source: branches/port5/ptpan/pt_prototypes.h

Last change on this file was 5968, checked in by westram, 16 years ago
  • new flag -w to aisc_mkpt (add include wrapper)
  • uniform style for several include wrappers
  • removed duplicated includes
  • removed useless nt_concatenate.hxx
File size: 12.0 KB
Line 
1/*
2 * This file is generated by aisc_mkpt.
3 * Any changes you make here will be overwritten later!
4 *
5 */
6
7#ifndef PT_PROTOTYPES_H
8#define PT_PROTOTYPES_H
9
10#ifndef P_
11# if defined(__STDC__) || defined(__cplusplus)
12#  define P_(s) s
13# else
14#  define P_(s) ()
15# endif
16#else
17# error P_ already defined elsewhere
18#endif
19
20
21/* PTP_new_design.cxx */
22extern "C" int pt_init_bond_matrix P_((PT_pdc *THIS));
23extern "C" char *get_design_info P_((PT_tprobes *tprobe));
24extern "C" char *get_design_hinfo P_((PT_tprobes *tprobe));
25ULONG MarkSpeciesGroup P_((struct PTPanGlobal *pg, STRPTR specnames));
26struct DesignQuery *AllocDesignQuery P_((struct PTPanGlobal *pg));
27void FreeDesignQuery P_((struct DesignQuery *dq));
28struct DesignHit *AddDesignHit P_((struct DesignQuery *dq));
29void RemDesignHit P_((struct DesignHit *dh));
30void CalcProbeQuality P_((struct DesignQuery *dq));
31BOOL FindProbeInPartition P_((struct DesignQuery *dq));
32extern "C" int PT_start_design P_((PT_pdc *pdc, int dummy_1x));
33
34/* PTP_main.cxx */
35struct PTPanGlobal *AllocPTPanGlobal P_((void));
36void FreePTPanGlobal P_((struct PTPanGlobal *pg));
37extern "C" int server_shutdown P_((PT_main *, aisc_string passwd));
38extern "C" int broadcast P_((PT_main *main, int dummy_1x));
39
40/* PTP_io.cxx */
41ULONG BenchTimePassed P_((struct PTPanGlobal *pg));
42void BenchOutput P_((struct PTPanGlobal *pg));
43ULONG CalcLengthForFilteredSequence P_((struct PTPanGlobal *pg, STRPTR srcseq));
44ULONG FilterSequenceTo P_((struct PTPanGlobal *pg, STRPTR srcstr, STRPTR filtptr));
45STRPTR FilterSequence P_((struct PTPanGlobal *pg, STRPTR srcseq));
46ULONG CompressSequenceTo P_((struct PTPanGlobal *pg, STRPTR srcseq, ULONG *seqptr));
47ULONG *CompressSequence P_((struct PTPanGlobal *pg, STRPTR srcseq));
48ULONG GetLengthOfCompressedSequence P_((struct PTPanGlobal *pg, ULONG *seqptr));
49UWORD GetCompressedLongSize P_((struct PTPanGlobal *pg, ULONG pval));
50ULONG DecompressSequenceTo P_((struct PTPanGlobal *pg, ULONG *seqptr, STRPTR tarseq));
51ULONG DecompressCompressedLongTo P_((struct PTPanGlobal *pg, ULONG pval, STRPTR tarseq));
52STRPTR DecompressSequence P_((struct PTPanGlobal *pg, ULONG *seqptr));
53LONG DecompressSequencePartTo P_((struct PTPanGlobal *pg, ULONG *seqptr, ULONG seqpos, ULONG length, STRPTR tarseq));
54UBYTE GetNextCharacter P_((struct PTPanGlobal *pg, UBYTE *buffer, ULONG &bitpos, ULONG &count));
55ULONG WriteManyChars P_((UBYTE *buffer, ULONG bitpos, BYTE c, ULONG i));
56ULONG CompressSequenceWithDotsAndHyphens P_((struct PTPanGlobal *pg, struct PTPanSpecies *ps));
57void ComplementSequence P_((struct PTPanGlobal *pg, STRPTR seqstr));
58void ReverseSequence P_((struct PTPanGlobal *, STRPTR seqstr));
59BOOL OpenDataBase P_((struct PTPanGlobal *pg));
60BOOL LoadEcoliSequence P_((struct PTPanGlobal *pg));
61void FreeAllSpecies P_((struct PTPanGlobal *pg));
62BOOL CacheSpeciesLoad P_((struct CacheHandler *, struct PTPanSpecies *ps));
