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12	<DIV ALIGN=RIGHT>
13	version 3.6
14	</DIV>
15	<P>
16	<DIV ALIGN=CENTER>
17	<H1>DRAWTREE and DRAWGRAM</H1>
18	</DIV>
19	<P>
20	© Copyright 1986-2002 by The University of
21	Washington. Written by Joseph Felsenstein. Permission is granted to copy
22	this document provided that no fee is charged for it and that this copyright
23	notice is not removed.
24	<P>
25	DRAWTREE and DRAWGRAM are interactive tree-plotting programs that take a
26	tree description in a file and read it, and then let you interactively make
27	various settings and then plot the tree on a laser printer, plotter,
28	or dot matrix printer. In many cases (with Macintosh or PC graphics,
29	with X windows, or with a Tektronix-compatible graphics terminal)
30	you can preview the resulting tree. This allows you to modify the tree
31	until you like the result, then plot the result. DRAWTREE plots
32	unrooted trees and DRAWGRAM plots rooted cladograms and phenograms. On
33	good laser printers or as files for good drawing programs both can produce
34	fully publishable
35	results. On dot matrix printers the results look grainy but are good
36	enough for overhead transparencies or slides for presentations.
37	<P>
38	These programs are descended from PLOTGRAM and PLOTREE written by
39	Christopher Meacham. I have incorporated his code for fonts and his
40	plotter drivers, and in DRAWTREE have used some of his code for drawing
41	unrooted trees. In both programs I have also included some plotter driver
42	code by David Swofford, Julian Humphries and George D.F. "Buz" Wilson,
43	to all of whom I am very grateful. Mostly, however, they consist of my own
44	code and that of my programmers. The font files are printable-character
45	recodings of the public-domain Hershey fonts, recoded by Christopher Meacham.
46	<P>
47	This document will describe the features common to both programs. The
48	documents for DRAWTREE and DRAWGRAM describe the particular choices you
49	can make in each of those programs. The Appendix to this documentation file
50	contains some pieces of C code that can be inserted to make the program
51	handle another plotting device -- the plotters by Calcomp.
52	<P>
53	<H2>A Short Introduction</H2>
54	<P>
55	To use DRAWTREE and DRAWGRAM, you must have
56	<P>
57	<DL COMPACT>
58	<DT>(1)</DT> <DD>The compiled version of the program. If you have not obtained a
59	version of PHYLIP precompiled for your machine, you will have to take
60	the source code given here and modify it for your C
61	compiler and then compile it. This is not too hard: it is discussed below.</DD>
62	<P>
63	<DT>(2)</DT> <DD>A tree file. Trees are described in the nested-parenthesis notation
64	used throughout PHYLIP and standardized in an informal meeting of
65	program authors in Durham, New Hampshire in June, 1986. Trees for
66	both programs may be either bifurcating or multifurcating, and may
67	either have or not have branch lengths. Tree files produced by
68	the PHYLIP programs are in this form. There is further description of the
69	tree file format later in this document.</DD>
70	<P>
71	<DT>(3)</DT> <DD>A font file. There are six font files distributed with PHYLIP:
72	these consist of three Roman, two Italic, and one Russian Cyrillic font,
73	all from the public-domain
74	Hershey Fonts, in ASCII readable form. The details of font
75	representation need not concern you; all you need to do is to copy the
76	font file corresponding to the font you want into the appropriate
77	directory under the appropriate file name, and let the program use it.
78	Or you can let the program ask you for the name of the font file, which
79	it will do if it does not find one itself.
80	The six fonts are, respectively, a one- and a two-stroke sans-serif
81	Roman font, a three-stroke serifed Roman font, a two- and a three-
82	stroke serifed Italic font, and a two-stroke Cyrillic font for the Russian
83	language. If this is not clear just try them all. Note that for some
84	printers several built-in fonts such as Times-Roman and Courier can be used
85	too.</DD>
86	<P>
87	<DT>(4)</DT> <DD>A plotting device, and if possible a screen on which you can preview
88	the plot. The programs work with Postscript-compatible laser printers,
89	laser printers compatible with the PCL printer language of the Hewlett-Packard
90	Laserjet series,
91	IBM PC graphics screens,
92	the PICT format for the MacDraw drawing program,
93	the PCX file format for the PC Paintbrush painting program,
94	the file format for the freeware X-windows drawing programs <TT>xfig</TT> and
95	<TT>idraw</TT>,
96	the X Bitmap format for X-windows,
97	plotters including Hewlett-Packard models, dot matrix printers including
98	models by Epson and Apple, graphics terminals from DEC and Tektronix,
99	the input format for the freeware ray-tracing (3-dimensional rendering)
100	programs <TT>POV</TT> and <TT>rayshade</TT>,
101	and, strangest and most wonderful of all,
102	the Virtual Reality Markup Language (VRML) which is a file format that is
103	used by freely-available virtual reality programs like Cosmo Player.
104	You can choose the plotting and previewing
105	devices from a menu at run time, and these can be different. There are
106	places in the source code for the program where you can insert code for
107	a new plotter, should you want to do that.</DD>
108	</DL>
109	<P>
110	Once you have all these, the programs should be fairly self explanatory,
111	particular if you can preview your plots so that you can discover the
112	meaning of the different options by trying them out.
