
#include "phylip.h"
#include "disc.h"
#include "moves.h"
#include "wagner.h"

/* version 3.6. (c) Copyright 1993-2004 by the University of Washington.
   Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
   Permission is granted to copy and use this program provided no fee is
   charged for it and provided that this copyright notice is not removed. */

#define overr           4
#define which           1

typedef enum {
  horiz, vert, up, overt, upcorner, downcorner, onne, zerro, question
} chartype;
typedef enum {
  arb, use, spec
} howtree;

typedef enum {
  rearr, flipp, reroott, none
} rearrtype;

#ifndef OLDC
/*function prototypes */
void   getoptions(void);
void   inputoptions(void);
void   allocrest(void);
void   doinput(void);
void   configure(void);
void   prefix(chartype);
void   postfix(chartype);
void   makechar(chartype);
void   move_fillin(node *);
void   move_postorder(node *);

void   evaluate(node *);
void   reroot(node *);
void   move_filltrav(node *);
void   move_hyptrav(node *);
void   move_hypstates(void);
void   grwrite(chartype, long, long *);
void   move_drawline(long, long);
void   move_printree(void);
void   arbitree(void);
void   yourtree(void);

void   initmovenode(node **, node **, node *, long, long, long *, long *,
        initops, pointarray, pointarray, Char *, Char *, FILE *);
void   buildtree(void);
void   rearrange(void);
void   tryadd(node *, node *, node *, double *);
void   addpreorder(node *, node *, node *, double *);
void   try(void);
void   undo(void);
void   treewrite(boolean);
void   clade(void);
void   flip(void);

void   changeoutgroup(void);
void   redisplay(void);
void   treeconstruct(void);
void   get_usertree(void);
void   initboolnames(node *p, boolean *names);
/*function prototypes */
#endif
 
char infilename[FNMLNGTH],intreename[FNMLNGTH],outtreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH], factfilename[FNMLNGTH];
node *root;
long outgrno, screenlines, col, treelines, leftedge, topedge,
  vmargin, hscroll, vscroll, scrollinc, screenwidth, farthest;
/* outgrno indicates outgroup */
boolean weights, thresh, outgropt, ancvar, questions, allsokal,
               allwagner, mixture, factors, noroot,  waswritten;
boolean *ancone, *anczero, *ancone0, *anczero0;
Char *factor;
pointptr treenode;   /* pointers to all nodes in tree */
double threshold;
double *threshwt;
bitptr wagner, wagner0;
unsigned char che[9];
boolean reversed[9];
boolean graphic[9];
howtree how;
gbit *garbage;
char* progname;
Char ch;

/* Variables for treeread */
boolean usertree, goteof, firsttree, haslengths;
pointarray nodep;
node *grbg;
long *zeros;

/* Local variables for treeconstruct, propagated globally for C vesion: */
long dispchar, dispword, dispbit, atwhat, what, fromwhere, towhere,
     oldoutgrno, compatible;
double like, bestyet, gotlike;
Char *guess;
boolean display, newtree, changed, subtree, written, oldwritten, restoring,
  wasleft, oldleft, earlytree;
boolean *in_tree;
steptr numsteps, numsone, numszero;
long fullset;
bitptr steps, zeroanc, oneanc;
node *nuroot;
rearrtype lastop;
boolean *names;


void getoptions()
{
  /* interactively set options */
  long loopcount;
  Char ch;
  boolean done, gotopt;

  how = arb;
  usertree = false;
  goteof = false;
  outgrno = 1;
  outgropt = false;
  thresh = false;
  threshold = spp;
  weights = false;
  ancvar = false;
  allsokal = false;
  allwagner = true;
  mixture = false;
  factors = false;
  loopcount = 0;
  do {
#ifdef WIN32
    if(ansi || ibmpc){
      phyClearScreen();
    } else {
      printf("\n");
    }
#else
    printf((ansi || ibmpc) ? "\033[2J\033[H" : "\n");
#endif
        printf("\n\nInteractive mixed parsimony algorithm, version %s\n\n",
           VERSION);
    printf("Settings for this run:\n");
    printf("  X                         Use Mixed method?  %s\n",
           mixture ? "Yes" : "No");
    printf("  P                         Parsimony method?  %s\n",
           (allwagner && !mixture)   ? "Wagner"       :
           (!(allwagner || mixture)) ? "Camin-Sokal"  : "(methods in mixture)");
        
    printf("  A                     Use ancestral states?  %s\n",
           ancvar ? "Yes" : "No");
    printf("  F                  Use factors information?  %s\n",
           factors ? "Yes" : "No");
    printf("  O                            Outgroup root?  %s %3ld\n",
           outgropt ? "Yes, at species number" : "No, use as outgroup species",
           outgrno);
    printf("  W                           Sites weighted?  %s\n",
           (weights ? "Yes" : "No"));
    printf("  T                  Use Threshold parsimony?");
    if (thresh)
      printf("  Yes, count steps up to%4.1f\n", threshold);
    else
      printf("  No, use ordinary parsimony\n");
    printf("  U  Initial tree (arbitrary, user, specify)?  %s\n",
           (how == arb) ? "Arbitrary"                   :
           (how == use) ? "User tree from tree file"    : "Tree you specify");
    printf("  0       Graphics type (IBM PC, ANSI, none)?  %s\n",
           ibmpc ? "IBM PC" : ansi  ? "ANSI" : "(none)");
    printf("  S                 Width of terminal screen?");
    printf("%4ld\n", screenwidth);
    printf("  L                Number of lines on screen?%4ld",screenlines);
    printf("\n\nAre these settings correct?");
    printf(" (type Y or the letter for one to change)\n");
#ifdef WIN32
    phyFillScreenColor();
#endif
    scanf("%c%*[^\n]", &ch);
    getchar();
    if (ch == '\n')
      ch = ' ';
    uppercase(&ch);
    done = (ch == 'Y');
    gotopt = (strchr("SFOTXPAU0WL",ch) != NULL) ? true : false;
    if (gotopt) {
      switch (ch) {

