| 1 | /* |
|---|
| 2 | * njproc.c Adachi, J. 1995.10.30 |
|---|
| 3 | * Copyright (C) 1993-1995 J. Adachi & M. Hasegawa. All rights reserved. |
|---|
| 4 | */ |
|---|
| 5 | |
|---|
| 6 | #include "tridist.h" |
|---|
| 7 | |
|---|
| 8 | #define REV 0 |
|---|
| 9 | |
|---|
| 10 | #define DMIN -1.0e300 |
|---|
| 11 | |
|---|
| 12 | void |
|---|
| 13 | distantree(tr, dmat, numspc) |
|---|
| 14 | Tree *tr; |
|---|
| 15 | dmatrix dmat; |
|---|
| 16 | int numspc; |
|---|
| 17 | { |
|---|
| 18 | int i, j, ii, jj, kk, otui, otuj, nsp2, cinode, restsp; |
|---|
| 19 | double dij, bix, bjx, bkx, sij, smax, dnsp2, dij2; |
|---|
| 20 | ivector otu; |
|---|
| 21 | dvector r; |
|---|
| 22 | Node **psotu, *cp, *ip, *jp, *kp; |
|---|
| 23 | |
|---|
| 24 | cinode = numspc; |
|---|
| 25 | nsp2 = numspc - 2; |
|---|
| 26 | dnsp2 = 1.0 / nsp2; |
|---|
| 27 | r = new_dvector(numspc); |
|---|
| 28 | otu = new_ivector(numspc); |
|---|
| 29 | psotu = (Node **)new_npvector(numspc); |
|---|
| 30 | for (i = 0; i < numspc; i++) { |
|---|
| 31 | otu[i] = i; |
|---|
| 32 | psotu[i] = tr->brnchp[i]->kinp; |
|---|
| 33 | } |
|---|
| 34 | |
|---|
| 35 | for (restsp = numspc; restsp > 3; restsp--) { |
|---|
| 36 | |
|---|
| 37 | if (Upgma_optn) { |
|---|
| 38 | for (i = 0, smax = DMIN; i < restsp-1; i++) { |
|---|
| 39 | ii = otu[i]; |
|---|
| 40 | for (j = i + 1; j < restsp; j++) { |
|---|
| 41 | jj = otu[j]; |
|---|
| 42 | sij = - dmat[ii][jj]; |
|---|
| 43 | /* printf("%3d%3d %10.5f\n",ii+1,jj+1,sij); */ |
|---|
| 44 | #if REV |
|---|
| 45 | sij = - sij; |
|---|
| 46 | #endif /* REV */ |
|---|
| 47 | if (sij > smax) { |
|---|
| 48 | smax = sij; otui = i; otuj = j; |
|---|
| 49 | } |
|---|
| 50 | } |
|---|
| 51 | } |
|---|
| 52 | } else { /* NJ */ |
|---|
| 53 | for (i = 0; i < restsp; i++) { |
|---|
| 54 | ii = otu[i]; |
|---|
| 55 | for (j = 0, sij = 0.0; j < restsp; j++) sij += dmat[ii][otu[j]]; |
|---|
| 56 | r[ii] = sij; |
|---|
| 57 | } |
|---|
| 58 | for (i = 0, smax = DMIN; i < restsp-1; i++) { |
|---|
| 59 | ii = otu[i]; |
|---|
| 60 | for (j = i + 1; j < restsp; j++) { |
|---|
| 61 | jj = otu[j]; |
|---|
| 62 | sij = ( r[ii] + r[jj] ) * dnsp2 - dmat[ii][jj]; /* max */ |
|---|
| 63 | /* printf("%3d%3d %9.3f %9.3f %9.3f\n", |
|---|
| 64 | ii+1,jj+1,sij,r[ii],r[jj]); */ |
|---|
| 65 | #if REV |
|---|
| 66 | sij = - sij; |
|---|
| 67 | #endif /* REV */ |
|---|
| 68 | if (sij > smax) { |
|---|
| 69 | smax = sij; otui = i; otuj = j; |
|---|
| 70 | } |
|---|
| 71 | } |
|---|
| 72 | } |
|---|
| 73 | } /* Upgma_optn */ |
|---|
| 74 | |
|---|
| 75 | ii = otu[otui]; |
|---|
| 76 | jj = otu[otuj]; |
|---|
| 77 | dij = dmat[ii][jj]; |
|---|
| 78 | dij2 = dij * 0.5; |
|---|
| 79 | if (Upgma_optn) { |
|---|
| 80 | bix = dij2; |
|---|
| 81 | bjx = dij2; |
|---|
| 82 | } else { |
|---|
| 83 | bix = (dij + r[ii]/nsp2 - r[jj]/nsp2) * 0.5; |
|---|
| 84 | bjx = dij - bix; |
|---|
| 85 | } |
|---|
| 86 | cp = tr->brnchp[cinode]; |
|---|
| 87 | ip = psotu[ii]; |
|---|
| 88 | jp = psotu[jj]; |
|---|
| 89 | cp->isop = ip; |
|---|
| 90 | ip->isop = jp; |
|---|
