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fast8.c
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#include "align3.h"
#include <math.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include <fcntl.h>
parameters *values_here;
extern int *cc_weights;
int NOTUs, NCharacters, NHTUs, NTaxa;
look_up_thang **Character;
unsigned char **Name;
unsigned char buf[1024];
NodeT *Node, **PlacedTaxa;
int NPlacedTaxa;
int NTrees = 0, NOptimizations = 0;
double Optimizations = 0;
int NDirtyNodes = 0;
NodeT **DirtyNode;
BitVectorT *SupportedClades;
int NSupportedClades;
unsigned int SupportedCladesHash;
int NConsensusClades;
BitVectorT *ConsensusClades;
BufferedTreeT *ScratchBufferedTree = NOBUFFEREDTREE;
int tasks_available = 0, max_tasks_available, n_workers = 0, next_task = 0;
int *PartialFinalMap;
struct hostinfo *hostp;
int nhost = 0, narch, tids[256];
struct {
int tid;
int treeid;
int ntasks;
char *name;
} task[256];
char **serverargv;
int treeserial = 0, buffertick = 0;
int EPSILON = 0;
int BACKUP = 1, VERBOSE = 0, PRUNE = 1, doSPR = 1, doTBR = 1,
LOCALREARRANGEMENT = 1,
PABLO = 0, INITIALPABLO = 0, STEEPEST = 0,
TREE = 0, INDENT = 0, STATS = 0,
MAXWORKERS = 0, MINWORKERS = 0, LOOPCHUNK = 10000,
DOUBLEBUFFER = 1,
MAXTREES, FINAL_MAXTREES = 1024, INITIAL_MAXTREES = 0, maxtrees_exceeded = 0,
CONSENSUS = 0, CONSENSUSBITS = 0, CONSENSUSTABLE = 0, NUMBERCONSENSUSNODES = 0,
RANDOMIZATIONS = 0, FILLMISSING = 0,
FILLINS = 0,
MISSINGREPORT = 0, MISSINGSTATS = 0, MISSINGCONSENSUS = 0, MISSINGCONSENSUSDATA = 0,
TAGS = 0;
char *POORHOST = NULL;
enum {CHARACTER, BITMAP} FORMAT = CHARACTER;
ComputeSupportT SupportComputer;
enum {STANDALONE, MASTER, SERVER} SERVERMODE = STANDALONE;
FILE *blather;
void NewReadData (sequences)
look_up_thang **sequences;
{
int taxon, character, i, j;
/* printf ("%d OTUs.\n", NOTUs);
printf ("%d characters.\n", NCharacters);*/
NHTUs = NOTUs - 1;
NTaxa = NOTUs + NHTUs;
NewMatrix (Character, NTaxa * 2, NCharacters, look_up_thang);
/* NewMatrix (BitPosition, 256, NCharacters, int);
NewArray (UsedPositions, NCharacters, int);*/
NewArray (Name, NTaxa, unsigned char *);
/*NewArray (MissingData, NCharacters, unsigned int);
LoopBelow (character, NCharacters) {
UsedPositions[character] = 0;
MissingData[character] = 0;
LoopBelow (i, 256)
BitPosition[i][character] = -1;
}*/
/*LoopBelow (taxon, NOTUs) memcpy(Character[taxon],sequences[taxon],NCharacters*sizeof(look_up_thang));*/
for (j=0;j<NOTUs;j++) {
for (i=0;i<NCharacters;i++) {
Character[j][i].base=sequences[j][i].base;
/*if (!i) fprintf(stderr,"%2d vs. %2d ",sequences[j][i].base,Character[j][i].base);*/
}
}
buf[0]='a';
buf[1]='\0';
LoopBelow (taxon, NOTUs) {
Name[taxon]=CopyString(buf);
}
}
int RandomCharacter (int universe) {
int i, j, character;
character = rand () % CountBits (universe);
j = 0;
for (i = 0;; i++)
if ((1 << i) & universe) {
if (j is character)
return (1 << i);
else
j++;
}
}
void WriteData (FILE *f) {
int taxon, character;
fprintf (f, "%d %d\n", NOTUs, NCharacters);
LoopBelow (taxon, NOTUs) {
fprintf (f, "%s", Node[taxon].name);
LoopBelow (character, NCharacters) {
fprintf (f, " %d", RandomCharacter (Character[taxon][character].base));
}
fprintf (f, "\n");
}
}
unsigned char **RawData;
/* tree buffer stuff */
BufferedTreeT *NewBufferedTree () {
int i;
BufferedTreeT *bt;
bt = New (1, BufferedTreeT);
NewArray (bt->nodes, NTaxa, BufferedTreeNodeT);
NewArray (bt->placed_taxa_indices, NTaxa, int);
NewArray (bt->supported_clades, NHTUs - 1, BitVectorT);
LoopBelow (i, NHTUs - 1)
