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Definitions for CPssmWithParameters

Type	Member of	File	Line
class		/include/objects/scoremat/PssmWithParameters.hpp	55
function prototype or declaration	CPssmWithParameters	/include/objects/scoremat/PssmWithParameters.hpp	60
function prototype or declaration	CPssmWithParameters	/include/objects/scoremat/PssmWithParameters.hpp	73
function definition	CPssmWithParameters	/include/objects/scoremat/PssmWithParameters.hpp	82

4 declarations in 1 files.

References to CPssmWithParameters

File	Line
/include/algo/blast/api/deltablast.hpp	103 108 147
/include/algo/blast/api/local_search.hpp	94 107
/include/algo/blast/api/prelim_stage.hpp	78 151
/include/algo/blast/api/psibl2seq.hpp	48 73 90
/include/algo/blast/api/psiblast.hpp	51 106 116 119 155
/include/algo/blast/api/pssm_engine.hpp	56 130 204 209 215 226 259 266 273 282 291 299 306 313 321
/include/algo/blast/api/remote_blast.hpp	52 127 206 368
/include/algo/blast/api/remote_search.hpp	101 117
/include/algo/blast/api/search_strategy.hpp	50 227 246
/include/algo/blast/api/traceback_stage.hpp	65 98
/include/algo/blast/api/uniform_search.hpp	272
/include/algo/blast/blastinput/blast_args.hpp	607 612 636 651
/include/algo/blast/blastinput/psiblast_args.hpp	57 60
/include/algo/blast/blastinput/tblastn_args.hpp	51 54
/include/algo/blast/format/blast_format.hpp	285
/include/algo/blast/format/blastfmtutil.hpp	96
/include/algo/blast/format/build_archive.hpp	52 92
/include/algo/blast/vdb/tblastn_vdb_args.hpp	55 58
/include/algo/blast/vdb/vdbblast_local.hpp	53 63 90
/include/algo/structure/cd_utils/cuBlast2Seq.hpp	79 80 119
/include/algo/structure/cd_utils/cuPssmMaker.hpp	143 167 168
/include/algo/structure/cd_utils/cuPssmScorer.hpp	51 61
/include/objects/blast/Blas_get_searc_resul_reply_.hpp	63 88
/include/objects/blast/Blast4_queries_.hpp	59 124
/include/objects/blast/Blast4_value_.hpp	64 155 167
/include/objects/blast/names.hpp	202
/include/objects/cdd/Cdd_.hpp	69 128
/include/objects/scoremat/PssmWithParameters.hpp	55 60 73 73 74 74 82 82
/src/algo/blast/api/blast_aux_priv.cpp	127 134
/src/algo/blast/api/blast_aux_priv.hpp	136
/src/algo/blast/api/blast_objmgr_priv.hpp	54
/src/algo/blast/api/deltablast.cpp	177 182 186 191
/src/algo/blast/api/local_blast.cpp	137
/src/algo/blast/api/local_search.cpp	149
/src/algo/blast/api/prelim_stage.cpp	70 83 94 128
/src/algo/blast/api/psibl2seq.cpp	49 57
/src/algo/blast/api/psiblast.cpp	67 83 88 101 146
/src/algo/blast/api/psiblast_aux_priv.cpp	77 240 264 288 312 338 356 374 391 409 426 440 466 485 569
/src/algo/blast/api/psiblast_aux_priv.hpp	61 82 91 135 159
/src/algo/blast/api/psiblast_impl.cpp	59 173 180 189
/src/algo/blast/api/psiblast_impl.hpp	52 70 91 94 103
/src/algo/blast/api/pssm_engine.cpp	284 339 365 375 399 411 436 624 632 632
/src/algo/blast/api/remote_blast.cpp	581 583 1156 1373
/src/algo/blast/api/remote_search.cpp	356
/src/algo/blast/api/search_strategy.cpp	337 525
/src/algo/blast/api/split_query_aux_priv.cpp	195
/src/algo/blast/api/traceback_stage.cpp	65 128
/src/algo/blast/blastinput/blast_args.cpp	1247 1336
/src/algo/blast/blastinput/psiblast_args.cpp	139 146
/src/algo/blast/blastinput/tblastn_args.cpp	155 162
/src/algo/blast/format/blast_format.cpp	1108
/src/algo/blast/format/blastfmtutil.cpp	173
/src/algo/blast/format/build_archive.cpp	190 196
/src/algo/blast/unit_tests/api/delta_unit_test.cpp	84 101 307 568
/src/algo/blast/unit_tests/api/psibl2seq_unit_test.cpp	68 137
/src/algo/blast/unit_tests/api/psiblast_unit_test.cpp	82 106 184 590 1112 1157 1217
/src/algo/blast/unit_tests/api/pssmcreate_cdd_unit_test.cpp	812 934 1015
/src/algo/blast/unit_tests/api/pssmcreate_unit_test.cpp	611 808
/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.cpp	135
/src/algo/blast/unit_tests/api/search_strategy_unit_test.cpp	205
/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.cpp	368 369
/src/algo/blast/vdb/tblastn_vdb_args.cpp	148 155
/src/algo/blast/vdb/vdbblast_local.cpp	225 272 288 292 381 754 762 806
/src/algo/structure/cd_utils/cuBlast2Seq.cpp	114 119
/src/algo/structure/cd_utils/cuCdUpdater.cpp	485
/src/algo/structure/cd_utils/cuPssmMaker.cpp	354 371 400 426 426 664
/src/algo/structure/cd_utils/cuPssmScorer.cpp	45
/src/algo/structure/struct_util/su_pssm.cpp	441 522
/src/app/blast/blast_app_util.cpp	89 268 323 376 377 640 787
/src/app/blast/blast_app_util.hpp	116 117 266 267 285
/src/app/blast/blast_formatter.cpp	91 170 436
/src/app/blast/deltablast_app.cpp	82 96 128 151 171 303 520 570 582
/src/app/blast/psiblast_app.cpp	82 96 103 110 149 168 184 195 329 385 450
/src/app/blast/tblastn_app.cpp	198
/src/app/blast/tblastn_node.cpp	112
/src/app/blastdb/makeprofiledb.cpp	252 259 260 262 263 266 272 617 821 841 878 906 931 1000 1049 1425 1567 1626
/src/app/blastvdb/blast_formatter_vdb.cpp	85 168
/src/app/blastvdb/tblastn_vdb.cpp	205
/src/app/cn3d/alignment_manager.cpp	233
/src/app/cn3d/cn3d_blast.cpp	327 330
/src/app/cn3d/cn3d_pssm.cpp	268
/src/app/cn3d/cn3d_pssm.hpp	58 73
/src/objects/blast/Blas_get_searc_resul_reply_.cpp	161
/src/objects/blast/Blast4_queries_.cpp	79 160
/src/objects/blast/Blast4_value_.cpp	143 470 482
/src/objects/blast/names.cpp	410 414
/src/objects/cdd/Cdd_.cpp	461
/src/objects/scoremat/NCBI_ScoreMat_module.cpp	68
/src/objects/scoremat/PssmWithParameters.cpp	50 55 61 67
/src/objects/scoremat/PssmWithParameters_.cpp	89

288 references in 90 files.