From 30d70077d3e8857e07c794c9662549fc08fccebb Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Wed, 12 Apr 2023 15:20:40 +0100 Subject: [PATCH] JAL-629 mild improvement to test --- test/jalview/io/uniref50-relaxed.phy | 48 ++++++++++++++++++++++++++++++++++ test/jalview/io/uniref50-strict.phy | 48 ++++++++++++++++++++++++++++++++++ test/jalview/io/uniref50.phy | 48 ++++++++++++++++++++++++++++++++++ test/jalview/util/FileUtilsTest.java | 6 ++--- 4 files changed, 147 insertions(+), 3 deletions(-) create mode 100644 test/jalview/io/uniref50-relaxed.phy create mode 100644 test/jalview/io/uniref50-strict.phy create mode 100644 test/jalview/io/uniref50.phy diff --git a/test/jalview/io/uniref50-relaxed.phy b/test/jalview/io/uniref50-relaxed.phy new file mode 100644 index 0000000..d444d13 --- /dev/null +++ b/test/jalview/io/uniref50-relaxed.phy @@ -0,0 +1,48 @@ +15 157 +FER_CAPAA -----------------------------------------------------------A +FER_CAPAN MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA +FER1_SOLLC MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +Q93XJ9_SOLTU MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +FER1_PEA MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA +Q7XA98_TRIPR MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA +FER1_MESCR MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA +FER1_SPIOL MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA +FER3_RAPSA -----------------------------------------------------------A +FER2_ARATH MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA +FER_BRANA -----------------------------------------------------------A +FER1_ARATH MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +Q93Z60_ARATH MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +FER1_MAIZE MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA +O80429_MAIZE MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA + +SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG +SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG +SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG +TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG +AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG +AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ +TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE +TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ + +NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +SFLDD-------------------------------- +SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- diff --git a/test/jalview/io/uniref50-strict.phy b/test/jalview/io/uniref50-strict.phy new file mode 100644 index 0000000..ae38cec --- /dev/null +++ b/test/jalview/io/uniref50-strict.phy @@ -0,0 +1,48 @@ +15 157 +FER_CAPAA -----------------------------------------------------------A +FER_CAPAN MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA +FER1_SOLLCMA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +Q93XJ9_SOLMA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +FER1_PEA MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA +Q7XA98_TRIMATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA +FER1_MESCRMAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA +FER1_SPIOLMAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA +FER3_RAPSA-----------------------------------------------------------A +FER2_ARATHMAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA +FER_BRANA -----------------------------------------------------------A +FER1_ARATHMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +Q93Z60_ARAMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +FER1_MAIZEMATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA +O80429_MAIMAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA + +SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG +SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG +SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG +TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG +AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG +AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ +TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE +TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ + +NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +SFLDD-------------------------------- +SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- diff --git a/test/jalview/io/uniref50.phy b/test/jalview/io/uniref50.phy new file mode 100644 index 0000000..ae38cec --- /dev/null +++ b/test/jalview/io/uniref50.phy @@ -0,0 +1,48 @@ +15 157 +FER_CAPAA -----------------------------------------------------------A +FER_CAPAN MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA +FER1_SOLLCMA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +Q93XJ9_SOLMA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +FER1_PEA MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA +Q7XA98_TRIMATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA +FER1_MESCRMAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA +FER1_SPIOLMAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA +FER3_RAPSA-----------------------------------------------------------A +FER2_ARATHMAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA +FER_BRANA -----------------------------------------------------------A +FER1_ARATHMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +Q93Z60_ARAMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +FER1_MAIZEMATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA +O80429_MAIMAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA + +SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG +SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG +SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG +TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG +AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG +AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ +TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE +TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ + +NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +SFLDD-------------------------------- +SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- diff --git a/test/jalview/util/FileUtilsTest.java b/test/jalview/util/FileUtilsTest.java index 79c703f..35853b0 100644 --- a/test/jalview/util/FileUtilsTest.java +++ b/test/jalview/util/FileUtilsTest.java @@ -114,9 +114,9 @@ public class FileUtilsTest return new Object[][] { // -1=startsWith, 0=equals, 1=endsWith { "~/hello/sailor", -1, homeDir, "sailor", "~" }, // { "~/hello/sailor", 1, "/hello", "sailor", "~" }, // - { "./examples/uniref50.fa", -1, "/", "uniref50", null }, // - { "./examples/uniref50.fa", 1, "/examples", "uniref50", null }, // - { "examples/uniref50.fa", 1, "/examples", "uniref50", null }, // + { "./examples/uniref50.fa", -1, "/", "uniref50", "." }, // + { "./examples/uniref50.fa", 1, "/examples", "uniref50", "." }, // + { "examples/uniref50.fa", 1, "/examples", "uniref50", ".fa" }, // }; } } -- 1.7.10.2