Class jalview.analysis.AlignmentUtilsTests
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testAddMappedPositions | 0.001s | passed |
| testAddMappedPositions_withStopCodon | 0.001s | passed |
| testAlignAsSameSequences | 0.001s | passed |
| testAlignAsSameSequencesMultipleSubSeq | 0.001s | passed |
| testAlignAs_alternateTranscriptsUngapped | 0s | passed |
| testAlignProteinAsDna | 0.001s | passed |
| testAlignProteinAsDna_incompleteStartCodon | 0s | passed |
| testAlignSequenceAs_keepIntronGapsOnly | 0.001s | passed |
| testAlignSequenceAs_mappedProteinProtein | 0.001s | passed |
| testAlignSequenceAs_withMapping_noIntrons | 0.001s | passed |
| testAlignSequenceAs_withMapping_withIntrons | 0s | passed |
| testAlignSequenceAs_withMapping_withUnmappedProtein | 0s | passed |
| testAlignSequenceAs_withTrailingPeptide | 0.001s | passed |
| testExpandContext | 0.005s | passed |
| testExpandContext_annotation | 0.001s | passed |
| testFindCdsPositions | 0.001s | passed |
| testFindCdsPositions_fivePrimeIncomplete | 0.001s | passed |
| testGetSequencesByName | 0.001s | passed |
| testHasCrossRef | 0.001s | passed |
| testHaveCrossRef | 0s | passed |
| testIsMappable | 0.001s | passed |
| testMakeCdsAlignment | 0.001s | passed |
| testMakeCdsAlignment_alternativeTranscripts | 0.001s | passed |
| testMakeCdsAlignment_filterProducts | 0s | passed |
| testMakeCdsAlignment_multipleProteins | 0.001s | passed |
| testMapCdnaToProtein_forSubsequence | 0s | passed |
| testMapCdsToProtein | 0.001s | passed |
| testMapProteinAlignmentToCdna_noXrefs | 0.001s | passed |
| testMapProteinAlignmentToCdna_prioritiseXrefs | 0.001s | passed |
| testMapProteinAlignmentToCdna_withStartAndStopCodons | 0.001s | passed |
| testMapProteinAlignmentToCdna_withXrefs | 0.001s | passed |
| testShowOrHideSequenceAnnotations | 0.001s | passed |
| testTransferFeatures | 0.001s | passed |
| testTransferFeatures_withOmit | 0s | passed |
| testTransferFeatures_withSelect | 0s | passed |
| testTransferGeneLoci | 0.001s | passed |
| testTranslatesAs | 0.001s | passed |
Standard output
CLUSTAL short/5-11 EFGHIJK short/7-13 GHIJKLM short/9-15 IJKLMNO short/11-17 KLMNOPQ short/13-19 MNOPQRS Flank size: -1 CLUSTAL short/1-40 --------abcdEFGHIJKlmnopqrstuvwxyzabcdefghijklm short/1-40 ------abcdefGHIJKLMnopqrstuvwxyzabcdefghijklm short/1-40 ----abcdefghIJKLMNOpqrstuvwxyzabcdefghijklm short/1-40 --abcdefghijKLMNOPQrstuvwxyzabcdefghijklm short/1-40 abcdefghijklMNOPQRStuvwxyzabcdefghijklm Flank size: 0 CLUSTAL short/5-12 EFGHIJK short/7-14 GHIJKLM short/9-16 IJKLMNO short/11-18 KLMNOPQ short/13-20 MNOPQRS Flank size: 1 CLUSTAL short/4-13 dEFGHIJKl short/6-15 fGHIJKLMn short/8-17 hIJKLMNOp