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  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2008-07-14 19:43:15 UTC
  • mfrom: (2.1.12 intrepid)
  • Revision ID: james.westby@ubuntu.com-20080714194315-ed44u9ek7txva2rz
Tags: 6.1.20080302-3
http://bugs.debian.org/490437
tools/readdb.c: enable madvise()-based code on all glibc (hence all
Debian) systems, not just Linux.  (Closes: #490437.)

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object/scoremat.h
 
1
/***********************************************************************
 
2
*
 
3
**
 
4
*        Automatic header module from ASNTOOL
 
5
*
 
6
************************************************************************/
 
7
 
 
8
#ifndef _ASNTOOL_
 
9
#include <asn.h>
 
10
#endif
 
11
 
 
12
static char * asnfilename = "scoremat.h";
 
13
static AsnValxNode avnx[14] = {
 
14
    {2,NULL,1,0.0,NULL } ,
 
15
    {2,NULL,0,0.0,NULL } ,
 
16
    {3,NULL,1,0.0,NULL } ,
 
17
    {20,"unassigned" ,0,0.0,&avnx[4] } ,
 
18
    {20,"threshold" ,1,0.0,&avnx[5] } ,
 
19
    {20,"minscore" ,2,0.0,&avnx[6] } ,
 
20
    {20,"maxscore" ,3,0.0,&avnx[7] } ,
 
21
    {20,"meanscore" ,4,0.0,&avnx[8] } ,
 
22
    {20,"variance" ,5,0.0,&avnx[9] } ,
 
23
    {20,"name" ,10,0.0,&avnx[10] } ,
 
24
    {20,"is-optional" ,20,0.0,&avnx[11] } ,
 
25
    {20,"other" ,255,0.0,NULL } ,
 
26
    {3,NULL,0,0.0,NULL } ,
 
27
    {3,NULL,100000,0.0,NULL } };
 
28
 
 
29
static AsnType atx[64] = {
 
30
  {401, "Pssm" ,1,0,0,0,0,1,0,0,NULL,&atx[24],&atx[1],0,&atx[16]} ,
 
31
  {0, "isProtein" ,128,0,0,0,1,0,0,0,&avnx[0],&atx[2],NULL,0,&atx[3]} ,
 
32
  {301, "BOOLEAN" ,0,1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
 
33
  {0, "identifier" ,128,1,0,1,0,0,0,0,NULL,&atx[4],NULL,0,&atx[5]} ,
 
34
  {406, "Object-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[14]} ,
 
35
  {0, "numRows" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[7]} ,
 
36
  {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
 
37
  {0, "numColumns" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[8]} ,
 
38
  {0, "rowLabels" ,128,4,0,1,0,0,0,0,NULL,&atx[11],&atx[9],0,&atx[12]} ,
 
39
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[10],NULL,0,NULL} ,
 
40
  {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
 
41
  {312, "SEQUENCE OF" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
 
42
  {0, "byRow" ,128,5,0,0,1,0,0,0,&avnx[1],&atx[2],NULL,0,&atx[13]} ,
 
43
  {0, "query" ,128,6,0,1,0,0,0,0,NULL,&atx[14],NULL,0,&atx[15]} ,
 
44
  {407, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[52]} ,
 
45
  {0, "intermediateData" ,128,7,0,1,0,0,0,0,NULL,&atx[16],NULL,0,&atx[25]} ,
 
46
  {402, "PssmIntermediateData" ,1,0,0,0,0,1,0,0,NULL,&atx[24],&atx[17],0,&atx[26]} ,
 
47
  {0, "resFreqsPerPos" ,128,0,0,1,0,0,0,0,NULL,&atx[11],&atx[18],0,&atx[19]} ,
 
48
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
 
49
  {0, "weightedResFreqsPerPos" ,128,1,0,1,0,0,0,0,NULL,&atx[11],&atx[20],0,&atx[22]} ,
 
