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Definitions for GetSegs

Type	Member of	File	Line
function prototype or declaration	CSeq_align_Base	/include/objects/seqalign/Seq_align_.hpp	292
function definition	CSeq_align_Base	/include/objects/seqalign/Seq_align_.hpp	589
function prototype or declaration	CSeq_align_Handle	/include/objmgr/seq_align_handle.hpp	95
function definition	CSeq_align_Handle	/include/objmgr/seq_align_handle.hpp	197
function prototype or declaration		/src/algo/align/util/align_filter.cpp	482

5 declarations in 3 files.

References to GetSegs

File	Line
/include/gui/objutils/density_map.hpp	582 586 588 589 641 648 661
/include/objects/seqalign/Seq_align_.hpp	292 589
/include/objects/seqalign/seqalign_macros.hpp	90 98 99 110 111 122 123
/include/objmgr/seq_align_handle.hpp	95 197 199
/include/objtools/alnmgr/aln_converters.hpp	285 375
/include/objtools/alnmgr/seqids_extractor.hpp	121
/src/algo/align/advanced_cleanup/advanced_cleanup.cpp	734 797
/src/algo/align/contig_assembly/contig_assembly.cpp	195 197 210 223 644 645 646 647 729 731 732 733 922
/src/algo/align/mergetree/equiv_range.cpp	760 762 768
/src/algo/align/mergetree/merge_tree.cpp	857 859
/src/algo/align/ngalign/alignment_scorer.cpp	87 105 107 335 338 343 413 505 763 765
/src/algo/align/ngalign/banded_aligner.cpp	79 651
/src/algo/align/ngalign/inversion_merge_aligner.cpp	266 267 284 285
/src/algo/align/ngalign/result_set.cpp	343 343 346 346 402 404 408 410 438 439
/src/algo/align/ngalign/unordered_spliter.cpp	187 476 478 534 539 549 550
/src/algo/align/prosplign/Info.cpp	599 600 604
/src/algo/align/prosplign/prosplign.cpp	1220 1244
/src/algo/align/splign/splign.cpp	1313 3297 3298 3350
/src/algo/align/splign/unit_test/unit_test_splign.cpp	120
/src/algo/align/util/align_compare.cpp	85 88 96 152 209 210 211 212 213 281 289 296 305 329 330 331 337 338 342 904 907 938 949
/src/algo/align/util/align_filter.cpp	482 711 716 721 726 731 736 741
/src/algo/align/util/align_shadow.cpp	57 74 75 120
/src/algo/align/util/align_sort.cpp	118 126 127 130 131 132 133
/src/algo/align/util/best_placement.cpp	263 269 314 315 366 369 387 444 446 459 463 496 500 527 533 544 548 579 580 582
/src/algo/align/util/blast_tabular.cpp	54
/src/algo/align/util/named_collection_score_impl.cpp	155 188 188 385 406
/src/algo/align/util/patch_sequence.cpp	313 321
/src/algo/align/util/score_builder.cpp	190 193 196 201 201 211 223 374 386 691 697 833 837 843 849 853
/src/algo/align/util/score_lookup.cpp	123 179 180 269 270 271 272 306 307 311 312 316 319 320 330 355 358 509 510 667 668 700 701 703 825 827 1060 1172 1316 1318 1327 1328 1555 1561 1671 1672 1679
/src/algo/align/util/tabular_fmt.cpp	581 584 607 646 649 656 1388 1390 1413 1747 1749 1753 1754 1991 1992 2076 2082 2083 2084 2450
/src/algo/align/util/unit_test/score_builder_unit_test.cpp	122 221 230 240 259 268 289 310 351 372 399 400
/src/algo/blast/api/blast_results.cpp	370 463 466 469
/src/algo/blast/api/cdd_pssm_input.cpp	162
/src/algo/blast/api/magicblast.cpp	476 476 588 588 589 590 591 592 607 607 617 617 618 619 620 621 636 636 670 675
/src/algo/blast/api/psi_pssm_input.cpp	248 258 271 317
/src/algo/blast/api/repeats_filter_cxx.cpp	148 149
/src/algo/blast/format/blastxml2_format.cpp	161 170 174 175 216 354 355 442 443 444 445 446 447 485
/src/algo/blast/format/blastxml_format.cpp	173 182 186 187 228 362 363 433 434 435 436 437 438 474
