeric
Character
9 ,
9
1
2
20
6
3
10
9
5
1
5
1
5
1
5
1
5
1
Dec
Dec
4
4
Contents
Temp background code
Temp plate counts
Temp background code
Temp plate counts
Temp background code
Temp plate counts
Temp background code
Contents
Experiment key
Negative control key
Upload status flag
Negative control code
Negative control name
Negative control amount
Negative control units
Negative control mean
Negative control sd
Negative plate counts
Background code
Negative plate counts
Background code
Negative plate counts
Background code
Negative plate counts
Background code
Negative plate counts
Background code
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Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
7
8
9
10
11
12
14
15
16
17
18
19
G POSDAT.DBF
POSITIVE
ExpKeys, PosKey
- positive control data
G POSIND (Str(ExpKeys,9)+Str(PosKey,9))
STORAGE
Field name
EXPKEYS
POSKEY
STATUS
POSCODE
POSCTRLNAM
POSAMT
POSUNT
POSMEAN
POSSTDEV
POSPLTCNT1
POSBKGRND1
POSPLTCNT2
POSBKGRND2
POSPLTCNT3
POSBKGRND3
POSPLTCNT4
POSBKGRND4
POSPLTCNT5
POSBKGRND5
Type Width
Numeric 9
Numeric 9
Character 1
Numeric 2
Character 20
Numeric 6
Character 3
Numeric 10
Numeric 9
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
Dec Contents
Experiment key
Positive control key
Upload status flag
Positive control code
Positive control name
2 Positive control amount
Positive control units
4 Positive control mean
4 Positive control sd
Positive plate counts
Background code
Positive plate counts
Background code
Positive plate counts
Background code
Positive plate counts
Background code
Positive plate counts
Background code
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Name:
Alias:
Keys:
Index:
T^pe:
Reid
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Name:
Alias:
Keys:
Index:
Type:
Held
1
2
3
4
5
6
7
8
9
10
11
GJTEST.DBF - test
TEST
ExpKeys, SampKey
dose data
G TESIND (Str(ExpKeys,9)+Str(SampKey,9))
STORAGE
Field name
EXPKEYS
SAMPKEY
TD STATUS
DOSE
TESTMEAN
TESTDEV
TP STATUS
TSTPLTCNT1
TSTBKGRND1
TSTPLTCNT2
TSTBKGRND2
TSTPLTCNT3
TSTBKGRND3
TSTPLTCNT4
TSTBKGRND4
TSTPLTCNT5
TSTBKGRND5
Type Width
Numeric 9
Numeric 9
Character 1
Numeric 9
Numeric 10
Numeric 10
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
G DOSE.DBF - dose response data
G_Dose
None
TEMPORARY
Field name
G DOSE
G DOSEPLT1
G DOSEBKG1
G DOSEPLT2
G DOSEBKG2
G DOSEPLT3
G DOSEBKG3
G DOSEPLT4
G DOSEBKG4
G~DOSEPLT5
G DOSEBKG5
,
Type Width
Numeric 9
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character 1
Numeric 5
Character' 1
Numeric 5
Character 1
Dec
3
4
4
Contents
Experiment key
Sample key
Test dose upload status
Dose amount used
Test mean
Test standard dev
Test plate upload status
Test plate counts
Background code
Test plate counts
Background code
Test plate counts
Background code
Test plate counts
Background code
Test plate counts
Background code
Contents
Dose amount
Plate counts
Background code
Plate counts
Background code
Plate counts
Background code
Plate counts
Background code
Plate counts
Background code
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Name: G_SUGG1.DBF
Alias: SUGG1
Keys: Var_Name
Index: G_SUGG1 (Var_Name)
Type: STORAGE
Field
1
2
3
4
5
6
Field name
VAR NAME
LIST
SUGG INDEX
NUM SUGG
REQUIRED
VERIFIED
Type Width
Character 10
Logical
Numeric
Numeric
Logical
Logical
1
5
5
1
1
Dec Contents
Variable name
Selectable/Help text flag
Suggestion key
Suggestion box number
Required field tag
Verified field tag
Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
G_SUGG2.DBF
SUGG2
Sugg_Index
G_SUGG2 (Suggjndex)
STORAGE
Field name
SUGG_INDEX
SUGGESTION
RETURN VAL
Type Width
Numeric 5
Character 48
Character 48
Dec Contents
Suggestion key
String displayed
Selectable field return value
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Name: G_SEP.DBF - used for the raw data report
Alias: SEPERATE
Index: G_SEPIND (Sep_Nam)
Type: STORAGE
field name Type Width
SEP_NAM Character 10
GJPINVST.DBF - principal investigator list
PINVST
P_Invest
G_PININD (P_Invest)
STORAGE
Field name
P INVEST
Type
Character
Width
4
Dec
Contents
Flagged names for raw data report
Dec
Contents
Principal investigator
Name:
Alias:
Keys:
Index:
Type:
Field
1
GJPITMP.DBF - principal investigator modification
PITMP
G_PI
None
TEMPORARY
Field name
G PI
Type
Character
Width
4
Dec
Contents
Principal investigator
Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
G_MODSUG.DBF - suggestion modification
MODSUG
Sugg_Index
None
TEMPORARY
Field name
SUGGJNDEX
SUGGESTION
RETURN VAL
Type Width
Numeric 5
Character 48
Character 48
Dec Contents
Suggestion key
String displayed
Selectable field return value
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Name:
Alias:
Keys:
Index:
Type:
Field
1
2
Name:
Alias:
Keys:
Index:
Type:
Field
1
IVHELP.DBF
ProcName
IVHELP (ProcName)
STORAGE
Field name
PROCNAME
HELPTEXT
GTMDIST.DBF
Type
Character
Memo
Width
10
10
Dec'
DistKey
G_DSTIND (DistKey)
STORAGE
Field name
DISTKEY
DISTSITE
Type
Numeric
Character
Width
9
35
Dec
Contents
Procedure name (not presently used)
Help text shown
Contents
Distribution Key (Millions number for all
keys generated by this GeneTox distribution
copy)
Person and/or place to receive GeneTox
distribution copy
Name:
Alias:
Keys:
Index:
Type:
Field
1
2
3
4
5
6
GTMARCHV.DBF
ArchiveDB
ExpNam
G ARCIND (ExpNam)
STORAGE
Field name
EXPNAM
PASSWORD
DRIVE
PATH
FILENAME
ARCHDATE
Type
Character
Character
Character
Character
Character
Date -
Width
10
20
1
24
12
8
Dec Contents
Experiment name
Archive Password
Drive Letter of Archive Location
DOS Path of Archive Location
Archive File DOS Filename
Date Experiment Archived
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CHAPTER?
