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ust.cpp
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// UST
// --- VERSION 1.1 ----
// Author: amatur
#include <cmath>
#include <cstring>
#include <fstream>
#include <iostream>
#include <vector>
#include <assert.h>
#include <stdint.h>
#include <unordered_set>
#include <map>
#include <set>
#include <sstream>
#include <algorithm>
#include <cstdlib>
#include <list>
#include <stack>
#include <unordered_map>
#include <utility>
#include <queue>
#include <deque>
#include <unistd.h>
#include <tuple>
using namespace std;
bool DEBUGMODE = false;
int K = 0;
string UNITIG_FILE = "examples/k11.unitigs.fa";
string OUTPUT_FILENAME;
enum DEBUGFLAG_T {
NONE = 0,
UKDEBUG = 6,
VERIFYINPUT = 1,
INDEGREEPRINT = 2,
DFSDEBUGG = 3,
PARTICULAR = 4,
NODENUMBER_DBG = 5,
OLDNEWMAP = 9,
PRINTER = 10,
SINKSOURCE = 12
};
enum ALGOMODE_T {
BASIC = 0,
INDEGREE_DFS = 1,
INDEGREE_DFS_1 = 2,
OUTDEGREE_DFS = 3,
OUTDEGREE_DFS_1 = 4,
INDEGREE_DFS_INVERTED = 5,
PLUS_INDEGREE_DFS = 6,
RANDOM_DFS = 7,
NODEASSIGN = 8,
SOURCEFIRST = 9,
TWOWAYEXT = 10,
PROFILE_ONLY = 11,
EPPRIOR = 12,
GRAPHPRINT = 13,
TIGHTUB = 14,
BRACKETCOMP = 15
};
bool FLG_NEWUB = true;
bool FLG_ABUNDANCE = false;
DEBUGFLAG_T DBGFLAG = NONE; // NODENUMBER_DBG
ALGOMODE_T ALGOMODE = TWOWAYEXT;
string mapmode[] = {"basic",
"indegree_dfs",
"indegree_dfs_initial_sort_only",
"outdegree_dfs",
"outdegree_dfs_initial_sort_only",
"inverted_indegree_dfs",
"plus_indegree_dfs",
"random_dfs",
"node_assign",
"source_first",
"twoway",
"profile_only",
"endpoint_priority",
"graph_print",
"tight_ub",
"tip"};
string modefilename[] = {"Fwd",
"indegree_dfs",
"indegree_dfs_initial_sort_only",
"outdegree_dfs",
"outdegree_dfs_initial_sort_only",
"inverted_indegree_dfs",
"plus_indegree_dfs",
"random_dfs",
"node_assign",
"source_first",
"",
"profile_only",
"endpoint_priority",
"graph_print",
"tight_ub",
"Tip"};
typedef tuple<int, int, int, int> fourtuple; // uid, walkid, pos, isTip
bool sort_by_walkId(const fourtuple& lhs, const fourtuple& rhs) {
return get<1>(lhs) < get<1>(rhs);
}
bool sort_by_pos(const fourtuple& lhs, const fourtuple& rhs) {
return get<2>(lhs) < get<2>(rhs);
}
bool sort_by_tipstatus(const fourtuple& lhs, const fourtuple& rhs) {
return get<3>(lhs) < get<3>(rhs);
}
typedef struct {
int serial = -1;
int startPosWithKOverlap;
int endPosWithKOVerlap;
bool isWalkEnd = false;
int pos_in_walk = -100;
int finalWalkId = -1; // renders some walkId as invalid
int isTip = 0;
} new_node_info_t;
typedef struct {
int serial;
int ln;
} unitig_struct_t;
typedef struct {
// 1 means +, 0 means -
bool left;
bool right;
int toNode;
} edge_t;
typedef struct {
edge_t edge;
int fromNode;
} edge_both_t;
typedef struct {
edge_t edge;
int kmerStartIndex;
int kmerEndIndex;
} newEdge_t;
int C_ustitch = 0;
int C_twoway_ustitch = 0;
int C_tip_ustitch = 0;
int V_ustitch = 0;
int V_twoway_ustitch = 0;
int V_tip_ustitch = 0;
int isolated_node_count = 0;
int sink_count = 0;
int source_count = 0;
int sharedparent_count = 0;
int sharparentCntRefined = 0;
int onecount = 0;
struct node_sorter {
int node;
int sortkey;
// bool operator() (struct node_sorter i, struct node_sorter j) { return
// (i.sortkey<j.sortkey);}
};
bool sort_by_key(struct node_sorter i, struct node_sorter j) {
