uchime_src/timers.h

   1 T(MxBase_Alloc)\r
   2 T(MxBase_FreeData)\r
   3 T(MxBase_AllocData)\r
   4 T(SortSeqIndexes)\r
   5 T(Alloc_Vectors)\r
   6 T(MainLoop_NotNW)\r
   7 T(WriteOutput)\r
   8 T(NWB)\r
   9 T(ReadAllStdioFile)\r
  10 T(Windex_Init)\r
  11 T(Windex_SetSeqIndex)\r
  12 T(SeqToWords)\r
  13 T(SeqToWordsStep)\r
  14 T(SeqToShortWords)\r
  15 T(SeqToShortWordsA)\r
  16 T(SeqToShortWordsB)\r
  17 T(GetFractIdB)\r
  18 T(Windex_UniqueWordsAlloc)\r
  19 T(Windex_UniqueWords)\r
  20 T(GetPctId)\r
  21 T(Windex_Reset)\r
  22 T(GetSig)\r
  23 T(NWEditDist)\r
  24 T(EditDist_Myers)\r
  25 T(EditDist_BlockTarget)\r
  26 T(NWBand)\r
  27 T(WordCounting)\r
  28 T(NWAff)\r
  29 T(NWAffBand)\r
  30 T(NWSimple)\r
  31 T(NWSimpleB)\r
  32 T(BandWrap)\r
  33 T(IncIdCounts)\r
  34 T(GetBestDiagB)\r
  35 T(GetBestDiagB1)\r
  36 T(GetBestDiagB2)\r
  37 T(ClusterInit)\r
  38 T(ClusterPrep)\r
  39 T(HotSort1)\r
  40 T(HotSort2)\r
  41 T(SortA)\r
  42 T(SortB)\r
  43 T(CountSort)\r
  44 T(AddWords)\r
  45 T(ClusterWindex)\r
  46 T(MainInit)\r
  47 T(Output)\r
  48 T(WindexTail)\r
  49 T(WindexExit)\r
  50 T(Sort)\r
  51 T(U_AllocSeqLength)\r
  52 T(U_AllocSeedCount)\r
  53 T(U_AddSeed)\r
  54 T(AddSeq)\r
  55 T(U_SetWordCounts)\r
  56 T(U_SetWordCountsHash)\r
  57 T(U_SetWordScores)\r
  58 T(U_SetHotHits)\r
  59 T(U_SetHotHitsHash)\r
  60 T(U_SetHotHitsScores)\r
  61 T(U_Search)\r
  62 T(U_SearchExact)\r
  63 T(WF_SeqToWords)\r
  64 T(WF_SeqToWordsA)\r
  65 T(WF_SeqToWordsB)\r
  66 T(WF_AllocLA)\r
  67 T(WF_AllocLB)\r
  68 T(WF_AllocDiags)\r
  69 T(WF_SetA)\r
  70 T(WF_SetA_Nb)\r
  71 T(WF_SetAZero)\r
  72 T(WF_SetA2)\r
  73 T(WF_SetB)\r
  74 T(WF_GetCommonWordCount)\r
  75 T(WF_GetBestDiag)\r
  76 T(GetFractIdGivenPath)\r
  77 T(WX_GetUniqueWords)\r
  78 T(CompressPath)\r
  79 T(GetHSPs1)\r
  80 T(GetHSPs2)\r
  81 T(AlignHSPs)\r
  82 T(WF_ResolveHSPs)\r
  83 T(WX_SetExcludes)\r
  84 T(ViterbiFast)\r
  85 T(ViterbiFastBand)\r
  86 T(ViterbiFastBand0)\r
  87 T(ViterbiFastBand1)\r
  88 T(ViterbiFastBand2)\r
  89 T(ViterbiFastBand3)\r
  90 T(ViterbiFastBand4)\r
  91 T(TraceBackBit)\r
  92 T(TraceBackBitSW)\r
  93 T(SF_GetNextSeq)\r
  94 T(SF_FillCache)\r
  95 T(OnGlobalAccept)\r
  96 T(UngappedBlast)\r
  97 T(UngappedBlastId)\r
  98 T(UngappedBlast2Hit)\r
  99 T(LogHSPs)\r
 100 T(BlastOutput)\r
 101 T(BlastLeft)\r
 102 T(BlastRight)\r
 103 T(Blast1)\r
 104 T(Blast2)\r
 105 T(Blast3)\r
 106 T(Blast4)\r
 107 T(GetBestSeg)\r
 108 T(SWLinearDP)\r
 109 T(SWLinearTB)\r
 110 T(SWLinearDP2)\r
 111 T(SWLinearTB2)\r
 112 T(Chain)\r
 113 T(XlatSeq)\r
 114 T(XlatSeqToLetters)\r
 115 T(XDropFwdSimple)\r
 116 T(XDropFwdFast)\r
 117 T(XDropFwdFastTB)\r
 118 T(XDropBwd)\r
 119 T(SWSimple)\r
 120 T(PathAlloc)\r
 121 T(SubPath)\r
 122 T(SWUngapped)\r
 123 T(SWFast)\r
 124 T(SWFastNTB)\r
 125 T(SWAT_CacheQuery)\r
 126 T(SWAT_AlignTarget)\r
 127 T(SWAT_CacheQueryNW)\r
 128 T(SWAT_AlignTargetNW)\r
 129 T(SeqDB_FromFasta)\r
 130 T(LocalUngappedHitToAD)\r
 131 T(LocalGappedHitToAD)\r
 132 T(GlobalHitToAD)\r
 133 T(ResolveOverlaps)\r
 134 T(GetORFs)\r
 135 T(ChainCov_AddHit)\r
 136 T(ChainCov_EndQuery)\r
 137 T(ChainCov_DoTarget)\r
 138 T(BuildNb)\r
 139 T(MakeIntSubstMx)\r
 140 T(UngappedExtendLeft)\r
 141 T(UngappedExtendRight)\r
 142 T(AlignSP)\r
 143 T(AlignHSP)\r
 144 \r
 145 // Background\r
 146 T(Bg_SearchLoop)\r
 147 T(Bg_MainInit)\r
 148 T(Bg_MainTerm)\r
 149 T(Bg_Other)\r
 150 T(Bg_1)\r
 151 T(Bg_2)\r
 152 T(Bg_3)\r
 153 T(Bg_4)\r
 154 T(Bg_5)\r
 155 T(Bg_6)\r
 156 T(Bg_7)\r
 157 T(Bg_8)\r
 158 T(Bg_9)\r
 159 T(Bg_XFrame2)\r
 160 T(Bg_Usearch1)\r
 161 T(Bg_Usearch2)\r
 162 T(Bg_Usearch3)\r
 163 T(Bg_Usearch4)\r
 164 T(Bg_Hot)\r
 165 \r
 166 // For Timer2\r
 167 T(Search_2)\r
 168 T(Search_Loop_2)\r
 169 T(Search_InnerLoop_2)\r
 170 T(OnHit_2)\r
 171 T(UngappedBlast_2)\r
 172 T(MainInit_2)\r
 173 T(MainTerm_2)\r