#include "phylip.h" #include "draw.h" /* Version 3.696. Written by Joseph Felsenstein and Christopher A. Meacham. Additional code written by Hisashi Horino, Sean Lamont, Andrew Keefe, Daniel Fineman, Akiko Fuseki, Doug Buxton, Michal Palczewski, and James McGill. Copyright (c) 1986-2014, Joseph Felsenstein All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifdef MAC char* about_message = "Drawgram unrooted tree plotting program\r" "PHYLIP version 3.696\r" "(c) Copyright 1986-2014 by Joseph Felsenstein\r" "Written by Joseph Felsenstein and Christopher A. Meacham.\r" "Additional code written by Hisashi Horino, Sean Lamont, Andrew Keefe,\r" "Daniel Fineman, Akiko Fuseki, Doug Buxton and Michal Palczewski.\r" #endif //#define JAVADEBUG #define gap 0.5 /* distance in character heights between the end of a branch and the start of the name */ FILE *plotfile; char pltfilename[FNMLNGTH]; char trefilename[FNMLNGTH]; char *progname; long nextnode, strpwide, strpdeep, strpdiv, strptop, strpbottom, payge, numlines, hpresolution, iteration; boolean dotmatrix, haslengths, uselengths, empty, rescaled, firstscreens, pictbold, pictitalic, pictshadow, pictoutline, multiplot, finished; double xmargin, ymargin, topoflabels, bottomoflabels, rightoflabels, leftoflabels, tipspacing,maxheight, scale, xscale, yscale, xoffset, yoffset, nodespace, stemlength, treedepth, xnow, ynow, xunitspercm, yunitspercm, xsize, ysize, xcorner, ycorner, labelheight,labelrotation,expand, rootx, rooty, bscale, xx0, yy0, fontheight, maxx, minx, maxy, miny; double pagex, pagey, paperx, papery, hpmargin, vpmargin; double *textlength, *firstlet; striptype stripe; plottertype plotter, oldplotter; growth grows; treestyle style; node *root; pointarray nodep; pointarray treenode; fonttype font; long filesize; Char ch, resopts; double trweight; /* starting here, needed to make sccs version happy */ boolean goteof; node *grbg; long *zeros; /* ... down to here */ boolean canbeplotted; enum {yes, no} penchange, oldpenchange; static enum {weighted, intermediate, centered, inner, vshaped} nodeposition; winactiontype winaction; #ifndef OLDC /* function prototypes */ void initdrawgramnode(node **, node **, node *, long, long, long *, long *, initops, pointarray, pointarray, Char *, Char *, FILE *); void initialparms(void); char showparms(void); void getparms(char); void calctraverse(node *, double, double *); void calculate(void); void rescale(void); void setup_environment(Char *argv[]); void user_loop(void); void drawgram(char* intreename, char* fontfilename, char* plotfilename, char* plotfileopt, char* treegrows, char* stylekind, int usebranchlengths, double labelangle, int scalebranchlength, double branchscale, double breadthdepthratio, double stemltreedratio, double chhttipspratio, double xmarginratio, double ymarginratio, char* ancnodes, int dofinalplot, char* finalplotkind); /* function prototypes */ #endif void initdrawgramnode(node **p, node **grbg, node *q, long len, long nodei, long *ntips, long *parens, initops whichinit, pointarray treenode, pointarray nodep, Char *str, Char *ch, FILE *intree) { /* initializes a node */ long i; boolean minusread; double valyew, divisor; switch (whichinit) { case bottom: gnu(grbg, p); (*p)->index = nodei; (*p)->tip = false; for (i=0;inayme[i] = '\0'; nodep[(*p)->index - 1] = (*p); break; case nonbottom: gnu(grbg, p); (*p)->index = nodei; break; case tip: (*ntips)++; gnu(grbg, p); nodep[(*ntips) - 1] = *p; setupnode(*p, *ntips); (*p)->tip = true; (*p)->naymlength = len ; strncpy ((*p)->nayme, str, MAXNCH); break; case length: processlength(&valyew, &divisor, ch, &minusread, intree, parens); if (!minusread) (*p)->oldlen = valyew / divisor; else (*p)->oldlen = 0.0; break; case hsnolength: haslengths = false; break; default: /* cases hslength,treewt,unittrwt,iter */ break; /* should never occur */ } } /* initdrawgramnode */ void initialparms() { /* initialize parameters */ plotter = DEFPLOTTER; paperx=20.6375; pagex=20.6375; papery=26.9875; pagey=26.9875; strcpy(fontname,"Times-Roman"); plotrparms(spp); /* initial, possibly bogus, parameters */ style = phenogram; grows = horizontal; labelrotation = 90.0; nodespace = 3.0; stemlength = 0.05; treedepth = 0.5 / 0.95; rescaled = true; bscale = 1.0; uselengths = haslengths; if (uselengths) nodeposition = weighted; else nodeposition = centered; xmargin = 0.08 * xsize; ymargin = 0.08 * ysize; hpmargin = 0.02*pagex; vpmargin = 0.02*pagey; } /* initialparms */ char showparms() { char input[32]; Char ch; char cstr[32]; if (!firstscreens) clearit(); printf("\nRooted tree plotting program version %s\n\n", VERSION); printf("Here are the settings: \n"); printf(" 0 Screen type (IBM PC, ANSI): %s\n", ibmpc ? "IBM PC" : ansi ? "ANSI" : "(none)"); printf(" P Final plotting device: "); switch (plotter) { case lw: printf(" Postscript printer\n"); break; case pcl: printf(" HP Laserjet compatible printer (%d DPI)\n", (int) hpresolution); break; case epson: printf(" Epson dot-matrix printer\n"); break; case pcx: printf(" PCX file for PC Paintbrush drawing program (%s)\n", (resopts == 1) ? "EGA 640x350" : (resopts == 2) ? "VGA 800x600" : "VGA 1024x768"); break; case pict: printf(" Macintosh PICT file for drawing program\n"); break; case idraw: printf(" Idraw drawing program\n"); break; case fig: printf(" Xfig drawing program\n"); break; case hp: printf(" HPGL graphics language for HP plotters\n"); break; case xbm: printf(" X Bitmap file format (%d by %d resolution)\n", (int)xsize, (int)ysize); break; case bmp: printf(" MS-Windows Bitmap (%d by %d resolution)\n", (int)xsize, (int)ysize); break; case gif: printf(" Compuserve GIF format (%d by %d)\n",(int)xsize,(int)ysize); break; case ibm: printf(" IBM PC graphics (CGA, EGA, or VGA)\n"); break; case tek: printf(" Tektronix graphics screen\n"); break; case decregis: printf(" DEC ReGIS graphics (VT240 or DECTerm)\n"); break; case houston: printf(" Houston Instruments plotter\n"); break; case toshiba: printf(" Toshiba 24-pin dot matrix printer\n"); break; case citoh: printf(" Imagewriter or C.Itoh/TEC/NEC 9-pin dot matrix printer\n"); break; case oki: printf(" old Okidata 9-pin dot matrix printer\n"); break; case ray: printf(" Rayshade ray-tracing program file format\n"); break; case pov: printf(" POV ray-tracing program file