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spr_supertree.cpp
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spr_supertree.cpp
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/*******************************************************************************
spr_supertree.cpp
Copyright 2013-2014 Chris Whidden
http://kiwi.cs.dal.ca/Software/SPR_Supertrees
March 3, 2014
Version 1.2.1
This file is part of spr_supertrees.
spr_supertrees is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
spr_supertrees is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with spr_supertrees. If not, see <http://www.gnu.org/licenses/>.
*******************************************************************************
ALGORITHM
*******************************************************************************
These options control what algorithm is used to determine the SPR distance
from the supertree to the input trees. By default -bb is used.
-fpt Calculate the exact rSPR distance with an FPT algorithm
-bb Calculate the exact rSPR distance with a branch-and-bound
FPT algorithm. This is the default option.
-approx Calculate just a linear -time 3-approximation of the rSPR distance
-max k Calculate the exact rSPR distance if it is k or less and
otherwise use the 3-approximation
-split_approx
-split_approx x Calculate the exact rSPR distance if it is k or less and
otherwise use the exponential-time approximation
*******************************************************************************
OPTIMIZATIONS
*******************************************************************************
These options control the use of optimized branching. All optimizations are
enabled by default. Specifying any subset of -cob, -cab, and -sc will use
just that subset of optimizations. See the README for more information.
-allopt Use -cob -cab -sc and a new set of optimizations. This is the default
option
-noopt Use 3-way branching for all FPT algorithms
-cob Use "cut one b" improved branching
-cab Use "cut all b" improved branching
-sc Use "separate components" improved branching
-bipartition_cluster x Do not consider supertree rearrangements that violate
biparitions supported by x% of gene trees containing
at least two members from each side of the bipartition.
Enabled by default with x=0.5
*******************************************************************************
MULTIFURCATING COMPARISON OPTIONS
*******************************************************************************
-allow_multi Allow multifurcating gene trees
-support x Collapse bipartitions with less than x support
*******************************************************************************
UNROOTED COMPARISON OPTIONS
*******************************************************************************
-unrooted Compare the supertree to each rooting of the input trees.
Use the best found distance
-unrooted_min_approx Compare the supertree to each rooting of the
input trees.
Run the exact algorithm on the rooting with the
minimum approximate rspr distance
-simple_unrooted Root the gene trees at each iteration using
a bipartition balanced accuracy measure
(fast but potentially less accurate)
Reports an unrooted SPR distance comparison
at the end of each iteration for comparable
iteration scores
-simple_unrooted x Root the gene trees at the first x iterations
-simple_unrooted_fast The same as -simple_unrooted but does not use
an unrooted comparison at the end of each
iteration
-outgroup FILE Root the gene trees with the outgroup taxa
listed in FILE, one per line. Trees with a
polyphyletic outgroup are considered invalid.
-reroot Reroot the super tree at each iteration using
a bipartition balanced accuracy measure
-rspr_reroot Root trees using the SPR distance instead
of the bipartition balanced accuracy
*******************************************************************************
SEARCH STRATEGY OPTIONS
*******************************************************************************
-i x Run for x iterations of the global rearrangement search
-r x Only consider transfers of length x in the global rearrangement
search. Default is infinite (All SPRs). For NNI search use
-r 1
-include_only <file> Build the supertree only from taxa included in
<file>, one per line
-initial_tree <file> Begin the search with the tree in <file>
-num_leaves x Build the supertree from the x taxa that are found
in the largest number of trees
-random_insert_order Insert taxa in random order when building the
greedy addition tree. The default order is
descending occurence
-rf_ties Break SPR distance ties with the RF distance
*******************************************************************************
LGT ANALYSIS
*******************************************************************************
-lgt_analysis Conduct an LGT analysis with the initial user-specified
or greedy addition tree
-lgt_csv Output the LGT analysis seperated by commas rather than
spaces.
-lgt_groups FILE Specify a set of groups (e.g. genus or class) to analyze
with -lgt_analysis. The group FILE contains a set of
groups consisting of a group name on one line, group
members one per line, and a blank line to seperate each
group.
