Identifier search

Type the full name of an identifier to look for (a function name, variable name, typedef, etc).
Matches are case-sensitive. As a convenience,extra N line numbers denote case-insensitive occurrences..

Definitions for alignment

Type	File	Line
function prototype or declaration	/src/algo/align/util/unit_test/align_filter_unit_test.cpp	105
function prototype or declaration	/src/algo/align/util/unit_test/blast_tabular_unit_test.cpp	80
function prototype or declaration	/src/algo/align/util/unit_test/genomic_compart_unit_test.cpp	159
function prototype or declaration	/src/algo/structure/cd_utils/cuCdFromFasta.cpp	205
function prototype or declaration	/src/app/cn3d/sequence_viewer_widget.cpp	758
function prototype or declaration	/src/gui/widgets/aln_multiple/build_sparse_aln_job.cpp	196
function prototype or declaration	/src/objtools/cddalignview/cav_alignset.cpp	138

7 declarations in 7 files.

References to alignment

File	Line
/include/algo/align/util/patch_sequence.hpp	49
/include/algo/blast/api/psiblast.hpp	157
/include/algo/cobalt/cobalt.hpp	621 627 638 642 647 673
/include/algo/structure/cd_utils/cuCdUpdater.hpp	197
/include/algo/structure/struct_dp/struct_dp.h	110 120 131 168 180
/include/algo/structure/struct_util/su_block_multiple_alignment.hpp	286 286
/include/objtools/readers/gff2_reader.hpp	158 177
/scripts/common/new_project.sh	45
/src/algo/align/prosplign/demo/prosplign_demo.cpp	113 118 120
/src/algo/align/util/patch_sequence.cpp	62 65 226 227 231 235 238 251 257 261
/src/algo/align/util/unit_test/align_filter_unit_test.cpp	105 107 112
/src/algo/align/util/unit_test/blast_tabular_unit_test.cpp	80 81 82
/src/algo/align/util/unit_test/genomic_compart_unit_test.cpp	159 160 161
/src/algo/align/util/unit_test/score_builder_unit_test.cpp	114 116 122 146 150 154 158 162 166 170 174 178 182 186 190 194 198 208 213 221 223 230 232 240 243 252 259 261 268 270 289 291 310 312 333 351 353 355 372 377 385 387 391 393 399 400 403 405
/src/algo/blast/api/psiblast.cpp	103 136
/src/algo/blast/api/repeats_filter_cxx.cpp	144 147
/src/algo/blast/format/blast_format.cpp	532 534 537 540
/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp	984 985 986
/src/algo/blast/unit_tests/api/blastengine_unit_test.cpp	389 390 392 393
/src/algo/blast/unit_tests/api/psiblast_unit_test.cpp	575 577 580 591 1095 1098 1101 1113 1140 1141 1143 1146 1158
/src/algo/blast/unit_tests/api/seqalign_cmp.cpp	76 78 79 80 81 82 83 84 85 86 88 89 91 106 108
/src/algo/cobalt/demo/hyperclust.cpp	325 328 340
/src/algo/cobalt/prog.cpp	383 460 461 465 466 700 761 762 796 804 805 824 837 850 911 915 931 941 967 990 1003 1059 1071 1072 1079 1084 1120 1121 1146 1216 1257 1283 1287 1304 1314 1417 1469 1488
/src/algo/sequence/unit_test/unit_test_gene_model.cpp	366 366 389 453
/src/algo/structure/cd_utils/cuCdCore.cpp	220 223 223 223 225 968 969 981 1005 1006 1010 1022
/src/algo/structure/cd_utils/cuCdFromFasta.cpp	205 206
/src/algo/structure/cd_utils/cuCdUpdater.cpp	596 603 607
/src/algo/structure/struct_dp/block_align.cpp	469 482 483 484 485 487 494 496 500 518 519 524 526 530 551 552 662 691 698 728 734 755 761 782 863 865 867 868