format\n"); break; case vrml: printf(" VRML, Virtual Reality Markup Language\n"); break; case mac: case other: printf(" (Current output device unannounced)\n"); break; default: /*case not handled */ break; } printf(" (Preview no longer available)\n"); printf(" H Tree grows: "); printf((grows == vertical) ? "Vertically\n" : "Horizontally\n"); printf(" S Tree style: %s\n", (style == cladogram) ? "Cladogram" : (style == phenogram) ? "Phenogram" : (style == curvogram) ? "Curvogram" : (style == eurogram) ? "Eurogram" : (style == swoopogram) ? "Swoopogram" : "Circular"); printf(" B Use branch lengths: "); if (haslengths) { if (uselengths) printf("Yes\n"); else printf("No\n"); } else printf("(no branch lengths available)\n"); if (style != circular) { printf(" L Angle of labels:"); if (labelrotation < 10.0) printf("%5.1f\n", labelrotation); else printf("%6.1f\n", labelrotation); } printf(" R Scale of branch length:"); if (rescaled) printf(" Automatically rescaled\n"); else printf(" Fixed:%6.2f cm per unit branch length\n", bscale); printf(" D Depth/Breadth of tree:%6.2f\n", treedepth); printf(" T Stem-length/tree-depth:%6.2f\n", stemlength); printf(" C Character ht / tip space:%8.4f\n", 1.0 / nodespace); printf(" A Ancestral nodes: %s\n", (nodeposition == weighted) ? "Weighted" : (nodeposition == intermediate) ? "Intermediate" : (nodeposition == centered) ? "Centered" : (nodeposition == inner) ? "Inner" : "So tree is V-shaped"); if (plotter == lw || plotter == idraw || (plotter == fig && (labelrotation == 90.0 || labelrotation == 180.0 || labelrotation == 270.0 || labelrotation == 0.0)) || (plotter == pict && ((grows == vertical && labelrotation == 0.0) || (grows == horizontal && labelrotation == 90.0)))) printf(" F Font: %s\n",fontname); if ((plotter == pict && ((grows == vertical && labelrotation == 0.0) || (grows == horizontal && labelrotation == 90.0))) && (strcmp(fontname,"Hershey") != 0)) printf(" Q Pict Font Attributes: %s, %s, %s, %s\n", (pictbold ? "Bold" : "Medium"), (pictitalic ? "Italic" : "Regular"), (pictshadow ? "Shadowed": "Unshadowed"), (pictoutline ? "Outlined" : "Unoutlined")); if (plotter == ray) { printf(" M Horizontal margins:%6.2f pixels\n", xmargin); printf(" M Vertical margins:%6.2f pixels\n", ymargin); } else { printf(" M Horizontal margins:%6.2f cm\n", xmargin); printf(" M Vertical margins:%6.2f cm\n", ymargin); } printf(" # Pages per tree: "); /* Add 0.5 to clear up truncation problems. */ if (((int) ((pagex / paperx) + 0.5) == 1) && ((int) ((pagey / papery) + 0.5) == 1)) /* If we're only using one page per tree, */ printf ("one page per tree\n") ; else printf ("%.0f by %.0f pages per tree\n", (pagey-vpmargin) / (papery-vpmargin), (pagex-hpmargin) / (paperx-hpmargin)) ; for (;;) { printf("\n Y to accept these or type the letter for one to change\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); uppercase(&input[0]); ch=input[0]; if (plotter == idraw || plotter == lw) strcpy(cstr,"#Y0PVHSBLMRDTCAF"); else if (((plotter == fig) && (labelrotation == 0.0)) || (labelrotation == 90.0 ) || (labelrotation == 180.0) || (labelrotation == 270.0)) strcpy(cstr,"#Y0PVHSBLMRDTCAFQ"); else if (plotter == pict){ if (((grows == vertical && labelrotation == 0.0) || (grows == horizontal && labelrotation == 90.0))) strcpy(cstr,"#Y0PVHSBLMRDTCAFQ"); else strcpy(cstr,"#Y0PVHSBLMRDTCA"); } else strcpy(cstr,"#Y0PVHSBLMRDTCA"); if (strchr(cstr,ch)) break; printf(" That letter is not one of the menu choices. Type\n"); } return ch; } /* showparms */ void getparms(char numtochange) { /* get from user the relevant parameters for the plotter and diagram */ long loopcount; Char ch; char input[100]; boolean ok; int i, m, n; n = (int)((pagex-hpmargin-0.01)/(paperx-hpmargin)+1.0); m = (int)((pagey-vpmargin-0.01)/(papery-vpmargin)+1.0); switch (numtochange) { case '0': initterminal(&ibmpc, &ansi); break; case 'P': getplotter(); break; case 'H': if (grows == vertical) grows = horizontal; else grows = vertical; break; case 'S': clearit() ; printf("What style tree is this to be (currently set to %s):\n", (style == cladogram) ? "Cladogram" : (style == phenogram) ? "Phenogram" : (style == curvogram) ? "Curvogram" : (style == eurogram) ? "Eurogram" : (style == swoopogram) ? "Swoopogram" : "Circular") ; printf(" C Cladogram -- v-shaped \n") ; printf(" P Phenogram -- branches are square\n") ; printf(" V Curvogram -- branches are 1/4 of an ellipse\n") ; printf(" E Eurogram -- branches angle outward, then up\n"); printf(" S Swoopogram -- branches curve outward then reverse\n") ; printf(" O Circular tree\n"); do { printf("\n Type letter of style to change to (C, P, V, E, S or O):\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%c%*[^\n]", &ch); getchar(); uppercase(&ch); } while (ch != 'C' && ch != 'P' && ch != 'V' && ch != 'E' && ch != 'S' && ch != 'O'); switch (ch) { case 'C': style = cladogram; break; case 'P': style = phenogram; break; case 'E': style = eurogram; break; case 'S': style = swoopogram; break; case 'V': style = curvogram; break; case 'O': style = circular; treedepth = 1.0; break; } break; case 'B': if (haslengths) { uselengths = !uselengths; if (!uselengths) nodeposition = weighted; else nodeposition = intermediate; } else { printf("Cannot use lengths since not all of them exist\n"); uselengths = false; } break; case 'L': clearit(); printf("\n(Considering the tree as if it \"grew\" vertically:)\n"); printf("Are the labels to be plotted vertically (90),\n"); printf(" horizontally (0), or at a 45-degree angle?\n"); loopcount = 0; do { printf(" Choose an angle in degrees from 90 to 0:\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%lf%*[^\n]", &labelrotation); getchar(); uppercase(&ch); countup(&loopcount, 10); } while (labelrotation < 0.0 && labelrotation > 90.0); break; case 'M': clearit(); printf("\nThe tree will be drawn to fit in a rectangle which has \n"); printf(" margins in the horizontal and vertical directions of:\n"); if (plotter == ray) { printf( "%6.2f pixels (horizontal margin) and%6.2f pixels (vertical margin)\n", xmargin, ymargin); } else { printf("%6.2f cm (horizontal margin) and%6.2f cm (vertical margin)\n", xmargin, ymargin); } putchar('\n'); loopcount = 0; do { if (plotter == ray) printf(" New value (in pixels) of horizontal margin?