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Description: draw
Keywords: draw

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# Drawtree and Drawgram

© Copyright 1986-2009 by The University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

Drawtree and Drawgram are interactive tree-plotting programs that take a tree description in a file and read it, and then let you interactively make various settings and then plot the tree on a laser printer, plotter, or dot matrix printer. In many cases (with Macintosh or PC graphics, with X windows, or with a Tektronix-compatible graphics terminal) you can preview the resulting tree. This allows you to modify the tree until you like the result, then plot the result. Drawtree plots unrooted trees and Drawgram plots rooted cladograms and phenograms. On good laser printers or as files for good drawing programs both can produce fully publishable results. On dot matrix printers the results look grainy but are good enough for overhead transparencies or slides for presentations.

These programs are descended from PLOTGRAM and PLOTREE written by Christopher Meacham. I have incorporated his code for fonts and his plotter drivers, and in Drawtree have used some of his code for drawing unrooted trees. In both programs I have also included some plotter driver code by David Swofford, Julian Humphries and George D.F. "Buz" Wilson, to all of whom I am very grateful. Mostly, however, they consist of my own code and that of my programmers. The font files are printable-character recodings of the public-domain Hershey fonts, recoded by Christopher Meacham.

This document will describe the features common to both programs. The documents for Drawtree and Drawgram describe the particular choices you can make in each of those programs. The Appendix to this documentation file contains some pieces of C code that can be inserted to make the program handle another plotting device -- the plotters by Calcomp.

## A Short Introduction

To use Drawtree and Drawgram, you must have

(1)
  The compiled version of the program. If you have not obtained a version of PHYLIP precompiled for your machine, you will have to take the source code given here and modify it for your C compiler and then compile it. This is not too hard: it is discussed below.

(2)
  A tree file. Trees are described in the nested-parenthesis notation used throughout PHYLIP and standardized in an informal meeting of program authors in Durham, New Hampshire in June, 1986. Trees for both programs may be either bifurcating or multifurcating, and may either have or not have branch lengths. Tree files produced by the PHYLIP programs are in this form. There is further description of the tree file format later in this document.

(3)
  A font file. There are six font files distributed with PHYLIP: these consist of three Roman, two Italic, and one Russian Cyrillic font, all from the public-domain Hershey Fonts, in ASCII readable form. The details of font representation need not concern you; all you need to do is to copy the font file corresponding to the font you want into the appropriate folder under the appropriate file name, and let the program use it. Or you can let the program ask you for the name of the font file, which it will do if it does not find one itself. The six fonts are, respectively, a one- and a two-stroke sans-serif Roman font, a three-stroke serifed Roman font, a two- and a three- stroke serifed Italic font, and a two-stroke Cyrillic font for the Russian language. If this is not clear just try them all. Note that for some printers several built-in fonts such as Times-Roman and Courier can be used too. The Hershey fonts were created by Dr. A. V. Hershey of the U. S. National Bureau of Standards in the late 1960s. They may be freely distributed except that they may not be distributed in the original format used the the U. S. National Technical Information Service. Our format is different from the NTIS one. See Appendix 2, below, if you need a detailed discussion of the format.

(4)
  A plotting device, and if possible a screen on which you can preview the plot. The programs work with Postscript-compatible laser printers, laser printers compatible with the PCL printer language of the Hewlett-Packard Laserjet series, the PICT format for the MacDraw drawing program, the file formats for the freeware X-windows drawing programs `xfig` and `idraw`, IBM PC graphics screens, the PCX file format for the PC Paintbrush painting program, the X Bitmap format for X-windows, plotters including Hewlett-Packard models, dot matrix printers including models by Epson and Apple, graphics terminals from DEC and Tektronix, the input format for the freeware ray-tracing (3-dimensional rendering) programs `POV` and `rayshade`, and, strangest and most wonderful of all, the Virtual Reality Markup Language (VRML) which is a file format that is used by freely-available virtual reality programs. You can choose the plotting and previewing devices from a menu at run time, and these can be different. There are places in the source code for the program where you can insert code for a new plotter, should you want to do that.

Once you have all these, the programs should be fairly self explanatory, particular if you can preview your plots so that you can discover the meaning of the different options by trying them out.

