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Definitions for Begin

Type Member of File Line
function definition CPhyTreeNodeGroupper /include/algo/phy_tree/phytree_format/phytree_simplify.hpp 80
function definition CPhyTreeLabelTracker /include/algo/phy_tree/phytree_format/phytree_simplify.hpp 119
function definition CPhyTreeNodeAnalyzer /include/algo/phy_tree/phytree_format/phytree_simplify.hpp 195
function prototype or declaration IMacroBioDataIter /include/gui/objutils/macro_biodata_iter.hpp 91
function prototype or declaration CMacroBioData_FeatIterBase /include/gui/objutils/macro_biodata_iter.hpp 267
function prototype or declaration CMacroBioData_FeatIntervalIter /include/gui/objutils/macro_biodata_iter.hpp 334
function prototype or declaration CMacroBioData_BioSourceIter /include/gui/objutils/macro_biodata_iter.hpp 377
function prototype or declaration CMacroBioData_PubdescIter /include/gui/objutils/macro_biodata_iter.hpp 431
function prototype or declaration CMacroBioData_SeqdescIter /include/gui/objutils/macro_biodata_iter.hpp 517
function prototype or declaration CMacroBioData_MolInfoIter /include/gui/objutils/macro_biodata_iter.hpp 560
function prototype or declaration CMacroBioData_UserObjectIter /include/gui/objutils/macro_biodata_iter.hpp 597
function prototype or declaration CMacroBioData_StructCommentIter /include/gui/objutils/macro_biodata_iter.hpp 632
function prototype or declaration CMacroBioData_DBLinkIter /include/gui/objutils/macro_biodata_iter.hpp 655
function prototype or declaration CMacroBioData_AutodefOptsIter /include/gui/objutils/macro_biodata_iter.hpp 678
function prototype or declaration CMacroBioData_SeqAlignIter /include/gui/objutils/macro_biodata_iter.hpp 699
function prototype or declaration CMacroBioData_SeqIter /include/gui/objutils/macro_biodata_iter.hpp 736
function prototype or declaration CMacroBioData_SeqNAIter /include/gui/objutils/macro_biodata_iter.hpp 777
function prototype or declaration CMacroBioData_SeqAAIter /include/gui/objutils/macro_biodata_iter.hpp 786
function prototype or declaration CMacroBioData_SeqSetIter /include/gui/objutils/macro_biodata_iter.hpp 799
function prototype or declaration CMacroBioData_TSEntryIter /include/gui/objutils/macro_biodata_iter.hpp 836
function prototype or declaration CGlDisplayList /include/gui/opengl/gldlist.hpp 75
function prototype or declaration CGlRenderDebug /include/gui/opengl/glrender.hpp 335
function prototype or declaration IRender /include/gui/opengl/irender.hpp 161
function prototype or declaration CRenderCommon /include/gui/opengl/render_common.hpp 67
function prototype or declaration /include/gui/widgets/seq_graphic/rendering_ctx.hpp 705
function prototype or declaration /include/gui/widgets/seq_graphic/rendering_ctx.hpp 721
function prototype or declaration /include/gui/widgets/seq_graphic/rendering_ctx.hpp 729
function definition GenericArray /include/misc/jsonwrapp/rapidjson11/document.h 2578
function prototype or declaration CSeqMap /include/objmgr/seq_map.hpp 122
function prototype or declaration CSeqDB /include/objtools/blast/seqdb_reader/seqdb.hpp 952
function definition CWriteDB_PackedSemiTree /include/objtools/blast/seqdb_writer/writedb_general.hpp 488
function definition /include/serial/iterator.hpp 1004
function definition /include/serial/iterator.hpp 1019
function definition /include/serial/iterator.hpp 1027
function definition /include/serial/iterator.hpp 1042
function prototype or declaration CSyncQueue_ConstAccessGuard /include/util/sync_queue.hpp 672
function prototype or declaration CSyncQueue_AccessGuard /include/util/sync_queue.hpp 793
function definition CSyncQueue_ConstAccessGuard /include/util/sync_queue.hpp 2216
function definition CSyncQueue_AccessGuard /include/util/sync_queue.hpp 2309
macro (un)definition /src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp 1774
function definition CLadderContainer /src/algo/ms/omssa/msladder.cpp 324
