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graph.cpp
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// graph.cpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* Graph utilities
*
*/
#undef NDEBUG
#include "graph.hpp"
#include "common.inc"
namespace Common_sp
{
//////////////////////////////// DiGraph /////////////////////////////////////
// DiGraph::Node
void DiGraph::Node::attach (DiGraph &graph_arg)
{
ASSERT (! graph);
#ifndef NDEBUG
for (const bool b : {false, true})
ASSERT (arcs [b]. empty ());
#endif
graph = & graph_arg;
graph_arg. nodes << this;
graphIt = graph_arg. nodes. end ();
graphIt--;
}
DiGraph::Node::~Node ()
{
for (const bool b : {false, true})
deleteNeighborhood (b);
if (graph)
const_cast <DiGraph*> (graph) -> nodes. erase (graphIt);
}
void DiGraph::Node::qc () const
{
if (! qc_on)
return;
Root::qc ();
QC_IMPLY (graph, *graphIt == this);
if (! graph)
for (const bool b : {false, true})
{ QC_ASSERT (arcs [b]. empty ()); }
}
void DiGraph::Node::saveText (ostream &os) const
{
os << getName () << " ";
saveContent (os);
if (orderDfs)
os << " DFS_order = " << orderDfs;
if (scc)
os << " SCC: " << scc->getName ();
os << endl;
for (const bool b : {false, true})
{
os << " " << (b ? "Out" : "In") << ":" << endl;
for (const Arc* arc : arcs [b])
{
os << " " << arc->node [b] -> getName ();
os << ": ";
arc->saveContent (os);
os << endl;
}
}
}
bool DiGraph::Node::isIncident (const DiGraph::Node* n,
bool out) const
{
ASSERT (n);
ASSERT (graph);
ASSERT (n->graph == graph);
for (const Arc* arc : arcs [out])
if (arc->node [out] == n)
return true;
return false;
}
bool DiGraph::Node::isIncidentExcept (const DiGraph::Node* n,
bool out) const
{
ASSERT (n);
ASSERT (graph);
ASSERT (n->graph == graph);
for (const Arc* arc : arcs [out])
if (arc->node [out] != n)
return true;
return false;
}
VectorPtr<DiGraph::Node> DiGraph::Node::getNeighborhood (bool out) const
{
VectorPtr<Node> s; s. reserve (arcs [out]. size ());
for (const Arc* arc : arcs [out])
s << arc->node [out];
return s;
}
void DiGraph::Node::deleteNeighborhood (bool out)
{
for (Iter <List<Arc*> > iter (arcs [out]); iter. next (); )
delete *iter; // changes arcs[i]
}
void DiGraph::Node::setReachable (bool reachItself)
{
if (reachable)
return;
if (reachItself)
reachable = true;
for (Arc* arc : arcs [false])
static_cast <Node*> (arc->node [false]) -> setReachable (true);
}
DiGraph::Node* DiGraph::Node::setScc (size_t &visitedNum,
stack<DiGraph::Node*,vector<DiGraph::Node*>> &sccStack)
// Tarjan's alogorithm:
/*
Input: Graph G = (V, E), Start node v0
index = 0 // DFS node number counter
S = empty // An empty stack of nodes
tarjan(v0) // Start a DFS at the start node
procedure tarjan(v)
v.index = index // Set the depth index for v
v.lowlink = index
index = index + 1
S.push(v) // Push v on the stack
forall (v, v') in E do // Consider successors of v
if (v'.index is undefined) // Was successor v' visited?
tarjan(v') // Recurse
v.lowlink = min(v.lowlink, v'.lowlink)
elseif (v' in S) // Is v' on the stack?
v.lowlink = min(v.lowlink, v'.lowlink)
if (v.lowlink == v.index) // Is v the root of an SCC?