Once you have a compiled version of the appropriate program, say Drawgram, and a file called (say) `intree` with the tree in it, and a font file (say `font2` which you have copied as a file called `fontfile`), all you do is run the program Drawgram. It should automatically read the font and tree files, and will allow you to change the graphics devices. Then it will let you see the options it has chosen, and ask you if you want to change these. Once you have modified those that you want to, you can tell it to accept those. The program will then allow you to preview the tree on your screen, if you have an appropriate graphics capability on your computer screen, and if you haven't told it in the menu not to preview the plot. After previewing the tree, the program will want to know whether you are ready to plot the tree. You answer this using the Plot choice in the File menu will be found in the upper-left corner of he preview window in Windows systems or X Windows systems such as Linux. In Mac OS X systems it is a choice in THE Upper-left corner of the preview window. If you have chosen not to preview the plot, plotting will occur after you close the menu by making the Y (yes) choice when you are asked whether you want to accept the plot as is. If you say no, it will once again allow you to change options and will the allow you to preview the tree again, and so on as many times as you want. If you say yes, then it will write a file called (say) `plotfile`. If you then copy this file to your printer or plotter, it should result in a beautifully plotted tree. If the final plotting device is a Macintosh or PC graphics screen, it may not write a plot file but will plot directly on the screen.

If you don't want to print the file immediately, but want to edit the figure first, you should have chosen an output format that is readable by a draw program. Postscript format is readable by drawing programs such as Adobe Illustrator, Canvas, Freehand, and Coreldraw, and can be displayed by the Unix utilities Ghostscript and Ghostview. Some Macintosh drawing programs such as MacDraw can read PICT format. On Windows systems bitmap drawing editors such as Paint can read Windows Bitmap files. We have provided output formats here for Xfig and Idraw drawing programs available on Linux or Unix systems. Drawing programs can be used to add branch length numbers (something too hard for us to do automatically in these programs) and to make scale bars. Another use is as a way of printing out the trees, as most drawing programs are set up to print out their figures.

Having read the above, you may be ready to run the program. Below you will find more information about representation of trees in the tree file, on the different kinds of graphics devices supported by this program, and on how to recompile these programs.

## Trees

The Newick Standard for representing trees in computer-readable form makes use of the correspondence between trees and nested parentheses, noticed in 1857 by the famous English mathematician Arthur Cayley. If we have this rooted tree:

                             A                 D
                              \         E     /
                               \   C   /     /
                                \  !  /     /
                                 \ ! /     /
                            B     \!/     /
                             \     o     /
                              \    !    /
                               \   !   /
                                \  !  /
                                 \ ! /
                                  \!/
                                   o
                                   !
                                   !

then in the tree file it is represented by the following sequence of printable characters, starting at the beginning of the file:

(B,(A,C,E),D);

The tree ends with a semicolon. Everything after the semicolon in the input file is ignored, including any other trees. The bottommost node in the tree is an interior node, not a tip. Interior nodes are represented by a pair of matched parentheses. Between them are representations of the nodes that are immediately descended from that node, separated by commas. In the above tree, the immediate descendants are B, another interior node, and D. The other interior node is represented by a pair of parentheses, enclosing representations of its immediate descendants, A, C, and E.

Tips are represented by their names. A name can be any string of printable characters except blanks, colons, semcolons, parentheses, and square brackets. In the programs a maximum of 20 characters are allowed for names: this limit can easily be increased by recompiling the program and changing the constant declaration for "MAXNCH" in `phylip.h`.

Because you may want to include a blank in a name, it is assumed that an underscore character ("_") stands for a blank; any of these in a name will be converted to a blank when it is read in. Any name may also be empty: a tree like

(,(,,),);

is allowed. Trees can be multifurcating at any level (while in many of the programs multifurcations of user-defined trees are not allowed or restricted to a trifurcation at the bottommost level, these programs do make any such restriction).

Branch lengths can be incorporated into a tree by putting a real number, with or without decimal point, after a node and preceded by a colon. This represents the length of the branch immediately below that node. Thus the above tree might have lengths represented as:

(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);

These programs will be able to make use of this information only if lengths exist for every branch, except the one at the bottom of the tree.

The tree starts on the first line of the file, and can continue to subsequent lines. It is best to proceed to a new line, if at all, immediately after a comma. Blanks can be inserted at any point except in the middle of a species name or a branch length.

The above description is of a subset of the Newick Standard. For example, interior nodes can have names in that standard, but if any are included the present programs will omit them.

To help you understand this tree representation, here are some trees in the above form:

    ((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,
    seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,
    weasel:18.87953):2.09460):3.87382,dog:25.46154);

    (Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268,
    Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);

    (Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147,
    (P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939,
    Rodent:1.21460);

    ();

    ((A,B),(C,D));

    (Alpha,Beta,Gamma,Delta,,Epsilon,,,);

The Newick Standard was adopted June 26, 1986 by an informal committee meeting during the Society for the Study of Evolution meetings in Durham, New Hampshire and consisting of James Archie, William H.E. Day, Wayne Maddison, Christopher Meacham, F. James Rohlf, David Swofford, and myself. A web page describing it will be found at http://evolution.gs.washington.edu/phylip/newicktree.html.

## Plotter file formats

When the programs run they have a menu which allows you to set (on its option P) the final plotting device, and another menu which allows you to set the type of preview screen. The choices for previewing are a subset of those available for plotting, and they can be different (the most useful combination will usually be a previewing graphics screen with a hard-copy plotter or a drawing program graphics file format).