| 91 | jp->isop = cp; |
|---|
| 92 | ip->length += bix; |
|---|
| 93 | jp->length += bjx; |
|---|
| 94 | ip->kinp->length = ip->length; |
|---|
| 95 | jp->kinp->length = jp->length; |
|---|
| 96 | cp = cp->kinp; |
|---|
| 97 | cp->length = - dij2; |
|---|
| 98 | psotu[ii] = cp; |
|---|
| 99 | psotu[jj] = NULL; |
|---|
| 100 | for (j = 0; j < restsp; j++) { |
|---|
| 101 | kk = otu[j]; |
|---|
| 102 | if (kk != ii && kk != jj) { |
|---|
| 103 | dij = (dmat[ii][kk] + dmat[jj][kk]) * 0.5; |
|---|
| 104 | dmat[ii][kk] = dij; |
|---|
| 105 | dmat[kk][ii] = dij; |
|---|
| 106 | } |
|---|
| 107 | dmat[jj][kk] = 0.0; |
|---|
| 108 | dmat[kk][jj] = 0.0; |
|---|
| 109 | } |
|---|
| 110 | Numbrnch = ++cinode; |
|---|
| 111 | dnsp2 = 1.0 / --nsp2; |
|---|
| 112 | if (Debug_optn) { |
|---|
| 113 | for (putchar('\n'), j = 0; j < restsp; j++) printf("%6d",otu[j]+1); |
|---|
| 114 | for (putchar('\n'), i = 0; i < restsp; i++, putchar('\n')) { |
|---|
| 115 | for (j = 0, ii = otu[i]; j < restsp; j++) { |
|---|
| 116 | printf("%6.0f", dmat[ii][otu[j]]*100); |
|---|
| 117 | } |
|---|
| 118 | } |
|---|
| 119 | } |
|---|
| 120 | for (j = otuj; j < restsp - 1; j++) otu[j] = otu[j + 1]; |
|---|
| 121 | |
|---|
| 122 | } /* for restsp */ |
|---|
| 123 | |
|---|
| 124 | ii = otu[0]; |
|---|
| 125 | jj = otu[1]; |
|---|
| 126 | kk = otu[2]; |
|---|
| 127 | if (Upgma_optn) { |
|---|
| 128 | if (dmat[ii][jj] < dmat[ii][kk]) { |
|---|
| 129 | if (dmat[jj][kk] < dmat[ii][jj]) { |
|---|
| 130 | i = ii; ii = jj; jj = kk; kk = i; |
|---|
| 131 | } |
|---|
| 132 | } else { |
|---|
| 133 | if (dmat[ii][kk] < dmat[jj][kk]) { |
|---|
| 134 | j = jj; jj = kk; kk = j; |
|---|
| 135 | } else { |
|---|
| 136 | i = ii; ii = jj; jj = kk; kk = i; |
|---|
| 137 | } |
|---|
| 138 | } |
|---|
| 139 | bix = dmat[ii][jj] * 0.5; |
|---|
| 140 | bjx = dmat[ii][jj] * 0.5; |
|---|
| 141 | bkx = (dmat[ii][kk] + dmat[jj][kk] - dmat[ii][jj]) * 0.5; |
|---|
| 142 | } else { /* NJ */ |
|---|
| 143 | bix = (dmat[ii][jj] + dmat[ii][kk] - dmat[jj][kk]) * 0.5; |
|---|
| 144 | bjx = dmat[ii][jj] - bix; |
|---|
| 145 | bkx = dmat[ii][kk] - bix; |
|---|
| 146 | } |
|---|
| 147 | ip = psotu[ii]; |
|---|
| 148 | jp = psotu[jj]; |
|---|
| 149 | kp = psotu[kk]; |
|---|
| 150 | ip->isop = jp; |
|---|
| 151 | jp->isop = kp; |
|---|
| 152 | kp->isop = ip; |
|---|
| 153 | ip->length += bix; |
|---|
| 154 | jp->length += bjx; |
|---|
| 155 | kp->length += bkx; |
|---|
| 156 | ip->kinp->length = ip->length; |
|---|
| 157 | jp->kinp->length = jp->length; |
|---|
| 158 | kp->kinp->length = kp->length; |
|---|
| 159 | tr->ablength = sij; |
|---|
| 160 | if (Upgma_optn) { |
|---|
| 161 | tr->rootp = kp; |
|---|
| 162 | } else { |
|---|
| 163 | if (Outgr_optn) { |
|---|
| 164 | reroot(tr, tr->brnchp[Outgroup]->kinp); |
|---|
| 165 | } else { |
|---|
| 166 | reroot(tr, tr->brnchp[numspc-1]->kinp); /* tr->rootp = kp; */ |
|---|
| 167 | } |
|---|
| 168 | } |
|---|
| 169 | free_dvector(r); |
|---|
| 170 | free_ivector(otu); |
|---|
| 171 | free_npvector(psotu); |
|---|
| 172 | } /*_ distantree */ |
|---|
