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PEDRAW.DOC v1.4 PEDRAW is a program which draws out family trees in either text or graphics mode. It is designed to be used to help with genetics research, especially linkage analysis using the LINKAGE and LINKSYS packages. * OVERVIEW Data about the structure of the pedigree and about the individuals within it is read in from a data file which can have one of a variety of formats. One individual is selected and his relatives are displayed either diagramatically using shaded symbols or else as paragraphs of text linked by the IBM box character set. The pedigree is saved to disk in either Microsoft Paint Format or as a text file. * SPECIFICATIONS Needs a PC, DOS 2.0 or higher, 350K of RAM, any graphics monitor type. To do graphics pedigrees of a reasonable size you'll need a hard disk with some free space on it. To print out graphics you need an Epson or IBM compatible dot matrix printer, or a PostScript or HP-compatible laser printer, or you need Microsoft Windows or some other program that can read Microsoft Paint (MSP) files so you can use its printer drivers. The number of individuals displayed is limited by the amount of available memory. Multiple marriages and in-breeding can be accommodated to a reasonable extent, though may require some trial and error to produce the best result. * PROGRAM MENU FUNCTIONS Options are selected using the Up and Down arrow keys, followed by Enter (CR). Jump straight to an option by pressing the key corresponding to the first letter of the option's name. The Esc key generally quits a menu to the one at a higher level. * Load pedigree file Loads a file in from disk. File must be of acceptable format (see section on "Data files"). If the file has extension .DAT, .SDF, .PED or .PPD then the appropriate format is assumed, otherwise the user must specify the format. * Edit a file A simple text editor is supplied enabling the user to read or edit a file on disk or create a new file. The F1 provides help listing the functions available and the Esc key quits the editor so that the file can be saved to disk. This editor can be used to edit data files if desired. 1 PEDRAW.DOC v1.4 * Save pedigree file The pedigree data in memory is saved to disk. You are advised to give the file the extension .DAT so that it will be correctly recognised when it is subsequently loaded by PEDRAW. * Adjust pedigree Use this option to alter current pedigree data or create new data (by adding members). Every individual must have a unique ID, and the structure of the pedigree is determined by specifying the ID's of parents where relevant. Only the last three digits of the ID will be displayed in the pedigree diagram, and the rest of the ID may refer e.g. to family number. The shading is determined by the diagnosis code: 1 for filled in, 2 for half-filled and other numbers up to 19 for patterned shading. The first few values from 20 produce special symbols (20 produces the little filled circle usually used to indicate carrier status). Values from 30 up give a variety of half- and quarter-shaded symbols, and values from 40 up produce the "negative image" of these. If 100 is added to the shading code the individual is marked as dead. When adding or editing a member, press F10 when the information is complete, or Esc to cancel the operation. Promoting and demoting members moves them to the start or end of the list of pedigree members, controlling the way the pedigree will be displayed (for further information see the section explaining the algorithm used). * Configure settings This option is used to adjust the way the pedigree is drawn. The current configuration can be saved to disk, or a previously saved configuration can be loaded. If a configuration is saved to the file PEDRAW.CFG in the current working directory, then that configuration will be automatically loaded the next time PEDRAW is run from that directory. When the option to change the configuration is selected, any of the command line flags can be entered if desired (see section on "Flags"), but unless the program is being run in batch mode it is best just to press Enter to edit the options individually. If "Graphic display" is set to N a text file will be created with extension .TRE. The default is instead to produce a graphical display of the pedigree structure. If "Conceal sex" is set to Y then all individuals will be displayed as diamonds. This is to improve confidentiality when pedigrees are published. If "Conceal diagnosis" is set to Y then no individuals will be shaded. This is to maintain blindness among other members of the research team, e.g. laboratory workers assigning genotype. 