This file is indexed.

/usr/include/trilinos/fei_ArrayUtils.hpp is in libtrilinos-dev 10.4.0.dfsg-1ubuntu2.

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
#ifndef _fei_ArrayUtils_hpp_
#define _fei_ArrayUtils_hpp_

/*--------------------------------------------------------------------*/
/*    Copyright 2005 Sandia Corporation.                              */
/*    Under the terms of Contract DE-AC04-94AL85000, there is a       */
/*    non-exclusive license for use of this work by or on behalf      */
/*    of the U.S. Government.  Export of this program may require     */
/*    a license from the United States Government.                    */
/*--------------------------------------------------------------------*/

#include "fei_fwd.hpp"

#include <algorithm>

namespace fei {

  /** Binary search of a list that's assumed to be sorted.

      @param item to be searched for.
      @param list List to be searched.
      @param len Length of list.

      @return offset Offset at which item was found, or -1 if not found.
   */
  template<typename T>
    int binarySearch(const T& item,
        const T* list,
        int len)
    {
      if (len < 2) {
        if (len < 1) {
          return(-1);
        }

        if (list[0] != item) {
          return(-1);
        }
        else {
          return(0);
        }
      }

      unsigned start = 0;
      unsigned end = len - 1;

      while(end - start > 1) {
        unsigned mid = (start + end) >> 1;
        if (list[mid] < item) start = mid;
        else end = mid;
      }

      if (list[end] == item) return(end);
      if (list[start] == item) return(start);

      return(-1);
    }

  /** sort the specified array, and move the contents
    of the specified companions array to match the new order.
    This is an implementation of the insertion sort algorithm. */
  template<typename T>
    void insertion_sort_with_companions(int len, int* array, T* companions)
    {
      int i, j, index;
      T companion;

      for (i=1; i < len; i++) {
        index = array[i];
        companion = companions[i];
        j = i;
        while ((j > 0) && (array[j-1] > index))
        {
          array[j] = array[j-1];
          companions[j] = companions[j-1];
          j = j - 1;
        }
        array[j] = index;
        companions[j] = companion;
      }
    }

  /** Lower bound finds the first entry in list that is not less than item.
      A binary search is used, and list is assumed to be sorted.
   */
  template<typename T>
  int lowerBound(const T& item,
		 const T* list,
		 int len)
  {
    //The correctness of this function is tested in
    // fei/test_utils/test_misc.cpp, in test_misc::serialtest2().

    if (len < 1) return 0;

    unsigned start = 0;
    unsigned end = len - 1;

    while(end - start > 1) {
      unsigned mid = (start + end) >> 1;
      if (list[mid] < item) start = mid;
      else end = mid;
    }

    if (list[end] < item) {
      return(end+1);
    }

    if (list[start] < item) {
      return(end);
    }

    return(start);
  }

  /** Binary search of a list that's assumed to be sorted.

      @param item to be searched for.
      @param list List to be searched.
      @param len Length of list.
      @param insertPoint If item is not found, this is the offset into list at
      which item could be inserted while maintaining sortedness. Not referenced
      if item is found.

      @return offset Offset at which item was found, or -1 if not found.
   */
  template<typename T>
    int binarySearch(const T& item,
		     const T* list,
		     int len,
		     int& insertPoint)
    {
      //The correctness of this function is tested in src/utils/test_Set.C,
      //in the function test_Set::test2.

      if (len < 2) {
        if (len < 1) {
          insertPoint = 0;
          return(-1);
        }

        if (list[0] < item) {
          insertPoint = 1;
          return(-1);
        }
        if (item < list[0]) {
          insertPoint = 0;
          return(-1);
        }
        else {
          return(0);
        }
      }

      unsigned start = 0;
      unsigned end = len - 1;

      while(end - start > 1) {
        unsigned mid = (start + end) >> 1;
        if (list[mid] < item) start = mid;
        else end = mid;
      }

      if (list[end] < item) {
        insertPoint = end+1;
        return(-1);
      }

      if (item < list[end]) {
        if (list[start] < item) {
          insertPoint = end;
          return(-1);
        }

        if (item < list[start]) {
          insertPoint = start;
          return(-1);
        }
        else {
          return(start);
        }
      }
      else {
        return(end);
      }
    }

  /** Binary search of an std::vector that's assumed to be sorted.
   */
  template<typename T>
    int binarySearch(const T& item, const std::vector<T>& list, int& insertPoint)
    {
      if (list.size() == 0) {
        insertPoint = 0;
        return(-1);
      }
      return( binarySearch(item, &list[0], list.size(), insertPoint) );
    }

  /** Binary search of an std::vector that's assumed to be sorted.
   */
  template<typename T>
    int binarySearch(const T& item, const std::vector<T>& list)
    {
      if (list.size() == 0) return(-1);
      return( binarySearch(item, &list[0], list.size()) );
    }