/src/algo/blast/format/sam.cpp	69
/src/algo/blast/igblast/igblast.cpp	217 221 222 223 230 231 238 239 240 247 248 302 308 314 322 328 337 338 343 1245 1264 1281 1301 1523 1678 1709 1736
/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp	129 592 643 676 677 703 704 732 796 1491 1492 1507 1635 1651 1698 1708 1717 1887 1913 1926 1937 1994 2047 2067 2082 2144 2173 2190 2206 2212 2226 2233 2251 2258 2276 2282 2313 2317 2319 2323 2325 2329 2361 2365 2613 3269 3292 3523 3537 3551 3589
/src/algo/blast/unit_tests/api/blast_test_util.cpp	103 106
/src/algo/blast/unit_tests/api/magicblast_unit_test.cpp	310 316 499 500 502 504 511
/src/algo/blast/unit_tests/api/psibl2seq_unit_test.cpp	163 165 195 197
/src/algo/blast/unit_tests/api/pssmcreate_cdd_unit_test.cpp	606
/src/algo/blast/unit_tests/api/pssmcreate_unit_test.cpp	699
/src/algo/blast/unit_tests/api/rps_unit_test.cpp	116 117 230
/src/algo/blast/unit_tests/api/seqalign_set_convert.cpp	135
/src/algo/cobalt/blast.cpp	241 244 263 268 416 419 438 442
/src/algo/cobalt/cobalt.cpp	315 322
/src/algo/cobalt/rps.cpp	456 777
/src/algo/cobalt/seq.cpp	278
/src/algo/cobalt/unit_test/cobalt_unit_test.cpp	829 833 1034 1035 1036 1038 1039 1054 1066 1078 1090
/src/algo/cobalt/unit_test/seq_unit_test.cpp	89
/src/algo/gnomon/gnomon_objmgr.cpp	76 82
/src/algo/id_mapper/app/id_mapper_app.cpp	558 566 650
/src/algo/phy_tree/phytree_calc.cpp	632
/src/algo/phy_tree/unit_test/phytree_calc_unit_test.cpp	709 712 742 745 747 752 784
/src/algo/primer/primercheck.cpp	490 749 1290 2012
/src/algo/seqqa/blastp_tests.cpp	114 133 160
/src/algo/seqqa/single_aln_tests.cpp	76 77 183 185 196 409 869
/src/algo/sequence/align_cleanup.cpp	127 129 427 428 464 464 465 519 520 527
/src/algo/sequence/gene_model.cpp	386 430 479 534 535 535 558 603 604 616 670 673 679 681 732 1333 1334 2248 2249 2351 2352 2770 2779 2811 2820 2823 2876 2878 2879 2880 3137 3138 4140 4144 4148
/src/algo/sequence/internal_stops.cpp	118 280 286
/src/algo/sequence/project_exons.cpp	135 173 179 180 191 192 220 229 1338 1372 1382 1525
/src/algo/sequence/transform_align.cpp	431 490 760
/src/algo/sequence/unit_test/unit_test_gene_model.cpp	552 621 623 702 704 770 772 830 832 911 913 1025 1026 1055 1061 1151 1152 1181 1187 1278 1280 1285 1362 1364 1369 1450 1452 1457
/src/algo/structure/cd_utils/cuAlign.cpp	66 68 69 383 384 440 441 622 624 687 689 691 708 710 793 794 796 813 814 820 821
/src/algo/structure/cd_utils/cuCdCore.cpp	769 1214 1215 1250 1251
/src/algo/structure/cd_utils/cuCdUpdater.cpp	607
/src/algo/structure/struct_util/su_alignment_set.cpp	74 74 90 91 92 93 94 95 108 109 110 111 112 113 211 212 213 214 215 216 243 245 246 279 281
/src/app/cn3d/alignment_manager.cpp	121 122 123
/src/app/cn3d/alignment_set.cpp	142 143 144 145 146 147 175 177 178 219 221
/src/app/cn3d/cn3d_blast.cpp	412 415
/src/app/cn3d/data_manager.cpp	255 255 928 931
/src/app/cn3d/structure_set.cpp	322 323 324 325 326 327 342 343 344 345 346 347
/src/app/hfilter/hitfilter_app.cpp	297
/src/app/magicblast/magicblast_util.cpp	448 450 490 501 503 504 1034 1036 1038 1095 1096 1238 1239 1286 1287 1703
/src/app/table2asn/feature_table_reader.cpp	1459 1462
/src/gui/core/prj_helper.cpp	67
/src/gui/objutils/alignment_smear.cpp	183 184 187 188 190
/src/gui/objutils/basic_converters.cpp	353 356 373
/src/gui/objutils/convert_raw_to_delta.cpp	200 201 1041 1129