*******************************************************************************
OTHER OPTIONS
*******************************************************************************
-time Print iteration and total CPU time used at each
iteration
-cc Calculate a potentially better approximation with a
quadratic time algorithm
-valid_trees Output the set of trees that appear valid
-valid_trees_rooted Output the set of trees that appear valid after applying
any rooting options.
-multi_trees Output the set of multifurcating or invalid trees
*******************************************************************************/
#include <cstdio>
#include <cstdlib>
#include <ctime>
#include <string>
#include <cstring>
#include <iostream>
#include <fstream>
#include <sstream>
#include <climits>
#include <vector>
#include <map>
#include <utility>
#include <algorithm>
#include <list>
#include <time.h>
#include "rspr.h"
#include "Forest.h"
#include "ClusterForest.h"
#include "LCA.h"
#include "ClusterInstance.h"
#include "UndoMachine.h"
#include "lgt.h"
#include "sparse_counts.h"
#include "node_glom.h"
using namespace std;
//#define DEBUG_ONE_TREE true
// options to pick default
bool DEFAULT_ALGORITHM=true;
bool DEFAULT_OPTIMIZATIONS=true;
bool DEFAULT_SEARCH_OPTIMIZATIONS=true;
bool FPT = false;
bool QUIET = false;
bool UNROOTED = false;
bool SIMPLE_UNROOTED = false;
bool SIMPLE_UNROOTED_FAST = false;
int SIMPLE_UNROOTED_NUM = INT_MAX;
bool REROOT = false;
bool REROOT_INITIAL = false;
bool APPROX_ROOTING = false;
bool EXACT_ROOTING = false;
bool RANDOM_ROOTING = false;
bool RANDOM_INSERT_ORDER = false;
bool APPROX = false;
bool TIMING = false;
int NUM_ITERATIONS = 25;
bool SMALL_TREES = false;
bool CONVERT_LIST = false;
bool INVALID_TREES = false;
bool VALID_TREES = false;
bool VALID_TREES_ROOTED = false;
bool LGT_ANALYSIS = false;
bool LGT_EVALUATION = false;
bool FIND_MAX_DEGREE = false;
bool MULTI_TREES = false;
int NUM_LEAVES=-1;
int APPROX_SIBLINGS = 0;
int C_SOURCE = -1;
int NUM_SOURCE = -1;
bool RF_TIES = false;
double SUPPORT_THRESHOLD = 0.5;
bool TABOO_SEARCH = false;
bool ONE_TREE_AT_A_TIME = false;
bool NODE_GLOM_CONSTRUCTION = false;
bool USE_PRECOMPUTED_DISTANCES = false;
/*variables Joel added*/
int R_DISTANCE;
bool R_VARIABLE = false;
bool R_LIMIT = false;
bool R_RAND = false;
bool R_CONTROL = false;
bool R_BIAS = false;
float R_PROB;
bool S_LIMIT = false;
int S_NUM = 10;
bool S_STATS = false;
bool D_STATS = false;
bool RANDOM_TREE = false;
bool GREEDY = false;
bool GREEDY_REFINED = false;
string USAGE =
"spr_supertrees, version 1.2.1\n"
"\n"
"usage: spr_supertrees [OPTIONS]\n"
"Calculate binary rooted supertrees that minimize the Subtree Prune and\n"
"Regraft (SPR) distance to a set of rooted or unrooted binary or\n"
"multifurcating trees from STDIN in newick format. Supports arbitrary\n"
"leaf labels. See the README for more information.\n"
"\n"
"Copyright 2011-14 Chris Whidden\n"
"http://kiwi.cs.dal.ca/Software/SPR_Supertrees\n"
"March 3, 2014\n"
"Version 1.2.1\n"
"\n"
"This program comes with ABSOLUTELY NO WARRANTY.\n"
"This is free software, and you are welcome to redistribute it\n"
"under certain conditions; See the README for details.\n"
"\n"
"*******************************************************************************\n"
"ALGORITHM\n"
"*******************************************************************************\n"
"\n"
"These options control what algorithm is used to determine the SPR distance\n"
"from the supertree to the input trees. By default -bb is used.\n"
