added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / uchime_src / timers.h

diff --git a/uchime_src/timers.h b/uchime_src/timers.h
new file mode 100644 (file)
index 0000000..81cf7d1
--- /dev/null
+++ b/uchime_src/timers.h
@@ -0,0 +1,173 @@
+T(MxBase_Alloc)\r
+T(MxBase_FreeData)\r
+T(MxBase_AllocData)\r
+T(SortSeqIndexes)\r
+T(Alloc_Vectors)\r
+T(MainLoop_NotNW)\r
+T(WriteOutput)\r
+T(NWB)\r
+T(ReadAllStdioFile)\r
+T(Windex_Init)\r
+T(Windex_SetSeqIndex)\r
+T(SeqToWords)\r
+T(SeqToWordsStep)\r
+T(SeqToShortWords)\r
+T(SeqToShortWordsA)\r
+T(SeqToShortWordsB)\r
+T(GetFractIdB)\r
+T(Windex_UniqueWordsAlloc)\r
+T(Windex_UniqueWords)\r
+T(GetPctId)\r
+T(Windex_Reset)\r
+T(GetSig)\r
+T(NWEditDist)\r
+T(EditDist_Myers)\r
+T(EditDist_BlockTarget)\r
+T(NWBand)\r
+T(WordCounting)\r
+T(NWAff)\r
+T(NWAffBand)\r
+T(NWSimple)\r
+T(NWSimpleB)\r
+T(BandWrap)\r
+T(IncIdCounts)\r
+T(GetBestDiagB)\r
+T(GetBestDiagB1)\r
+T(GetBestDiagB2)\r
+T(ClusterInit)\r
+T(ClusterPrep)\r
+T(HotSort1)\r
+T(HotSort2)\r
+T(SortA)\r
+T(SortB)\r
+T(CountSort)\r
+T(AddWords)\r
+T(ClusterWindex)\r
+T(MainInit)\r
+T(Output)\r
+T(WindexTail)\r
+T(WindexExit)\r
+T(Sort)\r
+T(U_AllocSeqLength)\r
+T(U_AllocSeedCount)\r
+T(U_AddSeed)\r
+T(AddSeq)\r
+T(U_SetWordCounts)\r
+T(U_SetWordCountsHash)\r
+T(U_SetWordScores)\r
+T(U_SetHotHits)\r
+T(U_SetHotHitsHash)\r
+T(U_SetHotHitsScores)\r
+T(U_Search)\r
+T(U_SearchExact)\r
+T(WF_SeqToWords)\r
+T(WF_SeqToWordsA)\r
+T(WF_SeqToWordsB)\r
+T(WF_AllocLA)\r
+T(WF_AllocLB)\r
+T(WF_AllocDiags)\r
+T(WF_SetA)\r
+T(WF_SetA_Nb)\r
+T(WF_SetAZero)\r
+T(WF_SetA2)\r
+T(WF_SetB)\r
+T(WF_GetCommonWordCount)\r
+T(WF_GetBestDiag)\r
+T(GetFractIdGivenPath)\r
+T(WX_GetUniqueWords)\r
+T(CompressPath)\r
+T(GetHSPs1)\r
+T(GetHSPs2)\r
+T(AlignHSPs)\r
+T(WF_ResolveHSPs)\r
+T(WX_SetExcludes)\r
+T(ViterbiFast)\r
+T(ViterbiFastBand)\r
+T(ViterbiFastBand0)\r
+T(ViterbiFastBand1)\r
+T(ViterbiFastBand2)\r
+T(ViterbiFastBand3)\r
+T(ViterbiFastBand4)\r
+T(TraceBackBit)\r
+T(TraceBackBitSW)\r
+T(SF_GetNextSeq)\r
+T(SF_FillCache)\r
+T(OnGlobalAccept)\r
+T(UngappedBlast)\r
+T(UngappedBlastId)\r
+T(UngappedBlast2Hit)\r
+T(LogHSPs)\r
+T(BlastOutput)\r
+T(BlastLeft)\r
+T(BlastRight)\r
+T(Blast1)\r
+T(Blast2)\r
+T(Blast3)\r
+T(Blast4)\r
+T(GetBestSeg)\r
+T(SWLinearDP)\r
+T(SWLinearTB)\r
+T(SWLinearDP2)\r
+T(SWLinearTB2)\r
+T(Chain)\r
+T(XlatSeq)\r
+T(XlatSeqToLetters)\r
+T(XDropFwdSimple)\r
+T(XDropFwdFast)\r
+T(XDropFwdFastTB)\r
+T(XDropBwd)\r
+T(SWSimple)\r
+T(PathAlloc)\r
+T(SubPath)\r
+T(SWUngapped)\r
+T(SWFast)\r
+T(SWFastNTB)\r
+T(SWAT_CacheQuery)\r
+T(SWAT_AlignTarget)\r
+T(SWAT_CacheQueryNW)\r
+T(SWAT_AlignTargetNW)\r
+T(SeqDB_FromFasta)\r
+T(LocalUngappedHitToAD)\r
+T(LocalGappedHitToAD)\r
+T(GlobalHitToAD)\r
+T(ResolveOverlaps)\r
+T(GetORFs)\r
+T(ChainCov_AddHit)\r
+T(ChainCov_EndQuery)\r
+T(ChainCov_DoTarget)\r
+T(BuildNb)\r
+T(MakeIntSubstMx)\r
+T(UngappedExtendLeft)\r
+T(UngappedExtendRight)\r
+T(AlignSP)\r
+T(AlignHSP)\r
+\r
+// Background\r
+T(Bg_SearchLoop)\r
+T(Bg_MainInit)\r
+T(Bg_MainTerm)\r
+T(Bg_Other)\r
+T(Bg_1)\r
+T(Bg_2)\r
+T(Bg_3)\r
+T(Bg_4)\r
+T(Bg_5)\r
+T(Bg_6)\r
+T(Bg_7)\r
+T(Bg_8)\r
+T(Bg_9)\r
+T(Bg_XFrame2)\r
+T(Bg_Usearch1)\r
+T(Bg_Usearch2)\r
+T(Bg_Usearch3)\r
+T(Bg_Usearch4)\r
+T(Bg_Hot)\r
+\r
+// For Timer2\r
+T(Search_2)\r
+T(Search_Loop_2)\r
+T(Search_InnerLoop_2)\r
+T(OnHit_2)\r
+T(UngappedBlast_2)\r
+T(MainInit_2)\r
+T(MainTerm_2)\r