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

⨍ Functions 4,043◇ Types & classes 931

↓ 4 callersMethodintronAt

returns the number of residual nucleotides f, if an intron is in the protein sequence at (j,f) located returns -1, if at (j,{0,1,2}) no intron is loca

src/pp_simscore.cc:146

↓ 4 callersFunctionis3UTRExon

include/types.hh:596

↓ 4 callersFunctionis5UTRExon

include/types.hh:582

↓ 4 callersFunctionisAA

src/pp_prepare_align.cc:80

↓ 4 callersMethodisCDS

auxprogs/homGeneMapping/include/gene.hh:78

↓ 4 callersMethodisCDS

include/graph.hh:96

↓ 4 callersFunctionisCodingIntron

include/types.hh:633

↓ 4 callersMethodisFirstMate

returns true if alignment is first mate on read */

auxprogs/filterBam/src/BamToolsAccess.cc:68

↓ 4 callersFunctionisNuc

src/types.cc:480

↓ 4 callersMethodisSecondMate

returns true if alignment is second mate on read */

auxprogs/filterBam/src/BamToolsAccess.cc:74

↓ 4 callersFunctionisSignalType

src/hints.cc:22

↓ 4 callersFunctionis_boolean

! @brief return whether value is a boolean This function returns true if and only if the JSON value is a boolean. @return `true` if type

include/json.hpp:18914

↓ 4 callersMethodlocalSSMalus

* localSSMalus */

src/extrinsicinfo.cc:1872

↓ 4 callersFunctionnongap

src/pp_prepare_align.cc:83

↓ 4 callersMethodnormalize

src/motif.cc:204

↓ 4 callersMethodnumFilledRows

src/alignment.cc:816

↓ 4 callersMethodnumGFs

auxprogs/homGeneMapping/src/gene.cc:123

↓ 4 callersFunctionpointer

src/googletest/include/gtest/internal/gtest-port.h:1826

↓ 4 callersMethodpointer

src/googletest/include/gtest/internal/gtest-port.h:1628

↓ 4 callersFunctionpredictAndEvaluate

src/evaluation.cc:848

↓ 4 callersFunctionprintChrOfPairCovSteps

auxprogs/filterBam/src/filterBam.cc:721

↓ 4 callersMethodprintProbabilities

src/dummy.cc:14

↓ 4 callersFunctionprintUsage

src/getSeq.cc:167

↓ 4 callersMethodprojectOntoGeneSequence

* StatePath::projectOntoGeneSequence * makes a sequence of (possibly partial) genes out of this state path */

src/gene.cc:394

↓ 4 callersFunctionrandom

Gets the random number generator.

src/googletest/src/gtest-internal-inl.h:812

↓ 4 callersFunctionreadPart

src/pp_profile.cc:581

↓ 4 callersFunctionrelative_error

include/lldouble.hh:255

↓ 4 callersMethodrepeater

Returns repeater that broadcasts the TestEventListener events to all subscribers.

src/googletest/src/gtest.cc:4489

↓ 4 callersFunctionreplace_substring

! @brief replace all occurrences of a substring by another string @param[in,out] s the string to manipulate; changed so that all

include/json.hpp:12351

↓ 4 callersFunctionreverse_accumulate

* accumulate all values in a vector in back-to-front order */

auxprogs/homGeneMapping/include/projectio.hh:109

↓ 4 callersMethodscoreFromScratch

src/pp_profile.cc:407

↓ 4 callersFunctionsearch_for_lines_to_ignore

(sourcepath, startwith, ignores, startblock=True)

tests/short/utils/aug_out_filter.py:37

↓ 4 callersMethodsetBonusMalus

* initialization of a feature with the info given * in the extrinsic config table */

src/extrinsicinfo.cc:2296

↓ 4 callersMethodsetKappa

include/codonevo.hh:48

↓ 4 callersMethodsetOmega

src/orthoexon.cc:133

↓ 4 callersMethodsetOmegas

* Chooses k values for omega around 1, for which matrices P will be stored. * Examples: * k set of omegas * 1 1 (does not make sense for select

src/codonevo.cc:34

↓ 4 callersMethodsetPi

src/codonevo.cc:16

↓ 4 callersMethodshowSubstateMemoryUsage

src/vitmatrix.cc:481

↓ 4 callersMethodstart

src/compgenepred.cc:127

↓ 4 callersFunctionstateEvidenceSummary

* stateEvidenceSummary * Only count each source once for each state. */

src/gene.cc:108

↓ 4 callersMethodswap

Swaps two AssertionResults.