TRANSFER FILE FORMATS
GeneTox manager uses flat file formats for storing experiment and sample data for
backup, uploading, archiving, and sharing files between machines. Two distinct file formats
exist: the "old" file format (particular to the database structures before version 2.2) and the
"new" format (used hi version 2.2). GeneTox has the ability to read transfer files of either type,
but generates files only hi the "new" format. New format files may be identified by a character
"N" in the 56th column of the STO1 header record.
Record Type ST01 - Required with all associated records below for EACH experiment/strain
combination.
Description
ST01 - Master record for an experiment strain
Experiment strain key
Data record status in PC databases:
(A)ctive, (inactive, (M)odified,
(R)ead Only,(V)ax Download, (X)Archived
Experiment Name
Strain Abbreviation
Strain Date (YYMMDD)
Activation Level
General Experiment Info included (Y/N)
Number of Samples included for this experiment strain xetyas
Number of negative controls for this experiment strain xdyas
Number of positive controls for this experiment strain adysis
Culture Density
Transfer file format flag (N = new)
Col
1-4
5-13
14
Field
RecType
ExpKeys
RecStat
Data Type
Character
Integer
Character
I/en
4
9
1
15-24
25-30
31-36
37
38
39-41
42-43
44-45
46-55
** New
56
ExpNam
StrnAbr
StrnDate
ActLevel
GenRec
NumSmp
NumNeg
NumPos
CultDnsy
File Format
TFFormat
Character
Character
Date
Character
Character
Integer
Integer
Integer
Character
Only **
Character
10
6
6
1
1
2
2
2
10
1
**End-of-record**
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Record Type GE01 - Required if GenRec field in ST01 record = Y.
Co!
1-4
5-13
14
15-20
21-22
23-28
29-32
33-67
Field
RecType
ExpKeys
RecStat
ExpDate
TesTypCod
S9TypLot
LabTech
TesTypDes
Data Tvne
Character
Integer
Character
Date
Integer
Character
Character
Character
Len
4
9
1
6
2
6
4
35
Description
GE01 - General experiment information - Rec 1
Experiment strain key
Data record status in PC databases:
(A)ctive, (I)nactive, (Modified,
(R)ead Only, (V)ax Download, (X)Archived
Experiment Date (YYMMDD)
Test type code
S9 Type and Lot
Lab Technician initials
Test type description
**End-of-record**
Record Type GE02 - Required if GenRec field hi ST01 record - Y.
Col
1-4
5-13
14-16
17-22
23-28
29-34
35-59
60-63
Held
RecType
ExpKeys
TimeMi
TimeHr
TempF
TempC
LabBook
ResLabID
Data Type
Character
Integer
Integer
Floating
Floating
Floating
Character
Character
Lei
4
9
3
6.1
6.1
6.1
25
4
GE02 - General experiment information - Rec 2
Experiment strain key
Experiment time in minutes
Experiment tune hi hours
Temperature hi Farenheit
Temperature hi Centigrade
LabBook Number
Research Lab ID
**End-of-record**
Record Type GE03 - Required if GenRec field in ST01 record = Y.
Col
1-4
5-13
14-48
49-54
55-58
59-62
Field
RecType
ExpKeys
AsyModf
EnDate
PJtavest
EntryTech
Data Type
Character
Integer
Character
Date
Character
Character
Le
4
9
35
6
4
4
Description
GE03 - General experiment information - Rec 3
Experiment strain key
Assay Modification
Data entry date (YYMMDD)
Principal investigator initials
Data entry technician initials
**End-of-record**
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Record Type GE04 - Required if GenRec field in ST01 record = Y.
Col
1-4
5-13
14
15
16-21
22-27
28-31
32-35
36
37-40
Field
RecType
ExpKeys
S9StrB
S9StrA
S9Levell
S9Level2
S9Unitsl
S9Units2
S9Used
NmS9Desc
Data Type
Character
Integer
Integer
Integer
Character
Character
Character
Character
Character
Integer
Lem
4
9
1
1
1
1
4
4
1
4
Description
GE04 - General experiment information - Rec 4
Experiment strain key
S9 sterility before
S9 sterility after
S9 level 1
S9 level 2
S9 units 1
S9 units 2
S9 used (+/-)
Number of S9 description records to follow
(i.e., number of GEOSs)
**End-of-record**
Record Type GE05 - Number of GE05 records must correspond to value in NmS9Desc field in
record.
GE04
Col
1-4
5-13
14-78
Field
RecType
ExpKeys
S9Desc
Data Type
Character
Integer
Character
Len
4
9
65
**End-of-record**
Description
GE05 - General experiment information - Rec 5
Experiment strain key
S9 description line
Record Type NP01 - Number of NP01/NP02 record sets must correspond to value hi NumNeg
hi ST01 record.
field
Col
1-4
5-13
14
15-16
17-36
37-45
46-48
49-58
59-68
69
record
Field
RecType
NegKey
RecStat
NegCode
NegName
NegAmt
NegUnit
NegMean
NegStDev
NmNegCnt
Data Type
Character
Integer
Character
Integer
Character
Floating
Character
Floating
Floating
Integer
Len
4
9
1
2
20
9.3
3
10.4
10.4
1
Description
NP01 - Negative control general information
Negative control key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Archived
Negative control code
Negative control name
Negative control amount
Negative control units
Negative control mean
Negative control standard deviation
Number of negative control plate counts to follow hi
NP02
**End-of-record**
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Record Type NP02 - Number of NP01/NP02 record sets must correspond to value in NumNeg field in ST01
record.
Description
NP02 - Negative control plate counts
Negative control key
Plate count 1
Background code 1
Plate count 2
Background code2
Plate count 3
Background code 3
Plate count 4
Background code 4
Plate count 5
Background code 5
**End-of-record**
Col
1-4
5-13
14-18
19
20-24
25
26-30
31
32-36
37
38-42
43
field
Recl^pe
NegKey
NegPlCntl
NegBkgndl
NegPlCnt2
NegBkgnd2
NegPlCntS
NegBkgndS
NegPlCnt4
NegBkgnd4
NegPlCntS
NegBkgndS
Data Type
Character
Integer
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Len
4
9
5
1
5
1
5
1
5
1
5
1
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Record Type PP01 - Number of PP01/PP02 record sets must correspond to value in NumPos field in ST01 record.
Description
PP01 - Positive control general information
Positive control key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Arcbiyed
Positive control code
Positive control name
Positive control amount
Positive control units
Positive control mean
Positive control standard deviation
Number of positive control plate counts to follow in
PP02 record
**End-of-record**
Record Type PP02 - Number of PP01/PP02 record sets must correspond to value in NumPos field in ST01 record.
