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Functions3,919 in github.com/bbuchfink/diamond

⨍ Functions 3,919◇ Types & classes 804

↓ 2 callersFunctionBlast_FreqRatioToScore

src/stats/comp_based_stats.cpp:294

↓ 2 callersFunctionBlast_KarlinBlkNew

src/lib/blast/blastn_score.cpp:1219

↓ 2 callersFunctionBlast_MessageWrite

src/lib/blast/blast_message.cpp:101

↓ 2 callersFunctionBlast_OptimizeTargetFrequencies

Documented in optimized_target_freq.h */

src/stats/matrix_adjust/ncbi.cpp:699

↓ 2 callersFunctionBlast_ProgramIsNucleotide

src/lib/blast/blastn_score.cpp:1954

↓ 2 callersFunctionBlast_ResFreqFree

src/lib/blast/blastn_score.cpp:1343

↓ 2 callersFunctionListNodeAdd

* * ListNodeAdd(head) * adds after last node in list if *head not NULL * If *head is NULL, sets it to the new ListNode * returns poin

src/lib/blast/ncbi_std.cpp:77

↓ 2 callersFunctionListNodeCopyStr

* * ListNodeCopyStr (head, choice, str) * adds like ListNodeAdd() * sets newnode->choice = choice (if choice does not matter, use 0) *

src/lib/blast/ncbi_std.cpp:124

↓ 2 callersFunctionListNodeNew

* * ListNodeNew(vnp) * adds after last node in list if vnp not NULL * *************************************************************************

src/lib/blast/ncbi_std.cpp:55

↓ 2 callersFunctionMultiplyByAtranspose

* Compute the product y = beta * y + alpha * A^T * x, where A^T is * the transpose of the constraint matrix for the problem of * generating optimal

src/stats/matrix_adjust/ncbi.cpp:204

↓ 2 callersFunctionNCBISM_GetIndex

src/lib/blast/blastn_score.cpp:744

↓ 2 callersFunctionNlm_AddVectors

Documented in nlm_linear_algebra.h. */

src/stats/matrix_adjust/linear_algebra_ncbi.h:213

↓ 2 callersFunctionReNewtonSystemFree

* Free the memory associated with a ReNewtonSystem. * * @param newton_system on entry *newton_system points to the *