113	<P>
114	Once you have a compiled version of the appropriate program, say
115	DRAWGRAM, and a file called (say) <TT>treefile</TT> with the tree in it, and
116	a font file (say <TT>font2</TT> which you have copied as a file called
117	<TT>fontfile</TT>),
118	all you do is run the program DRAWGRAM. It should automatically read the
119	font and tree files, and will allow you to change the graphics devices. Then
120	it will let you see the options it has chosen, and ask you if you
121	want to change these. Once you have modified those that you want to,
122	you can tell it to accept those. The program will then allow you to
123	preview the tree on your screen, if you have told it that you have
124	an appropriate graphics screen. After
125	previewing the tree, the program will want to know whether you are ready to
126	plot the tree. In Windows you answer this using the File menu of the preview
127	window. In X Windows and Macintosh systems you can close the preview
128	window by clicking on its corner. Whether or not you close it, if you
129	get back to the text window that had the menus, and it accepts typing in
130	that window, you will be asked whether you want to accept the plot as is.
131	If you say no, it will once again allow you to change options and
132	will the allow you to preview the tree again, and so on as many times
133	as you want. If you say yes, then it will write a file called (say)
134	<TT>plotfile</TT>. If you then copy this file to your printer or plotter,
135	it should result in a beautifully plotted tree. If the final plotting
136	device is a Macintosh or PC graphics screen, it may not write a plot file
137	but will plot directly on the screen.
138	<P>
139	Having read the above, you may be ready to run the program. Below you
140	Will find more information about representation of trees in the tree
141	file, on the different kinds of graphics devices supported by this
142	program, and on how to recompile these programs.
143	<P>
144	<H2>Trees</H2>
145	<P>
146	The Newick Standard for representing trees in computer-readable
147	form makes use of the correspondence between trees and nested
148	parentheses, noticed in 1857 by the famous English mathematician Arthur
149	Cayley. If we have this rooted tree:
150	<P>
151	<PRE>
152	A D
153	\ E /
154	\ C / /
155	\ ! / /
156	\ ! / /
157	B \!/ /
158	\ o /
159	\ ! /
160	\ ! /
161	\ ! /
162	\ ! /
163	\!/
164	o
165	!
166	!
167	</PRE>
168	<P>
169	then in the tree file it is represented by the following sequence of printable
170	characters, starting at the beginning of the file:
171	<P>
172	(B,(A,C,E),D);
173	<P>
174	The tree ends with a semicolon. Everything after the semicolon in the
175	input file is ignored, including any other trees. The bottommost node
176	in the tree is an interior node, not a tip. Interior nodes are
177	represented by a pair of matched parentheses. Between them are
178	representations of the nodes that are immediately descended from that
179	node, separated by commas. In the above tree, the immediate
180	descendants are B, another interior node, and D. The other interior
181	node is represented by a pair of parentheses, enclosing representations
182	of its immediate descendants, A, C, and E.
183	<P>
184	Tips are represented by their names. A name can be any string of
185	printable characters except blanks, colons, semcolons, parentheses, and
186	square brackets. In the programs a maximum of 20 characters are allowed
187	for names: this limit can easily be increased by recompiling the program
188	and changing the constant
189	declaration for "MAXNCH" in <TT>phylip.h</TT>.
190	<P>
191	Because you may want to include a blank in a name, it is assumed that
192	an underscore character ("_") stands for a blank; any of these in a
193	name will be converted to a blank when it is read in. Any name may also
194	be empty: a tree like
195	<P>
196	(,(,,),);
197	<P>
198	is allowed. Trees can be multifurcating at any level (while in many
199	of the programs multifurcations of user-defined trees are not allowed
200	or restricted to a trifurcation at the bottommost level, these programs
201	do make any such restriction).
202	<P>
203	Branch lengths can be incorporated into a tree by putting a real
204	number, with or without decimal point, after a node and preceded by
205	a colon. This represents the length of the branch immediately
206	below that node. Thus the above tree might have lengths
207	represented as:
208	<P>
209	(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);
210	<P>
211	These programs will be able to make use of this information only if
212	lengths exist for every branch, except the one at the bottom of
213	the tree.
214	<P>
215	The tree starts on the first line of the file, and can continue to
216	subsequent lines. It is best to proceed to a new line, if at all,
217	immediately after a comma. Blanks can be inserted at any point except
218	in the middle of a species name or a branch length.
219	<P>
220	The above description is of a subset of the Newick Standard. For
221	example, interior nodes can have names in that standard, but if
222	any are included the present programs will omit them.
223	<P>
224	To help you understand this tree representation, here are some trees
225	in the above form:
226	<P>
227	<PRE>
228	((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,
229	seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,
230	weasel:18.87953):2.09460):3.87382,dog:25.46154);
231	<P>
232	(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268,
233	Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);
234	<P>
235	(Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147,
236	(P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939,
237	Rodent:1.21460);
238	<P>
239	();
240	<P>
241	((A,B),(C,D));
242	<P>
243	(Alpha,Beta,Gamma,Delta,,Epsilon,,,);
244	</PRE>
245	<P>
246	The Newick Standard was adopted June 26, 1986 by an informal
247	committee meeting during the Society for the Study of Evolution
248	meetings in Durham, New Hampshire and consisting of James Archie,
249	William H.E. Day, Wayne Maddison, Christopher Meacham, F. James Rohlf,
250	David Swofford, and myself. A web page describing it will be found
251	at <A HREF="http://evolution.gs.washington.edu/phylip/newicktree.html">
252	http://evolution.gs.washington.edu/phylip/newicktree.html</A>.