Col
1-4
5-13
14
15-16
17-36
37-45
46-48
49-58
59-68
69
Field
RecType
PosKey
RecStat
PosCode
PosName
PosAmt
PosUnit
PosMean
PosStDev
NmPosCnt
Data Type
Character
Integer
Character
Integer
Character
Floating
Character
Floating
Floating
Integer
Lem
4
9
1
2
20
9.3
3
10.4
10.4
1
Col
1-4
5-13
14-18
19
20-24
25
26-30
31
32-36
37
38-42
43
Field
RecType
PosKey
PosPlCntl
PosBkgndl
PosPlCnt2
PosBkgnd2
PosPlCntS
PosBkgndS
PosPlCnt4
PosBkgnd4
PosPlCntS
PosBkgndS
Data Type
Character
Integer
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Len
4
9
5
I
5
1
5
1
5
1
5
1
Description
PP02 - Positive control plate counts
Positive control key
Plate count 1
Background code 1
Plate count 2
Background code 2
Plate count 3
Background code 3
Plate count 4
Background code 4
Plate count 5
Background code 5
**End-of-record**
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Record Type SM01 - Number of SM01 record sets must correspond to value in NumSmp
field in ST01 record.
Col
1-4
5-13
14
field
RecType
SampKey
RecStat
Data Type Len
Character 4
Integer 9
Character 1
15-18
19-22
23-24
25-28
29
30
31
32-55
56-57
58
Filler
SmpLabID
SmpYr
SmpNo
PhenoCod
SmplStrB
SmplStrA
DosUnits
NumDose
GenSm
Character
Integer
Integer
Integer
Integer
Integer
Character
Integer
Character
4
2
4
1
1
1
24
2
1
59-62 RemCt Integer 4
63-66 NumSDc Integer 4
67-75 OldKey Integer 9
**End-of-record**
Description
SM01 - Sample analysis header information
Sample key
Data record status hi PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)eadjOnly, (V)ax Download, (X)Archived
Not currently used
Sample lab ID
Sample year
Sample number
Phenocode check
Sample sterility before
Sample sterility after
Dose units
Number of doses
General sample information included (Y/N)
(i.e., do SM03-SM04 records follow?)
Number of remarks records that follow (SMOSs)
Number of sample description records that follow
Old sample key if the SampKey field is a replacement
In the "old" transfer file format, SM02, SM03 and SM04 records Ijave the following format:
Record Type SM02 - Number of SM02 records must correspond to value hi NumSDc field
hi SM01 record.
Reid
1-4 RecType
5-13 SampKey
14-64 SampDesc
**End-of-record**
Data Type Len
Character 4
Integer 9
Character 51
Description
SM02 - Sample description records
Sample key
Sample description line
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Record Type SM03 - Required if GenSm field = Y in SM01 record.
Col
1-4
5-13
14-38
39-42
43-45
46-60
Field
RecType
SampKey
SolvDesc
SolvAmtPt
SolvUnits
CasNum
Data Type
Character
Integer
Character
Integer
Character
Character
Len
4
9
25
4
3
15
Description
SM03 - General sample information
Sample key
Solvent description
Solvent amount per plate
Solvent units
CAS number
**End-of-record**
Record Type SM04 - Required if GenSm field = Y in SM01 record.
Col
1-4
5-13
14-64
65-70
Field
RecType
SampKey
Sc_Bat_Lot
IncubatHr
Data Type
Character
Integer
Character
Floating
Lem
4 .
9
51
6.2
Description
SM04 - General sample information
Sample key
Source/Batch/Lot
Incubation hours
**End-of-record**
In the "new" transfer file format SM02, SM03, and SM04 records have the following format:
Record Type SM02 - Required for each SM01 record.
Col Field
1-4 RecType
5-13 SampKey
14-38 SolvDesc
39-42 SolvAmtPt
43-45 SolvUnits
46-51 IncubatHr
**End-of-record**
Data Type Len
Character 4
Integer 9
Character 25
Integer 4
Character 3
Floating 6.2
Description
SM02 - Experiment specific sample information
Sample key
Solvent description
Solvent amount per plate
Solvent units
Incubation hours
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Record Type SM03 - Number of SM03 records must correspond to value in NumSDc field
in SM01 record.
Col
1-4
543
14-64
Field
RecType
SampKey
SampDesc
Data Type
Character
Integer
Character
Len
4
9
51
Description
SM03 - Sample description records
Sample key
Sample description line
**End-of-record**
Record Type SM04 - Required if GenSm field = Y in SM01 record.
Co!
1-4
5-13
14-64
65-79
Field
RecType
SampKey
Sc_Bat_Lot
CasNum
Data Type
Character
Integer
Character
Character
Len
4
9
51
15
Description
SM04 - General sample information
Sample key *
Source/Batch/Lot
CAS number
**End-of-record**
Record Type SM05 - Number of SM05 records must correspond to value in RemCt field in
SM01 record.
Col Field
1-4 RecType
5-13 SampKey
14-73 Remark
**End-of-record**
Data Type Len
Character 4
Integer 9
Character 60
Description
SM05 - Sample remarks records
Sample key
Sample remark line
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Record Type TD01 - Number of TD01/TD02 record sets must correspond to value in NumDose field in SM01
record.
Description
TD01 - Dose analysis information
Experiment strain key
Sample key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Archived
Dose amount
Test dose mean
Test dose standard deviation
Number of test plate counts to follow in
TD02 record
**End-of-record**
Record Type TD02 - Number of TD01/TD02 record sets must correspond to value in NumDose field in ST01
record.
Col
1-4
5-13
14-22
23
24-32
33-42
43-52
53
Field
RecType
ExpKeys
SampKey
RecStat
Dose
TestMean
TestDev
TestCnt
Data Type
Character
Integer
Integer
Character
Floating
Floating
Floating
Integer
Len
4
9
9
1
9.3
10.4
10.4
1
Col
1-4
5-13
14-18
19
20-24
25
26-30
31
32-36
37
38-42
43
Field
RecType
SampKey
TstPlCntl
TstBkgndl
TstPlCnt2
TstBkgnd2
TstPlCntS
TstBkgndS
TstPlCnt4
TstBkgnd4
TstPlCntS
TstBkgndS
Data Type
Character
Integer
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Len
4
9
5
1
5
1
5
1
5
1
5
1
Description
TD02 - Test plate counts
Sample key
Plate count 1
Background code 1
Plate count 2
Background code 2
Plate count 3
Background code 3
Plate count 4
Background code 4
Plate count 5
Background code 5
**End-of-record**
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CHAPTERS
POSSIBLE ENHANCEMENTS
1. Modify GeneTox Manager code and databases to allow for replication of Samples within an
Experiment. The current database structure is:
Exp= = => Strain = = = > ExpSamp = = = > Test
Dose ,
GenSamp = = =
(where GenSamp is general sample information shared between Experiments, and ExpSamp is
experiment specific sample information.)
