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Functions862 in github.com/Koeng101/dnadesign

⨍ Functions 862◇ Types & classes 212
FunctionSmithWaterman
SmithWaterman performs local alignment between two strings using the Smith-Waterman algorithm. It returns the max score and optimal local alignments b
lib/align/align.go:171
MethodStoreFeatureSequences
StoreFeatureSequences calls StoreSequence on all features. The resulting JSON is guaranteed to have useful Feature.Sequence values. Useful when export
lib/bio/genbank/genbank.go:129
MethodSwap
(i, j int)
lib/fold/linearfold/linearfold.go:408
FunctionTestAddCodonTable
(t *testing.T)
lib/synthesis/codon/codon_test.go:263
FunctionTestAllTypesImplementWriterTo
(t *testing.T)
lib/bio/iowriter_test.go:16
FunctionTestAlphabet
(t *testing.T)
lib/alphabet/alphabet_test.go:10
FunctionTestAlphabet_Symbols
(t *testing.T)
lib/alphabet/alphabet_test.go:66
FunctionTestAndronescu2007Params
(t *testing.T)
lib/fold/mfe/mfe_test.go:295
FunctionTestAndronescu2007ParamsNoDanglingEnergies
(t *testing.T)
lib/fold/mfe/mfe_test.go:23
FunctionTestBadCodonTable
(t *testing.T)
lib/synthesis/fix/synthesis_test.go:198
FunctionTestBasicParsing
(t *testing.T)
lib/bio/uniref/uniref_test.go:114
FunctionTestBenchlingGenbank
****************************************************************************** Gbk/gb/genbank related benchmarks end here. *************************
lib/bio/genbank/genbank_test.go:282
FunctionTestBtgZIComplexFix
(t *testing.T)
lib/synthesis/fix/synthesis_test.go:165
FunctionTestBufferFailure
(t *testing.T)
lib/synthesis/fix/synthesis_test.go:175
FunctionTestBufferSmall
(t *testing.T)
lib/bio/fasta/fasta_test.go:109
FunctionTestBuildFeatureString
(t *testing.T)
lib/bio/genbank/genbank_test.go:680
FunctionTestBuildLocationString
(t *testing.T)
lib/bio/genbank/genbank_test.go:625
FunctionTestCONTRAfold
(t *testing.T)
lib/fold/fold_test.go:10
FunctionTestCancelCause
(t *testing.T)
lib/bio/errgroup/go120_test.go:17
FunctionTestCapitalizationRegression
(t *testing.T)
lib/synthesis/codon/codon_test.go:302
FunctionTestCds
(t *testing.T)
lib/synthesis/fix/synthesis_test.go:74
FunctionTestCdsBadInput
(t *testing.T)
lib/synthesis/fix/synthesis_test.go:128
FunctionTestCdsWithAlteredCodonTable
(t *testing.T)
lib/synthesis/fix/synthesis_test.go:21
FunctionTestCheckLongRegresssion
(t *testing.T)
lib/synthesis/fragment/fragment_test.go:72
FunctionTestCircularCutRegression
(t *testing.T)
lib/clone/clone_test.go:206
FunctionTestCircularLigate
(t *testing.T)
lib/clone/clone_test.go:137
FunctionTestCodecGet
(t *testing.T)
lib/bio/slow5/svb/codec_test.go:8
FunctionTestCodonJSONRegression
(t *testing.T)
lib/synthesis/codon/codon_test.go:556
FunctionTestComplement
(t *testing.T)
lib/transform/transform_test.go:30
FunctionTestComplementBase
(t *testing.T)
lib/transform/transform_test.go:63
FunctionTestComplementBaseError
(t *testing.T)
lib/transform/transform_test.go:75
FunctionTestComplementBaseRNA
(t *testing.T)
lib/transform/transform_test.go:109
FunctionTestComplementRNA
(t *testing.T)
lib/transform/transform_test.go:135
FunctionTestComplementRNANoRandom
(t *testing.T)
lib/transform/transform_test.go:121
FunctionTestCompromiseCodonTable
* ***************************************************************************** Codon Compromise + Add related tests begin here. *******************
lib/synthesis/codon/codon_test.go:230
FunctionTestConsortiumRegression
(t *testing.T)
lib/bio/genbank/genbank_test.go:746
FunctionTestCreateBarcode
(t *testing.T)
lib/primers/primers_test.go:114
FunctionTestCutWithEnzyme
(t *testing.T)
lib/clone/clone_test.go:17
FunctionTestCutWithEnzymeByName
(t *testing.T)
lib/clone/clone_test.go:10
FunctionTestCutWithEnzymeRegression
(t *testing.T)
lib/clone/clone_test.go:97
FunctionTestDualBarcodesToPrimerSet
(t *testing.T)
lib/sequencing/barcoding/barcoding_test.go:81
FunctionTestEmptyHeader
(t *testing.T)
lib/bio/uniref/uniref_test.go:136
FunctionTestEncodeAndDecode
(t *testing.T)
lib/seqhash/seqhash_test.go:69
FunctionTestEncodeDecode128Uint32
(t *testing.T)
lib/bio/slow5/svb/decoder_amd64_test.go:104
FunctionTestEncodeDecode256Uint32
(t *testing.T)
lib/bio/slow5/svb/decoder_amd64_test.go:125
FunctionTestEncodeDecode512Uint32
(t *testing.T)
lib/bio/slow5/svb/decoder_amd64_test.go:146
FunctionTestEncodeUint32
(t *testing.T)
lib/bio/slow5/svb/encoder_test.go:8
FunctionTestEntry
(t *testing.T)
lib/bio/uniprot/uniprot_test.go:50
FunctionTestExport_error
(t *testing.T)
lib/bio/rebase/rebase_test.go:58
FunctionTestFeature_GetSequence_Legacy
this was hand-written and tests the same as the above suite.
