From: tcofoegbu Date: Thu, 23 Jul 2015 11:40:24 +0000 (+0100) Subject: JAL-1805 modified test setup's so the are ran for groups which requires them X-Git-Tag: Release_2_10_0~563^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=28fda83cbef0c9c82cd09a343af4e1721085c104;hp=4de381907ba9fbd6b079aaf5f1d089680f0d9c6f;p=jalview.git JAL-1805 modified test setup's so the are ran for groups which requires them --- diff --git a/examples/test.aln b/examples/test.aln deleted file mode 100644 index 08a7ac3..0000000 --- a/examples/test.aln +++ /dev/null @@ -1,53 +0,0 @@ -CLUSTAL - -FER_CAPAA/1-97 -----------------------------------------------------------A -FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA -FER1_SOLLC/1-144 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA -Q93XJ9_SOLTU/1-144 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA -FER1_PEA/1-149 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA -Q7XA98_TRIPR/1-152 MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA -FER1_MESCR/1-148 MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA -FER1_SPIOL/1-147 MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA -FER3_RAPSA/1-96 -----------------------------------------------------------A -FER1_ARATH/1-148 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA -FER_BRANA/1-96 -----------------------------------------------------------A -FER2_ARATH/1-148 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA -Q93Z60_ARATH/1-118 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA -FER1_MAIZE/1-150 MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA -O80429_MAIZE/1-140 MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA -1A70|/1-97 -----------------------------------------------------------A - -FER_CAPAA/1-97 SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG -FER_CAPAN/1-144 SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG -FER1_SOLLC/1-144 SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG -Q93XJ9_SOLTU/1-144 SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG -FER1_PEA/1-149 SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG -Q7XA98_TRIPR/1-152 TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG -FER1_MESCR/1-148 AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG -FER1_SPIOL/1-147 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ -FER3_RAPSA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ -FER1_ARATH/1-148 TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ -FER_BRANA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE -FER2_ARATH/1-148 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ -Q93Z60_ARATH/1-118 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ -FER1_MAIZE/1-150 TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ -O80429_MAIZE/1-140 TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ -1A70|/1-97 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ - -FER_CAPAA/1-97 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- -FER_CAPAN/1-144 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- -FER1_SOLLC/1-144 NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- -Q93XJ9_SOLTU/1-144 KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- -FER1_PEA/1-149 SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- -Q7XA98_TRIPR/1-152 SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- -FER1_MESCR/1-148 SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- -FER1_SPIOL/1-147 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- -FER3_RAPSA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- -FER1_ARATH/1-148 SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- -FER_BRANA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- -FER2_ARATH/1-148 SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- -Q93Z60_ARATH/1-118 SFLDD-------------------------------- -FER1_MAIZE/1-150 SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA -O80429_MAIZE/1-140 SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- -1A70|/1-97 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA - diff --git a/examples/test.amsa b/examples/test.amsa deleted file mode 100644 index be456bf..0000000 --- a/examples/test.amsa +++ /dev/null @@ -1,72 +0,0 @@ ->FER_CAPAA Ferredoxin ------------------------------------------------------------ASYKVKLITPDGP -IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV -TIETHKEAELVG- ->FER_CAPAN Ferredoxin, chloroplast precursor -MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP -IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV -TIETHKEAELVG- ->FER1_SOLLC Ferredoxin-1, chloroplast precursor -MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP -IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV -TIETHKEEELTA- ->Q93XJ9_SOLTU Ferredoxin I precursor -MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP -IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV -TIETHKEEELTA- ->FER1_PEA Ferredoxin-1, chloroplast precursor -MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT -QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV -VIETHKEEDLTA- ->Q7XA98_TRIPR Ferredoxin I -MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP -QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV -TIETHKEEELTA- ->FER1_MESCR Ferredoxin-1, chloroplast precursor -MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK -QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV -TIETHKEEELTA- ->FER1_SPIOL Ferredoxin-1, chloroplast precursor -MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN -VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV -TIETHKEEELTA- ->FER3_RAPSA Ferredoxin, leaf L-A ------------------------------------------------------------ATYKVKFITPEGE -QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV -TIETHREEDMV-- ->FER1_ARATH Ferredoxin-1, chloroplast precursor -MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE -LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV -TIETHKEEDIV-- ->FER_BRANA Ferredoxin ------------------------------------------------------------ATYKVKFITPEGE -QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV -TIETHKEEELV-- ->FER2_ARATH Ferredoxin-2, chloroplast precursor -MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE -QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV -VIETHKEEAIM-- ->Q93Z60_ARATH At1g10960/T19D16_12 -MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE -QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- -------------- ->FER1_MAIZE Ferredoxin-1, chloroplast precursor -MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE -VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV -VIETHKEEELTGA ->O80429_MAIZE Ferredoxin -MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE -VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV -VIETHKEDDLL-- ->1A70| ------------------------------------------------------------AAYKVTLVTPTGN -VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV -TIETHKKEELTA ->#_Secondary Structure New description - 1 2 - 3 F F F 4 5 6 7 F 9 - ->#_Iron Sulphur Contacts New description - - F F F F - diff --git a/examples/test.blc b/examples/test.blc deleted file mode 100644 index f419862..0000000 --- a/examples/test.blc +++ /dev/null @@ -1,175 +0,0 @@ ->FER_CAPAA/1-97 Ferredoxin ->FER_CAPAN/1-144 Ferredoxin, chloroplast precursor ->FER1_SOLLC/1-144 Ferredoxin-1, chloroplast precursor ->Q93XJ9_SOLTU/1-144 Ferredoxin I precursor ->FER1_PEA/1-149 Ferredoxin-1, chloroplast precursor ->Q7XA98_TRIPR/1-152 Ferredoxin I ->FER1_MESCR/1-148 Ferredoxin-1, chloroplast precursor ->FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor ->FER3_RAPSA/1-96 Ferredoxin, leaf L-A ->FER1_ARATH/1-148 Ferredoxin-1, chloroplast precursor ->FER_BRANA/1-96 Ferredoxin ->FER2_ARATH/1-148 Ferredoxin-2, chloroplast precursor ->Q93Z60_ARATH/1-118 At1g10960/T19D16_12 ->FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor ->O80429_MAIZE/1-140 Ferredoxin ->1A70|/1-97 -* iteration 1 --MMMMMMM-M-MMMM- --AAAAAAA-A-AAAA- -----TTAA-S-SSTA- -----TTTT-T-TTVT- --------------L-- --------------G-- -------TT-----S-- -----PPAT-----P-- --SSSAAAT-A-AAR-- --VIILLLM-L-LLA-- --SSSYYSM-S-SSP-- --AGGGGGG-S-SSA-- --TTTTTA--A-AAF-- --MMMAAT--I-IIFA- --IIIVVMM-V-VVFL- --SSSSSSA-G-SSSS- --TTTTTTT-T-TTSM- --SSSSSAT-S-SSSS- --FFFFFFF-F-FFSI- --MLLLMAV-I-LLLL- --PPPRRPP-R-RRRR- --RRRTRKK-R-RRA-- --KKKQQ-P-S-QQA-- --PPPPP-Q-P-QQP-- --AAVMVTA-A-TTAA- --VVVPPPP-P-PPPP- --TTTMMPP-I-IITP- --SSSSSMM-S-SSAP- --LLLVVTM-L-LLVC- -------AA-R-RR-F- --KKKTAAA-S-SS-S- --PAATTLL-L-LLAS- --IIITTPP-P-PPLP- --PSSKTTS-S-FFPL- --NNNATNN-A-AAAR- --VVVFTVT-N-NNAL- --GGGSKGG-T-TTKR- --EEENARR-Q-QQVV- ------F---------- ------P---------- --AAAGSAS-S-SSGA- --LLLFGLL-L-LLIV- --FFFLFFF-F-FFMA- --GGGGGGG-G-GGGK- --LLLLLLL-L-LLRP- --KKKKKKK-K-KKSL- --SSSTSST-S-SSAA- ------V---------- --AGGSSSG-G-SSSA- -----LTAS-T-TTSP- -----KKSR-A-AARM- --NRRRRR--R-RRRR- --GNNGG---G-GG-R- --GGGDDGG-G-GG-Q- --KRRLLRG-R-RRRL- --VIIAAVR-V-VVLL- --TTTVVTM-T-TTRR- --CCCAAAT-A-AAAA- --MMMMMMM-M-MMQQ- -AAAAAAAAAAAAAAAA -SSSSSTAATTTTTTTA -YYYYYYYYYYYYYYYY -KKKKKKKKKKKKKNNK -VVVVVVVVVVVVVVVV -KKKKKKTTKKKKKKKT -LLLLLLLLFFFFFLLL -IIIIVIVVIIIIIIIV -TTTTTTTTTTTTTTTT -PPPPPPPPPPPPPPPP -DDEDDEETEEEEEEET -GGGGGGGGGGGGGGGG -PPPPTPKNEEEEEEEN -IIIIQQQVQLQQQVVV -EEEEEEEEEEEEEEEE -FFFFFFLFVVVVVLLF -DDEEEDEQEEEEEQQQ -CCCCCCCCCCCCCVVC -PPPPPPPPDDDEEPPP -DDDDSDDDDDDEEDDD -DNDDDDDDDDDDDDDD -VVVVVVVVVVVVVVVV -YYYYYYYYYYYYYYYY -IIIIIIIIVVVVVIII -LLLLLLLLLLLLLLLL -DDDDDDDDDDDDDDDD -QQQQHHAAAAAAAQFA -AAAAAAAAAAAAAAAA -EEEEEEEEEEEEEEEE -EEEEEEEEEEEEEEEE -AAEEVVAEAAAAADEE -GGGGGGGGGGGGGGGG -HHHHIIIIIIILLIII -DDDDDEDDDDDDDDDD -LLLLLLLLLLLLLLLL -PPPPPPPPPPPPPPPP -YYYYYYYYYYYYYYFY -SSSSSSSSSSSSSSSS -CCCCCCCCCCCCCCCC -RRRRRRRRRRRRRRRR -AAAAAAAAAAAAAAAA -GGGGGGGGGGGGGGGG -SSSSSSSSSSSSSSSS -CCCCCCCCCCCCCCCC -SSSSSSSSSSSSSSSS -SSSSSSSSSSSSSSSS -CCCCCCCCCCCCCCCC -AAAAAAAAAAAAAAAA -GGGGGGGGGGGGGGGG -KKKKKKKKKKKKKKKK -IIVVVVVLVVVVVVVL -AATTVVTKVVVVVVVK -GGAAGNSTSSSSSSST -GGGGGGGGGGGGGGGG -AASTENSSSSFSSSSS -VVVVVVVLVVVIIVVL -DDDDDNNNDDDDDDDN -QQQQQQQQQQQQQQQQ -TTSSSEDDSSSSSSSD -DDDDDDDDDDDDDDDD -GGGGGGGQQQEQQQQQ -NNNKSSSSSSSSSSSS -FFFFFFFFFFFFFYFF -LLLLLLLLLLLLLLLL -DDDDDDDDDDDDDDND -DDEDDDDDDDDDDDDD -DDDDEEDDDEDE-GND -QQQQQQQQQQQQ-QQQ -LLEEIIIIIIIM-IVI -EEAAEEKDAGAS-AAD -EEAAAGEEEEEE-DDE -GGGGGGGGGGGG-GGG -WWFFFWWWFFFY-WWW -VVVVVVVVVVVV-VVV -LLLLLLLLLLLL-LLL -TTTTTTTTTTTT-TTT -CCCCCCCCCCCC-CCC -VVVVVVVAAAAV-HAA -AAAAAAAAAAAA-AAA -YYYYYFYYYYYY-YYY -PPPPPPPPPPPP-PPP -QQKKTTTVTTTT-TTV -SSGCSSGSSSSS-SSS -DDDDDDDDDDDD-DDD -VVVVVVVVVVVV-VVV -TTTTVTTTTTTV-VVT -IIIIIIIIIIII-III -EEEEEEEEEEEE-EEE -TTTTTTTTTTTT-TTT -HHHHHHHHHHHH-HHH -KKKKKKKKRKKK-KKK -EEEEEEEEEEEE-EEK -AAEEEEEEEEEE-EDE -EEEEDEEEDDEA-EDE -LLLLLLLLMILI-LLL -VVTTTTTTVVVM-TLT -GGAAAAAA-----G-A --------------A-- -* diff --git a/examples/test.html b/examples/test.html deleted file mode 100644 index 229596c..0000000 --- a/examples/test.html +++ /dev/null @@ -1,29 +0,0 @@ - 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- - \ No newline at end of file diff --git a/examples/test.jvp b/examples/test.jvp deleted file mode 100644 index f4eecc5..0000000 Binary files a/examples/test.jvp and /dev/null differ diff --git a/examples/test.msf b/examples/test.msf deleted file mode 100644 index 8a476aa..0000000 --- a/examples/test.msf +++ /dev/null @@ -1,93 +0,0 @@ -!!AA_MULTIPLE_ALIGNMENT 1.0 - - MSF: 157 Type: P Check: 4683 .. - - - Name: FER_CAPAA/1-157 Len: 157 Check: 3320 Weight: 1.00 - Name: FER_CAPAN/1-145 Len: 157 Check: 2597 Weight: 1.00 - Name: FER1_SOLLC/1-145 Len: 157 Check: 3815 Weight: 1.00 - Name: Q93XJ9_SOLTU/1-145 Len: 157 Check: 4240 Weight: 1.00 - Name: FER1_PEA/1-150 Len: 157 Check: 9547 Weight: 1.00 - Name: Q7XA98_TRIPR/1-153 Len: 157 Check: 4969 Weight: 1.00 - Name: FER1_MESCR/1-149 Len: 157 Check: 7664 Weight: 1.00 - Name: FER1_SPIOL/1-148 Len: 157 Check: 5892 Weight: 1.00 - Name: FER3_RAPSA/1-157 Len: 157 Check: 8715 Weight: 1.00 - Name: FER1_ARATH/1-150 Len: 157 Check: 3201 Weight: 1.00 - Name: FER_BRANA/1-157 Len: 157 Check: 7649 Weight: 1.00 - Name: FER2_ARATH/1-150 Len: 157 Check: 4904 Weight: 1.00 - Name: Q93Z60_ARATH/1-150 Len: 157 Check: 4436 Weight: 1.00 - Name: FER1_MAIZE/1-150 Len: 157 Check: 4392 Weight: 1.00 - Name: O80429_MAIZE/1-142 Len: 157 Check: 8858 Weight: 1.00 - Name: 1A70|/1-156 Len: 156 Check: 484 Weight: 1.00 - - -// - -FER_CAPAA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ -FER_CAPAN/1-145 MA......SV SATMISTSFM PRKPAVTSL. KPIPNVGE.. ALFGLKS.A. -FER1_SOLLC/1-145 MA......SI SGTMISTSFL PRKPAVTSL. KAISNVGE.. ALFGLKS.G. -Q93XJ9_SOLTU/1-145 MA......SI SGTMISTSFL PRKPVVTSL. KAISNVGE.. ALFGLKS.G. -FER1_PEA/1-150 MATT...PAL YGTAVSTSFL RTQPMPMSV. TTTKAFSN.. GFLGLKT.SL -Q7XA98_TRIPR/1-153 MATT...PAL YGTAVSTSFM RRQPVPMSV. ATTTTTKAFP SGFGLKSVST -FER1_MESCR/1-149 MAAT..TAAL SGATMSTAFA PK..TPPMTA ALPTNVGR.. ALFGLKS.SA -FER1_SPIOL/1-148 MAAT..TTTM MG..MATTFV PKPQAPPMMA ALPSNTGR.. SLFGLKT.GS -FER3_RAPSA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ -FER1_ARATH/1-150 MAST....AL SSAIVGTSFI RRSPAPISLR SLPSANTQ.. SLFGLKS.GT -FER_BRANA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ -FER2_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST -Q93Z60_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST -FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV. .ALPAAKV.. GIMGRSA.SS -O80429_MAIZE/1-142 MAAT...... ...ALSMSIL R...APPPCF SSPLRLRV.. AVAKPLA.AP -1A70|/1-156 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ - -FER_CAPAA/1-157 ~~~~~~~~~A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA -FER_CAPAN/1-145 .NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA -FER1_SOLLC/1-145 .RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA -Q93XJ9_SOLTU/1-145 .RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA -FER1_PEA/1-150 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA -Q7XA98_TRIPR/1-153 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA -FER1_MESCR/1-149 SR.GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA -FER1_SPIOL/1-148 R..GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA -FER3_RAPSA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA -FER1_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA -FER_BRANA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA -FER2_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA -Q93Z60_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA -FER1_MAIZE/1-150 RR..RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA -O80429_MAIZE/1-142 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA -1A70|/1-156 ~~~~~~~~~A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA - -FER_CAPAA/1-157 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK -FER_CAPAN/1-145 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK -FER1_SOLLC/1-145 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK -Q93XJ9_SOLTU/1-145 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK -FER1_PEA/1-150 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK -Q7XA98_TRIPR/1-153 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK -FER1_MESCR/1-149 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK -FER1_SPIOL/1-148 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK -FER3_RAPSA/1-157 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR -FER1_ARATH/1-150 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK -FER_BRANA/1-157 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK -FER2_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK -Q93Z60_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDD~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ -FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK -O80429_MAIZE/1-142 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK -1A70|/1-156 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK - -FER_CAPAA/1-157 EAELVG~ -FER_CAPAN/1-145 EAELVG~ -FER1_SOLLC/1-145 EEELTA~ -Q93XJ9_SOLTU/1-145 EEELTA~ -FER1_PEA/1-150 EEDLTA~ -Q7XA98_TRIPR/1-153 EEELTA~ -FER1_MESCR/1-149 EEELTA~ -FER1_SPIOL/1-148 EEELTA~ -FER3_RAPSA/1-157 EEDMV~~ -FER1_ARATH/1-150 EEDIV~~ -FER_BRANA/1-157 EEELV~~ -FER2_ARATH/1-150 EEAIM~~ -Q93Z60_ARATH/1-150 ~~~~~~~ -FER1_MAIZE/1-150 EEELTGA -O80429_MAIZE/1-142 EDDLL~~ -1A70|/1-156 KEELTA - diff --git a/examples/test.pfam b/examples/test.pfam deleted file mode 100644 index dfaadf7..0000000 --- a/examples/test.pfam +++ /dev/null @@ -1,17 +0,0 @@ -FER_CAPAA/1-97 -----------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- -FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- -FER1_SOLLC/1-144 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- -Q93XJ9_SOLTU/1-144 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- -FER1_PEA/1-149 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- -Q7XA98_TRIPR/1-152 MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- -FER1_MESCR/1-148 MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- -FER1_SPIOL/1-147 MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- -FER3_RAPSA/1-96 -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- -FER1_ARATH/1-148 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- -FER_BRANA/1-96 -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- -FER2_ARATH/1-148 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- -Q93Z60_ARATH/1-118 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------------------- -FER1_MAIZE/1-150 MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA -O80429_MAIZE/1-140 MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- -1A70|/1-97 -----------------------------------------------------------AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA - diff --git a/examples/test.pileup b/examples/test.pileup deleted file mode 100644 index d191e4b..0000000 --- a/examples/test.pileup +++ /dev/null @@ -1,93 +0,0 @@ -PileUp - - MSF: 157 Type: P Check: 1935 .. - - - Name: FER_CAPAA/1-97 oo Len: 157 Check: 5701 Weight: 1.00 - Name: FER_CAPAN/1-144 oo Len: 157 Check: 8823 Weight: 1.00 - Name: FER1_SOLLC/1-144 oo Len: 157 Check: 41 Weight: 1.00 - Name: Q93XJ9_SOLTU/1-144 oo Len: 157 Check: 466 Weight: 1.00 - Name: FER1_PEA/1-149 oo Len: 157 Check: 5889 Weight: 1.00 - Name: Q7XA98_TRIPR/1-152 oo Len: 157 Check: 1438 Weight: 1.00 - Name: FER1_MESCR/1-148 oo Len: 157 Check: 3943 Weight: 1.00 - Name: FER1_SPIOL/1-147 oo Len: 157 Check: 2139 Weight: 1.00 - Name: FER3_RAPSA/1-96 oo Len: 157 Check: 7694 Weight: 1.00 - Name: FER1_ARATH/1-148 oo Len: 157 Check: 6163 Weight: 1.00 - Name: FER_BRANA/1-96 oo Len: 157 Check: 6628 Weight: 1.00 - Name: FER2_ARATH/1-148 oo Len: 157 Check: 7866 Weight: 1.00 - Name: Q93Z60_ARATH/1-118 oo Len: 157 Check: 3003 Weight: 1.00 - Name: FER1_MAIZE/1-150 oo Len: 157 Check: 4097 Weight: 1.00 - Name: O80429_MAIZE/1-140 oo Len: 157 Check: 1696 Weight: 1.00 - Name: 1A70|/1-97 oo Len: 156 Check: 6348 Weight: 1.00 - - -// - -FER_CAPAA/1-97 ---------- ---------- ---------- ---------- ---------- -FER_CAPAN/1-144 MA------SV SATMISTSFM PRKPAVTSL- KPIPNVGE-- ALFGLKS-A- -FER1_SOLLC/1-144 MA------SI SGTMISTSFL PRKPAVTSL- KAISNVGE-- ALFGLKS-G- -Q93XJ9_SOLTU/1-144 MA------SI SGTMISTSFL PRKPVVTSL- KAISNVGE-- ALFGLKS-G- -FER1_PEA/1-149 MATT---PAL YGTAVSTSFL RTQPMPMSV- TTTKAFSN-- GFLGLKT-SL -Q7XA98_TRIPR/1-152 MATT---PAL YGTAVSTSFM RRQPVPMSV- ATTTTTKAFP SGFGLKSVST -FER1_MESCR/1-148 MAAT--TAAL SGATMSTAFA PK--TPPMTA ALPTNVGR-- ALFGLKS-SA -FER1_SPIOL/1-147 MAAT--TTTM MG--MATTFV PKPQAPPMMA