2 PEDRAW.DOC v1.4 If "Codes for Epson printer" is set to Y then at the start of a text file (TRE file) the codes to make an Epson printer output the IBM box character set correctly are added (otherwise you would get italics, etc.). This has no effect on ordinary graphics (MSP) files. If "File name for saved diagram" is left blank then a default filename will be used, consisting of the ID of the individual of used as the pedigree ancestor with the extension .MSP for graphics files or .TRE for text files. So the pedigree diagram produced by selecting individual 12099 as the ancestor would be saved to file 12099.MSP. If the filename is set to 0 then the diagram will not be saved to disk, only displayed on screen. Otherwise any filename can be specified and the diagram will be saved with that name. The "Title" can be set to say anything. It will be printed out under the pedigree diagram. The "Numbers of lines to show" refers to which lines are to be displayed. The default is the first 5. Line 1 is the ID line, and then lines 2 to 11 are the optional text lines. The line numbers are entered separated by commas. To display the ID, if the ID contains a hyphen it is assumed that the LINKSYS format is used so that members have ID's such as 1-2, 2-3, etc. Therefore the first digit before the hyphen and all subsequent characters are displayed. If there is no hyphen in the ID code, it is assumed that the last 3 digits of the ID refer to the code of an individual within a family, and that the earlier characters may refer to the family code. Accordingly only the last 3 digits are displayed (and leading zeroes are removed). With the text lines, the number of characters displayed depends on the width of the symbols and of the gap between symbols. The symbol and gap height and width in pixels can be set. The minimum values for these are 4 and the maximum depends on the screen type. The sum of the symbol width and gap width must be a multiple of eight. The extra line height refers to the vertical space taken up by extra lines which are created either when multiple marriages occur or when a line is drawn through the pedigree when an intermarriage has occurred. The tip is that if you want to leave room for more characters of text lines to be displayed, the best thing to do is to increase the width of the gap between symbols but leave other dimensions unchanged. It is possible to limit the number of generations to be printed, perhaps if you have trouble fitting them on paper. The "Show all members" option is quite important. If it is set to N (the default) then when a pedigree is drawn and an ancestor is selected, only his descendants and their spouses (and their spouses' descendants and their spouses' spouses) are displayed. If the "Show all members" option is set to Y then the program looks for the oldest ancestor of each person marrying in to the 3 PEDRAW.DOC v1.4 pedigree and shows all their descendants as well. In addition the original ancestor used is not the person selected by the user but that person's oldest ancestor, so this option can be useful if you have forgotten the pedigree structure and want to have the ancestor selected automatically. See the section explaining the algorithm used for fuller details of how the program behaves. The "Invisible" option allows the program to run invisibly - no pedigree will be drawn on screen, although the relevant pedigree diagram will still be created and will be saved on disk. The purpose of this is so that the program can be run (e.g. from a batch file) in background of a multitasking system such as DESQview without having to switch the display in and out of graphics mode. The maximum number of rows (generations) and columns in the pedigree diagram can be altered from the default values, though the numbers that can in practice be used are limited by the available memory. * Display pedigree Once the pedigree structure has been set up this option enables you to display it on screen and save the diagram to disk. Just select the individual whose descendants are to be drawn. * Make key Produce a simple key for the pedigree diagram indicating the scheme used for shading symbols. The file giving this information must already exist on disk (it can be created with the "Edit a file option"). The format of the file is that there is one optional title line for the key, followed by up to ten lines each beginning with a number followed by an explanation of the diagnosis this represents, e.g.: Key for manic depressive pedigree 1 Bipolar disorder 2 Unipolar depression 0 Unaffected 100 Deceased A male symbol shaded appropriately will be drawn followed by the text given. You will also be prompted