The altered structure could be (for example):
Exp = = = > Strain = = = > ExpSamp = = = > RepSamp = = = >
Test Dose
A.
GenSamp = = = = = = = = = = = = = +
(where GenSamp is general sample information shared between Experiments, ExpSamp is
experiment specific sample information, and RepSamp is information specific to each replication
of the sample in the experiment.)
Once this is done, GeneTox Manager spiral data import code could be modified to save Spiral
Systems multiple test data (tests A-D) under the same Experiment name and Sample ID (with
replications of the sample) rather than requiring the user to choose a different Experiment name
for each test.
2. The Defaults menu option "Communications Setup" could be fully implemented. The current
choices include 1200/2400 baud modem, terminal server, or DEC Pathworks (PCS A). The
terminal server and PCSA options have been implemented for the HERL site, although both are
not used interchangeably. The terminal server connections was used prior to networking PCs
with PCSA. PCSA is now used exclusively. However, both terminal server and PCSA
connection practices for GeneTox Manager have been created.
For terminal server connections, the XTALK communications program was used. Connection
was automated using script files. Specific script files were created for the following operations-
Execute VAX GeneTox Manager System (VAXONLY); Upload New Data to VAX Databases
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(VAXT); Upload Modified Data to VAX Databases (VAXM); and Download VAX Data to
Databases (VAXDOWN). The XTALK .XTK files contain connection settings, and all these
files were identical, while the .XTS files contain connection commands. XTALK could probably
be used for MODEM (1200/2400 baud) connections as well, although this was not implemented
for GeneTox Manager at this site.
For connections through DEC Pathworks (PCSA), the SETHOST terminal emulation program
that comes with Pathworks was used. This program provides better VAX terminal emulation
than XTALK. Connection was again automated using script files. Specific script files were
created for the following operations: Execute VAX GeneTox Manager System (GENETOX);
Upload New Data to VAX Databases (UPLNEW); Upload Modified Data to VAX Databases
(UPLMOD); and Download VAX Data to Databases (ONLOAD). These SETHOST .SRC files
contain connection settings and commands.
The VAX Databases for the HERL site were FOCUS databases. Data was uploaded/downloaded
in Transfer File Format (see Programmer's Guide, Chapter 7 for details). GeneTox Manager
users may obtain copies of the FOCUS database structures and code, and the FORTRAN source
code used for statistical models, from Dr. Claxton on request. Users may also wish to use other
mainframe or mini-computer databases for storing long term data. The details of the Transfer
File Format are provided for this purpose. Users will have to modify the communications files
to execute the specific upload/download procedures used at their site.
GeneTox Manager could be modified, for distribution, to use one of several communication
methods, and to allow the user to select between them, as the "Communication Setup" option
seems to suggest. One could also modify GeneTox Manager to allow users to save the name
of the communication program called and the script files used hi Clipper default files, rather than
hardwiring them into the code, which would allow users to tailor the communications system
(from the PC side) without reprogramming.
3. GeneTox Manager source code could be reorganized into larger files where the individual
procedures are specifically named and grouped according to function. Currently, many small
.PRG files exist and these files correspond to the procedure names of the procedures they
contain. Reorganization would necessitate rewriting the system make file (GTM.RMK) as well.
CA-Clipper technicians have recommend that .OBJ files produced for use in CLIPPER 5.0
executables be 64K or less (the swap segment size of the VMM). GeneTox Manager as
currently organized and compiled does not conform to that recommendation.
GeneTox Manager PC Programmer's Guide
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4. A system similar to GeneTox Manager but specifically tailored to Mutation Frequency
calculations (named MUTAGEN FREQUENCY) exists. This system is almost identical to
GeneTox Manager. Mutagen Frequency will additionally store survivor as well as mutations
data for each control/sample, and produces a mutation frequency calculations report. It also
allows for more that five plate counts per dose, up to maximum of 100 plates and 50 doses.
This feature has not been brought into GeneTox Manager, although it could be added (without
adding the mutation frequency specific parts). Also, most of the GeneTox Manager code is
duplicated for use hi the Mutagen Frequency application with few changes or additions.
However, two separate copies of the code exist, and both copies must be updated for bug fixes,
changes, etc. These two applications could be merged into one source code pool, with minor
changes to the current code so that a majority of the code is exactly the same for each
application. This would be especially true if the additional "unlimited" plates per dose feature
was brought into GeneTox Manager. Some changes to the code to isolate application specific
routines would be necessary.
5. Currently the GeneTox Manager system backs up data by saving it hi Transfer File Format
to the database directory. There are no other provisions for backing up GeneTox Manager data.
Users may backup database data using the DOS BackUp utility. Files with extensions of .DBF
and .DBT contain experiment data which users may want to back up. .DFT files contain system
default settings, and users may also want to back these up. A strategy for implementing
automatic backups as part of the GeneTox Manager system was developed, but never
implemented (see below).
Automatic Backups for GeneTox Manager:
~ It would eliminate the current practice of saving flat file backups with each data
entry/modification and upload. (A flat file will still have to be generated for
uploading/exporting/archiving, however. This can't be helped.)
- Instead we would provide a "Backup" utility that would backup the current databases,
indexes, and system default settings all at the same time. This utility could be accessed
manually (probably from the Utilities-PC Functions menu), or be automated. A manual
"Restore" utility would also be provided to recover to the last backup (probably from the
Defaults-Set Special Options menu).
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— Automated backups could be controlled from the Special Options menu also. The user could
specify the drive [and path] to backup to, whether to automatically backup, and the frequency
of backups if automated. The settings menu would look like this:
GENETOX DATA BACKUP SETTINGS
Drive:
[Path:
Automatic Backups (Y/N) _
Backup Every Day(s) (0-99)
— Backups could be done at either entry or exit of the program. Specifying a backup every 0
days would cause the system to backup every time the program was run.
— The backup will backup only modified files. However, since almost all files are affected by
entry of new data, the majority of the files would be backed up each time the backup was run,
assuming at least one experiment was entered/modified during the backup interval.
— Using PKZip to "write" the backup utility. PKZip compresses files and allows specification
of a path (and filename).
— Testing of backups on large sample databases machine yielded the following results:
Time* Disk Space Used** Compression Ratio
PKZip 3:30 0.28Mb 89%
* times are in minutes:seconds and are approximated
** disk space is measured in Megabytes and rounded to the nearest 0.01Mb
6. The current distribution strategy for GeneTox Manager is to provide the means to generate
additional distribution diskettes with each copy of the system (GTMLoad.EXE). Other
distributors may not wish to allow users to generate additional distribution copies, and may wish
to modify the load/install code accordingly.