ALPSNTGR-- SLFGLKT-GS -FER3_RAPSA/1-96 ---------- ---------- ---------- ---------- ---------- -FER1_ARATH/1-148 MAST----AL SSAIVGTSFI RRSPAPISLR SLPSANTQ-- SLFGLKS-GT -FER_BRANA/1-96 ---------- ---------- ---------- ---------- ---------- -FER2_ARATH/1-148 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST -Q93Z60_ARATH/1-118 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST -FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV- -ALPAAKV-- GIMGRSA-SS -O80429_MAIZE/1-140 MAAT------ ---ALSMSIL R---APPPCF SSPLRLRV-- AVAKPLA-AP -1A70|/1-97 ---------- ---------- ---------- ---------- ---------- - -FER_CAPAA/1-97 ---------A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA -FER_CAPAN/1-144 -NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA -FER1_SOLLC/1-144 -RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA -Q93XJ9_SOLTU/1-144 -RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA -FER1_PEA/1-149 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA -Q7XA98_TRIPR/1-152 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA -FER1_MESCR/1-148 SR-GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA -FER1_SPIOL/1-147 R--GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA -FER3_RAPSA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA -FER1_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA -FER_BRANA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA -FER2_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA -Q93Z60_ARATH/1-118 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA -FER1_MAIZE/1-150 RR--RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA -O80429_MAIZE/1-140 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA -1A70|/1-97 ---------A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA - -FER_CAPAA/1-97 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK -FER_CAPAN/1-144 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK -FER1_SOLLC/1-144 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK -Q93XJ9_SOLTU/1-144 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK -FER1_PEA/1-149 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK -Q7XA98_TRIPR/1-152 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK -FER1_MESCR/1-148 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK -FER1_SPIOL/1-147 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK -FER3_RAPSA/1-96 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR -FER1_ARATH/1-148 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK -FER_BRANA/1-96 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK -FER2_ARATH/1-148 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK -Q93Z60_ARATH/1-118 GSCSSCAGKV VSGSIDQSDQ SFLDD----- ---------- ---------- -FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK -O80429_MAIZE/1-140 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK -1A70|/1-97 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK - -FER_CAPAA/1-97 EAELVG- -FER_CAPAN/1-144 EAELVG- -FER1_SOLLC/1-144 EEELTA- -Q93XJ9_SOLTU/1-144 EEELTA- -FER1_PEA/1-149 EEDLTA- -Q7XA98_TRIPR/1-152 EEELTA- -FER1_MESCR/1-148 EEELTA- -FER1_SPIOL/1-147 EEELTA- -FER3_RAPSA/1-96 EEDMV-- -FER1_ARATH/1-148 EEDIV-- -FER_BRANA/1-96 EEELV-- -FER2_ARATH/1-148 EEAIM-- -Q93Z60_ARATH/1-118 ------- -FER1_MAIZE/1-150 EEELTGA -O80429_MAIZE/1-140 EDDLL-- -1A70|/1-97 KEELTA - diff --git a/examples/test.pir b/examples/test.pir deleted file mode 100644 index 689561f..0000000 --- a/examples/test.pir +++ /dev/null @@ -1,80 +0,0 @@ ->P1;FER_CAPAA/1-97 -Ferredoxin ------------------------------------------------------------ASYKVKLITPDGP -IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV -TIETHKEAELVG-* ->P1;FER_CAPAN/1-144 -Ferredoxin, chloroplast precursor -MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP -IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV -TIETHKEAELVG-* ->P1;FER1_SOLLC/1-144 -Ferredoxin-1, chloroplast precursor -MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP -IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV -TIETHKEEELTA-* ->P1;Q93XJ9_SOLTU/1-144 -Ferredoxin I precursor -MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP -IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV -TIETHKEEELTA-* ->P1;FER1_PEA/1-149 -Ferredoxin-1, chloroplast precursor -MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT -QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV -VIETHKEEDLTA-* ->P1;Q7XA98_TRIPR/1-152 -Ferredoxin I -MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP -QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV -TIETHKEEELTA-* ->P1;FER1_MESCR/1-148 -Ferredoxin-1, chloroplast precursor -MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK -QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV -TIETHKEEELTA-* ->P1;FER1_SPIOL/1-147 -Ferredoxin-1, chloroplast precursor -MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN -VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV -TIETHKEEELTA-* ->P1;FER3_RAPSA/1-96 -Ferredoxin, leaf L-A ------------------------------------------------------------ATYKVKFITPEGE -QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV -TIETHREEDMV--* ->P1;FER1_ARATH/1-148 -Ferredoxin-1, chloroplast precursor -MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE -LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV -TIETHKEEDIV--* ->P1;FER_BRANA/1-96 -Ferredoxin ------------------------------------------------------------ATYKVKFITPEGE -QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV -TIETHKEEELV--* ->P1;FER2_ARATH/1-148 -Ferredoxin-2, chloroplast precursor -MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE -QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV -VIETHKEEAIM--* ->P1;Q93Z60_ARATH/1-118 -At1g10960/T19D16_12 -MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE -QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- --------------* ->P1;FER1_MAIZE/1-150 -Ferredoxin-1, chloroplast precursor -MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE -VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV -VIETHKEEELTGA* ->P1;O80429_MAIZE/1-140 -Ferredoxin -MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE -VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV -VIETHKEDDLL--* ->P1;1A70|/1-97 -1A70| 97 residues ------------------------------------------------------------AAYKVTLVTPTGN -VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV -TIETHKKEELTA* diff --git a/examples/test.rnaml b/examples/test.rnaml deleted file mode 100644 index 0c716f9..0000000 --- a/examples/test.rnaml +++ /dev/null @@ -1,2200 +0,0 @@ - - - - - - - - - - 1 - 89 - - - - 1 2 3 4 5 6 7 8 9 10 - 11 12 13 14 15 16 17 18 19 20 - 21 22 23 24 25 26 27 28 29 30 - 31 32 33 34 35 36 37 38 39 40 - 41 42 43 44 45 46 47 48 49 50 - 51 52 53 54 55 56 57 58 59 60 - 61 62 63 64 65 66 67 68 69 70 - 71 72 73 74 75 76 77 78 79 80 - 81 82 83 84 85 86 87 88 89 - - - GGAGAGUAGA UGAUUCGCGU UAAGCGUGUG UGAAUGGGAU GUCGUCACAC AACGAAGCGA - GAGCGCGGUG AAUCAUUGCA UCCGCUCCA - - - - LOOP1 - 60 - 61 - - - - - - - Crystallography ? - ? Angstroms - - - 1 - G - - P - 39.406 -40.727 -8.772 - - - O3' - 35.728 -40.286 -12.682 - - - - 2 - G - - P - 34.946 -38.900 -12.475 - - - O3' - 30.080 -38.122 -13.566 - - - - 3 - A - - P - 29.830 -36.592 -13.144 - - - O3' - 25.299 -34.832 -11.157 - - - - 4 - G - - P - 25.525 -33.291 -10.748 - - - O3' - 22.725 -31.357 -6.447 - - - - 5 - A - - P - 23.004 -29.821 -6.080 - - - O3' - 21.811 -28.069 -1.298 - - - - 6 - G - - P - 21.792 -26.530 -1.767 - - - O3' - 24.489 -23.234 1.411 - - - - 7 - U - - P - 24.494 -21.833 0.618 - - - O3' - 26.796 -17.886 2.729 - - - - 8 - A - - P - 25.940 -16.593 2.288 - - - O3' - 27.995 -11.947 1.918 - - - - 9 - G - - P - 26.631 -11.127 1.714 - - - O3' - 25.187 -8.816 -3.450 - - - - 10 - A - - P - 23.765 -8.232 -3.892 - - - O3' - 22.114 -8.019 -8.607 - - - - 11 - U - - P - 20.793 -7.127 -8.411 - - - O3' - 16.589 -7.608 -11.167 - - - - 12 - G - - P - 15.563 -6.541 -10.537 - - - O3' - 10.446 -7.534 -10.495 - - - - 13 - A - - P - 9.719 -6.369 -9.662 - - - O3' - 5.301 -7.413 -7.169 - - - - 14 - U - - P - 4.913 -6.043 -6.428 - - - O3' - 2.471 -6.216 -1.841 - - - - 15 - U - - P - 2.306 -4.695 -1.355 - - - O3' - 2.523 -3.519 3.678 - - - - 16 - C - - P - 2.410 -1.916 3.716 - - - O3' - 4.861 0.478 7.750 - - - - 17 - G - - P - 5.097 2.068 7.705 - - - O3' - 9.837 5.342 8.056 - - - - 18 - C - - P - 9.957 6.906 7.713 - - - O3' - 14.285 9.278 6.633 - - - - 19 - G - - P - 13.701 10.760 6.394 - - - O3' - 16.027 13.756 2.831 - - - - 20 - U - - P - 15.167 15.091 3.070 - - - O3' - 13.625 17.842 -0.910 - - - - 21 - U - - P - 12.758 18.952 -0.136 - - - O3' - 18.055 19.867 1.942 - - - - 22 - A - - P - 19.169 19.634 0.806 - - - O3' - 21.578 14.723 -0.062 - - - - 23 - A - - P - 23.185 14.817 -0.069 - - - O3' - 24.197 10.234 2.787 - - - - 24 - G - - P - 25.187 9.332 1.904 - - - O3' - 23.533 4.428 0.543 - - - - 25 - C - - P - 24.698 3.762 -0.344 - - - O3' - 23.832 1.164 -4.830 - - - - 26 - G - - P - 25.358 0.687 -5.012 - - - O3' - 27.639 1.163 -9.624 - - - - 27 - U - - P - 29.215 0.976 -9.386 - - - O3' - 32.967 2.977 -11.808 - - - - 28 - G - - P - 34.192 2.205 -11.110 - - - O3' - 38.926 3.986 -11.102 - - - - 29 - U - - P - 39.673 2.760 -10.388 - - - O3' - 43.897 3.593 -7.402 - - - - 30 - G - - P - 44.247 2.191 -6.693 - - - O3' - 46.005 2.102 -1.916 - - - - 31 - U - - P - 46.082 0.594 -1.358 - - - O3' - 46.014 -0.378 3.660 - - - - 32 - G - - P - 46.093 -1.940 4.026 - - - O3' - 42.541 -5.286 7.182 - - - - 33 - A - - P - 42.384 -6.877 7.063 - - - O3' - 38.307 -9.190 8.881 - - - - 34 - A - - P - 38.548 -10.772 8.689 - - - O3' - 34.569 -13.953 8.211 - - - - 35 - U - - P - 34.833 -15.458 7.714 - - - O3' - 32.606 -18.340 3.220 - - - - 36 - G - - P - 33.272 -19.727 3.692 - - - O3' - 29.146 -23.892 4.012 - - - - 37 - G - - P - 29.023 -23.774 5.611 - - - O3' - 32.904 -25.203 8.677 - - - - 38 - G - - P - 34.031 -24.091 8.410 - - - O3' - 38.938 -24.200 8.769 - - - - 39 - A - - P - 39.341 -22.721 8.285 - - - O3' - 43.751 -21.471 6.096 - - - - 40 - U - - P - 43.479 -19.903 5.856 - - - O3' - 45.395 -17.759 1.488 - - - - 41 - G - - P - 44.930 -16.222 1.586 - - - O3' - 43.506 -13.581 -2.651 - - - - 42 - U - - P - 42.831 -12.121 -2.591 - - - O3' - 41.294 -10.286 -7.932 - - - - 43 - C - - P - 42.354 -9.284 -8.602 - - - O3' - 37.101 -8.296 -10.514 - - - - 44 - G - - P - 36.225 -7.381 -9.523 - - - O3' - 31.469 -8.612 -8.166 - - - - 45 - U - - P - 31.072 -7.255 -7.406 - - - O3' - 28.607 -6.549 -3.172 - - - - 46 - C - - P - 28.715 -4.958 -2.980 - - - O3' - 28.390 -3.209 1.978 - - - - 47 - A - - P - 28.521 -1.606 2.045 - - - O3' - 30.414 1.118 5.980 - - - - 48 - C - - P - 30.264 2.613 5.413 - - - O3' - 33.914 6.098 6.836 - - - - 49 - A - - P - 33.658 7.488 6.071 - - - O3' - 37.349 10.868 4.871 - - - - 50 - C - - P - 36.440 12.000 4.175 - - - O3' - 38.419 14.513 0.075 - - - - 51 - A - - P - 37.256 15.394 -0.597 - - - O3' - 37.356 16.350 -5.434 - - - - 52 - A - - P - 36.109 17.208 -5.963 - - - O3' - 32.771 16.782 -10.663 - - - - 53 - C - - P - 31.552 17.777 -10.378 - - - O3' - 27.305 16.113 -12.908 - - - - 54 - G - - P - 26.189 17.220 -12.567 - - - O3' - 21.401 15.463 -11.735 - - - - 55 - A - - P - 20.593 16.847 -11.641 - - - O3' - 14.995 15.270 -10.886 - - - - 56 - A - - P - 14.099 15.609 -12.176 - - - O3' - 11.604 16.216 -7.225 - - - - 57 - G - - P - 12.080 17.523 -6.429 - - - O3' - 7.183 20.279 -7.550 - - - - 58 - C - - P - 5.983 21.146 -6.947 - - - O3' - 0.457 20.033 -6.497 - - - - 59 - G - - P - -0.544 20.976 -5.664 - - - O3' - -5.064 19.435 -4.069 - - - - 60 - A - - P - -5.376 20.880 -3.446 - - - O3' - -4.674 20.226 1.852 - - - - 61 - G - - P - -3.473 19.173 1.806 - - - O3' - -4.399 14.900 5.084 - - - - 62 - A - - P - -3.268 13.764 4.956 - - - O3' - -4.326 8.891 5.778 - - - - 63 - G - - P - -2.954 8.206 5.320 - - - O3' - -2.345 6.516 -0.228 - - - - 64 - C - - P - -1.075 5.830 -0.928 - - - O3' - -0.362 6.130 -5.741 - - - - 65 - G - - P - 0.975 5.389 -6.226 - - - O3' - 5.254 7.641 -9.385 - - - - 66 - C - - P - 6.414 6.540 -9.525 - - - O3' - 11.228 8.547 -10.401 - - - - 67 - G - - P - 12.262 7.325 -10.276 - - - O3' - 17.393 8.076 -7.688 - - - - 68 - G - - P - 18.588 8.450 -8.699 - - - O3' - 17.674 3.102 -7.969 - - - - 69 - U - - P - 17.676 1.931 -6.877 - - - O3' - 19.344 2.058 -2.233 - - - - 70 - G - - P - 19.325 0.478 -1.917 - - - O3' - 20.086 -1.464 2.724 - - - - 71 - A - - P - 20.065 -3.053 2.482 - - - O3' - 18.093 -6.084 6.331 - - - - 72 - A - - P - 18.058 -7.629 5.887 - - - O3' - 14.491 -10.888 7.635 - - - - 73 - U - - P - 14.861 -12.252 6.871 - - - O3' - 11.261 -15.468 5.182 - - - - 74 - C - - P - 12.050 -16.617 4.382 - - - O3' - 9.736 -18.950 0.360 - - - - 75 - A - - P - 10.800 -19.899 -0.381 - - - O3' - 10.831 -20.869 -5.373 - - - - 76 - U - - P - 12.149 -21.782 -5.481 - - - O3' - 15.150 -21.466 -9.686 - - - - 77 - U - - P - 16.383 -22.407 -9.255 - - - O3' - 21.158 -21.098 -10.643 - - - - 78 - G - - P - 22.003 -22.328 -10.053 - - - O3' - 26.870 -21.574 -8.157 - - - - 79 - C - - P - 27.394 -22.916 -7.439 - - - O3' - 32.738 -22.221 -7.672 - - - - 80 - A - - P - 33.094 -23.432 -8.669 - - - O3' - 37.970 -23.709 -10.290 - - - - 81 - U - - P - 38.180 -25.262 -9.938 - - - O3' - 42.343 -27.512 -8.310 - - - - 82 - C - - P - 41.594 -28.924 -8.148 - - - O3' - 42.976 -31.766 -3.839 - - - - 83 - C - - P - 41.983 -33.022 -3.698 - - - O3' - 40.724 -35.051 0.999 - - - - 84 - G - - P - 39.499 -36.072 0.803 - - - O3' - 35.976 -36.466 4.801 - - - - 85 - C - - P - 34.990 -37.680 4.429 - - - O3' - 30.031 -37.549 5.509 - - - - 86 - U - - P - 29.628 -39.018 5.001 - - - O3' - 25.142 -40.312 3.037 - - - - 87 - C - - P - 25.378 -41.854 2.656 - - - O3' - 22.860 -43.926 -1.490 - - - - 88 - C - - P - 23.430 -45.414 -1.686 - - - O3' - 24.098 -47.533 -6.370 - - - - 89 - A - - P - 24.738 -48.976 -6.070 - - - O3' - 28.245 -51.062 -9.390 - - - - - 22 - syn - - - 68 - syn - - - - 1 - - - 88 - - + - + - c - - - - 2 - - - 87 - - + - + - c - - - - 3 - - - 86 - - - - - - c - - - - 4 - - - 85 - - + - + - c - - - - 5 - - - 84 - - W - W - c - - - - 6 - - - 37 - - S - H - c - - - - 8 - - - 44 - - S - S - t - - - - 8 - - - 78 - - H - S - t - - - - 9 - - - 77 - - W - W - c - - - - 10 - - - 76 - - - - - - c - - - - 11 - - - 75 - - - - - - c - - - - 12 - - - 74 - - + - + - c - - - - 13 - - - 73 - - - - - - c - - - - 14 - - - 72 - - - - - - c - - - - 15 - - - 71 - - - - - - c - - - - 16 - - - 70 - - + - + - c - - - - 17 - - - 69 - - W - W - c - - - - 18 - - - 67 - - + - + - c - - - - 19 - - - 22 - - S - S - c - - - - 19 - - - 66 - - + - + - c - - - - 20 - - - 65 - - W - W - c - - - - 23 - - - 55 - - H - W - t - - - - 23 - - - 67 - - W - S - t - - - - 24 - - - 54 - - H - S - t - - - - 26 - - - 52 - - W - W - c - - - - 27 - - - 51 - - - - - - c - - - - 28 - - - 50 - - + - + - c - - - - 29 - - - 49 - - - - - - c - - - - 30 - - - 48 - - + - + - c - - - - 31 - - - 47 - - - - - - c - - - - 32 - - - 46 - - + - + - c - - - - 33 - - - 45 - - - - - - c - - - - 34 - - - 44 - - W - W - c - - - - 35 - - - 42 - - W - H - t - - - - 37 - - - 83 - - + - + - c - - - - 38 - - - 82 - - + - + - c - - - - 39 - - - 81 - - - - - - c - - - - 40 - - - 80 - - - - - - c - - - - 41 - - - 79 - - W - W - c - - - - 56 - - - 65 - - S - S - t - - - - 57 - - - 64 - - + - + - c - - - - 58 - - - 63 - - + - + - c - - - - 59 - - - 62 - - W - H - t - - - - 7 - - - 35 - - ! - ! - ! - - - - 8 - - - 35 - - ! - ! - ! - - - - 23 - - - 54 - - ! - ! - ! - - - - 24 - - - 69 - - ! - ! - ! - - - - 35 - - - 79 - - ! - ! - ! - - - - 43 - - - 44 - - ! - ! - ! - - - - 54 - - - 55 - - ! - ! - ! - - - - 56 - - - 57 - - ! - ! - ! - - - - 68 - - - 69 - - ! - ! - ! - - - - 1 - - - 88 - - 5 - - - - 37 - - - 83 - - 5 - - - - 26 - - - 52 - - 9 - - - - 23 - - - 55 - - 2 - - - - 57 - - - 64 - - 3 - - - - 19 - - - 66 - - 2 - - - - 8 - - - 78 - - 10 - - - - SG1 - 6 - 7 - - - - - SG2 - 18 - 18 - - - - - SG3 - 21 - 22 - - - - - SG4 - 25 - 25 - - - - - SG5 - 35 - 36 - - - - - SG6 - 42 - 43 - - - - - SG7 - 53 - 53 - - - - - SG8 - 56 - 56 - - - - - SG9 - 60 - 61 - - - - - SG10 - 67 - 68 - - - - - SG11 - 89 - 89 - - - - - - 1 - 264.792 11.342 - - - 2 - 264.792 30.246 - - - 3 - 264.792 49.149 - - - 4 - 264.792 68.053 - - - 5 - 264.792 86.957 - - - 6 - 276.134 86.957 - - - 7 - 287.476 86.957 - - - 8 - 148.757 221.618 - - - 9 - 143.395 239.745 - - - 10 - 138.033 257.872 - - - 11 - 132.670 275.999 - - - 12 - 127.308 294.126 - - - 13 - 121.946 312.254 - - - 14 - 116.584 330.381 - - - 15 - 111.221 348.508 - - - 16 - 105.859 366.635 - - - 17 - 100.497 384.762 - - - 18 - 53.294 416.207 - - - 19 - 48.034 426.256 - - - 20 - 39.267 443.003 - - - 21 - 219.423 487.713 - - - 22 - 219.423 476.370 - - - 23 - 219.423 465.028 - - - 24 - 219.423 446.125 - - - 25 - 219.423 427.221 - - - 26 - 219.423 389.414 - - - 27 - 219.423 370.510 - - - 28 - 219.423 351.607 - - - 29 - 219.423 332.703 - - - 30 - 219.423 313.800 - - - 31 - 219.423 294.896 - - - 32 - 219.423 275.992 - - - 33 - 219.423 257.089 - - - 34 - 219.423 238.185 - - - 35 - 287.476 124.764 - - - 36 - 276.134 124.764 - - - 37 - 264.792 124.764 - - - 38 - 264.792 143.667 - - - 39 - 264.792 162.571 - - - 40 - 264.792 181.474 - - - 41 - 264.792 200.378 - - - 42 - 276.134 200.378 - - - 43 - 287.476 200.378 - - - 44 - 264.792 238.185 - - - 45 - 264.792 257.089 - - - 46 - 264.792 275.992 - - - 47 - 264.792 294.896 - - - 48 - 264.792 313.800 - - - 49 - 264.792 332.703 - - - 50 - 264.792 351.607 - - - 51 - 264.792 370.510 - - - 52 - 264.792 389.414 - - - 53 - 264.792 408.318 - - - 54 - 264.792 446.125 - - - 55 - 264.792 465.028 - - - 56 - 264.792 476.370 - - - 57 - 21.732 476.499 - - - 58 - 12.965 493.246 - - - 59 - 4.198 509.994 - - - 60 - 0.000 537.223 - - - 61 - 24.408 550.000 - - - 62 - 44.392 531.035 - - - 63 - 53.159 514.288 - - - 64 - 61.927 497.540 - - - 65 - 79.461 464.045 - - - 66 - 88.228 447.297 - - - 67 - 93.488 437.249 - - - 68 - 98.749 427.200 - - - 69 - 56.992 371.893 - - - 70 - 62.354 353.766 - - - 71 - 67.716 335.638 - - - 72 - 73.079 317.511 - - - 73 - 78.441 299.384 - - - 74 - 83.803 281.257 - - - 75 - 89.165 263.130 - - - 76 - 94.527 245.003 - - - 77 - 99.890 226.876 - - - 78 - 105.252 208.749 - - - 79 - 219.423 200.378 - - - 80 - 219.423 181.474 - - - 81 - 219.423 162.571 - - - 82 - 219.423 143.667 - - - 83 - 219.423 124.764 - - - 84 - 219.423 86.957 - - - 85 - 219.423 68.053 - - - 86 - 219.423 49.149 - - - 87 - 219.423 30.246 - - - 88 - 219.423 11.342 - - - 89 - 219.423 0.000 - - - - - - - - - - - - \ No newline at end of file diff --git a/examples/testdata/uniref50_test_annot b/examples/testdata/uniref50_test_annot deleted file mode 100644 index fd60c65..0000000 --- a/examples/testdata/uniref50_test_annot +++ /dev/null @@ -1,11 +0,0 @@ -JALVIEW_ANNOTATION -# Created: Wed Jul 08 18:48:01 BST 2015 - -NO_GRAPH Test Annotation Test Annotation ||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|||||||||||||||||||||||||||||||||||||||||||||||||E,β|E,β|E,β|E,β|E,β|||||||||||||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||||||||E,β|E,β|||| -BAR_GRAPH Conservation Conservation of total alignment less than 25% gaps 1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|1.0,1,hydrophobic ,[5d1500]|2.0,2,small tiny ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|8.0,8,hydrophobic !tiny !polar !negative !charged !small !positive !proline,[cea700]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,small polar !tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !tiny !aromatic !aliphatic,[7d3f00]|6.0,6, !tiny !aromatic !negative !charged !positive !proline,[ae7d00]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|7.0,7,hydrophobic !tiny !polar !negative !charged !positive !proline,[be9200]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|9.0,9,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|5.0,5, !tiny !aromatic !hydrophobic !positive !aliphatic,[9e6800]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|3.0,3, !negative !aliphatic !