add results of one Jpred test

diff --git a/binaries/src/jpred/tests/res_d16vpa_.align b/binaries/src/jpred/tests/res_d16vpa_.align
new file mode 100644 (file)
index 0000000..e846252
--- /dev/null
+++ b/binaries/src/jpred/tests/res_d16vpa_.align
@@ -0,0 +1,78 @@
+>QUERY
+SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA
+YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL
+HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES
+WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG
+YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL
+>UniRef90_Q00028
+-----PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD
+SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ
+LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ
+RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG
+FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA--------------
+>UniRef90_Q8B635
+-----PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN
+SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS
+IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH
+RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG
+FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA--------------
+>UniRef90_Q9E205
+-----PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS
+ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS
+SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE
+NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG
+FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS--------------
+>UniRef90_Q88530
+--LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE
+NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L
+NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ
+GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG
+YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS--------------
+>UniRef90_B4XS08
+------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S
+EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG
+VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ
+YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG
+FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP-------------
+>UniRef90_P09265
+---PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S
+TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT
+TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE
+RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG
+FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE-----------
+>UniRef90_Q2QBC8
+------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA
+HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL
+HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ
+ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG
+YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL-------------------
+>UniRef90_Q90603
+---------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK
+NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD
+LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ
+ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV
+YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD----------------
+>UniRef90_O89246
+--------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE
+EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP
+SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ
+LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA
+YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR----
+>UniRef90_Q5PP87
+----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA
+PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD
+-------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ
+ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG
+YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG----------------------------
+>UniRef90_Q65819
+----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL
+AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T
+AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ
+RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG
+FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS---------------
+>UniRef90_O56869
+-RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS
+GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV
+GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES
+-QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA
+YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP-------------

diff --git a/binaries/src/jpred/tests/res_d16vpa_.concise b/binaries/src/jpred/tests/res_d16vpa_.concise
new file mode 100644 (file)
index 0000000..38a9914
--- /dev/null
+++ b/binaries/src/jpred/tests/res_d16vpa_.concise
@@ -0,0 +1,25 @@
+align1;QUERY:S,R,M,P,S,P,P,M,P,V,P,P,A,A,L,F,N,R,L,L,D,D,L,G,F,S,A,G,P,A,L,C,T,M,L,D,T,W,N,E,D,L,F,S,A,L,P,T,N,A,D,L,Y,R,E,C,K,F,L,S,T,L,P,S,D,V,V,E,W,G,D,A,Y,V,P,E,R,T,Q,I,D,I,R,A,H,G,D,V,A,F,P,T,L,P,A,T,R,D,G,L,G,L,Y,Y,E,A,L,S,R,F,F,H,A,E,L,R,A,R,E,E,S,Y,R,T,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,V,R,Q,L,H,R,Q,A,H,M,R,G,R,D,R,D,L,G,E,M,L,R,A,T,I,A,D,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,T,R,E,I,L,W,A,A,Y,A,E,Q,M,M,R,P,D,L,F,D,C,L,C,C,D,L,E,S,W,R,Q,L,A,G,L,F,Q,P,F,M,F,V,N,G,A,L,T,V,R,G,V,P,I,E,A,R,R,L,R,E,L,N,H,I,R,E,H,L,N,L,P,L,V,R,S,A,A,T,E,E,P,G,A,P,L,T,T,P,P,T,L,H,G,N,Q,A,R,A,S,G,Y,F,M,V,L,I,R,A,K,L,D,S,Y,S,S,F,T,T,S,P,S,E,A,V,M,R,E,H,A,Y,S,R,A,P,T,K,N,N,Y,G,S,T,I,E,G,L,L,D,L,P,D,D,D,A,P,E,E,A,G,L,A,A,P,R,L,S,F,L,