function prototype or declaration CLadderContainer /src/algo/ms/omssa/msladder.hpp 493
function prototype or declaration /src/algo/ms/omssa/mspeak.cpp 166
function prototype or declaration /src/algo/ms/omssa/omssamerge.cpp 171
macro (un)definition /src/algo/phy_tree/lex.newick.cpp 97
function prototype or declaration CReadBlastApp /src/app/read_blast_result/read_blast_result.hpp 426
function definition CAnyAffinityJob /src/connect/services/netschedule_api_getjob.cpp 81
function definition CMostAffinityJob /src/connect/services/netschedule_api_getjob.cpp 115
function prototype or declaration /src/gui/graph/regular_grid.cpp 250
function prototype or declaration /src/gui/graph/regular_grid.cpp 266
function prototype or declaration /src/gui/objutils/macro_engine.cpp 402
function prototype or declaration /src/gui/objutils/macro_engine_parallel.cpp 832
function prototype or declaration /src/gui/objutils/macro_engine_parallel.cpp 945
function prototype or declaration /src/gui/objutils/test_macro/unit_test_field_resolver.cpp 86
function prototype or declaration /src/gui/opengl/MTLTextureGlyph.cpp 160
function definition CGlDisplayList /src/gui/opengl/gldlist.cpp 61
function prototype or declaration /src/gui/opengl/gldlist.cpp 106
function definition CGlRenderDebug /src/gui/opengl/glrender.cpp 486
function definition CRenderCommon /src/gui/opengl/render_common.cpp 305
function prototype or declaration /src/gui/packages/pkg_snp/ld/ld_glyph.cpp 164
function prototype or declaration /src/gui/widgets/aln_crossaln/cross_panel_ir.cpp 413
function prototype or declaration /src/gui/widgets/aln_crossaln/cross_panel_ir.cpp 454
function prototype or declaration /src/gui/widgets/aln_crossaln/cross_panel_ir.cpp 459
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 1382
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 1412
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 1482
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 1513
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 1606
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 2128
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 2415
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 2436
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 2493
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 2525
function prototype or declaration /src/gui/widgets/aln_multiple/align_row.cpp 2617
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header.cpp 139
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header.cpp 147
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header.cpp 157
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header.cpp 188
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header.cpp 197
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header_handler.cpp 577
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header_handler.cpp 605
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header_handler.cpp 639
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_header_handler.cpp 673
function prototype or declaration /src/gui/widgets/aln_multiple/alnmulti_renderer.cpp 224
function prototype or declaration /src/gui/widgets/aln_multiple/feature_graph.cpp 975
function prototype or declaration /src/gui/widgets/aln_multiple/trace_graph.cpp 458
function prototype or declaration /src/gui/widgets/aln_multiple/trace_graph.cpp 663
function prototype or declaration /src/gui/widgets/aln_multiple/trace_graph.cpp 747
function prototype or declaration /src/gui/widgets/gl/demo_wx/gl_demo_dlg.cpp 143
function prototype or declaration /src/gui/widgets/gl/demo_wx/gl_demo_dlg.cpp 151
function prototype or declaration /src/gui/widgets/gl/linear_sel_handler.cpp 501
function prototype or declaration /src/gui/widgets/gl/linear_sel_handler.cpp 541
function prototype or declaration /src/gui/widgets/gl/linear_sel_handler.cpp 560
function prototype or declaration /src/gui/widgets/gl/minimap_handler.cpp 200