lib/bio/genbank/genbank_test.go:291
FunctionTestFlagEncoding
(t *testing.T)
lib/seqhash/seqhash_test.go:142
FunctionTestFold
(t *testing.T)
lib/fold/zuker/fold_test.go:9
FunctionTestFragment
(t *testing.T)
lib/synthesis/fragment/fragment_test.go:16
FunctionTestFragmentSizes
(t *testing.T)
lib/synthesis/fragment/fragment_test.go:34
FunctionTestFragmentWithOverhangs
(t *testing.T)
lib/synthesis/fragment/fragment_test.go:98
FunctionTestGbLocationStringBuilder
(t *testing.T)
lib/bio/genbank/genbank_test.go:117
FunctionTestGbkIO
(t *testing.T)
lib/bio/genbank/genbank_test.go:36
FunctionTestGbkLocationStringBuilder
(t *testing.T)
lib/bio/genbank/genbank_test.go:89
FunctionTestGcContent
(t *testing.T)
lib/checks/checks_test.go:21
FunctionTestGenbankNewlineParsingRegression
(t *testing.T)
lib/bio/genbank/genbank_test.go:251
FunctionTestGenerateVCF
(t *testing.T)
external/bcftools/bcftools_test.go:14
FunctionTestGet
(t *testing.T)
lib/bio/uniprot/uniprot_test.go:62
FunctionTestGetCodonFrequency
(t *testing.T)
lib/synthesis/codon/codon_test.go:160
FunctionTestGetSequenceMethod
(t *testing.T)
lib/bio/genbank/genbank_test.go:197
FunctionTestGoLimit
(t *testing.T)
lib/bio/errgroup/errgroup_test.go:231
FunctionTestHash2
(t *testing.T)
lib/seqhash/seqhash_test.go:13
FunctionTestHash2Fragment
(t *testing.T)
lib/seqhash/seqhash_test.go:154
FunctionTestHeader
(t *testing.T)
lib/bio/uniprot/uniprot_test.go:38
FunctionTestHeader
(t *testing.T)
lib/bio/fasta/fasta_test.go:11
FunctionTestIUPAC
(t *testing.T)
lib/transform/variants/variants_test.go:11
FunctionTestIUPAC_errors
(t *testing.T)
lib/transform/variants/variants_test.go:29
FunctionTestIntListType_UnmarshalText
(t *testing.T)
lib/bio/uniprot/xml_test.go:7
FunctionTestIsDNA
(t *testing.T)
lib/checks/checks_test.go:28
FunctionTestIsPalindromic
This also needs an example test.
lib/checks/checks_test.go:10
FunctionTestIsRNA
(t *testing.T)
lib/checks/checks_test.go:59
FunctionTestIssue279PCRBug
Test to catch bug discovered by @Koeng101, see issue #279.
lib/primers/pcr/pcr_test.go:79
FunctionTestIssue303Regression
(t *testing.T)
lib/bio/genbank/genbank_test.go:729
FunctionTestIssue70PCRBug
(t *testing.T)
lib/primers/pcr/pcr_test.go:93
FunctionTestKmer
(t *testing.T)
lib/clone/kmer_test.go:15
FunctionTestKmerFailure
(t *testing.T)
lib/clone/kmer_test.go:63
FunctionTestLeastRotation
(t *testing.T)
lib/seqhash/seqhash_test.go:117
FunctionTestLinearFold
(t *testing.T)
lib/fold/linearfold/linearfold_test.go:25
FunctionTestLinearLigate
(t *testing.T)
lib/clone/clone_test.go:149
FunctionTestLocationParser
(t *testing.T)
lib/bio/genbank/genbank_test.go:208
FunctionTestLongFragment
(t *testing.T)
lib/synthesis/fragment/fragment_test.go:57
FunctionTestMain
(m *testing.M)
lib/bio/slow5/svb/perf/perf_test.go:22
FunctionTestMarmurDoty
(t *testing.T)
lib/primers/primers_test.go:21
FunctionTestMash
(t *testing.T)
lib/align/mash/mash_test.go:10
FunctionTestMatchesConversion
(t *testing.T)
lib/align/megamash/megamash_test.go:43
FunctionTestMegamash
(t *testing.T)
lib/align/megamash/megamash_test.go:10
FunctionTestMeltingTemp
(t *testing.T)
lib/primers/primers_test.go:78
FunctionTestMethylatedGoldenGate
(t *testing.T)
lib/clone/clone_test.go:219
FunctionTestMinimap2
TestMinimap2 tests the Minimap2Raw function
external/minimap2/minimap2_test.go:14
FunctionTestMinimumFreeEnergy
(t *testing.T)
lib/fold/mfe/mfe_test.go:596
FunctionTestMultiGenbankIO
(t *testing.T)
lib/bio/genbank/genbank_test.go:69
FunctionTestMultiLineFeatureParse
(t *testing.T)
lib/bio/genbank/genbank_test.go:57
FunctionTestNdeIFix
(t *testing.T)
lib/synthesis/fix/synthesis_test.go:219
FunctionTestNeedlemanWunsch
(t *testing.T)
lib/align/align_test.go:11
FunctionTestOptimize
(t *testing.T)
lib/synthesis/codon/codon_test.go:52
FunctionTestOptimizeDifferentSeed
(t *testing.T)
lib/synthesis/codon/codon_test.go:100
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