Lines Matching refs:WA
30 Work_Area_t * WA) { in Add_Match() argument
37 for (p = start; (* p) != 0; p = & (WA->Match_Node_Space [(* p)].Next)) { in Add_Match()
38 …expected_start = WA->Match_Node_Space [(* p)].Start + WA->Match_Node_Space [(* p)].Len - G.Kmer_Le… in Add_Match()
40 diag = WA->Match_Node_Space [(* p)].Offset - WA->Match_Node_Space [(* p)].Start; in Add_Match()
47 WA->Match_Node_Space [(* p)].Len += 1 + HASH_KMER_SKIP; in Add_Match()
50 (* p) = WA->Match_Node_Space [(* p)].Next; in Add_Match()
51 WA->Match_Node_Space [save].Next = (* start); in Add_Match()
61 if (WA->Next_Avail_Match_Node == WA->Match_Node_Size) { in Add_Match()
62 int32 newSize = WA->Match_Node_Size * 2; in Add_Match()
65 memcpy(newSpace, WA->Match_Node_Space, sizeof(Match_Node_t) * WA->Match_Node_Size); in Add_Match()
67 delete [] WA->Match_Node_Space; in Add_Match()
69 WA->Match_Node_Size = newSize; in Add_Match()
70 WA->Match_Node_Space = newSpace; in Add_Match()
80 (* start) = WA->Next_Avail_Match_Node; in Add_Match()
81 WA->Next_Avail_Match_Node ++; in Add_Match()
83 WA->Match_Node_Space [(* start)].Offset = getStringRefOffset(ref); in Add_Match()
84 WA->Match_Node_Space [(* start)].Len = G.Kmer_Len; in Add_Match()
85 WA->Match_Node_Space [(* start)].Start = offset; in Add_Match()
86 WA->Match_Node_Space [(* start)].Next = save; in Add_Match()
91 WA->Match_Node_Space [(* start)].Offset, in Add_Match()
92 WA->Match_Node_Space [(* start)].Len, in Add_Match()
93 WA->Match_Node_Space [(* start)].Start, in Add_Match()
94 WA->Match_Node_Space [(* start)].Next); in Add_Match()
105 Add_Ref(String_Ref_t Ref, int Offset, Work_Area_t * WA) { in Add_Ref() argument
116 while (WA->String_Olap_Space [Sub].Full in Add_Ref()
117 && WA->String_Olap_Space [Sub].String_Num != StrNum) { in Add_Ref()
119 Sub = WA->String_Olap_Space [Sub].Next; in Add_Ref()
121 if (WA->Next_Avail_String_Olap == WA->String_Olap_Size) { in Add_Ref()
122 int32 newSize = WA->String_Olap_Size * 2; in Add_Ref()
125 memcpy(newSpace, WA->String_Olap_Space, sizeof(String_Olap_t) * WA->String_Olap_Size); in Add_Ref()
127 delete [] WA->String_Olap_Space; in Add_Ref()
129 WA->String_Olap_Size = newSize; in Add_Ref()
130 WA->String_Olap_Space = newSpace; in Add_Ref()
133 Sub = WA->Next_Avail_String_Olap ++; in Add_Ref()
134 WA->String_Olap_Space [Prev].Next = Sub; in Add_Ref()
135 WA->String_Olap_Space [Sub].Full = false; in Add_Ref()
140 if (! WA->String_Olap_Space [Sub].Full) { in Add_Ref()
141 WA->String_Olap_Space [Sub].String_Num = StrNum; in Add_Ref()
142 WA->String_Olap_Space [Sub].Match_List = 0; in Add_Ref()
143 WA->String_Olap_Space [Sub].diag_sum = 0.0; in Add_Ref()
144 WA->String_Olap_Space [Sub].diag_ct = 0; in Add_Ref()
145 WA->String_Olap_Space [Sub].diag_bgn = AS_MAX_READLEN; in Add_Ref()
146 WA->String_Olap_Space [Sub].diag_end = 0; in Add_Ref()
147 WA->String_Olap_Space [Sub].Next = 0; in Add_Ref()
148 WA->String_Olap_Space [Sub].Full = true; in Add_Ref()
149 WA->String_Olap_Space [Sub].consistent = true; in Add_Ref()
152 consistent = WA->String_Olap_Space [Sub].consistent; in Add_Ref()
154 WA->String_Olap_Space [Sub].diag_sum += (double)getStringRefOffset(Ref) - Offset; in Add_Ref()
155 WA->String_Olap_Space [Sub].diag_ct ++; in Add_Ref()
156 if (WA->String_Olap_Space [Sub].diag_bgn > Offset) WA->String_Olap_Space [Sub].diag_bgn = Offset; in Add_Ref()
157 if (WA->String_Olap_Space [Sub].diag_end < Offset) WA->String_Olap_Space [Sub].diag_end = Offset; in Add_Ref()
158 Add_Match (Ref, & (WA->String_Olap_Space [Sub].Match_List), Offset, & consistent, WA); in Add_Ref()
160 WA->String_Olap_Space [Sub].consistent = consistent; in Add_Ref()
235 Find_Overlaps(char Frag [], int Frag_Len, uint32 Frag_Num, Direction_t Dir, Work_Area_t * WA) { in Find_Overlaps() argument
245 memset (WA->String_Olap_Space, 0, STRING_OLAP_MODULUS * sizeof (String_Olap_t)); in Find_Overlaps()
246 WA->Next_Avail_String_Olap = STRING_OLAP_MODULUS; in Find_Overlaps()
247 WA->Next_Avail_Match_Node = 1; in Find_Overlaps()
254 WA->left_end_screened = false; in Find_Overlaps()
255 WA->right_end_screened = false; in Find_Overlaps()
257 WA->A_Olaps_For_Frag = 0; in Find_Overlaps()
258 WA->B_Olaps_For_Frag = 0; in Find_Overlaps()
275 WA->left_end_screened = true; in Find_Overlaps()
280 Add_Ref (Ref, Offset, WA); in Find_Overlaps()
312 WA->left_end_screened = true; in Find_Overlaps()
315 WA->right_end_screened = true; in Find_Overlaps()
321 Add_Ref (Ref, Offset, WA); in Find_Overlaps()
335 Process_String_Olaps (Frag, Frag_Len, Frag_Num, Dir, WA); in Find_Overlaps()