The plotting device menu looks like this:

    Which plotter or printer will the tree be drawn on?
    (many other brands or models are compatible with these)

       type:       to choose one compatible with:

            L         Postscript printer file format
            M         PICT format (for drawing programs)
            J         HP Laserjet PCL file format
            W         MS-Windows Bitmap
            F         FIG 2.0 drawing program format
            A         Idraw drawing program format
            Z         VRML Virtual Reality Markup Language file
            P         PCX file format (for drawing programs)
            K         TeKtronix 4010 graphics terminal
            X         X Bitmap format
            V         POVRAY 3D rendering program file
            R         Rayshade 3D rendering program file
            H         Hewlett-Packard pen plotter (HPGL file format)
            D         DEC ReGIS graphics (VT240 terminal)
            E         Epson MX-80 dot-matrix printer
            C         Prowriter/Imagewriter dot-matrix printer
            T         Toshiba 24-pin dot-matrix printer
            O         Okidata dot-matrix printer
            B         Houston Instruments plotter
            U         other: one you have inserted code for
     Choose one:

Here are the choices, with some comments on each:

Postscript printer file format. This means that the program will generate a file containing Postscript commands as its plot file. This can be printed on any Postscript-compatible laser printer. The page size is assumed to be 8.5 by 11 inches, but as plotting is within this limit A4 metric paper should work well too. This is the best quality output option. For this printer the menu options in Drawgram and Drawtree that allow you to select one of the built-in fonts will work. The programs default to Times-Roman when this plotting option is in effect. I have been able to use fonts Courier, Times-Roman, and Helvetica. The others have eluded me for some reason known only to those who really understand Postscript.

If your laser printer, supposedly Postcript-compatible, refuses to print the plot file, you might consider whether the first line of the plot file, which starts with `%!` needs to be altered somehow or eliminated. If your Laserwriter is hooked to a Macintosh it will be necessary to persuade it to print the plot file. In recent versions of the Macintosh operating systems this can supposedly be done by dragging the file icon onto the printer icon on the desktop. In earlier versions of the MacOS operating system you might have to use a utility called the Laserwriter Font Utility, which was distributed with the operating system.

PICT format (for drawing programs). This file format is read by many drawing programs (an early example was MacDraw). It has support for some fonts, though if fonts are used the species names can only be drawn horizontally or vertically, not at other angles in between. The control over line widths is a bit rough also, so that some lines at different angles may turn out to be different widths when you do not want them to be. If you are working on a Macintosh system and have not been able to persuade it to print a Postscript file, this option may be the best solution, as you could then read the file into a drawing program and then order it to print the resulting screen. The PICT file format has font support, and the default font for this plotting option is set to Times. You can also choose font attributes for the labels such as Bold, Italic, Outline, and Shadowed.

HP Laserjet PCL file format. Hewlett-Packard's extremely popular line of laser printers has been emulated by many other brands of laser printer, so that this format is compatible with more printers than any other. One limitation of the PCL4 command language for these printers is that it does not have primitive operations for drawing arbitrary diagonal lines. This means that they must be treated by these programs as if they were dot matrix printers with a great many dots. This makes output files large, and output can be slow. The user will be asked to choose the dot resolution (75, 150, or 300 dots per inch). The 300 dot per inch setting should not be used if the laser printer's memory is less than 512k bytes. The quality of output is also not as good as it might be so that the Postscript file format will usually produce better results even at the same resolution. I am grateful to Kevin Nixon for inadvertently pointing out that on Laserjets one does not have to dump the complete bitmap of a page to plot a tree.

MS-Windows Bitmap. This file format is used by most Windows drawing and paint programs, including Windows Paint which comes with the Windows operating system. It asks you to choose the height and width of the graphic image in pixels. For the moment, the image is set to be a monochrome image which can only be black or white. We hope to change that soon, but note that by pasting the image into a copy of Paint that is set to have a color image of the appropriate size, one can get a version whose color can be changed. Note also that Windows Bitmap files can be used as "wallpaper" images for the background of a desktop.

IBM PC graphics screens. This form of graphics was supported on DOS computers in the pre-Windows era. The graphics modes supported are CGA, EGA, VGA, Hercules, and AT&T (Olivetti). This option is also available for previewing plots, and in either previewing or final plotting it draws directly on the screen and does not make a plot file.

FIG 2.0 drawing program format. This is the file format of the free drawing program Xfig, available for X-windows systems on Unix or Linux systems. Xfig can be obtained from `http://duke.usask.ca/~macphed/soft/fig/`

You should also get transfig, which contains the fig2dev program which converts xfig output to the various printer languages. Transfig is on the same machine in

        /contrib/R5fixes/transfig-patches/transfig.2.1.6.tar.Z.

