Home
last modified time | relevance | path

Searched refs:Maxspc (Results 1 – 25 of 30) sorted by relevance

12

/dports/biology/treepuzzle/tree-puzzle-5.2/src/
H A Dsplit.c43 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 …]
H A Dmrca.c54 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 …]
H A Drecur-old.c128 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 …]
H A Dpstep-split.c283 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 …]
H A Drecur.c115 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 …]
H A Dpstep.c337 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 …]
H A Dconsensus.c38 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 …]
H A Dpstep-trueID.c155 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 …]
H A Dpstep-mrca.c151 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 …]
H A Dpstep-recursive.c151 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 …]
H A Dpstep.h274 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) */
H A Dpstep-mrca.h83 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) */
H A Dpstep-recursive.h83 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) */
H A Dpstep-trueID.h83 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) */
H A Dpuzzle2.c353 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 …]
H A Dpstep-split.h109 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) */
H A Dpstep-deglob.h55 EXTERN int Maxspc; /* Maxspc */
101 int Maxspc, /* in: Number of species (n) */
110 int Maxspc, /* No. of species */
118 int Maxspc); /* No. of species */
H A Dpuzzle1.c403 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 …]
H A Dconsensus.h78 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 */
H A Dpuzzle.h440 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 …]
H A Dppuzzle.c178 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 …]
H A Dml2.c960 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 …]
H A Dpstep-deglob.c59 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()
H A Dtreesort.c114 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()
H A Dmlparam.c205 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()

12