return (i.sortkey < j.sortkey);
}
bool sort_by_key_inverted(struct node_sorter i, struct node_sorter j) {
return (i.sortkey > j.sortkey);
}
int* global_indegree;
int* global_outdegree;
int* global_plusindegree;
int* global_plusoutdegree;
int* global_issinksource;
// int* global_priority;
map<pair<int, int>, int> inOutCombo;
vector<vector<edge_t> > adjList;
vector<vector<edge_t> > reverseAdjList;
vector<unitig_struct_t> unitigs;
map<int, string> newSequences;
map<int, string> newNewSequences; // int is the unitig id (old id)
set<int> newNewMarker;
vector<list<int> > newToOld;
vector<int>
walkFirstNode; // given a walk id, what's the first node of that walk
unordered_map<int, vector<edge_t> >
sinkSrcEdges; // int is the unitig id (old id)
string getFileName(const string& s) {
char sep = '/';
size_t i = s.rfind(sep, s.length());
if (i != string::npos) { return (s.substr(i + 1, s.length() - i)); }
return s;
}
inline string plus_strings(const string& a, const string& b, size_t kmersize) {
if (a == "") return b;
if (b == "") return a;
string ret = a + b.substr(kmersize - 1, b.length() - (kmersize - 1));
return ret;
}
string delSpaces(string& str) {
str.erase(std::remove(str.begin(), str.end(), ' '), str.end());
return str;
}
bool charToBool(char c) {
if (c == '+') {
return true;
} else {
if (c != '-') cout << "Erroneus character in BCALM2 output." << endl;
return false;
}
}
string reverseComplement(string base) {
size_t len = base.length();
char* out = new char[len + 1];
out[len] = '\0';
for (int i = 0; i < len; i++) {
if (base[i] == 'A')
out[len - i - 1] = 'T';
else if (base[i] == 'C')
out[len - i - 1] = 'G';
else if (base[i] == 'G')
out[len - i - 1] = 'C';
else if (base[i] == 'T')
out[len - i - 1] = 'A';
}
string outString(out);
free(out);
return outString;
}
double readTimer() {
return clock() / (double)CLOCKS_PER_SEC;
}
inline string currentDateTime() {
// Get current date/time, format is YYYY-MM-DD HH:mm:ss
time_t now = time(0);
struct tm tstruct;
char buf[80];
tstruct = *localtime(&now);
strftime(buf, sizeof(buf), "%Y-%m-%d %X\n", &tstruct);
return buf;
}
int countOutArcs(int node) {
return (adjList.at(node)).size();
}
inline char boolToCharSign(bool sign) {
return (sign == true) ? '+' : '-';
}
// @@ --- ALL PRINTING CODE --- //
void printBCALMGraph(vector<vector<edge_t> > adjList) {
for (int i = 0; i < adjList.size(); i++) {
cout << i << "# ";
for (edge_t edge : adjList.at(i)) {
cout << boolToCharSign(edge.left) << ":" << edge.toNode << ":"
<< boolToCharSign(edge.right) << ", ";
}
cout << endl;
}
}
class GroupMerger {
public:
map<int, bool> fwdVisited;
map<int, bool> bwdVisited;
map<int, int> bwdWalkId;
map<int, int> fwdWalkId;
GroupMerger() {}
void connectGroups(int from, int to) {
fwdVisited[from] = false;
bwdVisited[to] = false;
fwdWalkId[from] = to;
bwdWalkId[to] = from;
}
~GroupMerger() {}
};
class DisjointSet {
unordered_map<int, int> parent;
public:
DisjointSet() {}
void make_set(int id) {
this->parent[id] = -1;
}
void Union(int xId, int yId) {
int xset = find_set(xId);
int yset = find_set(yId);
if (xset != yset) { parent[xset] = yset; }
}
int find_set(int id) {
if (parent[id] == -1) return id;
return find_set(parent[id]);
}
~DisjointSet() {}
};
class Graph {
public:
size_t V = adjList.size();
int countNewNode = 0;
int time = 0;