7. GeneTox Manager code could be modified to make it networkable. CLIPPER contains all
the necessary procedures for implementing a shared file database system (file locking, record
locking, etc.), but the GeneTox Manager code does not use these facilities. With minor
additions to the use of databases during data writes, a network version of the system could be
produced.
GeneTox Manager PC Programmer's Guide
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NOTE: See also Appendix E of the GeneTox Manager User's Guide,
"Known Problems and Limitations" for details of other problems
and limitations within GeneTox Manager that may be corrected.
GeneTox Manager PC Programmer's Guide
Version 2.21
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CHAPTER 9
SNAP! DIAGRAMS
The following tree diagram has been created using the SNAP! shareware mentioned
earlier in this document. The documentation for SNAP! is located on the PC in the SNAP
subdirectory. The programmer can also retrieve other useful outputs through SNAP!.
System: GeneTox Mutagen Frequency System
Author: CSC/EPA
06/24/93 15:29:30
Tree Diagram
G_MENU.PRG
+—HELP.PRG
| +—HELP.PRG
*** Truncating tree for recursive call to HELP.PRG
+—G_VPUBL.PRG
| +—GJNTCLR.PRG
+—G_WELCOM.PRG
+—G_PROTO.PRG
| +—G_PROTO.PRG
*** Truncating tree for recursive call to G_PROTO.PRG
+—GJTERMHE.PRG
+—G_SELSUG.PRG
+—G_GESCRN.PRG
+—G_MENTER.PRG
+—G_ENTER.PRG
+—GJNSTFV.PRG
+—G_PROTO.PRG
| +—G_PROTO.PRG
*** Truncating tree for recursive call to G_PROTO.PRG
+—GJTERMHE.PRG
+—SET_INST.PRG
+—G_SCNTRL.PRG
+—G_EXTRNL.PRG
+—G_EXPMNT.PRG
+—G_EXINIT.PRG
+—G_EXSCRN.PRG
+—G_SUGON.PRG
| | +—EDIT_SUG.PRG
I | +—EXPAND_SUG.PRG
I j +— -UP_BOX.PRG
| | +— -DOWN_BOX.PRG
j +—G_SELSUG.PRG
| +—-MOD_SAVE.PRG
I +—G_SUGOFF.PRG
+—G ASSAY.PRG
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+—G_ASSCRN.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
I +—EXPANDJSUG.PRG
I +—UP_BOX.PRG
I +—DOWNJ3OX.PRG
+—G_SELSUG.PRG
•f—MOD_SAVE.PRG
+—G_STRAIN.PRG
+—FAKE_LEFT.PRG
+—G_STSCRN.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
I +—EXPAND_SUG.PRG
j +—UP_BOX.PRG
| +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—MOD_SAVE.PRG
+—STRN_MOVE.PRG
+—G_MSVSTN.PRG
| +—G_SELSUG.PRG
+—G_SUGOFF.PRG
+—G_DILFAC.PRG
•FAKE_LEFT.PRG
H CHANGESTRAIN (procedure in G_DILFAC.PRG)
+—STRAINLIST.PRG
+—CHANGESTRAIN (procedure in G_DILFAC.PRG)
** runcating tree for recursive call to CHANGESTRAIN
+—EDIT_SUG.PRG
+—EXPANDJSUG.PRG
+—SETJNST.PRG
+—G_PROTO.PRG
+—G_PROTO.PRG
** runcating tree for recursive call to G_PROTO.PRG
+—G_DFSCRN.PRG
+—STRAINLIST.PRG
+—MOD_SAVE.PRG
+—G NPMUT.PRG
+—G_NPSRV.PRG
+—G_ACTSYS.PRG
+—ENTER_COMM.PRG
+—G_ACINIT.PRG
+—G_ACSCRN.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
+—EXPAND_SUG.PRG
+—UP_BOX.PRG
+—DOWN_BOX.PRG
_SELSUG.PRG
+—MOD_SAVE.PRG
—G_SMPSPC.PRG
+—G_SMSCRN.PRG
+—G~SUGON.PRG
| +—EDIT_SUG.PRG
I +—EXPAND SUG.PRG
I +—UP_BOX.PRG
I +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—ENTER COMM.PRG
I
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+—MOD_SAVE.PRG
+—G_SUGOFF.PRG
G_CURSTR.PRG
+—G_CUSCRN.PRG
+—STRAINLIST.PRG
+—G_SUGON.PRG
| +-—EDIT_SUG.PRG
I +—-EXPAND_SUG.PRG
| +—-UP_BOX.PRG
j +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—CUR_STRAIN.PRG
+—MOD_SAVE.PRG
+—G_SUGOFF.PRG
+—G_QUALTY.PRG
+—G_QUSCRN.PRG
+—G_SUGON.PRG
| +-—EDIT_SUG.PRG
j +—EXPAND_SUG.PRG
I +—UP_BOX.PRG
j +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—MOD_SAVE.PRG
G_MUTDOSE.PRG
G_SRVDOSE.PRG
—GJREMARK.PRG
+—G_SUGON.PRG
| +—-EDIT_SUG.PRG
I +—EXPAND_SUG.PRG
j +—UP_BOX.PRG
I +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—G_RESCRN.PRG