print "SCC:"
repeat
v' = S.pop
print v'
until (v' == v)
*/
{
if (orderDfs)
{
if (inStack)
return scc;
else
return nullptr;
}
ASSERT (! inStack);
visitedNum++;
orderDfs = visitedNum;
sccStack. push (this);
inStack = true;
scc = this;
for (Arc* arc : arcs [true])
if (Node* lowNode = arc->node [true] -> setScc (visitedNum, sccStack))
if (lowNode->orderDfs < scc->orderDfs)
scc = lowNode;
ASSERT (scc->orderDfs <= orderDfs);
if (scc->orderDfs < orderDfs)
{
ASSERT (scc != this);
return scc;
}
// this is the root of a SCC
ASSERT (scc->orderDfs == orderDfs);
ASSERT (scc == this);
for (;;)
{
Node* n = sccStack. top ();
sccStack. pop ();
n->inStack = false;
if (n == this)
break;
n->scc = this;
}
return nullptr;
}
void DiGraph::Node::contract (Node* from)
{
ASSERT (from);
ASSERT (this != from);
contractContent (from);
for (const bool b : {false, true})
{
unordered_map <Node*, Arc*> m; m. rehash (arcs [b]. size ());
for (Arc* arc : arcs [b])
m [arc->node [b]] = arc;
for (Iter <List<Arc*> > iter (from->arcs [b]); iter. next (); )
{
Arc* arc = *iter;
if (m. find (arc->node [b]) == m. end ())
{
iter. erase ();
arc->node [! b] = this;
arcs [b]. push_back (arc);
arc->arcsIt [! b] = arcs [b]. end ();
arc->arcsIt [! b] --;
}
else
m [arc->node [b]] -> contractContent (arc);
}
}
delete from;
}
void DiGraph::Node::isolate ()
{
for (const bool b : {false, true})
while (! arcs [b]. empty ())
{
Arc* a = arcs [b]. front ();
delete a;
}
}
void DiGraph::Node::detach ()
{
ASSERT (graph);
#ifndef NDEBUG
for (const bool b : {false, true})
ASSERT (arcs [b]. empty ());
#endif
var_cast (graph) -> nodes. erase (graphIt);
graphIt = var_cast (graph) -> nodes. end ();
graph = nullptr;
}
DiGraph::Node* DiGraph::Node::copyGraph (bool out,
Node2Node &node2node) const
{
{
const Node* n = nullptr;
if (find (node2node, this, n))
return var_cast (n);
}
Node* n = copy ();
node2node [this] = n;
for (const Arc* arc : arcs [out])
{
const Node* child = arc->node [out];
Node* child1 = child->copyGraph (out, node2node);
new Arc (child1, n);
}
return n;
}
// DiGraph::Arc
void DiGraph::Arc::attach (Node* start,
Node* end)
{
ASSERT (start);
ASSERT (end);
ASSERT (start->graph);
ASSERT (start->graph == end->graph);
ASSERT (! node [false]);
ASSERT (! node [true]);
node [false] = start;
node [true] = end;
for (const bool b : {false, true})
{
List<Arc*>& arcs = node [b] -> arcs [! b];
arcs. push_back (this);
arcsIt [b] = arcs. end ();
arcsIt [b] --;
}
}
DiGraph::Arc::~Arc ()
{
for (const bool b : {false, true})
node [b] -> arcs [! b]. erase (arcsIt [b]);
}
void DiGraph::Arc::setNode (Node* newNode,
bool out)
{
ASSERT (newNode);
ASSERT (node [out]);
ASSERT (node [out] -> graph == newNode->graph);
if (node [out] == newNode)
return;
node [out] -> arcs [! out]. erase (arcsIt [out]);
node [out] = newNode;
newNode->arcs [! out]. push_back (this);
arcsIt [out] = newNode->arcs [! out]. end ();
arcsIt [out] --;
}
// DiGraph
void DiGraph::init (const DiGraph &other,
Old2new &old2new)
{
ASSERT (old2new. empty ());
ASSERT (old2new. bucket_count () == other. nodes. size ());
for (const Node* node : other. nodes)
{
Node* n = node->copy ();
n->attach (*this);
old2new [node] = n;
}
ASSERT (old2new. size () == other. nodes. size ());
for (const Node* node : other. nodes)
{
Node* n = old2new [node];
ASSERT (n);
EXEC_ASSERT (n->parentDC = old2new [static_cast <Node*> (n->parentDC)]);
if (n->scc)
{
n->scc = old2new [n->scc];
ASSERT (n->scc);
}
for (const Arc* arc : node->arcs [true])
{
Arc* a = arc->copy ();
a->attach (n, old2new [arc->node [true]]);
}
}
}
void DiGraph::qc () const
{
if (! qc_on)
return;
Set<const Node*> nodes_;
Set<const Arc*> arcs_ [2];
Set<string> names;
size_t arcs = 0;
for (const Node* node : nodes)
{
QC_ASSERT (node);
