package Ġbio . rel atives . bio . y _ str . parser Ċ Ċ import Ġbio . rel atives . bio . y _ str . model . Marker Feature Ċ import Ġbio . rel atives . common . model . Feature Ċ import Ġorg . junit . Assert . assertEquals Ċ import Ġorg . junit . Test Ċ import Ġjava . nio . file . Path Ċ import Ġjava . nio . file . Paths Ċ import Ġjava . util . regex . Pattern Ċ Ċ /** Ċ Ġ* Ġ@ author ĠCreated Ġby ĠV lad isl av ĠMarch enko Ġon Ġ 0 3 . 0 2 . 2 0 2 1 Ċ Ġ*/ Ċ class ĠMarker Feature Parser Test Ġ{ ĊĠĠĠ Ġ@ Test ĊĠĠĠ Ġfun Ġparse Features From Correct B ED () Ġ{ ĊĠĠĠĠĠĠĠ Ġval Ġres Ġ= ĠM FP . parse Features ( PATH _ TO _ CORRECT _ B ED ) ĊĊĠĠĠĠĠĠĠ ĠassertEquals ( 3 , Ġres . size ) ĊĠĠĠĠĠĠĠ Ġassert Records Equal ( FIRST _ FEATURE _ 0 , Ġres [ 0 ]) ĊĠĠĠĠĠĠĠ Ġassert Records Equal ( FIRST _ FEATURE _ 1 , Ġres [ 1 ]) ĊĠĠĠĠĠĠĠ Ġassert Records Equal ( SECOND _ FEATURE , Ġres [ 2 ]) ĊĠĠĠ Ġ} ĊĊĠĠĠ Ġ@ Test ( expected Ġ= ĠIllegalArgumentException :: class ) ĊĠĠĠ Ġfun Ġparse Features From In Correct B ED () Ġ{ ĊĠĠĠĠĠĠĠ ĠM FP . parse Features ( PATH _ TO _ IN CORRECT _ B ED ) ĊĠĠĠ Ġ} ĊĊĠĠĠ Ġprivate Ġfun Ġassert Records Equal ( expected : ĠMarker Feature , Ġactual : ĠFeature ) Ġ{ ĊĠĠĠĠĠĠĠ Ġactual Ġas ĠMarker Feature ĊĠĠĠĠĠĠĠ ĠassertEquals ( expected . start , Ġactual . start ) ĊĠĠĠĠĠĠĠ ĠassertEquals ( expected . end , Ġactual . end ) ĊĠĠĠĠĠĠĠ ĠassertEquals ( expected . chrom osome , Ġactual . chrom osome ) ĊĠĠĠĠĠĠĠ ĠassertEquals ( expected . gene , Ġactual . gene ) ĊĠĠĠĠĠĠĠ ĠassertEquals ( expected . repeat Mot if . pattern (), Ġactual . repeat Mot if . pattern ()) ĊĠĠĠ Ġ} ĊĊĠĠĠ Ġprivate Ġcompanion Ġobject Ġ{ ĊĠĠĠĠĠĠĠ Ġval ĠPATH _ TO _ CORRECT _ B ED : ĠPath Ġ= ĠPaths . get (" src / test / resources / correct . bed ") ĊĠĠĠĠĠĠĠ Ġval ĠPATH _ TO _ IN CORRECT _ B ED : ĠPath Ġ= ĠPaths . get (" src / test / resources / incorrect . bed ") ĊĠĠĠĠĠĠĠ Ġval ĠFIRST _ FEATURE _ 0 Ġ= ĠMarker Feature (" SC YL 3 ", Ġ" chr 1 ", Ġ 1 5 0 0 0 , Ġ 1 5 1 2 0 , ĠPattern . compile (" ag ct ")) ĊĠĠĠĠĠĠĠ Ġval ĠFIRST _ FEATURE _ 1 Ġ= ĠMarker Feature (" SC YL 3 ", Ġ" chr 1 ", Ġ 1 5 1 2 1 , Ġ 1 5 2 3 9 , ĠPattern . compile (" ag ct ")) ĊĠĠĠĠĠĠĠ Ġval ĠSE COND _ FEATURE Ġ= ĠMarker Feature (" SC YL 3 ", Ġ" chr 1 ", Ġ 2 0 0 0 0 , Ġ 2 0 1 1 9 , ĠPattern . compile (" ag c ")) ĊĠĠĠĠĠĠĠ Ġval ĠM FP Ġ= ĠMarker Feature Parser () ĊĠĠĠ Ġ} Ċ }