function prototype or declaration /src/gui/widgets/gl/minimap_handler.cpp 213
function prototype or declaration /src/gui/widgets/gl/minimap_handler.cpp 222
function prototype or declaration /src/gui/widgets/gl/minimap_handler.cpp 229
function prototype or declaration /src/gui/widgets/gl/mouse_zoom_handler.cpp 183
function prototype or declaration /src/gui/widgets/gl/mouse_zoom_handler.cpp 201
function prototype or declaration /src/gui/widgets/gl/mouse_zoom_handler.cpp 280
function prototype or declaration /src/gui/widgets/gl/mouse_zoom_handler.cpp 331
function prototype or declaration /src/gui/widgets/gl/mouse_zoom_handler.cpp 364
function prototype or declaration /src/gui/widgets/gl/mouse_zoom_handler.cpp 373
function prototype or declaration /src/gui/widgets/gl/ruler.cpp 733
function prototype or declaration /src/gui/widgets/gl/ruler.cpp 1018
function prototype or declaration /src/gui/widgets/gl/ruler.cpp 1135
function prototype or declaration /src/gui/widgets/gl/ruler.cpp 1219
function prototype or declaration /src/gui/widgets/gl/seqmark_handler.cpp 349
function prototype or declaration /src/gui/widgets/gl/seqmark_handler.cpp 463
function prototype or declaration /src/gui/widgets/hit_matrix/hit_matrix_graph.cpp 487
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_node.cpp 792
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_node.cpp 832
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_render.cpp 239
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_render.cpp 286
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_render.cpp 316
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_render.cpp 549
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_render.cpp 693
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_render.cpp 706
function prototype or declaration /src/gui/widgets/phylo_tree/phylo_tree_render.cpp 766
function prototype or declaration /src/gui/widgets/phylo_tree/tree_graphics_model.cpp 978
function prototype or declaration /src/gui/widgets/seq_graphic/feature_panel.cpp 886
function prototype or declaration /src/gui/widgets/seq_graphic/histogram_glyph.cpp 1358
function prototype or declaration /src/gui/widgets/seq_graphic/histogram_glyph.cpp 1385
function prototype or declaration /src/gui/widgets/seq_graphic/histogram_glyph.cpp 1542
function prototype or declaration /src/gui/widgets/seq_graphic/layout_track_impl.cpp 645
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 180
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 225
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 347
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 392
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 400
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 416
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 441
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 491
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 548
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 586
function prototype or declaration /src/gui/widgets/seq_graphic/rendering_ctx.cpp 644
function prototype or declaration /src/gui/widgets/seq_graphic/seqgraphic_pane.cpp 1265
function prototype or declaration /src/gui/widgets/seq_graphic/trace_glyph.cpp 334
function prototype or declaration /src/gui/widgets/seq_graphic/trace_glyph.cpp 485
function prototype or declaration /src/gui/widgets/seq_graphic/trace_glyph.cpp 566
function prototype or declaration /src/gui/widgets/seq_text/seq_graph.cpp 125
function prototype or declaration /src/gui/widgets/seq_text/seq_graph.cpp 176
function prototype or declaration /src/gui/widgets/seq_text/seq_text_pane.cpp 806
function prototype or declaration /src/gui/widgets/seq_text/seq_text_pane.cpp 985
macro (un)definition /src/objects/valerr/ValidErrItem.cpp 2444
function definition CSeqDB /src/objtools/blast/seqdb_reader/seqdb.cpp 723
function prototype or declaration CProcessor /src/objtools/data_loaders/genbank/id1/reader_id1.cpp 722