50
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,NULL} ,
 
51
  {309, "REAL" ,0,9,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
 
52
  {0, "freqRatios" ,128,2,0,0,0,0,0,0,NULL,&atx[11],&atx[23],0,NULL} ,
 
53
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,NULL} ,
 
54
  {311, "SEQUENCE" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
 
55
  {0, "finalData" ,128,8,0,1,0,0,0,0,NULL,&atx[26],NULL,0,NULL} ,
 
56
  {403, "PssmFinalData" ,1,0,0,0,0,1,0,0,NULL,&atx[24],&atx[27],0,&atx[33]} ,
 
57
  {0, "scores" ,128,0,0,0,0,0,0,0,NULL,&atx[11],&atx[28],0,&atx[29]} ,
 
58
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
 
59
  {0, "lambda" ,128,1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,&atx[30]} ,
 
60
  {0, "kappa" ,128,2,0,0,0,0,0,0,NULL,&atx[21],NULL,0,&atx[31]} ,
 
61
  {0, "h" ,128,3,0,0,0,0,0,0,NULL,&atx[21],NULL,0,&atx[32]} ,
 
62
  {0, "scalingFactor" ,128,4,0,0,1,0,0,0,&avnx[2],&atx[6],NULL,0,NULL} ,
 
63
  {404, "PssmParameters" ,1,0,0,0,0,1,0,0,NULL,&atx[24],&atx[34],0,&atx[61]} ,
 
64
  {0, "pseudocount" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[35]} ,
 
65
  {0, "rpsdbparams" ,128,1,0,1,0,0,0,0,NULL,&atx[36],NULL,0,&atx[40]} ,
 
66
  {412, "FormatRpsDbParameters" ,1,0,0,0,0,0,0,0,NULL,&atx[24],&atx[37],0,NULL} ,
 
67
  {0, "matrixName" ,128,0,0,0,0,0,0,0,NULL,&atx[10],NULL,0,&atx[38]} ,
 
68
  {0, "gapOpen" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[39]} ,
 
69
  {0, "gapExtend" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
 
70
  {0, "constraints" ,128,2,0,1,0,0,0,0,NULL,&atx[41],NULL,0,NULL} ,
 
71
  {411, "CoreDef" ,1,0,0,0,0,0,0,0,NULL,&atx[24],&atx[42],0,&atx[36]} ,
 
72
  {0, "nblocks" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[43]} ,
 
73
  {0, "blocks" ,128,1,0,0,0,0,0,0,NULL,&atx[11],&atx[44],0,&atx[56]} ,
 
74
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[45],NULL,0,NULL} ,
 
75
  {409, "CoreBlock" ,1,0,0,0,0,0,0,0,NULL,&atx[24],&atx[46],0,&atx[58]} ,
 
76
  {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[47]} ,
 
77
  {0, "stop" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[48]} ,
 
78
  {0, "minstart" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[49]} ,
 
79
  {0, "maxstop" ,128,3,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[50]} ,
 
80
  {0, "property" ,128,4,0,1,0,0,0,0,NULL,&atx[11],&atx[51],0,NULL} ,
 
81
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[52],NULL,0,NULL} ,
 
82
  {408, "BlockProperty" ,1,0,0,0,0,0,0,0,NULL,&atx[24],&atx[53],0,&atx[45]} ,
 
83
  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[3],0,&atx[54]} ,
 
84
  {0, "intvalue" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[55]} ,
 
85
  {0, "textvalue" ,128,2,0,1,0,0,0,0,NULL,&atx[10],NULL,0,NULL} ,
 
86
  {0, "loops" ,128,2,0,0,0,0,0,0,NULL,&atx[11],&atx[57],0,NULL} ,
 
87
  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
 
88
  {410, "LoopConstraint" ,1,0,0,0,0,0,0,0,NULL,&atx[24],&atx[59],0,&atx[41]} ,
 
89
  {0, "minlength" ,128,0,0,0,1,0,0,0,&avnx[12],&atx[6],NULL,0,&atx[60]} ,
 
90
  {0, "maxlength" ,128,1,0,0,1,0,0,0,&avnx[13],&atx[6],NULL,0,NULL} ,
 
91
  {405, "PssmWithParameters" ,1,0,0,0,0,1,0,0,NULL,&atx[24],&atx[62],0,&atx[4]} ,
 
92
  {0, "pssm" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[63]} ,
 
93
  {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[33],NULL,0,NULL} };
 
94
 
 
95
static AsnModule ampx[1] = {
 
96
  { "NCBI-ScoreMat" , "scoremat.h",&atx[0],NULL,NULL,0,0} };
 