The present format does not write the species labels in fonts recognized by Xfig but draws them with lines. This often makes the names look rather bumpy. We hope to change this soon.

Idraw drawing program format. Idraw is a free drawing program for X windows systems (such as Unix and Linux systems). Its interface is loosely based on MacDraw, and I find it much more useable than Xfig. Though it was unsupported for a number of years, it has more recently been actively supported by Scott Johnston, of Vectaport, Inc. (`http://www.vectaport.com`). He has produced, in his `ivtools` package, a number of specialized versions of Idraw, and he also distributes the original Idraw as part of it. Linux executables for all these are available from http://www.ivtools.org/ivtools/.

The Idraw file format that our programs produce can be read into Idraw, or can be imported into the other Ivtools programs. The file format saved from Idraw (or which can be exported from the other Ivtools programs) is Postscript, and if one does not print directly from Idraw one can simply send the file to the printer. But the format we produce is missing some of the header information and will not work directly as a Postscript file. However if you read it into Idraw and then save it (or import it into one of the other Ivtools programs and then export it) you will get a Postscript version that is fully useable.

Drawgram and Drawtree have font support in their Idraw file format options. The default font is Times-Bold but you can also enter the name of any other font that is supported by your Postscript printer. Idraw labels can be rotated to any angle.

VRML Virtual Reality Markup Language file. This is by far the most interesting plotting file format. VRML files describe objects in 3-dimensional space with lighting on them. A number of freely available "virtual reality browsers" such as Cosmo Player or Cortona can read VRML files. A list of available virtual reality browsers and browser plugins can be found at `http://cic.nist.gov/vrml/vbdetect.html`, a site that also automatically detects which VRML plugins are appropriate for your web browser. VRML plugins for your web browser or standalone browsers allow you to wander around looking at the tree from various angles, including from behind! I found VRMLView particularly easy to download -- it is distributed as an executable. It is not particulary fast and somewhat mysterious to use (try your mouse buttons). At the moment our VRML output is unsophisticated. The branches are made of tubes, with spheres at their joints. The tree is made of three-dimensional tubes but is basically flat. Names are made of connected tubes (to get this make sure you use a simple default font such as the Hershey font in file `font1`). VRML itself has been superseded by a standard called X3D (see http://www.web3d.org/), and we will be moving toward X3D support. Fortunately X3D is backwards compatible with VRML. What's next? Trees whose branches stick out in three dimensions? Animated trees whose forks rotate slowly? A video game involving combat among schools of systematists?

PCX file format (for drawing programs). A bitmap format that was formerly much used on the PC platform, this has been largely superseded by the Windows Bitmap (BMP) format, but it is still useful. This file format is simple and is read by many other programs as well. The user must choose one of three resolutions for the file, 640x480, 800x600, or 1024x768. The file is a monochrome paint file. Our PCX format is correct but is not read correctly by versions of Microsoft Paint (PBrush) that are running on systems that have loaded Word97.

Tektronix 4010 graphics terminal. The plot file will contain commands for driving the Tektronix series of graphics terminals. Other graphics terminals were compatible with the Tektronix 4010 and its immediate descendants. The MSDOS version of the public domain communications program Kermit, versions 2.30 and later, can emulate a Tektronix graphics terminal if the command "set terminal tek" is given. Of course that assumes that you are communicating with another computer. There are also similar terminal emulation programs for Macintoshes that emulate Tektronix graphics. On workstations with X windows you can use one option of the "xterm" utility to create a Tektronix-compatible window. On Sun workstations there used to be a Tektronix emulator you can run called "tektool" which can be used to view the trees. The Tektronix option is also available in our programs for previewing the plots, in which case the plotting commands will be not be written into a file but will be sent directly to your terminal.

X Bitmap format. This produces an X-bitmap for the X Windows system on Unix or Linux systems, which can be displayed on X screens. You will be asked for the size of the bitmap (e.g., 16x16, or 256x256, etc.). This format cannot be printed out without further format conversion but is usable for backgrounds of windows ("wallpaper"). This can be a very bulky format if you choose a large bitmap. The bitmap is a structure that can actually be compiled into a C program (and thus built in to it), if you should have some reason for doing that.

POVRAY 3D rendering program file. This produces a file for the free ray-tracing program POVRay (Persistence of Vision Raytracer), which is available at `http://www.povray.org/`. It shows a tree floating above a flat landscape. The tree is flat but made out of tubes (as are the letters of the species names). It casts a realistic shadow across the landscape. lit from over the left shoulder of the viewer. You will be asked to confirm the colors of the tree branches, the species names, the background, and the bottom plane. These default to Blue, Yellow, White, and White respectively.

