/dports/biology/treepuzzle/tree-puzzle-5.2/src/ |
H A D | split.c | 43 for (j = 0; j < Maxspc; j++) tmpedgeofleaf[j]=-1; in inittree_split() 51 for (j = 0; j < Maxspc; j++) (tmpedge)[i].split[j]=-1; in inittree_split() 124 for (i = 0; i < 2 * Maxspc - 3; i++) { in freetree_split() 169 for (n = Maxspc - edge[m].downsize; n<Maxspc; n++) in check_split() 271 for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { in updatetreesplits_split() 302 edge, Maxspc, Maxbrnch, edgeofleaf, in updatetreesplits_split() 308 edge, Maxspc, Maxbrnch, edgeofleaf, in updatetreesplits_split() 343 if (nextleaf >= Maxspc) { in addnextleaf_split() 409 for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { in computepenalties_split() 484 neighbormatr = new_ulimatrix(Maxspc,Maxspc); in onepstep_split() [all …]
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H A D | mrca.c | 54 for (j = 0; j < Maxspc; j++) { in inittree_mrca() 86 for (i=0; i < Maxspc; i++) { in inittree_mrca() 134 for (i = 0; i < 2 * Maxspc - 3; i++) { in freetree_mrca() 221 for (n=0; n < Maxspc; n++) { in updatetreeclusters_mrca() 338 for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { 412 if (nextleaf >= Maxspc) { in addnextleaf_mrca() 635 computepenalties_mrca(left, Maxspc, in computepenaltiestree_mrca() 699 for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { 778 neighbormatr = new_ulimatrix(Maxspc,Maxspc); in onepstep_mrca() 784 mrcamatrix = new_imatrix(Maxspc,Maxspc); in onepstep_mrca() [all …]
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H A D | recur-old.c | 128 for (i = 0; i < 2 * Maxspc - 3; i++) { in freetree_recur() 175 for (n = Maxspc - edge[m].downsize; n<Maxspc; n++) 276 for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { 350 if (nextleaf >= Maxspc) { in addnextleaf_recur() 443 computepenalties_recur(left, Maxspc, in computepenalties_recur() 549 computepenalties_recur(left, Maxspc, in computepenaltiestree_recur() 554 computepenalties_recur(right, Maxspc, in computepenaltiestree_recur() 657 for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) 661 for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { 742 neighbormatr = new_ulimatrix(Maxspc,Maxspc); in onepstep_recur() [all …]
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H A D | pstep-split.c | 283 if (nextleaf >= Maxspc) { in addnextleaf_split() 619 for (i = 3; i < Maxspc; i++) { in onepstep_split() 695 bp[n] = new_cmatrix(Maxspc - 3, Maxspc); in allpstep_split() 701 trueIDtmp = new_ivector(Maxspc); in allpstep_split() 705 fixedchooser(Maxspc, Maxspc, trueIDtmp); in allpstep_split() 708 chooser(Maxspc, Maxspc, trueIDtmp); in allpstep_split() 710 permutetaxa_ss(Maxspc, trueIDtmp, Namestr, in allpstep_split() 725 biparts, outgroup, Maxspc); in allpstep_split() 727 makenewsplitentries(biparts, Maxspc-3, in allpstep_split() 730 &maxbiparts, Maxspc); in allpstep_split() [all …]
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H A D | recur.c | 115 for (i = 0; i < 2 * Maxspc - 3; i++) { in freetree_recur() 191 edge, Maxspc, Maxbrnch, edgeofleaf, in updatetreeclusters_recur() 230 for (n = Maxspc - edge[m].downsize; n<Maxspc; n++) 333 for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { 406 if (nextleaf >= Maxspc) { in addnextleaf_recur() 501 computepenalties_recur(left, Maxspc, in computepenalties_recur() 607 computepenalties_recur(left, Maxspc, in computepenaltiestree_recur() 612 computepenalties_recur(right, Maxspc, in computepenaltiestree_recur() 706 for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { 784 neighbormatr = new_ulimatrix(Maxspc,Maxspc); in onepstep_recur() [all …]
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H A D | pstep.c | 337 if (nextleaf >= Maxspc) { in addnextleaf_orig() 624 for (i = 3; i < Maxspc; i++) { in onepstep_orig() 736 bp[n] = new_cmatrix(Maxspc - 3, Maxspc); in allpstep() 745 trueIDtmp = new_ivector(Maxspc); in allpstep() 749 fixedchooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 752 chooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 768 &psteprootleaf, quartetinfo, Maxspc, in allpstep() 774 &psteprootleaf, quartetinfo, Maxspc, in allpstep() 780 &psteprootleaf, quartetinfo, Maxspc, in allpstep() 786 &psteprootleaf, quartetinfo, Maxspc, in allpstep() [all …]
