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Functions4,043 in github.com/Gaius-Augustus/Augustus

↓ 717 callersMethodbegin
src/scanner/scannerbase.h:318
↓ 614 callersMethodend
src/googletest/include/gtest/internal/gtest-internal.h:1144
↓ 567 callersMethodsize
Returns the number of TestPartResult objects in the array.
src/googletest/src/gtest-test-part.cc:77
↓ 458 callersMethodpush_back
! @brief append an unescaped token at the end of the reference pointer @param[in] token token to add @complexity Amortized constant.
include/json.hpp:11828
↓ 321 callersMethodend
return iterator end (needed for range-based for)
include/json.hpp:3947
↓ 244 callersMethodempty
src/pp_simscore.cc:80
↓ 188 callersMethodsize
auxprogs/utrrnaseq/src/UTRs.cpp:549
↓ 169 callersMethodresize
include/matrix.hh:121
↓ 164 callersMethodfind
include/json.hpp:16518
↓ 158 callersFunctioncreate
include/json.hpp:17401
↓ 157 callersMethodlength
src/pp_simscore.cc:36
↓ 156 callersFunctionitoa
* convert int to string */
include/types.hh:833
↓ 127 callersMethodclear
include/genbank.hh:119
↓ 123 callersFunctionmod3
* mod3, returns the number in {0,1,2} being congruent to the argument modulo 3 */
include/types.hh:527
↓ 122 callersMethodwrite_character
include/json.hpp:12652
↓ 116 callersMethodinsert
src/alignment.cc:924
↓ 112 callersMethodassign
include/matrix.hh:104
↓ 105 callersMethodsize
include/json.hpp:2691
↓ 99 callersMethoderase
src/vitmatrix.cc:260
↓ 99 callersMethodfront
include/pp_profile.hh:597
↓ 92 callersMethodgetMessage
* Get the message describing the error. * @return A string message. */
include/types.hh:475
↓ 82 callersFunctiongoto_line_after
include/projectio.hh:74
↓ 77 callersMethodread
src/motif.cc:388
↓ 75 callersMethodclose
src/sqliteDB.cc:48
↓ 72 callersMethodbegin
return iterator begin (needed for range-based for)
include/json.hpp:3941
↓ 69 callersFunctionisOnFStrand
include/types.hh:663
↓ 68 callersMethodget
src/scanner/lex.cc:235
↓ 66 callersFunctionsize
! @brief returns the number of elements Returns the number of elements in a JSON value. @return The return value depends on the differen
include/json.hpp:21494
↓ 64 callersFunctionto_string
include/graph.hh:404
↓ 58 callersMethodvalue
Gets the user supplied value.
src/googletest/include/gtest/gtest.h:549
↓ 57 callersMethodsort
include/gene.hh:665
↓ 54 callersFunctionget
include/json.hpp:3956
↓ 49 callersFunctionlog
* computes the element-wise natrual logarithm of a matrix P */
src/contTimeMC.cc:251
↓ 48 callersMethodwrite
src/motif.cc:373
↓ 46 callersFunctionStreamableToString
src/googletest/include/gtest/gtest-message.h:215
↓ 43 callersMethodempty
! @brief return whether pointer points to the root document @return true iff the JSON pointer points to the root document @complexity Co
include/json.hpp:11853
↓ 42 callersFunctionend
! @brief returns an iterator to one past the last element Returns an iterator to one past the last element. @image html range-begin-end.
include/json.hpp:21037
↓ 42 callersMethodpush
src/scanner/scannerbase.h:252
↓ 40 callersFunctionadd
add a character to token_buffer
include/json.hpp:7272
↓ 38 callersMethodrend
include/pp_hitseq.hh:319
↓ 36 callersFunctiontype_name
! @brief return the type as string Returns the type name as string to be used in error messages - usually to indicate that a function was
include/json.hpp:23411
↓ 35 callersMethodGetString
Gets the text streamed to this object so far as an std::string. Each '\0' character in the buffer is replaced with "\\0".
src/googletest/src/gtest.cc:1004
↓ 34 callersFunctionbegin
! @brief returns an iterator to the first element Returns an iterator to the first element. @image html range-begin-end.svg "Illustratio
include/json.hpp:20966
↓ 34 callersMethodmalus
include/extrinsicinfo.hh:396
↓ 34 callersMethodopen
src/sqliteDB.cc:16
↓ 33 callersMethodgetQueryName
Retrieve the Query template NAME of the alignment, i.e the QNAME Field */
auxprogs/filterBam/src/BamToolsAccess.cc:20
↓ 32 callersFunctionbasic_json
! @brief create an empty value with a given type Create an empty JSON value with a given type. The value will be default initialized with
include/json.hpp:17830
↓ 32 callersMethodbegin
src/googletest/include/gtest/internal/gtest-internal.h:1143
↓ 31 callersMethodclear
auxprogs/utrrnaseq/src/UTRs.cpp:140
↓ 31 callersMethodparse_error
include/json.hpp:2463
↓ 31 callersMethodupdate
src/pp_scoring.cc:276
↓ 29 callersMethodgeneBegin
include/gene.hh:389
↓ 29 callersMethodrbegin
include/pp_hitseq.hh:316
↓ 28 callersFunctionColoredPrintf
Helpers for printing colored strings to stdout. Note that on Windows, we cannot simply emit special characters and have the terminal change colors. Th
src/googletest/src/gtest.cc:3019
↓ 28 callersMethodgetSeqProb
src/statemodel.cc:312
↓ 28 callersFunctionimpl
Accessors for the implementation object.