bt->supported_clades[i] = NewBitVector ();
return (bt);
}
NodeT *FindRoot (NodeT *n)
{
assert (n);
while (n->parent) n = n->parent;
return (n);
}
void CopyBufferedTree (BufferedTreeT *dest, BufferedTreeT *source) {
int i;
dest->n_placed_taxa = source->n_placed_taxa;
LoopBelow (i, source->n_placed_taxa) {
dest->nodes[i] = source->nodes[i];
dest->placed_taxa_indices[i] = source->placed_taxa_indices[i];
}
dest->n_supported_clades = source->n_supported_clades;
LoopBelow (i, source->n_supported_clades)
CopyBitVector (dest->supported_clades[i], source->supported_clades[i]);
dest->supported_clades_hash = source->supported_clades_hash;
dest->cost = source->cost;
dest->generation = source->generation;
}
void StoreTree (BufferedTreeT *bt, int taxa_in_use, int cost) {
int i;
NodeT *n, *p;
/* fprintf (stderr, "store tree with %d taxa\n", taxa_in_use); */
LoopBelow (i, taxa_in_use) {
n = PlacedTaxa[i];
if (n->left && !n->right) fail ("left but no right");
if (n->right && !n->left) fail ("right but no left");
}
LoopBelow (i, taxa_in_use) {
n = PlacedTaxa[i];
p = n->parent;
if (p is NONODE)
bt->nodes[i].parent_index = -1;
else {
bt->nodes[i].parent_index = p->taxon;
bt->nodes[i].on_left = (n is p->left);
}
}
bt->n_placed_taxa = taxa_in_use;
LoopBelow (i, taxa_in_use)
bt->placed_taxa_indices[i] = PlacedTaxa[i]->taxon;
bt->n_supported_clades = NSupportedClades;
LoopBelow (i, NSupportedClades) {
CopyBitVector (bt->supported_clades[i], SupportedClades[i]);
}
bt->supported_clades_hash = SupportedCladesHash;
bt->cost = cost;
}
void RecomputeNode (NodeT *n) {
int i,ii,jj;
parameters *valuesI;
if (n->left) {
RecomputeNode (n->left);
RecomputeNode (n->right);
i=0;
for (ii=0;ii<max(1,values_here->number_of_input_alignments);ii++) {
if (!values_here->other_parm) valuesI=values_here;
else if (values_here->other_parm[ii]) valuesI=values_here->other_parm[ii];
else valuesI=values_here;
for (jj=values_here->start[ii];jj<values_here->stop[ii];jj++) {
n->character[i]=valuesI->lookup[n->left->character[i].base][n->right->character[i].base];
n->localcost+=(n->character[i].cost*cc_weights[i]);
i++;
} /*jj*/
} /*end of characters loop*/
n->totalcost = n->localcost + n->left->totalcost + n->right->totalcost;
}
}
void LoadTree (BufferedTreeT *bt, int restore_supported_clades) {
extern void ComputeSupportedClades ();
int i;
int taxa_in_use = bt->n_placed_taxa;
NodeT *n;
NPlacedTaxa = bt->n_placed_taxa;
/* fprintf (stderr, "loading tree with %d taxa\n", NPlacedTaxa); */
LoopBelow (i, NPlacedTaxa) {
n = PlacedTaxa[i] = Node + bt->placed_taxa_indices[i];
n->parent = n->left = n->right = NONODE;
}
LoopBelow (i, taxa_in_use) {
n = PlacedTaxa[i];
if (bt->nodes[i].parent_index < 0) {
if (n->parent isnt NONODE) fail ("parent already set");
n->parent = NONODE;
} else {
if (n->parent isnt NONODE) fail ("parent already set");
n->parent = Node + bt->nodes[i].parent_index;
if (bt->nodes[i].on_left) {
if (n->parent->left isnt NONODE) fail ("left already set");
n->parent->left = n;
} else {
if (n->parent->right isnt NONODE) fail ("right already set");
n->parent->right = n;
}
}
n->localcost = n->totalcost = n->dirty = 0;
}
LoopBelow (i, NPlacedTaxa) {
n = PlacedTaxa[i];
if (n->left && !n->right) fail ("left but no right");
if (n->right && !n->left) fail ("right but no left");
}
RecomputeNode (FindRoot (PlacedTaxa[0]));
if (restore_supported_clades) {
ComputeSupportedClades ();
}
}
/* int Combine (int x, int y) { */
/* int z; */
/* z = SETBITS & x & y; */
/* if (! z) */
/* z = SETBITS & (x | y); */