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|3.0,3, !aromatic !positive !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|5.0,5,hydrophobic !tiny !negative !small !proline,[9e6800]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged polar !tiny !aromatic !hydrophobic !negative !small !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged hydrophobic polar !tiny !aromatic !negative !small !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|3.0,3, !aromatic !negative !proline,[7d3f00]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !positive !aliphatic !proline,[7d3f00]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,polar !tiny !aromatic !hydrophobic !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|4.0,4, !aromatic !positive !aliphatic !proline,[8d5300]|5.0,5,polar !aromatic !negative !aliphatic !proline,[9e6800]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|0.0,0,[4d0000]|1.0,1,polar ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|2.0,2,aliphatic hydrophobic ,[6d2a00]|2.0,2,small polar ,[6d2a00]|2.0,2,small hydrophobic ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|2.0,2,proline small ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|4.0,4,small charged negative polar ,[8d5300]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|1.0,1,small ,[5d1500]|2.0,2,aliphatic hydrophobic ,[6d2a00]|3.0,3,charged negative polar ,[7d3f00]|2.0,2,small polar ,[6d2a00]|5.0,5,positive charged hydrophobic aromatic polar ,[9e6800]|3.0,3,positive charged polar ,[7d3f00]|3.0,3,charged negative polar ,[7d3f00]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]| -BAR_GRAPH Quality Alignment Quality based on Blosum62 scores 29.151815,29.151815,[cba200]|30.574812,30.574812,[d1aa00]|14.400199,14.400199,[8b5000]|16.93248,16.93248,[965e00]|2.1220763,2.1220763,[560c00]|2.2049963,2.2049963,[560c00]|3.647952,3.647952,[5c1400]|4.814642,4.814642,[611b00]|18.351393,18.351393,[9c6600]|17.532412,17.532412,[996200]|7.5054855,7.5054855,[6d2a00]|15.490477,15.490477,[905600]|14.241707,14.241707,[8a4f00]|9.905579,9.905579,[773700]|20.354017,20.354017,[a57100]|26.870352,26.870352,[c19600]|24.969187,24.969187,[b98b00]|27.419409,27.419409,[c39900]|15.350427,15.350427,[8f5600]|21.116522,21.116522,[a87600]|9.34032,9.34032,[753400]|14.1895275,14.1895275,[8a4f00]|10.104505,10.104505,[783800]|8.587312,8.587312,[723000]|18.694708,18.694708,[9e6800]|11.420612,11.420612,[7e4000]|6.8467255,6.8467255,[6a2600]|17.449827,17.449827,[986100]|16.825909,16.825909,[955e00]|2.4334474,2.4334474,[570e00]|15.685622,15.685622,[915700]|9.836516,9.836516,[773700]|3.4712791,3.4712791,[5c1300]|4.531816,4.531816,[601900]|7.8744216,7.8744216,[6f2c00]|0.0,0.0,[4d0000]|9.01113,9.01113,[743200]|3.174218,3.174218,[5a1200]|2.0395048,2.0395048,[550b00]|2.1654668,2.1654668,[560c00]|21.517344,21.517344,[aa7800]|15.738462,15.738462,[915800]|14.844854,14.844854,[8d5300]|22.159096,22.159096,[ad7c00]|13.956608,13.956608,[894e00]|20.147892,20.147892,[a47000]|25.067545,25.067545,[b98c00]|2.0943506,2.0943506,[560c00]|20.30842,20.30842,[a57100]|10.254437,10.254437,[793900]|6.5836596,6.5836596,[692500]|19.446732,19.446732,[a16c00]|6.2202287,6.2202287,[672300]|9.796006,9.796006,[773700]|6.0385494,6.0385494,[672200]|13.963727,13.963727,[894e00]|13.838549,13.838549,[884d00]|18.48424,18.48424,[9d6700]|18.302633,18.302633,[9c6600]|41.172745,41.172745,[ffe600]|32.59908,32.59908,[dab600]|41.172745,41.172745,[ffe600]|34.495945,34.495945,[e2c000]|41.172745,41.172745,[ffe600]|33.501804,33.501804,[debb00]|27.034466,27.034466,[c29700]|40.020737,40.020737,[fadf00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|29.252739,29.252739,[cba300]|41.172745,41.172745,[ffe600]|14.935498,14.935498,[8d5300]|0.88449144,0.88449144,[500500]|41.172745,41.172745,[ffe600]|20.81991,20.81991,[a77400]|31.73346,31.73346,[d6b100]|29.757969,29.757969,[cea600]|16.279755,16.279755,[935b00]|32.647984,32.647984,[dab600]|38.352337,38.352337,[f3d600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.6125,39.6125,[f8dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|9.671661,9.671661,[763600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|11.17141,11.17141,[7d3e00]|41.172745,41.172745,[ffe600]|3.2054348,3.2054348,[5a1200]|38.569283,38.569283,[f4d700]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.707684,39.707684,[f9dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.447525,39.447525,[f8dc00]|21.229778,21.229778,[a97600]|27.779364,27.779364,[c59b00]|41.172745,41.172745,[ffe600]|24.149143,24.149143,[b58700]|39.447525,39.447525,[f8dc00]|33.857655,33.857655,[dfbd00]|41.172745,41.172745,[ffe600]|28.69976,28.69976,[c9a000]|41.172745,41.172745,[ffe600]|14.611241,14.611241,[8c5100]|32.346375,32.346375,[d9b400]|39.24055,39.24055,[f7db00]|41.172745,41.172745,[ffe600]|38.352337,38.352337,[f3d600]|38.569283,38.569283,[f4d700]|22.374107,22.374107,[ae7d00]|36.98438,36.98438,[edce00]|12.34415,12.34415,[824500]|11.811655,11.811655,[804200]|14.798897,14.798897,[8d5200]|36.60138,36.60138,[ebcc00]|14.0762415,14.0762415,[8a4e00]|36.817875,36.817875,[eccd00]|36.53897,36.53897,[ebcc00]|37.583706,37.583706,[efd100]|35.536423,35.536423,[e7c600]|18.004925,18.004925,[9b6400]|37.633095,37.633095,[f0d200]|34.738743,34.738743,[e3c200]|36.451622,36.451622,[ebcb00]|19.948801,19.948801,[a36f00]|28.285,28.285,[c79e00]|35.93151,35.93151,[e8c800]|36.817875,36.817875,[eccd00]|26.762383,26.762383,[c19500]|36.37101,36.37101,[eacb00]|36.413998,36.413998,[eacb00]|37.583706,37.583706,[efd100]|36.282784,36.282784,[eaca00]|34.729824,34.729824,[e3c200]|36.413998,36.413998,[eacb00]|24.348654,24.348654,[b68800]|24.349539,24.349539,[b68800]|34.091675,34.091675,[e0be00]|21.114677,21.114677,[a87600]|13.676696,13.676696,[884c00]|2.1107035,2.1107035,[560c00]| -BAR_GRAPH Consensus PID 80.0,M,M 80%|80.0,A,A 80%|20.0,+,[AST] 20%|53.333332,T,T 53%|6.6666665,L,L 6%|6.6666665,G,G 6%|13.333333,T,T 13%|20.0,P,P 20%|40.0,A,A 40%|40.0,L,L 40%|46.666668,S,S 46%|40.0,G,G 40%|33.333332,T,T 33%|20.0,+,[AIM] 20%|33.333332,V,V 33%|66.666664,S,S 66%|66.666664,T,T 66%|66.666664,S,S 66%|66.666664,F,F 66%|46.666668,L,L 46%|46.666668,R,R 46%|46.666668,R,R 46%|26.666666,Q,Q 26%|46.666668,P,P 46%|40.0,A,A 40%|60.0,P,P 60%|26.666666,T,T 26%|53.333332,S,S 53%|40.0,L,L 40%|20.0,R,R 20%|26.666666,S,S 26%|33.333332,L,L 33%|40.0,P,P 40%|26.666666,S,S 26%|33.333332,+,[AN] 33%|26.666666,V,V 26%|33.333332,G,G 33%|20.0,+,[EQ] 20%|6.6666665,F,F 6%|6.6666665,P,P 6%|33.333332,+,[AS] 33%|53.333332,L,L 53%|60.0,F,F 60%|73.333336,G,G 73%|66.666664,L,L 66%|66.666664,K,K 66%|53.333332,S,S 53%|6.6666665,V,V 6%|40.0,S,S 40%|26.666666,T,T 26%|20.0,A,A 20%|66.666664,R,R 66%|40.0,G,G 40%|53.333332,G,G 53%|46.666668,R,R 46%|33.333332,V,V 33%|46.666668,T,T 46%|53.333332,A,A 53%|66.666664,M,M 66%|100.0,A,A 100%|53.333332,T,T 53%|100.0,Y,Y 100%|86.666664,K,K 86%|100.0,V,V 100%|86.666664,K,K 86%|66.666664,L,L 66%|80.0,I,I 80%|100.0,T,T 100%|100.0,P,P 100%|66.666664,E,E 66%|100.0,G,G 100%|46.666668,E,E 46%|46.666668,Q,Q 46%|100.0,E,E 100%|46.666668,F,F 46%|60.0,E,E 60%|86.666664,C,C 86%|66.666664,P,P 66%|80.0,D,D 80%|93.333336,D,D 93%|100.0,V,V 100%|100.0,Y,Y 100%|66.666664,I,I 66%|100.0,L,L 100%|100.0,D,D 100%|46.666668,A,A 46%|100.0,A,A 100%|100.0,E,E 100%|100.0,E,E 100%|53.333332,A,A 53%|100.0,G,G 100%|60.0,I,I 60%|93.333336,D,D 93%|100.0,L,L 100%|100.0,P,P 100%|93.333336,Y,Y 93%|100.0,S,S 100%|100.0,C,C 100%|100.0,R,R 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,S,S 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,K,K 100%|80.0,V,V 80%|60.0,V,V 60%|53.333332,S,S 53%|100.0,G,G 100%|60.0,S,S 60%|80.0,V,V 80%|80.0,D,D 80%|100.0,Q,Q 100%|66.666664,S,S 66%|100.0,D,D 100%|46.666668,+,[GQ] 46%|73.333336,S,S 73%|93.333336,F,F 93%|100.0,L,L 100%|93.333336,D,D 93%|93.333336,D,D 93%|53.333332,D,D 53%|93.333336,Q,Q 93%|53.333332,I,I 53%|40.0,A,A 40%|53.333332,E,E 53%|93.333336,G,G 93%|46.666668,W,W 46%|93.333336,V,V 93%|93.333336,L,L 93%|93.333336,T,T 93%|93.333336,C,C 93%|53.333332,V,V 53%|93.333336,A,A 93%|86.666664,Y,Y 86%|93.333336,P,P 93%|60.0,T,T 60%|73.333336,S,S 73%|93.333336,D,D 93%|93.333336,V,V 93%|66.666664,T,T 66%|93.333336,I,I 93%|93.333336,E,E 93%|93.333336,T,T 93%|93.333336,H,H 93%|86.666664,K,K 86%|93.333336,E,E 93%|73.333336,E,E 73%|60.0,E,E 60%|73.333336,L,L 73%|46.666668,T,T 46%|40.0,A,A 40%|6.6666665,A,A 6%| - -SEQUENCE_GROUP JGroup:666531415 14 37 -1 FER_CAPAN FER1_SOLLC Q93XJ9_SOLTU FER1_PEA Q7XA98_TRIPR -PROPERTIES JGroup:666531415 colour=Zappo outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false - diff --git a/examples/testdata/uniref50_test_features b/examples/testdata/uniref50_test_features deleted file mode 100644 index 60f995f..0000000 --- a/examples/testdata/uniref50_test_features +++ /dev/null @@ -1,5 +0,0 @@ -FER1_SOLLC Jalview test_feature 34 47 0.0 . . -Q93XJ9_SOLTU Jalview test_feature 34 47 0.0 . . -FER1_PEA Jalview test_feature 37 52 0.0 . . -Q7XA98_TRIPR Jalview test_feature 39 55 0.0 . . -FER1_MESCR Jalview test_feature 37 51 0.0 . . diff --git a/examples/uniref50_test_annot b/examples/uniref50_test_annot deleted file mode 100644 index fd60c65..0000000 --- a/examples/uniref50_test_annot +++ /dev/null @@ -1,11 +0,0 @@ -JALVIEW_ANNOTATION -# Created: Wed Jul 08 18:48:01 BST 2015 - -NO_GRAPH Test Annotation Test Annotation ||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|||||||||||||||||||||||||||||||||||||||||||||||||E,β|E,β|E,β|E,β|E,β|||||||||||||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||||||||E,β|E,β|||| -BAR_GRAPH Conservation Conservation of total alignment less than 25% gaps 1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|1.0,1,hydrophobic ,[5d1500]|2.0,2,small tiny ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|8.0,8,hydrophobic !tiny !polar !negative !charged !small !positive !proline,[cea700]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,small polar !tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !tiny !aromatic !aliphatic,[7d3f00]|6.0,6, !tiny !aromatic !negative !charged !positive !proline,[ae7d00]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|7.0,7,hydrophobic !tiny !polar !negative !charged !positive !proline,[be9200]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|9.0,9,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|5.0,5, !tiny !aromatic !hydrophobic !positive !aliphatic,[9e6800]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|3.0,3, !negative !aliphatic !