Commit 90246a83 authored by Rui Chen's avatar Rui Chen

[BioJava] Deleted two problematic file. Added a patch file for solving the stdout error

parent bf6bc760
benchmark biojava
class org.dacapo.harness.BioJava
thread-model per_cpu
jars "AAProperties-jar-with-dependencies.jar";
size default args "${SCRATCH}/dat/test.fasta"
output
stdout digest 0xd31deba48b76595f822b43217afefd6fec3aefb9,
stderr digest 0xda39a3ee5e6b4b0d3255bfef95601890afd80709;
\ No newline at end of file
diff -Nur build/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java tempbuild/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
--- build/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java 2018-12-11 13:56:09.000000000 +0800
+++ tempbuild/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java 2018-12-13 17:08:05.000000000 +0800
@@ -88,7 +88,7 @@
compute(output, entry.getValue().getOriginalHeader(), entry.getValue().getSequenceAsString().trim(), delimiter, aaTable, propertyList, specificList,
decimalPlace);
}
- output.close();
+// output.close();
}
public static void run(String[] args) throws Exception{
......@@ -24,7 +24,11 @@
<os family="windows"/>
</condition>
<target name="unpack" depends="untar"/>
<target name="unpack" depends="untar, patch"/>
<target name="patch">
<patch patchfile="${bm-files}/${bm-name}.patch" dir="${bm-files}" strip="0" ignorewhitespace="yes"/>
</target>
<target name="bm-build">
<exec executable="${mvn-exe}" dir="${bm-build-dir}" failonerror="yes">
......@@ -32,8 +36,6 @@
</exec>
</target>
<target name="data"/>
<target name="jar">
<copy file="${bm-build-dir}/biojava-aa-prop/target/AAProperties-jar-with-dependencies.jar"
tofile="${bm-jars}/${bm-name}-${bm-version}.jar"/>
......
>1u6d_1
GRLIYTAGGYF-----RQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGCVV
>1u6d_2
GGLLYAVGGRNNspdgNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVI
>1u6d_3
DGHIYAVGGSHG----CIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVL
>1u6d_4
NRLLYAVGGFDG----TNRLNSAECYYPERNEWRMITAMNTIRSGAGVCVL
>1u6d_5
HNCIYAAGGYDG----QDQLNSVERYDVETETWTFVAPMKHRRSALGITVH
>1u6d_6
QGRIYVLGGYDG----HTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT
This diff is collapsed.
>ENST00000380152 peptide: ENSP00000369497 pep:KNOWN_protein_coding
MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPN
LFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTV
KTKMDQADDVSCPLLNSCLSESPVVLQCTHVTPQRDKSVVCGSLFHTPKFVKGRQTPKHI
SESLGAEVDPDMSWSSSLATPPTLSSTVLIVRNEEASETVFPHDTTANVKSYFSNHDESL
KKNDRFIASVTDSENTNQREAASHGFGKTSGNSFKVNSCKDHIGKSMPNVLEDEVYETVV
DTSEEDSFSLCFSKCRTKNLQKVRTSKTRKKIFHEANADECEKSKNQVKEKYSFVSEVEP
NDTDPLDSNVANQKPFESGSDKISKEVVPSLACEWSQLTLSGLNGAQMEKIPLLHISSCD
QNISEKDLLDTENKRKKDFLTSENSLPRISSLPKSEKPLNEETVVNKRDEEQHLESHTDC
ILAVKQAISGTSPVASSFQGIKKSIFRIRESPKETFNASFSGHMTDPNFKKETEASESGL
EIHTVCSQKEDSLCPNLIDNGSWPATTTQNSVALKNAGLISTLKKKTNKFIYAIHDETSY
KGKKIPKDQKSELINCSAQFEANAFEAPLTFANADSGLLHSSVKRSCSQNDSEEPTLSLT
SSFGTILRKCSRNETCSNNTVISQDLDYKEAKCNKEKLQLFITPEADSLSCLQEGQCEND
PKSKKVSDIKEEVLAAACHPVQHSKVEYSDTDFQSQKSLLYDHENASTLILTPTSKDVLS
NLVMISRGKESYKMSDKLKGNNYESDVELTKNIPMEKNQDVCALNENYKNVELLPPEKYM
RVASPSRKVQFNQNTNLRVIQKNQEETTSISKITVNPDSEELFSDNENNFVFQVANERNN
LALGNTKELHETDLTCVNEPIFKNSTMVLYGDTGDKQATQVSIKKDLVYVLAEENKNSVK
QHIKMTLGQDLKSDISLNIDKIPEKNNDYMNKWAGLLGPISNHSFGGSFRTASNKEIKLS
EHNIKKSKMFFKDIEEQYPTSLACVEIVNTLALDNQKKLSKPQSINTVSAHLQSSVVVSD
CKNSHITPQMLFSKQDFNSNHNLTPSQKAEITELSTILEESGSQFEFTQFRKPSYILQKS
TFEVPENQMTILKTTSEECRDADLHVIMNAPSIGQVDSSKQFEGTVEIKRKFAGLLKNDC
NKSASGYLTDENEVGFRGFYSAHGTKLNVSTEALQKAVKLFSDIENISEETSAEVHPISL
SSSKCHDSVVSMFKIENHNDKTVSEKNNKCQLILQNNIEMTTGTFVEEITENYKRNTENE
DNKYTAASRNSHNLEFDGSDSSKNDTVCIHKDETDLLFTDQHNICLKLSGQFMKEGNTQI
KEDLSDLTFLEVAKAQEACHGNTSNKEQLTATKTEQNIKDFETSDTFFQTASGKNISVAK
ESFNKIVNFFDQKPEELHNFSLNSELHSDIRKNKMDILSYEETDIVKHKILKESVPVGTG
NQLVTFQGQPERDEKIKEPTLLGFHTASGKKVKIAKESLDKVKNLFDEKEQGTSEITSFS
HQWAKTLKYREACKDLELACETIEITAAPKCKEMQNSLNNDKNLVSIETVVPPKLLSDNL
CRQTENLKTSKSIFLKVKVHENVEKETAKSPATCYTNQSPYSVIENSALAFYTSCSRKTS
VSQTSLLEAKKWLREGIFDGQPERINTADYVGNYLYENNSNSTIAENDKNHLSEKQDTYL
SNSSMSNSYSYHSDEVYNDSGYLSKNKLDSGIEPVLKNVEDQKNTSFSKVISNVKDANAY
PQTVNEDICVEELVTSSSPCKNKNAAIKLSISNSNNFEVGPPAFRIASGKIVCVSHETIK
KVKDIFTDSFSKVIKENNENKSKICQTKIMAGCYEALDDSEDILHNSLDNDECSTHSHKV
FADIQSEEILQHNQNMSGLEKVSKISPCDVSLETSDICKCSIGKLHKSVSSANTCGIFST
ASGKSVQVSDASLQNARQVFSEIEDSTKQVFSKVLFKSNEHSDQLTREENTAIRTPEHLI
SQKGFSYNVVNSSAFSGFSTASGKQVSILESSLHKVKGVLEEFDLIRTEHSLHYSPTSRQ
NVSKILPRVDKRNPEHCVNSEMEKTCSKEFKLSNNLNVEGGSSENNHSIKVSPYLSQFQQ
DKQQLVLGTKVSLVENIHVLGKEQASPKNVKMEIGKTETFSDVPVKTNIEVCSTYSKDSE
NYFETEAVEIAKAFMEDDELTDSKLPSHATHSLFTCPENEEMVLSNSRIGKRRGEPLILV