"\n"
"-fpt Calculate the exact rSPR distance with an FPT algorithm\n"
"\n"
"-bb Calculate the exact rSPR distance with a branch-and-bound\n"
" FPT algorithm. This is the default option.\n"
"\n"
"-approx Calculate just a linear -time 3-approximation of the rSPR distance\n"
"\n"
"-max k Calculate the exact rSPR distance if it is k or less and\n"
" otherwise use the 3-approximation\n"
"\n"
"-split_approx\n"
"-split_approx x Calculate the exact rSPR distance if it is k or less and\n"
" otherwise use the exponential-time approximation\n"
"\n"
"*******************************************************************************\n"
"OPTIMIZATIONS\n"
"*******************************************************************************\n"
"\n"
"These options control the use of optimized branching. All optimizations are\n"
"enabled by default. Specifying any subset of -cob, -cab, and -sc will use\n"
"just that subset of optimizations. See the README for more information.\n"
"\n"
"-allopt Use -cob -cab -sc and a new set of optimizations. This is the default\n"
" option\n"
"\n"
"-noopt Use 3-way branching for all FPT algorithms\n"
"\n"
"-cob Use \"cut one b\" improved branching\n"
"\n"
"-cab Use \"cut all b\" improved branching\n"
"\n"
"-sc Use \"separate components\" improved branching\n"
"\n"
"-bipartition_cluster x Do not consider supertree rearrangements that violate\n"
" biparitions supported by x% of gene trees containing\n"
" at least two members from each side of the bipartition.\n"
" Enabled by default with x=0.5\n"
"\n"
"*******************************************************************************\n"
"MULTIFURCATING COMPARISON OPTIONS\n"
"*******************************************************************************\n"
"\n"
"-allow_multi Allow multifurcating gene trees\n"
"\n"
"-support x Collapse bipartitions with less than x support\n"
"\n"
"*******************************************************************************\n"
"UNROOTED COMPARISON OPTIONS\n"
"*******************************************************************************\n"
"\n"
"-unrooted Compare the supertree to each rooting of the input trees.\n"
" Use the best found distance\n"
"\n"
"-unrooted_min_approx Compare the supertree to each rooting of the\n"
" input trees.\n"
" Run the exact algorithm on the rooting with the\n"
" minimum approximate rspr distance\n"
"\n"
"-simple_unrooted Root the gene trees at each iteration using\n"
" a bipartition balanced accuracy measure\n"
" (fast but potentially less accurate)\n"
" Reports an unrooted SPR distance comparison\n"
" at the end of each iteration for comparable\n"
" iteration scores\n"
"\n"
"-simple_unrooted x Root the gene trees at the first x iterations\n"
"\n"
"-simple_unrooted_fast The same as -simple_unrooted but does not use\n"
" an unrooted comparison at the end of each\n"
" iteration\n"
"\n"
"-outgroup FILE Root the gene trees with the outgroup taxa\n"
" listed in FILE, one per line. Trees with a\n"
" polyphyletic outgroup are considered invalid.\n"
"\n"
"-reroot Reroot the super tree at each iteration using\n"
" a bipartition balanced accuracy measure\n"
"\n"
"-rspr_reroot Root trees using the SPR distance instead\n"
" of the bipartition balanced accuracy\n"
"\n"
"\n"
"\n"
"*******************************************************************************\n"
"SEARCH STRATEGY OPTIONS\n"
"*******************************************************************************\n"
"\n"
"-i x Run for x iterations of the global rearrangement search\n"