char* color;
int* p_dfs;
bool* nodeSign;
new_node_info_t* oldToNew;
bool* saturated;
struct node_sorter* sortStruct;
bool* countedForLowerBound;
DisjointSet disSet;
GroupMerger gmerge;
Graph() {
color = new char[V];
p_dfs = new int[V];
nodeSign = new bool[V];
oldToNew = new new_node_info_t[V];
saturated = new bool[V];
sortStruct = new struct node_sorter[V];
global_indegree = new int[V];
global_outdegree = new int[V];
global_plusindegree = new int[V];
global_plusoutdegree = new int[V];
global_issinksource = new int[V];
// global_priority = new int[V];
countedForLowerBound = new bool[V];
for (int i = 0; i < V; i++) {
if (ALGOMODE == TWOWAYEXT || ALGOMODE == BRACKETCOMP) {
disSet.make_set(i);
}
oldToNew[i].serial = -1;
saturated[i] = false;
sortStruct[i].sortkey = 0;
sortStruct[i].node = i;
global_indegree[i] = 0;
global_outdegree[i] = 0;
global_plusindegree[i] = 0;
global_plusoutdegree[i] = 0;
global_issinksource[i] = 0;
// global_priority[i] = 0;
countedForLowerBound[i] = false;
}
}
inline bool sRight(edge_t plusminusedge) {
return !(plusminusedge.right == true);
}
inline bool sLeft(edge_t plusminusedge) {
return (plusminusedge.left == true);
}
void indegreePopulate() {
int xc = 0;
for (vector<edge_t> elist : adjList) {
for (edge_t e : elist) {
global_indegree[e.toNode] += 1;
sortStruct[e.toNode].sortkey = sortStruct[e.toNode].sortkey + 1;
if (e.right == true) { global_plusindegree[e.toNode] += 1; }
if (e.left == true) { global_plusoutdegree[xc] += 1; }
}
global_outdegree[xc] = elist.size();
xc++;
}
for (int i = 0; i < 5; i++) {
for (int j = 0; j < 5; j++) { inOutCombo[make_pair(i, j)] = 0; }
}
for (int i = 0; i < V; i++) {
pair<int, int> a;
a = make_pair(global_plusindegree[i], global_plusoutdegree[i]);
inOutCombo[a] = (inOutCombo.count(a) ? inOutCombo[a] + 1 : 1);
if (DBGFLAG == SINKSOURCE) { cout << i << "is "; }
if (global_plusoutdegree[i] == 0 && global_plusindegree[i] != 0) {
sink_count++;
global_issinksource[i] = 1;
// global_priority[i] = 5;
countedForLowerBound[i] = true;
if (DBGFLAG == SINKSOURCE) { cout << "sink, "; }
}
if (global_plusindegree[i] == 0 && global_plusoutdegree[i] != 0) {
source_count++;
global_issinksource[i] = 1;
// global_priority[i] = 5;
countedForLowerBound[i] = true;
if (DBGFLAG == SINKSOURCE) { cout << "source, "; }
}
if (global_indegree[i] == 0) {
global_issinksource[i] = 1;
isolated_node_count++;
if (DBGFLAG == SINKSOURCE) { cout << "isolated, "; }
}
if (global_indegree[i] == 1) { onecount++; }
if (DBGFLAG == SINKSOURCE) { cout << endl; }
}
xc = 0; // current vertex while traversing the adjacency list
for (vector<edge_t> elist : adjList) {
int neighborCount = 0;
int spNeighborCount[2];
spNeighborCount[0] = 0;
spNeighborCount[1] = 0;
stack<int> countedNodes;
set<pair<int, bool> > countedSides;
// if(true){
if (FLG_NEWUB == true) {
// ENDPOINT SIDE UPPER BOUND - improved
for (edge_t e_xy : elist) { // central node: all neighbors of x
int y = e_xy.toNode;
vector<edge_t> adjY = adjList[y];
bool eligibleSp = true;
// pair<int, bool> pairr;
for (edge_t e_from_y :
adjY) { // check if this neighbor is speacial
// pairr =make_pair(e_from_y.toNode, sRight(e_xy) );
if (e_from_y.toNode != xc) {
if (sRight(e_xy) == sLeft(e_from_y)) {
eligibleSp = false;
break;
}
}
}
if (eligibleSp) { spNeighborCount[sLeft(e_xy)]++; }