\n"); else printf(" New value (in cm) of horizontal margin?\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%lf%*[^\n]", &xmargin); getchar(); ok = ((unsigned)xmargin < xsize / 2.0); if (!ok) printf(" Impossible value. Please retype it.\n"); countup(&loopcount, 10); } while (!ok); loopcount = 0; do { if (plotter == ray) printf(" New value (in pixels) of vertical margin?\n"); else printf(" New value (in cm) of vertical margin?\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%lf%*[^\n]", &ymargin); getchar(); ok = ((unsigned)ymargin < ysize / 2.0); if (!ok) printf(" Impossible value. Please retype it.\n"); countup(&loopcount, 10); } while (!ok); break; case 'R': rescaled = !rescaled; if (!rescaled) { printf("Centimeters per unit branch length?\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%lf%*[^\n]", &bscale); getchar(); } break; case 'D': printf("New value of depth of tree as fraction of its breadth?\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%lf%*[^\n]", &treedepth); getchar(); break; case 'T': loopcount = 0; do { printf("New value of stem length as fraction of tree depth?\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%lf%*[^\n]", &stemlength); getchar(); countup(&loopcount, 10); } while ((unsigned)stemlength >= 0.9); break; case 'C': printf("New value of character height as fraction of tip spacing?\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%lf%*[^\n]", &nodespace); getchar(); nodespace = 1.0 / nodespace; break; case '#': loopcount = 0; for (;;){ clearit(); printf(" Page Specifications Submenu\n\n"); printf(" L Output size in pages: %.0f down by %.0f across\n", (pagey / papery), (pagex / paperx)); printf(" P Physical paper size: %1.5f by %1.5f cm\n",paperx,papery); printf(" O Overlap Region: %1.5f %1.5f cm\n",hpmargin,vpmargin); printf(" M main menu\n"); getstryng(input); ch = input[0]; uppercase(&ch); switch (ch){ case 'L': printf("Number of pages in height:\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); m = atoi(input); printf("Number of pages in width:\n"); getstryng(input); n = atoi(input); break; case 'P': printf("Paper Width (in cm):\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); paperx = atof(input); printf("Paper Height (in cm):\n"); getstryng(input); papery = atof(input); break; case 'O': printf("Horizontal Overlap (in cm):"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); hpmargin = atof(input); printf("Vertical Overlap (in cm):"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); vpmargin = atof(input); case 'M': break; default: printf("Please enter L, P, O , or M.\n"); break; } pagex = ((double)n * (paperx-hpmargin)+hpmargin); pagey = ((double)m * (papery-vpmargin)+vpmargin); if (ch == 'M') break; countup(&loopcount, 10); } break; case 'A': clearit(); printf("Should interior node positions:\n"); printf(" be Intermediate between their immediate descendants,\n"); printf(" Weighted average of tip positions\n"); printf(" Centered among their ultimate descendants\n"); printf(" iNnermost of immediate descendants\n"); printf(" or so that tree is V-shaped\n"); loopcount = 0; do { printf(" (type I, W, C, N or V):\n"); #ifdef WIN32 phyFillScreenColor(); #endif fflush(stdout); scanf("%c%*[^\n]", &ch); getchar(); uppercase(&ch); countup(&loopcount, 10); } while (ch != 'I' && ch != 'W' && ch != 'C' && ch != 'N' && ch != 'V'); switch (ch) { case 'W': nodeposition = weighted; break; case 'I': nodeposition = intermediate; break; case 'C': nodeposition = centered; break; case 'N': nodeposition = inner; break; case 'V': nodeposition = vshaped; break; } break; case 'F': if (plotter == fig){ for (i=0;i<34;++i) printf("%s\n",figfontname(i)); loopcount = 0; for (;;){ printf("Fontname:"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(fontname); if (isfigfont(fontname)) break; printf("Invalid font name for fig.\n"); printf("Enter one of the following fonts or \"Hershey\" for default" " font\n"); countup(&loopcount, 10); } } else { printf("Enter font name or \"Hershey\" for the default font\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(fontname); } break; case 'Q': clearit(); loopcount = 0; do { printf("Italic? (Y/N)\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); input[0] = toupper(input[0]); countup(&loopcount, 10); } while (input[0] != 'Y' && input[0] != 'N'); pictitalic = (input[0] == 'Y'); loopcount = 0; do { printf("Bold? (Y/N)\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); input[0] = toupper(input[0]); countup(&loopcount, 10); } while (input[0] != 'Y' && input[0] != 'N'); pictbold = (input[0] == 'Y'); loopcount = 0; do { printf("Shadow? (Y/N)\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); input[0] = toupper(input[0]); countup(&loopcount, 10); } while (input[0] != 'Y' && input[0] != 'N'); pictshadow = (input[0] == 'Y'); loopcount = 0; do { printf("Outline? (Y/N)\n"); #ifdef WIN32 phyFillScreenColor(); #endif getstryng(input); input[0] = toupper(input[0]); countup(&loopcount, 10); } while (input[0] != 'Y' && input[0] != 'N'); pictoutline = (input[0] == 'Y');break; } } /* getparms */ void calctraverse(node *p, double lengthsum, double *tipx) { /* traverse to establish initial node coordinates */ double x1, y1, x2, y2, x3, x4, x5, w1, w2, sumwx, sumw, nodeheight; node *pp, *plast, *panc; if (p == root) nodeheight = 0.0; else if (uselengths) nodeheight = lengthsum + fabs(p->oldlen); else nodeheight = 1.0; if (nodeheight > maxheight) maxheight = nodeheight; if (p->tip) { p->xcoord = *tipx; p->tipsabove = 1; if (uselengths) p->ycoord = nodeheight; else p->ycoord = 1.0; *tipx += tipspacing; return; } sumwx = 0.0; sumw = 0.0; p->tipsabove = 0; pp = p->next; x3 = 0.0; do { calctraverse(pp->back, nodeheight, tipx); p->tipsabove += pp->back->tipsabove; sumw += pp->back->tipsabove; sumwx += pp->back->tipsabove * pp->back->xcoord; if (fabs(pp->back->xcoord - 0.5) < fabs(x3 - 0.5)) x3 = pp->back->xcoord; plast = pp; pp = pp->next; } while (pp != p); x1 = p->next->back->xcoord; x2 = plast->back->xcoord; y1 = p->next->back->ycoord; y2 = plast->back->ycoord; switch (nodeposition) { case weighted: w1 = y1 - p->ycoord; w2 = y2 - p->ycoord; if (w1 + w2 <= 0.0) p->xcoord = (x1 + x2) / 2.0; else p->xcoord = (w2 * x1 + w1 * x2) / (w1 + w2); break; case intermediate: p->xcoord = (x1 + x2) / 2.0; break; case centered: p->xcoord = sumwx / sumw; break; case inner: p->xcoord = x3; break; case vshaped: if (iteration > 1) { if (!