253	<P>
254	<H2>Plotter file formats</H2>
255	<P>
256	When the programs run they have a menu which allows you to set (on its
257	option P) the final plotting device, and another menu which allows you
258	to set the type of preview screen. The
259	choices for previewing are a subset of those available for plotting,
260	and they can be different (the most useful combination will usually be a
261	previewing graphics screen with a hard-copy plotter or a drawing program
262	graphics file format).
263	<P>
264	The plotting device menu looks like this:
265	<P>
266	<TABLE><TR><TD BGCOLOR=white>
267	<PRE>
268	type: to choose one compatible with:
269
270	L Postscript printer file format
271	M PICT format (for drawing programs)
272	J HP Laserjet PCL file format
273	W MS-Windows Bitmap
274	F FIG 2.0 drawing program format
275	A Idraw drawing program format
276	Z VRML Virtual Reality Markup Language file
277	P PCX file format (for drawing programs)
278	K TeKtronix 4010 graphics terminal
279	X X Bitmap format
280	V POVRAY 3D rendering program file
281	R Rayshade 3D rendering program file
282	H Hewlett-Packard pen plotter (HPGL file format)
283	D DEC ReGIS graphics (VT240 terminal)
284	E Epson MX-80 dot-matrix printer
285	C Prowriter/Imagewriter dot-matrix printer
286	T Toshiba 24-pin dot-matrix printer
287	O Okidata dot-matrix printer
288	B Houston Instruments plotter
289	U other: one you have inserted code for
290	Choose one:
291	</PRE>
292	</TD></TR></TABLE>
293	<P>
294	Here are the choices, with some comments on each:
295	<P>
296	<B>Postscript printer file format.</B> This means that the program will
297	generate a file containing Postscript commands as its plot file. This
298	can be printed on any Postscript-compatible laser printer. The page
299	size is assumed to be 8.5 by 11 inches, but as plotting is within this
300	limit A4 metric paper should work well too. This is the best
301	quality output option. For this printer the menu options in DRAWGRAM
302	and DRAWTREE that allow you to select one of the built-in fonts will
303	work. The programs default to Times-Roman when this plotting option
304	is in effect. I have been able to use fonts Courier, Times-Roman, and
305	Helvetica. The others have eluded me for some reason known only to those
306	who really understand Postscript.
307	<P>
308	If your laser printer, supposedly
309	Postcript-compatible, refuses to print the plot file, you might
310	consider whether the first line of the plot file, which starts with <TT>%!</TT>
311	needs to be altered somehow or eliminated. If your Laserwriter is hooked to
312	a Macintosh it will be necessary
313	to persuade it to print the plot file.
314	In recent versions of the Macintosh operating systems this can supposedly
315	be done by dragging the file icon onto the printer icon on the desktop.
316	In earlier versions of the MacOS operating system you might have to use
317	a utility called the Laserwriter Font Utility, which was distributed with the
318	operating system.
319	<P>
320	<B>PICT format (for drawing programs).</B> This file format is read by
321	many drawing programs (an early example was MacDraw). It has support for
322	some fonts, though if fonts are used the species names can only be drawn
323	horizontally or vertically, not at other angles in between. The control over
324	line widths is a bit rough also, so that some lines at different angles
325	may turn out to be different widths when you do not want them to be.
326	If you are working on a Macintosh system and have not been able to persuade
327	it to print a Postscript file, this option may be the best solution, as you
328	could then read the file into a drawing program and then order it to print
329	the resulting screen. The PICT file format has font support, and the
330	default font for this plotting option is set to Times. You can also
331	choose font attributes for the labels such as Bold, Italic, Outline, and
332	Shadowed.
333	<P>
334	<B>HP Laserjet PCL file format.</B> Hewlett-Packard's extremely popular line
335	of laser printers has been emulated by many other brands of laser printer,
336	so that this format is compatible with more printers than any other.
337	One limitation of the PCL4
338	command language for these printers is that it does not have primitive
339	operations for drawing arbitrary diagonal lines. This means that they must
340	be treated by these programs as if they were dot matrix printers with a
341	great many dots. This makes output files large, and output can be slow.
342	The user will be asked to choose
343	the dot resoluton (75, 150, or 300 dots per inch). The 300 dot per inch
344	setting should not be used if the laser printer's memory is less than
345	512k bytes. The quality of output is also not as good as it might
346	be so that the Postscript file format will usually produce better results even
347	at the same resolution. I am
348	grateful to Kevin Nixon for inadvertently pointing out that on Laserjets one
349	does not have to dump the complete bitmap of a page to plot a tree.
