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connectPairs.cpp
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connectPairs.cpp
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// connectPairs.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:
* Create sets of connected items
*
*/
#undef NDEBUG
#include "common.hpp"
using namespace Common_sp;
#include "version.inc"
#include "common.inc"
namespace
{
static const string ext ("component");
struct Item : Named, DisjointCluster
{
explicit Item (const string &name_arg)
: Named (name_arg)
{}
};
struct ThisApplication : Application
{
ThisApplication ()
: Application ("Create sets of connected items")
{
version = VERSION;
addPositional ("in", "List of pairs of connected items: <item1> <item2>\nwhere <item1>, <item2> are strings with no spaces");
addPositional ("out", "If not <pairs> then output directory with the sets of connected items. Each set is named by its lexicographycally smaller item with the added extension " + strQuote ("." + ext));
addKey ("subset", "List of items. Item pairs are restricted to this list");
addFlag ("pairs", "<out> is a list of pairs: <item1> <item_min>, where <item_min> is lexicographycally smallest item of the cluster");
}
void body () const final
{
const string inFName = getArg ("in");
const string outFName = getArg ("out");
const string subsetFName = getArg ("subset");
const bool pairs = getFlag ("pairs");
unique_ptr<StringVector> subset;
if (! subsetFName. empty ())
{
subset. reset (new StringVector (subsetFName, (size_t) 10000, true)); // PAR
subset->sort ();
QC_ASSERT (subset->isUniq ());
}
unordered_map<string/*Item::name*/,Item*> items; items. rehash (100000); // PAR
// Not delete'd
{
LineInput fIn (inFName);
string s1, s2;
Istringstream iss;
while (fIn. nextLine ())
{
iss. reset (fIn. line);
s2. clear ();
iss >> s1 >> s2;
QC_ASSERT (! s2. empty ());
if (subset. get ())
{
if (! subset->containsFast (s1))
continue;
if (! subset->containsFast (s2))
continue;
}
if (! contains (items, s1))
items [s1] = new Item (s1);
if (! contains (items, s2))
items [s2] = new Item (s2);
items [s1] -> DisjointCluster::merge (* items [s2]);
}
}
map<const DisjointCluster*,VectorPtr<Item>> clusters;
for (auto& it : items)
clusters [it. second->getDisjointCluster ()] << it. second;
unique_ptr<OFStream> fOut;
if (pairs)
fOut. reset (new OFStream (outFName));
for (auto& it : clusters)
{
VectorPtr<Item>& cluster = it. second;
cluster. sort (Named::lessPtr);
ASSERT (! cluster . empty ());
if (! pairs)
fOut. reset (new OFStream (outFName, cluster [0] -> name, ext));
for (const Item* item : cluster)
if (pairs)
*fOut << item->name << '\t' << cluster [0] -> name << endl;
else
*fOut << item->name << endl;
if (! pairs)
fOut. reset ();
}
}
};
} // namespace
int main (int argc,
const char* argv[])
{
ThisApplication app;
return app. run (argc, argv);
}