QC_ASSERT (node->graph == this);
nodes_ << node;
try { node->qc (); }
catch (const exception &e)
{ throw runtime_error ("In node " + node->getHumanName () + ": " + e. what ()); }
for (const bool b : {false, true})
for (const Arc* arc : node->arcs [b])
{
QC_ASSERT (arc);
arcs_ [b] << arc;
arcs++;
if (b)
{
Unverbose unv;
arc->qc ();
}
}
if (names. contains (node->getName ()))
throw runtime_error ("Duplicate name: " + node->getName ());
names << node->getName ();
}
QC_ASSERT (nodes. size () == nodes_. size ());
for (const bool b : {false, true})
QC_ASSERT (2 * arcs_ [b]. size () == arcs);
QC_ASSERT (arcs_ [false] == arcs_ [true]);
}
void DiGraph::saveText (ostream &os) const
{
for (const Node* node : nodes)
{
node->saveText (os);
os << endl;
}
}
void DiGraph::deleteNodes ()
{
while (! nodes. empty ())
{
Node* n = nodes. front ();
if (! n)
errorExit ("DiGraph::Node is nullptr");
delete n;
}
}
void DiGraph::connectedComponents ()
{
for (Node* node : nodes)
node->DisjointCluster::init ();
for (Node* node : nodes)
for (const bool b : {false, true})
for (Arc* arc : node->arcs [b])
arc->node [b] -> DisjointCluster::merge (* arc->node [! b]);
}
void DiGraph::scc ()
{
size_t visitedNum = 0;
vector<Node*> vec (nodes. size ());
vec. clear ();
stack<Node*,vector<Node*>> sccStack (vec);
for (Node* node : nodes)
{
if (! node->orderDfs)
node->setScc (visitedNum, sccStack);
ASSERT (sccStack. empty ());
}
}
void DiGraph::contractScc ()
{
for (Iter <List<Node*> > iter (nodes); iter. next (); )
{
Node* n = *iter;
ASSERT (n->scc);
if (n->scc != n)
n->scc->contract (n);
}
}
VectorPtr<DiGraph::Node> DiGraph::getEnds (bool out) const
{
VectorPtr<Node> s;
for (const Node* node : nodes)
if (node->arcs [out]. empty ())
s << node;
return s;
}
DiGraph::Node2Node DiGraph::reverse (const Node2Node& old2new)
{
Node2Node new2old (old2new. size ());
for (const auto& it : old2new)
new2old [it. second] = it. first;
return new2old;
}
void DiGraph::borrowArcs (const Node2Node &other2this,
bool parallelAllowed)
{
#ifndef NDEBUG
const DiGraph* otherGraph = nullptr;
#endif
for (const auto& it : other2this)
{
const Node* other = it. first;
const Node* from = it. second;
ASSERT (other);
ASSERT (from);
ASSERT (other->graph);
ASSERT (from ->graph);
#ifndef NDEBUG
if (otherGraph)
{ ASSERT (otherGraph == other->graph); }
else
otherGraph = other->graph;
#endif
ASSERT (this == from->graph);
ASSERT (otherGraph != this);
const VectorPtr<Node> otherNeighborhood (other->getNeighborhood (true));
for (const Node* otherNeighbor : otherNeighborhood)
if (const Node* to = findPtr (other2this, otherNeighbor))
if (parallelAllowed || ! from->isIncident (to, true))
new Arc ( var_cast (from)
, var_cast (to)
);
}
}
////////////////////////////////////////// Tree ////////////////////////////////////////////
// Tree::TreeNode
void Tree::TreeNode::qc () const
{
if (! qc_on)
return;
DiGraph::Node::qc ();
if (graph)
{
QC_ASSERT (! (isLeafType () && isInteriorType ()));
QC_IMPLY (isLeaf (), isLeafType ());
QC_IMPLY (isInteriorType () && getParent (), getParent () -> isInteriorType ());
}
if (contains (getName (), objNameSeparator))
throw runtime_error (strQuote (getName ()) + " contains separator " + strQuote (string (1, objNameSeparator)));
}
void Tree::TreeNode::saveText (ostream &os) const
{
os << getName () << ": ";
saveContent (os);
bool saveSubtreeP = false;
for (const Arc* arc : arcs [false])
if (static_cast <const TreeNode*> (arc->node [false]) -> getSaveSubtreeP ())
{
saveSubtreeP = true;
break;
}
if (saveSubtreeP)
{
Offset ofs;
for (const Arc* arc : arcs [false])
{
Offset::newLn (os);
static_cast <TreeNode*> (arc->node [false]) -> saveText (os);
}
}
else
if (! isLeaf ())
os << " (" << getLeavesSize () << ")"; // Time ??
