Description: Renamed ChunkPool class to bowtieChunkPool. SeqAn has a class with the same name and fatal name collision happens. Forwarded: no Author: Ognyan Kulev Last-Update: 2013-04-18 --- a/aligner.h +++ b/aligner.h @@ -337,7 +337,7 @@ public: bool verbose, bool quiet, int maxBts, - ChunkPool *pool, + bowtieChunkPool *pool, int *btCnt = NULL, AlignerMetrics *metrics = NULL) : Aligner(true, rangeMode), @@ -544,7 +544,7 @@ protected: bool quiet_; // don't print informational/warning info const int maxBts_; - ChunkPool *pool_; + bowtieChunkPool *pool_; int *btCnt_; AlignerMetrics *metrics_; }; @@ -585,7 +585,7 @@ public: bool verbose, bool quiet, int maxBts, - ChunkPool *pool, + bowtieChunkPool *pool, int *btCnt) : Aligner(true, rangeMode), refs_(refs), @@ -1358,7 +1358,7 @@ protected: bool quiet_; int maxBts_; - ChunkPool *pool_; + bowtieChunkPool *pool_; int *btCnt_; // Range-finding state for first mate @@ -1482,7 +1482,7 @@ public: bool verbose, bool quiet, int maxBts, - ChunkPool *pool, + bowtieChunkPool *pool, int *btCnt) : Aligner(true, rangeMode), refs_(refs), @@ -2035,7 +2035,7 @@ protected: TDriver* driver_; // Pool for distributing chunks of best-first path descriptor memory - ChunkPool *pool_; + bowtieChunkPool *pool_; bool verbose_; bool quiet_; --- a/aligner_0mm.h +++ b/aligner_0mm.h @@ -32,7 +32,7 @@ public: RangeCache* cacheFw, RangeCache* cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool maqPenalty, @@ -124,7 +124,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; bool maqPenalty_; @@ -164,7 +164,7 @@ public: RangeCache* cacheFw, RangeCache* cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool reportSe, @@ -366,7 +366,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; const bool reportSe_; --- a/aligner_1mm.h +++ b/aligner_1mm.h @@ -32,7 +32,7 @@ public: RangeCache *cacheFw, RangeCache *cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool maqPenalty, @@ -161,7 +161,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; const bool maqPenalty_; @@ -201,7 +201,7 @@ public: RangeCache *cacheFw, RangeCache *cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool reportSe, @@ -478,7 +478,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; const bool reportSe_; --- a/aligner_23mm.h +++ b/aligner_23mm.h @@ -33,7 +33,7 @@ public: RangeCache *cacheFw, RangeCache *cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool maqPenalty, @@ -231,7 +231,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; const bool maqPenalty_; @@ -273,7 +273,7 @@ public: RangeCache *cacheFw, RangeCache *cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool reportSe, @@ -675,7 +675,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; const bool reportSe_; --- a/aligner_seed_mm.h +++ b/aligner_seed_mm.h @@ -37,7 +37,7 @@ public: RangeCache* cacheFw, RangeCache* cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool maqPenalty, @@ -554,7 +554,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; bool strandFix_; @@ -598,7 +598,7 @@ public: RangeCache* cacheFw, RangeCache* cacheBw, uint32_t cacheLimit, - ChunkPool *pool, + bowtieChunkPool *pool, BitPairReference* refs, vector >& os, bool reportSe, @@ -1375,7 +1375,7 @@ private: RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; - ChunkPool *pool_; + bowtieChunkPool *pool_; BitPairReference* refs_; vector >& os_; const bool reportSe_; --- a/ebwt_search.cpp +++ b/ebwt_search.cpp @@ -111,7 +111,7 @@ static bool strandFix; // attempt to fi static bool randomizeQuals; // randomize quality values static bool stats; // print performance stats static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread -static int chunkSz; // size of single chunk disbursed by ChunkPool +static int chunkSz; // size of single chunk disbursed by bowtieChunkPool static bool chunkVerbose; // have chunk allocator output status messages? static bool recal; static int recalMaxCycle; @@ -223,7 +223,7 @@ static