GEPSIKRNLLNEFDRIIENQEKSLKASKSTPDGTIKDRRLFMHHVSLEPITCVPFRTTKE
RQEIQNPNFTAPGQEFLSKSHLYEHLTLEKSSSNLAVSGHPFYQVSATRNEKMRHLITTG
RPTKVFVPPFKTKSHFHRVEQCVRNINLEENRQKQNIDGHGSDDSKNKINDNEIHQFNKN
NSNQAVAVTFTKCEEEPLDLITSLQNARDIQDMRIKKKQRQRVFPQPGSLYLAKTSTLPR
ISLKAAVGGQVPSACSHKQLYTYGVSKHCIKINSKNAESFQFHTEDYFGKESLWTGKGIQ
LADGGWLIPSNDGKAGKEEFYRALCDTPGVDPKLISRIWVYNHYRWIIWKLAAMECAFPK
EFANRCLSPERVLLQLKYRYDTEIDRSRRSAIKKIMERDDTAAKTLVLCVSDIISLSANI
SETSSNKTSSADTQKVAIIELTDGWYAVKAQLDPPLLAVLKNGRLTVGQKIILHGAELVG
SPDACTPLEAPESLMLKISANSTRPARWYTKLGFFPDPRPFPLPLSSLFSDGGNVGCVDV
IIQRAYPIQWMEKTSSGLYIFRNEREEEKEAAKYVEAQQKRLEALFTKIQEEFEEHEENT
TKPYLPSRALTRQQVRALQDGAELYEAVKNAADPAYLEGYFSEEQLRALNNHRQMLNDKK
QAQIQLEIRKAMESAEQKEQGLSRDVTTVWKLRIVSYSKKEKDSVILSIWRPSSDLYSLL
TEGKRYRIYHLATSKSKSKSERANIQLAATKKTQYQQLPVSDEILFQIYQPREPLHFSKF
LDPDFQPSCSEVDLIGFVVSVVKKTGLAPFVYLSDECYNLLAIKFWIDLNEDIIKPHMLI
AASNLQWRPESKSGLLTLFAGDFSVFSASPKEGHFQETFNKMKNTVENIDILCNEAENKL
MHILHANDPKWSTPTKDCTSGPYTAQIIPGTGNKLLMSSPNCEIYYQSPLSLCMAKRKSV
STPVSAQMTSKSCKGEKEIDDQKNCKKRRALDFLSRLPLPPPVSPICTFVSPAAQKAFQP
PRSCGTKYETPIKKKELNSPQMTPFKKFNEISLLESNSIADEELALINTQALLSGSTGEK
QFISVSESTRTAPTSSEDYLRLKRRCTTSLIKEQESSQASTEECEKNKQDTITTKKYI
\ No newline at end of file
>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
AASQAALGL
\ No newline at end of file
>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
AASQAALGL
This source diff could not be displayed because it is too large. You can view the blob instead.
>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
AASQAALGL
>sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1
MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA
TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG
NGMNAWVAWRNRCKGTDVQAWIRGCRL
\ No newline at end of file
>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
AASQAALGL
>sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1
MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA
TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG
NGMNAWVAWRNRCKGTDVQAWIRGCRL
\ No newline at end of file
>SAOV_0114
MAVNVRDYIAENYGLFINGEFVKGSSDETIEVTNPATGETLSHITRAKDKDVDHAVEVAQ
EAFESWSLTSKSERAQMLRDIGDKLMAQKDKIAMIETLNNGKPIRETTAIDIPFAARHFH
YFASVIETEEGTVNDIDKDTMSIVRHEPIGVVGAVVAWNFPMLLAAWKIAPAIAAGNTIV
IQPSSSTPLSLLEVAKIFQEVLPKGVVNILTGKGSESGNAIFNHDGVDKLSFTGSTDVGY