}
void Tree::TreeNode::printNewick_ (ostream &os,
bool internalNames,
bool minimalLeafName) const
{
// Cf. saveText() ??
if (isLeaf ())
os << name2newick (getNewickName (minimalLeafName));
else
{
string internalName;
if (internalNames)
internalName = name2newick (getNewickName (minimalLeafName));
ASSERT (! arcs [false]. empty ());
#if 0
bool done = false;
if ( internalName. empty ()
&& arcs [false]. size () == 1
)
{
const TreeNode* n = static_cast <TreeNode*> (arcs [false]. front () -> node [false]);
ASSERT (n);
const double dist = n->getParentDistance ();
if (dist == dist && ! dist)
{
n->printNewick_ (os, internalNames, minimalLeafName);
done = true;
}
}
if (! done)
#endif
{
os << "(";
bool first = true;
for (const Arc* arc : arcs [false])
{
const TreeNode* n = static_cast <TreeNode*> (arc->node [false]);
if (! first)
os << ",";
n->printNewick_ (os, internalNames, minimalLeafName);
first = false;
}
os << ")" << internalName;
}
}
const double dist = getParentDistance ();
if (dist == dist && dist != -1.0)
os << ":" << fixed << dist;
}
#if 0
string Tree::TreeNode::name2newick (const string &s)
{
string s1 (s);
replace (s1, "\"\' ():;,[]<>=", '_');
return s1;
//return s1. substr (0, 100 /*50*/); // PAR
// Newick allowes the name length >= 50 characters, but http://www.trex.uqam.ca/ breaks with 50
}
#endif
const Tree::TreeNode* Tree::TreeNode::getAncestor (size_t height) const
{
const TreeNode* n = this;
FOR (size_t, i, height)
if (n)
n = n->getParent ();
else
break;
if (n)
return n;
return getTree(). root;
}
void Tree::TreeNode::setParent (TreeNode* newParent)
{
ASSERT (newParent != this);
#if 0
// Breaks sort()'ing
if (newParent && getParent () == newParent)
return;
#endif
if (! arcs [true]. empty ())
{
Arc* a = arcs [true]. front ();
delete a;
}
ASSERT (arcs [true]. empty ());
if (newParent)
{
new Arc (this, newParent);
ASSERT (getParent () == newParent);
}
else
var_cast (getTree ()). root = this;
}
void Tree::TreeNode::printAncestors (const TreeNode* end) const
{
const TreeNode* node = this;
for (;;)
{
cout << ' ' << node;
if (! node || node == end)
break;
node = node->getParent ();
}
cout << endl;
}
Tree::TreeNode::TipName Tree::TreeNode::getTipName () const
{
if (isLeaf ())
return TipName (getName (), 0);
TipName tn_best;
for (const DiGraph::Arc* arc : arcs [false])
{
const TipName tn = static_cast <const TreeNode*> (arc->node [false]) -> getTipName ();
if (tn_best. name. empty () || tn_best. name > tn. name)
tn_best = tn;
}
tn_best.depth ++;
return tn_best;
}
void Tree::TreeNode::getSubtreeHeights (Vector<Tree::TreeNode::NodeDist> &nodeHeights) const
{
if (isLeaf ())
return;
double height = 0.0;
for (const DiGraph::Arc* arc : arcs [false])
{
const TreeNode* node = static_cast <const TreeNode*> (arc->node [false]);
const double dist = node->getParentDistance ();
ASSERT (dist >= 0.0);
node->getSubtreeHeights (nodeHeights);
maximize (height, dist + (node->isLeaf () ? 0.0 : nodeHeights. back (). dist));
}
nodeHeights << NodeDist {this, height};
}
void Tree::TreeNode::getLeafDepths_ (Vector<Tree::TreeNode::NodeDist> &leafDepths,
bool first) const
{
const size_t start = leafDepths. size ();
if (isLeaf ())
leafDepths << NodeDist {this, 0.0};
else
for (const DiGraph::Arc* arc : arcs [false])
{
const TreeNode* node = static_cast <const TreeNode*> (arc->node [false]);
node->getLeafDepths_ (leafDepths, false);
}
if (! first)
{
const double parentDistance = getParentDistance ();
FFOR_START (size_t, i, start, leafDepths. size ())