function prototype or declaration CProcessor /src/objtools/data_loaders/genbank/id1/reader_id1.cpp 787
function prototype or declaration /src/serial/test/test_serial.cpp 731
function prototype or declaration /src/serial/test/test_serial.cpp 738
function prototype or declaration /src/serial/test/test_serial.cpp 771
function prototype or declaration /src/serial/test/test_serial.cpp 785
function definition CMurmurHash2A /src/util/checksum/murmurhash/MurmurHash2.cxx 265

153 declarations in 60 files.

References to Begin

File Line
/include/algo/phy_tree/phytree_format/phytree_simplify.hpp 80 119 195
/include/corelib/ncbimisc.hpp 800 802 804 804
/include/gui/objutils/macro_biodata_iter.hpp 91 267 334 377 431 517 560 597 632 655 678 699 736 777 786 799 836
/include/gui/opengl/gldlist.hpp 75
/include/gui/opengl/glrender.hpp 335
/include/gui/opengl/irender.hpp 161
/include/gui/opengl/render_common.hpp 67
/include/gui/widgets/seq_graphic/rendering_ctx.hpp 705 721 729
/include/misc/jsonwrapp/jsonwrapp11.hpp 1607 1614
/include/misc/jsonwrapp/rapidjson11/document.h 1577 1583 1583 1698 1701 1701 1863 2578 2578 2592
/include/misc/jsonwrapp/rapidjson11/pointer.h 749
/include/misc/jsonwrapp/rapidjson11/schema.h 394 401 437 445 484 502 536 952 1900
/include/objmgr/seq_map.hpp 122
/include/objtools/alnmgr/aln_asn_reader.hpp 118 122 130 133 147 148 156 157 165 166 174
/include/objtools/blast/seqdb_reader/seqdb.hpp 952
/include/objtools/blast/seqdb_writer/writedb_general.hpp 488
/include/objtools/eutils/efetch/PubmedArticle.hpp 158
/include/serial/iterator.hpp 1004 1019 1027 1042
/include/util/sync_queue.hpp 672 793 2216 2245 2309 2338
/src/algo/blast/api/msa_pssm_input.cpp 189
/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp 2664 2690
/src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp 1774 1813 1816 1936 1940 2007 2011 3026
/src/algo/ms/omssa/msladder.cpp 324
/src/algo/ms/omssa/msladder.hpp 493
/src/algo/ms/omssa/mspeak.cpp 166
/src/algo/ms/omssa/omssa.cpp 453 503 531 1264 1292
/src/algo/ms/omssa/omssamerge.cpp 171 182 183
/src/algo/phy_tree/lex.newick.cpp 97 702 747 1512 1523 1655
/src/algo/phy_tree/phytree_format/phytree_format.cpp 380 389 589 657
/src/algo/seqqa/demo/demo_seqtest.cpp 141
/src/algo/seqqa/single_aln_tests.cpp 652
/src/algo/sequence/demo/regexplocdemo.cpp 116
/src/algo/sequence/project_exons.cpp 1823
/src/algo/sequence/unit_test/unit_test_gap_analysis.cpp 126
/src/app/blastdb/makeblastdb.cpp 465 471 479 489
/src/app/id2_fetch/id2_fetch_simple.cpp 740
/src/app/oligofar/cseqvecprocessor.hpp 131
/src/app/pubseq_gateway/server/osg_connection.cpp 233
/src/app/read_blast_result/collect_simple.cpp 42 66 310
/src/app/read_blast_result/copy_loc.cpp 44 60 80
/src/app/read_blast_result/problems.cpp 259 276 305 720
/src/app/read_blast_result/read_blast.cpp 59 380 551
/src/app/read_blast_result/read_blast_result.hpp 426
/src/app/read_blast_result/read_blast_result_lib.cpp 665 667 668 670
/src/app/read_blast_result/shortcuts.cpp 38 51
/src/build-system/configure 38762
/src/connect/services/netschedule_api_getjob.cpp 81 115 217 229 240
/src/gui/framework/app_task_service.cpp 126 332 440
/src/gui/graph/regular_grid.cpp 250 266
/src/gui/objutils/attached_handles.cpp 136
/src/gui/objutils/macro_biodata_iter.cpp 504 686 822 1005 1133 1421 1555 1638 1709 1765 1921 2028 2132 2152 2176 2277
/src/gui/objutils/macro_engine.cpp 402
/src/gui/objutils/macro_engine_parallel.cpp 832 945
/src/gui/objutils/test_macro/unit_test_field_resolver.cpp 86
/src/gui/opengl/MTLTextureGlyph.cpp 160
/src/gui/opengl/gldlist.cpp 61 106
/src/gui/opengl/glrender.cpp 486
/src/gui/opengl/render_common.cpp 125 134 305
/src/gui/packages/pkg_sequence_edit/subprep_util.cpp 1963
/src/gui/packages/pkg_snp/ld/ld_glyph.cpp 164
/src/gui/widgets/aln_crossaln/cross_panel_ir.cpp 413 454 459
/src/gui/widgets/aln_multiple/align_row.cpp 1382 1412 1482 1513 1606 2128 2415 2436 2493 2525 2617
/src/gui/widgets/aln_multiple/alnmulti_header.cpp 139 147 157 188 197