  /** Perform a binary search but limit the search to a given range.
      @param item Value to be searched for.
      @param list
      @param listLength
      @param start Starting offset of search 'window'.
      @param end Ending offset of search 'window'. end should be less than 
      listLength.
      @param insertPoint
      @return offset position at which item was found. If not found, returns -1.
      (Since 0-based indexing is used, 'end' can't be greater than listLength-1.)
  */
  template<typename T>
    int binarySearch(const T& item, const T* list, int /*listLength*/,
		     int start, int end, int& insertPoint)
    {
      int length = end - start + 1;

      if (length < 2) {
        if (length < 1) {
          insertPoint = start;
          return(-1);
        }

        if (list[start] < item) {
          insertPoint = start+1;
          return(-1);
        }
        if (item < list[start]) {
          insertPoint = start;
          return(-1);
        }
        else {
          return(start);
        }
      }

      unsigned ustart = start;
      unsigned uend = end;

      while(uend - ustart > 1) {
        unsigned mid = (ustart + uend) >> 1;
        if (list[mid] < item) ustart = mid;
        else uend = mid;
      }

      //if list[uend] < item, then insertPoint = end+1
      if (list[uend] < item) {
        insertPoint = uend+1;
        return(-1);
      }

      if (item < list[uend]) {
        if (list[ustart] < item) {
          insertPoint = uend;
          return(-1);
        }

        if (item < list[ustart]) {
          insertPoint = ustart;
          return(-1);
        }
        else {
          //list[ustart] == item
          return(ustart);
        }
      }

      // list[uend] == item
      return(uend);
    }

   /** Perform a binary search for each item in a sorted input list.

       \param numItems   number of items to be searched for
       \param items      list of items (length numItems) to be searched for
       \param offsets    list (length numItems) allocated by caller. On exit,
                         offsets[i] contains the offset of item in 'list', or
                         -1 if item is not present in 'list'.
       \param list       array (length 'listLength') to be searched
       \param listLength length of input array 'list'
    */
  template<typename T>
    int binarySearch(int numItems, const T* items, int* offsets,
		     const T* list, int listLength)
    {
      int i;
      if (numItems < 1 || listLength < 1) {
        if (listLength < 1) {
          for(i=0; i<numItems; ++i) offsets[i] = -1;
        }
      }

      int tmp, start = 0;
      int end = listLength -1;
      int insertPoint = -1;
      for(i=0; i<numItems; ++i) {
        tmp = binarySearch(items[i], list, listLength, start, end, insertPoint);
        start = tmp > -1 ? tmp : insertPoint;
        offsets[i] = tmp;
      }

      return(0);
    }

  /** Insert an item into a sorted list, maintaining sortedness.
      If the item is inserted, return the offset at which it was inserted.
      If the item was already present, return -1.
   */
  template<class T>
    int sortedListInsert(const T& item, std::vector<T>& list)
    {
      typename std::vector<T>::iterator iter =
        std::lower_bound(list.begin(), list.end(), item);

      if (iter == list.end() || *iter != item) {
        iter = list.insert(iter, item);
        return( iter - list.begin() );
      }

      return(-1);
    }

  /** Insert an item into a sorted list, maintaining sortedness.
   */
  template<class T>
    int sortedListInsert(const T& item, T*& list, int& len, int& allocLen)
    {
      int i, insertPoint = -1;
      int index = binarySearch(item, list, len, insertPoint);
      if (index < 0) {
        if (len >= allocLen) {
          allocLen = len+2;
          T* newlist = new T[allocLen];
          for(i=0; i<insertPoint; ++i) newlist[i] = list[i];
          newlist[insertPoint] = item;
          for(i=insertPoint; i<len; ++i) newlist[i+1] = list[i];
          delete [] list;
          list = newlist;
        }
        else {
          for(i=len; i>insertPoint; --i) {
            list[i] = list[i-1];
          }
          list[insertPoint] = item;
        }
        ++len;
        return(insertPoint);
      }

      return(-1);
    }

  /** Insert an item into a list at a specified position.
   */
  template<class T>
    int listInsert(const T& item, int offset, T*& list,
		   int& usedLength, int& allocatedLength,
		   int allocChunkSize=200)
    {
      if (offset < 0 || offset > usedLength) {
        return(-1);
      }

      if (usedLength < allocatedLength) {
        for(int i=usedLength; i>offset; --i) {
          list[i] = list[i-1];
        }
        list[offset] = item;
        ++usedLength;
        return(0);
      }

      T* newlist = new T[allocatedLength+allocChunkSize];

      allocatedLength += allocChunkSize;
      int i;
      for(i=0; i<offset; ++i) {
        newlist[i] = list[i];
      }

      newlist[offset] = item;

      for(i=offset+1; i<=usedLength; ++i) {
        newlist[i] = list[i-1];
      }

      ++usedLength;
      delete [] list;
      list = newlist;
      return(0);
    }

  /** Simple exhaustive search of a list.
      @return offset at which item is found, or -1 if not found.
  */
  template<class T>
    int searchList(const T& item, const T* list, int len)
    {
      for(int i=0; i<len; ++i) {
        if (list[i] == item) {
          return(i);
        }
      }
      return(-1);
    }

} //namespace fei

#endif // _fei_ArrayUtils_hpp_