350	<P>
351	<B>MS-Windows Bitmap.</B> This file format is used by most Windows
352	drawing and paint programs, including Windows Paint which comes with the
353	Windows operating system. It asks you to choose the height and width
354	of the graphic image in pixels. For the moment, the image is set to be
355	a monochrome image which can only be black or white. We hope to change
356	that soon, but note that by pasting the image into a copy of Paint that
357	is set to have a color image of the appropriate size, one can get a version
358	whose color can be changed. Note also that Windows Bitmap files can be
359	used as "wallpaper" images for the background of a desktop.
360	<P>
361	<B>IBM PC graphics screens.</B> The code for this in the programs is available
362	in the precompiled PC executables or if you compile the programs
363	yourself in C. The graphics modes supported are CGA, EGA, VGA,
364	Hercules, and AT&T (Olivetti).
365	This option is also available for previewing plots, and
366	in either previewing or final plotting it draws directly on the screen
367	and does not make a plot file.
368	<P>
369	<B>FIG 2.0 drawing program format.</B> This is the file format of the
370	free drawing program Xfig, available for X-windows systems on Unix or
371	Linux systems. Xfig
372	can be <A HREF="http://duke.usask.ca/~macphed/soft/fig/">obtained from</A>
373	<TT>http://duke.usask.ca/~macphed/soft/fig/</TT>
374	<P>
375	You should also get transfig, which contains the fig2dev program which converts
376	xfig output to the various printer languages. Transfig is on the same machine
377	in
378	<P>
379	<PRE>
380	/contrib/R5fixes/transfig-patches/transfig.2.1.6.tar.Z.
381	</PRE>
382	<P>
383	The present format
384	does not write the species labels in fonts recognized by
385	Xfig but draws them with lines. This often makes the names look rather
386	bumpy. We hope to change this soon.
387	<P>
388	<B>Idraw drawing program format.</B> Idraw is a free drawing program for
389	X windows systems (such as Unix and Linux systems). Its interface is
390	loosely based on MacDraw, and I find it much more useable than Xfig.
391	Though it was unsupported for a number of years, it has more recently
392	been actively supported by Scott Johnston, of
393	<A HREF="http://www.vectaport.com/index.html">Vectaport, Inc.</A> (<TT>http://www.vectaport.com</TT>). He has produced, in his <TT>ivtools</TT> package, a number
394	of specialized versions of Idraw, and he also distributes the original
395	Idraw as part of it. Linux executables for all these are available from
396	Vectaport, or from various archive machines.
397	<P>
398	The Idraw file format that our programs produce can be read into Idraw, or
399	can be imported into the other Ivtools programs. The file format saved
400	from Idraw (or which can be exported from the other Ivtools programs)
401	is Postscript, and if one does not print directly from Idraw one can
402	simply send the file to the printer. But the format we produce is missing
403	some of the header information and will not work directly as a Postscript
404	file. However if you read it into Idraw and then save it (or import it into
405	one of the other Ivtools programs and then export it) you will get a Postscript
406	version that is fully useable.
407	<P>
408	DRAWGRAM and DRAWTREE have font support in their Idraw file format options.
409	The default font is Times-Bold but you can also enter the name of any
410	other font that is supported by your Postscript printer. Idraw labels
411	can be rotated to any angle.
412	<P>
413	<B>VRML Virtual Reality Markup Language file.</B> This is by far the most
414	interesting plotting file format. VRML files describe objects in 3-dimensional
415	space with lighting on them. A number of freely available "virtual reality
416	browsers" such as Cosmo Player can read VRML files.
417	<A HREF="http://www.web3d.org/vrml/browpi.htm">A list of available virtual reality browsers and browser plugins</A>
418	can be found at <TT>http://www.web3d.org/vrml/browpi.htm</TT>.
419	These allow you to
420	wander around looking at the tree from various angles, including from
421	behind! At the moment our VRML output is primitive, with labels that
422	always look the same no matter what angle you look at them from, and
423	with a "sun" that is always behind you. The tree is made of three-dimensional
424	tubes but is basically flat. We hope to change these soon. What's
425	next? Trees whose branches stick out in three dimensions? Animated trees
426	whose forks rotate slowly?
427	A video game involving combat among schools of systematists?
428	<P>
429	<B>PCX file format (for drawing programs).</B> A bitmap format that was
430	formerly much used on the PC platform, this has been largely superseded by
431	the Windows Bitmap (BMP) format, but it is still useful. This file format
432	is simple and is read by many other programs as well. The user must
433	choose one of three resolutions for the file, 640x480, 800x600, or 1024x768.
434	The file is a monochrome paint file. Our PCX format is correct but is not
435	read correctly by versions of Microsoft Paint (PBrush) that are running on
436	systems that have loaded Word97.
437	<P>
438	<B>Tektronix 4010 graphics terminal.</B> The plot file will contain commands
439	for driving the Tektronix series of graphics terminals. Other
440	graphics terminals were compatible with the Tektronix 4010 and its
441	immediate descendants. The PCDOS version of the public domain communications
442	program Kermit, versions 2.30 and later, can emulate a Tektronix
443	graphics terminal if the command "set terminal tek" is given. Of course
444	that assumes that you are communicating with another computer. There are
445	also similar terminal emulation programs for Macintoshes that emulate
446	Tektronix graphics. On workstations with X windows you can use one option of
447	the "xterm" utility to create a Tektronix-compatible window. On Sun
448	workstations there used to be a
449	Tektronix emulator you can run called "tektool" which can be used to
450	view the trees. The Tektronix option is also available in our programs
451	for previewing the plots, in which case the plotting commands will be not be
452	written into a file but will be sent directly to your terminal.
