This file is indexed.

/usr/include/polymake/external/permlib/bsgs.h is in libpolymake-dev-common 3.2r2-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
// ---------------------------------------------------------------------------
//
//  This file is part of PermLib.
//
// Copyright (c) 2009-2011 Thomas Rehn <thomas@carmen76.de>
// All rights reserved.
// 
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
// 1. Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
// 3. The name of the author may not be used to endorse or promote products
//    derived from this software without specific prior written permission.
// 
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
// NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// ---------------------------------------------------------------------------


#ifndef BSGS_H_
#define BSGS_H_

#include <map>
#include <list>
#include <vector>

#include <boost/cstdint.hpp>
#include <boost/foreach.hpp>
#include <boost/scoped_ptr.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/utility.hpp>

#include <permlib/bsgs_core.h>

#include <permlib/transversal/orbit_set.h>
#include <permlib/transversal/transversal.h>
#include <permlib/predicate/pointwise_stabilizer_predicate.h>
#include <permlib/predicate/stabilizes_point_predicate.h>

#include <permlib/redundant_base_point_insertion_strategy.h>

namespace permlib {

template <class PERM, class TRANS>
struct BSGS;

template <class PERM, class TRANS>
std::ostream &operator<< (std::ostream &out, const BSGS<PERM,TRANS> &bsgs) {
	out << "BASE[" << bsgs.B.size() << "]" << std::endl;
	BOOST_FOREACH(unsigned long beta, bsgs.B) {
		out << static_cast<unsigned int>(beta+1) << ",";
	}
	out << std::endl;
	out << "SGS[" << bsgs.S.size() << "]" << std::endl;
	BOOST_FOREACH(const typename PERM::ptr &g, bsgs.S) {
		out << *g << ",";
	}
	out << std::endl;
	out << "U" << std::endl;
	BOOST_FOREACH(const TRANS &U, bsgs.U) {
		for (unsigned int i=0; i<bsgs.n; ++i)
			// trigger transversal depth reload
			boost::scoped_ptr<PERM> dummy(U.at(i));
		out << U.size() << "{" << U.m_statMaxDepth << "}" << ",";
	}
	out << " = " << bsgs.order() << std::endl;
	BOOST_FOREACH(const TRANS &U, bsgs.U) {
		out << U << std::endl;
	}
	return out;
}

/// Represents a base and strong generating set (BSGS)
template <class PERM, class TRANS>
struct BSGS : public BSGSCore<PERM,TRANS> {
	typedef typename BSGSCore<PERM,TRANS>::PERMlist PERMlist;
	
	/// constructs an empty group of degree n
	explicit BSGS(dom_int n);
	/// copy constructor
	/**
	 * creates a deep copy of generator list and transversals,
	 * so there is no link between the original BSGS and the copy
	 */
	BSGS(const BSGS<PERM,TRANS>& bsgs);
	
	/// assignment operator
	/**
	 * creates a deep copy of generator list and transversals,
	 * so there is no link between the original BSGS and the copy
	 */
	BSGS<PERM,TRANS>& operator=(const BSGS<PERM,TRANS>&);
    
	/// order of the group
	/**
	 * read from the transversal product
	 */
	template<typename Integer>
	Integer order() const;
	
	/// order of the group
	/**
	 * read from the transversal product
	 */
	boost::uint64_t order() const;
	
	/// sifts an element through the specified transversal range
	/**
	 * @param g permutation to sift
	 * @param siftee 
	 * @param j lowest transversal index to sift; i.e. sift through transversal U[j], U[j+1], ...
	 */
	unsigned int sift(const PERM& g, PERM& siftee, unsigned int j = 0) const;
	/// sifts an element through the specified transversal range
	/**
	 * @param g permutation to sift
	 * @param siftee 
	 * @param j lowest transversal index to sift
	 * @param k highest transversal index to sift plus one
	 */
	unsigned int sift(const PERM& g, PERM& siftee, unsigned int j, unsigned int k) const;
	/// true iff g sifts through transversal system
	bool sifts(const PERM& g) const;