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H A D | consensus.c | 38 biparts = new_cmatrix(Maxspc-3, Maxspc); in initconsensus() 41 if (Maxspc % 32 == 0) in initconsensus() 42 splitlength = Maxspc/32; in initconsensus() 43 else splitlength = (Maxspc + 32 - (Maxspc % 32))/32; in initconsensus() 92 for (i = 0; i < Maxspc - 3; i++) in computebiparts() 93 for (j = 0; j < Maxspc; j++) in computebiparts() 105 for (j = 0; j < Maxspc; j++) { in computebiparts() 309 for(n=0; n<Maxspc; n++) { in quartsupport() 459 consbiparts = new_cmatrix( (Maxspc-3) + 1, Maxspc + 1); in makeconsensus() 824 ymin = 2*Maxspc - 2; in nodecoordinates() [all …]
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H A D | pstep-trueID.c | 155 if (nextleaf >= Maxspc) { in addnextleaf_orig() 491 for (i = 3; i < Maxspc; i++) { in onepstep() 566 bp[n] = new_cmatrix(Maxspc - 3, Maxspc); in allpstep() 572 trueIDtmp = new_ivector(Maxspc); in allpstep() 576 fixedchooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 579 chooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 581 permutetaxa_ss(Maxspc, trueIDtmp, Namestr, in allpstep() 597 biparts, outgroup, Maxspc); in allpstep() 599 makenewsplitentries(biparts, Maxspc-3, in allpstep() 602 &maxbiparts, Maxspc); in allpstep() [all …]
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H A D | pstep-mrca.c | 151 if (nextleaf >= Maxspc) { in addnextleaf_orig() 480 for (i = 3; i < Maxspc; i++) { in onepstep() 554 bp[n] = new_cmatrix(Maxspc - 3, Maxspc); in allpstep() 560 trueIDtmp = new_ivector(Maxspc); in allpstep() 565 fixedchooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 567 chooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 577 biparts, outgroup, Maxspc); in allpstep() 579 makenewsplitentries(biparts, Maxspc-3, in allpstep() 582 &maxbiparts, Maxspc); in allpstep() 591 makenewsplitentries(bp[Currtrial], Maxspc-3, in allpstep() [all …]
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H A D | pstep-recursive.c | 151 if (nextleaf >= Maxspc) { in addnextleaf_orig() 480 for (i = 3; i < Maxspc; i++) { in onepstep() 554 bp[n] = new_cmatrix(Maxspc - 3, Maxspc); in allpstep() 560 trueIDtmp = new_ivector(Maxspc); in allpstep() 565 fixedchooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 567 chooser(Maxspc, Maxspc, trueIDtmp); in allpstep() 577 biparts, outgroup, Maxspc); in allpstep() 579 makenewsplitentries(biparts, Maxspc-3, in allpstep() 582 &maxbiparts, Maxspc); in allpstep() 591 makenewsplitentries(bp[Currtrial], Maxspc-3, in allpstep() [all …]
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H A D | pstep.h | 274 int Maxspc, /* in: Number of species (n) */ 290 int Maxspc, /* No. of species */ 299 int Maxspc); /* No. of species */ 315 int Maxspc, /* in: Number of species (n) */ 327 int Maxspc, /* in: Number of species (n) */ 345 int Maxspc, /* No. of species */ 354 int Maxspc); /* No. of species */ 372 int Maxspc, /* in: Number of species (n) */ 384 int Maxspc, /* in: Number of species (n) */
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H A D | pstep-mrca.h | 83 int Maxspc, /* in: Number of species (n) */ 92 int Maxspc, /* No. of species */ 100 int Maxspc); /* No. of species */ 149 int Maxspc, /* in: Number of species (n) */ 156 int Maxspc, /* in: Number of species (n) */
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H A D | pstep-recursive.h | 83 int Maxspc, /* in: Number of species (n) */ 92 int Maxspc, /* No. of species */ 100 int Maxspc); /* No. of species */ 149 int Maxspc, /* in: Number of species (n) */ 156 int Maxspc, /* in: Number of species (n) */
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H A D | pstep-trueID.h | 83 int Maxspc, /* in: Number of species (n) */ 92 int Maxspc, /* No. of species */ 100 int Maxspc); /* No. of species */ 149 int Maxspc, /* in: Number of species (n) */ 156 int Maxspc, /* in: Number of species (n) */
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H A D | puzzle2.c | 353 if (*Maxspc < 3) { in getsizesites() 361 if (*Maxspc < 4) { in getsizesites() 366 if (*Maxspc > 257) { in getsizesites() 377 if (*Maxspc < 4) { in getsizesites() 384 if (*Maxspc > 257) { in getsizesites() 447 if (ss_maxspc != Maxspc) { in readsubsetfile() 464 for(n = 0; n<Maxspc; n++) { in readsubsetfile() 465 if (ss_maxspc != Maxspc) { in readsubsetfile() 490 for (n=0; n<Maxspc; n++) { in readsubsetfile() 880 for (i = 0; i < Maxspc; i++) in estimatebasefreqs() [all …]