453	<P>
454	<B>X Bitmap format.</B> This produces an X-bitmap for the X Windows system
455	on Unix or Linux systems,
456	which can be displayed on X screens. You will be asked for the
457	size of the bitmap (e.g., 16x16, or 256x256, etc.). This format
458	cannot be printed out without further format conversion but is
459	usable for backgrounds of windows ("wallpaper"). This can be a very
460	bulky format if you choose a large bitmap. The bitmap is a structure
461	that can actually be compiled into a C program (and thus built in to it),
462	if you should have some reason for doing that.
463	<P>
464	<B>POVRAY 3D rendering program file.</B> This produces a file for the
465	free ray-tracing program POVRay (Persistence of Vision Raytracer),
466	which is <A HREF="http://www.povray.org/">available at</A>
467	<TT>http://www.povray.org/</TT>.
468	It shows a tree floating above a flat landscape. The tree is flat but
469	made out of tubes (as are the letters of the species names). It
470	casts a realistic shadow across the landscape. lit from over the left
471	shoulder of the viewer. You will be asked to confirm the colors of the
472	tree branches, the species names, the background, and the bottom plane.
473	These default to Blue, Yellow, White, and White respectively.
474	<P>
475	<B>Rayshade 3D rendering program file.</B> The input format for the
476	free ray-tracing program "rayshade" which is
477	<A HREF="http://www-graphics.stanford.edu/~cek/rayshade/rayshade.html">available</A>
478	at <TT>http://www-graphics.stanford.edu/~cek/rayshade/rayshade.html</TT>
479	for many kinds of systems. Rayshade
480	takes files of this format and turns them into color scenes in "raw"
481	raster format (also called "MTV" format after a raytracing
482	program of that name). If you get the pbmplus package
483	(<A HREF="http://sourceforge.net/projects/netpbm/">available from</A>
484	<TT>http://sourceforge.net/projects/netpbm/</TT>).
485	and compile it on your system
486	you can use the "mtvtoppm" and "ppmtogif" programs to convert this
487	into the widely-used GIF raster format. (the pbmplus package will also
488	allow you to convert into tiff, pcx and many other formats) The
489	resultant image will show a tree floating above a landscape, rendered
490	in a real-looking 3-dimensional scene with shadows and illumination.
491	It is possible to use Rayshade to
492	make two scenes that together are a stereo pair. When producing
493	output for Rayshade you will be asked by the DRAWGRAM or DRAWTREE
494	whether you want to reset the values for the colors you want for the
495	tree, the species names, the background, and the desired resolution.
496	<P>
497	<B>Hewlett-Packard pen plotter (HPGL file format).</B>
498	This means that the program will generate a
499	file as its plot file which uses the HPGL graphics language. Hewlett-Packard
500	7470, 7475, and many other plotters are compatible with this. The
501	paper size is again assumed to be 8.5 by 11 inches (again, A4 should
502	work well too). It is assumed that there are two pens, a finer one for
503	drawing names, and the HPGL commands will call for switching between
504	these. The Hewlett-Packard Laserjet III printer can emulate an HP plotter,
505	and this feature is included in its PCL5 command language (but not in the
506	PCL4 command languages of earlier Hewlett-Packard models). As plotters
507	are now rare the main use of HPGL will be when they are emulated by
508	laser printers, but other file formats such as PCL and Postscript will be
509	better choices in those cases.
510	<P>
511	<B>DEC ReGIS graphics (VT240 terminal).</B> The DEC ReGIS standard is
512	used by the VT240 and VT340 series terminals by DEC (Digital Equipment
513	Corporation). There used to be many graphics terminals that emulate the
514	VT240 or VT340 as well. The DECTerm windows in many versions
515	of Digital's (now Compaq's) DECWindows windowing system do so.
516	This option is available in our programs for
517	previewing trees as well. In preview mode it does not write a plot file
518	but sends the commands directly to the screen; in final mode it writes a
519	plot file. In DEC's version of Unix, Ultrix version 4.1 and later,
520	the windowing system allows DEC ReGIS graphics as a default.
521	<P>
522	<B>Epson MX-80 dot-matrix printer.</B> This file format is for the dot-matrix
523	printers by Epson (starting with the MX80 and continuing on to many other
524	models), as well as the IBM Graphics printers. The code here plots in
525	double-density graphics mode. Many of the later models are capable of
526	higher-density graphics but not with every dot printed. This
527	density was chosen for reasonably wide compatibility. Many other dot-matrix
528	printers on the market have graphics modes compatible with the
529	Epson printers. I cannot guarantee that the plot files generated by
530	these programs will be compatible with all of these, but they do work on
531	Epsons. They have also worked, in our hands, on IBM Graphics Printers. There
532	used to be many printers that claimed compatibility with these too, but I
533	do not know whether it will work on all of them. If you have trouble
534	with any of these you might consider trying in the epson option of
535	procedure initplotter to put in a fprintf statement
536	that writes to plotfile an escape sequence that changes line spacing.