short/10-19 jKLMNOPQr short/12-21 lMNOPQRSt Flank size: 2 CLUSTAL short/3-14 cdEFGHIJKlm short/5-16 efGHIJKLMno short/7-18 ghIJKLMNOpq short/9-20 ijKLMNOPQrs short/11-22 klMNOPQRStu Flank size: 3 CLUSTAL short/2-15 bcdEFGHIJKlmn short/4-17 defGHIJKLMnop short/6-19 fghIJKLMNOpqr short/8-21 hijKLMNOPQrst short/10-23 jklMNOPQRStuv Flank size: 4 CLUSTAL short/1-16 abcdEFGHIJKlmno short/3-18 cdefGHIJKLMnopq short/5-20 efghIJKLMNOpqrs short/7-22 ghijKLMNOPQrstu short/9-24 ijklMNOPQRStuvw Flank size: 5 CLUSTAL short/1-17 -abcdEFGHIJKlmnop short/2-19 bcdefGHIJKLMnopqr short/4-21 defghIJKLMNOpqrst short/6-23 fghijKLMNOPQrstuv short/8-25 hijklMNOPQRStuvwx Flank size: 6 CLUSTAL short/1-18 --abcdEFGHIJKlmnopq short/1-20 abcdefGHIJKLMnopqrs short/3-22 cdefghIJKLMNOpqrstu short/5-24 efghijKLMNOPQrstuvw short/7-26 ghijklMNOPQRStuvwxy Flank size: 7 CLUSTAL short/1-19 ---abcdEFGHIJKlmnopqr short/1-21 -abcdefGHIJKLMnopqrst short/2-23 bcdefghIJKLMNOpqrstuv short/4-25 defghijKLMNOPQrstuvwx short/6-27 fghijklMNOPQRStuvwxyz Flank size: 8 CLUSTAL short/1-20 ----abcdEFGHIJKlmnopqrs short/1-22 --abcdefGHIJKLMnopqrstu short/1-24 abcdefghIJKLMNOpqrstuvw short/3-26 cdefghijKLMNOPQrstuvwxy short/5-28 efghijklMNOPQRStuvwxyza Flank size: 9 CLUSTAL short/1-21 -----abcdEFGHIJKlmnopqrst short/1-23 ---abcdefGHIJKLMnopqrstuv short/1-25 -abcdefghIJKLMNOpqrstuvwx short/2-27 bcdefghijKLMNOPQrstuvwxyz short/4-29 defghijklMNOPQRStuvwxyzab Flank size: 10 CLUSTAL short/1-22 ------abcdEFGHIJKlmnopqrstu short/1-24 ----abcdefGHIJKLMnopqrstuvw short/1-26 --abcdefghIJKLMNOpqrstuvwxy short/1-28 abcdefghijKLMNOPQrstuvwxyza short/3-30 cdefghijklMNOPQRStuvwxyzabc Flank size: 11 CLUSTAL short/1-23 -------abcdEFGHIJKlmnopqrstuv short/1-25 -----abcdefGHIJKLMnopqrstuvwx short/1-27 ---abcdefghIJKLMNOpqrstuvwxyz short/1-29 -abcdefghijKLMNOPQrstuvwxyzab short/2-31 bcdefghijklMNOPQRStuvwxyzabcd Flank size: 12 CLUSTAL short/1-24 --------abcdEFGHIJKlmnopqrstuvw short/1-26 ------abcdefGHIJKLMnopqrstuvwxy short/1-28 ----abcdefghIJKLMNOpqrstuvwxyza short/1-30 --abcdefghijKLMNOPQrstuvwxyzabc short/1-32 abcdefghijklMNOPQRStuvwxyzabcde Flank size: 13 CLUSTAL short/1-25 --------abcdEFGHIJKlmnopqrstuvwx short/1-27 ------abcdefGHIJKLMnopqrstuvwxyz short/1-29 ----abcdefghIJKLMNOpqrstuvwxyzab short/1-31 --abcdefghijKLMNOPQrstuvwxyzabcd short/1-33 abcdefghijklMNOPQRStuvwxyzabcdef Flank size: 14 CLUSTAL short/1-26 --------abcdEFGHIJKlmnopqrstuvwxy short/1-28 ------abcdefGHIJKLMnopqrstuvwxyza short/1-30 ----abcdefghIJKLMNOpqrstuvwxyzabc short/1-32 --abcdefghijKLMNOPQrstuvwxyzabcde short/1-34 abcdefghijklMNOPQRStuvwxyzabcdefg Flank size: 15 CLUSTAL short/1-27 --------abcdEFGHIJKlmnopqrstuvwxyz short/1-29 ------abcdefGHIJKLMnopqrstuvwxyzab