"\n"
"-r x Only consider transfers of length x in the global rearrangement\n"
" search. Default is infinite (All SPRs). For NNI search use\n"
" -r 1\n"
"\n"
"-include_only <file> Build the supertree only from taxa included in\n"
" <file>, one per line\n"
"\n"
"-initial_tree <file> Begin the search with the tree in <file>\n"
"\n"
"-num_leaves x Build the supertree from the x taxa that are found\n"
" in the largest number of trees\n"
"\n"
"-random_insert_order Insert taxa in random order when building the\n"
" greedy addition tree. The default order is\n"
" descending occurence\n"
"\n"
"-rf_ties Break SPR distance ties with the RF distance\n"
"\n"
"*******************************************************************************\n"
"LGT ANALYSIS\n"
"*******************************************************************************\n"
"\n"
"-lgt_analysis Conduct an LGT analysis with the initial user-specified\n"
" or greedy addition tree\n"
"\n"
"-lgt_csv Output the LGT analysis seperated by commas rather than\n"
" spaces.\n"
"\n"
"-lgt_groups FILE Specify a set of groups (e.g. genus or class) to analyze\n"
" with -lgt_analysis. The group FILE contains a set of\n"
" groups consisting of a group name on one line, group\n"
" members one per line, and a blank line to seperate each\n"
" group.\n"
" \n"
"*******************************************************************************\n"
"OTHER OPTIONS\n"
"*******************************************************************************\n"
"-time Print iteration and total CPU time used at each\n"
" iteration\n"
"\n"
"-cc Calculate a potentially better approximation with a\n"
" quadratic time algorithm\n"
"\n"
"-valid_trees Output the set of trees that appear valid\n"
"-valid_trees_rooted Output the set of trees that appear valid after applying\n"
" any rooting options.\n"
"\n"
"-multi_trees Output the set of multifurcating or invalid trees\n";
Node *find_best_sibling(Node *super_tree, vector<Node *> &gene_trees,
int label);
Node *find_best_sibling(Node *super_tree, vector<Node *> &gene_trees,
vector<Node *> *best_siblings, int label);
void find_best_sibling_helper(Node *n, Node *new_leaf, Node *super_tree,
vector<Node *> &gene_trees, int &min_distance, int &min_tie_distance,
int &num_ties, Node **best_sibling);
vector<Node *> *find_best_siblings(Node *super_tree, vector<Node *> &gene_trees, int label, int num_siblings);
void find_best_siblings_helper(Node *n, Node *new_leaf, Node *super_tree,
vector<Node *> &gene_trees, int &min_distance, int &min_tie_distance,
int &num_ties, multimap<int, Node*> *best_siblings, int num_siblings);
void test_sibling_helper(Node *n, Node *new_leaf, Node *super_tree,
vector<Node *> &gene_trees, int &min_distance, int &min_tie_distance,
int &num_ties, Node **best_sibling);
void find_best_spr(Node *super_tree, vector<Node *> &gene_trees,
Node *&best_spr_move, Node *&best_sibling);
void find_best_spr_helper(Node *n, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties);
void find_best_spr_helper(Node *n, Node *new_sibling, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties);
void get_support(Node *super_tree, vector<Node *> *gene_trees);
void get_support(Node *n, Node *super_tree, vector<Node *> *gene_trees);
void get_transfer_support(Node *super_tree, vector<Node *> *gene_trees);
void get_transfer_support(Node *n, Node *super_tree, vector<Node *> *gene_trees);
void get_bipartition_support(Node *super_tree, vector<Node *> *gene_trees,
enum RELAXATION relaxed);