63BOOL CacheSpeciesUnload P_((struct CacheHandler *, struct PTPanSpecies *ps));
64ULONG CacheSpeciesSize P_((struct CacheHandler *, struct PTPanSpecies *ps));
65BOOL LoadSpecies P_((struct PTPanGlobal *pg));
66BOOL LoadIndexHeader P_((struct PTPanGlobal *pg));
67BOOL LoadAllPartitions P_((struct PTPanGlobal *pg));
68void FreeAllPartitions P_((struct PTPanGlobal *pg));
69
70/* PTP_etc.cxx */
71void SetARBErrorMsg P_((PT_local *locs, const STRPTR error));
72extern "C" STRPTR virt_name P_((PT_probematch *ml));
73extern "C" STRPTR virt_fullname P_((PT_probematch *ml));
74extern "C" bytestring *PT_unknown_names P_((struct_PT_pdc *pdc));
75
76/* PTP_family.cxx */
77extern "C" int ff_find_family P_((PT_local *locs, bytestring *species));
78extern "C" int find_family P_((PT_local *locs, bytestring *species));
79
80/* PT_lowlevel.cxx */
81ULONG WriteBits P_((UBYTE *adr, ULONG bitpos, ULONG code, UWORD len));
82ULONG ReadBits P_((UBYTE *adr, ULONG bitpos, UWORD len));
83
84/* PT_huffman.cxx */
85void BuildHuffmanCodeRec P_((struct HuffCode *hcbase, struct HuffCodeInternal *hc, ULONG len, ULONG rootidx, ULONG codelen, ULONG code));
86BOOL BuildHuffmanCode P_((struct HuffCode *hcbase, ULONG len, LONG threshold));
87void WriteHuffmanTree P_((struct HuffCode *hc, ULONG size, FILE *fh));
88struct HuffTree *ReadHuffmanTree P_((FILE *fh));
89struct HuffTree *BuildHuffmanTreeFromTable P_((struct HuffCode *hc, ULONG maxid));
90void FreeHuffmanTree P_((struct HuffTree *root));
91struct HuffTree *FindHuffTreeID P_((struct HuffTree *ht, UBYTE *adr, ULONG bitpos));
92
93/* PT_treepack.cxx */
94BOOL WriteIndexHeader P_((struct PTPanGlobal *pg));
95BOOL WriteTreeHeader P_((struct PTPanPartition *pp));
96BOOL CachePartitionLoad P_((struct CacheHandler *, struct PTPanPartition *pp));
97void CachePartitionUnload P_((struct CacheHandler *, struct PTPanPartition *pp));
98ULONG CachePartitionSize P_((struct CacheHandler *, struct PTPanPartition *pp));
99BOOL WriteStdSuffixTreeHeader P_((struct PTPanPartition *pp));
100BOOL CacheStdSuffixPartitionLoad P_((struct CacheHandler *, struct PTPanPartition *pp));
101void CacheStdSuffixPartitionUnload P_((struct CacheHandler *, struct PTPanPartition *pp));
102ULONG FixRelativePointersRec P_((struct PTPanPartition *pp, ULONG pos, ULONG level, ULONG elen));
103LONG ULONGCompare P_((const ULONG *node1, const ULONG *node2));
104ULONG CalcPackedNodeSize P_((struct PTPanPartition *pp, ULONG pos));
105ULONG CalcPackedLeafSize P_((struct PTPanPartition *pp, ULONG pos));
106void DebugTreeNode P_((struct TreeNode *tn));
107void GetTreePath P_((struct TreeNode *tn, STRPTR strptr, ULONG len));
108struct TreeNode *GoDownStdSuffixNodeChild P_((struct TreeNode *oldtn, UWORD seqcode));
109struct TreeNode *GoDownNodeChild P_((struct TreeNode *oldtn, UWORD seqcode));
110struct TreeNode *GoDownNodeChildNoEdge P_((struct TreeNode *oldtn, UWORD seqcode));
111struct TreeNode *ReadPackedNode P_((struct PTPanPartition *pp, ULONG pos));
112struct TreeNode *ReadPackedNodeNoEdge P_((struct PTPanPartition *pp, ULONG pos));
113struct TreeNode *ReadPackedLeaf P_((struct PTPanPartition *pp, ULONG pos));
114ULONG WritePackedNode P_((struct PTPanPartition *pp, ULONG pos, UBYTE *buf));
115ULONG WritePackedLeaf P_((struct PTPanPartition *pp, ULONG pos, UBYTE *buf));
