int run_sequential( char *dataset_file, pltb_config_t *config, model_space_t *model_space )
{
FILE *out = DEBUG_PROCESS_STATISTICS_OPEN_OUTPUT;
pltb_model_stat_t stats[model_space->matrix_count];
TIME_STRUCT_INIT(timer);
fprint_eval_header(out);
pllAlignmentData *data = read_alignment_data(dataset_file);
pltb_result_t result;
for(unsigned i = 0; i < IC_MAX; i++) {
result.ic[i] = FLT_MAX;
}
while (next_model(model_space)) {
partitionList *parts = init_partitions(data, config->base_freq_kind);
pllInstance *inst = setup_instance(model_space->matrix_repr, &config->attr_model_eval, data, parts);
pltb_model_stat_t *stat = &stats[model_space->matrix_index];
stat->matrix_index = model_space->matrix_index;
TIME_START(timer);
optimize_model_parameters(inst, parts);
TIME_END(timer);
stat->time_cpu = TIME_CPU(timer);
stat->time_real = TIME_REAL(timer);
stat->likelihood = inst->likelihood;
calculate_model_ICs(stat, data, inst, model_space->free_parameter_count, config);
merge_into_result(&result, stat, model_space->matrix_index);
fprint_eval_row(out, model_space, stat);
pllPartitionsDestroy(inst, &parts);
pllDestroyInstance(inst);
}
fprint_eval_summary(out, model_space, &stats, &result);
DEBUG_PROCESS_STATISTICS_CLOSE_OUTPUT(out);
evaluate_result(model_space, &result, data, config);
pllAlignmentDataDestroy(data);
return 0;
}
void evaluate_result(model_space_t *relative_model_space, pltb_result_t *result, pllAlignmentData *data, pltb_config_t *config)
{
pllInstance *tree;
/* TODO: inplace modifications. ugly! */
make_indices_absolute(relative_model_space, &result->matrix_index);
unsigned *models = malloc(sizeof(unsigned) * (IC_MAX + config->n_extra_models));
unsigned n_models = prepare_unique_model_tasks(models, &result->matrix_index, config->extra_models, config->n_extra_models);
model_space_t model_space;
init_selection_model_space(&model_space, models, n_models);
PRINT_TREE_SEARCH_HEADER();
while (next_model(&model_space)) {
PRINT_TREE_SEARCH_PRETEXT_BEGIN(model_space.matrix_repr_short);
bool first = true;
for (unsigned i = 0; i < IC_MAX; i++) {
if (result->matrix_index[i] == models[model_space.matrix_index]) {
if (first) {
PRINT_TREE_SEARCH_PRETEXT_IC(get_IC_name_short(i));
first = false;
} else {
PRINT_TREE_SEARCH_PRETEXT_IC_SEP(get_IC_name_short(i));
}
}
}
if (first) {
PRINT_TREE_SEARCH_PRETEXT_IC("extra");
}
PRINT_TREE_SEARCH_PRETEXT_END();
partitionList *parts = init_partitions(data, config->base_freq_kind);
/* do the actual work */
tree = setup_instance(model_space.matrix_repr, &config->attr_tree_search, data, parts);
tree_search(tree, parts);
prepare_tree_string(tree, parts);
PRINT_TREE(tree->tree_string);
pllPartitionsDestroy(tree, &parts);
pllDestroyInstance(tree);
}
destroy_model_space(&model_space);
}
int main (int argc, char * argv[])
{
pllAlignmentData * alignmentData;
pllInstance * tr;
pllNewickTree * newick;
partitionList * partitions;
pllQueue * partitionInfo;
int i;
pllInstanceAttr attr;
pllRearrangeList * rearrangeList;
#ifdef _FINE_GRAIN_MPI
pllInitMPI (&argc, &argv);
#endif
if (argc < 4)
{
fprintf (stderr, "usage: %s [phylip-file] [newick-file] [partition-file] [threads]\n", argv[0]);
return (EXIT_FAILURE);
}
/* Set the PLL instance attributes */
attr.rateHetModel = PLL_GAMMA;
attr.fastScaling = PLL_FALSE;
attr.saveMemory = PLL_FALSE;
attr.useRecom = PLL_FALSE;
attr.randomNumberSeed = 0xDEADBEEF;
attr.numberOfThreads = (argc > 4) ? (atoi(argv[4]) > 0 ? atoi(argv[4]) : 8) : 8; /* This only affects the pthreads version */
/* Create a PLL tree */
tr = pllCreateInstance (&attr);
/* Parse a PHYLIP file */
alignmentData = pllParseAlignmentFile (PLL_FORMAT_PHYLIP, argv[1]);
if (!alignmentData)
{
fprintf (stderr, "Error while parsing %s\n", argv[1]);
return (EXIT_FAILURE);
}
/* Parse a NEWICK file */
newick = pllNewickParseFile (argv[2]);
if (!newick)
{
fprintf (stderr, "Error while parsing newick file %s\n", argv[2]);
return (EXIT_FAILURE);
}
if (!pllValidateNewick (newick)) /* check whether the valid newick tree is also a tree that can be processed with our nodeptr structure */
{
fprintf (stderr, "Invalid phylogenetic tree\n");
printf ("%d\n", errno);
//return (EXIT_FAILURE);
}
/* Parse the partitions file into a partition queue structure */
partitionInfo = pllPartitionParse (argv[3]);
/* Validate the partitions */
if (!pllPartitionsValidate (partitionInfo, alignmentData))
{
fprintf (stderr, "Error: Partitions do not cover all sites\n");
return (EXIT_FAILURE);
}
/* Commit the partitions and build a partitions structure */
partitions = pllPartitionsCommit (partitionInfo, alignmentData);
/* We don't need the the intermedia partition queue structure anymore */