Rayshade 3D rendering program file. The input format for the free ray-tracing program "rayshade" which is available at `http://www-graphics.stanford.edu/~cek/rayshade/rayshade.html` for many kinds of systems. Rayshade takes files of this format and turns them into color scenes in "raw" raster format (also called "MTV" format after a raytracing program of that name). If you get the pbmplus package (available from `http://sourceforge.net/projects/netpbm/`). and compile it on your system you can use the "mtvtoppm" and "ppmtogif" programs to convert this into the widely-used GIF raster format. (the pbmplus package will also allow you to convert into tiff, pcx and many other formats) The resultant image will show a tree floating above a landscape, rendered in a real-looking 3-dimensional scene with shadows and illumination. It is possible to use Rayshade to make two scenes that together are a stereo pair. When producing output for Rayshade you will be asked by the Drawgram or Drawtree whether you want to reset the values for the colors you want for the tree, the species names, the background, and the desired resolution.

Hewlett-Packard pen plotter (HPGL file format). This means that the program will generate a file as its plot file which uses the HPGL graphics language. Hewlett-Packard 7470, 7475, and many other plotters are compatible with this. The paper size is again assumed to be 8.5 by 11 inches (again, A4 should work well too). It is assumed that there are two pens, a finer one for drawing names, and the HPGL commands will call for switching between these. The Hewlett-Packard Laserjet III printer can emulate an HP plotter, and this feature is included in its PCL5 command language (but not in the PCL4 command languages of earlier Hewlett-Packard models). As plotters are now rare the main use of HPGL will be when they are emulated by laser printers, but other file formats such as PCL and Postscript will be better choices in those cases.

DEC ReGIS graphics (VT240 terminal). The DEC ReGIS standard is used by the VT240 and VT340 series terminals by DEC (Digital Equipment Corporation). There used to be many graphics terminals that emulate the VT240 or VT340 as well. The DECTerm windows in many versions of Digital's (now Compaq's) DECWindows windowing system do so. This option is available in our programs for previewing trees as well. In preview mode it does not write a plot file but sends the commands directly to the screen; in final mode it writes a plot file. In DEC's version of Unix, Ultrix version 4.1 and later, the windowing system allows DEC ReGIS graphics as a default.

Epson MX-80 dot-matrix printer. This file format is for the dot-matrix printers by Epson (starting with the MX80 and continuing on to many other models), as well as the IBM Graphics printers. The code here plots in double-density graphics mode. Many of the later models are capable of higher-density graphics but not with every dot printed. This density was chosen for reasonably wide compatibility. Many other dot-matrix printers on the market have graphics modes compatible with the Epson printers. I cannot guarantee that the plot files generated by these programs will be compatible with all of these, but they do work on Epsons. They have also worked, in our hands, on IBM Graphics Printers. There used to be many printers that claimed compatibility with these too, but I do not know whether it will work on all of them. If you have trouble with any of these you might consider trying in the epson option of procedure initplotter to put in a fprintf statement that writes to plotfile an escape sequence that changes line spacing. As dot matrix printers are rare these days, I suspect this option will not get much testing.

Prowriter/Imagewriter dot-matrix printer. The trading firm C. Itoh distributed this line of dot-matrix printers, which was made by Tokyo Electric (TEC) and also was sold by NEC under the product number PC8023. These were 9-pin dot matrix printers. In a slightly modified form they were also the Imagewriter printer sold by Apple for their Macintosh line. The same escape codes seem to work on both machines, the Apple version being a serial interface version. They are not related to the IBM Proprinter, despite the name.

Toshiba 24-pin dot-matrix printer. The 24-pin printers from Toshiba were covered by this option. These included the P1340, P1350, P1351, P351, 321, and later models. For a 24-pin printer the plot file can get fairly large as it contains a bit map of the image and there are more bits with a 24-pin image. Printing was usually slow.

Okidata dot-matrix printer. The ML81, 82, 83 and ML181, 182, 183 line of dot-matrix printers from Okidata had their own graphics codes and those are dealt with by this option. The later Okidata ML190 series emulated IBM Graphics Printers so that you would not want to use this option for them but the option for that printer.

Houston Instruments plotter. The Houston Instruments line of plotters were also known as Bausch and Lomb plotters. The code in the programs for these has not been tested recently; I would appreciate anyone who tries it out telling me whether it works. I do not have access to such a plotter myself, and doubt most users will come across one.

Conversion from these formats to others is also possible. There is a free program by Jef Poskanzer called "PBMPLUS" that interconverts many bitmap formats (see above under Rayshade).

## Drivers for Preview of Plots

Plots may be previewed in a number of formats which are chosen using the menu option. Previewing defaults to different drivers depending on which kind of system you are running the programs on. For Unix or Linux systems it defaults to X Windows, for Windows systems to Windows graphics, and for Macintosh systems to macintosh graphics screens.

