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Definitions for starts

Type	File	Line
function prototype or declaration	/src/algo/align/util/align_shadow.cpp	121
function prototype or declaration	/src/algo/align/util/blast_tabular.cpp	63
function prototype or declaration	/src/gui/packages/pkg_sequence_edit/convert_selected_gaps.cpp	587
function prototype or declaration	/src/gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.cpp	566
function prototype or declaration	/src/gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.cpp	619

5 declarations in 4 files.

References to starts

File	Line
/include/algo/gnomon/gnomon.hpp	90
/include/algo/sequence/find_pattern.hpp	45 52 59
/include/algo/structure/cd_utils/cuAlign.hpp	90 96 98
/include/algo/structure/cd_utils/cuCdCore.hpp	93
/include/algo/structure/cd_utils/cuSeqAnnotFromFasta.hpp	99
/include/objtools/edit/rna_edit.hpp	63 67
/include/objtools/readers/gff2_reader.hpp	229 234
/include/sra/readers/bam/bamindex.hpp	1667
/src/algo/align/util/align_shadow.cpp	121 130 130 131 143 145 147 149 151 153 155 160 163
/src/algo/align/util/blast_tabular.cpp	63 65 65
/src/algo/blast/api/blast_seqalign.cpp	171 187 212 213 226 227 240 241 255 256 274 293 308 330 344 629 640 643 666 729 734 747 751 1295 1296 1298 1300 1303 1305
/src/algo/blast/api/cdd_pssm_input.cpp	353 360 361
/src/algo/blast/api/psi_pssm_input.cpp	334 370 371 424 429 431
/src/algo/blast/api/repeats_filter_cxx.cpp	156 159 166 167 169 170
/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp	2575 2576 2577 2578 2579 2580 2582 2600 2600 2631 2633 2636 2638 2657 2672 2673 2683 2698 2699
/src/algo/blast/unit_tests/api/delta_unit_test.cpp	256 258 258 258 259 270 274 274 274 275 286 288 288 288 289 335 337 337 337 338 349 351 351 351 352 363 367 367 367 368 379 381 381 381 382 394 396 396 396 397 408 410 410 410 411 422 424 424 424 425 437 439 439 439 440 452 454 454 454 455 517 519 519 519 520 531 535 535 535 536 547 549 549 549 550 596 598 598 598 599 611 613 613 613 614 625 629 629 629 630 641 643 643 643 644 656 658 658 658 659 670 672 672 672 673
/src/algo/blast/unit_tests/api/neutral_seqalign.hpp	92 106
/src/algo/blast/unit_tests/api/psiblast_unit_test.cpp	229 230 235 241 241 241 242 249 257 257 257 258 314 315 323 324 325 326 327 328 329 330 331 332 344 345 354 355 356 357 358 359 399 400 408 417 417 417 418 425 436 436 436 437 491 492 500 509 509 509 510 518 529 529 529 530 619 625 625 625 626 633 639 639 639 640 647 657 657 657 658 668 669 674 680 680 680 681 688 694 694 694 695 705 706 738 746 746 746 747 754 762 762 762 763 770 782 782 782 783 794 795 805 806 857 863 863 863 864 871 877 877 877 878 885 895 895 895 896 906 907 912 918 918 918 919 926 932 932 932 933 943 944 976 982 982 982 983 990 996 996 996 997 1004 1014 1014 1014 1015 1025 1026 1031 1037 1037 1037 1038 1045 1051 1051 1051 1052 1062 1063
/src/algo/blast/unit_tests/api/pssmcreate_cdd_unit_test.cpp	609 651 652 897 899 900 901 902 903 904 1086 1088 1089
/src/algo/blast/unit_tests/api/pssmcreate_unit_test.cpp	703 707 708 721
/src/algo/blast/unit_tests/api/seqalign_cmp.cpp	86 88 295 301 304 307 384 384 394 394 401 403
/src/algo/blast/unit_tests/api/seqalign_set_convert.cpp	98
/src/algo/cobalt/hit.cpp	56 61 63 66 66 67 67 79 81 81 82 82
/src/algo/cobalt/seq.cpp	279 321 331
/src/algo/cobalt/traceback.cpp	83 88 89
/src/algo/cobalt/unit_test/cobalt_unit_test.cpp	830 838 840 841
/src/algo/gnomon/gnomon_seq.cpp	158 160 183 240 250 268 270 298 299 299 300
/src/algo/gnomon/gnomon_seq.hpp	102 104
/src/algo/gnomon/score.cpp	1325 1479 1479 1480 1483 1486 1560 1562 1596 1597 1598 1599 1636 1662 1676 1677 1686 1715
/src/algo/phy_tree/unit_test/phytree_calc_unit_test.cpp	459 460 461 461