+align2;UniRef90_Q00028:-,-,-,-,-,P,P,K,A,T,S,P,T,A,L,Y,Q,R,L,Q,A,E,L,G,F,P,E,G,Q,A,M,L,F,A,M,E,K,W,N,E,D,M,F,S,A,I,P,V,H,V,D,L,Y,T,E,I,A,L,L,S,T,S,V,N,E,V,V,K,A,G,L,D,S,L,P,I,P,T,E,V,D,L,N,A,H,G,S,E,P,F,P,E,V,P,A,L,E,D,E,L,E,T,Y,V,I,S,A,Q,R,F,Y,L,S,E,L,R,A,R,E,E,H,Y,S,R,L,L,R,G,Y,C,V,A,L,L,H,Y,L,Y,G,S,A,K,R,Q,L,R,G,A,-,-,-,G,S,D,S,A,L,M,H,K,F,K,Q,V,V,R,D,R,Y,Y,R,E,T,A,N,L,A,R,L,L,Y,L,H,L,Y,I,S,V,T,R,E,V,S,W,R,L,H,A,S,Q,V,V,N,Q,G,I,F,V,S,L,H,Y,T,W,P,Q,R,R,K,F,E,C,L,F,H,P,V,L,F,N,H,G,V,V,I,L,E,N,D,P,L,E,F,N,D,L,Q,R,I,N,Y,R,R,R,E,L,G,L,P,L,I,R,A,G,L,I,E,E,E,N,L,P,L,E,S,E,P,T,F,S,G,K,L,P,R,T,I,G,F,L,T,H,Q,I,R,T,K,M,E,A,Y,S,N,A,H,P,S,T,P,L,F,P,L,A,E,H,S,Y,S,R,I,D,G,R,L,S,Y,G,T,T,A,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align3;UniRef90_Q8B635:-,-,-,-,-,P,I,K,A,S,S,P,S,S,L,I,K,N,L,L,D,E,L,N,F,P,E,G,P,S,L,L,S,S,M,E,K,W,N,E,D,L,F,S,C,I,P,R,F,L,E,I,Y,I,E,N,S,I,L,S,T,S,V,D,E,V,I,K,N,L,D,N,S,L,N,Y,D,D,V,I,D,F,Q,V,H,G,P,E,T,F,P,K,T,P,L,L,E,E,E,L,E,N,Y,V,T,S,V,Q,K,Y,F,L,S,E,L,K,A,R,E,V,T,Y,S,F,L,L,T,K,Y,C,K,A,L,L,L,Y,L,R,Y,N,T,K,S,S,I,K,G,-,-,-,-,-,-,N,K,D,I,N,Q,K,F,K,Q,N,V,R,E,R,Y,Y,R,E,V,A,N,I,A,R,L,L,Y,L,H,L,Y,L,S,V,T,R,E,V,S,W,K,L,H,A,D,Q,V,L,L,Q,S,V,F,V,S,L,S,Y,S,W,S,H,R,R,Q,F,E,C,I,F,H,P,I,L,F,N,H,G,I,V,N,L,E,N,N,P,L,T,F,K,E,L,Q,K,I,N,Y,R,R,H,I,L,G,L,P,L,I,R,A,G,L,V,E,E,D,N,Q,P,L,M,I,P,P,E,F,S,S,K,L,P,R,T,I,G,F,L,T,Q,Q,I,R,A,K,M,E,A,Y,S,D,N,H,P,V,T,P,K,F,P,R,I,E,H,S,Y,A,K,P,I,D,P,I,N,Y,G,T,T,I,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align4;UniRef90_Q9E205:-,-,-,-,-,P,P,R,V,A,S,P,A,V,L,Y,Q,Q,L,I,N,D,L,H,F,S,E,G,P,R,I,I,A,L,L,E,T,C,N,E,D,I,F,S,C,F,P,L,N,E,D,L,Y,T,D,T,I,V,F,S,T,N,P,S,D,I,I,E,L,E,T,S,E,T,P,E,-,-,P,I,N,L,I,T,K,G,-,C,D,L,P,S,L,P,S,T,Y,T,E,L,P,M,Y,V,E,N,V,Q,N,T,F,F,T,E,L,R,V,R,E,K,A,Y,L,R,L,L,I,L,Y,C,K,S,L,L,R,H,L,Q,G,I,S,R,R,S,S,V,G,A,R,S,Q,D,C,E,H,K,Y,I,T,Q,F,K,Q,S,I,R,L,R,Y,Y,R,E,V,A,K,L,A,R,L,L,Y,L,H,L,Y,I,T,V,T,R,Q,F,S,W,R,L,F,A,Q,Q,S,K,Y,P,D,V,F,A,A,M,K,F,M,W,L,E,N,R,Q,F,T,C,A,F,H,P,I,L,C,N,H,G,I,V,L,L,E,G,K,P,L,S,S,Q,R,L,R,E,V,N,Y,R,R,R,Q,L,G,L,P,L,V,R,C,A,L,I,E,E,K,G,V,P,L,V,Q,R,P,E,F,S,A,H,M,P,R,S,L,G,F,L,T,H,H,I,K,A,K,L,D,V,Y,S,S,K,H,S,Q,E,P,G,N,V,R,V,D,H,P,Y,A,R,N,V,N,N,I,N,Y,G,S,S,V,E,A,M,I,V,S,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align5;UniRef90_Q88530:-,-,L,P,S,P,E,-,A,A,S,P,N,L,L,Y,D,R,L,I,L,E,L,D,F,A,E,G,P,S,L,L,A,K,L,E,R,V,N,V,D,L,F,S,C,L,P,L,N,S,H,L,Y,K,H,A,K,I,L,S,T,C,P,R,E,V,L,D,A,V,Y,E,N,T,W,Q,Y,T,A,L,N,L,N,E,H,G,K,S,S,I,P,P,V,P,A,S,K,D,D,L