We have already mentioned (above) some of the options that are also used for previewing. These include:

MSDOS Graphics Screens. These were mentioned above as possible output images.

Macintosh graphics screens. Using the windowing features of Codewarrior C from Metrowerks, our Macintosh executables open a graphics window and draw preview trees in it. We have not provided this option for final plotting of the tree. The window is about 2/3 the height of the desktop screen and has the tree drawn in black on a white background. After the preview appears, you can dismiss the window by closing it using the usual little box in its corner, or by typing Command-Q.

The windows are created using the Carbon windowing system on Mac OS X, and the trees drawn in it using Quickdraw calls. However, with the release of Snow Leopard (Mac OS X 10.6), the Cocoa windowing system is to be standard on Mac OS X, for Intel-based 64-bit systems. As of this release, Mac OS X 10.6 is too new for us to have any tests yet. We have made sure to compile Drawtree and Drawgram as 32-bit executables, as for those the Carbon windowing system is still supported. Likewise Quickdraw calls are to be replaced by Quartz 2D calls. However Quickdraw calls in the executables will continue to be supported for a while. We know that we have to put in some effort to replace the Carbon and Quickdraw functions by Cocoa and Quart 2D functions.

X Windows display. Our Unix and Linux code tries to do previews in X Windows. We hope that the Unix/Linux Makefle will find the correct libraries to link from. An X window appears with the preview of the tree in it. To dismiss this window one needs to put the mouse over the text window that had the menus in it (or click on them) and then type Y or N to plot the tree or return to the menu.

Sometimes the X windows code does not find the proper libraries on an X11 system, especially if they have been moved to a new location. This may require recompiling and alteration of the Makefile to specify the location of these libraries.

MS Windows display. The executables produced using the Cygwin Gnu C++ compiler should produce this graphics preview window. The preview window can be dismissed using its File menu. In its menu the Change Parameters otion will lead you back to the text menu to make more changes, and the Plot option will cause the final plot file to be written. The Quit option will interrupt the program, causing no plot file to be produced. Normally you will not want to use that option.

Tektronix 4010 graphics terminal. This previewing option was described above as a final plot option.

DEC ReGIS graphics (VT240 terminal). This previewing option was described above as a final plot option.

## Problems Copying Files to Printers

A problem may arose in how to get the plot files to the plotting device or printer. One has to copy them directly, but one should be careful to not let your serial or parallel port strip off the high-order bits in the bytes if you are using one of the options that generate nonprintable characters. This will be true for most of the dot matrix printers and for bitmaps dumped to an HP Laserjet-compatible printer. This can be a problem under Unix or MSDOS. If, for example, you have a dot-matrix printer connected to a parallel port under PCDOS, to copy the file PLOTFILE to the printer without losing the high-order bits, you must use the /B switch on the COPY command:

      COPY/B PLOTFILE PRN:

## The VAX VMS Line Length Problem

A problem that may occur under some operating systems, particularly the VMS operating system for Digital VAXes, is having a plot file with lines that exceed some operating system limit such as 255 characters. This can happen if you are using the Tektronix option. You should set your terminal type with the command

       $ SET TERM/NOWRAP/ESCAPE

which will allow Tektronix and DEC ReGIS plots to successfully appear on your terminal. That way, if you have a terminal capable of plotting one of these kinds of plots, the operating system will not interfere with the process. It will not be possible to use files of Tektronix commands as final plot files, however, as the TYPE command usually used to get them to appear on the screen does not allow lines longer than 2048 bytes, and Tektronix plots are single lines longer than that.

## Other problems and opportunities

Another problem is adding labels (such as vertical scales and branch lengths) to the plots produced by this program. This may require you to use the BMP, PICT, Idrawm, Xfig, PCX or Postscript file format and use a draw or paint program to add them.

I would like to add more fonts. The present fonts are recoded versions of the Hershey fonts. They are legally publicly distributable. Most other font families on the market are not public domain and I cannot afford to license them for distribution. Some people have noticed that the Hershey fonts, which are drawn by a series of straight lines, have noticeable angles in what are supposed to be curves, when they are printed on modern laser printers and looked at closely. This is less a problem than one might think since, fortunately, when scientific journals print a tree it is usually shrunk so small that these imperfections (and often the tree itself) are hard to see!

One more font that could be added from the Hershey font collection would be a Greek font. If Greek users would find that useful I could add it, but my impression is that they publish mostly in English anyway.

## Writing Code for a new Plotter, Printer or File Format

The C version of these programs consists of two C programs, "drawgram.c" and "drawtree.c". Each of these has common sections of code compiled into it called "draw.c", "draw2.c" and a common header file, "draw.h". In addition the Macintosh version requires two more files, "interface.c" and "interface.h". All of the graphics commands that are common to both programs will be found in "draw.c" and "draw2.c". The following instructions for writing your own code to drive a different kind of printer, plotter, or graphics file format, require you only to make changes in "draw.c" and "draw2.c". The two programs can then be recompiled.