}
if (spNeighborCount[0] > 1) {
sharedparent_count += spNeighborCount[0] - 1;
}
if (spNeighborCount[1] > 1) {
sharedparent_count += spNeighborCount[1] - 1;
}
}
if (FLG_NEWUB == false) {
// ENDPOINT SIDE UPPER BOUND
for (edge_t e_xy : elist) {
int y = e_xy.toNode;
vector<edge_t> adjY = adjList[y];
bool eligible = true;
pair<int, bool> pairr;
for (edge_t e_from_y : adjY) {
pairr = make_pair(e_from_y.toNode, sRight(e_xy));
if (e_from_y.toNode != xc) {
if (sRight(e_xy) == sLeft(e_from_y)) {
eligible = false;
break;
}
}
}
if (eligible) { neighborCount++; }
}
if (global_issinksource[xc] == 1) {
if (neighborCount > 1) {
sharedparent_count += neighborCount - 1;
}
} else {
if (neighborCount > 2) {
sharedparent_count += neighborCount - 2;
}
}
}
// sharedparent_count_wrong =sharedparent_count;
// if(true){
if (1 == 0) {
// OLDER UPPER BOUND CALC
int neighborCount = 0;
for (edge_t e_xy : elist) {
int y = e_xy.toNode;
if (!countedForLowerBound[y]) {
vector<edge_t> adjY = adjList[y];
bool eligible = true;
for (edge_t e_from_y : adjY) {
if (e_from_y.toNode != xc) {
if (sRight(e_xy) == sLeft(e_from_y)) {
eligible = false;
break;
}
}
}
if (eligible) {
countedForLowerBound[y] = true;
// global_priority[y] = 4;
neighborCount++;
countedNodes.push(y);
}
}
}
if (global_issinksource[xc] == 1) {
if (neighborCount > 1) {
sharedparent_count += neighborCount - 1;
} else {
while (!countedNodes.empty()) {
countedForLowerBound[countedNodes.top()] = false;
countedNodes.pop();
}
}
} else {
if (neighborCount > 2) {
sharedparent_count += neighborCount - 2;
} else {
while (!countedNodes.empty()) {
countedForLowerBound[countedNodes.top()] = false;
countedNodes.pop();
}
}
}
}
xc++;
}
// check if not ALGOMODE == INDEGREE_DFS_INVERTED
delete[] global_indegree;
delete[] global_outdegree;
delete[] global_plusindegree;
delete[] global_plusoutdegree;
}
void DFS_visit(int u) {
if (ALGOMODE == BRACKETCOMP) {
if (global_issinksource[u] == 1) {
vector<edge_t> adju = adjList.at(u);
vector<edge_t> myvector;
for (edge_t e : adju) { myvector.push_back(e); }
sinkSrcEdges[u] = myvector;
return;
}
}
stack<edge_t> s;
edge_t uEdge;
uEdge.toNode = u;
s.push(uEdge);
while (!s.empty()) {
edge_t xEdge = s.top();
int x = xEdge.toNode;
s.pop();
if (color[x] == 'w') {
// Original DFS code
time = time + 1;
color[x] = 'g';
s.push(xEdge);
vector<edge_t> adjx = adjList.at(x);
if (ALGOMODE == RANDOM_DFS) {
random_shuffle(adjx.begin(), adjx.end());
}
// if(ALGOMODE == EPPRIOR){
// sort( adjx.begin( ), adjx.end( ), [ ](
// const edge_t& lhs, const edge_t& rhs )
// {
// return
// global_priority[lhs.toNode] <
// global_priority[rhs.toNode] ;
// });
// }
if (ALGOMODE == INDEGREE_DFS) {
sort(adjx.begin(), adjx.end(),
[](const edge_t& lhs, const edge_t& rhs) {
return global_indegree[lhs.toNode] <
global_indegree[rhs.toNode];
});
}
if (ALGOMODE == PLUS_INDEGREE_DFS) {
sort(adjx.begin(), adjx.end(),
[](const edge_t& lhs, const edge_t& rhs) {
return global_indegree[lhs.toNode] -
global_plusindegree[lhs.toNode] >
global_indegree[lhs.toNode] -
global_plusindegree[rhs.toNode];
});
}
if (ALGOMODE == INDEGREE_DFS_INVERTED) {
sort(adjx.begin(), adjx.end(),
[](const edge_t& lhs, const edge_t& rhs) {
return global_indegree[lhs.toNode] >
global_indegree[rhs.toNode];
});
}
if (ALGOMODE == OUTDEGREE_DFS) {