for the name of the file to save the key to, and this should have the extension MSP, e.g. KEY.MSP. Alternatively entering 0 for the filename will prevent the key being saved to disk. * Use DOS Enter any DOS commands, e.g. to copy, rename or delete files, or 4 PEDRAW.DOC v1.4 run another program if there is enough memory left. * Quit program Quit program. Beware, all unsaved data will be lost! * FLAGS These can either be entered on the command line, when the program is first run, or when the "Configure settings" option is chosen, or in batch mode instead of an ID. All flags may be upper or lower case. To use flags on the command line enter: PEDRAW /FLAG1 /FLAG2 etc. or: PEDRAW datafile.dat /FLAG1 /FLAG2 etc. The section on the "Configure settings" option clarifies the effects of some of the flags. /P or /P1 - draw Pictures, enter graphics mode. /P0 - leave graphics mode, display text. /E or /E1 - send a code to the text file which instructs Epson- compatible printers to print the graphics character set correctly - this is the default. /E0 - do not insert special characters into text file, to allow output to e.g. IBM compatible printers and some word processors. /Gx - print only first x generations, default is 6. /Lx - determines whether or not a line from an individual's entry is displayed; the default is to just display the last three digits of an individual's ID number (line 1 displayed) and the first four text lines but up eleven lines can be displayed. To turn, for example, line 6 on enter /L6. To turn a line off again the negative number is used, e.g. /L-2. x = 1 to 11 or -1 to -11. /Ttitle - set the title to the words following /T, until the next / is encountered. This will not work for more than one word if the switch is used on the command line. /Ffile - sets the filename to save the pedigree diagram to. /F0 means don't save it. /F means use default name. 5 PEDRAW.DOC v1.4 /A - attempts to display all relatives; when an ancestor is entered the program seeks to find his oldest ancestor; when all that ancestor's descendants have been displayed the family trees of everybody marrying into the pedigree are then mapped out, and so on. /B or /B1 - blanks out diagnoses, all symbols are left unshaded. /B0 - shades symbols according to coding. /U or /U1 - unsexes individuals so that all symbols are displayed as diamonds regardless of gender. /U0 - displays males as squares, females as circles. /M - use menus, quit batch mode. /Cx - set maximum number of columns in the pedigree diagram to x. Default is 200. /Rx - set maximum number of rows (generations) in the pedigree diagram to x (though number actually displayed can be limited by /G). Default is 8. /SWx - Set symbol width in pixels to x. Default is 24. /GWx - Set width of gap between symbols in pixels to x. Note that the width of the symbol plus the width of the gap must sum to a multiple of 8. Default is 16. /SHx - Set symbol height in pixels to x. Default is 24. /GHx - Set height of gap between symbols in pixels to x. Default is 16. /Hx - Set height of extra lines (for second marriages, etc. ) in pixels to x. Default is 12. /I or /I1 - Run the program "invisibly", without drawing the diagram on screen, just save it to an MSP file. /I0 - Resume normal mode, displaying diagrams on screen. * DATA FILES PEDRAW accepts pedigree data arranged in one of four formats: as a PEDRAW data file, as a LINKSYS SDF file, or as a LINKAGE PED file either before or after passing through MAKEPED. PEDRAW determines the format of the file by its extension. If the filename ends .DAT then it is assumed to be in PEDRAW format. If it ends .SDF it is assumed to be in LINKSYS SDF format (produced 6 PEDRAW.DOC v1.4 by using the "Export" option of LINKSYS). If it has the extension .PED it is assumed to be a LINKAGE pedigree data file before MAKEPED has been run on it (i.e. without sibling pointers), and if it has the extension .PPD then it is assumed to be a LINKAGE pedigree file output from MAKEPED. If the data file has none of these extensions then the program will ask which format the file is in. Note that there is no way to override the default interpretation. That is if you have a LINKAGE file called PEDATAIN.DAT, PEDRAW will misread the file and report an error. The file would have to be renamed e.g. to PEDATAIN.PPD before PEDRAW could use it. * PEDRAW data file format This is the format in which PEDRAW itself saves files. The file should be saved with the extension .DAT. This format will be created automatically when pedigree data is saved using the "Save pedigree file" option. The file is a plain text file which can be created by a word processor or the text editor supplied