src/googletest/src/gtest.cc:1017

↓ 4 callersMethodtest_to_run_count

Gets the number of tests that should run.

src/googletest/src/gtest.cc:811

↓ 4 callersMethodtextColumn

auxprogs/homGeneMapping/include/sqliteDB.hh:82

↓ 4 callersFunctiontoStateType

include/types.hh:540

↓ 4 callersFunctionuniqueKeys

auxprogs/filterBam/src/filterBam.cc:532

↓ 4 callersMethodupdateExonSpecificValues

auxprogs/joingenes/jg_transcript.h:537

↓ 3 callersFunctionAbort

src/googletest/include/gtest/internal/gtest-port.h:2168

↓ 3 callersMethodAddTestPartResult

Adds a test part result to the list.

src/googletest/src/gtest.cc:2066

↓ 3 callersMethodAppend

src/googletest/src/gtest.cc:3384

↓ 3 callersMethodArgv

src/googletest/src/gtest-death-test.cc:861

↓ 3 callersFunctionArrayAsVector

src/googletest/src/gtest.cc:2119

↓ 3 callersFunctionAssertionResult

src/googletest/include/gtest/gtest.h:306

↓ 3 callersMethodBaseGenerator

src/googletest/include/gtest/internal/gtest-param-util.h:227

↓ 3 callersFunctionCaptureStderr

Starts capturing stderr.

src/googletest/src/gtest-port.cc:1180

↓ 3 callersMethodClear

Clears the object.

src/googletest/src/gtest.cc:2174

↓ 3 callersMethodClone

src/googletest/include/gtest/internal/gtest-param-util.h:234

↓ 3 callersFunctionFlagToEnvVar

Returns the name of the environment variable corresponding to the given flag. For example, FlagToEnvVar("foo") will return "GTEST_FOO" in the open-so

src/googletest/src/gtest-port.cc:1273

↓ 3 callersFunctionFormatTimeInMillisAsDuration

Formats the given time in milliseconds as seconds.

src/googletest/src/gtest.cc:4035

↓ 3 callersFunctionFormatTimeInMillisAsSeconds

Formats the given time in milliseconds as seconds.

src/googletest/src/gtest.cc:3658

↓ 3 callersFunctionGetPrefixUntilComma

Returns the prefix of 'str' before the first comma in it; returns the entire string if it contains no comma.

src/googletest/include/gtest/internal/gtest-internal.h:668

↓ 3 callersMethodGetTestPartResultReporterForCurrentThread

Returns the test part result reporter for the current thread.

src/googletest/src/gtest.cc:742

↓ 3 callersFunctionGetTestSuite

Gets the i-th test suite among all the test suites. i can range from 0 to total_test_suite_count() - 1. If i is not in that range, returns NULL.

src/googletest/src/gtest-internal-inl.h:587

↓ 3 callersFunctionGetTestTypeId

Returns the type ID of ::testing::Test. We should always call this instead of GetTypeId< ::testing::Test>() to get the type ID of testing::Test. Thi

src/googletest/src/gtest.cc:647

↓ 3 callersFunctionInitGoogleTestImpl

src/googletest/src/gtest.cc:5977

↓ 3 callersFunctionInsert

Insert after position P */

auxprogs/compileSpliceCands/list.c:83

↓ 3 callersFunctionInt32FromGTestEnv

Reads and returns a 32-bit integer stored in the environment variable corresponding to the given flag; if it isn't set or doesn't represent a valid 32

src/googletest/src/gtest-port.cc:1344

↓ 3 callersFunctionIsLast

Return "true" if P is the last position in list L. (Parameter L is unused in this implementation) */

auxprogs/compileSpliceCands/list.c:44

↓ 3 callersFunctionMakeAndRegisterTestInfo

Creates a new TestInfo object and registers it with Google Test; returns the created object. Arguments: test_suite_name: name of the test suite na

src/googletest/src/gtest.cc:2572

↓ 3 callersFunctionMatchRegexAtHead

Returns true iff regex matches a prefix of str. regex must be a valid simple regular expression and not start with "^", or the result is undefined.

