void doinit(void) { /* initializes variables */ inputnumbersstate(phylostates[0], &spp, &chars, &nonodes, 1); words = chars / bits + 1; // if (printdata) // fprintf(outfile, "%2ld species, %3ld characters\n\n", spp, chars); alloctree(&treenode); setuptree(treenode); allocrest(); } /* doinit */
void maketree() { /* construct the tree */ long i ; inputdata(replicates, printdata, lower, upper, x, reps); /* if (njoin && (spp < 3)) { mexPrintf("\nERROR: Neighbor-Joining runs must have at least 3 species\n\n"); exxit(-1); } */ if (progress) putchar('\n'); if (ith == 1) setuptree(&curtree, nonodes2 + 1); for (i = 1; i <= spp; i++) enterorder[i - 1] = i; if (jumble) randumize(seed, enterorder); for (i = 0; i < spp; i++) cluster[i] = curtree.nodep[i]; jointree(); if (njoin) curtree.start = curtree.nodep[outgrno - 1]->back; printree(curtree.start, treeprint, njoin, (boolean)(!njoin)); if (treeprint) summarize(); if (trout) { col = 0; if (njoin) treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start); else curtree.root = curtree.start, treeoutr(curtree.start,&col,&curtree); } if (progress) { mexPrintf("\nOutput written on file \"%s\"\n\n", outfilename); if (trout) mexPrintf("Tree written on file \"%s\"\n\n", outtreename); } } /* maketree */
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(factors) openfile(&factfile,FACTFILE,"factors file", "r",progname,factfilename); alloctree(&treenode); setuptree(treenode); allocrest(); inputoptions(); inputdata(treenode, dollo, false, stdout); } /* doinput */
void maketree() { /* construct the tree */ long i ; inputdata(replicates, printdata, lower, upper, x, reps); if (progress) putchar('\n'); if (ith == 1) setuptree(&curtree, nonodes2 + 1); for (i = 1; i <= spp; i++) enterorder[i - 1] = i; if (jumble) randumize(seed, enterorder); for (i = 0; i < spp; i++) cluster[i] = curtree.nodep[i]; jointree(); if (outgropt) curtree.start = curtree.nodep[outgrno - 1]->back; printree(&curtree, curtree.start->next, treeprint, njoin, !njoin); if (treeprint) summarize(); if (trout) { col = 0; if (njoin) treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start); else curtree.root = curtree.start, treeoutr(curtree.start,&col,&curtree); } if (progress) { printf("\nOutput written on output file\n\n"); if (trout) printf("Tree written on tree file\n\n"); } } /* maketree */
void globrearrange() { /* does global rearrangements */ tree globtree; tree oldtree; int i,j,k,num_sibs,num_sibs2; node *where,*sib_ptr,*sib_ptr2; double oldbestyet = curtree.likelihood; int success = false; alloctree(&globtree.nodep,nonodes2); alloctree(&oldtree.nodep,nonodes2); setuptree(&globtree,nonodes2); setuptree(&oldtree,nonodes2); allocview(&oldtree, nonodes2, totalleles); allocview(&globtree, nonodes2, totalleles); copy_(&curtree,&globtree); copy_(&curtree,&oldtree); for ( i = spp ; i < nonodes2 ; i++ ) { num_sibs = count_sibs(curtree.nodep[i]); sib_ptr = curtree.nodep[i]; if ( (i - spp) % (( nonodes2 / 72 ) + 1 ) == 0 ) putchar('.'); fflush(stdout); for ( j = 0 ; j <= num_sibs ; j++ ) { re_move(&sib_ptr,&where); copy_(&curtree,&priortree); if (where->tip) { copy_(&oldtree,&curtree); copy_(&oldtree,&bestree); sib_ptr = sib_ptr->next; continue; } else num_sibs2 = count_sibs(where); sib_ptr2 = where; for ( k = 0 ; k < num_sibs2 ; k++ ) { addwhere = NULL; addtraverse(sib_ptr,sib_ptr2->back,true); if ( addwhere && where != addwhere && where->back != addwhere && bestree.likelihood > globtree.likelihood) { copy_(&bestree,&globtree); success = true; } sib_ptr2 = sib_ptr2->next; } copy_(&oldtree,&curtree); copy_(&oldtree,&bestree); sib_ptr = sib_ptr->next; } } copy_(&globtree,&curtree); copy_(&globtree,&bestree); if (success && globtree.likelihood > oldbestyet) { succeeded = true; } else { succeeded = false; } freeview(&oldtree, nonodes2); freeview(&globtree, nonodes2); freetree(&globtree.nodep,nonodes2); freetree(&oldtree.nodep,nonodes2); }
