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221 lines (179 loc) · 6.1 KB
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// min_spanning_forest.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:
* Minimum spanning forest
*
*/
#undef NDEBUG
#include "common.hpp"
#include "graph.hpp"
using namespace Common_sp;
#include "version.inc"
#include "common.inc"
namespace
{
struct Item final : DiGraph::Node
{
const string name;
Item (DiGraph &graph_arg,
const string &name_arg)
: DiGraph::Node (graph_arg)
, name (name_arg)
{}
};
struct Link final : DiGraph::Arc
{
const double weight;
Link (Item* start,
Item* end,
double weight_arg)
: DiGraph::Arc (start, end)
, weight (weight_arg)
{
ASSERT (! isNan (weight));
}
void saveText (ostream &os) const final
{ os << static_cast <const Item*> (node [false]) -> name
<< '\t' << weight
<< '\t' << static_cast <const Item*> (node [true]) -> name
<< '\n';
}
bool operator< (const Link &other) const
{ return weight > other. weight; }
};
struct ThisApplication final : Application
{
ThisApplication ()
: Application ("Print minimum spanning forest per connected component")
{
version = VERSION;
addPositional ("in", "File with lines: <item1> <item2> <weight>. Sorted by <weight> ascending, or descending if -max");
addFlag ("max", "<weight> must be maximized in the forest, otherwise minimized");
addKey ("rename", "File with pairs: <item> <tab> <new name>");
}
void body () const final
{
const string inFName = getArg ("in");
const bool maxP = getFlag ("max");
const string matchFName = getArg ("rename");
KeyValue old2new;
if (! matchFName. empty ())
{
LineInput fIn (matchFName);
Set<string> newNames;
while (fIn. nextLine ())
{
string& newName = fIn. line;
const string oldName (findSplit (newName, '\t'));
QC_ASSERT (! newName. empty ());
if (contains (old2new, oldName))
throw runtime_error ("Duplicate old name: " + strQuote (oldName));
if (newNames. contains (newName))
throw runtime_error ("Duplicate new name: " + strQuote (newName));
old2new [oldName] = newName;
}
}
unordered_map<string/*Item::name*/,Item*> items; items. rehash (100000); // PAR
DiGraph gr; // Of Item, DAG
{
double weight_prev = - numeric_limits<double>::max ();
if (maxP)
weight_prev *= -1;
LineInput fIn (inFName);
Istringstream iss;
while (fIn. nextLine ())
{
string s1;
string s2;
double weight = NaN;
iss. reset (fIn. line);
iss >> s1 >> s2 >> weight;
QC_ASSERT (! s2. empty ());
QC_ASSERT (! isNan (weight));
if ( (maxP && weight > weight_prev)
|| (! maxP && weight < weight_prev)
)
throw runtime_error ("Weight disorder: " + fIn. lineStr ());
trim (s1);
trim (s2);
if (s1 == s2)
continue;
s1 = nvl (key2value (old2new, s1, true), s1);
s2 = nvl (key2value (old2new, s2, true), s2);
// n1, n2
if (! contains (items, s1))
items [s1] = new Item (gr, s1);
if (! contains (items, s2))
items [s2] = new Item (gr, s2);
Item* n1 = items [s1];
Item* n2 = items [s2];
ASSERT (n1);
ASSERT (n2);
ASSERT (n1 != n2);
if (n1->getDisjointCluster () != n2->getDisjointCluster ())
{
new Link (n1, n2, weight);
n1->DisjointCluster::merge (*n2);
}
weight_prev = weight;
}
}
ASSERT (gr. nodes. size () == items. size ());
gr. qc ();
map<const DisjointCluster*,VectorPtr<Item>> clusters;
for (auto& it : items)
clusters [it. second->getDisjointCluster ()] << it. second;
bool first = false;
for (const auto& it : clusters)
{
const VectorPtr<Item>& cluster = it. second;
ASSERT (! cluster . empty ());
VectorPtr<Link> links; links. reserve (cluster. size () * 10); // PAR
for (const Item* item : cluster)
for (const DiGraph::Arc* arc : item->arcs [true])
{
ASSERT (arc);
links << static_cast <const Link*> (arc);
}
links. sortPtr ();
if (first)
first = false;
else
cout << endl;
for (const Link* link : links)
link->saveText (cout);
}
}
};
} // namespace
int main (int argc,
const char* argv[])
{
ThisApplication app;
return app. run (argc, argv);
}