      case 'F':
        factors = !factors;
        break;

      case 'X':
        mixture = !mixture;
        break;

      case 'W':
          weights = !weights;
          break;

      case 'P':
        allwagner = !allwagner;
        break;

      case 'A':
        ancvar = !ancvar;
        break;

      case 'O':
        outgropt = !outgropt;
        if (outgropt)
          initoutgroup(&outgrno, spp);
        break;

      case 'T':
        thresh = !thresh;
        if (thresh)
          initthreshold(&threshold);
        break;

      case 'U':
        if (how == arb)
          how = use;
        else if (how == use)
          how = spec;
        else
          how = arb;
        break;

      case '0':
        initterminal(&ibmpc, &ansi);
        break;

      case 'S':
        screenwidth= readlong("Width of terminal screen (in characters)?\n");
        break;

      case 'L':
        initnumlines(&screenlines);
        break;
      }
    }
    if (!(gotopt || done))
      printf("Not a possible option!\n");
    countup(&loopcount, 100);
  } while (!done);
  allsokal = (!allwagner && !mixture);
  if (scrollinc < screenwidth / 2.0)
    hscroll = scrollinc;
  else
    hscroll = screenwidth / 2;
  if (scrollinc < screenlines / 2.0)
    vscroll = scrollinc;
  else
    vscroll = screenlines / 2;
}  /* getoptions */


void inputoptions()
{
  /* input the information on the options */
  long i;
  scan_eoln(infile);
  for (i = 0; i < (chars); i++)
    weight[i] = 1;
    if (ancvar)
        inputancestors(anczero0, ancone0);
    if (factors) {
      factor = (Char *)Malloc(chars*sizeof(Char));
      inputfactors(chars, factor, &factors);
    }
    if (mixture)
        inputmixture(wagner0);
    if (weights)
      inputweights(chars, weight, &weights);
  putchar('\n');
  if (weights)
    printweights(stdout, 0, chars, weight, "Characters");
  for (i = 0; i < (words); i++) {
    if (mixture)
      wagner[i] = wagner0[i];
    else if (allsokal)
      wagner[i] = 0;
    else
      wagner[i] = (1L << (bits + 1)) - (1L << 1);
  }
  if (allsokal && !mixture)
    printf("Camin-Sokal parsimony method\n\n");
  if (allwagner && !mixture)
    printf("Wagner parsimony method\n\n");
  if (mixture)
    printmixture(stdout, wagner);
  for (i = 0; i < (chars); i++) {
    if (!ancvar) {
      anczero[i] = true;
      ancone[i] = (((1L << (i % bits + 1)) & wagner[i / bits]) != 0);
    } else {
      anczero[i] = anczero0[i];
      ancone[i] = ancone0[i];
    }
  }
  if (factors)
    printfactors(stdout, chars, factor, "");
  if (ancvar)
    printancestors(stdout, anczero, ancone);
  noroot = true;
  questions = false;
  for (i = 0; i < (chars); i++) {
    if (weight[i] > 0) {
      noroot = (noroot && ancone[i] && anczero[i] &&
          ((((1L << (i % bits + 1)) & wagner[i / bits]) != 0)
            || threshold <= 2.0));
    }
    questions = (questions || (ancone[i] && anczero[i]));
    threshwt[i] = threshold * weight[i];
  }
}  /* inputoptions */


void allocrest()
{
  nayme = (naym *)Malloc(spp*sizeof(naym));
  in_tree = (boolean *)Malloc(nonodes*sizeof(boolean));
  extras = (steptr)Malloc(chars*sizeof(long));
  weight = (steptr)Malloc(chars*sizeof(long));
  numsteps = (steptr)Malloc(chars*sizeof(long));
  numsone = (steptr)Malloc(chars*sizeof(long));
  numszero = (steptr)Malloc(chars*sizeof(long));
  threshwt = (double *)Malloc(chars*sizeof(double));
  guess = (Char *)Malloc(chars*sizeof(Char));
  ancone = (boolean *)Malloc(chars*sizeof(boolean));
  anczero = (boolean *)Malloc(chars*sizeof(boolean));
  ancone0 = (boolean *)Malloc(chars*sizeof(boolean));
  anczero0 = (boolean *)Malloc(chars*sizeof(boolean));
  wagner = (bitptr)Malloc(words*sizeof(long));
  wagner0 = (bitptr)Malloc(words*sizeof(long));
  steps = (bitptr)Malloc(words*sizeof(long));
  zeroanc = (bitptr)Malloc(words*sizeof(long));
  oneanc = (bitptr)Malloc(words*sizeof(long));
}  /* allocrest */


void doinput()
{
  /* reads the input data */

  inputnumbers(&spp, &chars, &nonodes, 1);
  words = chars / bits + 1;
  printf("%2ld species, %3ld characters\n", spp, chars);
  printf("\nReading input file ...\n\n");
  getoptions();
  if (weights)
    openfile(&weightfile,WEIGHTFILE,"weights file","r",progname,weightfilename);
  if(ancvar)
      openfile(&ancfile,ANCFILE,"ancestors file", "r",progname,ancfilename);
  if(mixture)
      openfile(&mixfile,MIXFILE,"mixture file", "r",progname,mixfilename);
  if(factors)
      openfile(&factfile,FACTFILE,"factors file", "r",progname,factfilename);

  alloctree(&treenode);
  setuptree(treenode);
  allocrest();
  inputoptions();
  inputdata(treenode, true, false, stdout);
}  /* doinput */


void configure()
{
  /* configure to machine -- set up special characters */
  chartype a;