src/stats/matrix_adjust/ncbi.cpp:404

↓ 2 callersFunctionSegParametersFree

Comments in blast_seg.h */

src/lib/blast/blast_seg.cpp:2250

↓ 2 callersFunctionSegParametersNewAa

Comments in blast_seg.h */

src/lib/blast/blast_seg.cpp:2203

↓ 2 callersFunction_PSIAllocateMatrix

src/lib/blast/blastn_score.cpp:290

↓ 2 callersFunction_PSIMatrixFrequencyRatiosFree

src/lib/blast/matrix_freq_ratios.c:1742

↓ 2 callersFunctionabsolute_path

src/util/system/system.cpp:404

↓ 2 callersMethodacquire

src/util/parallel/semaphore.h:170

↓ 2 callersFunctionadd

src/util/simd/vector8_sse.h:92

↓ 2 callersFunctionadd_self_aln

src/align/extend.cpp:133

↓ 2 callersFunctionalign

src/align/gapped_final.cpp:80

↓ 2 callersFunctionalignPointer

src/lib/ips4o/memory.hpp:60

↓ 2 callersFunctionalign_right

src/dp/swipe/anchored_wrapper.cpp:64

↓ 2 callersMethodalloc_buffer

src/search/hit_buffer.cpp:323

↓ 2 callersMethodalloc_size

src/util/text_buffer.h:143

↓ 2 callersMethodallocate_read_buffer

src/contrib/mcl/sparse_matrix_stream.h:273

↓ 2 callersFunctionanchored_swipe

src/tools/benchmark.cpp:401

↓ 2 callersFunctionapply_filters

src/align/culling.cpp:193

↓ 2 callersFunctionassign_stats

src/dp/swipe/stat_cell.h:208

↓ 2 callersFunctionauto_append_extension_if_exists

src/util/system/system.cpp:170

↓ 2 callersMethodbackground_freqs_f

src/stats/score_matrix.h:209

↓ 2 callersFunctionbanded_3frame_swipe

src/dp/swipe/banded_3frame_swipe.cpp:409

↓ 2 callersMethodbegin

src/util/data_structures/sparse_flat_array.h:152

↓ 2 callersMethodbegin

src/util/data_structures/range_partition.h:65

↓ 2 callersMethodbegin_old

src/basic/match.h:377

↓ 2 callersFunctionbisection

src/lib/alp/njn_root.hpp:206

↓ 2 callersMethodblock_size

src/legacy/daa/daa_file.h:185

↓ 2 callersMethodbytes

src/data/fasta/fasta_file.cpp:245

↓ 2 callersMethodcbs_mask

src/dp/swipe/target_iterator.h:160

↓ 2 callersMethodcheck

src/util/geo/interval.h:69

↓ 2 callersFunctioncigar_to_hsp

src/contrib/dna/extension.cpp:195

↓ 2 callersMethodclear

src/util/ptr_vector.h:60

↓ 2 callersMethodclear

src/util/parallel/parallelizer.cpp:103

↓ 2 callersFunctionclip_diag

src/util/geo/geo.h:49

↓ 2 callersFunctioncluster_sorted

src/cluster/helpers.cpp:119

↓ 2 callersMethodcollect_components

src/contrib/mcl/sparse_matrix_stream.h:338

↓ 2 callersFunctioncompute_chains

src/contrib/dna/extension_chain.cpp:352

↓ 2 callersFunctioncompute_score

src/contrib/dna/chain.cpp:185

↓ 2 callersMethodcompute_self_aln

src/data/block/block.cpp:188

↓ 2 callersMethodconsume

src/contrib/mcl/sparse_matrix_stream.h:126

↓ 2 callersFunctioncontaining_directory

src/util/system/system.h:60

↓ 2 callersFunctionconvert_size

src/util/string/string.cpp:45

↓ 2 callersMethodcorrected_bit_score

src/basic/match.h:390

↓ 2 callersMethodcount

src/basic/packed_transcript.h:63

↓ 2 callersMethodcount

src/basic/shape_config.h:46

↓ 2 callersFunctioncount_targets

src/align/load_hits.h:30

↓ 2 callersMethodcreate_partition

src/legacy/dmnd/dmnd.cpp:428

↓ 2 callersMethodcrend

src/lib/mio/mmap.hpp:250

↓ 2 callersFunctiondecode_deflines

src/data/blastdb/phr.cpp:202

↓ 2 callersFunctiondecode_protein_sequence

src/data/blastdb/psq.cpp:36

↓ 2 callersMethoddeflines

src/data/blastdb/blastdb.cpp:253

↓ 2 callersFunctiondiag_sub_matrix

src/util/geo/geo.h:33

↓ 2 callersFunctiondict_file_name

src/data/sequence_file.cpp:71

↓ 2 callersMethoddict_len

src/data/sequence_file.cpp:748

↓ 2 callersMethoddict_title

src/data/sequence_file.cpp:740

↓ 2 callersFunctiondisjoint

src/chaining/backtrace.cpp:36

↓ 2 callersFunctiondiv_up

src/util/util.h:29

↓ 2 callersMethoddone

src/contrib/mcl/sparse_matrix_stream.h:256

↓ 2 callersMethodend

src/util/data_structures/array.h:58

↓ 2 callersMethodend

src/util/data_structures/sparse_flat_array.h:156

↓ 2 callersMethodenqueue_or_abort

src/util/data_structures/queue.h:78

↓ 2 callersMethodenvelopes

src/align/legacy/query_mapper.cpp:43

↓ 2 callersMethoderase

* Erases the element pointed to be iter. */

src/lib/interval_tree/interval_tree.hpp:751

↓ 2 callersFunctionerfc8_sum

src/lib/gsl/gsl.h:251

↓ 2 callersMethodevalue_norm

src/stats/score_matrix.cpp:226

↓ 2 callersFunctionextend

src/align/global_ranking/extend.cpp:88

↓ 2 callersFunctionextend_between_anchors

src/contrib/dna/extension_chain.cpp:113

↓ 2 callersMethodextend_left

src/dp/dp.h:129

↓ 2 callersFunctionextend_new_at_peak

src/contrib/dna/extension_chain.cpp:74

↓ 2 callersFunctionextend_query

src/align/global_ranking/extend.cpp:45

↓ 2 callersMethodextend_right

src/dp/dp.h:125

↓ 2 callersFunctionextract_stats

src/dp/swipe/stat_cell.h:175

↓ 2 callersMethodfile_name

src/cluster/file_array.h:114

↓ 2 callersMethodfilter_by_taxonomy

src/data/sequence_file.cpp:765

↓ 2 callersFunctionfilter_hsp

src/align/culling.cpp:146

↓ 2 callersMethodfind_entry

src/util/data_structures/hash_table.h:83

↓ 2 callersMethodfinish

src/util/parallel/thread_pool.h:77

↓ 2 callersMethodfinished

src/util/parallel/thread_pool.h:83

↓ 2 callersFunctionfmadd

src/util/simd/vector8_sse.h:124

↓ 2 callersMethodforThread

src/lib/ips4o/memory.hpp:163

↓ 2 callersFunctionformat_seqid

src/data/blastdb/phr.cpp:244

↓ 2 callersMethodframe

src/search/hit.h:77

↓ 2 callersMethodframe

src/basic/match.h:396

↓ 2 callersFunctionframe_mask

src/data/sequence_file.cpp:279

↓ 2 callersMethodfread

src/util/io/zstd_bridge.cpp:44

↓ 2 callersMethodfree_buffer

src/search/hit_buffer.cpp:357

↓ 2 callersFunctiongapped_filter

src/align/gapped_filter.cpp:33

↓ 2 callersFunctiongenerate_intermediate_output

src/align/output.cpp:115

↓ 2 callersMethodget32

src/dp/swipe/target_iterator.h:136

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