/* return (z); */
/* } */
void ComputeFinal (NodeT *n) {
int i;
look_up_thang n_ch;
NodeT *parent = n->parent;
LoopBelow (i, NCharacters) {
/*n_ch = n->character[i] & SETBITS;*/
n_ch=n->character[i];
n_ch.union_bit=0;
/*if root*/
if (parent is NONODE) n->final_character[i].base = n_ch.base;
/*if parent is contained in node -- should be OK*/
else if (((~n_ch.base) & parent->final_character[i].base) is 0) n->final_character[i].base = parent->final_character[i].base;
/*if union on down add parent--needs to be fixed wrt matrix*/
else if (n->character[i].union_bit) n->final_character[i].base = n_ch.base | parent->final_character[i].base;
/*if was inrtersection add anything in parent and one of the descendents--need to be fixed wrt matrix*/
else if (n->left) n->final_character[i].base = n_ch.base | (parent->final_character[i].base & (n->left->character[i].base | n->right->character[i].base));
/*if terminal*/
else n->final_character[i].base = n_ch.base;
n->final_character[i].union_bit=0; /*cost should not matter*/
/* if (parent && n->left) { */
/* NodeT *left = n->left, *right = n->right; */
/* int z = */
/* Combine (parent->final_character[i], Combine (left->character[i], right->character[i])) & */
/* Combine (left->character[i], Combine (parent->final_character[i], right->character[i])) & */
/* Combine (right->character[i], Combine (left->character[i], parent->final_character[i])); */
/* if (z isnt n->final_character[i]) */
/* fprintf (stderr, "Discrepancy at taxon %d character %d: sm = %d, fitch = %d\n", */
/* n->taxon, i, z, n->final_character[i]); */
/* } */
}
if (n->left) {
ComputeFinal (n->left);
ComputeFinal (n->right);
}
}
void ComputeSupportEverything (NodeT *n) {
if (n->left is NONODE) {
ClearBitVector (n->taxa);
SetBit (n->taxa, n->taxon);
} else {
ComputeSupportEverything (n->left);
ComputeSupportEverything (n->right);
OrBitVectors (n->taxa, n->left->taxa, n->right->taxa);
if (n->parent isnt NONODE)
SupportedClades[NSupportedClades++] = n->taxa;
}
}
void FindSupportMust (NodeT *n) {
int supported = 0, i;
NodeT *p = n->parent;
if (p) {
LoopBelow (i, NCharacters)
if (!(n->final_character[i].base & p->final_character[i].base)) {
/* fprintf (stderr, "taxon %d character %d supported\n", n->taxon, i); */
supported = 1;
break;
}
}
if (n->left is NONODE) {
ClearBitVector (n->taxa);
SetBit (n->taxa, n->taxon);
} else {
FindSupportMust (n->left);
FindSupportMust (n->right);
OrBitVectors (n->taxa, n->left->taxa, n->right->taxa);
if (supported) {
SupportedClades[NSupportedClades++] = n->taxa;
}
}
}
void ComputeSupportMust (NodeT *root) {
ComputeFinal (root);
FindSupportMust (root);
}
int IsSingleton (look_up_thang x) {
int i, y;
y = 1;
LoopBelow (i, 26) /*wordsize in yapp but 26 bits in structure*/
if (x.base is y)
return (1);
else
y <<= 1;
return (0);
}
void FindSupportMay (NodeT *n) {
int supported = 0, i;
NodeT *p = n->parent;
if (p) {
LoopBelow (i, NCharacters)
if (n->final_character[i].base isnt p->final_character[i].base) {
supported = 1;
break;
}
}
if (n->left is NONODE) {
ClearBitVector (n->taxa);
SetBit (n->taxa, n->taxon);
} else {
FindSupportMay (n->left);
FindSupportMay (n->right);
OrBitVectors (n->taxa, n->left->taxa, n->right->taxa);
if (supported) {
SupportedClades[NSupportedClades++] = n->taxa;
}
}
}
void ComputeSupportMay (NodeT *root) {
ComputeFinal (root);
FindSupportMay (root);
}
void FindSupportNotSameSingleton (NodeT *n) {
int supported = 0, i;
NodeT *p = n->parent;
if (p) {
LoopBelow (i, NCharacters)