src/googletest/src/gtest-port.cc:908

↓ 3 callersFunctionParseFlagValue

Parses a string as a command line flag. The string should have the format "--flag=value". When def_optional is true, the "=value" part can be omitte

src/googletest/src/gtest.cc:5640

↓ 3 callersFunctionParseInt32

Parses 'str' for a 32-bit signed integer. If successful, writes the result to *value and returns true; otherwise leaves *value unchanged and returns

src/googletest/src/gtest-port.cc:1288

↓ 3 callersFunctionParseInt32Flag

Parses a string for an Int32 flag, in the form of "--flag=value". On success, stores the value of the flag in *value, and returns true. On failure,

src/googletest/src/gtest.cc:5694

↓ 3 callersFunctionPrintByteSegmentInObjectTo

Prints a segment of bytes in the given object.

src/googletest/src/gtest-printers.cc:60

↓ 3 callersFunctionPrintRawArrayTo

src/googletest/include/gtest/gtest-printers.h:593

↓ 3 callersMethodPushLine

src/googletest/src/gtest.cc:1156

↓ 3 callersMethodRemoveTrailingPathSeparator

If input name has a trailing separator character, remove it and return the name, otherwise return the name string unmodified. On Windows platform, use

src/googletest/src/gtest-filepath.cc:339

↓ 3 callersFunctionReportFailureInUnknownLocation

src/googletest/src/gtest.cc:2272

↓ 3 callersFunctionShuffleRange

src/googletest/src/gtest-internal-inl.h:309

↓ 3 callersFunctionStripTrailingSpaces

src/googletest/include/gtest/internal/gtest-port.h:2042

↓ 3 callersFunctionaddExonpartHint

check and insert new hint into the list of exonpart hints

auxprogs/bam2hints/bam2hints.cc:110

↓ 3 callersMethodaddFeature

* HintGroup::addFeature * put the feature at the right place: sorted increasingly by end positions */

src/hints.cc:577

↓ 3 callersMethodaddFragment

src/alignment.cc:71

↓ 3 callersMethodaliEnd

src/alignment.cc:64

↓ 3 callersMethodalignRight

move interval such that max equals newmax

include/pp_profile.hh:211

↓ 3 callersFunctionalternativeVariants

auxprogs/joingenes/jg_transcript.cpp:1414

↓ 3 callersFunctionback

! @brief access the last element Returns a reference to the last element in the container. For a JSON container `c`, the expression `c.ba

include/json.hpp:20449

↓ 3 callersFunctionbool_cast

auxprogs/filterBam/src/filterBam.cc:523

↓ 3 callersFunctioncbegin

! @brief returns a const iterator to the first element Returns a const iterator to the first element. @image html range-begin-end.svg "I

include/json.hpp:21006

↓ 3 callersMethodcgp_with_db_execution

(self, resfolder, reffolder, *args)

tests/short/examples/test_examples.py:542

↓ 3 callersMethodclone

include/gene.hh:364

↓ 3 callersMethodclose

src/scanner/scannerbase.h:94

↓ 3 callersMethodcompatibleWith

* Feature::compatibleWith * True if a gene structure could exist that is compatible with both features. */

src/hints.cc:290

↓ 3 callersMethodcompileExtrinsicEvidence

* Gene::initializeGroupLists */

src/gene.cc:1661

↓ 3 callersFunctioncreateDir

* create directory if not existing */

auxprogs/homGeneMapping/include/projectio.hh:80

↓ 3 callersFunctioncross_entropy_error_f

src/train_logReg_param.cc:215

↓ 3 callersMethoddeleteModelParameterFiles

src/etraining.cc:255

↓ 3 callersFunctiondoViterbi

any changes made to the order above needs to be reflected in the following functions */

include/vitmatrix.hh:135

↓ 3 callersMethoddoViterbiPiecewise

* NAMGene::doViterbiPiecewise * Iterate the viterbi algorithm on pieces of DNA small enough so that the DP matrices fit into memory. */

src/namgene.cc:516

↓ 3 callersFunctiondownload

(url, target_dir, unzip=False, set_trset=False, set_testseq=False, set_refanno=False)

tests/longrunning/single_genome/test_single.py:112

↓ 3 callersMethodempty

include/vitmatrix.hh:263

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