with PEDRAW (selected by the "Edit a file" option), or if pedigree information is kept in a database a report can be set up to export information in the correct format. Each individual needs at least 13 lines. The first line contains the ID. The second line is the gender (M, F or X) and an optional diagnosis code which is a number from 0 to 99 to indicate how the symbol will be shaded (currently only some numbers produce shades, the highest at present being 46). If 100 is added to this number the individual is marked as dead. The diagnosis code is separated from the gender by a comma. The next line optionally contains the ID's of the father then mother, separated by a comma. The next ten lines can contain any text. The maximum length of a an ID or text line is 20 characters. Example: 12032 F,4 12048,12060 Miss Linda Smith Schizophrenic AB pos wx Rr ... four more lines, some can be blank. Note that there is no obligation to keep separate pedigrees in separate files. Information about several pedigrees can be stored in the same data file, provided each individual has a unique ID. A diagnosis code of 1 shades solid, 2 is half-filled and the other numbers produce different patterns. Males are squares, females circles and unknowns (X) diamonds. 7 PEDRAW.DOC v1.4 * Other data formats These are only worth using if you are actually using the LINKSYS and/or LINKAGE programs, so the format of the files will not be described. Files can only be read in from these formats, not saved (though the data input can then be saved in PEDRAW format). The SDF format is created from LINKSYS by using the "Export" option. If PEDRAW reads such a file in it treats it in the following way: 1. A new ID is created by concatenating the individual's family name with the LINKSYS ID to create a new unique name (meaning that information about several different pedigrees can be contained in the one SDF file). So individual 2-5 from pedigree F9 becomes F92-5. 2. Each of the (up to) ten phenotype codes is read into the ten text lines. 3. In a somewhat feeble attempt to guess diagnosis the program assumes that the first phenotype code refers to affection status. If it begins with a "2" or contains a "-2" (e.g. if the phenotype code is "1-2") then the PEDRAW diagnosis code is set to 1 (for solid shading). Otherwise it is set to 0. If this does not end up right the diagnosis codes can be adjusted subsequently by hand using the "Adjust pedigree" option. LINKAGE pedigree files can be read in directly (handy for checking coding). There must be at least two spaces between locus codes, and only single spaces between the symbols within a locus code, i.e. PEDRAW expects to find codes such as: 2 1 1 1 0 1 0 1 1 PEDRAW expects to find a file with extension .PED to be in a format suitable to be read by MAKEPED, and with .PPD if the file has been output by MAKEPED. This clashes with the convention suggested in the most recent LINKAGE documentation of having the former with an extension .DAT and the latter with an extension .PED. The PEDRAW convention is the one used by LINKSYS and files may have to be renamed accordingly. LINKAGE files are treated as follows: 1. A unique ID number is constructed by multiplying the pedigree number by 1000 and adding the individual number, so that individual 2 from pedigree 3 gets an ID of 3002. 2. Each of the locus codes is read into a text line. Single spaces within locus codes are removed, so that 0 1 1 becomes 011. 8 PEDRAW.DOC v1.4 3. As for LINKSYS files, PEDRAW attempts to guess the diagnosis code by assuming that the first locus code is affection status. If the first digit of the first locus code is 2 the diagnosis code is set to 1 (for solid shading), otherwise it is set to 0. * USING PEDRAW IN BATCH MODE Usually PEDRAW is operated interactively from menus. It is also possible to run PEDRAW in batch mode so that it takes all its entry from standard input, meaning that input can be redirected into PEDRAW using DOS commands. The way to start PEDRAW in batch mode is to give the name of a data file on the command line e.g.: PEDRAW EXPED.DAT The data file must exist and must have the extension .DAT or .SDF or .PED or .PPD so that PEDRAW knows what format to expect. PEDRAW then moves directly to the "Display pedigree" option and awaits the input of the ID of an individual whose descendants are to be displayed. However in batch mode it is possible instead to enter flags at this point. PEDRAW carries on reading commands from standard input until either there is an error, or until the end of the input file is reached, or until an 'X' is input or until the /M flag is selected. If the end of file is reached or an 'X' is