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H A D | pstep-split.h | 109 int Maxspc, /* in: Number of species (n) */ 118 int Maxspc, /* No. of species */ 126 int Maxspc); /* No. of species */ 175 int Maxspc, /* in: Number of species (n) */ 182 int Maxspc, /* in: Number of species (n) */
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H A D | pstep-deglob.h | 55 EXTERN int Maxspc; /* Maxspc */ 101 int Maxspc, /* in: Number of species (n) */ 110 int Maxspc, /* No. of species */ 118 int Maxspc); /* No. of species */
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H A D | puzzle1.c | 403 Numquartets = (uli) Maxspc*(Maxspc-1)*(Maxspc-2)*(Maxspc-3)/24; in compnumqts() 716 2*Maxspc-3); 1179 Maxspc); 1187 Maxspc); 1841 useqs = new_cvector(Maxspc); 3102 distdone = new_imatrix(Maxspc,Maxspc); 3883 if (locroot<Maxspc) { 4222 if (locroot<Maxspc) { 5726 Maxbrnch = 2*Maxspc - 3; 6325 psteptreestrlen = (Maxspc * (int)(1 + log10((double)Maxspc))) + [all …]
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H A D | consensus.h | 78 int Maxspc); /* in: number of species in tree */ 86 int Maxspc); /* in: number of taxa in tree */ 93 int Maxspc); /* number of taxa */ 104 int Maxspc); /* in: no. of species */
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H A D | puzzle.h | 440 int Maxspc, /* in: number of taxa */ 460 int *Maxspc, /* out: number of taxa */ 465 int *Maxspc, /* out: number of taxa */ 473 int Maxspc, /* in: number of taxa */ 485 void permutetaxa_ss(int Maxspc, /* in: number of taxa */ 499 int Maxspc, /* in: number of taxa */ 511 int Maxspc, /* in: number of taxa */ 523 int Maxspc, /* number of taxa */ 580 int Maxspc); /* in: number of species in tree */ 589 int Maxspc); /* in: number of taxa in tree */ [all …]
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H A D | ppuzzle.c | 178 for (n2=0; n2<Maxspc; n2++) in PP_Printbiparts() 340 int jobs = .5*Maxspc*(Maxspc-1); in PP_Final_Update() 386 initsched(&sched, .5*Maxspc*(Maxspc-1), PP_NumProcs-1, 1); in PP_Mldistance() 515 while ((chunk>0)&&(lx<Maxspc-1)) in PP_NextCoord() 519 chunk -= Maxspc - ly - 1; in PP_NextCoord() 911 Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ; in PP_RecvData() 1006 Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ; in PP_SendData() 1508 for (i = 3; i < Maxspc; i++) in PP_RecvQuartBlock() 2390 psteptreestrlen = (Maxspc * (int)(1 + log10((double)Maxspc))) + in slave_main() 2409 Distanmat = new_dmatrix(Maxspc, Maxspc); in slave_main() [all …]
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H A D | ml2.c | 960 Numbrnch = 2*Maxspc-3; in readusertree() 961 Numibrnch = Maxspc-3; in readusertree() 962 Numspc = Maxspc; in readusertree() 1064 Distanmat = new_dmatrix(Maxspc, Maxspc); in mlstart() 1410 Numbrnch = 2*Maxspc-3; in njtree() 1411 Numibrnch = Maxspc-3; in njtree() 1412 Numspc = Maxspc; in njtree() 1432 distan = new_dmatrix(Maxspc,Maxspc); in njdistantree() 1437 nsp2 = Maxspc - 2; in njdistantree() 1440 r = new_dvector(Maxspc); in njdistantree() [all …]
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H A D | pstep-deglob.c | 59 int Maxspc, /* in: Number of species (n) */ in inittree_orig() argument 76 tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); in inittree_orig() 126 int Maxspc, /* No. of species */ in addnextleaf_orig() argument 147 if (nextleaf >= Maxspc) { in addnextleaf_orig() 274 int Maxspc) /* No. of species */ in freetree_orig() argument 278 for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].edgemap); in freetree_orig()
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H A D | treesort.c | 114 for (n=0; n < 2*Maxspc; n++) { in printctree() 136 snodes = (int *) calloc((size_t) (4 * 2 * Maxspc), sizeof(int)); in initctree() 139 for (n=0; n<(4 * 2 * Maxspc); n++) { in initctree() 219 ct_nextnode = Maxspc; 298 ct_nextnode = Maxspc; in copytree() 369 for(n=0; n<Maxspc; n++) { in sortctree() 410 for(n=0; n<Maxspc; n++) { in fprintfsortctree() 459 for(n=0; n<Maxspc; n++) { in sprintfctree()
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H A D | mlparam.c | 205 minqts = (uli) floor(0.25 * MINPERTAXUM * Maxspc) + 1; in optimseqevolparamsquart() 206 maxqts = (uli) floor(0.25 * MAXPERTAXUM * Maxspc) + 1; in optimseqevolparamsquart() 207 if (Maxspc == 4) { in optimseqevolparamsquart() 225 chooser(Maxspc, 4, taxon); in optimseqevolparamsquart()
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