pllQueuePartitionsDestroy (&partitionInfo);
/* eliminate duplicate sites from the alignment and update weights vector */
pllAlignmentRemoveDups (alignmentData, partitions);
/* Set the topology of the PLL tree from a parsed newick tree */
pllTreeInitTopologyNewick (tr, newick, PLL_TRUE);
/* Or instead of the previous function use the next commented line to create
a random tree topology
pllTreeInitTopologyRandom (tr, alignmentData->sequenceCount, alignmentData->sequenceLabels); */
/* Connect the alignment and partition structure with the tree structure */
if (!pllLoadAlignment (tr, alignmentData, partitions))
{
fprintf (stderr, "Incompatible tree/alignment combination\n");
return (EXIT_FAILURE);
}
/* Initialize the model. Note that this function will also perform a full
tree traversal and evaluate the likelihood of the tree. Therefore, you
have the guarantee that tr->likelihood the valid likelihood */
pllInitModel(tr, partitions);
pllOptimizeBranchLengths (tr, partitions, 64);
printf ("Log-likelihood of topology: %f\n", tr->likelihood);
/* Create a list that will hold information for at most 20 rearrangement moves */
rearrangeList = pllCreateRearrangeList (20);
/* The next flag specifies that PLL optimizes the length of the new branch
that is created by an SPR move */
tr->thoroughInsertion = PLL_FALSE;
/* Note that the following commands will fill the list with at most 20
SPR and NNI rearrangement moves, i.e. the best 20 will appear in the
list */
printf ("Computing the best 20 SPR and NNI rearrangements in radius (1,20)\n");
pllRearrangeSearch (tr,
partitions,
PLL_REARRANGE_SPR,
tr->nodep[tr->mxtips + 1],
1,
20,
rearrangeList);
pllRearrangeSearch (tr,
partitions,
PLL_REARRANGE_NNI,
tr->nodep[tr->mxtips + 1],
1,
20,
rearrangeList);
printf ("Number of computed rearrangements: %d\n", rearrangeList->entries);
printf ("------------------------------------\n");
for (i = 0; i < rearrangeList->entries; ++ i)
{
printf ("%2d Type: %s Log-likelihood: %f\n",
i,
rearrangeList->rearr[i].rearrangeType == PLL_REARRANGE_SPR ?
"SPR" : "NNI",
rearrangeList->rearr[i].likelihood);
}
printf ("Committing move 0\n");
pllRearrangeCommit(tr, partitions, &(rearrangeList->rearr[0]), PLL_TRUE);
pllEvaluateLikelihood (tr, partitions, tr->start, PLL_TRUE, PLL_FALSE);
printf ("New log-likelihood: %f\n\n", tr->likelihood);
/* We don't need the rearrange list anymore */
pllDestroyRearrangeList (&rearrangeList);
/* Now let's create another list and compute 30 rearrangement moves */
rearrangeList = pllCreateRearrangeList (30);
/* The next flag specifies that the length of the new branch that is created
by an SPR move need not be optimized */
tr->thoroughInsertion = PLL_TRUE;
printf ("Computing the best 30 SPR in radius (1,30)\n");
pllRearrangeSearch (tr, partitions,
PLL_REARRANGE_SPR,
tr->nodep[tr->mxtips + 1],
1,
30,
rearrangeList);
printf ("Number of computed rearrangements: %d\n", rearrangeList->entries);
printf ("------------------------------------\n");
for (i = 0; i < rearrangeList->entries; ++ i)
{
printf ("%2d Type: SPR Likelihood: %f\n", i, rearrangeList->rearr[i].likelihood);
}
printf ("Committing rearrangeList->rearr[0]\n");
pllRearrangeCommit (tr, partitions, &(rearrangeList->rearr[0]), PLL_TRUE);
pllEvaluateLikelihood (tr, partitions, tr->start, PLL_FALSE, PLL_FALSE);
printf ("New log-likelihood: %f\n\n", tr->likelihood);
/* Rolling back to the previous topology. Note that if we evaluate the
likelihood with a partial traversal we might get an invalid log likelihood.
This is due to the fact that the likelihood vectors no longer correspond
to the old topology, hence we need to do full traversal. I left the
partial traversal here as an example */
printf ("Rolling back...\n");
pllRearrangeRollback (tr, partitions);
pllEvaluateLikelihood (tr, partitions, tr->start, PLL_FALSE, PLL_FALSE);
printf ("New log-likelihood: %f\n\n", tr->likelihood);
/* We do one more rollback to get to the original topology, but this time we
do a full traversal to fix the log-likelihood to the correct value plus we
do branch-length optimization */
printf ("Rolling back...\n");
pllRearrangeRollback (tr, partitions);
pllEvaluateLikelihood (tr, partitions, tr->start, PLL_TRUE, PLL_FALSE);
pllOptimizeBranchLengths (tr, partitions, 64);
printf ("New log-likelihood: %f\n\n", tr->likelihood);
/* DEallocate the rearrange list */
pllDestroyRearrangeList (&rearrangeList);
/* Do some cleanup */
pllAlignmentDataDestroy (alignmentData);
pllNewickParseDestroy (&newick);
pllPartitionsDestroy (tr, &partitions);
pllDestroyInstance (tr);
return (EXIT_SUCCESS);
}