If you want to write code for other printers, plotters, or vector file formats, this is not too hard. The plotter option "U" is provided as a place for you to insert your own code. Chris Meacham's system was to draw everything, including the characters in the names and all curves, by drawing a series of straight lines. Thus you need only master your plotter's commands for drawing straight lines. In function "plotrparms" you must set up the values of variables "xunitspercm" and "yunitspercm", which are the number of units in the x and y directions per centimeter, as well as variables "xsize" and "ysize" which are the size of the plotting area in centimeters in the x direction and the y direction. A variable "penchange" of a user-defined type is set to "yes" or "no" depending on whether the commands to change the pen must be issued when switching between plotting lines and drawing characters. Even though dot-matrix printers do not have pens, penchange should be set to "yes" for them. In function "plot" you must issue commands to draw a line from the current position (which is at (xnow, ynow) in the plotter's units) to the position (xabs, yabs), under the convention that the lower-left corner of the plotting area is (0.0, 0.0). In functions "initplotter" and "finishplotter" you must issue commands to initialize the plotter and to finish plotting, respectively. If the pen is to be changed an appropriate piece of code must be inserted in function "penchange". The code to print the text needs to be added to the "plottext" function.

For dot matrix printers and raster graphics matters are a bit more complex. The functions "plotrparms", "initplotter", "finishplotter" and "plot" still respectively set up the parameters for the plotter, initialize it, finish a plot, and plot one line. But now the plotting consists of drawing dots into a two-dimensional array called "stripe". Once the plot is finished this array is printed out. In most cases the array is not as tall as a full plot: instead it is a rectangular strip across it. When the program has finished drawing in ther strip, it prints it out and then moves down the plot to the next strip. For example, for Hewlett-Packard Laserjets we have defined the strip as 2550 dots wide and 20 dots deep. When the program goes to draw a line, it draws it into the strip and ignores any part of it that falls outside the strip. Thus the program does a complete plotting into the strip, then prints it, then moves down the diagram by (in this case) 20 dots, then does a complete plot into that strip, and so on.

To work with a new raster or dot matrix format, you will have to define the desired width of a strip ("strpwide"), the desired depth ("strpdeep"), and how many lines of bytes must be printed out to print a strip. For example Toshiba P351 printers in graphics mode print strips of dots 1350 bits wide by 24 bits deep, each column of 24 bits printing out as consecutive four bytes with 6 bits each. In that case, one prints out a strip by printing up to 1350 groups of 4 bytes. "strpdiv" is 4, and "strpwide" is 1350, and "strpdeep" is 24. Procedure "striprint" is the one that prints out a strip, and has special-case code for the different printers and file formats. For file formats, all of which print out a single row of dots at a time, the variable "strpdiv" is not used. The variable "dotmatrix" is set to "true" or "false" in function "plotrparms" according to whether or not "strpdiv" is to be used. Procedure "plotdot" sets a single dot in the array "strip" to 1 at position (xabs, yabs). The coordinates run from 1 at the top of the plot to larger numbers as we proceed down the page. Again, there is special-case code for different printers and file formats in that function. You will probably want to read the code for some of the dot matrix or file format options if you want to write code for one of them. Many of them have provision for printing only part of a line, ignoring parts of it that have no dots to print.

I would be happy to obtain the resulting code from you to consider adding it to this listing so we can cover more kinds of plotters, printers, and file formats.

## APPENDIX 1. Code to drive some other graphics devices.

These pieces of code are to be inserted in the places reserved for the "Y" plotter option. The variables necessary to run this have already been incorporated into the programs.

### Calcomp plotters:

Calcomp's industrial-strength plotters are not as much a fixture of University computer centers as they once were, but just in case you need to use one, this code should work:

A global declaration needed near the front of drawtree.c:

    Char cchex[16];

Code to be inserted into function plotrparms:

      case 'Y':
        plotter = other;
        xunitspercm = 39.37;
        yunitspercm = 39.37;
        xsize = 25.0;
        ysize = 25.0;
        xposition = 12.5;
        yposition = 0.0;
        xoption = center;
        yoption = above;
        rotation = 0.0;
        break;

Code to be inserted into function plot:

