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180 lines (146 loc) · 5.62 KB
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// index_find.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:
* Find approximately closest objects ordered by proximity using an index
*
*/
#undef NDEBUG
#include "common.hpp"
using namespace Common_sp;
#include "version.inc"
#include "common.inc"
namespace
{
struct ObjNum
{
string obj;
size_t num {0};
bool operator< (const ObjNum &other) const
{ LESS_PART (other, *this, num);
LESS_PART (*this, other, obj);
return false;
}
};
struct ThisApplication : Application
{
ThisApplication ()
: Application ("Find approximately closest objects ordered by proximity using an index.\n\
An object is a file with a list of attributes.\n\
Average time: O(A S (A (log A + log S) + log N)), where N is the number of objects, and A is the average number of attributes in an object, S = attr_size_max.\n\
")
{
version = VERSION;
addPositional ("dir", "Directory with objects");
addPositional ("index", "Directory with an attribute index for <dir>");
addPositional ("attr_size_max", "Attribute file size limit; objects having only attrbutes whose index files exceed <attr_size_max> are indiscernible");
addPositional ("target", "Target object");
addFlag ("large", "Directory <dir> is large: it is subdivided into subdirectories \"0\" .. \"" + to_string (small_hash_class_max - 1) + "\" which are the hashes of file names");
}
void body () const final
{
const string dir = getArg ("dir");
const string index = getArg ("index");
const streamsize attr_size_max = (streamsize) arg2uint ("attr_size_max");
const string target = getArg ("target");
const bool large = getFlag ("large");
// size(index) = O(N A)
StringVector attrObjs; // Repeated objects
{
StringVector bigAttrs;
// Time = O(A (log N + log A + S))
{
LineInput f (target);
while (f. nextLine ())
{
string& attr = f. line;
trim (attr);
const string attrFName (index + "/" + attr);
if (! fileExists (attrFName))
continue;
if (getFileSize (attrFName) >= attr_size_max)
bigAttrs << attr;
else
attrObjs << StringVector (attrFName, (size_t) 1000, true); // PAR
}
}
// size(attrObjs) = O(A S)
// size(bigAttrs) = O(A)
if (verbose ())
{
PRINT (attrObjs. size ());
PRINT (bigAttrs. size ());
}
// Time: O(A log A)
bigAttrs. sort ();
QC_ASSERT (bigAttrs. isUniq ());
// Time: O(A S (log A + log S))
StringVector objs (attrObjs);
objs. sort ();
objs. uniq ();
// size(objs) = O(A S)
if (verbose ())
PRINT (objs. size ());
// Append: attrObjs
// Time: O(A S (log N + A log A))
if (! bigAttrs. empty ())
for (const string& obj : objs)
{
const string objFName (dir + (large ? "/" + to_string (str2hash_class (obj, false)) : "") + "/" + obj);
if (! fileExists (objFName))
continue;
StringVector attrs (objFName, (size_t) 1000, true); // PAR
attrs. sort ();
QC_ASSERT (attrs. isUniq ());
const size_t n = bigAttrs. getIntersectionSize (attrs); // O(A)
FOR (size_t, i, n)
attrObjs << obj;
}
}
// size(attrObjs) = O(A^2 S)
// Time: O(A^2 S)
unordered_map<string,size_t> obj2num; obj2num. rehash (attrObjs. size ());
for (const string& obj : attrObjs)
obj2num [obj] ++;
// size(obj2num) = O(A^2 S)
// Time: O(A^2 S (log A + log S))
Vector<ObjNum> objNums; objNums. reserve (obj2num. size ());
for (const auto& it : obj2num)
objNums << std::move (ObjNum {it. first, it. second});
objNums. sort ();
// size(objNums) = O(A^2 S)
for (const ObjNum& objNum : objNums)
cout << objNum. obj << endl;
}
};
} // namespace
int main (int argc,
const char* argv[])
{
ThisApplication app;
return app. run (argc, argv);
}