/src/gui/widgets/aln_multiple/alnmulti_header_handler.cpp 577 605 639 673
/src/gui/widgets/aln_multiple/alnmulti_renderer.cpp 224
/src/gui/widgets/aln_multiple/feature_graph.cpp 975
/src/gui/widgets/aln_multiple/trace_graph.cpp 458 663 747
/src/gui/widgets/gl/demo_wx/gl_demo_dlg.cpp 143 151
/src/gui/widgets/gl/linear_sel_handler.cpp 501 541 560
/src/gui/widgets/gl/minimap_handler.cpp 200 213 222 229
/src/gui/widgets/gl/mouse_zoom_handler.cpp 183 201 280 331 364 373
/src/gui/widgets/gl/ruler.cpp 733 1018 1135 1219
/src/gui/widgets/gl/seqmark_handler.cpp 349 463
/src/gui/widgets/hit_matrix/hit_matrix_graph.cpp 487 555 625 671 681 693 727
/src/gui/widgets/phylo_tree/phylo_tree_node.cpp 792 832
/src/gui/widgets/phylo_tree/phylo_tree_render.cpp 239 286 316 549 693 706 766
/src/gui/widgets/phylo_tree/tree_graphics_model.cpp 362 978
/src/gui/widgets/seq_graphic/alignment_glyph.cpp 2152 2354 2370
/src/gui/widgets/seq_graphic/feature_panel.cpp 886
/src/gui/widgets/seq_graphic/histogram_glyph.cpp 1253 1358 1385 1495 1542 1604 1607 1651 1785
/src/gui/widgets/seq_graphic/layout_track_impl.cpp 645
/src/gui/widgets/seq_graphic/rendering_ctx.cpp 180 225 347 392 400 416 441 491 548 586 644 754 823 898 922 968 1018 1048 1116 1221
/src/gui/widgets/seq_graphic/segment_smear_glyph.cpp 155
/src/gui/widgets/seq_graphic/seqgraphic_pane.cpp 1265 1474
/src/gui/widgets/seq_graphic/trace_glyph.cpp 334 485 566
/src/gui/widgets/seq_text/seq_graph.cpp 125 176
/src/gui/widgets/seq_text/seq_text_pane.cpp 806 985
/src/misc/hgvs/hgvs_parser.cpp 1488
/src/misc/hgvs/hgvs_parser2.cpp 345 2050 2101
/src/misc/hgvs/hgvs_writer2.cpp 213 829 868
/src/misc/hgvs/test/hgvs2variation.cpp 204 235 392
/src/misc/hgvs/test/test_hgvs_parser_app.cpp 81
/src/misc/hgvs/variation_util.cpp 106 183 1607 1623
/src/misc/hgvs/variation_util2.cpp 117 770 1089 2239 3360 3469 3981 4711
/src/objects/general/test/test_uoconv.cpp 62 64
/src/objects/mmdb1/Biostruc.cpp 66
/src/objects/ncbimime/Ncbi_mime_asn1.cpp 66
/src/objects/valerr/ValidErrItem.cpp 2444
/src/objmgr/seq_map.cpp 799 820
/src/objmgr/test/unit_test_objmgr.cpp 630
/src/objmgr/util/seq_loc_util.cpp 575
/src/objmgr/util/unit_test/unit_test_fasta_ostream.cpp 570
/src/objtools/blast/seqdb_reader/seqdb.cpp 723
/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp 2778 2779
/src/objtools/blast/seqdb_writer/writedb_isam.cpp 308
/src/objtools/cleanup/test/test_cases/+run_tests 392 413 416
/src/objtools/data_loaders/genbank/id1/reader_id1.cpp 722 787
/src/objtools/data_loaders/genbank/processors.cpp 914 1131 1444 1592 1654 1674 1746
/src/objtools/data_loaders/genbank/reader_id2_base.cpp 2011 2038
/src/objtools/data_loaders/genbank/reader_snp.cpp 287 305
/src/objtools/data_loaders/genbank/request_result.cpp 560
/src/objtools/flatfile/asci_blk.cpp 2768 3138 3143 3208 3213 3265 3270 3364 3383 3430 3438 3529
/src/objtools/flatfile/citation.cpp 312 320 330 335
/src/objtools/flatfile/fcleanup.cpp 82 413 417 517
/src/objtools/flatfile/ftanet.cpp 730 740
/src/objtools/flatfile/gb_ascii.cpp 2326 2357
/src/objtools/flatfile/genref.cpp 2621 2625 2891 2896 2969
/src/objtools/flatfile/nucprot.cpp 293 1498 1599 2356 2367 2573 2629 2666
/src/objtools/flatfile/utilfeat.cpp 318 323 427
/src/objtools/readers/unit_test/unit_test_agp_converter.cpp 159
/src/objtools/test/objmgr/id64_unit_test.cpp 589 1322
/src/objtools/test/objmgr/id_unit_test.cpp 709
/src/objtools/writers/agp_write.cpp 162
/src/sample/app/alnmgr/alnmgr_sample.cpp 131
/src/serial/test/test_serial.cpp 729 731 733 736 738 758 767 771 774 785 788 829
/src/sra/data_loaders/csra/test/test_csra_loader.cpp 2043 2056 2125 2138 2220 2233 2314 2327 2410 2423
/src/sra/readers/sra/test/sra_test.cpp 130
/src/sra/readers/sra/test/vdb_test.cpp 978
/src/sra/readers/sra/wgsread.cpp 3753
/src/util/checksum/murmurhash/MurmurHash2.cxx 265
/src/util/test/test_queue_mt.cpp 204 230 237 289 304
/src/util/thread_pool.cpp 862 1763 1870 1949

429 references in 132 files.