if (! (n->final_character[i].base is p->final_character[i].base &&
IsSingleton(n->final_character[i]))) {
supported = 1;
break;
}
}
if (n->left is NONODE) {
ClearBitVector (n->taxa);
SetBit (n->taxa, n->taxon);
} else {
FindSupportNotSameSingleton (n->left);
FindSupportNotSameSingleton (n->right);
OrBitVectors (n->taxa, n->left->taxa, n->right->taxa);
if (supported) {
SupportedClades[NSupportedClades++] = n->taxa;
}
}
}
void ComputeSupportNotSameSingleton (NodeT *root) {
ComputeFinal (root);
FindSupportNotSameSingleton (root);
}
void ComputeSupportedClades () {
int i;
NodeT *root = FindRoot (PlacedTaxa[0]);
NSupportedClades = 0;
(*SupportComputer) (root);
/* fprintf (stderr, "%d supported clades\n", NSupportedClades); */
qsort (SupportedClades, NSupportedClades, sizeof (BitVectorT), QsortCompareBitVectors);
SupportedCladesHash = 0;
LoopBelow (i, NSupportedClades)
SupportedCladesHash += BitVectorHash (SupportedClades[i]);
}
int CladeIsSupported (BitVectorT taxa) {
return ((int)bsearch (&taxa, SupportedClades, NSupportedClades,
sizeof (BitVectorT), QsortCompareBitVectors));
}
int IsSupported (NodeT *n) {
return (CladeIsSupported (n->taxa));
}
void PrintConsensusTable (FILE *f) {
int i, j;
LoopBelow (i, NConsensusClades) {
fprintf (f, "%d ", i+1);
LoopBelow (j, NOTUs)
if (GetBit (ConsensusClades[i], j))
fprintf (f, "%s ", Node[j].name);
fprintf (f, "\n");
}
}
void PrintConsensusBits (FILE *f) {
int i;
char *tag = TAGS? "ConsensusBits ": "";
fprintf (f, "%s%d\n", tag, NOTUs);
LoopBelow (i, NConsensusClades) {
fputs (tag, f);
fprintfBitVector (f, ConsensusClades[i]);
fprintf (f, "\n");
}
}
void InitConsensus () {
int i, n_clades = NSupportedClades + NOTUs + 1;
NewArray (ConsensusClades, n_clades, BitVectorT);
LoopBelow (i, n_clades)
ConsensusClades[i] = NewBitVector ();
LoopBelow (i, NSupportedClades)
CopyBitVector (ConsensusClades[i], SupportedClades[i]);
NConsensusClades = NSupportedClades;
}
void Consense () {
int i, j;
j = 0;
LoopBelow (i, NConsensusClades) {
if (CladeIsSupported (ConsensusClades[i])) {
BitVectorT temp;
temp = ConsensusClades[i];
ConsensusClades[i] = ConsensusClades[j];
ConsensusClades[j] = temp;
j++;
}
}
NConsensusClades = j;
}
BitVectorT *oldconsensusclades;
int noldconsensusclades;
void PrintConsensusNode (FILE *f, ConsensusNodeT *n) {
int i, j;
if (n->n_kids is 0) {
LoopBelow (i, NTaxa)
if (GetBit (ConsensusClades[n->clade], i)) {
fprintf (f, "%s", Node[i].name);
break;
}
} else {
LoopBelow (i, n->n_kids) {
if (i is 0) {
LoopBelow (j, noldconsensusclades)
if (! CompareBitVectors (ConsensusClades[n->clade], oldconsensusclades[j]))
break;
if (j < noldconsensusclades)
fprintf (f, "%d", j+1);
fprintf (f, "(");
} else
fprintf (f, " ");
PrintConsensusNode (f, n->kids[i]);
}
fprintf (f, ")");
}
}
void PrintConsensus (FILE *f) {
ConsensusNodeT *nodes;
int i, j;
if (NUMBERCONSENSUSNODES) {
NewArray (oldconsensusclades, NConsensusClades, BitVectorT);
LoopBelow (i, NConsensusClades) {
oldconsensusclades[i] = NewBitVector ();
CopyBitVector (oldconsensusclades[i], ConsensusClades[i]);
}
noldconsensusclades = NConsensusClades;
} else
noldconsensusclades = 0;
ClearBitVector (ConsensusClades[NConsensusClades + NOTUs]);
LoopBelow (i, NOTUs) {
ClearBitVector (ConsensusClades[NConsensusClades + i]);
SetBit (ConsensusClades[NConsensusClades + i], i);
SetBit (ConsensusClades[NConsensusClades + NOTUs], i);
}
NConsensusClades += NOTUs + 1;
qsort (ConsensusClades, NConsensusClades, sizeof (BitVectorT), QsortCompareBitVectors);
NewArray (nodes, NConsensusClades, ConsensusNodeT);