(p == root)) { panc = nodep[p->back->index-1]; w1 = p->ycoord - panc->ycoord; w2 = y1 - p->ycoord; if (w1+w2 < 0.000001) x4 = (x1+panc->xcoord)/2.0; else x4 = (w1*x1+w2*panc->xcoord)/(w1+w2); w2 = y2 - p->ycoord; if (w1+w2 < 0.000001) x5 = (x2+panc->xcoord)/2.0; else x5 = (w1*x2+w2*panc->xcoord)/(w1+w2); if (panc->xcoord < p->xcoord) p->xcoord = x5; else p->xcoord = x4; } else { if ((y1-2*p->ycoord+y2) < 0.000001) p->xcoord = (x1+x2)/2; else p->xcoord = ((y2-p->ycoord)*x1+(y1-p->ycoord))/(y1-2*p->ycoord+y2); } } break; } if (uselengths) { p->ycoord = nodeheight; return; } if (nodeposition != inner) { p->ycoord = (y1 + y2 - sqrt((y1 + y2) * (y1 + y2) - 4 * (y1 * y2 - (x2 - p->xcoord) * (p->xcoord - x1)))) / 2.0; /* this formula comes from the requirement that the vector from (x,y) to (x1,y1) be at right angles to that from (x,y) to (x2,y2) */ return; } if (fabs(x1 - 0.5) > fabs(x2 - 0.5)) { p->ycoord = y1 + x1 - x2; w1 = y2 - p->ycoord; } else { p->ycoord = y2 + x1 - x2; w1 = y1 - p->ycoord; } if (w1 < epsilon) p->ycoord -= fabs(x1 - x2); } /* calctraverse */ void calculate() { /* compute coordinates for tree */ double tipx; double sum, temp, maxtextlength, maxfirst=0, leftfirst, angle; double lef = 0.0, rig = 0.0, top = 0.0, bot = 0.0; double *firstlet, *textlength; long i; firstlet = (double *)Malloc(nextnode*sizeof(double)); textlength = (double *)Malloc(nextnode*sizeof(double)); for (i = 0; i < nextnode; i++) { nodep[i]->xcoord = 0.0; nodep[i]->ycoord = 0.0; if (nodep[i]->naymlength > 0) firstlet[i] = lengthtext(nodep[i]->nayme, 1L,fontname,font); else firstlet[i] = 0.0; } i = 0; do i++; while (!nodep[i]->tip); leftfirst = firstlet[i]; maxheight = 0.0; maxtextlength = 0.0; //printf("fontname: %s\n",fontname); for (i = 0; i < nextnode; i++) { if (nodep[i]->tip) { textlength[i] = lengthtext(nodep[i]->nayme, nodep[i]->naymlength, fontname, font); //printf("i: %li textlength[i]: %f nodep[i]->nayme: %s nodep[i]->naymlength: %li\n", i, textlength[i], nodep[i]->nayme, nodep[i]->naymlength); if (textlength[i]-0.5*firstlet[i] > maxtextlength) { maxtextlength = textlength[i]-0.5*firstlet[i]; maxfirst = firstlet[i]; } } } //printf("maxtextlength: %f maxfirst: %f\n", maxtextlength, maxfirst); maxtextlength = maxtextlength + 0.5*maxfirst; fontheight = heighttext(font,fontname); if (style == circular) { if (grows == vertical) angle = pi / 2.0; else angle = 2.0*pi; } else angle = pi * labelrotation / 180.0; maxtextlength /= fontheight; maxfirst /= fontheight; leftfirst /= fontheight; for (i = 0; i < nextnode; i++) { if (nodep[i]->tip) { textlength[i] /= fontheight; firstlet[i] /= fontheight; } } if (spp > 1) labelheight = 1.0 / (nodespace * (spp - 1)); else labelheight = 1.0 / nodespace; if (angle < pi / 6.0) tipspacing = (nodespace + cos(angle) * (maxtextlength - 0.5*maxfirst)) * labelheight; else if (spp > 1) { if (style == circular) { tipspacing = 1.0 / spp; } else tipspacing = 1.0 / (spp - 1.0); } else tipspacing = 1.0; finished = false; iteration = 1; do { if (style == circular) tipx = 1.0/(2.0*(double)spp); else tipx = 0.0; sum = 0.0; calctraverse(root, sum, &tipx); iteration++; } while ((nodeposition == vshaped) && (iteration < 4*spp)); rooty = root->ycoord; labelheight *= 1.0 - stemlength; for (i = 0; i < nextnode; i++) { if (rescaled) { if (style != circular) nodep[i]->xcoord *= 1.0 - stemlength; nodep[i]->ycoord = stemlength * treedepth + (1.0 - stemlength) * treedepth * (nodep[i]->ycoord - rooty) / (maxheight - rooty); nodep[i]->oldtheta = angle; } else { nodep[i]->xcoord = nodep[i]->xcoord * (maxheight - rooty) / treedepth; nodep[i]->ycoord = stemlength / (1 - stemlength) * (maxheight - rooty) + nodep[i]->ycoord; nodep[i]->oldtheta = angle; } } topoflabels = 0.0; bottomoflabels = 0.0; leftoflabels = 0.0; rightoflabels = 0.0; if (style == circular) { for (i = 0; i < nextnode; i++) { temp = nodep[i]->xcoord; if (grows == vertical) { nodep[i]->xcoord = (1.0+nodep[i]->ycoord * cos((1.5-2.0*temp)*pi)/treedepth)/2.0; nodep[i]->ycoord = (1.0+nodep[i]->ycoord * sin((1.5-2.0*temp)*pi)/treedepth)/2.0; nodep[i]->oldtheta = (1.5-2.0*temp)*pi; } else { nodep[i]->xcoord = (1.0+nodep[i]->ycoord * cos((1.0-2.0*temp)*pi)/treedepth)/2.0; nodep[i]->ycoord = (1.0+nodep[i]->ycoord * sin((1.0-2.0*temp)*pi)/treedepth)/2.0; nodep[i]->oldtheta = (1.0-2.0*temp)*pi; } } tipspacing *= 2.0*pi; } maxx = nodep[0]->xcoord; maxy = nodep[0]->ycoord; minx = nodep[0]->xcoord; if (style == circular) miny = nodep[0]->ycoord; else miny = 0.0; for (i = 1; i < nextnode; i++) { if (nodep[i]->xcoord > maxx) maxx = nodep[i]->xcoord; if (nodep[i]->ycoord > maxy) maxy = nodep[i]->ycoord; if (nodep[i]->xcoord < minx) minx = nodep[i]->xcoord; if (nodep[i]->ycoord < miny) miny = nodep[i]->ycoord; } if (style == circular) { for (i = 0; i < nextnode; i++) { if (nodep[i]->tip) { angle = nodep[i]->oldtheta; if (cos(angle) < 0.0) angle -= pi; top = (nodep[i]->ycoord - maxy) / labelheight + sin(nodep[i]->oldtheta); rig = (nodep[i]->xcoord - maxx) / labelheight + cos(nodep[i]->oldtheta); bot = (miny - nodep[i]->ycoord) / labelheight - sin(nodep[i]->oldtheta); lef = (minx - nodep[i]->xcoord) / labelheight - cos(nodep[i]->oldtheta); if (cos(nodep[i]->oldtheta) > 0) { if (sin(angle) > 0.0) top += sin(angle) * textlength[i]; top += sin(angle - 1.25 * pi) * gap * firstlet[i]; if (sin(angle) < 0.0) bot -= sin(angle) * textlength[i]; bot -= sin(angle - 0.75 * pi) * gap * firstlet[i]; if (sin(angle) > 0.0) rig += cos(angle - 0.75 * pi) * gap * firstlet[i]; else rig += cos(angle - 1.25 * pi) * gap * firstlet[i]; rig += cos(angle) * textlength[i]; if (sin(angle) > 0.0) lef -= cos(angle - 1.25 * pi) * gap * firstlet[i]; else lef -= cos(angle - 0.75 * pi) * gap * firstlet[i]; } else { if (sin(angle) < 0.0) top -= sin(angle) * textlength[i]; top += sin(angle + 0.25 * pi) * gap * firstlet[i]; if (sin(angle) > 0.0) bot += sin(angle) * textlength[i]; bot -= sin(angle - 0.25 * pi) * gap * firstlet[i]; if (sin(angle) > 0.0) rig += cos(angle - 0.25 * pi) * gap * firstlet[i]; else rig += cos(angle + 0.25 * pi) * gap * firstlet[i]; if (sin(angle) < 0.0) rig += cos(angle) * textlength[i]; if (sin(angle) > 0.0) lef -= cos(angle + 0.25 * pi) * gap * firstlet[i]; else