bool supported_spr(Node *source, Node *target);
bool pair_comparator (pair<int, int> a, pair<int, int> b);
/*Prototypes of Joel's functions*/
void find_best_spr_r(Node *super_tree, vector<Node *> &gene_trees, Node *&best_spr_move, Node *&best_sibling, int r);
void find_best_spr_r(Node *super_tree, vector<Node *> &gene_trees, Node *&best_spr_move, Node *&best_sibling, int r, vector<int> *original_scores);
void find_best_spr_r_helper(Node *n, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, int r);
void find_best_spr_r_helper(Node *n, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &min_tie_distance,
int &num_ties, int r,
vector<int> *original_scores);
void find_best_spr_r_helper(Node *n, Node *new_sibling, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, int r, int origin);
void find_best_spr_r_helper(Node *n, Node *new_sibling, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &min_tie_distance,
int &num_ties, int r, int origin, int offset);
void find_best_spr(Node *super_tree, vector<Node *> &gene_trees, Node *&best_spr_move, Node *&best_sibling, vector <pair <int, pair<int, int> > > &stats);
void find_best_spr_helper(Node *n, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, vector<pair <int, pair<int, int> > > &stats);
void find_best_spr_helper(Node *n, Node *new_sibling, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, vector<pair <int, pair<int, int> > > &stats);
void find_best_spr(Node *super_tree, vector<Node *> &gene_trees, Node *&best_spr_move, Node *&best_sibling, vector<pair <pair<Node*,Node*>, int> > &approx_moves);
void find_best_spr_helper(Node *n, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, vector<pair <pair<Node*,Node*>, int> > &approx_moves);
void find_best_spr_helper(Node *n, Node *new_sibling, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, vector<pair <pair<Node*,Node*>, int> > &approx_moves);
void find_best_spr_helper(Node *n, Node *new_sibling, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, vector<pair <pair<Node*,Node*>, int> > &approx_moves, int offset);
bool sort_approx_moves(const pair<pair<Node*,Node*>, int> &a, const pair<pair<Node*,Node*>, int> &b);
int find_r();
int find_r(double probability);
void find_best_distance(Node * n, Node * super_tree, vector<Node *> &gene_trees, vector< pair<Node*, int> > &scores, int &num_zeros, int &best_distance);
//void find_best_distance_helper(Node *n, Forest *f, vector<Node *> &gene_trees, vector< pair<Node *, int> > &scores);
vector<pair<Node *, int> > get_best_scores(vector<pair<Node *, int> > &scores);
void find_best_spr_r_helper(Node *n, Node *new_sibling, Node *super_tree,
vector<Node *> &gene_trees, Node *&best_spr_move,
Node *&best_sibling, int &min_distance, int &num_ties, int r, int origin, vector<pair <pair<Node*,Node*>, int> > &approx_moves);
bool is_taboo(list<Node> taboo_trees, Node *super_tree);
map<string, int> label_map;
map<int, string> reverse_label_map;
bool is_pow_2(int n) {
return (n) && !(n & (n - 1));
}
bool BIPARTITION_CLUSTER = false;
list<Node> taboo_trees = list<Node>();
int main(int argc, char *argv[]) {
// ignore multifurcating trees by default
IGNORE_MULTI = true;
string INCLUDE_ONLY = "";
bool OUTGROUP_ROOT = false;
string OUTGROUP = "";
string INITIAL_SUPER_TREE = "";
string LGT_GROUPS = "";
bool INITIAL_SUPER_TREE_UNROOTED = false;
bool FIND_SUPPORT = false;
bool FIND_BIPARTITION_SUPPORT = false;
enum RELAXATION RELAXED_BIPARTITION_SUPPORT = NEGATIVE_RELAXED;
bool FIND_CLADE_TRANSFERS = false;
bool LGT_CSV = false;
int max_args = argc-1;