LoopBelow (i, NConsensusClades) {
nodes[i].n_kids = 0;
NewArray (nodes[i].kids, NConsensusClades, ConsensusNodeT *);
nodes[i].has_parent = 0;
nodes[i].clade = i;
}
LoopBelow (i, NConsensusClades) {
LoopInterval (j, i + 1, NConsensusClades - 1) {
if (BitVectorSubsetEq (ConsensusClades[i], ConsensusClades[j])) {
nodes[j].kids[nodes[j].n_kids++] = &nodes[i];
nodes[i].has_parent = 1;
break;
}
}
}
LoopBelow (i, NConsensusClades) {
if (! nodes[i].has_parent)
PrintConsensusNode (f, &nodes[i]);
}
}
void CompressTreeBuffer (TreeBufferT *tb) {
int max_acceptable_cost = tb->min_tree_cost + Max (0, EPSILON);
int i, j;
j = 0;
LoopBelow (i, tb->n_buffered_trees) {
if (tb->buffered_tree[i]->cost <= max_acceptable_cost) {
BufferedTreeT *temp = tb->buffered_tree[i];
tb->buffered_tree[i] = tb->buffered_tree[j];
tb->buffered_tree[j] = temp;
j++;
}
}
tb->n_buffered_trees = j;
tb->compressed = 1;
}
#define INITIALMAXBUFFEREDTREES 1024
TreeBufferT *NewTreeBuffer () {
int i;
TreeBufferT *tb = New (1, TreeBufferT);
tb->n_buffered_trees = 0;
tb->max_buffered_trees = INITIALMAXBUFFEREDTREES;
NewArray (tb->buffered_tree, tb->max_buffered_trees, BufferedTreeT *);
LoopBelow (i, tb->max_buffered_trees)
tb->buffered_tree[i] = NOBUFFEREDTREE;
tb->min_tree_cost = INFINITY;
tb->compressed = 0;
return (tb);
}
BufferedTreeT *NextAvailableBufferedTree (TreeBufferT *b) {
if (b->n_buffered_trees >= MAXTREES)
return (NOBUFFEREDTREE);
if (b->n_buffered_trees >= b->max_buffered_trees) {
int i, m = b->max_buffered_trees;
b->max_buffered_trees = Min (MAXTREES, b->max_buffered_trees * 2);
fprintf (stderr, "\nIncreasing buffer size to %d\n", b->max_buffered_trees);
b->buffered_tree = (BufferedTreeT **)Reallocate_D ((void *) b->buffered_tree,
b->max_buffered_trees * sizeof (BufferedTreeT *));
LoopInterval (i, m, b->max_buffered_trees - 1)
b->buffered_tree[i] = NOBUFFEREDTREE;
}
if (b->buffered_tree[b->n_buffered_trees] is NOBUFFEREDTREE) {
b->buffered_tree[b->n_buffered_trees] = NewBufferedTree ();
}
return (b->buffered_tree[b->n_buffered_trees++]);
}
int NCandidateTrees = 0, NCandidatesRejected = 0, NCandidatesDiscarded = 0, NTreesReceived = 0;
int NServerDiscards = 0;
void BufferTree (TreeBufferT *b, int n_placed_taxa, int cost, BufferedTreeT *bt) {
int i, j, old_cost;
BufferedTreeT *t;
if (bt is NOBUFFEREDTREE)
NCandidateTrees++;
if (bt) {
SupportedCladesHash = bt->supported_clades_hash;
NSupportedClades = bt->n_supported_clades;
LoopBelow (i, NSupportedClades) {
SupportedClades[i] = bt->supported_clades[i];
}
} else {
ComputeSupportedClades ();
}
if (b->n_buffered_trees >= MAXTREES) {
if (cost < b->min_tree_cost) {
b->min_tree_cost = cost;
/*fprintf (blather, "->%d", cost);*/
CompressTreeBuffer (b);
} else if (! b->compressed) {
CompressTreeBuffer (b);
}
if (b->n_buffered_trees >= MAXTREES) {
if (! maxtrees_exceeded) {
/*fprintf (blather, "\nmaxtrees = %d exceeded\n", MAXTREES);*/
maxtrees_exceeded = 1;
}
NCandidatesDiscarded++;
return;
}
}
LoopBelow (i, b->n_buffered_trees) {
t = b->buffered_tree[i];
if (t->supported_clades_hash is SupportedCladesHash &&
t->n_supported_clades is NSupportedClades &&
t->cost is cost) {
LoopBelow (j, NSupportedClades) {
if (CompareBitVectors (t->supported_clades[j], SupportedClades[j])) {
break;
}
}
if (j >= NSupportedClades) {
NCandidatesRejected++;
return;
}
}
}
/* fprintf (stderr, "BufferTree storing tree with %d taxa\n", n_placed_taxa); */
t = NextAvailableBufferedTree (b);
if (bt) {
assert (bt->n_placed_taxa is n_placed_taxa);