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|3.0,3, !aromatic !positive !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|5.0,5,hydrophobic !tiny !negative !small !proline,[9e6800]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged polar !tiny !aromatic !hydrophobic !negative !small !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged hydrophobic polar !tiny !aromatic !negative !small !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|3.0,3, !aromatic !negative !proline,[7d3f00]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !positive !aliphatic !proline,[7d3f00]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,polar !tiny !aromatic !hydrophobic !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|4.0,4, !aromatic !positive !aliphatic !proline,[8d5300]|5.0,5,polar !aromatic !negative !aliphatic !proline,[9e6800]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|0.0,0,[4d0000]|1.0,1,polar ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|2.0,2,aliphatic hydrophobic ,[6d2a00]|2.0,2,small polar ,[6d2a00]|2.0,2,small hydrophobic ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|2.0,2,proline small ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|4.0,4,small charged negative polar ,[8d5300]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|1.0,1,small ,[5d1500]|2.0,2,aliphatic hydrophobic ,[6d2a00]|3.0,3,charged negative polar ,[7d3f00]|2.0,2,small polar ,[6d2a00]|5.0,5,positive charged hydrophobic aromatic polar ,[9e6800]|3.0,3,positive charged polar ,[7d3f00]|3.0,3,charged negative polar ,[7d3f00]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]| -BAR_GRAPH Quality Alignment Quality based on Blosum62 scores 29.151815,29.151815,[cba200]|30.574812,30.574812,[d1aa00]|14.400199,14.400199,[8b5000]|16.93248,16.93248,[965e00]|2.1220763,2.1220763,[560c00]|2.2049963,2.2049963,[560c00]|3.647952,3.647952,[5c1400]|4.814642,4.814642,[611b00]|18.351393,18.351393,[9c6600]|17.532412,17.532412,[996200]|7.5054855,7.5054855,[6d2a00]|15.490477,15.490477,[905600]|14.241707,14.241707,[8a4f00]|9.905579,9.905579,[773700]|20.354017,20.354017,[a57100]|26.870352,26.870352,[c19600]|24.969187,24.969187,[b98b00]|27.419409,27.419409,[c39900]|15.350427,15.350427,[8f5600]|21.116522,21.116522,[a87600]|9.34032,9.34032,[753400]|14.1895275,14.1895275,[8a4f00]|10.104505,10.104505,[783800]|8.587312,8.587312,[723000]|18.694708,18.694708,[9e6800]|11.420612,11.420612,[7e4000]|6.8467255,6.8467255,[6a2600]|17.449827,17.449827,[986100]|16.825909,16.825909,[955e00]|2.4334474,2.4334474,[570e00]|15.685622,15.685622,[915700]|9.836516,9.836516,[773700]|3.4712791,3.4712791,[5c1300]|4.531816,4.531816,[601900]|7.8744216,7.8744216,[6f2c00]|0.0,0.0,[4d0000]|9.01113,9.01113,[743200]|3.174218,3.174218,[5a1200]|2.0395048,2.0395048,[550b00]|2.1654668,2.1654668,[560c00]|21.517344,21.517344,[aa7800]|15.738462,15.738462,[915800]|14.844854,14.844854,[8d5300]|22.159096,22.159096,[ad7c00]|13.956608,13.956608,[894e00]|20.147892,20.147892,[a47000]|25.067545,25.067545,[b98c00]|2.0943506,2.0943506,[560c00]|20.30842,20.30842,[a57100]|10.254437,10.254437,[793900]|6.5836596,6.5836596,[692500]|19.446732,19.446732,[a16c00]|6.2202287,6.2202287,[672300]|9.796006,9.796006,[773700]|6.0385494,6.0385494,[672200]|13.963727,13.963727,[894e00]|13.838549,13.838549,[884d00]|18.48424,18.48424,[9d6700]|18.302633,18.302633,[9c6600]|41.172745,41.172745,[ffe600]|32.59908,32.59908,[dab600]|41.172745,41.172745,[ffe600]|34.495945,34.495945,[e2c000]|41.172745,41.172745,[ffe600]|33.501804,33.501804,[debb00]|27.034466,27.034466,[c29700]|40.020737,40.020737,[fadf00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|29.252739,29.252739,[cba300]|41.172745,41.172745,[ffe600]|14.935498,14.935498,[8d5300]|0.88449144,0.88449144,[500500]|41.172745,41.172745,[ffe600]|20.81991,20.81991,[a77400]|31.73346,31.73346,[d6b100]|29.757969,29.757969,[cea600]|16.279755,16.279755,[935b00]|32.647984,32.647984,[dab600]|38.352337,38.352337,[f3d600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.6125,39.6125,[f8dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|9.671661,9.671661,[763600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|11.17141,11.17141,[7d3e00]|41.172745,41.172745,[ffe600]|3.2054348,3.2054348,[5a1200]|38.569283,38.569283,[f4d700]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.707684,39.707684,[f9dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.447525,39.447525,[f8dc00]|21.229778,21.229778,[a97600]|27.779364,27.779364,[c59b00]|41.172745,41.172745,[ffe600]|24.149143,24.149143,[b58700]|39.447525,39.447525,[f8dc00]|33.857655,33.857655,[dfbd00]|41.172745,41.172745,[ffe600]|28.69976,28.69976,[c9a000]|41.172745,41.172745,[ffe600]|14.611241,14.611241,[8c5100]|32.346375,32.346375,[d9b400]|39.24055,39.24055,[f7db00]|41.172745,41.172745,[ffe600]|38.352337,38.352337,[f3d600]|38.569283,38.569283,[f4d700]|22.374107,22.374107,[ae7d00]|36.98438,36.98438,[edce00]|12.34415,12.34415,[824500]|11.811655,11.811655,[804200]|14.798897,14.798897,[8d5200]|36.60138,36.60138,[ebcc00]|14.0762415,14.0762415,[8a4e00]|36.817875,36.817875,[eccd00]|36.53897,36.53897,[ebcc00]|37.583706,37.583706,[efd100]|35.536423,35.536423,[e7c600]|18.004925,18.004925,[9b6400]|37.633095,37.633095,[f0d200]|34.738743,34.738743,[e3c200]|36.451622,36.451622,[ebcb00]|19.948801,19.948801,[a36f00]|28.285,28.285,[c79e00]|35.93151,35.93151,[e8c800]|36.817875,36.817875,[eccd00]|26.762383,26.762383,[c19500]|36.37101,36.37101,[eacb00]|36.413998,36.413998,[eacb00]|37.583706,37.583706,[efd100]|36.282784,36.282784,[eaca00]|34.729824,34.729824,[e3c200]|36.413998,36.413998,[eacb00]|24.348654,24.348654,[b68800]|24.349539,24.349539,[b68800]|34.091675,34.091675,[e0be00]|21.114677,21.114677,[a87600]|13.676696,13.676696,[884c00]|2.1107035,2.1107035,[560c00]| -BAR_GRAPH Consensus PID 80.0,M,M 80%|80.0,A,A 80%|20.0,+,[AST] 20%|53.333332,T,T 53%|6.6666665,L,L 6%|6.6666665,G,G 6%|13.333333,T,T 13%|20.0,P,P 20%|40.0,A,A 40%|40.0,L,L 40%|46.666668,S,S 46%|40.0,G,G 40%|33.333332,T,T 33%|20.0,+,[AIM] 20%|33.333332,V,V 33%|66.666664,S,S 66%|66.666664,T,T 66%|66.666664,S,S 66%|66.666664,F,F 66%|46.666668,L,L 46%|46.666668,R,R 46%|46.666668,R,R 46%|26.666666,Q,Q 26%|46.666668,P,P 46%|40.0,A,A 40%|60.0,P,P 60%|26.666666,T,T 26%|53.333332,S,S 53%|40.0,L,L 40%|20.0,R,R 20%|26.666666,S,S 26%|33.333332,L,L 33%|40.0,P,P 40%|26.666666,S,S 26%|33.333332,+,[AN] 33%|26.666666,V,V 26%|33.333332,G,G 33%|20.0,+,[EQ] 20%|6.6666665,F,F 6%|6.6666665,P,P 6%|33.333332,+,[AS] 33%|53.333332,L,L 53%|60.0,F,F 60%|73.333336,G,G 73%|66.666664,L,L 66%|66.666664,K,K 66%|53.333332,S,S 53%|6.6666665,V,V 6%|40.0,S,S 40%|26.666666,T,T 26%|20.0,A,A 20%|66.666664,R,R 66%|40.0,G,G 40%|53.333332,G,G 53%|46.666668,R,R 46%|33.333332,V,V 33%|46.666668,T,T 46%|53.333332,A,A 53%|66.666664,M,M 66%|100.0,A,A 100%|53.333332,T,T 53%|100.0,Y,Y 100%|86.666664,K,K 86%|100.0,V,V 100%|86.666664,K,K 86%|66.666664,L,L 66%|80.0,I,I 80%|100.0,T,T 100%|100.0,P,P 100%|66.666664,E,E 66%|100.0,G,G 100%|46.666668,E,E 46%|46.666668,Q,Q 46%|100.0,E,E 100%|46.666668,F,F 46%|60.0,E,E 60%|86.666664,C,C 86%|66.666664,P,P 66%|80.0,D,D 80%|93.333336,D,D 93%|100.0,V,V 100%|100.0,Y,Y 100%|66.666664,I,I 66%|100.0,L,L 100%|100.0,D,D 100%|46.666668,A,A 46%|100.0,A,A 100%|100.0,E,E 100%|100.0,E,E 100%|53.333332,A,A 53%|100.0,G,G 100%|60.0,I,I 60%|93.333336,D,D 93%|100.0,L,L 100%|100.0,P,P 100%|93.333336,Y,Y 93%|100.0,S,S 100%|100.0,C,C 100%|100.0,R,R 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,S,S 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,K,K 100%|80.0,V,V 80%|60.0,V,V 60%|53.333332,S,S 53%|100.0,G,G 100%|60.0,S,S 60%|80.0,V,V 80%|80.0,D,D 80%|100.0,Q,Q 100%|66.666664,S,S 66%|100.0,D,D 100%|46.666668,+,[GQ] 46%|73.333336,S,S 73%|93.333336,F,F 93%|100.0,L,L 100%|93.333336,D,D 93%|93.333336,D,D 93%|53.333332,D,D 53%|93.333336,Q,Q 93%|53.333332,I,I 53%|40.0,A,A 40%|53.333332,E,E 53%|93.333336,G,G 93%|46.666668,W,W 46%|93.333336,V,V 93%|93.333336,L,L 93%|93.333336,T,T 93%|93.333336,C,C 93%|53.333332,V,V 53%|93.333336,A,A 93%|86.666664,Y,Y 86%|93.333336,P,P 93%|60.0,T,T 60%|73.333336,S,S 73%|93.333336,D,D 93%|93.333336,V,V 93%|66.666664,T,T 66%|93.333336,I,I 93%|93.333336,E,E 93%|93.333336,T,T 93%|93.333336,H,H 93%|86.666664,K,K 86%|93.333336,E,E 93%|73.333336,E,E 73%|60.0,E,E 60%|73.333336,L,L 73%|46.666668,T,T 46%|40.0,A,A 40%|6.6666665,A,A 