input the program exits, otherwise it just reverts back to ordinary menu-driven operation. To use PEDRAW with redirected input one might run it like so: PEDRAW EXPED.DAT < INPUT.JF Here INPUT.JF would contain a list of ID's and flags as follows: 12880 13990 /l-2 /l-3 /f1out.msp /tRelatives of number 14001 /a 14001 x This would display the descendants of 12880 and 13990, saving the diagrams to 12880.MSP and 13990.MSP, then would draw a diagram of all the relatives of 14001 and save it in the file 1OUT.MSP with an appropriate title. The x at the end is not strictly necessary but marks the end of file and quits PEDRAW. Note that in batch mode the normal editing keys do not work (cursor keys, control-left-arrow, etc.). The pedigree diagram is not displayed for long on screen, just drawn and then saved to disk. You may wish to run the program "invisibly" in batch mode, particularly in a multitasking environment such as DESQview. The pedigree diagram will not be displayed on the screen, just saved 9 PEDRAW.DOC v1.4 to disk. The advantage is that the monitor is never switched into graphics mode, an operation which can sometimes cause problems with some multitaskers. * SETTING THE GRAPHICS DISPLAY If the program won't display graphics and prints the message "fg_init() failed" then you will have to set an environment variable to the name of your display type. To do this, before you run PEDRAW type the following line: SET FG_DISPLAY=xxxx except instead of xxxx type one of the following: HERC CGAHIRES EGAECD VGA11 VGA12 EGAMONO EGACOLOR TOSHIBA 8514A Which one you type depends on the kind of display you have which you will have to determine from reading your computer manual or by asking your supplier. So if you have a Hercules-compatible display you would type: SET FG_DISPLAY=HERC and if you had a CGA display you would type: SET FG_DISPLAY=CGAHIRES and so on. You may want to put this line in your AUTOEXEC.BAT file. * PRINTING OUT PEDIGREES Text pedigrees can be read into a word processor and printed out from there, or can be printed directly to an Epson or IBM compatible printer with the following command: COPY filename.tre PRN Graphics pedigrees can be input into Microsoft Paint, edited if necessary, and then output to a printer. New versions of Paint no longer work correctly with large diagrams. Other programs designed to work with Microsoft Paint files can also be used, for example WordPerfect 5 works well (at least for small 10 PEDRAW.DOC v1.4 pedigrees) and can be used to incorporate pedigree diagrams into text. To print out pedigrees without using Microsoft Windows the program PRMSP.EXE can be used to print MSP files to an Epson or IBM compatible dot-matrix printer or a laser printer: PRMSP filename.msp The full details of the options available with PRMSP are as follows: Format: PRMSP infile.msp [outfile.prn] [/flag1 /flag2 etc.] infile.msp - the name of the saved MSP file to be printed out. outfile.prn - the name of a file to be printed to. This is optional and if no name is given then the printer (PRN) will be used instead. /I - this flag means print to an IBM-compatible printer instead of an Epson-compatible printer. /P - this flag means print the pedigree with the paper in "portrait" orientation - across the page - instead of the default "landscape" orientation - down the page. Note that in earlier versions of PRMSP this had the opposite effect because it was taken to refer to the orientation of the diagram rather than the paper. /H - high density - will work only with Epson-compatible 24-pin printer to give a picture three times smaller than above, or twice as small on a Hewlett-Packard compatible laser printer. /D - draught mode - should be quicker but lower quality for dot matrix printers in high density mode or "portrait" orientation. On Hewlett-Packard compatible laser printers prints out double normal size. /Snumber - this flag means print "number" spaces before each line of the picture - use it to control where the diagram appears on the page. The default is 6. (Only for dot matrix printers.) /Lnumber - this flag controls the line spacing on the printer, as used by the ESC A command. By default "number" is set to 8, but if the lines of your diagram come out separated or overlapping, then using this flag may help you to adjust the line-spacing to produce a better picture. (Only for dot matrix printers.) /Fnumber - this flag lets you determine whether a line feed (new line) character is sent to your printer with each carriage return character. If number is 0 then no line feed is sent, if it is 1 then a line feed is sent. The default is 1. If your 11 PEDRAW.DOC v1.4 diagram comes out "double-spaced" - with