  for (a = horiz; (long)a <= (long)question; a = (chartype)((long)a + 1))
    reversed[(long)a] = false;
  for (a = horiz; (long)a <= (long)question; a = (chartype)((long)a + 1))
    graphic[(long)a] = false;
  if (ibmpc) {
    che[(long)horiz] = 205;
    graphic[(long)horiz] = true;
    che[(long)vert] = 186;
    graphic[(long)vert] = true;
    che[(long)up] = 186;
    graphic[(long)up] = true;
    che[(long)overt] = 205;
    graphic[(long)overt] = true;
    che[(long)onne] = 219;
    reversed[(long)onne] = true;
    che[(long)zerro] = 176;
    graphic[(long)zerro] = true;
    che[(long)question] = 178;   /* or try CHR(177) */
    graphic[(long)question] = true;
    che[(long)upcorner] = 200;
    graphic[(long)upcorner] = true;
    che[(long)downcorner] = 201;
    graphic[(long)downcorner] = true;
    return;
  }
  if (ansi) {
    che[(long)onne] = ' ';
    reversed[(long)onne] = true;
    che[(long)horiz] = che[(long)onne];
    reversed[(long)horiz] = true;
    che[(long)vert] = che[(long)onne];
    reversed[(long)vert] = true;
    che[(long)up] = 'x';
    graphic[(long)up] = true;
    che[(long)overt] = 'q';
    graphic[(long)overt] = true;
    che[(long)zerro] = 'a';
    graphic[(long)zerro] = true;
    reversed[(long)zerro] = true;
    che[(long)question] = '?';
    reversed[(long)question] = true;
    che[(long)upcorner] = 'm';
    graphic[(long)upcorner] = true;
    che[(long)downcorner] = 'l';
    graphic[(long)downcorner] = true;
    return;
  }
  che[(long)horiz] = '=';
  che[(long)vert] = ' ';
  che[(long)up] = '!';
  che[(long)overt] = '-';
  che[(long)onne] = '*';
  che[(long)zerro] = '=';
  che[(long)question] = '.';
  che[(long)upcorner] = '`';
  che[(long)downcorner] = ',';
}  /* configure */


void prefix(chartype a)
{
  /* give prefix appropriate for this character */
  if (reversed[(long)a])
    prereverse(ansi);
  if (graphic[(long)a])
    pregraph(ansi);
}  /* prefix */


void postfix(chartype a)
{
  /* give postfix appropriate for this character */
  if (reversed[(long)a])
    postreverse(ansi);
  if (graphic[(long)a])
    postgraph(ansi);
}  /* postfix */


void makechar(chartype a)
{
  /* print out a character with appropriate prefix or postfix */
  prefix(a);
  putchar(che[(long)a]);
  postfix(a);
}  /* makechar */


void move_fillin(node *p)
{
  /* Sets up for each node in the tree two statesets.
     stateone and statezero are the sets of character
     states that must be 1 or must be 0, respectively,
     in a most parsimonious reconstruction, based on the
     information at or above this node.   Note that this
     state assignment may change based on information further
     down the tree.   If a character is in both sets it is in
     state "P".   If in neither, it is "?". */
  long i;
  long l0, l1, r0, r1, st, wa, za, oa;

  for (i = 0; i < (words); i++) {
    l0 = p->next->back->statezero[i];
    l1 = p->next->back->stateone[i];
    r0 = p->next->next->back->statezero[i];
    r1 = p->next->next->back->stateone[i];
    wa = wagner[i];
    za = zeroanc[i];
    oa = oneanc[i];
    st = (l1 & r0) | (l0 & r1);
    steps[i] = st;
    p->stateone[i] = (l1 | r1) & (~(st & (wa | za)));
    p->statezero[i] = (l0 | r0) & (~(st & (wa | oa)));
  }
}  /* move_fillin */


void move_postorder(node *p)
{
  /* traverses a binary tree, calling function fillin at a
     node's descendants before calling fillin at the node */
  if (p->tip)
    return;
  move_postorder(p->next->back);
  move_postorder(p->next->next->back);
  move_fillin(p);
  count(steps, zeroanc, numszero, numsone);
}  /* move_postorder */


void evaluate(node *r)
{
  /* Determines the number of steps needed for a tree.
     This is the minimum number needed to evolve chars on this tree */
  long i, stepnum, smaller;
  double sum;
  boolean nextcompat, thiscompat, done;

  sum = 0.0;
  for (i = 0; i < (chars); i++) {
    numszero[i] = 0;
    numsone[i] = 0;
  }
  for (i = 0; i < (words); i++) {
    zeroanc[i] = fullset;
    oneanc[i] = 0;
  }
  compatible = 0;
  nextcompat = true;
  move_postorder(r);
  count(r->stateone, zeroanc, numszero, numsone);
  for (i = 0; i < (words); i++) {
    zeroanc[i] = 0;
    oneanc[i] = fullset;
  }
  move_postorder(r);
  count(r->statezero, zeroanc, numszero, numsone);
  for (i = 0; i < (chars); i++) {
    smaller = spp * weight[i];
    numsteps[i] = smaller;
    if (anczero[i]) {
      numsteps[i] = numszero[i];
      smaller = numszero[i];
    }
    if (ancone[i] && numsone[i] < smaller)
     numsteps[i] = numsone[i];
    stepnum = numsteps[i] + extras[i];
    if (stepnum <= threshwt[i])
      sum += stepnum;
    else
      sum += threshwt[i];
    thiscompat = (stepnum <= weight[i]);
    if (factors) {
      done = (i + 1 == chars);
      if (!done)
        done = (factor[i + 1] != factor[i]);
      nextcompat = (nextcompat && thiscompat);
      if (done) {
        if (nextcompat)
          compatible += weight[i];
        nextcompat = true;
      }
    } else if (thiscompat)
      compatible += weight[i];
    guess[i] = '?';
    if (!ancone[i] ||
        (anczero[i] && numszero[i] < numsone[i]))
      guess[i] = '0';
    else if (!anczero[i] ||
             (ancone[i] && numsone[i] < numszero[i]))
     guess[i] = '1';
  }
  like = -sum;
}  /* evaluate */