/src/gui/objutils/fingp_seqalign.cpp	341
/src/gui/objutils/label.cpp	2308 2335 2363 2366 2405 2430 2435 2438 2573 2586 2599 2608 2609 2650 2656
/src/gui/objutils/macro_fn_do.cpp	1540
/src/gui/objutils/report_trim.cpp	503 506 571 605
/src/gui/objutils/sparse_functions.cpp	103
/src/gui/objutils/utils.cpp	1020 1021 1029 1211 1212 1222 1231 1813
/src/gui/packages/pkg_alignment/align_span_view.cpp	323 327 328
/src/gui/packages/pkg_alignment/align_tab_export_job.cpp	106 111 114
/src/gui/packages/pkg_alignment/blast_seq_tool_job.cpp	608 610
/src/gui/packages/pkg_alignment/cleanup_alignments_tool_manager.cpp	303 305
/src/gui/packages/pkg_alignment/multi_align_view.cpp	262 263 270 271
/src/gui/packages/pkg_alignment/prosplign_tool.cpp	487 629 630 631
/src/gui/packages/pkg_alignment/tree_builder_tool.cpp	227 228
/src/gui/packages/pkg_sequence_edit/apply_rna_its_dlg.cpp	349 365 366 1009 1009 1010 1037
/src/gui/packages/pkg_sequence_edit/convert_selected_gaps.cpp	583 584 584 587 588
/src/gui/packages/pkg_sequence_edit/create_seq_hist_for_tpa.cpp	485 486 486 489 490
/src/gui/packages/pkg_sequence_edit/dll_register.cpp	1173
/src/gui/packages/pkg_sequence_edit/edit_seq_ends_with_align.cpp	302 304 305
/src/gui/packages/pkg_sequence_edit/edit_seq_id.cpp	797 807 814
/src/gui/packages/pkg_sequence_edit/far_pointer_seq.cpp	279 280 561 562 562 569 570
/src/gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.cpp	562 563 563 566 567 571 572 576 577
/src/gui/packages/pkg_sequence_edit/recompute_intervals.cpp	92 96 105
/src/gui/packages/pkg_sequence_edit/remove_sequences_from_alignments.cpp	287 290 290 294 297 297 305 308 308 313 314 315 316 320 322 322 343 346 346 350 352 359 359 373 373 377 377 382 383 384 385 389 392 392 399 431 432 432 434 438 438 446 446 448 455 455 456 456 462 462 467 467 475 475 478 478 483 484 492 493 499 499 507 507 508 508 513 514
/src/gui/packages/pkg_sequence_edit/subprep_util.cpp	783 786 796
/src/gui/packages/pkg_sequence_edit/update_align.cpp	199 269 304
/src/gui/packages/pkg_sequence_edit/update_seq.cpp	545
/src/gui/packages/pkg_sequence_edit/update_seq_panel.cpp	948 949
/src/gui/widgets/aln_multiple/alnmulti_ds_builder.cpp	310
/src/gui/widgets/aln_multiple/build_alnvec_job.cpp	374 375
/src/gui/widgets/aln_table/aln_table_ds.cpp	121 122
/src/gui/widgets/aln_table/alnspan_vertmodel.cpp	127 129
/src/gui/widgets/edit/alignment_assistant.cpp	561 563 605 607 747 793 909 1548 1710 1759 1763 1763 1771 1773 1780 1780 1781 1781 1787 1787 1792 1792 1800 1800 1803 1803 1807 1808
/src/gui/widgets/edit/assembly_tracking_panel.cpp	351 352 352 355 356
/src/gui/widgets/edit/cds_translation_panel.cpp	1264 1268 1271 1278 1279 1287 1288 1296
/src/gui/widgets/edit/edit_object_feature_propagate.cpp	326
/src/gui/widgets/edit/paint_alignment.cpp	143 145 224 313
/src/gui/widgets/edit/vectortrimpanel.cpp	1051 1209 1452 1455
/src/gui/widgets/hit_matrix/dense_ds.cpp	220 232 244 430 474 733 758 760 790 793
/src/gui/widgets/hit_matrix/dense_hit.cpp	86 87
/src/gui/widgets/hit_matrix/std_seg_hit.cpp	91 95
/src/gui/widgets/object_list/text_item_seq_align.cpp	57 68
/src/gui/widgets/seq_graphic/alignment_glyph.cpp	854 857 2491
/src/gui/widgets/seq_graphic/alignment_job.cpp	358 359 443 2100 2108 2194 2195 2196 2199 2199 2201 2217 2217 2223 2403 2404
/src/gui/widgets/seq_graphic/denseg_ci.cpp	83 173
/src/gui/widgets/seq_graphic/denseg_graphic_ds.cpp	70 72 74