lef -= cos(angle - 0.25 * pi) * gap * firstlet[i]; lef += cos(angle) * textlength[i]; } } if (top > topoflabels) topoflabels = top; if (bot > bottomoflabels) bottomoflabels = bot; if (rig > rightoflabels) rightoflabels = rig; if (lef > leftoflabels) leftoflabels = lef; } topoflabels *= labelheight; bottomoflabels *= labelheight; leftoflabels *= labelheight; rightoflabels *= labelheight; } if (style != circular) { //printf("labelheight: %f angle: %f maxtextlength: %f maxfirst: %f\n", labelheight, angle, maxtextlength, maxfirst); topoflabels = labelheight * (1.0 + sin(angle) * (maxtextlength - 0.5 * maxfirst) + cos(angle) * 0.5 * maxfirst); rightoflabels = labelheight * (cos(angle) * (textlength[nextnode-1] - 0.5 * maxfirst) + sin(angle) * 0.5); leftoflabels = labelheight * (cos(angle) * leftfirst * 0.5 + sin(angle) * 0.5); } rooty = miny; free(firstlet); free(textlength); } /* calculate */ void rescale() { /* compute coordinates of tree for plot device */ long i; double treeheight, treewidth, extrax, extray, temp; //printf("maxy: %f miny: %f maxx: %f minx: %f\n", maxy, miny, maxx, minx); treeheight = maxy - miny; treewidth = maxx - minx; if (style == circular) { treewidth = 1.0; treeheight = 1.0; if (!rescaled) { if (uselengths) { labelheight *= (maxheight - rooty) / treedepth; topoflabels *= (maxheight - rooty) / treedepth; bottomoflabels *= (maxheight - rooty) / treedepth; leftoflabels *= (maxheight - rooty) / treedepth; rightoflabels *= (maxheight - rooty) / treedepth; treewidth *= (maxheight - rooty) / treedepth; } } } treewidth += rightoflabels + leftoflabels; treeheight += topoflabels + bottomoflabels; //printf("rightoflabels: %f leftoflabels: %f topoflabels: %f bottomoflabels: %f treewidth: %f treeheight: %f\n", rightoflabels, leftoflabels, topoflabels, bottomoflabels, treewidth, treeheight); if (grows == vertical) { if (!rescaled) expand = bscale; else { expand = (xsize - 2 * xmargin) / treewidth; if ((ysize - 2 * ymargin) / treeheight < expand) expand = (ysize - 2 * ymargin) / treeheight; } extrax = (xsize - 2 * xmargin - treewidth * expand) / 2.0; extray = (ysize - 2 * ymargin - treeheight * expand) / 2.0; } else { if (!rescaled) expand = bscale; else { expand = (ysize - 2 * ymargin) / treewidth; if ((xsize - 2 * xmargin) / treeheight < expand) expand = (xsize - 2 * xmargin) / treeheight; } extrax = (xsize - 2 * xmargin - treeheight * expand) / 2.0; extray = (ysize - 2 * ymargin - treewidth * expand) / 2.0; } //printf("in rescale rescaled: %i treewidth: %f treeheight: %f expand: %f\n", rescaled, treewidth, treeheight, expand); //printf("xsize: %f xmargin: %f ysize: %f ymargin: %f\n", xsize, xmargin, ysize, ymargin); for (i = 0; i < nextnode; i++) { //printf("before rescale i: %li, nodep[i]: %f, %f\n", i, nodep[i]->xcoord, nodep[i]->ycoord); nodep[i]->xcoord = expand * (nodep[i]->xcoord + leftoflabels); nodep[i]->ycoord = expand * (nodep[i]->ycoord + bottomoflabels); if ((style != circular) && (grows == horizontal)) { temp = nodep[i]->ycoord; nodep[i]->ycoord = expand * treewidth - nodep[i]->xcoord; nodep[i]->xcoord = temp; } nodep[i]->xcoord += xmargin + extrax; nodep[i]->ycoord += ymargin + extray; //printf("after rescale i: %li, nodep[i]: %f, %f\n", i, nodep[i]->xcoord, nodep[i]->ycoord); } if (style == circular) { xx0 = xmargin+extrax+expand*(leftoflabels + 0.5); yy0 = ymargin+extray+expand*(bottomoflabels + 0.5); } else if (grows == vertical) rooty = ymargin + extray; else rootx = xmargin + extrax; } /* rescale */ void plottree(node *p, node *q) { /* plot part or all of tree on the plotting device */ long i; double x00=0, y00=0, x1, y1, x2, y2, x3, y3, x4, y4, cc, ss, f, g, fract=0, minny, miny; node *pp; //printf("p: %p q: %p xscale: %f xoffset: %f yscale: %f yoffset %f\n", p, q, xscale, xoffset, yscale, yoffset); // fflush(stdout); x2 = xscale * (xoffset + p->xcoord); y2 = yscale * (yoffset + p->ycoord); if (style == circular) { x00 = xscale * (xx0 + xoffset); y00 = yscale * (yy0 + yoffset); } if (p != root) { x1 = xscale * (xoffset + q->xcoord); y1 = yscale * (yoffset + q->ycoord); //printf("branch p: %f, %f q: %f, %f\n",p->xcoord, p->ycoord, q->xcoord, q->ycoord); //fflush(stdout); switch (style) { case cladogram: plot(penup, x1, y1); plot(pendown, x2, y2); break; case phenogram: plot(penup, x1, y1); if (grows == vertical) plot(pendown, x2, y1); else plot(pendown, x1, y2); plot(pendown, x2, y2); break; case curvogram: plot(penup, x1, y1) ; curvespline(x1,y1,x2,y2,(boolean)(grows == vertical),20); break; case eurogram: plot(penup, x1, y1); if (grows == vertical) plot(pendown, x2, (2 * y1 + y2) / 3); else plot(pendown, (2 * x1 + x2) / 3, y2); plot(pendown, x2, y2); break; case swoopogram: plot(penup, x1, y1); if ((grows == vertical && fabs(y1 - y2) >= epsilon) || (grows == horizontal && fabs(x1 - x2) >= epsilon)) { if (grows == vertical) miny = p->ycoord; else miny = p->xcoord; pp = q->next; while (pp != q) { if (grows == vertical) minny = pp->back->ycoord; else minny = pp->back->xcoord; if (minny < miny) miny = minny; pp = pp->next; } if (grows == vertical) miny = yscale * (yoffset + miny); else miny = xscale * (xoffset + miny); if (grows == vertical) fract = 0.3333 * (miny - y1) / (y2 - y1); else fract = 0.3333 * (miny - x1) / (x2 - x1); } if ((grows == vertical && fabs(y1 - y2) >= epsilon) || (grows == horizontal && fabs(x1 - x2) >= epsilon)) { if (grows == vertical) miny = p->ycoord; else miny = p->xcoord; pp = q->next; while (pp != q) { if (grows == vertical) minny = pp->back->ycoord; else minny = pp->back->xcoord; if (minny < miny) miny = minny; pp = pp->next; } if (grows == vertical) miny = yscale * (yoffset + miny); else miny = xscale * (xoffset + miny); if (grows == vertical) fract = 0.3333 * (miny - y1) / (y2 - y1); else fract = 0.3333 * (miny - x1) / (x2 - x1); } swoopspline(x1,y1,x1+fract*(x2-x1),y1+fract*(y2-y1), x2,y2,(boolean)(grows != vertical),segments); break; case circular: plot(penup, x1, y1); if (fabs(x1-x00)+fabs(y1-y00) > 0.00001) { g = ((x1-x00)*(x2-x00)+(y1-y00)*(y2-y00)) /sqrt(((x1-x00)*(x1-x00)+(y1-y00)*(y1-y00)) *((x2-x00)*(x2-x00)+(y2-y00)*(y2-y00))); if (g > 1.0) g = 1.0; if (g < -1.0) g = -1.0; f = acos(g); if ((x2-x00)*(y1-y00)>(x1-x00)*(y2-y00)) f = -f; if (fabs(g-1.0) > 0.0001) { cc = cos(f/segments); ss = sin(f/segments); x3 = x1; y3 = y1; for (i = 1; i <= segments; i++) { x4 = x00 + cc*(x3-x00) - ss*(y3-y00); y4 = y00 + ss*(x3-x00) + cc*(y3-y00); x3 = x4; y3 = y4; plot(pendown, x3, y3); } } } plot(pendown, x2, y2); break; } } else { if (style == circular) { x1 = x00; y1 = y00; } else { if (grows == vertical) { x1 = xscale * (xoffset + p->xcoord); y1 = yscale * (yoffset + rooty); } else { x1 = xscale * (xoffset + rootx); y1 = yscale * (yoffset + p->ycoord); } } //printf("root p: %f, %f q: %f, %f\n",x2, y2, x1, y1); //fflush(stdout); plot(penup, x1, y1); plot(pendown, x2, y2); } if (p->tip) return; pp = p->next; while (pp != p) { plottree(pp->back, p); pp = pp->next; } } /* plottree */ void plotlabels(char *fontname) { long i; double compr, dx = 0, dy = 0, labangle, cosl, sinl, cosv, sinv, vec; boolean left, right; node *lp; double *firstlet; firstlet = (double *)Malloc(nextnode*sizeof(double)); textlength = (double *)Malloc(nextnode*sizeof(double)); compr = xunitspercm / yunitspercm; if (penchange == yes) changepen(labelpen); for (i = 0; i < nextnode; i++) { if (nodep[i]->tip) { lp = nodep[i]; firstlet[i] = lengthtext(nodep[i]->nayme,1L,fontname,font) /fontheight; textlength[i] = lengthtext(nodep[i]->nayme, nodep[i]->naymlength, fontname, font)/fontheight; labangle = nodep[i]->oldtheta; if (cos(labangle) < 0.0) labangle += pi; cosl = cos(labangle); sinl = sin(labangle); vec = sqrt(1.0+firstlet[i]*firstlet[i]); cosv = firstlet[i]/vec; sinv = 1.0/vec; if (style == circular) { right = cos(nodep[i]->oldtheta) > 0.0; left = !right; if (right) { dx = labelheight * expand * cos(nodep[i]->oldtheta); dy = labelheight * expand * sin(nodep[i]->oldtheta); dx += labelheight * expand * 0.5 * vec * (-cosl*sinv+sinl*cosv); dy += labelheight * expand * 0.5 * vec * (-sinl*sinv-cosl*cosv); } if (left) { dx = labelheight * expand * cos(nodep[i]->oldtheta); dy = labelheight * expand * sin(nodep[i]->oldtheta); dx -= labelheight * expand * textlength[i] * cosl; dy -= labelheight * expand * textlength[i] * sinl; dx += labelheight * expand * 0.5 * vec * (cosl*cosv+sinl*sinv); dy += labelheight * expand * 0.5 * vec * (-sinl*cosv-cosl*sinv); } } else { dx = labelheight * expand * cos(nodep[i]->oldtheta); dy = labelheight * expand * sin(nodep[i]->oldtheta); dx -= labelheight * expand * 0.5 * firstlet[i] * (cosl-sinl*sinv); dy -= labelheight * expand * 0.5 * firstlet[i] * (sinl+cosl*sinv); } if (style == circular) { plottext(lp->nayme, lp->naymlength, labelheight * expand * xscale / compr, compr, xscale * (lp->xcoord + dx + xoffset), yscale * (lp->ycoord + dy + yoffset), 180 * (-labangle) / pi, font,fontname); } else { if (grows == vertical) plottext(lp->nayme, lp->naymlength, labelheight * expand * xscale / compr, compr, xscale * (lp->xcoord + dx + xoffset), yscale * (lp->ycoord + dy + yoffset), -labelrotation, font,fontname); else plottext(lp->nayme, lp->naymlength, labelheight * expand * yscale, compr, xscale * (lp->xcoord + dy + xoffset), yscale * (lp->ycoord - dx + yoffset), 90.0 - labelrotation, font,fontname); } } } if (penchange == yes) changepen(treepen); free(firstlet); free(textlength); } /* plotlabels */ void setup_environment(Char *argv[]) { boolean firsttree; /* Set up all kinds of fun stuff */ #ifdef TURBOC if ((registerbgidriver(EGAVGA_driver) <0) || (registerbgidriver(Herc_driver) <0) || (registerbgidriver(CGA_driver) <0)){ printf("Graphics error: %s ",grapherrormsg(graphresult())); exit(-1);} #endif /* Open in binary: ftell() is broken for UNIX line-endings under WIN32 */ openfile(&intree,INTREE,"input tree file", "rb",argv[0],trefilename); printf("DRAWGRAM from PHYLIP version %s\n",VERSION); printf("Reading tree ... \n"); firsttree = true; allocate_nodep(&nodep, &intree, &spp); treeread (intree, &root, treenode, &goteof, &firsttree, nodep, &nextnode, &haslengths, &grbg, initdrawgramnode,true,-1); root->oldlen = 0.0; printf("Tree has been read.\n"); printf("Loading the font .... \n"); loadfont(font,FONTFILE,argv[0]); printf("Font loaded.\n"); ansi = ANSICRT; ibmpc = IBMCRT; firstscreens = true; initialparms(); canbeplotted = false; } /* setup_environment */ void user_loop() { char input_char; long stripedepth; while (!canbeplotted) { do { input_char=showparms(); firstscreens = false; if (input_char != 'Y') getparms(input_char); } while (input_char != 'Y'); #ifdef JAVADEBUG // JRM Debug printf("\n***internal parameters***\n"); printf("fontname: %s\n", fontname); printf("plotter: %i\n",plotter); printf("paperx: %f\n",paperx); printf("papery: %f\n",papery); printf("hpmargin: %f\n",hpmargin); printf("vpmargin: %f\n",vpmargin); printf("pagex: %f\n",pagex); printf("pagey: %f\n",pagey); printf("xmargin: %f\n",xmargin); printf("ymargin: %f\n",ymargin); printf("firstscreens: %i\n",firstscreens); printf("canbeplotted: %i\n",canbeplotted); printf("style: %i\n",style); printf("grows: %i\n",grows); printf("labelrotation: %f\n",labelrotation); printf("nodespace: %f\n",nodespace); printf("stemlength: %f\n",stemlength); printf("treedepth: %f\n",treedepth); printf("bscale: %f\n",bscale); printf("uselengths: %i\n",uselengths); printf("nodeposition: %i\n",nodeposition); printf("dotmatrix: %i\n",dotmatrix); printf("xsize: %f\n", xsize); printf("ysize: %f\n", ysize); fflush(stdout); #endif if (dotmatrix) { stripedepth = allocstripe(stripe,(strpwide/8), ((long)(yunitspercm * ysize))); //printf("strpwide: %li, yunitspercm: %f, ysize: %f\n",strpwide, yunitspercm, ysize); //printf("stripedepth: %li\n", stripedepth); //fflush(stdout); strpdeep = stripedepth; strpdiv = stripedepth; } plotrparms(spp); //printf("after plotrparms\n"); //printf("strpdeep: %li, yunitspercm: %f, ysize: %f\n",strpdeep, yunitspercm, ysize); //fflush(stdout); numlines = dotmatrix ? ((long)floor(yunitspercm * ysize + 0.5) / strpdeep) :1; //printf("dotmatrix: %i numlines: %li\n",dotmatrix, numlines); //fflush(stdout); xscale = xunitspercm; yscale = yunitspercm; calculate(); rescale(); canbeplotted = true; } } /* user_loop */ void drawgram( char *intreename, char *fontfilename, char *plotfilename, char *plotfileopt, char *treegrows, char *stylekind, int usebranchlengths, double labelangle, int scalebranchlength, double branchscale, double breadthdepthratio, double stemltreedratio, double chhttipspratio, double xmarginratio, double ymarginratio, char *ancnodes, int