537	As dot matrix printers are rare these days, I suspect this option will
538	not get much testing.
539	<P>
540	<B>Prowriter/Imagewriter dot-matrix printer.</B>
541	The trading firm C. Itoh distributed this line of
542	dot-matrix printers, which was made by Tokyo Electric (TEC) and also was
543	sold by NEC under the product number PC8023. These were 9-pin dot matrix
544	printers. In a slightly modified form they were also the Imagewriter
545	printer sold by Apple for their Macintosh line. The same escape codes
546	seem to work on both machines, the Apple version being a serial
547	interface version. They are not related to the IBM Proprinter, despite
548	the name.
549	<P>
550	<B>Toshiba 24-pin dot-matrix printer.</B>
551	The 24-pin printers from Toshiba were covered
552	by this option. These included the P1340, P1350, P1351, P351, 321, and
553	later models. For a 24-pin printer the plot file can get fairly large
554	as it contains a bit map of the image and there are more bits with a
555	24-pin image. Printing was usually slow.
556	<P>
557	<B>Okidata dot-matrix printer.</B>
558	The ML81, 82, 83 and ML181, 182, 183 line of dot-matrix
559	printers from Okidata had their own graphics codes and those are dealt
560	with by this option. The later Okidata ML190 series emulated IBM Graphics
561	Printers so that you would not want to use this option for them but the option
562	for that printer.
563	<P>
564	<B>Houston Instruments plotter.</B> The Houston Instruments line of plotters
565	were also known as Bausch and Lomb plotters. The code in the
566	programs for these has not been tested recently; I would appreciate
567	anyone who tries it out telling me whether it works. I do not have
568	access to such a plotter myself, and doubt most users will come across one.
569	<P>
570	Conversion from these formats to others is also possible.
571	There is a free program by Jef Poskanzer called "PBMPLUS" that interconverts
572	many bitmap formats (see above under Rayshade).
573	<P>
574	<H2>Drivers for Preview of Plots</H2>
575	<P>
576	Plots may be previewed in a number of formats which are chosen using the
577	menu option. Previewing defaults to different drivers depending on which
578	kind of system you are running the programs on. For Unix or Linux systems
579	it defaults to X Windows, for Windows systems to Windows graphics, and
580	for Macintosh systems to macintosh graphics screens.
581	<P>
582	We have already mentioned (above) some of the options that are also used
583	for previewing. These include:
584	<P>
585	<B>MSDOS Graphics Screens.</B> These were mentioned
586	above as possible output images.
587	<P>
588	<B>Macintosh graphics screens.</B> Using the windowing features of
589	Codewarrior C from Metrowerks, our Macintosh executables
590	open a graphics window and draw preview trees in it. We have
591	not provided this option for final plotting of the tree.
592	The window is about 2/3 the height of the desktop screen and has the tree drawn
593	in black on a white background.
594	After the preview appears, you can dismiss the window by closing it
595	using the usual little box in its corner, or by typing Command-Q.
596	<P>
597	<B>X Windows display.</B> Our Unix and Linux code tries to do previews
598	in X Windows. We hope that the Unix/Linux Makefle will find the correct
599	libraries to link from. An X window appears with the preview of the tree
600	in it. To dismiss this window one needs to put the mouse over the
601	text window that had the menus in it (or click on them) and then type Y
602	or N to plot the tree or return to the menu.
603	<P>
604	<B>MS Windows display.</B> The executables produced using the Cygwin
605	Gnu C++ compiler should produce this graphics preview window. The preview
606	window can be dismissed using its File menu. In its menu the Change
607	Parameters otion will lead you back to the text menu to make more
608	changes, and the Plot option will cause the final plot file to be written.
609	The Quit option will interrupt the program, causing no plot file to b produced.
610	Normally you will not want to use that option.
611	<P>
612	<B>Tektronix 4010 graphics terminal.</B> This previewing option was
613	described above as a final plot option.
614	<P>
615	<B>DEC ReGIS graphics (VT240 terminal).</B> This previewing option was
616	described above as a final plot option.
617	<P>
618	<H2>Problems Copying Files to Printers</H2>
619	<P>
620	A problem may arose in how to get the plot files to the plotting device
621	or printer. One has to copy them directly, but one should be careful to
622	not let your serial or parallel port strip off the high-order bits in the
623	bytes if you are using one of the options that generate nonprintable
624	characters. This will be true for most of the dot matrix printers and
625	for bitmaps dumped to an HP Laserjet-compatible printer. This can be
626	a problem under Unix or MSDOS. If, for example, you have a dot-matrix
627	printer connected to a parallel port under PCDOS, to copy the file
628	PLOTFILE to the printer without losing the high-order bits, you must use
629	the /B switch on the COPY command:
630	<P>
631	<PRE>
632	COPY/B PLOTFILE PRN:
633	</PRE>
634	<P>
635	<H2>The VAX VMS Line Length Problem</H2>
636	<P>
637	A problem that may occur under some operating systems, particularly the
638	VMS operating system for Digital VAXes, is having a plot file with lines
639	that exceed some operating system limit such as 255 characters. This can
640	happen if you are using the Tektronix option.