Declare these variables at the beginning of the function:

    long n, inc, xinc, yinc, xlast, ylast, xrel,
       yrel, xhigh, yhigh, xlow, ylow;
    Char quadrant;

and insert this into the switch statement:

      case other:
        if (penstatus == pendown)
          putc('H', plotfile);
        else
          putc('D', plotfile);
        xrel = (long)floor(xabs + 0.5) - xnow;
        yrel = (long)floor(yabs + 0.5) - ynow;
        xnow = (long)floor(xabs + 0.5);
        ynow = (long)floor(yabs + 0.5);
        if (xrel > 0) {
          if (yrel > 0)
            quadrant = 'P';
          else
            quadrant = 'T';
        } else if (yrel > 0)
          quadrant = 'X';
        else
          quadrant = '1';
        xrel = labs(xrel);
        yrel = labs(yrel);
        if (xrel > yrel)
          n = xrel / 255 + 1;
        else
          n = yrel / 255 + 1;
        xinc = xrel / n;
        yinc = yrel / n;
        xlast = xrel % n;
        ylast = yrel % n;
        xhigh = xinc / 16;
        yhigh = yinc / 16;
        xlow = xinc & 15;
        ylow = yinc & 15;
        for (i = 1; i <= n; i++)
          fprintf(plotfile, "%c%c%c%c%c",
                  quadrant, cchex[xhigh - 1], cchex[xlow - 1], cchex[yhigh - 1],
                  cchex[ylow - 1]);
        if (xlast != 0 || ylast != 0)
          fprintf(plotfile, "%c%c%c%c%c",
                  quadrant, cchex[-1], cchex[xlast - 1], cchex[-1],
                  cchex[ylast - 1]);
        break;

Code to be inserted into function initplotter:

      case other:
        cchex[-1] = 'C';
        cchex[0] = 'D';
        cchex[1] = 'H';
        cchex[2] = 'L';
        cchex[3] = 'P';
        cchex[4] = 'T';
        cchex[5] = 'X';
        cchex[6] = '1';
        cchex[7] = '5';
        cchex[8] = '9';
        cchex[9] = '/';
        cchex[10] = '=';
        cchex[11] = '#';
        cchex[12] = '"';
        cchex[13] = '\'';
        cchex[14] = '^';
        xnow = 0.0;
        ynow = 0.0;
        fprintf(plotfile, "CCCCCCCCCC");
        break;

Code to be inserted into function finishplotter:

      case other:
        plot(penup, 0.0, yrange + 50.0);
        break;

## Appendix 2. Our Hershey font encoding.

The Hershey fonts were digitized fonts created by Dr. A. V. Hershey in the late 1960s when he was working at the U. S. Naval Weapons Laboratory. They were published in U. S. National Bureau of Standards Special Publication No. 424, distributed by the U. S. National Technical Information Service. Legally, it is possible to freely distribute these fonts in any encoding system except the original one used by the U. S. National Technical Information Service, provided that you acknowledge that the original fonts were produced by Dr. Hershey and published by NBS. Fortunately, Chris Meacham developed the software we use to read the Hershey fonts, and it uses a simple coding system that he developed. The original Hershey fonts were transformed by him into this encoding system. Six of them are distributed with PHYLIP: three Roman fonts, one unserifed and two serifed, two Italic fonts, one unserifed and one serifed, and a Russian Cyrillic font.

Each font file consists of groups of lines, one for each character. Here are the lines for character "h" in the font #1 in this encoding:

    Ch 608 21 19 28
     -1456 1435 -1445 1748 1949 2249 2448 2545 2535 -12935

The group of lines starts with the letter C (for Character). Then follows the character that this font will draw (in this case "h"). It is the byte which, when read by the computer, signals that character. Then there is the number of this character in the original Hershey fonts (608). This is not used by our software.

The Hershey fonts are drawn on a grid of points as a series of lines. The next three numbers (21, 19, and 28) are the height (21), and two widths (19, and 28, which we don't use). Then comes a new line which shows the individual pen moves. When these are negative, they indicate that the pen is to be up when moving; when they are positive, the pen is to be down. They are integers. The last of them is greater than 10,000, and that is the signal to end after that move.

Each number has a final four digits that give the coordinate to which the pen is to move. These are given as (x,y) coordinates. Thus the first number (-1456) indicates the pen is to be up and the plotting is to move to coordinate (14, 56), which is x = 14, y = 56. Then the pen is put down and moved to (14, 35). This draws a line from (14, 56) to (14, 35), in fact the vertical line that forms the back of the "h". Then the pen is picked up and moved to (14, 45). Then there follow a series of moves with pen down to (14, 35), (14, 45), (17, 48), (19, 49), (22, 49), (24, 48), (25, 45), and finally (25, 35). This draws a series of connected line segments that make the arch and right-hand vertical, ending up at the bottom-right of the character. -12935 then signals a pen-up move to (29, 35). This moves to a point where the next character can start, putting in a little "white space".

As you can see, the coding system is quite simple. Does anyone want to draw us some new fonts to add to our repertoire? I have spared you the Gothic, Old English, and Greek Hershey fonts, but perhaps there are some other nice ones people might want to use.