+—APNDINST (procedure in G_REMARK.PRG)
| +—GJNSTFV.PRG
| +—G_APPEND (procedure in G_REMARK.PRG)
| +—GJNVffiW.PRG
+—-MOD_SAVE.PRG
J20NTNU.PRG
+—G_SAVEAL.PRG
+—G_SAVEXP.PRG
+—G_SAVSMP.PRG
+—G_SAVGEN.PRG
+—G_SAVNP.PRG
| +—G_QUTTAL.PRG
+—G_SAVSMD.PRG
| +—G_QUITAL.PRG
+—G_SAVTST.PRG
| +—G_QUITAL.PRG
+—G_SELSUG.PRG
G_SAVNEW.PRG
+— G_SAVSMP.PRG
+—G_SAVSMD.PRG
| +—G_QUITAL.PRG
+—G_SAVTST.PRG
+—G_QUITAL.PRG
+—G_VAXFLE.PRG
+—G_CHKCNT.PRG
+—G_GENREC.PRG
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I +—G_RPPAGE.PRG
+—G_GENNPS.PRG
+—G_CHKTPN.PRG
+—G_GENREC.PRG
| +—G_RPPAGE.PRG
+—G_GENTST.PRG
+—G_MODIFY.PRG
+—G_SUGON.PRG
| +~ED1T_SUG.PRG
I +—EXPAND_SUG.PRG
I +—UP_BOX.PRG
I +—DOWN BOX.PRG
+—G_SELSUG7PRG
+—G_INSTFV.PRG
H-—G_PROTO.PRG
| +—G_PROTO.PRG
** runcating tree for recursive call to G_PROTO.PRG
+—FAKB_LEFT.PRG
+—G_MOGEN.PRG
| +^-G MOGINT.PRG
+—G_MOCN'flLPRG
I +—G_MOCINT.PRG
+—G_MOSMPL.PRG
| +~G_MOSINT.PRG
+—G SUGON.PRG
| +—EDIT_SUG.PRG
j +—EXPAND_SUG.PRG
I +—UPJ3OX.PRG
j +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—PRNT_STRAI.PRG
+—CUR_STRAIN.PRG
—G_MODOSE.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
I +—EXPAND SUG.PRG
j +—UPJ3OX.PRG
I +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—PRNT_STRAI.PRG
+—CUR_STRAIN.PRG
—G_ADSMPL.PRG
+—G_ADSINT.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
I +—EXPAND SUG.PRG
j +—UPJBOX.PRG
I -f—DOWNJBOX.PRG
+—G_SELSUG.PRG
+—CUR_STRAIN.PRG
—G_DELSMP.PRG
•t-—G_SUGON.PRG
| +—EDIT_SUG.PRG
j +—EXPAND SUG.PRG
j +—UP_BOX.PRG
I +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—PRNT.STRAI.PRG
+—CUR STRAIN.PRG
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—G_SCNTRL.PRG
+—G_EXTRNL.PRG
+—G_EXPMNT.PRG
+—G_EXINIT.PRG
+—G_EXSCRN.PRG
+—G_SUGON.PRG
| +—-EDIT_SUG.PRG
| +—EXPAND_SUG.PRG
| +—UP_BOX.PRG
| +—-DOWN_BOX.PRG
+—G_SELSUG.PRG
+-—MOD_SAVE.PRG
+—G_SUGOFF.PRG
—G_ASSAY.PRG
+—G_ASSCRN.PRG
+—G_SUGON.PRG
| +—-EDIT_SUG.PRG
I +—EXPAND_SUG.PRG
| +—-UP_BOX.PRG
| +-—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—MOD_SAVE.PRG
—G_STRAIN.PRG
+—FAKE_LEFT.PRG
+—GJSTSCRN.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
[ +—EXPAND_SUG.PRG
| +—UP_BOX.PRG
I +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+— -MOD_SAVE.PRG
+—STRN_MOVE.PRG
+—G_MSVSTN.PRG
| +—G_SELSUG.PRG
+—G_SUGOFF.PRG
—G_DILFAC.PRG
+—FAKEJLEFT.PRG
+—CHANGESTRAIN (procedure in GJDELFAC.PRG)
| +—STRAINLIST.PRG
| +—CHANGESTRAIN (procedure in G_DILFAC.PRG)
Truncating tree for recursive call to CHANGESTRAIN
| +—-EDIT_SUG.PRG
| +—EXPAND_SUG.PRG
| +—SETJNST.PRG
I +—G_PROTO.PRG
| +—G_PROTO.PRG
Truncating tree for recursive call to G_PROTO.PRG
+—G_DFSCRN.PRG
+—STRAINLIST.PRG
+— -MOD_SAVE.PRG
+—G_NPMUT.PRG
+—G_NPSRV.PRG
+—G_ACTSYS.PRG
| +— -ENTER_COMM.PRG
| +—G_ACINIT.PRG
| +—G_ACSCRN.PRG
| +—G_SUGON.PRG
I I +-—EDIT SUG.PRG
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I I +—EXPAND_SUG.PRG
j j +—UP BOX.PRG
j j +—DOWNJ3OX.PRG
j +—G SBLSUG.PRG
j +—MOD_SAVE.PRG
+—G_SMPSPC.PRG
| +—G_SMSCRN.PRG
(„, -f—G_SUGON.PRG
| +—EDIT_SUG.PRG
| +—EXPAND_SUG.PRG
j +—UP_BOX.PRG
I +—DOWN_BOX.PRG
+—G SELSUG.PRG
+—CENTER COMM.PRG
•f—MODJSAVE.PRG
+—G_SUGOFF.PRG
+—G_CURSTR.PRG
+—G_CUSCRN.PRG
+—STRAINLIST.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
I +—EXPAND SUG.PRG
| +—UP_BOX.PRG
j +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—CUR STRAIN.PRG
+—MOD~ SAVE.PRG
+—G_SUGOFF.PRG
-G_QUALTY.PRG
+—G QUSCRN.PRG
+—G^SUGON-PRG
| +—EDIT_SUG.PRG
I +—^EXPAND_SUG.PRG
j +—UP BOX.PRG
| +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—^MOD_SAVE.PRG
+—G MUTDOSE.PRG
+—GJiRVDOSRPRG
+—G REMARK.PRG
+Z_G_SUGON.PRG
| +—EDIT_SUG.PRG