gaps between each line - then specifying /F0 may cure the problem. (Only for dot matrix printers.) /FF - send a formfeed (new page) after printing the file. (You must use this flag on the last file you print on a PostScript printer, but other files can be printed on the same page first.) /HP - produce output for a Hewlett-Packard compatible laser printer. /PS - produce output for a PostScript printer. For Hewlett-Packard or PostScript printers only: /OXnumber - x origin, default 72. Measured in points (1/72") approximately from the left hand edge of the page. /OYnumber - y origin from the bottom of an A4 page, default 72 in "portrait" orientation for the bottom left corner, or 720 in "landscape" orientation for the top left corner. For PostScript printers only: /SXnumber - x scale, default 1.0. /SYnumber - y scale, default 1.0. /ROnumber - rotation about origin, default 0.0 Example use of PRMSP: PRMSP 12990.MSP TEMP.PRN /S12 /I The file 12990.MSP would be printed out to the file TEMP.PRN, in a format suitable for sending to an IBM-compatible printer. Then later TEMP.PRN could be printed by entering: PRINT TEMP.PRN The advantage of this is that by using the DOS PRINT command printing occurs in background - you can get on with other things while the diagram is being printed. Note: except in the case of PostScript printers, PRMSP cannot work if your computer does not send 8 data bits to the printer. This is sometimes altered by the MODE command which is usually in the AUTOEXEC.BAT file - see your DOS manual for details - and it is especially likely to have been used if your printer is on a serial cable rather than the ordinary "Centronics" parallel cable. Also make sure that your printer is set to receive 8 bits rather than 7 - see your printer manual if you have problems. Note that you must always use the /FF flag when you wish to 12 PEDRAW.DOC v1.4 produce output from a laser printer, otherwise the image will be stored in the printer's memory but will never be displayed. However you may wish to print a number of graphs onto different parts of the same page and then only use the /FF flag with the last one. * EXPLANATION OF MAPPING ALGORITHM This is provided so that the optimum order for including people in the data file can be decided upon. The aim would be to reduce the number of crossings over of lines, and to avoid having to repeat individuals in different parts of the diagram. In general people are added to the pedigree diagram in order from top to bottom and from left to right. The algorithm used is as follows: 1. An individual whose descendants are to be displayed is selected by the user. 2. If the option to extend the pedigree and show all members is selected then instead of starting with the individual given the program attempts to begin with the oldest ancestor of this individual it can find. 3. The following process is repeated (recursively) for each individual in turn, beginning with the common ancestor provided. A. The index individual is marked as "dealt with", and is drawn. B. The next spouse of the index individual is selected. The next spouse is the one who has a child which appears in the data file before the children of other spouses, provided that the spouse is not marked as "dealt with". C. Each of the children of the index individual and this spouse is in turn selected. If the child has already been drawn then a line will be drawn from the current sibship to the place where the child appears in the pedigree, unless the child has been shown in an earlier generation (when the line would have to go "uphill"), in which case the child is drawn again but is marked as a repeat ("REP"). If the child is not marked as "dealt with" it is set as the new index individual and the process beginning in 3A is applied to it (i.e. it's spouses and children will be displayed). D. If the option to extend the pedigree and show all members is selected then the oldest ancestor of the spouse is added to a "to-be-done-later" list. E. The spouse is set to be the new index individual and the process beginning in 3A is applied to it. 13 PEDRAW.DOC v1.4 4. If the option to extend the pedigree and show all members is selected then for everyone in the "to-be-done-later" list the process beginning in 3A is applied. The above algorithm actually works quite well, even for fairly complex pedigrees. However it does fall down if there is a complete marriage loop, as when a husband has children by his ex-wife's ex-husband's ex-wife. If H1 has children by W1 and W1 has children by H2 and H2 has children by W2, then if W2 has children by H1 the program will not display them (or the marriage between H1 and W2) because H1 