while (argc > 1) {
char *arg = argv[--argc];
if (strcmp(arg, "-fpt") == 0) {
FPT = true;
DEFAULT_ALGORITHM=false;
}
else if (strcmp(arg, "-bb") == 0) {
BB = true;
DEFAULT_ALGORITHM=false;
}
else if (strcmp(arg, "-approx") == 0) {
APPROX=true;
}
else if (strcmp(arg, "-q") == 0)
QUIET = true;
else if (strcmp(arg, "-cc") == 0)
APPROX_CHECK_COMPONENT = true;
else if (strcmp(arg, "-unrooted") == 0)
UNROOTED = true;
else if (strcmp(arg, "-simple_unrooted") == 0) {
SIMPLE_UNROOTED = true;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
SIMPLE_UNROOTED_NUM = atoi(arg2);
cout << "SIMPLE_UNROOTED_NUM=" << SIMPLE_UNROOTED_NUM << endl;
}
}
else if (strcmp(arg, "-simple_unrooted_rspr") == 0) {
SIMPLE_UNROOTED = true;
EXACT_ROOTING = true;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
SIMPLE_UNROOTED_NUM = atoi(arg2);
cout << "SIMPLE_UNROOTED_NUM=" << SIMPLE_UNROOTED_NUM << endl;
}
}
else if (strcmp(arg, "-simple_unrooted_random") == 0) {
SIMPLE_UNROOTED = true;
RANDOM_ROOTING = true;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
SIMPLE_UNROOTED_NUM = atoi(arg2);
cout << "SIMPLE_UNROOTED_NUM=" << SIMPLE_UNROOTED_NUM << endl;
}
}
else if (strcmp(arg, "-simple_unrooted_fast") == 0) {
SIMPLE_UNROOTED=true;
SIMPLE_UNROOTED_FAST=true;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
SIMPLE_UNROOTED_NUM = atoi(arg2);
cout << "SIMPLE_UNROOTED_NUM=" << SIMPLE_UNROOTED_NUM << endl;
}
}
else if (strcmp(arg, "-random_insert_order") == 0) {
RANDOM_INSERT_ORDER = true;
}
else if (strcmp(arg, "-reroot") == 0) {
REROOT = true;
REROOT_INITIAL = true;
}
else if (strcmp(arg, "-reroot_initial") == 0) {
REROOT_INITIAL = true;
}
else if (strcmp(arg, "-rspr_root") == 0) {
EXACT_ROOTING = true;
}
else if (strcmp(arg, "-random_root") == 0) {
RANDOM_ROOTING = true;
}
else if (strcmp(arg, "-unrooted_min_approx") == 0) {
UNROOTED = true;
UNROOTED_MIN_APPROX = true;
}
else if (strcmp(arg, "-noopt") == 0) {
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-cut_one_b") == 0 ||
strcmp(arg, "-cob") == 0) {
CUT_ONE_B = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-reverse_cut_one_b") == 0 ||
strcmp(arg, "-rcob") == 0) {
REVERSE_CUT_ONE_B = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-cut_all_b") == 0 ||
strcmp(arg, "-cab") == 0) {
CUT_ALL_B = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-cut_ac_separate_components") == 0 ||
strcmp(arg, "-sc") == 0) {
CUT_AC_SEPARATE_COMPONENTS = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-cut_one_ab") == 0) {
CUT_ONE_AB = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-h") == 0) {
cout << USAGE;
return 0;
}
/* else if (strcmp(arg, "-cluster") == 0) {
CLUSTER_REDUCTION = true;
PREFER_RHO = true;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
MAX_CLUSTERS = atoi(arg2);
cout << "MAX_CLUSTERS=" << MAX_CLUSTERS << endl;
}
}
*/
else if (strcmp(arg, "-prefer_rho") == 0) {
PREFER_RHO = true;
}
/*
else if (strcmp(arg, "-memoize") == 0) {
MEMOIZE = true;
}
else if (strcmp(arg, "-all_mafs") == 0) {
ALL_MAFS= true;
}
*/
else if (strcmp(arg, "-i") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
NUM_ITERATIONS = atoi(arg2);
cout << "NUM_ITERATIONS=" << NUM_ITERATIONS << endl;
}
}
/*Joel: limit SPR radius*/
else if (strcmp(arg, "-r") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] == 'r'){
R_LIMIT = true;
R_RAND = true;
R_DISTANCE = find_r();
cout << "RANDOM R_DISTANCE=" << R_DISTANCE << endl;
}
else if (arg2[0] != '-'){
R_LIMIT = true;
R_DISTANCE = atoi(arg2);
cout << "R_DISTANCE=" << R_DISTANCE << endl;