,P,A,Y,V,T,A,V,Q,E,F,Y,L,E,E,L,E,A,R,E,Q,I,Y,A,K,L,F,F,G,Y,C,R,A,L,I,M,H,I,I,K,S,V,-,-,L,N,E,S,R,G,V,R,V,S,D,D,Y,V,Q,N,K,A,R,W,Y,I,S,N,N,Y,Y,R,D,A,V,R,I,A,K,L,L,Y,L,H,L,Y,L,S,T,T,E,I,V,S,Q,R,L,E,A,M,Q,T,S,L,Q,D,L,F,V,Y,L,R,C,E,W,G,Q,G,R,Q,F,W,C,I,F,Q,P,M,I,Y,N,H,G,V,P,M,I,E,G,R,A,L,T,S,L,E,L,G,S,S,N,Y,I,R,S,E,L,G,L,P,L,I,R,C,E,L,L,E,E,L,E,S,P,V,V,F,P,P,T,F,T,A,T,A,P,R,S,S,G,Y,L,F,H,N,I,R,A,K,M,E,L,Y,S,N,I,H,P,S,P,Q,L,S,G,L,S,D,H,T,Y,V,R,T,H,V,P,V,N,Y,G,T,T,V,E,V,L,L,D,A,S,D,P,D,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align6;UniRef90_B4XS08:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,F,P,E,A,S,T,I,L,S,T,F,E,L,M,N,M,D,L,F,S,C,L,P,R,N,E,D,L,Y,R,N,A,A,L,L,S,G,S,V,T,E,V,I,E,A,-,-,S,E,I,P,I,D,G,E,I,D,L,N,A,H,G,S,K,Q,L,P,I,P,P,S,N,E,W,E,I,P,N,Y,V,E,A,V,Q,Q,F,F,L,S,E,L,R,A,R,E,E,S,Y,L,K,L,F,L,G,Y,C,R,A,I,V,N,Y,I,K,S,A,A,T,R,G,V,R,G,C,R,I,M,D,R,K,S,E,A,N,K,R,M,R,R,M,I,A,D,R,Y,Y,R,E,A,A,R,L,A,K,V,L,Y,L,H,L,Y,L,S,V,A,R,E,I,S,S,R,L,C,A,T,Q,M,Q,V,Q,N,V,F,V,Y,M,R,Y,E,W,Q,Q,Y,R,Q,F,T,C,L,F,H,P,I,M,F,N,H,G,V,V,L,L,N,G,E,P,L,Q,A,Q,K,L,R,E,V,N,Y,I,R,F,K,L,G,L,P,V,I,R,C,G,L,V,E,E,H,D,K,P,L,V,E,E,P,R,F,Y,G,N,L,P,R,S,S,G,F,L,T,E,L,I,R,S,K,M,E,A,Y,S,E,L,R,P,T,S,P,S,S,I,S,N,D,H,T,Y,A,K,Q,L,D,K,V,N,F,G,S,T,R,E,A,I,L,D,T,I,D,T,E,G,P,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align7;UniRef90_P09265:-,-,-,P,S,P,P,W,V,A,S,P,K,I,L,Y,Q,Q,L,I,R,D,L,D,F,S,E,G,P,R,L,L,S,C,L,E,T,W,N,E,D,L,F,S,C,F,P,I,N,E,D,L,Y,S,D,M,M,V,L,S,P,D,P,D,D,V,I,-,-,-,-,S,T,V,S,T,K,D,H,V,N,L,T,T,R,G,S,V,R,L,P,S,P,P,K,Q,P,T,G,L,P,A,Y,V,Q,E,V,Q,D,S,F,T,V,E,L,R,A,R,E,E,A,Y,T,K,L,L,V,T,Y,C,K,S,I,I,R,Y,L,Q,G,T,A,K,R,T,T,I,G,L,N,I,Q,N,P,D,Q,K,A,Y,T,Q,L,R,Q,S,I,L,L,R,Y,Y,R,E,V,A,S,L,A,R,L,L,Y,L,H,L,Y,L,T,V,T,R,E,F,S,W,R,L,Y,A,S,Q,S,A,H,P,D,V,F,A,A,L,K,F,T,W,T,E,R,R,Q,F,T,C,A,F,H,P,V,L,C,N,H,G,I,V,L,L,E,G,K,P,L,T,A,S,A,L,R,E,I,N,Y,R,R,R,E,L,G,L,P,L,V,R,C,G,L,V,E,E,N,K,S,P,L,V,Q,Q,P,S,F,S,V,H,L,P,R,S,V,G,F,L,T,H,H,I,K,R,K,L,D,A,Y,A,V,K,H,P,Q,E,P,R,H,V,R,A,D,H,P,Y,A,K,V,V,E,N,R,N,Y,G,S,S,I,E,A,M,I,L,A,P,-,-,P,S,P,S,E,-,-,-,-,-,-,-,-,-,-,-,
+align8;UniRef90_Q2QBC8:-,-,-,-,-,-,-,-,-,-,-,-,A,A,L,Y,N,R,L,L,E,D,L,G,F,G,D,G,P,A,L,C,T,I,L,D,S,W,N,E,D,L,F,S,G,L,P,A,N,P,D,L,Y,R,E,C,R,F,L,S,T,L,P,G,D,V,V,V,W,G,D,A,H,A,P,D,R,G,P,I,D,I,R,A,H,G,S,A,P,F,P,S,L,P,A,R,R,E,G,L,P,A,Y,C,E,A,L,T,R,F,F,H,S,E,L,R,A,R,E,E,S,Y,R,R,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,T,R,Q,L,H,R,Q,A,A,L,K,G,R,P,R,D,L,Q,E,M,L,R,A,A,V,A,E,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,V,R,E,I,L,W,A,V,Y,A,E,Q,V,M,R,Q,D,L,F,E,G,L,R,C,D,L,E,Q,A,R,Q,L,S,C,L,F,Q,P,L,L,F,V,H,G,A,L,S,V,G,G,E,P,V,S,P,A,R,L,R,E,L,N,H,V,R,E,R,L,N,L,P,L,I,R