diff options
Diffstat (limited to 'random_util.h')
| -rw-r--r-- | random_util.h | 26 |
1 files changed, 19 insertions, 7 deletions
diff --git a/random_util.h b/random_util.h index 7f4823e..39f8c04 100644 --- a/random_util.h +++ b/random_util.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead <blangmea@jhsph.edu> + * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu> * * This file is part of Bowtie 2. * @@ -20,6 +20,7 @@ #ifndef RANDOM_UTIL_H_ #define RANDOM_UTIL_H_ +#include <algorithm> #include "random_source.h" #include "ds.h" @@ -37,18 +38,24 @@ public: // A set with fewer than this many elements should kick us into swap-list // mode immediately. Otherwise we start in seen-list mode and then // possibly proceed to swap-list mode later. - static const size_t SWAPLIST_THRESH = 128; + static const size_t SWAPLIST_THRESH; - // Convert seen-list to swap-list after this many - static const size_t CONVERSION_THRESH = 16; + // Convert seen-list to swap-list after this many entries in the seen-list. + static const size_t CONVERSION_THRESH; + + // Convert seen-list to swap-list after this (this times n_) many entries + // in the seen-list. + static const float CONVERSION_FRAC; Random1toN(int cat = 0) : sz_(0), n_(0), cur_(0), - list_(SWAPLIST_THRESH, cat), seen_(CONVERSION_THRESH, cat) {} + list_(SWAPLIST_THRESH, cat), seen_(CONVERSION_THRESH, cat), + thresh_(0) {} Random1toN(size_t n, int cat = 0) : sz_(0), n_(n), cur_(0), - list_(SWAPLIST_THRESH, cat), seen_(CONVERSION_THRESH, cat) {} + list_(SWAPLIST_THRESH, cat), seen_(CONVERSION_THRESH, cat), + thresh_(0) {} /** * Initialize the set of pseudo-randoms to be given out without replacement. @@ -60,6 +67,7 @@ public: cur_ = 0; list_.clear(); seen_.clear(); + thresh_ = std::max(CONVERSION_THRESH, (size_t)(CONVERSION_FRAC * n)); } /** @@ -69,6 +77,7 @@ public: void reset() { sz_ = n_ = cur_ = 0; swaplist_ = converted_ = false; list_.clear(); seen_.clear(); + thresh_ = 0; } /** @@ -120,7 +129,8 @@ public: cur_++; assert_leq(cur_, n_); // Move on to using the swap-list? - if(seen_.size() >= CONVERSION_THRESH && cur_ < n_) { + assert_gt(thresh_, 0); + if(seen_.size() >= thresh_ && cur_ < n_) { // Add all elements not already in the seen list to the // swap-list assert(!seen_.empty()); @@ -204,6 +214,8 @@ protected: EList<T> list_; // pseudo-random swapping list EList<T> seen_; // prior to swaplist_ mode, list of // pseudo-randoms given out + size_t thresh_; // conversion threshold for this instantiation, which + // depends both on CONVERSION_THRESH and on n_ }; #endif |