void reroot(node *outgroup)
{
  /* reorients tree, putting outgroup in desired position. */
  node *p, *q, *newbottom, *oldbottom;
  boolean onleft;

  if (outgroup->back->index == root->index)
    return;
  newbottom = outgroup->back;
  p = treenode[newbottom->index - 1]->back;
  while (p->index != root->index) {
    oldbottom = treenode[p->index - 1];
    treenode[p->index - 1] = p;
    p = oldbottom->back;
  }
  onleft = (p == root->next);
  if (restoring)
    if (!onleft && wasleft){
      p = root->next->next;
      q = root->next;
    } else {
      p = root->next;
      q = root->next->next;
    }
  else {
    if (onleft)
      oldoutgrno = root->next->next->back->index;
    else
      oldoutgrno = root->next->back->index;
    wasleft = onleft;
    p = root->next;
    q = root->next->next;
  }
  p->back->back = q->back;
  q->back->back = p->back;
  p->back = outgroup;
  q->back = outgroup->back;
  if (restoring) {
    if (!onleft && wasleft) {
      outgroup->back->back = root->next;
      outgroup->back = root->next->next;
    } else {
      outgroup->back->back = root->next->next;
      outgroup->back = root->next;
    }
  } else {
    outgroup->back->back = root->next->next;
    outgroup->back = root->next;
  }
  treenode[newbottom->index - 1] = newbottom;
}  /* reroot */


void move_filltrav(node *r)
{
  /* traverse to fill in interior node states */
  if (r->tip)
    return;
  move_filltrav(r->next->back);
  move_filltrav(r->next->next->back);
  move_fillin(r);
}  /* move_filltrav */


void move_hyptrav(node *r)
{
  /* compute states at one interior node */
  long i;
  boolean bottom;
  long l0, l1, r0, r1, s0, s1, a0, a1, temp, wa;
  gbit *zerobelow = NULL, *onebelow = NULL;

  disc_gnu(&zerobelow, &garbage);
  disc_gnu(&onebelow, &garbage);
  bottom = (r->back == NULL);
  if (bottom) {
    memcpy(zerobelow->bits_, zeroanc, words*sizeof(long));
    memcpy(onebelow->bits_, oneanc, words*sizeof(long));
  } else {
    memcpy(zerobelow->bits_, treenode[r->back->index - 1]->statezero,
           words*sizeof(long));
    memcpy(onebelow->bits_, treenode[r->back->index - 1]->stateone,
           words*sizeof(long));
  }
  for (i = 0; i < (words); i++) {
    s0 = r->statezero[i];
    s1 = r->stateone[i];
    a0 = zerobelow->bits_[i];
    a1 = onebelow->bits_[i];
    if (!r->tip) {
      wa = wagner[i];
      l0 = r->next->back->statezero[i];
      l1 = r->next->back->stateone[i];
      r0 = r->next->next->back->statezero[i];
      r1 = r->next->next->back->stateone[i];
      s0 = (wa & ((a0 & l0) | (a0 & r0) | (l0 & r0))) |
           (fullset & (~wa) & s0);
      s1 = (wa & ((a1 & l1) | (a1 & r1) | (l1 & r1))) |
           (fullset & (~wa) & s1);
      temp = fullset & (~(s0 | s1 | l1 | l0 | r1 | r0));
      s0 |= temp & a0;
      s1 |= temp & a1;
      r->statezero[i] = s0;
      r->stateone[i] = s1;
    }
  }
  if (((1L << dispbit) & r->stateone[dispword - 1]) != 0) {
    if (((1L << dispbit) & r->statezero[dispword - 1]) != 0)
      r->state = '?';
    else
      r->state = '1';
  } else {
    if (((1L << dispbit) & r->statezero[dispword - 1]) != 0)
      r->state = '0';
    else
      r->state = '?';
  }
  if (!r->tip) {
    move_hyptrav(r->next->back);
    move_hyptrav(r->next->next->back);
  }
  disc_chuck(zerobelow, &garbage);
  disc_chuck(onebelow, &garbage);
}  /* move_hyptrav */


void move_hypstates()
{
  /* fill in and describe states at interior nodes */
  long i, j, k;

  for (i = 0; i < (words); i++) {
    zeroanc[i] = 0;
    oneanc[i] = 0;
  }
  for (i = 0; i < (chars); i++) {
    j = i / bits + 1;
    k = i % bits + 1;
    if (guess[i] == '0')
      zeroanc[j - 1] = ((long)zeroanc[j - 1]) | (1L << k);
    if (guess[i] == '1')
      oneanc[j - 1] = ((long)oneanc[j - 1]) | (1L << k);
  }
  move_filltrav(root);
  move_hyptrav(root);
}  /* move_hypstates */


void grwrite(chartype c, long num, long *pos)
{
  long i;

  prefix(c);
  for (i = 1; i <= num; i++) {
    if ((*pos) >= leftedge && (*pos) - leftedge + 1 < screenwidth)
      putchar(che[(long)c]);
    (*pos)++;
  }
  postfix(c);
}  /* grwrite */


void move_drawline(long i, long lastline)
{
  /* draws one row of the tree diagram by moving up tree */
  node *p, *q, *r, *first =NULL, *last =NULL;
  long n, j, pos;
  boolean extra, done;
  Char st;
  chartype c, d;