116struct SearchQuery *CloneSearchQuery P_((struct SearchQuery *oldsq));
117struct SearchQuery *AllocSearchQuery P_((struct PTPanGlobal *pg));
118void FreeSearchQuery P_((struct SearchQuery *sq));
119void SearchTree P_((struct SearchQuery *sq));
120void PostFilterQueryHits P_((struct SearchQuery *sq));
121BOOL AddQueryHit P_((struct SearchQuery *sq, ULONG hitpos));
122void RemQueryHit P_((struct QueryHit *qh));
123void MergeQueryHits P_((struct SearchQuery *tarsq, struct SearchQuery *srcsq));
124void PrintSearchQueryState P_((const char *s1, const char *s2, struct SearchQuery *sq));
125void SearchTreeRec P_((struct SearchQuery *sq));
126void CollectTreeRec P_((struct SearchQuery *sq));
127BOOL MatchSequence P_((struct SearchQuery *sq));
128BOOL MatchSequenceRec P_((struct SearchQuery *sq));
129BOOL FindSequenceMatch P_((struct SearchQuery *sq, struct QueryHit *qh, STRPTR tarstr));
130BOOL FindSequenceMatchRec P_((struct SearchQuery *sq, struct QueryHit *qh, STRPTR tarptr));
131
132/* PTP_buildtree.cxx */
133BOOL BuildStdSuffixTree P_((struct PTPanGlobal *pg));
134BOOL BuildMemoryStdSuffixTree P_((struct PTPanPartition *pp));
135ULONG SplitStdSfxNode P_((struct PTPanPartition *pp, ULONG leafnum));
136ULONG FindStdSfxNode P_((struct PTPanPartition *pp, ULONG snum, ULONG &sfxstart, ULONG sfxend));
137ULONG FastFindStdSfxNode P_((struct PTPanPartition *pp, ULONG snum, ULONG sfxstart, ULONG sfxend));
138ULONG InsertStdSfxNode P_((struct PTPanPartition *pp, ULONG sfxstart, ULONG sfxend, ULONG parnum));
139BOOL WriteStdSuffixTreeToDisk P_((struct PTPanPartition *pp));
140BOOL BuildPTPanIndex P_((struct PTPanGlobal *pg));
141BOOL BuildMergedDatabase P_((struct PTPanGlobal *pg));
142BOOL PartitionPrefixScan P_((struct PTPanGlobal *pg));
143BOOL CreateTreeForPartition P_((struct PTPanPartition *pp));
144BOOL BuildMemoryTree P_((struct PTPanPartition *pp));
145ULONG CommonSequenceLength P_((struct PTPanPartition *pp, ULONG spos1, ULONG spos2, ULONG maxlen));
146LONG CompareCompressedSequence P_((struct PTPanGlobal *pg, ULONG spos1, ULONG spos2));
147BOOL InsertTreePos P_((struct PTPanPartition *pp, ULONG pos, ULONG window));
148BOOL CalculateTreeStats P_((struct PTPanPartition *pp));
149void GetTreeStatsDebugRec P_((struct PTPanPartition *pp, ULONG pos, ULONG level));
150void GetTreeStatsTreeDepthRec P_((struct PTPanPartition *pp, ULONG pos, ULONG level));
151void GetTreeStatsLevelRec P_((struct PTPanPartition *pp, ULONG pos, ULONG level));
152void GetTreeStatsShortEdgesRec P_((struct PTPanPartition *pp, ULONG pos, ULONG level, ULONG elen));
153void GetTreeStatsLongEdgesRec P_((struct PTPanPartition *pp, ULONG pos, ULONG level, ULONG elen));
154void GetTreeStatsBranchHistoRec P_((struct PTPanPartition *pp, ULONG pos, ULONG level, ULONG elen));
155void GetTreeStatsVerifyRec P_((struct PTPanPartition *pp, ULONG pos, ULONG treepos, ULONG hash));
156ULONG GetTreeStatsLeafCountRec P_((struct PTPanPartition *pp, ULONG pos));
157void GetTreeStatsLeafCollectRec P_((struct PTPanPartition *pp, ULONG pos));
158LONG LongEdgeLengthCompare P_((const struct SfxNode **node1, const struct SfxNode **node2));
159LONG LongEdgePosCompare P_((const struct SfxNode **node1, const struct SfxNode **node2));
160LONG LongEdgeLabelCompare P_((struct SfxNode **node1, struct SfxNode **node2));