void maketree() { /* construct the tree */ long i; if (usertree) { /* Open in binary: ftell() is broken for UNIX line-endings under WIN32 */ openfile(&intree,INTREE,"input tree file", "rb",progname,intreename); numtrees = countsemic(&intree); if(numtrees > MAXSHIMOTREES) shimotrees = MAXSHIMOTREES; else shimotrees = numtrees; if (numtrees > 2) initseed(&inseed, &inseed0, seed); if (treeprint) { fprintf(outfile, "User-defined tree"); if (numtrees > 1) putc('s', outfile); putc('\n', outfile); } setuptree(&curtree, nonodes2); for (which = 1; which <= spp; which++) inittip(which, &curtree); which = 1; while (which <= numtrees) { for (i = 0 ; i < nonodes2 ; i++) { if ( i > spp) { /* must do this since not all nodes may be used if an unrooted tree is read in after a rooted one */ curtree.nodep[i]->back = NULL; curtree.nodep[i]->next->back = NULL; curtree.nodep[i]->next->next->back = NULL; } else curtree.nodep[i]->back = NULL; } treeread2 (intree, &curtree.start, curtree.nodep, lengths, &trweight, &goteof, &haslengths, &spp,false,nonodes2); curtree.start = curtree.nodep[outgrno - 1]->back; treevaluate(); printree(); summarize(); which++; } FClose(intree); if (numtrees > 1 && loci > 1 ) { weight = (long *)Malloc(loci*sizeof(long)); for (i = 0; i < loci; i++) weight[i] = 1; standev2(numtrees, maxwhich, 0, loci-1, maxlogl, l0gl, l0gf, seed); free(weight); fprintf(outfile, "\n\n"); } } else { /* if ( !usertree ) */ if (jumb == 1) { setuptree(&curtree, nonodes2); setuptree(&priortree, nonodes2); setuptree(&bestree, nonodes2); if (njumble > 1) setuptree(&bestree2, nonodes2); } for (i = 1; i <= spp; i++) enterorder[i - 1] = i; if (jumble) randumize(seed, enterorder); nextsp = 3; buildsimpletree(&curtree); curtree.start = curtree.nodep[enterorder[0] - 1]->back; if (jumb == 1) numtrees = 1; nextsp = 4; if (progress) { printf("Adding species:\n"); writename(0, 3, enterorder); #ifdef WIN32 phyFillScreenColor(); #endif } while (nextsp <= spp) { buildnewtip(enterorder[nextsp - 1], &curtree, nextsp); copy_(&curtree, &priortree); bestree.likelihood = -DBL_MAX; addtraverse(curtree.nodep[enterorder[nextsp - 1] - 1]->back, curtree.start, true ); copy_(&bestree, &curtree); if (progress) { writename(nextsp - 1, 1, enterorder); #ifdef WIN32 phyFillScreenColor(); #endif } if (global && nextsp == spp) { if (progress) { printf("\nDoing global rearrangements\n"); printf(" !"); for (i = 1; i <= spp - 2; i++) if ( (i - spp) % (( nonodes2 / 72 ) + 1 ) == 0 ) putchar('-'); printf("!\n"); printf(" "); } } succeeded = true; while (succeeded) { succeeded = false; if ( global && nextsp == spp ) globrearrange(); else rearrange(curtree.start); if (global && nextsp == spp) putc('\n', outfile); } if (global && nextsp == spp && progress) putchar('\n'); if (njumble > 1) { if (jumb == 1 && nextsp == spp) copy_(&bestree, &bestree2); else if (nextsp == spp) { if (bestree2.likelihood < bestree.likelihood) copy_(&bestree, &bestree2); } } if (nextsp == spp && jumb == njumble) { if (njumble > 1) copy_(&bestree2, &curtree); curtree.start = curtree.nodep[outgrno - 1]->back; printree(); summarize(); } nextsp++; } } if ( jumb < njumble) return; if (progress) { printf("\nOutput written to file \"%s\"\n", outfilename); if (trout) printf("\nTree also written onto file \"%s\"\n", outtreename); } freeview(&curtree, nonodes2); if (!usertree) { freeview(&bestree, nonodes2); freeview(&priortree, nonodes2); } for (i = 0; i < spp; i++) free(x[i]); if (!contchars) { free(locus); free(pbar); } } /* maketree */