  pos = 1;
  p = nuroot;
  q = nuroot;
  extra = false;
  if (i == (long)p->ycoord && (p == root || subtree)) {
    extra = true;
    c = overt;
    if (display) {
      switch (p->state) {

      case '1':
        c = onne;
        break;

      case '0':
        c = zerro;
        break;

      case '?':
        c = question;
        break;
      }
    }
    if ((subtree))
      stwrite("Subtree:", 8, &pos, leftedge, screenwidth);
    if (p->index >= 100)
      nnwrite(p->index, 3, &pos, leftedge, screenwidth);
    else if (p->index >= 10) {
      grwrite(c, 1, &pos);
      nnwrite(p->index, 2, &pos, leftedge, screenwidth);
    } else {
      grwrite(c, 2, &pos);
      nnwrite(p->index, 1, &pos, leftedge, screenwidth);
    }
  } else {
    if (subtree)
      stwrite("          ", 10, &pos, leftedge, screenwidth);
    else
      stwrite("  ", 2, &pos, leftedge, screenwidth);
  }
  do {
    if (!p->tip) {
      r = p->next;
      done = false;
      do {
        if (i >= r->back->ymin && i <= r->back->ymax) {
          q = r->back;
          done = true;
        }
        r = r->next;
      } while (!(done || r == p));
      first = p->next->back;
      r = p->next;
      while (r->next != p)
        r = r->next;
      last = r->back;
    }
    done = (p == q);
    n = (long)p->xcoord - (long)q->xcoord;
    if (n < 3 && !q->tip)
      n = 3;
    if (extra) {
      n--;
      extra = false;
    }
    if ((long)q->ycoord == i && !done) {
      if ((long)q->ycoord > (long)p->ycoord)
        d = upcorner;
      else
        d = downcorner;
      c = overt;
      if (display) {
        switch (q->state) {

        case '1':
          c = onne;
          break;

        case '0':
          c = zerro;
          break;

        case '?':
          c = question;
          break;
        }
        d = c;
      }
      if (n > 1) {
        grwrite(d, 1, &pos);
        grwrite(c, n - 3, &pos);
      }
      if (q->index >= 100)
        nnwrite(q->index, 3, &pos, leftedge, screenwidth);
      else if (q->index >= 10) {
        grwrite(c, 1, &pos);
        nnwrite(q->index, 2, &pos, leftedge, screenwidth);
      } else {
        grwrite(c, 2, &pos);
        nnwrite(q->index, 1, &pos, leftedge, screenwidth);
      }
      extra = true;
    } else if (!q->tip) {
      if ((long)last->ycoord > i && (long)first->ycoord < i
        && i != (long)p->ycoord) {
        c = up;
        if (i < (long)p->ycoord)
          st = p->next->back->state;
        else
          st = p->next->next->back->state;
        if (display) {
          switch (st) {

          case '1':
            c = onne;
            break;

          case '0':
            c = zerro;
            break;

          case '?':
            c = question;
            break;
          }
        }
        grwrite(c, 1, &pos);
        chwrite(' ', n - 1, &pos, leftedge, screenwidth);
      } else
        chwrite(' ', n, &pos, leftedge, screenwidth);
    } else
      chwrite(' ', n, &pos, leftedge, screenwidth);
    if (p != q)
      p = q;
  } while (!done);
  if ((long)p->ycoord == i && p->tip) {
    n = 0;
    for (j = 1; j <= nmlngth; j++) {
      if (nayme[p->index - 1][j - 1] != '\0')
        n = j;
    }
    chwrite(':', 1, &pos, leftedge, screenwidth);
    for (j = 0; j < n; j++)
      chwrite(nayme[p->index - 1][j], 1, &pos, leftedge, screenwidth);
  }
  putchar('\n');
}  /* move_drawline */


void move_printree()
{
  /* prints out diagram of the tree */
  long tipy, i, dow;

  if (!subtree)
    nuroot = root;
  if (changed || newtree)
    evaluate(root);
  if (display)
    move_hypstates();
  if (ansi || ibmpc)
    printf("\033[2J\033[H");
  else
    putchar('\n');
  tipy = 1;
  dow = down;
  if (spp * dow > screenlines && !subtree) {
    dow--;
  }
  if (noroot)
    printf("(unrooted)");
  if (display) {
    printf(" ");
    makechar(onne);
    printf(":1 ");
    makechar(question);
    printf(":? ");
    makechar(zerro);
    printf(":0 ");
  } else
    printf("             ");
  if (!earlytree) {
    printf("%10.1f Steps", -like);
  }
  if (display)
    printf("  CHAR%3ld", dispchar);
  else
    printf("         ");
  if (!earlytree) {
    printf("  %3ld chars compatible\n", compatible);
  }
  printf("                            ");
  if (changed && !earlytree) {
    if (-like < bestyet) {
      printf("     BEST YET!");
      bestyet = -like;
    } else if (fabs(-like - bestyet) < 0.000001)
      printf("  (as good as best)");
    else {
      if (-like < gotlike)
        printf("     better");
      else if (-like > gotlike)
        printf("     worse!");
    }
  }
  printf("\n");

  farthest = 0;
  coordinates(nuroot, &tipy, 1.5, &farthest);
  vmargin = 4;
  treelines = tipy - dow;
  if (topedge != 1) {
    printf("** %ld lines above screen **\n", topedge - 1);
    vmargin++;
  }

  if ((treelines - topedge + 1) > (screenlines - vmargin))
    vmargin++;
  for (i = 1; i <= treelines; i++) {
    if (i >= topedge && i < topedge + screenlines - vmargin)
      move_drawline(i, treelines);
  }

  if ((treelines - topedge + 1) > (screenlines - vmargin)) {
    printf("** %ld", treelines - (topedge - 1 + screenlines - vmargin));
    printf(" lines below screen **\n");
  }
  if (treelines - topedge + vmargin + 1 < screenlines)
    putchar('\n');
  gotlike = -like;
  changed = false;
}  /* move_printree */