}
}
}
else if (strcmp(arg, "-r_variable") == 0) {
R_VARIABLE = true;
DEFAULT_SEARCH_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-p") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (!R_RAND)
R_PROB = 0.500;
else if (arg2[0] != '-'){
R_BIAS = true;
R_PROB = atof(arg2);
cout << "PROBABILITY=" << R_PROB << endl;
}
}
DEFAULT_SEARCH_OPTIMIZATIONS=false;
}
/*Joel: refined greedy search*/
else if(strcmp(arg, "-r_greedy")==0){
GREEDY_REFINED = true;
if(max_args > argc){
char *arg2 = argv[argc+1];
if(arg2[0] != '-')
S_NUM = atoi(arg2);
else
S_NUM = 5;
}
if(max_args > argc){
char *arg2 = argv[argc+2];
if(arg2[0] != '-')
R_DISTANCE = atoi(arg2);
else
R_DISTANCE = 1;
}
DEFAULT_SEARCH_OPTIMIZATIONS=false;
}
/*Joel: limit starting points*/
else if (strcmp(arg, "-num_start") == 0){
S_LIMIT = true;
if(max_args > argc) {
char *arg2 = argv[argc+1];
if(arg2[0] != '-'){
S_NUM = atoi(arg2);
}
}
cout << "STARTING POINTS TO CHECK: " << S_NUM << endl;
DEFAULT_SEARCH_OPTIMIZATIONS=false;
}
/*Joel: limit SPR radius options*/
else if (strcmp(arg, "-stats") == 0){
S_STATS = true;
}
else if (strcmp(arg, "-control") == 0) {
R_CONTROL = true;
DEFAULT_SEARCH_OPTIMIZATIONS=false;
}
/*Joel: stats on approx distance vs total distance*/
else if (strcmp(arg, "-d_stats") == 0)
D_STATS = true;
/*Joel: greedy search*/
else if(strcmp(arg, "-greedy")==0) {
GREEDY = true;
DEFAULT_SEARCH_OPTIMIZATIONS=false;
}
/*Joel: random starting tree*/
else if (strcmp(arg, "-rand_tree") == 0)
RANDOM_TREE = true;
else if (strcmp(arg, "-max") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
MAX_SPR = atoi(arg2);
cout << "MAX_SPR=" << MAX_SPR << endl;
}
}
else if (strcmp(arg, "-cluster_max") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-') {
CLUSTER_MAX_SPR = atoi(arg2);
cout << "CLUSTER_MAX_SPR=" << CLUSTER_MAX_SPR << endl;
}
}
}
else if (strcmp(arg, "-num_leaves") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
NUM_LEAVES = atoi(arg2);
cout << "NUM_LEAVES=" << NUM_LEAVES << endl;
}
}
else if (strcmp(arg, "-time") == 0) {
TIMING= true;
}
else if (strcmp(arg, "-clamp") == 0) {
CLAMP= true;
}
else if (strcmp(arg, "-small_trees") == 0) {
SMALL_TREES=true;
}
else if (strcmp(arg, "-convert_list") == 0) {
CONVERT_LIST=true;
}
else if (strcmp(arg, "-valid_trees") == 0) {
VALID_TREES=true;
}
else if (strcmp(arg, "-invalid_trees") == 0) {
VALID_TREES=true;
INVALID_TREES=true;
}
else if (strcmp(arg, "-valid_trees_rooted") == 0) {
VALID_TREES_ROOTED=true;
}
else if (strcmp(arg, "-lgt_analysis") == 0) {
LGT_ANALYSIS=true;
}
else if (strcmp(arg, "-lgt_evaluation") == 0) {
LGT_EVALUATION=true;
}
else if (strcmp(arg, "-lgt_csv") == 0) {
LGT_CSV=true;
}
else if (strcmp(arg, "-max_degree") == 0) {
FIND_MAX_DEGREE=true;
}
else if (strcmp(arg, "-multi_trees") == 0) {
MULTI_TREES=true;
}
else if (strcmp(arg, "-rf_ties") == 0) {
RF_TIES=true;
}
else if (strcmp(arg, "-allow_multi") == 0) {
IGNORE_MULTI = false;
}
else if (strcmp(arg, "-protect_edges") == 0) {
EDGE_PROTECTION = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-allow_abort") == 0) {
ABORT_AT_FIRST_SOLUTION = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-preorder_sib_pairs") == 0) {
PREORDER_SIBLING_PAIRS = true;
NEAR_PREORDER_SIBLING_PAIRS = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-near_preorder_sib_pairs") == 0) {
NEAR_PREORDER_SIBLING_PAIRS = true;
DEFAULT_OPTIMIZATIONS=false;
}
else if (strcmp(arg, "-leaf_reduction") == 0) {
LEAF_REDUCTION = true;
}
else if (strcmp(arg, "-leaf_reduction2") == 0) {