void maketree() { /* contruct the tree */ long nextsp,numtrees; boolean succeeded=false; long i, j, which; if (usertree) { inputdata(replicates, printdata, lower, upper, x, reps); setuptree(&curtree, nonodes2); for (which = 1; which <= spp; which++) setuptipf(which, &curtree); if (eoln(infile)) { fscanf(infile, "%*[^\n]"); getc(infile); } openfile(&intree,INTREE,"input tree file","r",progname,intreename); fscanf(intree, "%ld%*[^\n]", &numtrees); getc(intree); if (numtrees > MAXNUMTREES) { printf("\nERROR: number of input trees is read incorrectly from %s\n", intreename); exxit(-1); } if (treeprint) { fprintf(outfile, "User-defined tree"); if (numtrees > 1) putc('s', outfile); fprintf(outfile, ":\n\n"); } first = true; which = 1; while (which <= numtrees) { treeread2 (intree, &curtree.start, curtree.nodep, lengths, &trweight, &goteof, intreename, "Fitch", &haslengths, &spp); nums = spp; curtree.start = curtree.nodep[outgrno - 1]->back; treevaluate(); printree(&curtree, curtree.start, treeprint, false, false); summarize(numtrees); which++; } FClose(intree); } else { if (jumb == 1) { inputdata(replicates, printdata, lower, upper, x, reps); setuptree(&curtree, nonodes2); setuptree(&priortree, nonodes2); setuptree(&bestree, nonodes2); if (njumble > 1) setuptree(&bestree2, nonodes2); } for (i = 1; i <= spp; i++) enterorder[i - 1] = i; if (jumble) randumize(seed, enterorder); nextsp = 3; buildsimpletree(&curtree, nextsp); curtree.start = curtree.nodep[enterorder[0] - 1]->back; if (jumb == 1) numtrees = 1; nextsp = 4; if (progress) { printf("Adding species:\n"); writename(0, 3, enterorder); #ifdef WIN32 phyFillScreenColor(); #endif } while (nextsp <= spp) { nums = nextsp; buildnewtip(enterorder[nextsp - 1], &curtree, nextsp); copy_(&curtree, &priortree); bestree.likelihood = -99999.0; addtraverse(curtree.nodep[enterorder[nextsp - 1] - 1]->back, curtree.start, true, &numtrees,&succeeded); copy_(&bestree, &curtree); if (progress) { writename(nextsp - 1, 1, enterorder); #ifdef WIN32 phyFillScreenColor(); #endif } if (global && nextsp == spp) { if (progress) { printf("Doing global rearrangements\n"); printf(" !"); for (j = 1; j <= (spp - 2); j++) putchar('-'); printf("!\n"); printf(" "); } } succeeded = true; while (succeeded) { succeeded = false; rearrange(curtree.start, &numtrees,&nextsp,&succeeded); if (global && ((nextsp) == spp) && progress) printf("\n "); } if (global && nextsp == spp) { putc('\n', outfile); if (progress) putchar('\n'); } if (njumble > 1) { if (jumb == 1 && nextsp == spp) copy_(&bestree, &bestree2); else if (nextsp == spp) { if (bestree2.likelihood < bestree.likelihood) copy_(&bestree, &bestree2); } } if (nextsp == spp && jumb == njumble) { if (njumble > 1) copy_(&bestree2, &curtree); curtree.start = curtree.nodep[outgrno - 1]->back; printree(&curtree, curtree.start, treeprint, true, false); summarize(numtrees); } nextsp++; } } if (jumb == njumble && progress) { printf("\nOutput written to output file\n\n"); if (trout) { printf("Tree also written onto file\n"); putchar('\n'); } } } /* maketree */