641	You should set your terminal type with the
642	command
643	<P>
644	<PRE>
645	$ SET TERM/NOWRAP/ESCAPE
646	</PRE>
647	<BR>
648	which will allow Tektronix and DEC ReGIS
649	plots to successfully appear on your terminal. That way, if you have a
650	terminal capable of plotting one of these kinds of plots, the operating
651	system will not interfere with the process. It will not be possible to
652	use files of Tektronix commands as final plot files, however, as the TYPE
653	command usually used to get them to appear on the screen does not allow
654	lines longer than 2048 bytes, and Tektronix plots are single lines longer
655	than that.
656	<P>
657	<H2>Other problems and opportunities</H2>
658	<P>
659	Another problem is adding labels (such as vertical scales and branch
660	lengths) to the plots produced by this program. This may require you to
661	use the BMP, PICT, Idrawm, Xfig, PCX or Postscript file format and use a draw
662	or paint program to add them.
663	<P>
664	I would like to add more fonts. The present fonts are recoded versions of
665	the Hershey fonts. They are legally publicly distributable. Most other font
666	families on the market are not public domain and I cannot
667	afford to license them for distribution. Some people have noticed that the
668	Hershey fonts, which are drawn by a series of straight lines, have noticeable
669	angles in what are supposed to be curves, when they are printed on modern
670	laser printers and looked at closely. This is less a problem than one might
671	think since, fortunately, when scientific journals print a tree it is usually
672	shrunk so small that these imperfections (and often the tree itself)
673	are hard to see!
674	<P>
675	One more font that could be added from the Hershey font collection would be a
676	Greek font. If Greek users would
677	find that useful I could add it, but my impression is that they publish
678	mostly in English anyway.
679	<P>
680	<H2>Writing Code for a new Plotter, Printer or File Format</H2>
681	<P>
682	The C version of these programs consists of two C programs, "drawgram.c"
683	and "drawtree.c". Each of these has common sections of code compiled
684	into it called
685	"draw.c", "draw2.c" and a common header file, "draw.h". In addition
686	the Macintosh version requires two more files, "interface.c" and
687	"interface.h". All of the graphics commands that are common to both
688	programs will be found in "draw.c" and "draw2.c". The following instructions
689	for writing your own code to drive a different kind of printer,
690	plotter, or graphics file format, require you only to make changes in
691	"drawgraphics.c". The two programs can then be recompiled.
692	<P>
693	If you want to write code for other printers, plotters, or vector
694	file formats, this is not
695	too hard. The plotter option "U" is provided as a place for you to insert
696	your own code. Chris Meacham's system was to draw everything, including the
697	characters in the names and all curves, by drawing a series of straight
698	lines. Thus you need only master your plotter's commands for drawing
699	straight lines. In function "plotrparms"
700	you must set up the values of
701	variables "xunitspercm" and "yunitspercm", which are the number of units in
702	the x and y directions per centimeter, as well as variables "xsize" and
703	"ysize" which are the size of the plotting area in centimeters in the x
704	direction and the y direction. A variable "penchange" of a user-defined type
705	is set to "yes" or "no" depending on whether the commands to change the pen
706	must be issued when switching between plotting lines and drawing
707	characters. Even though dot-matrix printers do not have pens, penchange
708	should be set to "yes" for them. In function "plot" you must issue commands
709	to draw a line from the current
710	position (which is at (xnow, ynow) in the plotter's units) to the position
711	(xabs, yabs), under the
712	convention that the lower-left corner of the plotting area is (0.0, 0.0). In
713	functions "initplotter" and "finishplotter"
714	you must issue commands to
715	initialize the plotter and to finish plotting, respectively. If the pen is
716	to be changed an appropriate piece of code must be inserted in
717	function "penchange".
718	<P>
719	For dot matrix printers and raster graphics matters are a bit more complex. The
720	functions "plotrparms", "initplotter", "finishplotter" and "plot"
721	still respectively set up the parameters for the plotter, initialize it,
722	finish a plot, and plot one line. But now the plotting consists of drawing
723	dots into a two-dimensional array called "stripe". Once the plot is
724	finished this array is printed out. In most cases the array is not as tall
725	as a full plot: instead it is a rectangular strip across it. When the
726	program has finished drawing in ther strip, it prints it out and then
727	moves down the plot to the next strip. For example, for Hewlett-Packard
728	Laserjets we have defined the strip as 2550 dots wide and 20 dots deep. When
729	the program goes to draw a line, it draws it into the strip and ignores
730	any part of it that falls outside the strip. Thus the program does a complete
731	plotting into the strip, then prints it, then moves down the diagram by (in
732	this case) 20 dots, then does a complete plot into that strip, and so on.