	/// tries to find a new base element
	/**
	 * find an element which is moved by h
	 * @param h
	 * @param beta element moved by h
	 * @return true iff an element h could be found
	 */
	bool chooseBaseElement(const PERM &h, dom_int &beta) const;
	/// inserts a redundant base beta
	/**
	 * @param beta
	 * @param minPos insert point not before the minPos-th base element
	 * @return insertion position
	 */
	unsigned int insertRedundantBasePoint(unsigned int beta, unsigned int minPos = 0);
	/// strips redundant base points from the end to the minPos-th base element
	void stripRedundantBasePoints(int minPos = 0);
	
	/// removes redundant generators
	/**
	 * The remaining set S is still a strong generating set. Its size will be at most log |G|.
	 *
	 * Note that applying this method may result in a difference between transversals and 
	 * strong generating set. If you use a SchreierTree, then the transversal will no longer 
	 * automatically return elements from the strong generating set.
	 */
	void stripRedundantStrongGenerators();
	
	/// re-computes the j-th fundamental orbit with the given orbit generators
	/**
	 * @see Transversal<PERM>::orbit
	 */
	void orbit(unsigned int j, const PERMlist &generators);
	/// updates the j-th fundamental orbit with the given orbit generators and a new generator g
	/**
	 * @see Transversal<PERM>::orbitUpdate
	 */
	void orbitUpdate(unsigned int j, const PERMlist &generators, const typename PERM::ptr &g);
	
	/// adds a new group generator
	/**
	 * @param g group generator
	 * @param updateOrbit true iff transversals/orbits should be updates
	 * @return index up to which transversals/orbits need update
	 */
	int insertGenerator(const typename PERM::ptr& g, bool updateOrbit);
	/// updates transversals/orbits
	/**
	 * @param pos index up to which transversals should be updated
	 * @see insertGenerator
	 */
	void updateOrbits(int pos);
	
	/// generates a uniformly distributed random element of \f$G^{[i]}\f$
	/**
	 * @param i the stabilizer chain index to generate the random element of. If set to 0 a random element of the whole group is returned.
	 */
	PERM random(const int i = 0) const;

	/// conjugate group with a permutation
	/**
	 * If S is the generating set of this group, then after conjugation the group will be generated by c^{-1} S c.
	 * @param g permutation the group should be conjugated by
	 */
	void conjugate(const PERM& g);
	
	/// writes base, SGS and transversals
	friend std::ostream &operator<< <> (std::ostream &out, const BSGS<PERM,TRANS> &bsgs);
private:
	/// sifts an element through the specified transversal range
	template <class BaseIterator, class TransversalIterator>
	unsigned int sift(const PERM& g, PERM& siftee, BaseIterator begin, BaseIterator end, TransversalIterator beginT, TransversalIterator endT) const;

	/// id counter of all BSGS instances
	static int ms_bsgsId;
	
	/// deep-copy transversals and group generators
	void copyTransversals(const BSGS<PERM,TRANS>& bsgs);
};

//
//     ----       IMPLEMENTATION
//

template <class PERM, class TRANS>
int BSGS<PERM,TRANS>::ms_bsgsId = 0;

template <class PERM, class TRANS>
BSGS<PERM,TRANS>::BSGS(dom_int n_) 
	: BSGSCore<PERM,TRANS>(++ms_bsgsId, n_, 0)
{}

template <class PERM, class TRANS>
BSGS<PERM,TRANS>::BSGS(const BSGS<PERM,TRANS>& bsgs)
	: BSGSCore<PERM,TRANS>(bsgs.m_id, bsgs.B, bsgs.U, bsgs.n)
{ 
	copyTransversals(bsgs);
}

template <class PERM, class TRANS>
BSGS<PERM,TRANS>& BSGS<PERM,TRANS>::operator=(const BSGS<PERM,TRANS>& bsgs) {
	if (this == &bsgs)
		return *this;
	