short/1-31 ----abcdefghIJKLMNOpqrstuvwxyzabcd short/1-33 --abcdefghijKLMNOPQrstuvwxyzabcdef short/1-35 abcdefghijklMNOPQRStuvwxyzabcdefgh Flank size: 16 CLUSTAL short/1-28 --------abcdEFGHIJKlmnopqrstuvwxyza short/1-30 ------abcdefGHIJKLMnopqrstuvwxyzabc short/1-32 ----abcdefghIJKLMNOpqrstuvwxyzabcde short/1-34 --abcdefghijKLMNOPQrstuvwxyzabcdefg short/1-36 abcdefghijklMNOPQRStuvwxyzabcdefghi Flank size: 17 CLUSTAL short/1-29 --------abcdEFGHIJKlmnopqrstuvwxyzab short/1-31 ------abcdefGHIJKLMnopqrstuvwxyzabcd short/1-33 ----abcdefghIJKLMNOpqrstuvwxyzabcdef short/1-35 --abcdefghijKLMNOPQrstuvwxyzabcdefgh short/1-37 abcdefghijklMNOPQRStuvwxyzabcdefghij Flank size: 18 CLUSTAL short/1-30 --------abcdEFGHIJKlmnopqrstuvwxyzabc short/1-32 ------abcdefGHIJKLMnopqrstuvwxyzabcde short/1-34 ----abcdefghIJKLMNOpqrstuvwxyzabcdefg short/1-36 --abcdefghijKLMNOPQrstuvwxyzabcdefghi short/1-38 abcdefghijklMNOPQRStuvwxyzabcdefghijk Flank size: 19 CLUSTAL short/1-31 --------abcdEFGHIJKlmnopqrstuvwxyzabcd short/1-33 ------abcdefGHIJKLMnopqrstuvwxyzabcdef short/1-35 ----abcdefghIJKLMNOpqrstuvwxyzabcdefgh short/1-37 --abcdefghijKLMNOPQrstuvwxyzabcdefghij short/1-39 abcdefghijklMNOPQRStuvwxyzabcdefghijkl Flank size: 20 CLUSTAL short/1-32 --------abcdEFGHIJKlmnopqrstuvwxyzabcde short/1-34 ------abcdefGHIJKLMnopqrstuvwxyzabcdefg short/1-36 ----abcdefghIJKLMNOpqrstuvwxyzabcdefghi short/1-38 --abcdefghijKLMNOPQrstuvwxyzabcdefghijk short/1-40 abcdefghijklMNOPQRStuvwxyzabcdefghijklm Flank size: 21 CLUSTAL short/1-33 --------abcdEFGHIJKlmnopqrstuvwxyzabcdef short/1-35 ------abcdefGHIJKLMnopqrstuvwxyzabcdefgh short/1-37 ----abcdefghIJKLMNOpqrstuvwxyzabcdefghij short/1-39 --abcdefghijKLMNOPQrstuvwxyzabcdefghijkl short/1-40 abcdefghijklMNOPQRStuvwxyzabcdefghijklm Flank size: 22 CLUSTAL short/1-34 --------abcdEFGHIJKlmnopqrstuvwxyzabcdefg short/1-36 ------abcdefGHIJKLMnopqrstuvwxyzabcdefghi short/1-38 ----abcdefghIJKLMNOpqrstuvwxyzabcdefghijk short/1-40 --abcdefghijKLMNOPQrstuvwxyzabcdefghijklm short/1-40 abcdefghijklMNOPQRStuvwxyzabcdefghijklm Flank size: 23 CLUSTAL short/1-35 --------abcdEFGHIJKlmnopqrstuvwxyzabcdefgh short/1-37 ------abcdefGHIJKLMnopqrstuvwxyzabcdefghij short/1-39 ----abcdefghIJKLMNOpqrstuvwxyzabcdefghijkl short/1-40 --abcdefghijKLMNOPQrstuvwxyzabcdefghijklm short/1-40 abcdefghijklMNOPQRStuvwxyzabcdefghijklm Flank size: 24 CLUSTAL short/1-36 --------abcdEFGHIJKlmnopqrstuvwxyzabcdefghi short/1-38 ------abcdefGHIJKLMnopqrstuvwxyzabcdefghijk short/1-40 ----abcdefghIJKLMNOpqrstuvwxyzabcdefghijklm short/1-40 --abcdefghijKLMNOPQrstuvwxyzabcdefghijklm short/1-40 abcdefghijklMNOPQRStuvwxyzabcdefghijklm
Standard error
SO term type4 invalid SO term type8 invalid