,S,A,A,T,E,E,P,G,A,A,L,T,A,A,P,A,L,Q,T,Q,R,A,R,S,S,G,Y,F,M,T,L,I,R,V,K,L,D,A,Y,S,E,W,S,A,G,S,E,G,A,V,L,R,E,H,A,Y,S,R,R,R,E,R,T,N,Y,G,S,S,I,E,G,L,L,E,L,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align9;UniRef90_Q90603:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,Y,T,R,L,L,H,E,L,D,F,V,E,G,P,S,I,L,A,R,L,E,K,I,N,V,D,L,F,S,C,F,P,H,N,K,H,L,Y,E,H,A,K,I,L,S,V,S,P,S,E,V,L,E,E,L,S,K,N,T,W,T,Y,T,A,L,N,L,N,E,H,G,E,V,A,L,P,M,P,P,T,T,K,A,D,L,P,S,Y,V,D,D,I,Q,N,F,Y,L,G,E,L,E,A,R,E,K,S,Y,A,T,M,F,Y,G,Y,C,R,A,L,A,E,Y,I,R,Q,S,A,I,K,D,L,R,D,A,-,-,R,V,E,D,K,N,I,G,A,C,S,K,A,R,Q,Y,I,A,E,R,Y,Y,R,E,A,F,A,N,V,L,Y,V,H,L,Y,L,S,T,T,R,D,V,S,Q,R,L,E,A,S,Q,M,G,R,Q,N,I,F,V,Y,L,K,C,E,W,L,Q,E,R,H,F,H,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,V,L,T,A,P,E,L,R,A,Q,N,Y,I,R,S,E,F,G,L,P,L,I,R,C,K,L,V,E,E,P,D,M,P,L,I,S,P,P,P,F,S,G,D,A,P,R,A,S,V,Y,L,L,Q,C,I,R,S,K,L,E,V,Y,S,S,H,P,P,N,P,Q,L,H,V,H,K,E,H,V,H,Q,K,L,E,S,P,P,N,Y,G,T,T,V,E,A,L,L,M,D,S,S,D,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align10;UniRef90_O89246:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,E,L,D,F,T,E,G,P,S,L,L,S,R,L,E,K,L,N,V,D,L,F,S,C,F,P,I,N,G,H,L,Y,E,H,A,T,L,L,S,V,S,P,S,E,V,L,D,A,A,S,E,E,K,W,A,Y,T,A,I,N,L,N,E,H,C,G,M,E,V,P,R,P,P,L,T,K,D,G,L,P,V,Y,V,T,E,I,Q,K,F,F,S,M,E,L,E,A,R,E,K,S,Y,V,T,L,L,C,G,Y,C,R,A,L,A,C,Y,L,R,Q,G,A,N,E,P,S,R,C,D,M,C,V,G,G,S,-,-,-,-,E,T,P,R,R,S,I,A,G,A,Y,Y,R,E,A,A,R,F,A,R,L,L,Y,M,H,L,Y,L,S,V,T,R,D,V,S,R,R,L,E,A,S,Q,R,K,R,Q,N,L,F,A,H,L,R,C,D,W,H,Q,L,R,H,F,Q,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,A,L,T,A,A,E,L,R,T,Q,N,Y,V,R,S,E,L,G,L,P,V,M,R,C,E,L,V,E,E,R,G,M,P,L,T,A,P,P,A,F,L,A,N,A,P,R,A,S,A,Y,L,F,Q,C,I,K,S,K,L,E,V,Y,S,L,M,H,P,P,R,P,R,S,S,A,R,G,E,S,G,R,A,G,K,A,G,P,S,H,G,T,I,V,K,A,M,L,R,D,S,T,H,P,G,P,A,I,A,D,I,A,A,A,R,-,-,-,-,
+align11;UniRef90_Q5PP87:-,-,-,-,-,-,-,-,-,-,S,P,D,A,L,Y,Q,R,L,I,S,D,L,A,F,D,E,G,P,A,L,L,G,A,M,E,R,W,N,E,D,L,F,S,C,L,P,G,N,E,D,L,Y,A,R,L,V,M,L,S,A,S,A,D,E,V,A,A,Q,V,R,A,P,T,A,D,A,S,-,V,D,L,G,V,P,G,A,E,P,M,P,R,V,P,A,V,E,E,E,L,P,A,Y,V,A,A,V,E,R,F,F,V,S,T,L,R,A,R,E,E,R,Y,A,R,L,L,D,A,Y,C,R,A,V,L,R,Y,L,H,A,Q,A,R,R,D,-,-,-,-,-,-,-,-,-,-,-,-,-,E,G,K,L,R,Q,L,V,R,G,R,Y,Y,R,D,V,A,R,L,A,P,W,L,F,L,H,L,Y,V,A,T,A,R,E,L,S,W,R,L,H,A,D,Q,V,V,A,Q,D,V,F,M,S,L,R,Y,E,W,D,Q,A,R,Q,L,T,C,L,F,H,P,V,L,F,N,H,G,V,V,L,L,S,G,A,P,V,P,A,A,Q,L,R,A,V,N,H,R,R,R,E,L,G,L,P,L,V,R,A,G,L,I,E,E,D,G,A,D,L,V,E,E,P,P,F,S,A,A,L,P,R,A,A,G,Y,L,S,H,Q,V,R,I,K,M,E,A,Y,S,-,-,-,-,-,-,-,-,R,E,Y,R,D,H,T,Y,C,R,P,P,S,P,V,S,Y,G,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align12;UniRef90_Q65819:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,R,M,Q,A,E,L,G,F,P,D,G,P,A,L,L,R,A,M,E,R,W