QVAEAAAKHLVPATLELGGKSANIILDDANLDLAVEGIQLGILFNQGEVCSAGSRLLVHE
KIYDQLVPRLQEAFSNIKVGDPQDEATQMGSQTGKDQLDKIQSYIDAAKESDAQILAGGH
RLTENGLDKGFFFEPTLIAVPDNHHKLAQEEIFGPVLTVIKVKDDQEAIDIANDSEYGLA
GGVFSQNITRALNIAKAVRTGRIWINTYNQVPEGAPFGGYKKSGIGRETYKGALSNYQQV
KNIYIDTSNALKGLY
>SAOV_0094
MFIGKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSY
FISEQPEELLINSVDKHSIAFRAKNYKVSTKLLNKQYYQAMYLSNLTSYLFSFVKIPDNI
ILSLINNLDDLLNGNLESLNKKESIKEIAKVVRAKILQDESNEALLFMLEKAGIVIYEKR
INDSIDAYSFWSKDLTPFIILGTNKGVAVRRNFDLAHELGHLVLHRHIQFDLLSPEEYKT
IEHEADIFASEFLLPEEAFKKDFDQMTKKSNPDYLAVLKEKWYVSIQAIAMRAYYLGLMS
STQYRYFWASLNKKGYKSKEPLDDVIEMSRPVKMNSLLKLYFDRNILTPQKLLNYLKVDE
TFLNHLAGINLKLFKDYVNENREYNITNLYK
>SAA6008_00126
MLTIPEKENRGSKEQEVAIMIDALADKGKKALEALSKKSQEEINHIVHQMSLAAVDQHMV
LAKLAHEETGRGIYEDKAIKNLYASEYIWNSIKDNKTVGIIGEDKEKGLTYVAEPIGVIC
GVTPTTNPTSTTIFKAMIAIKTGNPIIFAFHPSAQESSKRAAEVVLEAAMKAGAPKDIIQ
WIEVPSIEATKQLMNHKGIALVLATGGSGMVKSAYSTGKPALGVGPGNVPSYIEKTAHIK
RAVNDIIGSKTFDNGMICASEQVVVIDKEIYKDVTNEFKAHQAYFVKKDELQRLENAIMN
EQKTSIKPDIVGKSAVEIAELAGIPVPENTKLIIAEISGVGSDYPLSREKLSPVLALVKA
QSTKQAFQICEDTLHFGGLGHTAVIHTEDETLQKDFGLRMKACRVLVNTPSAVGGIGDM0
NELIPSLTLGCGSYGRNSISHNVSATDLLNIKTIAKRRNNTQIFKVPAQIYFEENAIMSL
TTMDKIEKVMIVCDPGMVEFGYTKTVENVLRQRTEQPQIKIFSEVEPNPSTNTVYKGLE1
MVDFQPDTIIALGGGSAMDAAKAMWMFFEHPETSFFGAKQKFLDIGKRTYKIGMPENAT0
ICIPTTSGTGSEVTPFAVITDSETNVKYPLADFALTPDVAIIDPQFVMSVPKSVTADTGM
DVLTHAMESYVSVMASDYTRGLSLQAIKLTFEYLKSSVEKGDKVSREKMHNASTLAGMAF
ANAFLGIAHSIAHKIGGEYGIPHGRANAILLPHIIRYNAKDPQKHALFPKYEFFRADTDY
ADIAKFLGLKGNTTEALVESLAKAVYELGQSVGIEMNLKSQGVSEEELNESIDRMAELAF
EDQCTTANPKEALISEIKDIIQTSYDYKQ
\ No newline at end of file
>SAOV_0114
MAVNVRDYIAENYGLFINGEFVKGSSDETIEVTNPATGETLSHITRAKDKDVDHAVEVAQ
EAFESWSLTSKSERAQMLRDIGDKLMAQKDKIAMIETLNNGKPIRETTAIDIPFAARHFH
YFASVIETEEGTVNDIDKDTMSIVRHEPIGVVGAVVAWNFPMLLAAWKIAPAIAAGNTIV
IQPSSSTPLSLLEVAKIFQEVLPKGVVNILTGKGSESGNAIFNHDGVDKLSFTGSTDVGY
QVAEAAAKHLVPATLELGGKSANIILDDANLDLAVEGIQLGILFNQGEVCSAGSRLLVHE
KIYDQLVPRLQEAFSNIKVGDPQDEATQMGSQTGKDQLDKIQSYIDAAKESDAQILAGGH
RLTENGLDKGFFFEPTLIAVPDNHHKLAQEEIFGPVLTVIKVKDDQEAIDIANDSEYGLA
GGVFSQNITRALNIAKAVRTGRIWINTYNQVPEGAPFGGYKKSGIGRETYKGALSNYQQV
KNIYIDTSNALKGLY
>SAOV_0094
MFIGKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSY
FISEQPEELLINSVDKHSIAFRAKNYKVSTKLLNKQYYQAMYLSNLTSYLFSFVKIPDNI
ILSLINNLDDLLNGNLESLNKKESIKEIAKVVRAKILQDESNEALLFMLEKAGIVIYEKR