	this->B = bsgs.B;
	this->n = bsgs.n;
	this->m_id = bsgs.m_id;
	
	copyTransversals(bsgs);
	return *this;
}

template <class PERM, class TRANS>
template <class BaseIterator, class TransversalIterator>
unsigned int BSGS<PERM, TRANS>::sift(const PERM& g, PERM& siftee, BaseIterator begin, BaseIterator end, TransversalIterator beginT, TransversalIterator endT) const{
	unsigned int k = 0;
	siftee = g;
	BaseIterator baseIt;
	TransversalIterator transIt;
	for (baseIt = begin, transIt = beginT; baseIt != end && transIt != endT; ++baseIt, ++transIt) {
		unsigned long b = *baseIt;
		const TRANS& U_i = *transIt;
		//std::cout << " ~~~ sift " << siftee << " b" << b << std::endl;
		boost::scoped_ptr<PERM> u_b(U_i.at(siftee / b));
		if (u_b == 0)
			return k;
		u_b->invertInplace();
		siftee *= *u_b;
		++k;
	}
	return k;
}

template <class PERM, class TRANS>
unsigned int BSGS<PERM, TRANS>::sift(const PERM& g, PERM& siftee, unsigned int j) const {
	return sift(g, siftee, this->B.begin() + j, this->B.end(), this->U.begin() + j, this->U.end());
}

template <class PERM, class TRANS>
unsigned int BSGS<PERM, TRANS>::sift(const PERM& g, PERM& siftee, unsigned int j, unsigned int k) const {
	return sift(g, siftee, this->B.begin() + j, this->B.begin() + k, this->U.begin() + j, this->U.begin() + k);
}

template <class PERM, class TRANS>
bool BSGS<PERM, TRANS>::sifts(const PERM& g) const {
	PERM siftee(this->n);
	unsigned int m = sift(g, siftee);
	return this->B.size() == m && siftee.isIdentity();
}

template <class PERM, class TRANS>
bool BSGS<PERM, TRANS>::chooseBaseElement(const PERM &h, dom_int &beta) const {
	for (beta = 0; beta < this->n; ++beta) {
		if (std::find(this->B.begin(), this->B.end(), beta) != this->B.end())
			continue;
		if (h / beta != beta)
			return true;
	}
	return false;
}

template <class PERM, class TRANS>
void BSGS<PERM, TRANS>::orbit(unsigned int j, const PERMlist &generators) {
	this->U[j].orbit(this->B[j], generators);
}
	
template <class PERM, class TRANS>
void BSGS<PERM, TRANS>::orbitUpdate(unsigned int j, const PERMlist &generators, const typename PERM::ptr &g) {
	this->U[j].orbitUpdate(this->B[j], generators, g);
}

template <class PERM, class TRANS>
PERM BSGS<PERM, TRANS>::random(const int i) const {
	BOOST_ASSERT( i >= 0 );
    PERM g(this->n);
    for (int l = this->U.size()-1; l>=i ; --l) {
		//std::cout << l << " : " << U[l] << " : " << U[l].size() << std::endl;
        unsigned long beta = *(boost::next(this->U[l].begin(), randomInt(this->U[l].size())));
        boost::scoped_ptr<PERM> u_beta(this->U[l].at(beta));
        g *= *u_beta;
    }
    return g;
}

template <class PERM, class TRANS>
void BSGS<PERM, TRANS>::conjugate(const PERM& g) {
	PERM gInv(g);
	gInv.invertInplace();