CopyBufferedTree (t, bt);
} else
StoreTree (t, n_placed_taxa, cost);
b->compressed = 0;
t->generation = b->current_generation;
old_cost = b->min_tree_cost;
if (cost < old_cost) {
b->min_tree_cost = cost;
/* fprintf (blather, "->%d", cost);*/
}
}
#ifdef _CLYDE_
void TransmitTreeToParent (TreeBufferT *b, int n_placed_taxa, int cost, BufferedTreeT *bt) {
int me, parent;
if (b->n_buffered_trees < MAXTREES ||
cost < b->min_tree_cost) {
/* fprintf (stderr, "transmitting tree with %d taxa\n", n_placed_taxa); */
assert (bt is NOBUFFEREDTREE);
me = pvm_mytid ();
parent = pvm_parent ();
ComputeSupportedClades ();
StoreTree (ScratchBufferedTree, n_placed_taxa, cost);
pvm_initsend (PvmDataDefault);
PackBufferedTree (ScratchBufferedTree, 1);
assert (! pvm_send (pvm_parent (), RETURNTREE));
if (ScratchBufferedTree->cost < b->min_tree_cost) {
b->min_tree_cost = ScratchBufferedTree->cost;
}
} else {
NServerDiscards++;
}
}
#endif
#ifdef _CLYDE_
void TellParentDone () {
pvm_initsend (PvmDataDefault);
assert (! pvm_send (pvm_parent (), LOOPISDONE));
}
#endif
void DoNothing () {
}
void (*LOOPDONE) () = DoNothing;
void (*BUFFERTREE) (TreeBufferT *b, int n_placed_taxa, int cost, BufferedTreeT *bt) = BufferTree;
void ResetTreeBuffer (TreeBufferT *b) {
b->n_buffered_trees = 0;
b->min_tree_cost = INFINITY;
b->compressed = 1;
}
void ResetGeneration (TreeBufferT *b) {
int i;
b->current_generation = 0;
LoopBelow (i, b->n_buffered_trees)
b->buffered_tree[i]->generation = 0;
}
void NextGeneration (TreeBufferT *b) {
/* fprintf (blather, ";");*/
b->current_generation++;
}
int NodeCost (NodeT *n)
{
int character, c = 0;
LoopBelow (character, NCharacters)
if (n->character[character].union_bit) c++;
return (c);
}
#define costof(c) ((c&UNIONBIT)? 1 : 0)
#define totalcostof(p) (p? p->totalcost: 0)
void SaveNode (NodeT *n)
{
NodeT *b = n->backupnode;
b->localcost = n->localcost;
b->totalcost = n->totalcost;
memcpy (b->character, n->character, NCharacters * sizeof (look_up_thang));
n->dirty = 1;
DirtyNode[NDirtyNodes++] = n;
/* fprintf (stderr, "save node %s cost %d\n", n->name, n->totalcost); */
}
void RestoreNodes ()
{
int i;
NodeT *n, *b;
/* fprintf (stderr, "restoring %d dirty nodes: ", NDirtyNodes); */
LoopBelow (i, NDirtyNodes) {
n = DirtyNode[i];
b = n->backupnode;
/* fprintf (stderr, "%s (cost %d->%d) ", n->name, n->totalcost, b->totalcost); */
n->localcost = b->localcost;
n->totalcost = b->totalcost;
memcpy (n->character, b->character, NCharacters * sizeof (look_up_thang));
n->dirty = 0;
}
/* fprintf (stderr, "\n"); */
NDirtyNodes = 0;
}
#define BILLION 1000000000
int Repair (NodeT *node, int force, BackupT backup, int grandtotalcost, TreeBufferT *buffer)
{
int character, count, highcount, newtotalcost, d, retval;
look_up_thang newcharacter, oldcharacter;
/* unsigned int newcharacter, oldcharacter;*/
NodeT *n;
static int lasthighcount = -1;
int ii,jj;
parameters *valuesI;
/* fprintf (blather, "repair node %s\n", node? node->name: "null"); */
assert ((int) backup is NOBACKUP || backup is FROMBACKUP || backup is TOBACKUP);
if (!node) {
/* fprintf (stderr, "Repair NULL\n"); */
if (BACKUP && backup is FROMBACKUP)
RestoreNodes ();
if (PRUNE && backup is FROMBACKUP)
lasthighcount = -1;
return (0);
} else {
if (BACKUP && backup is FROMBACKUP) {
RestoreNodes ();
} else {
highcount = -1;
if (PRUNE && backup is FROMBACKUP && lasthighcount > force)
force = lasthighcount;
character=0;
for (ii=0;ii<max(1,values_here->number_of_input_alignments);ii++) {
if (!values_here->other_parm) valuesI=values_here;