/src/algo/seqqa/single_aln_tests.cpp	837 838 840 841
/src/algo/seqqa/xcript_tests.cpp	932 938 958 961 964
/src/algo/sequence/find_pattern.cpp	42 50 56 69 75 85 92
/src/algo/sequence/internal_stops.cpp	60 62 67 139 171 265
/src/algo/sequence/orf.cpp	82 83 94 99 176 178 181 194 194 195
/src/algo/sequence/unit_test/unit_test_internal_stops.cpp	443 446
/src/algo/structure/cd_utils/cuAlign.cpp	351 365 366 366 412 413 418 426 430 724 743
/src/algo/structure/cd_utils/cuBlock.cpp	200 202 203 206 585 586 587
/src/algo/structure/cd_utils/cuCD.cpp	468 509 510 513
/src/algo/structure/cd_utils/cuCdCore.cpp	301 307 308 308
/src/algo/structure/cd_utils/cuCdUpdater.cpp	610 615 615 616 617
/src/algo/structure/cd_utils/cuSeqAnnotFromFasta.cpp	576 603 608 615 620
/src/algo/structure/struct_util/su_alignment_set.cpp	299 303 304 306 307
/src/app/cn3d/alignment_set.cpp	245 249 250 252 253
/src/app/magicblast/magicblast_util.cpp	1240 1256 1258 1258 1261
/src/app/nmer_repeats/nmer_repeats.cpp	141 156 159 160 161 178 182
/src/app/pubseq_gateway/server/timing.cpp	69 73 77
/src/gui/objutils/convert_raw_to_delta.cpp	200 209
/src/gui/objutils/sparse_functions.cpp	239 249 250
/src/gui/packages/pkg_sequence_edit/convert_selected_gaps.cpp	587 592 604 609
/src/gui/packages/pkg_sequence_edit/create_seq_hist_for_tpa.cpp	489 495
/src/gui/packages/pkg_sequence_edit/edit_seq_ends_with_align.cpp	304 310 314
/src/gui/packages/pkg_sequence_edit/far_pointer_seq.cpp	569 579 580
/src/gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.cpp	566 582 619 624 646 705 716 729 755
/src/gui/packages/pkg_sequence_edit/remove_sequences_from_alignments.cpp	450 464 483
/src/gui/widgets/edit/alignment_assistant.cpp	1775 1789 1807
/src/gui/widgets/hit_matrix/dense_hit.cpp	67 71 72
/src/gui/widgets/seq_graphic/denseg_ci.cpp	84 86 96 119 141 142 143 144 195 201 202 203 204
/src/objects/general/Date_std.cpp	171 172 190 200 214 219 288 298 316
/src/objects/seqalign/Dense_seg.cpp	111 130 169 182 191 207 220 229 276 307 671 676 676 954 975 987 987 1014 1111 1177 1246 1287 1288 1352 1357 1416 1420
/src/objects/seqalign/Seq_align.cpp	748 785 835 912
/src/objects/seqalign/Spliced_seg.cpp	454 455 457 458
/src/objects/seqfeat/PCRPrimerSeq.cpp	217 222 223 224
/src/objtools/align_format/tabular.cpp	1534 1566 1568 1568 1571
/src/objtools/alnmgr/aln_converters.cpp	151 165 166 216 249 263 264 667 674 674
/src/objtools/alnmgr/aln_generators.cpp	309 310 311 312 312 322 381 382 410 458 459 479 486 882 901 920 920 1042 1043 1075 1118 1119 1142 1151
/src/objtools/alnmgr/alnmap.cpp	1445 1480
/src/objtools/alnmgr/alnmerger.cpp	379 394 395 396 468 495 497 507 508 511 517 531 569 573 581 582 649 655 657 661 673 680 809 813 1174 1183 1207 1250 1250
/src/objtools/alnmgr/alnsegments.cpp	288 290 303
/src/objtools/alnmgr/alnvecprint.cpp	98 115 123 261 279 287
/src/objtools/cddalignview/cav_alignset.cpp	284 288 289 291 292
/src/objtools/edit/rna_edit.cpp	127 131 132 133 134 135 145 154 164 209 221 228 235 263
/src/objtools/readers/aln_reader.cpp	540 609 612 614
/src/objtools/readers/gff2_reader.cpp	781 784 795 801 804 810 812 826 829 840 846 849 855 857
/src/objtools/readers/phrap.cpp	1185 1187 1188 1210 1216 1232
/src/objtools/validator/validerror_align.cpp	1007 1010 1062 1066 1067 1441 1459 1463 1469 1470 1479 1489 1490 1493
/src/objtools/writers/psl_record.cpp	447 450 450 451 452
/src/sra/readers/bam/bamindex.cpp	738 739 743 2719 2766 2767
/src/sra/readers/bam/bamread.cpp	2950 2955 3007 3008 3020 3023
/src/sra/readers/sra/csraread.cpp	1520 1522 1580 1581 1591 1594
/src/sra/readers/sra/wgsread.cpp	6698 6732
/src/util/test/test_histogram_mt.cpp	140 141 142 152

805 references in 82 files.