if (p_dfs[x] == -1) {
sort(adjx.begin(), adjx.end(),
[](const edge_t& lhs, const edge_t& rhs) {
return global_outdegree[lhs.toNode] <
global_outdegree[rhs.toNode];
});
} else if (nodeSign[x] == false) {
sort(adjx.begin(), adjx.end(),
[](const edge_t& lhs, const edge_t& rhs) {
return global_outdegree[lhs.toNode] -
global_plusoutdegree[lhs.toNode] <
global_outdegree[rhs.toNode] -
global_plusoutdegree[rhs.toNode];
});
} else if (nodeSign[x] == true) {
sort(adjx.begin(), adjx.end(),
[](const edge_t& lhs, const edge_t& rhs) {
return global_plusoutdegree[lhs.toNode] <
global_plusoutdegree[rhs.toNode];
});
}
}
// Now our branching code ::
// For a white x
// Consider 2 case:
// Case 1. p[x] = -1, it can happen in two way, x is the first
// one ever in this connected component, or no one wanted to
// take x either way, if p[x] = -1, i can be representative of a
// new node in new graph Case 2. p[x] != -1, so x won't be the
// representative/head of a newHome. x just gets added to its
// parent's newHome.
int u = unitigs.at(x).ln; // unitig length
if (p_dfs[x] == -1) {
list<int> xxx;
xxx.push_back(x);
newToOld.push_back(xxx);
oldToNew[x].serial =
countNewNode++; // countNewNode starts at 0, then keeps
// increasing
oldToNew[x].finalWalkId = oldToNew[x].serial;
// added while doing bracket comp
walkFirstNode.push_back(x);
oldToNew[x].pos_in_walk = 1;
oldToNew[x].startPosWithKOverlap = 1;
if (u < K) {
oldToNew[x].endPosWithKOVerlap =
1; // do we actually see this? yes
if (DBGFLAG == UKDEBUG) {
cout << "node: " << x << "u< k ***** u = " << u
<< endl;
}
} else {
oldToNew[x].endPosWithKOVerlap = u - K + 1;
}
} else {
newToOld[oldToNew[p_dfs[x]].serial].push_back(x);
oldToNew[x].serial = oldToNew[p_dfs[x]].serial;
oldToNew[x].finalWalkId = oldToNew[x].serial;
if (ALGOMODE == TWOWAYEXT || ALGOMODE == BRACKETCOMP) {
disSet.Union(x, p_dfs[x]);
}
oldToNew[x].startPosWithKOverlap =
oldToNew[p_dfs[x]].endPosWithKOVerlap + 1;
oldToNew[x].pos_in_walk =
oldToNew[p_dfs[x]].pos_in_walk + 1;
if (u < K) {
oldToNew[x].endPosWithKOVerlap =
oldToNew[x].startPosWithKOverlap +
1; // do we actually see this? yes
if (DBGFLAG == UKDEBUG) {
cout << "node: " << x << "u< k ***** u = " << u
<< endl;
}
} else {
oldToNew[x].endPosWithKOVerlap =
u - K +
(oldToNew[x]
.startPosWithKOverlap); // check correctness
}
}
// x->y is the edge, x is the parent we are extending
for (edge_t yEdge : adjx) { // edge_t yEdge = adjx.at(i);
int y = yEdge.toNode;
if (ALGOMODE == BRACKETCOMP) {
if (global_issinksource[y] == true) { continue; }
}
// Normal DFS
if (color[y] == 'w') { s.push(yEdge); }
// handle self-loop, self-loop will always be an extra edge
// redundant, because we remove self-loop anyway
if (y == x) {
edge_both_t e;
e.edge = yEdge;
e.fromNode = x;
} else if (saturated[x]) {
// Since x is saturated, we only add resolveLater edges
// no need to check for consistency
if (y != p_dfs[x]) {
edge_both_t e;
e.edge = yEdge;
e.fromNode = x;
}
} else {
// If x has space to take a child, meaning x is not
// saturated hunting for potential child
if (color[y] == 'w' && p_dfs[y] == -1) {
// y has white color & got no parent => means it's
// homeless, so let's see if we can take it as a
// child of x
// But just see if it is eligible to be a child,
// i.e. is it consistent (sign check)?