/src/gui/widgets/seq_graphic/gui_object_info_seq_align.cpp	90 95 98 107 110 133 140 554 556
/src/misc/hgvs/hgvs_parser2.cpp	811
/src/misc/hgvs/objcoords.cpp	334 726 739
/src/misc/hgvs/variation_util.cpp	159 171 480 480 481 506 507
/src/misc/hgvs/variation_util2.cpp	267 277 505 506 508 531 532 3526
/src/objects/seq/seq_align_mapper_base.cpp	191 193 196 199 202 205 208 211 2477 2478 2941
/src/objects/seq/seq_loc_mapper_base.cpp	1353 1356 1386 1412 1446 1472 1483 1488 1514 1517 1527 1533 1543 1550 1563 1574
/src/objects/seqalign/Seq_align.cpp	75 77 83 94 112 130 155 157 160 165 176 236 243 254 256 258 260 275 277 279 281 296 298 300 302 304 306 308 319 321 324 330 343 364 381 651 653 658 661 669 672 687 703 730 760 955 964 976 1017 1039 1041 1042 1226 1230 1273 1464 1467 1504 1512 1517 1528 1606 1617 1626 1658 1799 1802 1823 1831 1833 1874 1877 1903 1919 1967 1973 1979 2031 2034 2042 2047 2057 2069 2117 2120 2141 2163 2168 2188 2196 2216 2222 2236
/src/objmgr/annot_object.cpp	568 576 614 659 685 721 730 782 843
/src/objmgr/seq_annot_info.cpp	852 856
/src/objmgr/split/id_range.cpp	179
/src/objmgr/util/seq_align_util.cpp	117 122
/src/objtools/align/alngraphic.cpp	303
/src/objtools/align_format/align_format_util.cpp	709 762 898 926 955 1008 1028 1049 1346 1356 1360 1361 1377 1387 1391 1392 4311 4663 4703
/src/objtools/align_format/aln_printer.cpp	98
/src/objtools/align_format/seqalignfilter.cpp	103 119 139 155 196 226 365 384 400 562
/src/objtools/align_format/showalign.cpp	1828 1835 1842 2010 2014 2015 2045 2048 3169 3223
/src/objtools/align_format/tabular.cpp	909 922 926 927 1532 1533 1744 1748 1773 1777 1803 1807 1924 1952 1954 1955 1956 1958 1959 2520
/src/objtools/align_format/unit_test/blast_test_util.cpp	81 84
/src/objtools/alnmgr/aln_container.cpp	59 63
/src/objtools/alnmgr/aln_converters.cpp	75
/src/objtools/alnmgr/alnmix.cpp	102 103 104 108 111
/src/objtools/alnmgr/alntext.cpp	262 399
/src/objtools/alnmgr/demo/alnvwrapp.cpp	90 91 92
/src/objtools/alnmgr/score_builder_base.cpp	153 310 313 352 370 509 510 514 515 553 554 556 568 569 571 572 573 575 589 609 610 1017 1277
/src/objtools/alnmgr/unit_test/unit_test_alnmgr.cpp	990
/src/objtools/cddalignview/cav_alignset.cpp	83 83 85 85 105 106 107 178 179 180 211 213 214 257 259
/src/objtools/edit/feature_propagate.cpp	70 72 74 76 77 107 109 111 113 114 269 325 417 436
/src/objtools/edit/seq_entry_edit.cpp	1019 1142 1187 1234 2229 2232 2902 3043 3078
/src/objtools/edit/unit_test/unit_test_entry_edit.cpp	823 826 875 878 927 930
/src/objtools/format/cigar_formatter.cpp	87 89 96 116 117 124
/src/objtools/format/comment_item.cpp	276 278 279
/src/objtools/format/primary_item.cpp	417 419 420
/src/objtools/readers/gff2_reader.cpp	540 563 570
/src/objtools/validator/utilities.cpp	402 414 415
/src/objtools/validator/validatorp.cpp	1045 1045
/src/objtools/validator/validerror_align.cpp	97 424 425 448 448 1302 1305 1312 1315 1316 1320
/src/objtools/writers/aln_writer.cpp	90 92 94 96
/src/objtools/writers/gff3_writer.cpp	374 395 416 419 421 768
/src/objtools/writers/psl_writer.cpp	124 132 136 143
/src/sra/data_loaders/bam/test/test_bam_loader.cpp	200 260 319 377 444 504 564 652 745
/src/sra/data_loaders/csra/test/test_csra_loader.cpp	202 287 370 461 721 812 891 967 1045 1215 1234 1379 1398 1586 1605 1771 1790 1997 2680 2760

1303 references in 170 files.