void resetOptions() { randomizeQuals = false; // randomize quality values stats = false; // print performance stats chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread - chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB) + chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB) chunkVerbose = false; // have chunk allocator output status messages? recal = false; recalMaxCycle = 64; @@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); UnpairedExactAlignerV1Factory alSEfact( ebwt, NULL, @@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat // Global initialization PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); Unpaired1mmAlignerV1Factory alSEfact( ebwtFw, @@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); Unpaired23mmAlignerV1Factory alSEfact( ebwtFw, &ebwtBw, @@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt // Global initialization PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); AlignerMetrics *metrics = NULL; if(stats) { --- a/ebwt_search_backtrack.h +++ b/ebwt_search_backtrack.h @@ -2724,7 +2724,7 @@ public: bool verbose, bool quiet, bool mate1, - ChunkPool* pool, + bowtieChunkPool* pool, int *btCnt) : SingleRangeSourceDriver( params, rs, fw, sink, sinkPt, os, verbose, @@ -2927,7 +2927,7 @@ public: bool verbose, bool quiet, bool mate1, - ChunkPool* pool, + bowtieChunkPool* pool, int *btCnt = NULL) : params_(params), rs_(rs), @@ -2986,7 +2986,7 @@ protected: bool verbose_; bool quiet_; bool mate1_; - ChunkPool* pool_; + bowtieChunkPool* pool_; int *btCnt_; }; --- a/pool.h +++ b/pool.h @@ -19,13 +19,13 @@ * is set at construction time. Heap memory is only allocated at * construction and deallocated at destruction. */ -class ChunkPool { +class bowtieChunkPool { public: /** * Initialize a new pool with an initial size of about 'bytes' * bytes. Exit with an error message if we can't allocate it. */ - ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : + bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : verbose(verbose_), patid(0), pool_(NULL), cur_(0), chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz), bits_(lim_), exhaustCrash_(false), @@ -38,7 +38,7 @@ public: } } catch(std::bad_alloc& e) { ThreadSafe _ts(&gLock); - std::cerr << "Error: Could not allocate ChunkPool of " + std::cerr << "Error: Could not allocate bowtieChunkPool of " << totSz << " bytes" << std::endl; exhausted(); throw 1; // Exit if we haven't already @@ -48,7 +48,7 @@ public: /** * Delete all the pools. */ - ~ChunkPool() { + ~bowtieChunkPool() { if(pool_ != NULL) delete[] pool_; } @@ -189,7 +189,7 @@ public: * Initialize a new pool with an initial size of about 'bytes' * bytes. Exit with an error message if we can't allocate it. */ - AllocOnlyPool(ChunkPool* pool, const char *name) : + AllocOnlyPool(bowtieChunkPool* pool, const char *name) : pool_(pool), name_(name), curPool_(0), cur_(0) { assert(pool != NULL); @@ -388,7 +388,7 @@ protected: lastCurInPool_.pop_back(); } - ChunkPool* pool_; + bowtieChunkPool* pool_; const char *name_; std::vector pools_; /// the memory pools uint32_t curPool_; /// pool we're current allocating from --- a/range_source.h +++ b/range_source.h @@ -1388,7 +1388,7 @@ class PathManager { public: - PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : + PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : branchQ_(verbose, quiet), cpool(cpool_), bpool(cpool, "branch"), @@ -1637,7 +1637,7 @@ protected: public: - ChunkPool *cpool; // pool for generic chunks of memory + bowtieChunkPool *cpool; // pool for generic chunks of memory AllocOnlyPool bpool; // pool for allocating Branches AllocOnlyPool rpool; // pool for allocating RangeStates AllocOnlyPool epool; // pool for allocating Edits @@ -1811,7 +1811,7 @@ public: bool quiet, bool mate1, uint32_t minCostAdjustment, - ChunkPool* pool, + bowtieChunkPool* pool, int *btCnt) : RangeSourceDriver(true, minCostAdjustment), len_(0), mate1_(mate1),