// 2 case, Does x's child have grandparent?
// If No:
if (p_dfs[x] == -1 && ALGOMODE != NODEASSIGN) {
// case 1: child has no grandparent
// so extend path without checking any sign
nodeSign[x] = yEdge.left;
nodeSign[y] = yEdge.right;
p_dfs[y] = x;
saturated[x] = true; // found a child
} else if (nodeSign[x] == yEdge.left) {
// case 2: child (=y) has grandparent, i.e. x's
// parent exists
nodeSign[y] = yEdge.right;
p_dfs[y] = x;
saturated[x] = true; // found a child
} else {
// do we reach this case?
edge_both_t e;
e.edge = yEdge;
e.fromNode = x;
}
} else {
// merger
if (ALGOMODE == TWOWAYEXT ||
ALGOMODE == BRACKETCOMP) {
// y is not white
bool consistentEdge =
(nodeSign[y] == yEdge.right &&
(p_dfs[x] == -1 ||
(p_dfs[x] != -1 &&
nodeSign[x] == yEdge.left)));
if (p_dfs[y] == -1 && consistentEdge &&
oldToNew[x].serial != oldToNew[y].serial) {
// cout<<"x: "<<x<<":"
// <<disSet.find_set(x)<<" "; cout<<"y:
// "<<y<<":" <<disSet.find_set(y) <<endl;
// not in same group already, prevent cycle
if (disSet.find_set(x) !=
disSet.find_set(y)) {
nodeSign[x] = yEdge.left;
nodeSign[y] = yEdge.right;
p_dfs[y] = x;
saturated[x] = true; // found a child
// oldToNew[y].serial
disSet.Union(x, y);
gmerge.connectGroups(
oldToNew[x].serial,
oldToNew[y].serial);
}
}
}
if (y != p_dfs[x]) {
edge_both_t e;
e.edge = yEdge;
e.fromNode = x;
}
}
}
}
} else if (color[x] == 'g') {
time = time + 1;
color[x] = 'b';
}
}
}
void DFS() {
if (ALGOMODE == NODEASSIGN) {
for (int i = 0; i < V; i++) {
nodeSign[i] = true;
if (global_plusindegree[i] <
global_indegree[i] - global_plusindegree[i]) {
nodeSign[i] = true;
}
}
}
if (ALGOMODE == SOURCEFIRST) {
for (int i = 0; i < V; i++) {
sortStruct[i].node = i;
sortStruct[i].sortkey = global_issinksource[i];
}
vector<struct node_sorter> myvector(sortStruct, sortStruct + V);
sort(myvector.begin(), myvector.end(), sort_by_key_inverted);
copy(myvector.begin(), myvector.end(), sortStruct);
}
// if(ALGOMODE == EPPRIOR){
// for (int i = 0; i < V; i++) {
// sortStruct[i].node = i;
// sortStruct[i].sortkey = global_priority[i];
// }
// vector<struct node_sorter> myvector (sortStruct,
// sortStruct+V); sort (myvector.begin(), myvector.end(),
// sort_by_key_inverted); copy(myvector.begin(),
// myvector.end(), sortStruct);
// }
if (ALGOMODE == INDEGREE_DFS_INVERTED) {
for (int i = 0; i < V; i++) {
sortStruct[i].node = i;
sortStruct[i].sortkey = global_indegree[i];
}
vector<struct node_sorter> myvector(sortStruct, sortStruct + V);
sort(myvector.begin(), myvector.end(), sort_by_key_inverted);
// random_shuffle ( myvector.begin(), myvector.end() );
copy(myvector.begin(), myvector.end(), sortStruct);
}
if (ALGOMODE == INDEGREE_DFS || ALGOMODE == INDEGREE_DFS_1) {
for (int i = 0; i < V; i++) {
sortStruct[i].node = i;
sortStruct[i].sortkey = global_indegree[i];
}
vector<struct node_sorter> myvector(sortStruct, sortStruct + V);
sort(myvector.begin(), myvector.end(), sort_by_key);
copy(myvector.begin(), myvector.end(), sortStruct);
if (DBGFLAG == INDEGREEPRINT) {
cout << "print in degrees" << endl;
for (int i = 0; i < V; i++) {
