JAL-629 mild improvement to test

diff --git a/test/jalview/io/uniref50-relaxed.phy b/test/jalview/io/uniref50-relaxed.phy
new file mode 100644 (file)
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 (file)
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 (file)
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 (file)
--- 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" }, //
     };
   }
 }