INDSIDAYSFWSKDLTPFIILGTNKGVAVRRNFDLAHELGHLVLHRHIQFDLLSPEEYKT
IEHEADIFASEFLLPEEAFKKDFDQMTKKSNPDYLAVLKEKWYVSIQAIAMRAYYLGLMS
STQYRYFWASLNKKGYKSKEPLDDVIEMSRPVKMNSLLKLYFDRNILTPQKLLNYLKVDE
TFLNHLAGINLKLFKDYVNENREYNITNLYK
>SAA6008_00126
MLTIPEKENRGSKEQEVAIMIDALADKGKKALEALSKKSQEEINHIVHQMSLAAVDQHMV
LAKLAHEETGRGIYEDKAIKNLYASEYIWNSIKDNKTVGIIGEDKEKGLTYVAEPIGVIC
GVTPTTNPTSTTIFKAMIAIKTGNPIIFAFHPSAQESSKRAAEVVLEAAMKAGAPKDIIQ
WIEVPSIEATKQLMNHKGIALVLATGGSGMVKSAYSTGKPALGVGPGNVPSYIEKTAHIK
RAVNDIIGSKTFDNGMICASEQVVVIDKEIYKDVTNEFKAHQAYFVKKDELQRLENAIMN
EQKTSIKPDIVGKSAVEIAELAGIPVPENTKLIIAEISGVGSDYPLSREKLSPVLALVKA
QSTKQAFQICEDTLHFGGLGHTAVIHTEDETLQKDFGLRMKACRVLVNTPSAVGGIGDMY
NELIPSLTLGCGSYGRNSISHNVSATDLLNIKTIAKRRNNTQIFKVPAQIYFEENAIMSL
TTMDKIEKVMIVCDPGMVEFGYTKTVENVLRQRTEQPQIKIFSEVEPNPSTNTVYKGLEM
MVDFQPDTIIALGGGSAMDAAKAMWMFFEHPETSFFGAKQKFLDIGKRTYKIGMPENATF
ICIPTTSGTGSEVTPFAVITDSETNVKYPLADFALTPDVAIIDPQFVMSVPKSVTADTGM
DVLTHAMESYVSVMASDYTRGLSLQAIKLTFEYLKSSVEKGDKVSREKMHNASTLAGMAF
ANAFLGIAHSIAHKIGGEYGIPHGRANAILLPHIIRYNAKDPQKHALFPKYEFFRADTDY
ADIAKFLGLKGNTTEALVESLAKAVYELGQSVGIEMNLKSQGVSEEELNESIDRMAELAF
EDQCTTANPKEALISEIKDIIQTSYDYKQ
\ No newline at end of file
>2gox
---S-tDaErLkhl--IvTpSgAgeq----NmIgMtPt-viAv---HyL-dEt-eqWe
>2gox
GsrS-tDAeRLkh--LiVTpSGaGEqn---MiGMtPTviA-vh--YlDE-tEqwE-Kf
>2gox
GS-rsTDaERLkhl-IvTPSgAGEqnmig--MTPtVIavH-Yld-ETEqwEKf-G-LE
\ No newline at end of file
>1mbc
VLSEGEWQLVLHVWAKVEADVAghgqdil--IRLFKSHPeTlekfdrfkhlkteaemkasedlkkhgvtvltalgailkkkghheaelkplaqshatkhkipikylefiseaiihvlhsrhpgdf-GADAQGAMNKAL
>1hlb
DLTLaQKKiVRKTWHQlMRNKtsfvtdvf--IRIFAYDPsAqnkfpqmagmsasqlrssrqmqahairvssimseyveeldsdilpellatlarthdlnkvgadhynlfakvlmealqaelgsdf-NEKTRDAWAKAF
>1thb.A
VLSPaDKTNVKAAWGKVGAHAGeygaeal--ERMFLSFPtTktyfphfdlshgsaqvkghgkkvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaahlpaef-------TPAVHASLDKFL
>1ith.A
GLTAaQIKAIQDHWFLnIKGCLqaaadsif-FKYLTAYPgDlaffhkfssvplyglrsnpaykaqtltvinyldkvvdalggnagalmkakvpshdamgitpkhfgqllklvggvfqeefsa----DPTTVAAWGDAA
\ No newline at end of file
>SAOV_0114
MAVNVRDYIAENYGLFINGEFVKGSSDETIEVTNPATGETLSHITRAKDKDVDHAVEVAQ
EAFESWSLTSKSERAQMLRDIGDKLMAQKDKIAMIETLNNGKPIRETTAIDIPFAARHFH
YFASVIETEEGTVNDIDKDTMSIVRHEPIGVVGAVVAWNFPMLLAAWKIAPAIAAGNTIV
IQPSSSTPLSLLEVAKIFQEVLPKGVVNILTGKGSESGNAIFNHDGVDKLSFTGSTDVGY