| +—EXPAND_SUG.PRG
j +—UP_BOX.PRG
| +—DOWN_BOX.PRG
+—G SELSUGJPRG
+—G~RESCRN.PRG
+—^APNDINST (procedure in G_REMARK.PRG)
| +—G INSTFV.PRG
j +—G~APPEND (procedure in G_REMARK.PRG)
I +—GJNVIEW.PRG
+—^MOD_SAVE.PRG
+—G_CONTNU.PRG
+—G_SAVEAL.PRG
+—G_SAVEXP.PRG
+—G_SAVSMP.PRG
+—G_SAVGEN.PRG
+—G SAVNP.PRG
| +JL-G_QUITAL.PRG
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I +—G_SAVSMD.PRG
| | +—G_QUITAL.PRG
j +—G_SAVTST.PRG
| | +—G_QUITAL.PRG
| +—G_SELSUG.PRG
+—G_SAVNEW.PRG
| +—G_SAVSMP.PRG
| +—G_SAVSMD.PRG
| | +—G_QUITAL.PRG
| +—G_SAVTST.PRG
| +—G_QUITAL.PKG
+—G_VAXFLE.PRG
+—G_CHKCNT.PRG
+—G_GENREC.PRG
| +—G_RPPAGE.PRG
+—G_GENNPS.PRG
+—G_CHKTPN.PRG
+—G_GENREC.PRG
| +—G_RPPAGE.PRG
+—G_GENTST.PRG
~G_MODSMP.PRG f
+—G SCNTRL.PRG
_EXTRNL.PRG
+—G_EXPMNT.PRG
_EXINIT.PRG
_EXSCRN.PRG
4-—G_SUGON.PRG
| +—EDITJSUG.PRG
| +—EXPAND_SUG.PRG
| +—UP_BOX.PRG
j +—DOWNJ8OX.PRG
+—G_SELSUG7PRG
+—MOD_S AVE.PRG
+—G_SUGOFF.PRG
h—G_ASSAY.PRG
+—G ASSCRN.PRG
+—GJSUGON.PRG
[ +—EDIT_SUG.PRG
| +—EXPAND_SUG.PRG
I +—-UP_BOX.PRG
| +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+_ -MOD_SAVE.PRG
H—G_STRAIN.PRG
+—FAKE_LEFT.PRG
+—G_STSCRN.PRG
+—G_SUGON.PRG
| +—EDITJSUG.PRG
| +-—EXPAND_SUG.PRG
I +—UP_BOX.PRG
| +—DOWN_BOX.PRG
+—GJSELSUG.PRG
+—-MOD_SAVE.PRG
+—STRN_MOVE.PRG
+—G_MSVSTN.PRG
| +—G_SELSUG.PRG
+—G_SUGOFF.PRG
+—G_DILFAC.PRG
| +—-FAKE_LEFT.PRG
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+—CHANGESTRAIN (procedure in G DELFAC.PRG)
| +—STRAINLIST.PRG
,| +—CHANGESTRAIN (procedure in G_DELFAC.PRG)
*** Truncating tree for recursive call to CHANGESTRAIN
| +—EDIT_SUG.PRG
I +—EXPAND_SUG.PRG
j +—SET_INST.PRG
| +—G_PROTO.PRG
j +—G_PROTO.PRG
*** Truncating tree for recursive call to G_PROTO.PRG
+—G_DFSCRN.PRG
+—STRAINLIST.PRG
4-—MODJSAVE.PRG
+—G_NPMUT.PRG
4.—G_NPSRV.PRG
+—G_ACTSYS.PRG
+—ENTER_COMM.PRG
+—G_ACINrr.PRG
+—G_ACSCRN.PRG
4.—G_SUGON.PRG
| +—EDIT_SUG.PRG
| +—EXPAND_SUG.PRG
j +—UP_BOX.PRG
| +—DOWN_BOX.PRG
4-—G_SELSUG.PRG
+—MOD_SAVE.PRG
SMPSPC.PRG
+™Q_SMSCRN.PRG
-I G SUGON.PRG
| 4-^-EDIT_SUG.PRG
| +—EXPAND SUG.PRG
j +—UP_BOX.PRG
| • 4-—-DOWN BOX.PRG
+_^G SELSUG.PRG
+—ENTER COMM.PRG
4-—MOD_SAVE.PRG
4-_G SUGOFF.PRG
+—G_CURSTR.PRG
+—G CUSCRN.PRG
+—STRAINLIST.PRG
+—G_SUGON.PRG
| 4.—EDIT SUG.PRG
| +—EXPAND_SUG.PRG
j +—UP_BOX.PRG
j +—DOWN_BOX.PRG
4-—G_SELSUG.PRG
H-—CUR_STRAIN.PRG
4-—MOD_SAVE.PRG
4.—G_SUGOFF.PRG
—G_QUALTY.PRG
4.—G_QUSCRN.PRG
4-—G_SUGON.PRG
| +—^EDIT_SUG.PRG
| +—EXPAND_SUG.PRG
j 4-—UP_BOX.PRG
| 4.—DOWN_BOX.PRG
4-—G^SELSUG.PRG
4.—MOD_SAVE.PRG
G MUTDOSE.PRG
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+—G.
+-•
I I
—G_SRVDOSE.PRG
—G_REMARK.PRG
+—G_SUGON.PRG
| +—EDIT_SUG.PRG
I +-—EXPAND_SUG.PRG
| +—UP_BOX.PRG
| +—DOWN_BOX.PRG
+—G_SELSUG.PRG
+—G_RESCRN.PRG
+—-APNDINST (procedure in G_REMARK.PRG)
| +—GJNSTFV.PRG
j + —G_APPEND (procedure in G_REMARK.PRG)
j +—G_INVffiW.PRG
+—MOD_SAVE.PRG
+—G_CONTNU.PRG
+—G_SAVEAL.PRG
+—G_SAVEXP.PRG
+—G_SAVSMP.PRG
+—G_SAVGEN.PRG
+—G_SAVNP.PRG
| +—G_QUITAL.PRG
+—G_SAVSMD.PRG
| +—G_QUITAL.PRG
+—G_SAVTST.PRG
| +—G_QUITAL.PRG
+-—GJSELSUG.PRG
+—G_SAVNEW.PRG
+—G_SAVSMP.PRG
+—G_SAVSMD.PRG
| +—G_QUITAL.PRG
| +—G_SAVTST.PRG
| +—G_QUTTAL.PRG
+—G_VAXFLE.PRG
+—G_CHKCNT.PRG
+—G_GENREC.PRG
| +-—G_RPPAGE.PRG
+—G_GENNPS.PRG
+—G_CHKTPN.PRG
+—G_GENREC.PRG
| +—G_RPPAGE.PRG
+—G_GENTST.PRG
-GJNSTRC.PRG
+—G_INAD0.PRG
| +—GJNASCR.PRG
+—GJNVIEW.PRG
+—G_INSTFV.PRG
UTIL.PRG
--GJLISTEX.PRG
-G_DBRIND.PRG
--GJEXPLOD.PRG
+— -DP_SCRN (procedure in G_EXPORT.PRG)
+—RMVEXP.PRG
--GJMPEXP.PRG
+—GJMPORT.PRG
I + —EXIT_PROC (procedure in G_IMPORT.PRG)
+—RMVEXP.PRG
—-G_EXPORT.PRG
+—-DP_SCRN (procedure in GJ3XPORT.PRG)
+—G VAXFLE.PRG