dofinalplot, char* finalplotkind) { //printf("hello from DrawGram\n"); // setup before data is translated char *previewfilename = "JavaPreview.ps"; // from init javarun = true; ansi = ANSICRT; ibmpc = IBMCRT; firstscreens = false; canbeplotted = true; dotmatrix = false; boolean wasplotted = false; grbg = NULL; progname = "Drawgram"; initialparms(); // translate Java doubles to Drawgram local variables labelrotation = labelangle; stemlength = stemltreedratio; treedepth = breadthdepthratio; bscale = branchscale; nodespace = 1.0 / chhttipspratio; xmargin = xmarginratio * paperx; ymargin = ymarginratio * papery; // translate Java boolean to Phylip boolean boolean doplot; if (dofinalplot != 0) doplot = true; else doplot = false; if (usebranchlengths != 0) uselengths = true; else uselengths = false; if (scalebranchlength != 0) rescaled = true; else rescaled = false; // plot style style = phenogram; if (!strcmp(stylekind,"cladogram")) style = cladogram; if (!strcmp(stylekind,"phenogram")) style = phenogram; if (!strcmp(stylekind,"curvogram")) style = curvogram; if (!strcmp(stylekind,"eurogram")) style = eurogram; if (!strcmp(stylekind,"swoopogram")) style = swoopogram; if (!strcmp(stylekind,"circular")) style = circular; // tree growth direction grows = horizontal; if (!strcmp(treegrows,"vertical")) grows = vertical; // node positions if (!strcmp(ancnodes,"weighted")) nodeposition = weighted; if (!strcmp(ancnodes,"intermediate")) nodeposition = intermediate; if (!strcmp(ancnodes,"centered")) nodeposition = centered; if (!strcmp(ancnodes,"inner")) nodeposition = inner; if (!strcmp(ancnodes,"vshaped")) nodeposition = vshaped; plotter = lw; strcpy(afmfile,"none"); if(dofinalplot) { if (!strcmp(finalplotkind,"lw")) { plotter = lw; } /* // not currently available if(!strcmp(finalplotkind,"svg")) { plotter = svg; } */ else if(!strcmp(finalplotkind,"hp")) { plotter = hp; } if(!strcmp(finalplotkind,"tek")) { plotter = tek; } if(!strcmp(finalplotkind,"ibm")) { plotter = ibm; } if(!strcmp(finalplotkind,"mac")) { plotter = mac; } if(!strcmp(finalplotkind,"houston")) { plotter = houston; } if(!strcmp(finalplotkind,"decregis")) { plotter = decregis; } if(!strcmp(finalplotkind,"epson")) { plotter = epson; } if(!strcmp(finalplotkind,"oki")) { plotter = oki; } if(!strcmp(finalplotkind,"fig")) { plotter = fig; } if(!strcmp(finalplotkind,"citoh")) { plotter = citoh; } if(!strcmp(finalplotkind,"toshiba")) { plotter = toshiba; } if(!strcmp(finalplotkind,"pcx")) { plotter = pcx; } if(!strcmp(finalplotkind,"pcl")) { plotter = pcl; } if(!strcmp(finalplotkind,"pict")) { plotter = pict; } if(!strcmp(finalplotkind,"ray")) { plotter = ray; } if(!strcmp(finalplotkind,"pov")) { plotter = pov; } if(!strcmp(finalplotkind,"xbm")) { plotter = xbm; } if(!strcmp(finalplotkind,"bmp")) { plotter = bmp; } if(!strcmp(finalplotkind,"gif")) { plotter = gif; } if(!strcmp(finalplotkind,"idraw")) { plotter = idraw; } if(!strcmp(finalplotkind,"vrml")) { plotter = vrml; } if(!strcmp(finalplotkind,"other")) { plotter = other; } } else { // preview plotter = lw; // hardwired to ps } // choose the best Hershey approximation of the font int fontid = figfontid(fontfilename); //printf("fontfilename: %s id: %i ", fontfilename, fontid); char* hersheyfontname = "font1"; switch (fontid) { case 4: //AvantGarde-Book case 8: //Bookman-Light case 16: //Helvetica case 20: //Helvetica-Narrow hersheyfontname = "font1"; // romans sans break; case 6: //AvantGarde-Demi case 10: //Bookman-Demi case 18: //Helvetica-Bold case 22: //Helvetica-Narrow-Bold hersheyfontname = "font2"; // romans sans bold break; case 0: //Times-Roman case 2: //Times-Bold case 12: //Courier case 14: //Courier-Bold case 24: //NewCenturySchlbk-Roman case 26: //NewCenturySchlbk-Bold case 28: //Palatino-Roman case 30: //Palatino-Bold hersheyfontname = "font3"; // romans serif break; case 1: //Times-Italic case 5: //AvantGarde-BookOblique case 9: //Bookman-LightItalic case 13: //Courier-Italic case 17: //Helvetica-Oblique case 21: //Helvetica-Narrow-Oblique case 25: //NewCenturySchlbk-Italic case 29: //Palatino-Italic case 33: //ZapfChancery-MediumItalic hersheyfontname = "font4"; // romans serif italic break; case 3: //Times-BoldItalic case 7: //AvantGarde-DemiOblique case 11: //Bookman-DemiItalic case 15: //Courier-BoldItalic case 19: //Helvetica-BoldOblique case 23: //Helvetica-Narrow-BoldOblique case 27: //NewCenturySchlbk-BoldItalic case 31: //Palatino-BoldItalic hersheyfontname = "font5"; // romans serif italic bold break; default: /* case 32: //Symbol case 34: //ZapfDingbats */ hersheyfontname = "font1"; // romans sans break; } //printf("hersheyfontname: %s\n", hersheyfontname); loadfont(font,hersheyfontname,progname); #ifdef JAVADEBUG // JRM Debug // dump translated parameters from Java to make sure they made it printf("Starting parameters: \n"); printf("intreename: %s\n",intreename); printf("fontfilename: %s\n",fontfilename); printf("plotfilename: %s\n",plotfilename); printf("plotfileopt: %s\n",plotfileopt); printf("previewfilename: %s\n",previewfilename); printf("rescaled: %i\n",rescaled); printf("finalplotkind: %s\n",finalplotkind); printf("doplot: %i\n",doplot); fflush(stdout); #endif // start drawgram code /* printf("hello from DrawGram\n"); printf("DRAWGRAM from PHYLIP version %s\n",VERSION); fflush(stdout); */ // read tree intree = fopen(intreename,"r"); boolean firsttree = true; allocate_nodep(&nodep, &intree, &spp); plotrparms(spp); treeread (intree, &root, treenode, &goteof, &firsttree, nodep, &nextnode, &haslengths, &grbg, initdrawgramnode,true,-1); root->oldlen = 0.0; // if there are no lengths, shut uselengths off if (haslengths==0) uselengths = false; //printf("Tree has been read.