void arbitree()
{
  long i;

  root = treenode[0];
  add2(treenode[0], treenode[1], treenode[spp], &root,
    restoring, wasleft, treenode);
  for (i = 3; i <= (spp); i++)
    add2(treenode[spp+ i - 3], treenode[i - 1], treenode[spp + i - 2],
      &root, restoring, wasleft, treenode);
  for (i = 0; i < (nonodes); i++)
    in_tree[i] = true;
}  /* arbitree */


void yourtree()
{
  long i, j;
  boolean ok;

  root = treenode[0];
  add2(treenode[0], treenode[1], treenode[spp], &root,
    restoring, wasleft, treenode);
  i = 2;
  do {
    i++;
    move_printree();
    printf("\nAdd species%3ld: \n", i);
    printf("   \n");
    for (j = 0; j < nmlngth; j++)
      putchar(nayme[i - 1][j]);
    do {
      printf("\nbefore node (type number): ");
      inpnum(&j, &ok);
      ok = (ok && ((j >= 1 && j < i) || (j > spp && j < spp + i - 1)));
      if (!ok)
        printf("Impossible number. Please try again:\n");
    } while (!ok);
    add2(treenode[j - 1], treenode[i - 1], treenode[spp + i - 2], &root,
      restoring, wasleft, treenode);
  } while (i != spp);
  for (i = 0; i < (nonodes); i++)
    in_tree[i] = true;
}  /* yourtree */


void initmovenode(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 */
  /* LM 7/27  I added this function and the commented lines around */
  /* treeread() to get the program running, but all 4 move programs*/
  /* are improperly integrated into the v4.0 support files.  As is */
  /* this is a patchwork function              */
  boolean minusread;
  double valyew, divisor;

  switch (whichinit) {
  case bottom:
    gnutreenode(grbg, p, nodei, chars, zeros);
    treenode[nodei - 1] = *p;
    break;
  case nonbottom:
    gnutreenode(grbg, p, nodei, chars, zeros);
    break;
  case tip:
    match_names_to_data (str, treenode, p, spp);
    break;
  case length:
    processlength(&valyew, &divisor, ch, &minusread, intree, parens);
    /* process lengths and discard */
  default:      /*cases hslength,hsnolength,treewt,unittrwt,iter,*/
    break;
  }
} /* initmovenode */


void initboolnames(node *p, boolean *names)
{
  /* sets BOOLEANs that indicate tips */
  node *q;

  if (p->tip) {
    names[p->index - 1] = true;
    return;
  }
  q = p->next;
  while (q != p) {
    initboolnames(q->back, names);
    q = q->next;
  }
}
/* initboolnames */


void get_usertree() 
{
  long i, j, nextnode;
  node *p;

  openfile(&intree,INTREE,"input tree file", "r",progname,intreename);
  names = (boolean *)Malloc(spp*sizeof(boolean));
  firsttree = true;                                            
  nodep = NULL;                                       
  nextnode = 0;                                           
  haslengths = 0;                                         
  zeros = (long *)Malloc(chars*sizeof(long));         
  for (i = 0; i < chars; i++)                           
    zeros[i] = 0;                                         
  treeread(intree, &root, treenode, &goteof, &firsttree, nodep, &nextnode, 
                  &haslengths, &grbg, initmovenode,false,nonodes); 
  for (i = spp; i < (nonodes); i++) {
    p = treenode[i];
    for (j = 1; j <= 3; j++) {
      p->stateone = (bitptr)Malloc(words*sizeof(long));
      p->statezero = (bitptr)Malloc(words*sizeof(long));
      p = p->next;
    }
  } 
  for (i = 0; i < spp; i++)
    names[i] = false;
  initboolnames(root, names);
  for (i = 0; i < (spp); i++)
    in_tree[i] = names[i];
  free(names);
  FClose(intree);
}

void buildtree()
{

  changed = false;
  newtree = false;
  switch (how) {

  case arb:
    arbitree();
    break;

  case use:
    get_usertree(); 
    break;

  case spec:
    yourtree();
    break;
  }
  if (!outgropt)
    outgrno = root->next->back->index;
  if (outgropt && in_tree[outgrno - 1])
    reroot(treenode[outgrno - 1]);
}  /* buildtree */


void rearrange()
{
  long i, j;
  boolean ok1, ok2;
  node *p, *q;

  printf("Remove everything to the right of which node? ");
  inpnum(&i, &ok1);
  ok1 = (ok1 && i >= 1 && i < spp * 2 && i != root->index);
  if (ok1) {
    printf("Add before which node? ");
    inpnum(&j, &ok2);
    ok2 = (ok2 && j >= 1 && j < spp * 2);
    if (ok2) {
      ok2 = (treenode[j - 1] != treenode[treenode[i - 1]->back->index - 1]);
      p = treenode[j - 1];
      while (p != root) {
        ok2 = (ok2 && p != treenode[i - 1]);
        p = treenode[p->back->index - 1];
      }
      if (ok1 && ok2) {
        what = i;
        q = treenode[treenode[i - 1]->back->index - 1];
        if (q->next->back->index == i)
          fromwhere = q->next->next->back->index;
        else
          fromwhere = q->next->back->index;
        towhere = j;
        re_move2(&treenode[i - 1], &q, &root, &wasleft, treenode);
        add2(treenode[j - 1], treenode[i - 1], q, &root,
          restoring, wasleft, treenode);
      }
      lastop = rearr;
    }
  }
  changed = (ok1 && ok2);
  move_printree();
  if (!(ok1 && ok2))
    printf("Not a possible rearrangement.   Try again: ");
  else {
    oldwritten =written;
    written = false;
  }
}  /* rearrange */