	//
	// to conjugate a BSGS, all three components (B,S,U) have to be adjusted
	//

	// STEP 1: conjugate generating set S
	BOOST_FOREACH(typename PERM::ptr& p, this->S) {
		*p ^= gInv;
		*p *= g;
	}

	std::vector<dom_int> oldB(this->B);
	for (unsigned int i = 0; i < this->U.size(); ++i) {
		// STEP 2: adapt base B
		this->B[i] = g / oldB[i];
		// STEP 3: conjugate transversal U
		this->U[i].permute(g, gInv);
	}
}

template <class PERM, class TRANS>
int BSGS<PERM, TRANS>::insertGenerator(const typename PERM::ptr& g, bool updateOrbit) {
	int pos = 0;
	for (; static_cast<unsigned int>(pos) < this->B.size(); ++pos) {
		if (*g / this->B[pos] != this->B[pos])
			break;
	}
	
	if (static_cast<unsigned int>(pos) == this->B.size()) {
		dom_int beta;
		bool newBaseElement __attribute__((unused)) = chooseBaseElement(*g, beta);
		BOOST_ASSERT( newBaseElement );
		this->B.push_back(beta);
		this->U.push_back(TRANS(this->n));
	}
	
	const int insertionPosition = pos;
	this->S.push_back(g);
	
	if (updateOrbit) {
		bool groupOrderChanged = false;
		for (; pos >= 0; --pos) {
			PERMlist orbitGenerators;
			const unsigned int oldTransversalSize = this->U[pos].size();
			//std::cout << "INSERT orbit @ " << pos << " : " << g << std::endl;
			std::copy_if(this->S.begin(), this->S.end(), std::back_inserter(orbitGenerators), 
					PointwiseStabilizerPredicate<PERM>(this->B.begin(), this->B.begin() + pos));
			if (orbitGenerators.size() > 0) {
				orbitUpdate(pos, orbitGenerators, g);
				
				// group order can only increase by adding generators
				if (this->U[pos].size() > oldTransversalSize)
					groupOrderChanged = true;
			}
		}
		
		if (!groupOrderChanged) {
			this->S.pop_back();
			return -1;
		}
	}
	
	return insertionPosition;
}

template <class PERM, class TRANS>
void BSGS<PERM, TRANS>::updateOrbits(int pos) {
	if (pos < 0)
		return;
	for (; pos >= 0; --pos) {
		PERMlist orbitGenerators;
		std::copy_if(this->S.begin(), this->S.end(), std::back_inserter(orbitGenerators), 
					PointwiseStabilizerPredicate<PERM>(this->B.begin(), this->B.begin() + pos));
		if (orbitGenerators.size() > 0)
			orbit(pos, orbitGenerators);
	}
}

template <class PERM, class TRANS>
template <typename Integer>
Integer BSGS<PERM, TRANS>::order() const {
	Integer orderValue(1);
	BOOST_FOREACH(const TRANS &Ui, this->U) {
		orderValue *= Ui.size();
	}
	return orderValue;
}

template <class PERM, class TRANS>
boost::uint64_t BSGS<PERM, TRANS>::order() const {
	return order<boost::uint64_t>();
}


template <class PERM, class TRANS>
unsigned int BSGS<PERM, TRANS>::insertRedundantBasePoint(unsigned int beta, unsigned int minPos) {
	PERMlist S_i;
	TrivialRedundantBasePointInsertionStrategy<PERM,TRANS> is(*this);
	int pos = is.findInsertionPoint(beta, S_i);
	if (pos < 0)
		return -(pos+1);
    pos = std::max(static_cast<unsigned int>(pos), minPos);
	
	this->B.insert(this->B.begin() + pos, beta);
	this->U.insert(this->U.begin() + pos, TRANS(this->n));
	this->U[pos].orbit(beta, S_i);
	return pos;
}

template <class PERM, class TRANS>
void BSGS<PERM, TRANS>::stripRedundantBasePoints(int minPos) {
	for (int i = this->B.size()-1; i >= minPos; --i) {
		if (this->U[i].size() <= 1) {
			if (i == static_cast<int>(this->B.size()-1)) {
				this->B.pop_back();
				this->U.pop_back();
			} else {
				this->B.erase(this->B.begin() + i);
				this->U.erase(this->U.begin() + i);
			}
		}
	}
}