QVAEAAAKHLVPATLELGGKSANIILDDANLDLAVEGIQLGILFNQGEVCSAGSRLLVHE
KIYDQLVPRLQEAFSNIKVGDPQDEATQMGSQTGKDQLDKIQSYIDAAKESDAQILAGGH
RLTENGLDKGFFFEPTLIAVPDNHHKLAQEEIFGPVLTVIKVKDDQEAIDIANDSEYGLA
GGVFSQNITRALNIAKAVRTGRIWINTYNQVPEGAPFGGYKKSGIGRETYKGALSNYQQV
KNIYIDTSNALKGLY
>SAOV_0094
MFIGKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSY
FISEQPEELLINSVDKHSIAFRAKNYKVSTKLLNKQYYQAMYLSNLTSYLFSFVKIPDNI
ILSLINNLDDLLNGNLESLNKKESIKEIAKVVRAKILQDESNEALLFMLEKAGIVIYEKR
INDSIDAYSFWSKDLTPFIILGTNKGVAVRRNFDLAHELGHLVLHRHIQFDLLSPEEYKT
IEHEADIFASEFLLPEEAFKKDFDQMTKKSNPDYLAVLKEKWYVSIQAIAMRAYYLGLMS
STQYRYFWASLNKKGYKSKEPLDDVIEMSRPVKMNSLLKLYFDRNILTPQKLLNYLKVDE
TFLNHLAGINLKLFKDYVNENREYNITNLYK
>SAA6008_00126
MLTIPEKENRGSKEQEVAIMIDALADKGKKALEALSKKSQEEINHIVHQMSLAAVDQHMV
LAKLAHEETGRGIYEDKAIKNLYASEYIWNSIKDNKTVGIIGEDKEKGLTYVAEPIGVIC
GVTPTTNPTSTTIFKAMIAIKTGNPIIFAFHPSAQESSKRAAEVVLEAAMKAGAPKDIIQ
WIEVPSIEATKQLMNHKGIALVLATggsgmvksaySTGKPALGVGPGNVPSYIEKTAHIK
RAVNDIIGSKTFDNGMICASEQVVVIDKEIYKDVTNEFKAHQAYFVKKDELQRLENAIMN
EQKTSIKPDIVGKSAVEIAELAGIPVPENTKLIIAEISGVGSDYPLSREKLSPVLALVKA
QSTKQAFQICEDTLHFGGLGHTAVIHTEDETLQKDFGLRMKACRVLVNTPSAVGGIGDMY
NELIPSLTLGCGSYGRNSISHNVSATDLLNIKTIAKRRNNTQIFKVPAQIYFEENAIMSL
TTMDKIEKVMIVCDPGMVEFGYTKTVENVLRQRTEQPQIKIFSEVEPNPSTNTVYKGLEM
MVDFQPDTIIALGGGSAMDAAKAMWMFFEHPETSFFGAKQKFLDIGKRTYKIGMPENATF
ICIPTTSGTGSEVTPFAVITDSETNVKYPLADFALTPDVAIIDPQFVMSVPKSVTADTGM
DVLTHAMESYVSVMASDYTRGLSLQAIKLTFEYLKSSVEKGDKVSREKMHNASTLAGMAF
ANAFLGIAHSIAHKIGGEYGIPHGRANAILLPHIIRYNAKDPQKHALFPKYEFFRADTDY
ADIAKFLGLKGNTTEALVESLAKAVYELGQSVGIEMNLKSQGVSEEELNESIDRMAELAF
EDQCTTANPKEALISEIKDIIQTSYDYKQ
\ No newline at end of file
>rna-Apple3
TTCTTGGGGTTTGCGTCAGATAGCAACTTCCGGCGGCAGTAGAGATGATATTTTATCCGA
TTGAGCTTGCCCAGCGCACCCTCGGGCCCCGTGGCTCTTCTCTTAAATGTGCCCTGCACG
ATGTTAGCGGTTCCTACTCCTCCCCGAGCCCTATGGGTGGACAGACTCGCCCTCTGAGGC
TGCGTGTTCAACTGGTTCCAAGTCCGGCGCCTGTGGATCTACGACGCGACCAGCAACATT
ATACCAATGTCTAGGCTTAGCTCGAAAACTAGTAAGCCTTAGAACTAGGGTCGTAGCTTC
TTCTAAATGAAGGGCAGCGTCATAGCCATCCACGTTAGCGCTTACTCAATCGCCTGTCGG
CTGTCATGTTACCGCTGCCGTAAGTTCGTGAACATAAAATACAACACATTTTAGGTTTAA
CAAGGATTGTTTACCGCCACGTACTGGTGCCGGTAGTGAAACGAAAAACCTCAGCATCGG
GAGGAGGAGAACGGAATCCCTACCAATCTTATCTCTACTTAAAGAACAAAGCGCGCGGTA
CATGGCGCAGACGAGAATGAATCCCCGAACGGGCCGAGTTAGACTCCTCAACCTGTCGAA
AAGTTGCGATCCGCTAGATCGTAGAGTACGGACTTAAAAAAGAAAAGAAGGTCTCTACCC
GAGCGGTGAGCCCAACCAGTTCCAGGTTGCTGCCGGATTCTTCCACACGGCGGTGCCATA