will already be marked as "dealt with" by the time the circle comes round to him again. A similar thing would happen if a man had children by his ex- wife's ex-husband's daughter. In practice this should rarely be a problem and I have no intention of fixing it at present. You will have to work round it by creating a dummy individual to break the loop. To avoid having unnecessary repeated individuals, make sure that the ancestor belonging to the earliest generation is given first. Note that to force a sibship of a given parent to be shown first it is only necessary to promote one of the sibs in it to be first in the data file. However to force a sibship to be last all the sibs must come after all the other children of that parent. I don't know whether to recommend that the easiest way to get the best-looking pedigree is to try to understand the algorithm or just use trial and error. In my experience it is almost always possible to get whole the pedigree displayed without any repeats. * EXAMPLE SESSION To help explain the above I have enclosed an example data file called EXPED.DAT. Use a text editor or word processor to read it or print it out by entering: PRINT EXPED.DAT To produce pedigrees proceed as follows. First make sure that you are logged on to the disk containing the above programs, and that you have changed directory (using CHDIR) to the one that contains them. Then enter: PEDRAW Using the up-and-down arrows highlight the "Load pedigree file" option and press Enter. Press Enter twice more to see a list of all files in the subdirectory. Highlight EXPED.DAT and select it by pressing Enter. The data file should be loaded in without problems. 14 PEDRAW.DOC v1.4 Highlight the "Display pedigree" option and select it with Enter. Press Enter again to see a list of ID's of everyone in the pedigree. Highlight 12119 and select it with Enter. The pedigree should be displayed (if not see the section on "Setting the graphics display"). Press Esc and the diagram will be saved to disk with the name 12119.MSP. Press Esc again to return to the main menu, then select "Quit" to leave PEDRAW. If you have Microsoft Windows then you may wish to run that and then select the file 12119.MSP to open with Paint. You can label the pedigree with that and then print it out in the usual way. If you do not have Microsoft Windows, print out the pedigree by entering: PRMSP 12119.MSP To see how PEDRAW uses .PED files, try selecting EXPED.PED instead of EXPED.DAT and choose the ancestor 4001. * MICROSOFT PAINT UTILITIES In addition to PRMSP, a number of utility programs for manipulating Microsoft paint files are provided. These programs are for resizing, joining and viewing files. They all work only on "old format" paint files, so they will not work on files saved from newer versions of Microsoft paint, or on .BMP files. However it should be possible to read the results in to Windows Paint without any difficulty (I think). Later versions (3.x) of Windows Paint(brush) will read in an MSP file OK (if that option is selected) but will then save it as a BMP file, and these utilities will therefore not work on the edited file, nor can the BMP file be read into some versions of WordPerfect. To get round this I have introduced a small conversion utility to convert back from BMP to MSP format. Please note that these programs may be quite slow on some computers. * Resizing paint files This can be done using the SIZEMSP.EXE program. Running this program on its own gives you the current size of a paint file in pixels: SIZEMSP filename.msp The size of the file is adjusted by entering four numbers to increase the left, right, top, and bottom margins by that number of pixels. The numbers for the left and right margins must be divisible by eight. Negative numbers cut off that number of pixels from the appropriate edge. E.g.: 15 PEDRAW.DOC v1.4 SIZEMSP filename.msp 16 16 4 -6 Adds white space 16 pixels wide to the left and right edges, adds 4 blank lines of pixels at the top, and snips off 6 lines of pixels at the bottom. * Viewing paint files You can view files without having to print them out or load Windows by entering: VIEWMSP filename.msp If the file is too big to be displayed on the screen you can move around it using the cursor keys. Pressing the Escape key quits the program. * Joining paint files Files can be combined into a larger paint file, either side by side using SPLICMSP.EXE, or one under the other using TAGMSP.EXE. The format for both programs is the same: TAGMSP file1.msp file2.msp [file3.msp ...] newfile.msp Several files can be joined at once in this way. * Converting BMP to MSP files To do this use the BMP2MSP program. You only