src/googletest/include/gtest/gtest.h:1405
↓ 28 callersMethodname
include/json.hpp:2369
↓ 26 callersMethodkey
include/json.hpp:5847
↓ 26 callersMethodpop_back
! @brief remove last reference token @pre not `empty()` @liveexample{The example shows the usage of `pop_back`.,json_pointer__pop_back}
include/json.hpp:11782
↓ 26 callersMethodsize
include/gene.hh:221
↓ 25 callersMethodframe
reading frame, in case it is a (coding) exon, usually depends only on the type
src/gene.cc:152
↓ 25 callersMethodrc
include/geneticcode.hh:174
↓ 25 callersMethodtest_case
(self, testfilename, refsamfilename, filterbamoptions)
tests/short/auxprogs/filterbam/test_filterbam.py:56
↓ 24 callersFunctionGetUnitTestImpl
Convenience function for accessing the global UnitTest implementation object.
src/googletest/src/gtest-internal-inl.h:945
↓ 24 callersFunctionassert_invariant
! @brief checks the class invariants This function asserts the class invariants. It needs to be called at the end of every constructor to
include/json.hpp:17710
↓ 24 callersFunctionis_object
! @brief return whether value is an object This function returns true if and only if the JSON value is an object. @return `true` if type
include/json.hpp:19051
↓ 24 callersMethodset
src/googletest/include/gtest/internal/gtest-port.h:1631
↓ 23 callersMethodchrStart
src/alignment.cc:51
↓ 23 callersMethodgeneEnd
include/gene.hh:390
↓ 23 callersMethodsize
include/merkmal.hh:176
↓ 22 callersFunctionEq
src/googletest/include/gtest/gtest-matchers.h:759
↓ 22 callersMethodblockSize
include/pp_profile.hh:759
↓ 22 callersFunctionnewstrcpy
* copy string to newly allocated character array */
include/types.hh:851
↓ 22 callersMethodnumSpecies
include/geneMSA.hh:127
↓ 21 callersMethodbindInt
src/sqliteDB.cc:203
↓ 21 callersMethodchrEnd
src/alignment.cc:57
↓ 21 callersMethodclose
auxprogs/homGeneMapping/src/sqliteDB.cc:50
↓ 21 callersMethodcount
include/json.hpp:16506
↓ 21 callersMethodgetAliStart
include/orthoexon.hh:64
↓ 21 callersMethodinv
include/geneticcode.hh:186
↓ 21 callersMethodlength
src/scanner/scannerbase.h:298
↓ 21 callersMethodreset
src/vitmatrix.cc:242
↓ 20 callersMethodbindText
src/sqliteDB.cc:224
↓ 20 callersMethoddoubleValue
* conversion to other types */
include/lldouble.hh:70
↓ 20 callersMethodoperator[]
! @brief access to successor @pre The iterator is initialized; i.e. `m_object != nullptr`. */
include/json.hpp:11347
↓ 19 callersFunctionAssertionSuccess
Makes a successful assertion result.
src/googletest/src/gtest.cc:1031
↓ 19 callersMethodblockCount
include/pp_profile.hh:756
↓ 19 callersMethoddistance_faded_bonus
src/hints.cc:557
↓ 19 callersMethodnumRows
chromosomal range, maximized over rows
include/alignment.hh:175
↓ 19 callersMethodnumber_integer
include/json.hpp:5817
↓ 18 callersMethodadd
src/gene.cc:41
↓ 18 callersMethodgetAliEnd
length of HECT + 1
include/orthoexon.hh:66
↓ 18 callersMethodgetBiologicalState
src/gene.cc:176
↓ 18 callersFunctioninput_adapter
include/json.hpp:5088
↓ 18 callersFunctionloadError
auxprogs/joingenes/jg_ios.cpp:6
↓ 18 callersMethodsax_parse
include/json.hpp:10265
↓ 17 callersFunctionAssertionFailure
Makes a failed assertion result.
src/googletest/src/gtest.cc:1036
↓ 17 callersFunctionFilePath
src/googletest/include/gtest/internal/gtest-filepath.h:65
↓ 17 callersMethodINV
include/geneticcode.hh:194
↓ 17 callersFunctionfind
include/json.hpp:20812
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