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+—G CHKCNT.PRG
+—GJ3ENREC.PRG
| +—G RPPAGE.PRG
+—GJ3ENNPS.PRG
+—G_CHKTPN.PRG
+—G_GENREC.PRG
| +—G_RPPAGE.PRG
+—G GENTST.PRG
+—G_DELRV.PRG ~
| +—RMVEXP.PRG
+—G ARCMNU.PRG
+-^-G_ARCHIV.PRG
+—G VAXFLE.PRG
+~G_CHKCNT.PRG
+—G GENREC.PRG
| +^-G RPPAGE.PRG
+—GJ3ENNPS.PRG
+—G_CHKTPN.PRG
+—G_GENREC.PRG
| 4-—G_RPPAGE.PRG
+—G GENTST.PRG
-ARCH SCRN (procedure in G_ARCHIV.PRG)
f—RMVEXP.PRG
•G_DEARCH.PRG
f—ARCH_SCRN2 (procedure in G_DEARCH.PRG)
f—DP_SCRN2 (procedure in G_DEARCH.PRG)
f—EXIT PROC (procedure in G_IMPORT.PRG)
f—RMVEXP.PRG
4-—G_RESET (procedure in G_ACCEPT.PRG)
+—G ACCEPT.PRG
+™EXrr_PROC (procedure in GJMPORT.PRG)
+—RMVEXP.PRG
+—G_RESET procedure in G_ACCEPT.PRG)
-G RBPORT.PRG
•»•—G_RPTCHS.PRG
RAWDAT.PRG
+—G_CLRSEP.PRG
+—G RPRAWH.PRG
| +H-G_RPPAGE.PRG
+—G_RPRWHM.PRG
+—G RPRAWD.PRG
+—G~RPRWFM.PRG
+—G~RPRWTM.PRG
| +—G_RPPAGE.PRG
+—G_RPRWOM.PRG
| +—G_RPPAGE.PRG
+—G_RPRWHS.PRG
+—G_RPRWFS.PRG
+—GJRPRWTS.PRG
| +—G_RPPAGE.PRG
+—G_RPRWOS.PRG
| +—G RPPAGE.PRG
+—G_RPRAWG.PRG
| +—G_RPPAGE.PRG
+—G_RPRAWR.PRG
| +—G_RPPAGB.PRG
| +—G_GENREC.PRG
j +—G_RPPAGE.PRG
+—G RPRAWS.PRG
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I +—G_RPRASH.PRG
| | +—G_RPPAGE.PRG
| +—G_GENREC.PRG
| +—G_RPPAGE.PRG
+—G_RPRAW9.PRG
+—G_RPRASH.PRG
| +—G_RPPAGE.PRG
+—G_GENREC.PRG
+—G_RPPAGE.PRG
h—G_STATS.PRG
+—DSRCH.PRG
+—-BBRIDGE.PRG
| +—G_RPTOUT.PRG
+—-HBRIDGE.PRG
| +—G_RPTOUT.PRG
+—SBRIDGE.PRG
| +—G_RPTOUT.PRG
+—G_ALLRPT.PRG
+—G_RPTOUT.PRG
+—CSRCH.PRG
—G_MDEFLT.PRG
+—G_COMMUN.PRG
+—G_COLORS.PRG
+—G_INTCLR.PRG
+—G_SPEOPT.PRG
+—G_QUITAL.PRG
+—G_NEWPAS.PRG
+---GJSPMENU.PRG
+—G_NEWPAS.PRG
+—G_SUGGES.PRG
+—G_SELSUG.PRG
+—G_SUSEL.PRG
+—G_SUEXP.PRG
+—G_SUMOD.PRG
+—G_SULIST.PRG
| +—GJSULMOD.PRG
+—G_SUHELP.PRG
+—G_SULMOD.PRG
+—G_SUHMOD.PRG
+—G_SUHELP.PRG
G_SUASSY.PRG
• +—G_SUMOD.PRG
+—G_SULIST.PRG
| +—G_SULMOD.PRG
+—G_SUHELP.PRG
+—G_SULMOD.PRG
+—GJ5UHMOD.PRG
+—G_SUHELP.PRG
H—G_SUFINL.PRG
+—G_SUMOD.PRG
h—G SULIST.PRG
--GJSULMOD.PRG
_SUHELP.PRG
JSULMOD.PRG
_SUHMOD.PRG
~-G_SUHELP.PRG
-G_SUNP.PRG
+—G_SUMOD.PRG
+—G SULIST.PRG
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—G_SULMOD.PRG
_SUHELP.PRG
+—G_SULMOD.PRG
+—G_SUHMOD.PRG
+—G_SUHELP.PRG
G_SUACT.PRG
SUMOD.PRG
^-G_SULIST.PRG
+—G SULMOD.PRG
JSUHELP.PRG
+—G_SULMOD.PRG
+—G_SUHMOD.PRG
+—G_SUHELP.PRG
+—G_SUSAMP.PRG
-G_SUMOD.PRG
+~G_SULIST.PRG
| +—GJSULMOD.PRG
+—G_SUHELP.PRG
+—G_SULMOD.PRG
+—G_SUHMOD.PRG
+—G_SUHELP.PRG
+—G SUCUR.PRG
+^-G_SUMOD.PRG
+—G_SUL1ST.PRG
| +—GJSULMOD.PRG
+—G_SUHELP.PRG
+—G_SULMOD.PRG
+—G SUHMOD.PRG
+—GJSUHELP.PRG
-G_SUQUAL.PRG
+—G_SUMOD.PRG
+—G SULIST.PRG
| +—G_SULMOD.PRG
+—G_SUHELP.PRG
+—G_SULMOD.PRG
+—G_SUHMOD.PRG
+—G SUHELP.PRG
+—G_SUDOSE.pllG
+—G_SUMOD.PRG
+—G_SULIST.PRG
• | +—G SULMOD.PRG
+—G SUHELP.PRG
+—GISULMOD.PRG
+—G SUHMOD.PRG
+-Z-G_SUHELP.PRG
+—G_SURMRK.PRG
+—G SUMOD.PRG
+-^-G_SULIST.PRG
| +—G_SULMOD.PRG
+—G_SUHELP.PRG
+—G_SULMOD.PRG
+—Q_SUHMOD.PRG
+—G_SUHELP.PRG
-G_SUREP.PRG
-G_SUREXT.PRG
+—G_SUMOD.PRG
+—G_SULIST.PRG
| +—G_SULMOD.PRG
+—G SUHELP.PRG
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+—G_SULMOD.PRG
+—G_SUHMOD.PRG
+—G_SUHELP.PRG
—G_PIMENU.PRG
+—-G_PIADD.PRG
| +-—PI_SAVE (procedure in G_PIADD.PRG)
+—G_PIMOD.PRG
+—G_PIADD.PRG
+-—PI_SAVE (procedure in G_PIADD.PRG)
—G_DBZAP.PRG
—G_AMASSY.PRG
+—G_AMASSC.PRG
+—G_SELSUG.PRG
+—G_SUGOFF.PRG
+—G_PLTITR.PRG
+—-HELP.PRG
| +—-HELP.PRG
*** Truncating tree for recursive call to HELP.PRG
+—G_LSTARC.PRG
•+—G_DELEXP.PRG
+—RMVEXP.PRG
—G_MQUIT.PRG
—G_QUITAL.PRG
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•iSrU.S. GOVERNMENT PRINTING OFFICE: 1994 - 550-001/80379
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|