have to give the name of the BMP file (the .BMP can also be omitted) and a file with the same name but extension .MSP will be created: BMP2MSP file1.bmp * HYPERTEXT HELP This documentation is available as a set of files which can be read as pop-up hypertext help using MaxThink's HyperRez program. If you have these files (generally distributed in the HELPINST archive) then to read them first change into the directory in which the files are located, then enter HR to load the program. One can then change to another directory, and thereafter pressing the hot key combination (by default Control-B) at any time will pop up the help. The hot key combination can be changed using the HRK program supplied. Pressing F1 then provides brief instructions on using the utility. With some monitor types it would probably be unwise to attempt to pop up the help when the monitor is in graphics mode, i.e. while a pedigree diagram is actually being drawn or displayed. Otherwise it can provide a useful reminder of how to use PEDRAW, although having the program loaded (or any other pop-up program) does take up a small amount of memory which therefore becomes 16 PEDRAW.DOC v1.4 unavailable to PEDRAW. * CLOSING COMMENTS All trademarks acknowledged. PEDRAW is freely distributed to educational institutions, public health institutions and individuals for their private use. All other users (including private hospitals) must register the program before using it. Contact me at the address below for details. I would be very glad to hear of comments/problems/suggestions for improvements. One thing that is somewhat unsatisfactory but that I probably will not be changing is the way that diagonal lines which mark someone as deceased are rather short and get truncated at the edges of the screen. I probably won't be improving the facilities to print out pedigrees either, as programs such as Windows do exist to do this and it is a rather tedious way of reinventing the wheel. The text mode has now fallen behind the graphics mode, but I have no real plans to bring it back in line. Other features can be adjusted within limits according to user demand, and if somebody has special requirements then I may well be able to accommodate them. PEDRAW is written in C++ and makes fairly heavy use of routines from the Zortech Flash Graphics library and C++ toolkit. I would be willing to distribute to the source code to appropriate individuals who wish to modify it (though it is not well documented). Unfortunately I have made various modifications to the toolkit and so I would have to pass that on as well, so anybody wanting this code would have to furnish me with proof that they had a copy of the toolkit already, e.g. by sending me a listing of a header file or two. As far as upgrades are concerned, I will try to maintain a list of people I know who are using PEDRAW and I may periodically send out a notice announcing if I have made any significant changes. If you did not obtain the program directly from me it may be worth sending me your address so that I can add you to this list. I aim to keep up-to-date versions at the following sites from which they will be available by e-mail or anonymous ftp: USA: SIMTEL collection Numerous mirror sites available by anonymous ftp and e-mail. Europe mailserver: mailserv@fi.uwasa.garbo Send mail with Subject: garbo-request and message: send help gene-server: Internet gene-server@bchs.uh.edu 17 PEDRAW.DOC v1.4 BITNET/ EARN gene-server%bchs.uh.edu@CUNYVM UUCP gene-server@bchs.UUCP (new style) Send mail with Subject: SEND DOS HELP Anonymous ftp: ftp.bchs.uh.edu European: Anonymous ftp: nic.fun.com E-mail: mailserver@nic.funet.fi Send mail message: HELP European EMBL server: NetServ@EMBL-Heidelberg.DE Send mail message: DIR DOS_SOFTWARE Anonymous ftp: ftp.embl-heidelberg.de (/pub/software/dos) Manager: Rainer Fuchs, Fuchs@EMBL-Heidelberg.DE Problems: NetHelp@EMBL-Heidelberg.DE USA anonymous FTP: ftp.bio.indiana.edu UK only (JANET): call: uk.ac.lancs.pdsoft mailserver: archive-server@uk.ac.lancs.pdsoft Send message: send micros/ibmpc/INDEX Reference: CURTIS D. A program to draw pedigrees using LINKAGE or LINKSYS data files. Annals of Human Genetics 1990 54: 365- 367. This work was supported in part by a post-doctoral training fellowship from the John D. and Catherine T. MacArthur Foundation Mental Health Research Network I (Psychobiology of Depression). Copyright Dave Curtis 1990 Academic Department of Psychiatry St Mary's Hospital Medical School Praed Street London W2 1NY, England Phone: 071 725 1993 Janet: dcurtis@UK.AC.CRC Elsewhere: dcurtis@CRC.AC.UK EARN/Bitnet: dcurtis%CRC@UKACRL Usenet: ...!mcsun!ukc!mrccrc!D.Curtis 18