else if (values_here->other_parm[ii]) valuesI=values_here->other_parm[ii];
else valuesI=values_here;
/*fprintf(stderr,"%d->%d ",values_here->start[ii],values_here->stop[ii]);*/
for (jj=values_here->start[ii];jj<values_here->stop[ii];jj++) {
/* LoopBelow (character, NCharacters) {*/
for (n = node, count = 0; n; n = n->parent, count++) {
/*NOptimizations++;
newcharacter = SETBITS & n->left->character[character] & n->right->character[character];
if (! newcharacter) newcharacter = UNIONBIT | n->left->character[character] | n->right->character[character];
*/
newcharacter=valuesI->lookup[n->left->character[character].base][n->right->character[character].base];
oldcharacter = n->character[character];
if (count < force || (*((unsigned int *) &newcharacter)) isnt *((unsigned int *) &oldcharacter)) {
/*if (count < force || newcharacter isnt oldcharacter) {*/
if (BACKUP && backup is TOBACKUP && !n->dirty) SaveNode (n);
d=newcharacter.cost - oldcharacter.cost;
n->localcost += (cc_weights[character]*d);
/*d = (costof (newcharacter) - costof (oldcharacter));
n->localcost += d;*/
n->character[character] = newcharacter;
if (count > highcount) highcount = count;
if (backup is TOBACKUP) {
assert ((int) buffer);
grandtotalcost += (cc_weights[character]*d);
}
}
else break;
}
if (backup is TOBACKUP && PRUNE && grandtotalcost > buffer->min_tree_cost + EPSILON) return (grandtotalcost);
/*}character loop*/
character ++;
} /*jj*/
} /*end of characters loop*/
if (PRUNE && backup is TOBACKUP && highcount > lasthighcount)
lasthighcount = highcount;
for (n = node, count = 0;
n;
n = n->parent, count++) {
newtotalcost = n->localcost + totalcostof (n->left) + totalcostof (n->right);
if (count <= highcount ||
newtotalcost isnt n->totalcost) {
/* if (BACKUP && backup is TOBACKUP) { */
/* fprintf (stderr, "node %s is %sdirty\n", n->name, n->dirty? "": "not "); */
/* } */
if (BACKUP && backup is TOBACKUP && !n->dirty)
SaveNode (n);
n->totalcost = newtotalcost;
/* fprintf (stderr, "%s->totalcost = %d\n", n->name, n->totalcost); */
if (PRUNE && backup is TOBACKUP && count > lasthighcount)
lasthighcount = count;
} else {
break;
}
}
}
}
retval = (FindRoot (node))->totalcost;
if (backup is TOBACKUP)
assert ((int) retval is grandtotalcost);
/* fprintf (blather, "Repair returns %d\n", retval); */
if (PRUNE && backup is FROMBACKUP)
lasthighcount = -1;
return (retval);
}
void ClearNode (NodeT *n)
{
n->localcost = 0;
memset (n->character, 0, NCharacters * sizeof (look_up_thang));
}
int correct_predictions = 0, incorrect_predictions = 0;
int AddSib (NodeT *old_node, NodeT *new_node, NodeT *HTU, BackupT backup, TreeBufferT *buffer)
{
int grandtotalcost;
NodeT *old_node_parent = old_node->parent;
NodeT *n;
/* fprintf (blather, "Add %s to %s via %s\n", new_node->name, old_node->name, HTU->name); */
ClearNode (HTU);
n = FindRoot (old_node);
grandtotalcost = n->totalcost + new_node->totalcost + HTU->localcost;
/* fprintf (stderr, "grandtotalcost %d = %s(%d) + %s(%d) + %s(%d)\n", */
/* grandtotalcost, n->name, n->totalcost, */
/* new_node->name, new_node->totalcost, */
/* HTU->name, HTU->localcost); */
HTU->parent = old_node->parent;
HTU->left = old_node;
HTU->right = new_node;
old_node->parent = new_node->parent = HTU;
if (old_node_parent) {
if (old_node_parent->left is old_node) old_node_parent->left = HTU;
else if (old_node_parent->right is old_node) old_node_parent->right = HTU;
else fail ("Bogus adoption in AddSib");
}
return (Repair (HTU, 1, backup, grandtotalcost, buffer));