void tryadd(node *p, node *item, node *nufork, double *place)
{
  /* temporarily adds one fork and one tip to the tree.
     Records scores in array place */
  add2(p, item, nufork, &root, restoring, wasleft, treenode);
  evaluate(root);
  place[p->index - 1] = -like;
  re_move2(&item, &nufork, &root, &wasleft, treenode);
}  /* tryadd */


void addpreorder(node *p, node *item, node *nufork, double *place)
{
  /* traverses a binary tree, calling function tryadd
     at a node before calling tryadd at its descendants */
  if (p == NULL)
    return;
  tryadd(p,item,nufork,place);
  if (!p->tip) {
    addpreorder(p->next->back, item, nufork, place);
    addpreorder(p->next->next->back, item, nufork, place);
  }
}  /* addpreorder */


void try()
{
  /* Remove node, try it in all possible places */
  double *place;
  long i, j, oldcompat;
  double current;
  node *q, *dummy, *rute;
  boolean tied, better, ok;

  printf("Try other positions for which node? ");
  inpnum(&i, &ok);
  if (!(ok && i >= 1 && i <= nonodes && i != root->index)) {
    printf("Not a possible choice! ");
    return;
  }
  printf("WAIT ...\n");
  place = (double *)Malloc(nonodes*sizeof(double));
  for (j = 0; j < (nonodes); j++)
    place[j] = -1.0;
  evaluate(root);
  current = -like;
  oldcompat = compatible;
  what = i;
  q = treenode[treenode[i - 1]->back->index - 1];
  if (q->next->back->index == i)
    fromwhere = q->next->next->back->index;
  else
    fromwhere = q->next->back->index;
  rute = root;
  if (root->index == treenode[i - 1]->back->index) {
    if (treenode[treenode[i - 1]->back->index - 1]->next->back == treenode[i - 1])
      rute = treenode[treenode[i - 1]->back->index - 1]->next->next->back;
    else
      rute = treenode[treenode[i - 1]->back->index - 1]->next->back;
  }
  re_move2(&treenode[i - 1], &dummy, &root, &wasleft, treenode);
  oldleft = wasleft;
  root = rute;
  addpreorder(root, treenode[i - 1], dummy, place);
  wasleft =oldleft;
  restoring = true;
  add2(treenode[fromwhere - 1], treenode[what - 1],dummy, &root,
    restoring, wasleft, treenode);
  like = -current;
  compatible = oldcompat;
  restoring = false;
  better = false;
  printf("          BETTER: ");
  for (j = 1; j <= (nonodes); j++) {
    if (place[j - 1] < current && place[j - 1] >= 0.0) {
      printf("%3ld:%6.2f", j, place[j - 1]);
      better = true;
    }
  }
  if (!better)
    printf(" NONE");
  printf("\n          TIED:    ");
  tied = false;
  for (j = 1; j <= (nonodes); j++) {
    if (fabs(place[j - 1] - current) < 1.0e-6 && j != fromwhere) {
      if (j < 10)
        printf("%2ld", j);
      else
        printf("%3ld", j);
      tied = true;
    }
  }
  if (tied)
    printf(":%6.2f\n", current);
  else
    printf("NONE\n");
  changed = true;
  free(place);
}  /* try */


void undo()
{
  /* restore to tree before last rearrangement */
  long temp;
  boolean btemp;
  node *q;

  switch (lastop) {

  case rearr:
    restoring = true;
    oldleft = wasleft;
    re_move2(&treenode[what - 1], &q, &root, &wasleft, treenode);
    btemp = wasleft;
    wasleft = oldleft;
    add2(treenode[fromwhere - 1], treenode[what - 1],q, &root,
      restoring, wasleft, treenode);
    wasleft = btemp;
    restoring = false;
    temp = fromwhere;
    fromwhere = towhere;
    towhere = temp;
    changed = true;
    break;

  case flipp:
    q = treenode[atwhat - 1]->next->back;
    treenode[atwhat - 1]->next->back =
      treenode[atwhat - 1]->next->next->back;
    treenode[atwhat - 1]->next->next->back = q;
    treenode[atwhat - 1]->next->back->back = treenode[atwhat - 1]->next;
    treenode[atwhat - 1]->next->next->back->back =
      treenode[atwhat - 1]->next->next;
    break;

  case reroott:
    restoring = true;
    temp = oldoutgrno;
    oldoutgrno = outgrno;
    outgrno = temp;
    reroot(treenode[outgrno - 1]);
    restoring = false;
    break;

  case none:
    /* blank case */
    break;
  }
  move_printree();
  if (lastop == none) {
    printf("No operation to undo! \n");
    return;
  }
  btemp = oldwritten;
  oldwritten = written;
  written = btemp;
}  /* undo */


void treewrite(boolean done)
{
  /* write out tree to a file */
  Char ch;

  treeoptions(waswritten, &ch, &outtree, outtreename, progname);
  if (!done)
    move_printree();
  if (waswritten && ch == 'N')
    return;
  col = 0;
  treeout(root, 1, &col, root);
  printf("\nTree written to file \"%s\"\n\n", outtreename);
  waswritten = true;
  written = true;
  FClose(outtree);
#ifdef MAC
  fixmacfile(outtreename);
#endif
}
  /* treewrite */


void clade()
{
  /* pick a subtree and show only that on screen */
  long i;
  boolean ok;

  printf("Select subtree rooted at which node (0 for whole tree)? ");
  inpnum(&i, &ok);
  ok = (ok && (unsigned)i <= nonodes);
  if (ok) {
    subtree = (i > 0);
    if (subtree)
      nuroot = treenode[i - 1];
    else
      nuroot = root;
  }
  move_printree();
  if (!ok)
    printf("Not possible to use this node. ");
}  /* clade */


void flip()
{
  /* flip at a node left-right */
  long i;
  boolean ok;
  node *p;