leafDepths [i]. dist += parentDistance;
}
}
size_t Tree::TreeNode::getHeight () const
{
size_t n = 0;
for (const Arc* arc : arcs [false])
maximize (n, 1 + static_cast <const TreeNode*> (arc->node [false]) -> getHeight ());
return n;
}
size_t Tree::TreeNode::getInteriorHeight () const
{
ASSERT (isInteriorType ());
size_t n = 0;
for (const Arc* arc : arcs [false])
{
const TreeNode* node = static_cast <const TreeNode*> (arc->node [false]);
if (node->isInteriorType ())
maximize (n, 1 + node->getInteriorHeight ());
}
return n;
}
double Tree::TreeNode::getDistanceHeight () const
{
double n = 0.0;
for (const Arc* arc : arcs [false])
{
const TreeNode* child = static_cast <const TreeNode*> (arc->node [false]);
const double parentDistance = child->getParentDistance ();
ASSERT (parentDistance >= 0.0);
maximize (n, parentDistance + child->getDistanceHeight ());
}
return n;
}
void Tree::TreeNode::getBifurcatingInteriorBranching (size_t &bifurcatingInteriorNodes,
size_t &branches) const
{
ASSERT (isInteriorType ());
ASSERT (/*a*/ arcs [false]. size () >= 2); // transient nodes are prohibited
// Make *this bifurcating
branches += arcs [false]. size () - 2; // b
bifurcatingInteriorNodes += arcs [false]. size () - 2; // n
size_t interiorArcs = 0; // i
for (const Arc* arc : arcs [false])
{
const TreeNode* node = static_cast <const TreeNode*> (arc->node [false]);
if (node->isInteriorType ())
{
interiorArcs++;
node->getBifurcatingInteriorBranching (bifurcatingInteriorNodes, branches);
}
}
branches += interiorArcs;
if (interiorArcs)
bifurcatingInteriorNodes++;
ASSERT (branches >= bifurcatingInteriorNodes);
ASSERT (branches <= 2 * bifurcatingInteriorNodes);
/*Proof:
a >= 2.
i <= a.
For each parent node:
b = a - 2 + i.
n = a - 2 + (bool) i.
x := 2 n - b = a - 2 + 2 (bool) i - i = (a - i) + 2 ((bool) i - 1).
if i > 0 then x = a - i >= 0.
if i = 0 then x = a - 2 >= 0.
*/
}
size_t Tree::TreeNode::getSubtreeSize (bool countLeaves) const
{
size_t n = 0;
for (const Arc* arc : arcs [false])
{
const TreeNode* child = static_cast <TreeNode*> (arc->node [false]);
if (! countLeaves && child->arcs [false]. empty ())
continue;
n += 1 + child->getSubtreeSize (countLeaves);
}
return n;
}
void Tree::TreeNode::subtreeSize2leaves ()
{
leaves = 0;
for (const Arc* arc : arcs [false])
{
const TreeNode* child = static_cast <TreeNode*> (arc->node [false]);
var_cast (child) -> subtreeSize2leaves ();
leaves += 1 + child->leaves;
}
}
double Tree::TreeNode::getSubtreeLength () const
{
double len = 0.0;
for (const Arc* arc : arcs [false])
{
const TreeNode* node = static_cast <TreeNode*> (arc->node [false]);
len += node->getParentDistance () + node->getSubtreeLength ();
}
return len;
}
void Tree::TreeNode::setLeaves ()
{
leaves = 0;
for (const Arc* arc : arcs [false])
{
TreeNode* child = static_cast <TreeNode*> (arc->node [false]);
child->setLeaves ();
ASSERT (child->leaves);
leaves += child->leaves;
}
if (! leaves)
leaves = 1;
}
void Tree::TreeNode::setLeaves (size_t leaves_arg)
{
leaves = leaves_arg;
for (const Arc* arc : arcs [false])
{
TreeNode* child = static_cast <TreeNode*> (arc->node [false]);
child->setLeaves (leaves_arg);
}
}
size_t Tree::TreeNode::getLeavesSize () const
{
size_t n = 0;
for (const Arc* arc : arcs [false])
n += static_cast <TreeNode*> (arc->node [false]) -> getLeavesSize ();
return max<size_t> (n, 1);
}
namespace
{
struct ChildFreq
{
Tree::TreeNode* node;
size_t freq;
ChildFreq (Tree::TreeNode* node_arg,
size_t freq_arg)
: node (node_arg)