\n"); //printf("haslengths: %i\n",haslengths); //fflush(stdout); // printer specific details to simulate interactive setup // mostly from getplotter with some from plotrparms // after treeread as some formats need some of the tree data dotmatrix = false; long stripedepth; switch (plotter) { case lw: strcpy(fontname, fontfilename); break; case hp: strcpy(fontname, "Hershey"); break; case tek: strcpy(fontname, "Hershey"); break; case ibm: strcpy(fontname, "Hershey"); break; case mac: strcpy(fontname, "Hershey"); break; case houston: strcpy(fontname, "Hershey"); break; case decregis: strcpy(fontname, "Hershey"); break; case epson: dotmatrix = true; strcpy(fontname, "Hershey"); strpdiv = 1; stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); break; case oki: dotmatrix = true; strcpy(fontname, "Hershey"); strpdiv = 1; stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); break; case fig: strcpy(fontname, fontfilename); break; case citoh: dotmatrix = true; strcpy(fontname, "Hershey"); strpdiv = 1; stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); break; case toshiba: dotmatrix = true; strcpy(fontname, "Hershey"); strpdiv = 4; stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); break; case pcx: dotmatrix = true; strcpy(fontname, "Hershey"); // assume VGA 1024 x 768 strpwide = 1024; yunitspercm = 768 / ysize; resopts = 3; strpdiv = 10; stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); break; case pcl: dotmatrix = true; strcpy(fontname, "Hershey"); // assume 300 dpi hpresolution = 300; xunitspercm = 118.11023622; /* 300 DPI = 118.1 DPC */ yunitspercm = 118.11023622; strpwide = 2550; /* 8.5 * 300 DPI */ strpdeep = DEFAULT_STRIPE_HEIGHT; /* height of the strip */ strpdiv = DEFAULT_STRIPE_HEIGHT; /* in this case == strpdeep */ stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); break; case pict: strcpy(fontname, fontfilename); break; case ray: strcpy(fontname, "Hershey"); break; case pov: strcpy(fontname, "Hershey"); break; case xbm: dotmatrix = true; strcpy(fontname, "Hershey"); // assume 1000 x 1000 xunitspercm = 1.0; yunitspercm = 1.0; xsize = 1000; ysize = 1000; xmargin = 0.08 * xsize; ymargin = 0.08 * ysize; strpdeep = DEFAULT_STRIPE_HEIGHT; strpdiv = DEFAULT_STRIPE_HEIGHT; strpwide = (long)xsize; stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); break; case bmp: dotmatrix = true; strcpy(fontname, "Hershey"); // assume 1000 x 1000 xunitspercm = 1.0; yunitspercm = 1.0; xsize = 1000; ysize = 1000; xmargin = 0.08 * xsize; ymargin = 0.08 * ysize; strpdeep = DEFAULT_STRIPE_HEIGHT; strpdiv = DEFAULT_STRIPE_HEIGHT; strpwide = (long)xsize; stripedepth = allocstripe(stripe,(strpwide/8),((long)(yunitspercm * ysize))); /* printf("***bmp setup done\n"); printf("xsize: %f\n", xsize); printf("ysize: %f\n", ysize); printf("xmargin: %f\n",xmargin); printf("ymargin: %f\n",ymargin); printf("strpwide: %li, yunitspercm: %f, ysize: %f\n" ,strpwide, yunitspercm, ysize); fflush(stdout); */ break; case gif: strcpy(fontname, fontfilename); break; case idraw: strcpy(fontname, "Times-Bold"); break; case vrml: strcpy(fontname, "Hershey"); treecolor = 5; namecolor = 4; vrmlskycolornear = 6; vrmlskycolorfar = 6; vrmlgroundcolornear = 3; vrmlgroundcolorfar = 3; break; case other: strcpy(fontname, "Hershey"); break; default: break; } numlines = dotmatrix ? ((long)floor(yunitspercm * ysize + 0.5) / strpdeep) :1; xscale = xunitspercm; yscale = yunitspercm; #ifdef JAVADEBUG // jrmdebug dump final parameter settings printf("\n***internal parameters***\n"); printf("fontname: %s\n", fontname); printf("plotter: %i\n",plotter); printf("paperx: %f\n",paperx); printf("papery: %f\n",papery); printf("hpmargin: %f\n",hpmargin); printf("vpmargin: %f\n",vpmargin); printf("pagex: %f\n",pagex); printf("pagey: %f\n",pagey); printf("xmargin: %f\n",xmargin); printf("ymargin: %f\n",ymargin); printf("firstscreens: %i\n",firstscreens); printf("canbeplotted: %i\n",canbeplotted); printf("style: %i\n",style); printf("grows: %i\n",grows); printf("labelrotation: %f\n",labelrotation); printf("nodespace: %f\n",nodespace); printf("stemlength: %f\n",stemlength); printf("treedepth: %f\n",treedepth); printf("bscale: %f\n",bscale); printf("uselengths: %i\n",uselengths); printf("nodeposition: %i\n",nodeposition); printf("dotmatrix: %i\n",dotmatrix); printf("xsize: %f\n", xsize); printf("ysize: %f\n", ysize); printf("---internal vars---\n"); printf("nodespace: %f\n",nodespace); printf("spp: %li\n",spp); printf("doplot: %i\n",doplot); printf("dotmatrix: %i numlines: %li\n",dotmatrix, numlines); fflush(stdout); #endif calculate(); rescale(); //printf("passed rescale\n"); //fflush(stdout); int lenname; if (doplot) { lenname = strlen(plotfilename); } else { lenname = strlen(previewfilename); } char* usefilename = (char*) malloc(lenname + 1); if (doplot) { strcpy(usefilename, plotfilename); strcpy(pltfilename, plotfilename); } else { strcpy(usefilename, previewfilename); } strcpy(trefilename, intreename); // Open plot files in binary mode. plotfile = fopen(usefilename,plotfileopt); //printf("initializing plotter\n"); //fflush(stdout); initplotter(spp,fontname); //printf("plotter initialized\n"); //printf("numlines: %li\n",numlines); //fflush(stdout); //printf("\nWriting plot file ...\n"); //fflush(stdout); if (!dofinalplot) { /* printf("calling makebox\n"); printf("fontname: %s\n",fontname); printf("xoffset: %f\n",xoffset); printf("yoffset: %f\n",yoffset); printf("scale: %f\n",scale); printf("spp: %li\n",spp); fflush(stdout); */ changepen(labelpen); makebox(fontname,&xoffset,&yoffset,&scale,spp); /* printf("back from makebox\n"); printf("fontname: %s\n",fontname); printf("xoffset: %f\n",xoffset); printf("yoffset: %f\n",yoffset); printf("scale: %f\n",scale); printf("spp: %li\n",spp); fflush(stdout); */ changepen(treepen); } drawit(fontname,&xoffset,&yoffset,numlines,root); //printf("drawit done\n"); //fflush(stdout); finishplotter(); //printf("finishplotter done\n"); //fflush(stdout); fclose(plotfile); //printf("\nPlot written to file \"%s\"\n\n", pltfilename); wasplotted = true; fclose(intree); //printf("Drawgram Done.\n\n"); return; } int main(int argc, Char *argv[]) { boolean wasplotted = false; javarun = false; argv[0] = "Drawgram"; grbg = NULL; progname = argv[0]; init(argc, argv); setup_environment(argv); user_loop(); if (!(winaction == quitnow)) { /* Open plot files in binary mode. */ openfile(&plotfile,PLOTFILE,"plot file", "wb",argv[0],pltfilename); initplotter(spp,fontname); numlines = dotmatrix ? ((long)floor(yunitspercm * ysize + 0.5)/strpdeep) : 1; //printf("numlines: %li\n",numlines); if (plotter != ibm) printf("\nWriting plot file ...\n"); drawit(fontname,&xoffset,&yoffset,numlines,root); finishplotter(); FClose(plotfile); wasplotted = true; printf("\nPlot written to file \"%s\"\n\n", pltfilename); } FClose(intree); printf("Done.\n\n"); #ifdef WIN32 phyRestoreConsoleAttributes(); #endif return 0; }