/src/algo/structure/struct_dp/demo/struct_dp_demo.cpp	148 149 153 154 156 158 159 160 162 163 171
/src/app/cn3d/alignment_manager.cpp	136 138 142
/src/app/cn3d/block_multiple_alignment.hpp	370 370
/src/app/cn3d/cdd_annot_dialog.cpp	247 248 250 260 267 628 632 634 672 673 809 810 819 1069 1070 1072 1074 1076
/src/app/cn3d/cdd_ibis_annot_dialog.cpp	876 877 901 906 1654 1660 1666
/src/app/cn3d/conservation_colorer.cpp	72 79 99 231 257
/src/app/cn3d/conservation_colorer.hpp	54
/src/app/cn3d/sequence_display.cpp	98 239 241 298 370 376 376 382 384 441 442 446 448 454 456 468 475 500 508 514 520 523 541 556 558 572 579 586 593 600 607 614 623 623 623 630 631 641 650 658 677 678 678 681 683 688 690 700 712 713 714 723 724 731 733 746 747 756 757 766 768 822 849 850 853 856 875 881 883 889 937 938 948 961 962 967 967 972 973 973 974 979 980 985 986 1036 1052 1068 1069 1072 1123 1128 1130 1140 1141 1143 1153 1154 1157 1238 1292 1321
/src/app/cn3d/sequence_display.hpp	77 80 83 86 95 100 106 144 150 158 158
/src/app/cn3d/sequence_viewer.cpp	116 119 120 123 126 193 198 199 210 211 258 259 280 307 316 318 328 328 330 332 360 365 369 423 425 432 500 501 503 508
/src/app/cn3d/sequence_viewer_widget.cpp	75 124 180 201 203 205 217 261 296 327 378 578 584 586 642 688 758 764 810 823 825 838 842 857 874 902 922 944 949 951 969 986
/src/app/cn3d/sequence_viewer_window.cpp	337 341 353 370 377
/src/app/cn3d/structure_set.cpp	895 896 896 898 907
/src/app/cn3d/taxonomy_tree.cpp	266 276 277
/src/app/cn3d/taxonomy_tree.hpp	62
/src/app/cn3d/update_viewer.cpp	522 524 524 525 526 527 528 529 530 531 532 533 534 535 542 543 544 559 933 944 948 964 977 981 983
/src/app/cn3d/update_viewer.hpp	91
/src/app/read_blast_result/read_blast.cpp	286 287 303 313 329 335 346 352 357 357 449
/src/app/read_blast_result/read_blast_result.hpp	220 443
/src/app/read_blast_result/read_blast_result_lib.cpp	108 111
/src/app/speedtest/speedtest.cpp	460 464
/src/app/streamtest/process_prosplign.hpp	100 104
/src/app/table2asn/feature_table_reader.cpp	1438 1443 1450 1459 1459 1462
/src/gui/opengl/glbitmapfont.cpp	910 916 934
/src/gui/opengl/gltexture.cpp	211 212 215
/src/gui/packages/pkg_sequence_edit/recompute_intervals.cpp	79 82 86 92 92 92 96 105
/src/gui/packages/pkg_sequence_edit/subprep_util.cpp	776 783 783 783 786 796
/src/gui/widgets/aln_multiple/build_sparse_aln_job.cpp	176 177 184 187 191 196
/src/gui/widgets/aln_table/annot_compare_ds.cpp	516 529 531
/src/gui/widgets/edit/cds_translation_panel.cpp	1243 1246 1251 1255 1264 1264 1264 1268 1271 1278 1279 1287 1288 1296
/src/gui/widgets/phylo_tree/phylo_tree_widget.cpp	676 677 680
/src/gui/widgets/wx/image_grabber.cpp	122 123 185 218 219 264
/src/objects/seq/unit_test/seqalign_unit_test.cpp	88 89 91 111 112
/src/objtools/cddalignview/cav_alignset.cpp	138 140 140 141 145 145 149
/src/objtools/cddalignview/cav_function.cpp	162 166 186 191 200 205 216 228 233 242 254 264 265
/src/objtools/readers/gff2_reader.cpp	319 326 330 440 441 445 470 478
/src/objtools/readers/gff3_reader.cpp	363 364 368
/src/sra/readers/bam/bamindex.cpp	2674 2675 2676
/src/util/test/formatguess_unit_test.cpp	504

601 references in 67 files.