733	<P>
734	To work with a new raster or dot matrix format, you will have to define the
735	desired width of a strip ("strpwide"), the desired depth ("strpdeep"), and
736	how many lines of bytes must be printed out to print a strip. For example
737	Toshiba P351 printers in graphics mode print strips of dots 1350 bits wide
738	by 24 bits deep, each column of 24 bits printing out as consecutive four bytes
739	with 6 bits each. In that case, one prints out a
740	strip by printing up to 1350 groups of 4 bytes. "strpdiv" is 4, and
741	"strpwide" is 1350, and "strpdeep" is 24. Procedure "striprint"
742	is the one that prints out a strip, and has special-case code for the
743	different printers and file formats. For file formats, all of which
744	print out a single row of dots at a time, the variable "strpdiv" is not
745	used. The variable "dotmatrix" is set to
746	"true" or "false" in function "plotrparms"
747	according to whether or not "strpdiv" is to be used. Procedure "plotdot"
748	sets a single dot in the array "strip" to 1 at position (xabs, yabs). The
749	coordinates run from 1 at the top of the plot to larger numbers as we
750	proceed down the page. Again, there is special-case code for different
751	printers and file formats in that
752	function.
753	You will probably want to read the code for some of the dot matrix or file
754	format options if you want to write code for one of them. Many of them
755	have provision for printing only part of a line, ignoring parts of it that
756	have no dots to print.
757	<P>
758	I would be happy to obtain the resulting code from you to consider
759	adding it to this listing so we can cover more kinds of plotters, printers,
760	and file formats.
761	<P>
762	<HR>
763	<P>
764	<H2>APPENDIX 1.</H2> Code to drive some other graphics devices.
765	These pieces of code are to be
766	inserted in the places reserved for the "Y" plotter option. The variables
767	necessary to run this
768	have already been incorporated into the
769	programs.
770	<P>
771	<H3>Calcomp plotters:</H3>
772	<P>
773	Calcomp's industrial-strength plotters are not as much a fixture of
774	University computer centers as they one were, but just in case you need to
775	use one, this code should work:
776	<P>
777	A global declaration needed near the front of drawtree.c:
778	<P>
779	<PRE>Char cchex[16];</PRE>
780	<P>
781	Code to be inserted into function plotrparms:
782	<P>
783	<PRE>
784	case 'Y':
785	plotter = other;
786	xunitspercm = 39.37;
787	yunitspercm = 39.37;
788	xsize = 25.0;
789	ysize = 25.0;
790	xposition = 12.5;
791	yposition = 0.0;
792	xoption = center;
793	yoption = above;
794	rotation = 0.0;
795	break;
796	</PRE>
797	<P>
798	Code to be inserted into function plot:
799	<P>
800	Declare these variables at the beginning of the function:
801	<P>
802	<PRE>
803	long n, inc, xinc, yinc, xlast, ylast, xrel,
804	yrel, xhigh, yhigh, xlow, ylow;
805	Char quadrant;
806	</PRE>
807	<P>
808	and insert this into the switch statement:
809	<P>
810	<PRE>
811	case other:
812	if (penstatus == pendown)
813	putc('H', plotfile);
814	else
815	putc('D', plotfile);
816	xrel = (long)floor(xabs + 0.5) - xnow;
817	yrel = (long)floor(yabs + 0.5) - ynow;
818	xnow = (long)floor(xabs + 0.5);
819	ynow = (long)floor(yabs + 0.5);
820	if (xrel > 0) {
821	if (yrel > 0)
822	quadrant = 'P';
823	else
824	quadrant = 'T';
825	} else if (yrel > 0)
826	quadrant = 'X';
827	else
828	quadrant = '1';
829	xrel = labs(xrel);
830	yrel = labs(yrel);
831	if (xrel > yrel)
832	n = xrel / 255 + 1;
833	else
834	n = yrel / 255 + 1;
835	xinc = xrel / n;
836	yinc = yrel / n;
837	xlast = xrel % n;
838	ylast = yrel % n;
839	xhigh = xinc / 16;
840	yhigh = yinc / 16;
841	xlow = xinc & 15;
842	ylow = yinc & 15;
843	for (i = 1; i <= n; i++)
844	fprintf(plotfile, "%c%c%c%c%c",
845	quadrant, cchex[xhigh - 1], cchex[xlow - 1], cchex[yhigh - 1],
846	cchex[ylow - 1]);
847	if (xlast != 0 \|\| ylast != 0)
848	fprintf(plotfile, "%c%c%c%c%c",
849	quadrant, cchex[-1], cchex[xlast - 1], cchex[-1],
850	cchex[ylast - 1]);
851	break;
852	</PRE>
853	<P>
854	Code to be inserted into function initplotter:
855	<P>
856	<PRE>
857	case other:
858	cchex[-1] = 'C';
859	cchex[0] = 'D';
860	cchex[1] = 'H';
861	cchex[2] = 'L';
862	cchex[3] = 'P';
863	cchex[4] = 'T';
864	cchex[5] = 'X';
865	cchex[6] = '1';
866	cchex[7] = '5';
867	cchex[8] = '9';
868	cchex[9] = '/';
869	cchex[10] = '=';
870	cchex[11] = '#';
871	cchex[12] = '"';
872	cchex[13] = '\'';
873	cchex[14] = '^';
874	xnow = 0.0;
875	ynow = 0.0;
876	fprintf(plotfile, "CCCCCCCCCC");
877	break;
878	</PRE>
879	<P>
880	Code to be inserted into function finishplotter:
881	<P>
882	<PRE>
883	case other:
884	plot(penup, 0.0, yrange + 50.0);
885	break;
886	</PRE>
887	</BODY>
888	</HTML>

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