6%| - -SEQUENCE_GROUP JGroup:666531415 14 37 -1 FER_CAPAN FER1_SOLLC Q93XJ9_SOLTU FER1_PEA Q7XA98_TRIPR -PROPERTIES JGroup:666531415 colour=Zappo outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false - diff --git a/examples/uniref50_test_features b/examples/uniref50_test_features deleted file mode 100644 index 60f995f..0000000 --- a/examples/uniref50_test_features +++ /dev/null @@ -1,5 +0,0 @@ -FER1_SOLLC Jalview test_feature 34 47 0.0 . . -Q93XJ9_SOLTU Jalview test_feature 34 47 0.0 . . -FER1_PEA Jalview test_feature 37 52 0.0 . . -Q7XA98_TRIPR Jalview test_feature 39 55 0.0 . . -FER1_MESCR Jalview test_feature 37 51 0.0 . . diff --git a/examples/uniref50_test_tree b/examples/uniref50_test_tree deleted file mode 100644 index 585b68b..0000000 --- a/examples/uniref50_test_tree +++ /dev/null @@ -1 +0,0 @@ -(((FER_BRANA:112.15387,FER3_RAPSA:110.84613):46.4375,FER_CAPAA:144.0625):177.2998,(O80429_MAIZE:184.40039,(FER1_MAIZE:195.79102,(((FER1_SPIOL:111.687515,FER1_MESCR:84.312485):51.929688,((Q93Z60_ARATH:398.14285,(FER2_ARATH:53.65625,FER1_ARATH:48.34375):0.0):86.725006,(Q7XA98_TRIPR:78.65277,FER1_PEA:68.34723):63.774994):7.7578125):0.58332825,((Q93XJ9_SOLTU:23.647736,FER1_SOLLC:20.352264):31.71875,FER_CAPAN:52.28125):101.7448):41.498047):37.208984):177.2998); diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java index e2e7534..3f6afbc 100644 --- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java +++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java @@ -20,6 +20,10 @@ */ package jalview.ws.dbsources.das.datamodel; +import jalview.bin.Cache; +import jalview.ws.dbsources.das.api.DasSourceRegistryI; +import jalview.ws.dbsources.das.api.jalviewSourceI; + import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; @@ -39,10 +43,6 @@ import org.biodas.jdas.schema.sources.SOURCE; import org.biodas.jdas.schema.sources.SOURCES; import org.biodas.jdas.schema.sources.VERSION; -import jalview.bin.Cache; -import jalview.ws.dbsources.das.api.DasSourceRegistryI; -import jalview.ws.dbsources.das.api.jalviewSourceI; - /** * */ @@ -56,7 +56,8 @@ public class DasSourceRegistry implements DasSourceRegistryI, private Hashtable localSources = null; - public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das/"; + // public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das/"; + public static String DEFAULT_REGISTRY = "http://www.ebi.ac.uk/das-srv/registry/das/"; /** * true if thread is running and we are talking to DAS registry service diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java index da49f22..fda4e1b 100644 --- a/test/MCview/PDBChainTest.java +++ b/test/MCview/PDBChainTest.java @@ -31,7 +31,7 @@ public class PDBChainTest final Atom a4 = new Atom(2f, 1f, 7f); - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { System.out.println("setup"); diff --git a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java index 7ba2035..b68842a 100644 --- a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java +++ b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java @@ -118,7 +118,7 @@ public class AlignmentAnnotationUtilsTest * * @throws IOException */ - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws IOException { alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA, diff --git a/test/jalview/analysis/AnnotationSorterTest.java b/test/jalview/analysis/AnnotationSorterTest.java index 37bfca4..1731302 100644 --- a/test/jalview/analysis/AnnotationSorterTest.java +++ b/test/jalview/analysis/AnnotationSorterTest.java @@ -30,7 +30,7 @@ public class AnnotationSorterTest /* * Set up 6 sequences and 7 annotations. */ - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { al = buildAlignment(NUM_SEQS); diff --git a/test/jalview/analysis/ParsePropertiesTest.java b/test/jalview/analysis/ParsePropertiesTest.java index 221d47e..1325671 100644 --- a/test/jalview/analysis/ParsePropertiesTest.java +++ b/test/jalview/analysis/ParsePropertiesTest.java @@ -23,7 +23,7 @@ public class ParsePropertiesTest /** * Construct an alignment with 4 sequences with varying description format */ - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { SequenceI[] seqs = new SequenceI[] diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java index 81514a4..3c84189 100644 --- a/test/jalview/analysis/TestAlignSeq.java +++ b/test/jalview/analysis/TestAlignSeq.java @@ -46,7 +46,7 @@ public class TestAlignSeq /** * @throws java.lang.Exception */ - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws Exception { s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS"); diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index 8bd484a..adc24db 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -109,7 +109,6 @@ public class CommandLineOperations { BufferedReader outputReader = new BufferedReader( new InputStreamReader(ls2_proc.getInputStream())); - BufferedReader errorReader = new BufferedReader( new InputStreamReader(ls2_proc.getErrorStream())); worker = new Worker(ls2_proc); @@ -127,20 +126,20 @@ public class CommandLineOperations return worker; } - @BeforeTest + @BeforeTest(alwaysRun = true) public void initialize() { new CommandLineOperations(); } - @BeforeTest + @BeforeTest(alwaysRun = true) public void setUpForHeadlessCommandLineInputOperations() throws IOException { String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo " + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com " - + "-features examples/uniref50_test_features -annotations examples/uniref50_test_annot -tree examples/uniref50_test_tree"; + + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree"; Worker worker = jalviewDesktopRunner(true, cmds, 9000); String ln = null; while ((ln = worker.getOutputReader().readLine()) != null) @@ -150,7 +149,7 @@ public class CommandLineOperations } } - @BeforeTest + @BeforeTest(alwaysRun = true) public void setUpForCommandLineInputOperations() throws IOException { String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats"; @@ -232,13 +231,14 @@ public class CommandLineOperations { "CMD [-dasserver nickname=www.test.com] executed successfully!", "Failed command : -dasserver nickname=www.test.com" }, { - "CMD [-features examples/uniref50_test_features] executed successfully!", - "Failed command : -features examples/uniref50_test_features" }, + "CMD [-features examples/testdata/plantfdx.features] executed successfully!", + "Failed command : -features examples/testdata/plantfdx.features" }, + { + "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!", + "Failed command : -annotations examples/testdata/plantfdx.annotations" }, { - "CMD [-annotations examples/uniref50_test_annot] executed successfully!", - "Failed command : -annotations examples/uniref50_test_annot" }, - { "CMD [-tree examples/uniref50_test_tree] executed successfully!", - "Failed command : -tree examples/uniref50_test_tree" }, + "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!", + "Failed command : -tree examples/testdata/uniref50_test_tree" }, // non headless mode input operations { "CMD [-nousagestats] executed successfully!", "Failed command : -nousagestats" }, diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java index 3591648..375ae55 100644 --- a/test/jalview/commands/EditCommandTest.java +++ b/test/jalview/commands/EditCommandTest.java @@ -30,7 +30,7 @@ public class EditCommandTest private Alignment al; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { testee = new EditCommand(); diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index e885733..2eaae94 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -79,7 +79,7 @@ public class AlignmentTest * Read in Stockholm format test data including secondary structure * annotations. */ - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws IOException { al = loadAlignment(TEST_DATA, "STH"); diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java index 68c3ddf..2e6f3f9 100644 --- a/test/jalview/datamodel/PDBEntryTest.java +++ b/test/jalview/datamodel/PDBEntryTest.java @@ -9,7 +9,7 @@ import org.testng.annotations.Test; public class PDBEntryTest { - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws Exception { } diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java index 78eb66c..4d08b15 100644 --- a/test/jalview/datamodel/SequenceTest.java +++ b/test/jalview/datamodel/SequenceTest.java @@ -15,7 +15,7 @@ public class SequenceTest { SequenceI seq; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { seq = new Sequence("FER1", "AKPNGVL"); diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java index 301c70d..fd465cf 100644 --- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java +++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java @@ -50,7 +50,7 @@ public class PDBFileWithJmolTest // "./examples/DNMT1_MOUSE.pdb" // }; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java index 44b5d58..0c5d7fa 100644 --- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java +++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java @@ -19,7 +19,7 @@ public class JalviewChimeraView /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { jalview.bin.Jalview.main(new String[] diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index b49352b..4c55386 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -19,7 +19,7 @@ public class AlignViewportTest AlignmentI al; AlignViewport testee; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { SequenceI seq1 = new Sequence("Seq1", "ABC"); diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java index a7e84b1..ae56fb4 100644 --- a/test/jalview/gui/AnnotationChooserTest.java +++ b/test/jalview/gui/AnnotationChooserTest.java @@ -52,7 +52,7 @@ public class AnnotationChooserTest AlignFrame af; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws IOException { // pin down annotation sort order for test diff --git a/test/jalview/gui/JAL1353bugdemo.java b/test/jalview/gui/JAL1353bugdemo.java index 868e19e..e90e3d9 100644 --- a/test/jalview/gui/JAL1353bugdemo.java +++ b/test/jalview/gui/JAL1353bugdemo.java @@ -42,7 +42,7 @@ import org.testng.annotations.Test; public class JAL1353bugdemo { - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { } diff --git a/test/jalview/gui/PDBSearchPanelTest.java b/test/jalview/gui/PDBSearchPanelTest.java index 514fd7a..7697bda 100644 --- a/test/jalview/gui/PDBSearchPanelTest.java +++ b/test/jalview/gui/PDBSearchPanelTest.java @@ -13,7 +13,7 @@ import org.testng.annotations.Test; public class PDBSearchPanelTest { - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws Exception { } @@ -69,7 +69,7 @@ public class PDBSearchPanelTest } @Test(groups = - { "Network" }, timeOut = 5000) + { "Network", "External" }, timeOut = 5000) public void txt_search_ActionPerformedTest() { PDBSearchPanel searchPanel = new PDBSearchPanel(null); diff --git a/test/jalview/gui/PaintRefresherTest.java b/test/jalview/gui/PaintRefresherTest.java index 6916cef..1705e90 100644 --- a/test/jalview/gui/PaintRefresherTest.java +++ b/test/jalview/gui/PaintRefresherTest.java @@ -22,7 +22,7 @@ import org.testng.annotations.Test; public class PaintRefresherTest { // TODO would prefer PaintRefresher to be a single rather than static - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { PaintRefresher.components.clear(); diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index f984dfc..46397d3 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -41,7 +41,7 @@ public class PopupMenuTest PopupMenu testee = null; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws IOException { alignment = new FormatAdapter().readFile(TEST_DATA, diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index 2baee84..71d062c 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -18,7 +18,7 @@ public class StructureChooserTest { Sequence seq; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws Exception { seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java index feba9cb..31bfd9d 100644 --- a/test/jalview/io/AnnotatedPDBFileInputTest.java +++ b/test/jalview/io/AnnotatedPDBFileInputTest.java @@ -32,7 +32,7 @@ public class AnnotatedPDBFileInputTest String pdbId; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setup() throws Exception { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", @@ -156,7 +156,7 @@ public class AnnotatedPDBFileInputTest /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { jalview.bin.Jalview.main(new String[] diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java index 0d66b21..2404ea9 100644 --- a/test/jalview/io/FileIOTester.java +++ b/test/jalview/io/FileIOTester.java @@ -38,7 +38,7 @@ public class FileIOTester /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { } diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java index 108dd31..b6a3e4a 100644 --- a/test/jalview/io/JSONFileTest.java +++ b/test/jalview/io/JSONFileTest.java @@ -62,7 +62,7 @@ public class JSONFileTest private JSONFile jf; - @BeforeTest + @BeforeTest(alwaysRun = true) public void setup() throws Exception { // create and add sequences @@ -228,7 +228,7 @@ public class JSONFileTest } - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void methodSetup() { passedCount = 0; diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index c03dd71..2afcdc2 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -47,7 +47,7 @@ public class Jalview2xmlTests /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { jalview.bin.Jalview.main(new String[] diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java index a783b1e..261ffc6 100644 --- a/test/jalview/io/NewickFileTests.java +++ b/test/jalview/io/NewickFileTests.java @@ -84,7 +84,7 @@ public class NewickFileTests /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { } diff --git a/test/jalview/io/RNAMLfileTest.java b/test/jalview/io/RNAMLfileTest.java index d9d0b7f..fc54ef1 100644 --- a/test/jalview/io/RNAMLfileTest.java +++ b/test/jalview/io/RNAMLfileTest.java @@ -29,7 +29,7 @@ import org.testng.annotations.Test; public class RNAMLfileTest { - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { } diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java index 1e4a866..e3612a5 100644 --- a/test/jalview/structure/StructureSelectionManagerTest.java +++ b/test/jalview/structure/StructureSelectionManagerTest.java @@ -15,7 +15,7 @@ public class StructureSelectionManagerTest { private StructureSelectionManager ssm; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { ssm = new StructureSelectionManager(); diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index c5d1db9..3354e38 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -57,7 +57,7 @@ public class AAStructureBindingModelTest /** * Set up test conditions with three aligned sequences, */ - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { SequenceI seq1 = new Sequence("1YCS", "-VPSQK"); diff --git a/test/jalview/util/QuickSortTest.java b/test/jalview/util/QuickSortTest.java index fac463a..ea55779 100644 --- a/test/jalview/util/QuickSortTest.java +++ b/test/jalview/util/QuickSortTest.java @@ -23,7 +23,7 @@ public class QuickSortTest private final Object[] sortedThings = new Object[] { c4, c2, c1, c3 }; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { things = new Object[] diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java index e54d5b9..2963ef2 100644 --- a/test/jalview/ws/PDBSequenceFetcherTest.java +++ b/test/jalview/ws/PDBSequenceFetcherTest.java @@ -37,7 +37,7 @@ public class PDBSequenceFetcherTest SequenceFetcher sf; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws Exception { // ensure 'add annotation from structure' is selected @@ -50,7 +50,7 @@ public class PDBSequenceFetcherTest } @Test(groups = - { "Functional" }, enabled = false) + { "Network" }, enabled = true) public void testRnaSeqRetrieve() throws Exception { List sps = sf.getSourceProxy("PDB"); diff --git a/test/jalview/ws/dbsources/PDBRestClientTest.java b/test/jalview/ws/dbsources/PDBRestClientTest.java index 00c1e02..9ae5b26 100644 --- a/test/jalview/ws/dbsources/PDBRestClientTest.java +++ b/test/jalview/ws/dbsources/PDBRestClientTest.java @@ -34,7 +34,7 @@ import com.sun.jersey.api.client.config.DefaultClientConfig; public class PDBRestClientTest { - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() throws Exception { } @@ -45,7 +45,7 @@ public class PDBRestClientTest } @Test(groups = - { "External" }) + { "External", "Network" }) public void executeRequestTest() { List wantedFields = new ArrayList(); @@ -95,7 +95,7 @@ public class PDBRestClientTest } @Test(groups = - { "External" }) + { "External, Network" }) public void parsePDBJsonExceptionStringTest() { List wantedFields = new ArrayList(); @@ -134,7 +134,7 @@ public class PDBRestClientTest } @Test(groups = - { "External" }, expectedExceptions = Exception.class) + { "External", "Network" }, expectedExceptions = Exception.class) public void testForExpectedRuntimeException() throws Exception { List wantedFields = new ArrayList(); diff --git a/test/jalview/ws/gui/Jws2ParamView.java b/test/jalview/ws/gui/Jws2ParamView.java index b22f0f7..41ead2f 100644 --- a/test/jalview/ws/gui/Jws2ParamView.java +++ b/test/jalview/ws/gui/Jws2ParamView.java @@ -62,7 +62,7 @@ public class Jws2ParamView public static Jws2Discoverer disc = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { Cache.initLogger(); @@ -75,7 +75,7 @@ public class Jws2ParamView */ @Test(groups = - { "Functional" }, enabled = false) + { "Interactive" }, enabled = true) public void testJws2Gui() { Iterator presetEnum = presetTests.iterator(); diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java index 03fca21..35110a4 100644 --- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java +++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java @@ -52,7 +52,7 @@ public class DisorderAnnotExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java index e6b7c58..08bb405 100644 --- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java +++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java @@ -34,7 +34,7 @@ import org.testng.annotations.Test; public class JalviewJabawsTestUtils { - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { } diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java index e347e55..e458876 100644 --- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java +++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java @@ -62,7 +62,7 @@ public class JpredJabaStructExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index dc33cbf..87a4ec6 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -61,7 +61,7 @@ public class RNAStructExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { diff --git a/test/jalview/ws/jws2/ParameterUtilsTest.java b/test/jalview/ws/jws2/ParameterUtilsTest.java index d76a532..523ccb3 100644 --- a/test/jalview/ws/jws2/ParameterUtilsTest.java +++ b/test/jalview/ws/jws2/ParameterUtilsTest.java @@ -51,7 +51,7 @@ public class ParameterUtilsTest private static Jws2Discoverer disc = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { serviceTests.add("AAConWS".toLowerCase()); diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java index abaa7ec..d9b1d90 100644 --- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java +++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java @@ -48,7 +48,7 @@ public class DbRefFetcherTest /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { jalview.bin.Cache.initLogger();