/// Class that can be used to sort a strong generating set.
/**
 * The goal is to sort a list of strong generators so that generators for the stabilizers in the
 * stabilizer chain are next to each other.
 */
template <class PERM>
class StrongGeneratingSetSorter : public std::binary_function<typename PERM::ptr, typename PERM::ptr, bool> {
public:
	/**
	 * @param baseBegin begin-iterator(dom_int) to the base relative to which the strong generating set is to be sorted
	 * @param baseEnd   end-iterator(dom_int) to the base relative to which the strong generating set is to be sorted
	 */
	template<class InputIterator>
	StrongGeneratingSetSorter(InputIterator baseBegin, InputIterator baseEnd) : m_base(baseBegin, baseEnd) { }
	
	/// true iff p1 stabilizes more base points (in increasing order) than p2
	bool operator()(const typename PERM::ptr& p1, const typename PERM::ptr& p2) const {
		BOOST_FOREACH(const dom_int b, m_base) {
			if ( p1->at(b) == b  &&  p2->at(b) != b )
				return true;
			if ( p1->at(b) != b )
				return false;
		}
		return false;
	}
private:
	std::vector<dom_int> m_base;
};

template <class PERM, class TRANS>
void BSGS<PERM, TRANS>::stripRedundantStrongGenerators() {
	PERMlist sortedSGS(this->S);
	sortedSGS.sort(StrongGeneratingSetSorter<PERM>(this->B.begin(), this->B.end()));
	
	PERMlist filteredSGS;
	OrbitSet<PERM, dom_int>* oldOrbit = new OrbitSet<PERM, dom_int>();
	dom_int oldBaseElement = static_cast<dom_int>(-1);
	BOOST_FOREACH(const typename PERM::ptr& gen, sortedSGS) {
		if (gen->isIdentity())
			continue;
		filteredSGS.push_back(gen);
	
		// Compute to which base element this strong generator belongs.
		// That is, gen stabilizes all base points up to baseElement.
		// No generator can stabilize all base elements because we excluded
		//  identity permutations before.
		dom_int baseElement = this->B.front();
		BOOST_FOREACH(const dom_int b, this->B) {
			baseElement = b;
			if (*gen / b != b)
				break;
		}
		PERMLIB_DEBUG(std::cout << "gen " << *gen << "   @ " << baseElement << std::endl;)

		OrbitSet<PERM, dom_int>* newOrbit = new OrbitSet<PERM, dom_int>();
		newOrbit->orbit(baseElement, filteredSGS, typename Transversal<PERM>::TrivialAction());
		if (oldBaseElement == baseElement && newOrbit->size() == oldOrbit->size()) {
			delete newOrbit;
			PERMLIB_DEBUG(std::cout << "  removed\n";)
			filteredSGS.pop_back();
		} else {
			delete oldOrbit;
			oldOrbit = newOrbit;
		}
		oldBaseElement = baseElement;
	}
	delete oldOrbit;
	
	this->S = filteredSGS;
}

template <class PERM, class TRANS>
void BSGS<PERM,TRANS>::copyTransversals(const BSGS<PERM,TRANS>& bsgs) {
	std::map<PERM*,typename PERM::ptr> genMap;
	BOOST_FOREACH(const typename PERM::ptr& p, bsgs.S) {
		typename PERM::ptr deepcopy(new PERM(*p));
		//std::cout << "found " << p.get() << " = " << *p << std::endl;
		genMap.insert(std::make_pair(p.get(), deepcopy));
		this->S.push_back(deepcopy);
	}
	
	BOOST_ASSERT(this->B.size() == bsgs.B.size());
	BOOST_ASSERT(bsgs.B.size() == bsgs.U.size());
	this->U.clear();
	this->U.resize(bsgs.U.size(), TRANS(bsgs.n));
	BOOST_ASSERT(this->U.size() == bsgs.U.size());
	
	for (unsigned int i=0; i<this->U.size(); ++i) {
		this->U[i] = bsgs.U[i].clone(genMap);
	}
}

}

#endif // -- BSGS_H_