161ULONG GetSeqHash P_((struct PTPanGlobal *pg, ULONG seqpos, ULONG len, ULONG hash));
162ULONG GetSeqHashBackwards P_((struct PTPanGlobal *pg, ULONG seqpos, ULONG len, ULONG hash));
163BOOL CheckLongEdgeMatch P_((struct PTPanPartition *pp, ULONG seqpos, ULONG edgelen, ULONG dictpos));
164BOOL BuildLongEdgeDictionary P_((struct PTPanPartition *pp));
165BOOL WriteTreeToDisk P_((struct PTPanPartition *pp));
166BOOL CreatePartitionLookup P_((struct PTPanGlobal *pg));
167
168/* PTP_match.cxx */
169void SearchPartition P_((struct PTPanPartition *pp, struct SearchQuery *sq));
170void QueryTests P_((struct PTPanGlobal *pg));
171void PP_convertBondMatrix P_((PT_pdc *pdc, PTPanGlobal *pg));
172void PP_buildPosWeight P_((SearchQuery *sq));
173extern "C" int probe_match P_((PT_local *locs, aisc_string probestring));
174void SortHitsList P_((struct SearchQuery *sq));
175void CreateHitsGUIList P_((struct SearchQuery *sq));
176extern "C" STRPTR get_match_info P_((PT_probematch *ml));
177STRPTR GetMatchListHeader P_((STRPTR seq));
178extern "C" STRPTR get_match_hinfo P_((PT_probematch *));
179extern "C" STRPTR c_get_match_hinfo P_((PT_probematch *));
180extern "C" bytestring *match_string P_((PT_local *locs));
181extern "C" bytestring *MP_match_string P_((PT_local *locs));
182extern "C" bytestring *MP_all_species_string P_((PT_local *));
183extern "C" int MP_count_all_species P_((PT_local *));
184
185/* PTP_findEx.cxx */
186extern "C" int PT_find_exProb P_((PT_exProb *pep));
187
188/* PT_cachehandler.cxx */
189struct CacheHandler *AllocCacheHandler P_((void));
190void FreeCacheHandler P_((struct CacheHandler *ch));
191struct CacheNode *CacheLoadData P_((struct CacheHandler *ch, struct CacheNode *cn, APTR ud));
192ULONG CacheMemUsage P_((struct CacheHandler *ch));
193void DisableCache P_((struct CacheHandler *ch));
194void EnableCache P_((struct CacheHandler *ch));
195BOOL CacheDataLoaded P_((struct CacheNode *cn));
196void FreeCacheNode P_((struct CacheHandler *ch, struct CacheNode *cn));
197BOOL CacheUnloadData P_((struct CacheHandler *ch, struct CacheNode *cn));
198ULONG FlushCache P_((struct CacheHandler *ch));
199
200/* PT_hashing.cxx */
201struct HashArray *AllocHashArray P_((ULONG size));
202void FreeHashArray P_((struct HashArray *ha));
203void ClearHashArray P_((struct HashArray *ha));
204struct HashEntry *GetHashEntry P_((struct HashArray *ha, ULONG hashkey));
205BOOL EnlargeHashArray P_((struct HashArray *ha));
206BOOL InsertHashEntry P_((struct HashArray *ha, ULONG hashkey, ULONG data));
207
208/* dlist.cxx */
209void NewList P_((struct List *lh));
210void AddHead P_((struct List *lh, struct Node *nd));
211void AddTail P_((struct List *lh, struct Node *nd));
212void Remove P_((struct Node *nd));
213LONG NodePriCompare P_((const struct Node **node1, const struct Node **node2));
214BOOL SortList P_((struct List *lh));
215struct BinTree *BuildBinTreeRec P_((struct Node **nodearr, ULONG left, ULONG right));
216struct BinTree *BuildBinTree P_((struct List *list));
217void FreeBinTree P_((struct BinTree *root));
218struct Node *FindBinTreeLowerKey P_((struct BinTree *root, LLONG key));
219
220#undef P_
221
222#else
223#error pt_prototypes.h included twice
224#endif /* PT_PROTOTYPES_H */
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