LEAF_REDUCTION2 = true;
}
else if (strcmp(arg, "-split_approx") == 0) {
SPLIT_APPROX = true;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
SPLIT_APPROX_THRESHOLD = atoi(arg2);
cout << "SPLIT_APPROX_THRESHOLD=" << SPLIT_APPROX_THRESHOLD
<< endl;
}
}
else if (strcmp(arg, "-support") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
REQUIRED_SUPPORT = atof(arg2);
cout << "REQUIRED_SUPPORT=" << REQUIRED_SUPPORT
<< endl;
}
}
else if (strcmp(arg, "-approx_siblings") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
APPROX_SIBLINGS = atoi(arg2);
cout << "APPROX_SIBLINGS=" << APPROX_SIBLINGS
<< endl;
}
}
else if (strcmp(arg, "-include_only") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
INCLUDE_ONLY = string(arg2);
cout << "INCLUDE_ONLY=" << INCLUDE_ONLY
<< endl;
}
}
else if (strcmp(arg, "-outgroup") == 0) {
OUTGROUP_ROOT = true;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
OUTGROUP = string(arg2);
cout << "OUTGROUP=" << OUTGROUP
<< endl;
}
}
else if (strcmp(arg, "-initial_tree") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
INITIAL_SUPER_TREE = string(arg2);
cout << "INITIAL_TREE=" << INITIAL_SUPER_TREE
<< endl;
}
}
else if (strcmp(arg, "-lgt_groups") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
LGT_GROUPS = string(arg2);
cout << "LGT_GROUPS=" << LGT_GROUPS
<< endl;
}
}
else if (strcmp(arg, "-initial_tree_unrooted") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
INITIAL_SUPER_TREE = string(arg2);
cout << "INITIAL_TREE=" << INITIAL_SUPER_TREE
<< endl;
INITIAL_SUPER_TREE_UNROOTED=true;
REROOT_INITIAL=true;
}
}
else if (strcmp(arg, "-count_losses") == 0) {
COUNT_LOSSES = true;
}
else if (strcmp(arg, "-cut_lost") == 0) {
CUT_LOST = true;
}
else if (strcmp(arg, "-find_support") == 0) {
FIND_SUPPORT = true;
}
else if (strcmp(arg, "-find_bipartition_support") == 0) {
FIND_BIPARTITION_SUPPORT = true;
}
else if (strcmp(arg, "-relaxed_bipartition_support") == 0) {
RELAXED_BIPARTITION_SUPPORT = ALL_RELAXED;
}
else if (strcmp(arg, "-strict_bipartition_support") == 0) {
RELAXED_BIPARTITION_SUPPORT = STRICT;
}
else if (strcmp(arg, "-bipartition_cluster") == 0) {
BIPARTITION_CLUSTER = true;
cout << "BIPARTITION_CLUSTER=true" << endl;
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-')
SUPPORT_THRESHOLD = atof(arg2);
}
cout << "CLUSTER THRESHOLD=" << SUPPORT_THRESHOLD
<< endl;
}
else if (strcmp(arg, "-find_clade_transfers") == 0) {
FIND_CLADE_TRANSFERS = true;
}
else if (strcmp(arg, "-taboo_search") == 0) {
TABOO_SEARCH = true;
}
else if (strcmp(arg, "-one_tree_at_a_time") == 0
|| (strcmp(arg, "-one_tree") == 0) ) {
ONE_TREE_AT_A_TIME = true;
}
else if (strcmp(arg, "-node_glom_construction") == 0
|| (strcmp(arg, "-node_glom") == 0) ) {
NODE_GLOM_CONSTRUCTION = true;
}
else if (strcmp(arg, "-precompute") == 0 ) {
USE_PRECOMPUTED_DISTANCES = true;
}
else if (strcmp(arg, "-cluster_tune") == 0) {
if (max_args > argc) {
char *arg2 = argv[argc+1];
if (arg2[0] != '-') {
CLUSTER_TUNE = atoi(arg2);
cout << "CLUSTER_TUNE=" << CLUSTER_TUNE << endl;
}
}
}
else if (strcmp(arg, "--help") == 0) {
cout << USAGE;
return 0;
}
}
if (DEFAULT_OPTIMIZATIONS) {
CUT_ALL_B=true;
CUT_ONE_B = true;
CUT_TWO_B = true;
// CUT_TWO_B_ROOT = true;
REVERSE_CUT_ONE_B = true;
REVERSE_CUT_ONE_B_3 = true;
CUT_AC_SEPARATE_COMPONENTS = true;
EDGE_PROTECTION = true;
EDGE_PROTECTION_TWO_B = true;
PREFER_NONBRANCHING = true;
// CHECK_MERGE_DEPTH = true;
// ABORT_AT_FIRST_SOLUTION = true;
PREORDER_SIBLING_PAIRS = true;
NEAR_PREORDER_SIBLING_PAIRS = true;
LEAF_REDUCTION = true;