cout << sortStruct[i].node << "->" << sortStruct[i].sortkey
<< endl;
}
}
}
if (ALGOMODE == RANDOM_DFS) {
for (int i = 0; i < V; i++) {
sortStruct[i].node = i;
sortStruct[i].sortkey = global_indegree[i];
}
vector<struct node_sorter> myvector(sortStruct, sortStruct + V);
sort(myvector.begin(), myvector.end(), sort_by_key);
random_shuffle(myvector.begin(), myvector.end());
copy(myvector.begin(), myvector.end(), sortStruct);
}
if (ALGOMODE == OUTDEGREE_DFS || ALGOMODE == OUTDEGREE_DFS_1) {
for (int i = 0; i < V; i++) {
sortStruct[i].node = i;
sortStruct[i].sortkey = global_outdegree[i];
}
vector<struct node_sorter> myvector(sortStruct, sortStruct + V);
sort(myvector.begin(), myvector.end(), sort_by_key);
copy(myvector.begin(), myvector.end(), sortStruct);
}
double time_a = readTimer();
for (int i = 0; i < V; i++) {
color[i] = 'w';
p_dfs[i] = -1;
}
cout << "Basic V loop time: " << readTimer() - time_a << " sec" << endl;
time_a = readTimer();
for (int j = 0; j < V; j++) {
int i;
if (ALGOMODE == OUTDEGREE_DFS || ALGOMODE == OUTDEGREE_DFS_1 ||
ALGOMODE == INDEGREE_DFS || ALGOMODE == INDEGREE_DFS_1 ||
ALGOMODE == SOURCEFIRST) {
i = sortStruct[j].node;
} else {
i = j;
}
if (color[i] == 'w') {
if (DBGFLAG == DFSDEBUGG) {
cout << "visit start of node: " << i << endl;
}
DFS_visit(i);
}
}
cout << "DFS time: " << readTimer() - time_a << " sec" << endl;
/***MERGE START***/
bool* merged = new bool[countNewNode];
for (int i = 0; i < countNewNode; i++) { merged[i] = false; }
if (ALGOMODE == TWOWAYEXT || ALGOMODE == BRACKETCOMP) {
ofstream uidSequenceFile;
uidSequenceFile.open("uidSeq" + modefilename[ALGOMODE] + ".txt");
for (const auto& p : gmerge.fwdWalkId) {
if (gmerge.fwdVisited[p.first] == false) {
int fromnode = p.first;
int tonode = p.second;
deque<int> lst;
lst.push_back(fromnode);
lst.push_back(tonode);
gmerge.fwdVisited[fromnode] = true;
gmerge.bwdVisited[tonode] = true;
if (gmerge.fwdVisited.count(tonode) > 0) {
while (gmerge.fwdVisited[tonode] == false) {
gmerge.fwdVisited[tonode] = true;
tonode = gmerge.fwdWalkId[tonode];
gmerge.bwdVisited[tonode] = true;
lst.push_back(tonode);
if (gmerge.fwdVisited.count(tonode) == 0) break;
}
}
if (gmerge.bwdVisited.count(fromnode) > 0) {
while (gmerge.bwdVisited[fromnode] == false) {
gmerge.bwdVisited[fromnode] = true;
fromnode = gmerge.bwdWalkId[fromnode];
gmerge.fwdVisited[fromnode] = true;
lst.push_front(fromnode);
if (gmerge.bwdVisited.count(fromnode) == 0) break;
}
}
int headOfThisWalk =
walkFirstNode[lst.at(0)]; // CHECK AGAIN
assert(!lst.empty());
int commonWalkId = lst.at(0);
int posOffset = 1;
int lastWalk = -1;
for (auto i : lst) {
// i is new walk id before merging
merged[i] = true;
walkFirstNode[i] = headOfThisWalk;
// travesing the walk list of walk ID i
for (int uid : newToOld[i]) {
oldToNew[uid].serial = commonWalkId;
oldToNew[uid].finalWalkId = commonWalkId;
oldToNew[uid].pos_in_walk = posOffset++;
}
}
oldToNew[newToOld[lst.back()].back()].isWalkEnd = true;
V_twoway_ustitch++;
}
}
for (int newNodeNum = 0; newNodeNum < countNewNode; newNodeNum++) {