97
 
 
98
static AsnValxNodePtr avn = avnx;
 
99
static AsnTypePtr at = atx;
 
100
static AsnModulePtr amp = ampx;
 
101
 
 
102
 
 
103
 
 
104
/**************************************************
 
105
*
 
106
*    Defines for Module NCBI-ScoreMat
 
107
*
 
108
**************************************************/
 
109
 
 
110
#define PSSM &at[0]
 
111
#define PSSM_isProtein &at[1]
 
112
#define PSSM_identifier &at[3]
 
113
#define PSSM_numRows &at[5]
 
114
#define PSSM_numColumns &at[7]
 
115
#define PSSM_rowLabels &at[8]
 
116
#define PSSM_rowLabels_E &at[9]
 
117
#define PSSM_byRow &at[12]
 
118
#define PSSM_query &at[13]
 
119
#define PSSM_intermediateData &at[15]
 
120
#define PSSM_finalData &at[25]
 
121
 
 
122
#define PSSMINTERMEDIATEDATA &at[16]
 
123
#define PSSMINTERMEDIATEDATA_resFreqsPerPos &at[17]
 
124
#define PSSMINTERMEDIATEDATA_resFreqsPerPos_E &at[18]
 
125
#define PSSMINTERMEDIATEDATA_weightedResFreqsPerPos &at[19]
 
126
#define PSSMINTERMEDIATEDATA_weightedResFreqsPerPos_E &at[20]
 
127
#define PSSMINTERMEDIATEDATA_freqRatios &at[22]
 
128
#define PSSMINTERMEDIATEDATA_freqRatios_E &at[23]
 
129
 
 
130
#define PSSMFINALDATA &at[26]
 
131
#define PSSMFINALDATA_scores &at[27]
 
132
#define PSSMFINALDATA_scores_E &at[28]
 
133
#define PSSMFINALDATA_lambda &at[29]
 
134
#define PSSMFINALDATA_kappa &at[30]
 
135
#define PSSMFINALDATA_h &at[31]
 
136
#define PSSMFINALDATA_scalingFactor &at[32]
 
137
 
 
138
#define PSSMPARAMETERS &at[33]
 
139
#define PSSMPARAMETERS_pseudocount &at[34]
 
140
#define PSSMPARAMETERS_rpsdbparams &at[35]
 
141
#define PSSMPARAMETERS_constraints &at[40]
 
142
 
 
143
#define PSSMWITHPARAMETERS &at[61]
 
144
#define PSSMWITHPARAMETERS_pssm &at[62]
 
145
#define PSSMWITHPARAMETERS_params &at[63]
 
146
 
 
147
#define BLOCKPROPERTY &at[52]
 
148
#define BLOCKPROPERTY_type &at[53]
 
149
#define BLOCKPROPERTY_intvalue &at[54]
 
150
#define BLOCKPROPERTY_textvalue &at[55]
 
151
 
 
152
#define COREBLOCK &at[45]
 
153
#define COREBLOCK_start &at[46]
 
154
#define COREBLOCK_stop &at[47]
 
155
#define COREBLOCK_minstart &at[48]
 
156
#define COREBLOCK_maxstop &at[49]
 
157
#define COREBLOCK_property &at[50]
 
158
#define COREBLOCK_property_E &at[51]
 
159
 
 
160
#define LOOPCONSTRAINT &at[58]
 
161
#define LOOPCONSTRAINT_minlength &at[59]
 
162
#define LOOPCONSTRAINT_maxlength &at[60]
 
163
 
 
164
#define COREDEF &at[41]
 
165
#define COREDEF_nblocks &at[42]
 
166
#define COREDEF_blocks &at[43]
 
167
#define COREDEF_blocks_E &at[44]
 
168
#define COREDEF_loops &at[56]
 
169
#define COREDEF_loops_E &at[57]
 
170
 
 
171
#define FORMATRPSDBPARAMETERS &at[36]
 
172
#define FORMATRPSDBPARAMETERS_matrixName &at[37]
 
173
#define FORMATRPSDBPARAMETERS_gapOpen &at[38]
 
174
#define FORMATRPSDBPARAMETERS_gapExtend &at[39]