TGGACGACCCCGTACTTTGGGCATTCTAGGCTACCTACTGCGAACGCCTCGCGTTCATGC
GCAAAGTTTTCTCTAGATAGGTCCCATGTACGGTTCGCATTGCGAAAGTATGGGATACTA
GAGGTTTTATCGGGCCTCGCTTGAGGTCTGTCTGGGACTGGCGCACATCGCTCGTCGCCC
AGTCGATAGCGGGGTGATTAAATAAGAAATATGTTAGTGCCCGGATTTGGAACCAACCAG
TCCCGGTAGCGGTACAAAAAGCCTTTCCTGCTAGTTCTATGCTTAAAGCGTACTCCTGTT
ACAATCCGTAGGCAACCTGAAGAGGCAACCTGGTTTTCCTTTATTTCGACTTTGTTTGCC
ATTTCCAATGTGATACTGTGCGGCGACCTTAATGCTTTTTGGTAAAACCATACCGAGATC
CAGCGCACGCGACATTCAGACCGGTCCCGGTTTGGCGGTCAACCTCGTACTCTGCACTGT
TCAGCTAGAGGGGTCTCCTATCCCGAGGTACCGGTCGTCTAACGGGTGGTTACAGGGGCT
GGTCCTACTCTACCAACAGTTAAGGAGGGCAACAAGTTCGATCCACGAGTGAGACCTGGA
TCCGGGGGGATGGCATACATCCCATACGCTCACTCAGCATGCACGTTCCTAGCACATGCT
GGAATCTTGCAAGCTGGACAGAGTGTATTGTGGCCCTTGAGCTATACTTCTAACGCCAGA
TCCATGTTTGCAAACATAGCTCCAGTGGCCTATTCGACGGTTTAGCCTCTGCACCATGTT
ATG
\ No newline at end of file
>rna-Apple3
FLGFASDSNFRRQ*R*YFIRLSLPSAPSGPVALLLNVPCTMLAVPTPPRALWVDRLAL*G
CVFNWFQVRRLWIYDATSNIIPMSRLSSKTSKP*N*GRSFF*MKGSVIAIHVSAYSIACR
LSCYRCRKFVNIKYNTF*V*QGLFTATYWCR**NEKPQHREEENGIPTNLIST*RTKRAV
HGADENESPNGPS*TPQPVEKLRSARS*STDLKKKRRSLPER*AQPVPGCCRILPHGGAI
WTTPYFGHSRLPTANASRSCAKFSLDRSHVRFALRKYGILEVLSGLA*GLSGTGAHRSSP
SR*RGD*IRNMLVPGFGTNQSR*RYKKPFLLVLCLKRTPVTIRRQPEEATWFSFISTLFA
ISNVILCGDLNAFW*NHTEIQRTRHSDRSRFGGQPRTLHCSARGVSYPEVPVV*RVVTGA
GPTLPTVKEGNKFDPRVRPGSGGMAYIPYAHSACTFLAHAGILQAGQSVLWPLSYTSNAR
SMFANIAPVAYSTV*PLHHVM
\ No newline at end of file
package org.dacapo.harness;
import org.dacapo.parser.Config;
import java.io.File;
import java.io.PrintStream;
public class BioJava extends Benchmark {
String[] args;
public BioJava(Config config, File scratch, File data) throws Exception {
super(config, scratch, data, false);
Class<?> clazz = Class.forName("org.biojava.nbio.aaproperties.CommandPrompt", true, loader);
this.method = clazz.getMethod("main", String[].class);
}
@Override
protected void prepare(String size) throws Exception {
super.prepare(size);
args = config.preprocessArgs(size, scratch, data);
}
@Override
public void iterate(String size) throws Exception {
System.out.println(System.out.toString());
this.method.invoke(null, (Object) new String[]{"-i", args[0], "-a"});
System.out.println(System.out.toString());
System.out.println("in here I am out");
}
}
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