}
NodeT *RemoveAsSib (NodeT *node, BackupT backup)
{
NodeT *parent, *sibling, *grandparent;
parent = node->parent;
assert (parent);
if (node is parent->left)
sibling = parent->right;
else
sibling = parent->left;
grandparent = parent->parent;
/* fprintf (blather, "Remove %s and %s from %s leaving %s\n", node->name, parent->name, grandparent? grandparent->name: "none", sibling->name); */
parent->parent = parent->left = parent->right = NONODE;
node->parent = NONODE;
sibling->parent = grandparent;
if (grandparent) {
if (grandparent->left is parent) grandparent->left = sibling;
else if (grandparent->right is parent) grandparent->right = sibling;
else fail ("Bogus adoption in RemoveAsSib");
}
Repair (grandparent, 0, backup, 0, 0);
return (parent);
}
#ifdef PARANOID
#define FindSlot(node,parent) (node is parent->left? &(parent->left): (node is parent->right? &(parent->right): (fail ("can't find slot"),&(parent->left))))
#define FindOtherSlot(node,parent) (node is parent->left? &(parent->right): (node is parent->right? &(parent->left): (fail ("can't find other slot"),&(parent->left))))
#define FindSib(node,parent) (node is parent->left? (parent->right): (node is parent->right? (parent->left): (fail ("can't find other slot"),(parent->left))))
#else
#define FindSlot(node,parent) (node is parent->left? &(parent->left): &(parent->right))
#define FindOtherSlot(node,parent) (node is parent->left? &(parent->right): &(parent->left))
#define FindSib(node,parent) (node is parent->left? (parent->right): (parent->left))
#endif
#ifdef _CLYDE_
void ReceiveTree (TreeBufferT *tb) {
int bytes, tag, tid, thiscost, i;
assert (! pvm_bufinfo (pvm_recv (-1, -1), &bytes, &tag, &tid));
switch (tag) {
case RETURNTREE:
NTreesReceived++;
UnpackBufferedTree (ScratchBufferedTree, 1);
thiscost = ScratchBufferedTree->cost;
/* fprintf (stderr, "received tree with %d taxa\n", ScratchBufferedTree->n_placed_taxa); */
if (thiscost < tb->min_tree_cost) {
int i;
pvm_initsend (PvmDataDefault);
PackInt (buffertick);
PackInt (thiscost);
PackInt (tb->compressed? tb->n_buffered_trees: 0);
LoopBelow (i, n_workers)
if (task[i].tid isnt tid)
assert (! pvm_send (task[i].tid, NEWMINTREECOST));
}
if (thiscost <= tb->min_tree_cost + EPSILON) {
/* fprintf (stderr, "buffering it\n"); */
(*BUFFERTREE) (tb, ScratchBufferedTree->n_placed_taxa, thiscost, ScratchBufferedTree);
} else {
/* fprintf (stderr, "cost of %d is too high compared to %d.\n", thiscost, ScratchBufferedTree->cost); */
}
break;
case LOOPISDONE:
LoopBelow (i, n_workers)
if (task[i].tid is tid)
break;
assert (i < n_workers);
task[i].ntasks--;
tasks_available++;
next_task = i;
break;
default:
assert (0);
}
}
#endif
#ifdef _CLYDE_
int GetAServer (TreeBufferT *tb) {
int tid, i;
while (tasks_available is 0 || pvm_probe (-1, -1) > 0) {
ReceiveTree (tb);
}
for (i = 0; i < n_workers && task[next_task].ntasks is DOUBLEBUFFER; i++)
next_task = (next_task + 1) % n_workers;
assert (i < n_workers);
task[next_task].ntasks++;
tasks_available--;
tid = task[next_task].tid;
next_task = (next_task + 1) % n_workers;
return (tid);
}
#endif
#ifdef _CLYDE_
void WaitForServers (TreeBufferT *tb) {
int i;
while (tasks_available isnt max_tasks_available)
ReceiveTree (tb);
buffertick++;
pvm_initsend (PvmDataDefault);
LoopBelow (i, n_workers)
assert (! pvm_send (task[i].tid, BUFFERTICK));
}
#endif
void IgnoreTreeBuffer (TreeBufferT *tb) {
}
void (*WAITFORSERVERS) (TreeBufferT *tb) = IgnoreTreeBuffer;
int SERVERTASKSWITH = 0, SERVERTASKSWITHOUT = 0;
#ifdef _CLYDE_