  printf("Flip branches at which node? ");
  inpnum(&i, &ok);
  ok = (ok && i > spp && i <= nonodes);
  if (ok) {
    p = treenode[i - 1]->next->back;
    treenode[i - 1]->next->back = treenode[i - 1]->next->next->back;
    treenode[i - 1]->next->next->back = p;
    treenode[i - 1]->next->back->back = treenode[i - 1]->next;
    treenode[i - 1]->next->next->back->back = treenode[i - 1]->next->next;
    atwhat = i;
    lastop = flipp;
  }
  move_printree();
  if (ok) {
    oldwritten = written;
    written = false;
    return;
  }
  if (i >= 1 && i <= spp)
    printf("Can't flip there. ");
  else
    printf("No such node. ");
}  /* flip */


void changeoutgroup()
{
  long i;
  boolean ok;

  oldoutgrno = outgrno;
  do {
    printf("Which node should be the new outgroup? ");
    inpnum(&i, &ok);
    ok = (ok && in_tree[i - 1] && i >= 1 && i <= nonodes &&
          i != root->index);
    if (ok)
      outgrno = i;
  } while (!ok);
  if (in_tree[outgrno - 1])
    reroot(treenode[outgrno - 1]);
  changed = true;
  lastop = reroott;
  move_printree();
  oldwritten = written;
  written = false;
}  /* changeoutgroup */


void redisplay()
{
  boolean done=false;
  waswritten = false;
  do {
    printf("\nNEXT? (Options: R # + - S . T U W O F H J K L C ? X Q) ");
    printf("(? for Help) ");
#ifdef WIN32
    phyFillScreenColor();
#endif
    scanf("%c%*[^\n]", &ch);
    getchar();
    if (ch == '\n')
      ch = ' ';
    uppercase(&ch);
    if (strchr("R#+-S.TUWOFHJKLC?XQ",ch) != NULL){
      switch (ch) {

      case 'R':
        rearrange();
        break;

      case '#':
        nextinc(&dispchar, &dispword, &dispbit, chars, bits, &display,
                  numsteps, weight);
        move_printree();
        break;

      case '+':
        nextchar(&dispchar, &dispword, &dispbit, chars, bits, &display);
        move_printree();
        break;

      case '-':
        prevchar(&dispchar, &dispword, &dispbit, chars, bits, &display);
        move_printree();
        break;

      case 'S':
        show(&dispchar, &dispword, &dispbit, chars, bits, &display);
        move_printree();
        break;

      case '.':
        move_printree();
        break;

      case 'T':
        try();
        break;

      case 'U':
        undo();
        break;

      case 'W':
        treewrite(done);
        break;

      case 'O':
        changeoutgroup();
        break;

      case 'F':
        flip();
        break;

      case 'H':
        window(left, &leftedge, &topedge, hscroll, vscroll, treelines,
                 screenlines, screenwidth, farthest, subtree);
        move_printree();
        break;

      case 'J':
        window(downn, &leftedge, &topedge, hscroll, vscroll, treelines,
                 screenlines, screenwidth, farthest, subtree);
        move_printree();
        break;

      case 'K':
        window(upp, &leftedge, &topedge, hscroll, vscroll, treelines,
                 screenlines, screenwidth, farthest, subtree);
        move_printree();
        break;

      case 'L':
        window(right, &leftedge, &topedge, hscroll, vscroll, treelines,
                 screenlines, screenwidth, farthest, subtree);
        move_printree();
        break;

      case 'C':
        clade();
        break;

      case '?':
        help("character");
        move_printree();
        break;

      case 'X':
        done = true;
        break;

      case 'Q':
        done = true;
        break;
      }
    }
  } while (!done);
  if (!written) {
    do {
      printf("Do you want to write out the tree to a file? (Y or N) ");
#ifdef WIN32
      phyFillScreenColor();
#endif
      scanf("%c%*[^\n]", &ch);
      getchar();
      if (ch == '\n')
        ch = ' ';
    } while (ch != 'Y' && ch != 'y' && ch != 'N' && ch != 'n');
  }
  if (ch == 'Y' || ch == 'y')
    treewrite(done);
}  /* redisplay */


void treeconstruct()
{
  /* constructs a binary tree from the pointers in treenode. */

  restoring = false;
  subtree = false;
  display = false;
  dispchar = 0;
  fullset = (1L << (bits + 1)) - (1L << 1);
  earlytree = true;
  buildtree();
  waswritten = false;
  printf("\nComputing steps needed for compatibility in characters...\n\n");
  newtree = true;
  earlytree = false;
  move_printree();
  bestyet = -like;
  gotlike = -like;
  lastop = none;
  newtree = false;
  written = false;
  redisplay();
}  /* treeconstruct */


int main(int argc, Char *argv[])
{  /* Interactive mixed parsimony                                      */
   /* reads in spp, chars, and the data. Then calls treeconstruct to   */
   /*  construct the tree and query the user                           */
#ifdef MAC
  argc = 1;                /* macsetup("Move","");                */
  argv[0] = "Move";
#endif
  init(argc, argv);
  progname = argv[0];
  strcpy(infilename,INFILE);
  strcpy(intreename,INTREE);
  strcpy(outtreename,OUTTREE);
  openfile(&infile,infilename,"input file", "r",argv[0],infilename);

  screenlines = 24;
  scrollinc = 20;
  screenwidth = 80;
  topedge = 1;
  leftedge = 1;
  ibmpc = IBMCRT;
  ansi = ANSICRT;
  root = NULL;
  bits = 8*sizeof(long) - 1;
  doinput();
  configure();
  treeconstruct();
  FClose(outtree);
#ifdef MAC
  fixmacfile(outtreename);
#endif
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  return 0;
}  /* Interactive mixed parsimony */