,N,E,D,L,F,S,C,L,P,T,N,A,D,L,Y,A,D,A,A,L,L,S,A,D,A,D,A,V,V,G,A,M,Y,L,A,V,P,D,A,E,R,L,D,L,N,A,H,A,N,Q,P,L,P,A,P,P,A,S,E,E,G,L,P,E,Y,V,A,G,V,Q,A,H,F,L,A,E,L,R,A,R,E,E,R,Y,A,G,L,F,L,G,Y,C,R,A,L,L,Q,H,L,R,A,-,-,-,-,T,A,A,R,G,R,G,A,A,G,A,G,A,Q,A,D,R,L,R,Q,L,V,A,A,R,Y,Y,R,E,A,S,R,L,A,R,L,A,F,A,H,M,Y,V,A,T,A,R,E,V,S,W,R,L,H,S,Q,Q,S,Q,A,Q,G,V,F,V,S,L,Y,Y,A,W,P,Q,R,R,Q,F,T,C,L,F,H,P,V,L,F,N,H,G,V,V,A,L,E,D,G,F,L,D,A,A,E,L,R,R,L,N,Y,R,R,R,E,L,G,L,P,L,V,R,A,G,L,V,E,V,E,V,G,P,L,V,E,E,P,P,F,S,G,S,L,P,R,A,L,G,F,L,N,Y,Q,V,R,A,K,M,G,A,P,A,E,-,-,A,G,G,R,L,A,P,E,R,E,H,S,Y,A,R,P,R,G,A,I,N,Y,G,T,T,P,E,A,M,L,R,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+align13;UniRef90_O56869:-,R,N,P,G,P,P,A,L,V,S,A,S,F,L,A,K,N,A,L,T,E,L,Q,F,A,D,W,D,K,I,Q,H,V,L,K,T,I,N,I,D,I,F,S,C,V,P,V,G,E,N,G,L,C,N,M,D,W,F,S,L,D,T,E,K,I,W,T,L,M,D,S,G,T,P,N,V,S,P,N,L,L,I,T,P,G,P,P,-,-,P,E,C,I,K,T,P,E,E,A,P,A,Y,F,E,A,I,S,N,Y,F,E,S,V,L,A,A,R,E,A,E,Y,A,K,L,L,A,E,Y,A,K,S,L,A,K,Y,I,R,H,K,S,Q,K,V,G,R,-,-,G,L,R,A,L,E,L,D,T,E,E,A,K,K,R,L,M,K,S,E,Y,Y,K,G,I,E,K,L,L,I,I,F,L,V,H,L,V,L,N,A,C,R,D,V,A,R,I,I,W,V,Q,Q,R,D,S,S,S,V,L,Q,K,V,T,Y,R,W,E,S,-,Q,Q,L,H,C,I,F,Q,P,L,L,V,S,P,G,P,V,F,L,D,N,D,P,L,P,L,Q,T,L,Q,H,V,N,Y,V,R,Y,L,L,G,V,P,V,L,R,F,S,M,I,E,E,S,P,S,A,Q,Y,I,P,-,-,-,-,Y,D,K,T,A,P,S,A,Y,D,V,L,A,T,I,A,R,-,-,-,-,T,C,L,T,S,S,G,C,S,R,A,S,H,D,H,T,Y,A,R,D,N,E,K,P,N,Y,S,S,S,R,I,V,L,L,A,D,S,A,L,D,T,P,-,-,-,-,-,-,-,-,-,-,-,-,-,
+
+jnetpred:-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,-,-,-,-,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,E,E,E,E,E,E,E,-,-,-,H,-,H,H,E,E,-,-,-,-,E,E,-,-,-,-,E,E,E,E,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,H,H,H,-,-,-,-,-,E,E,E,E,E,-,-,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+JNETCONF:9,9,8,8,8,8,8,7,7,6,3,6,8,8,9,9,9,9,8,7,4,4,7,8,8,8,7,4,6,8,8,9,9,9,9,9,8,5,4,2,3,2,2,2,3,2,3,5,6,6,5,1,0,1,2,2,2,4,0,5,7,6,1,6,8,8,8,7,6,3,2,3,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,4,1,0,2,3,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,7,3,2,1,4,1,1,1,5,7,7,7,7,5,1,7,8,9,9,9,9,9,9,9,9,9,8,5,4,6,8,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,6,1,1,1,4,4,5,5,2,1,3,5,4,5,6,4,4,6,3,0,1,1,1,1,1,1,3,4,5,1,1,2,5,6,4,5,7,7,5,3,6,8,7,7,6,5,4,1,0,0,1,1,1,0,4,3,2,1,0,5,7,5,1,1,1,1,1,0,0,1,7,8,7,7,5,2,1,0,3,6,7,6,5,6,7,7,6,2,1,2,6,6,8,9,9,9,9,8,8,7,5,1,0,2,4,6,7,7,7,7,7,6,7,7,7,7,7,7,6,4,1,4,6,7,7,7,7,7,7,7,6,5,1,0,3,3,3,2,1,6,7,7,7,7,6,5,4,4,5,7,7,7,7,6,3,3,4,2,6,
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diff --git a/binaries/src/jpred/tests/res_d16vpa_.hmm b/binaries/src/jpred/tests/res_d16vpa_.hmm
new file mode 100644 (file)
index 0000000..c07a517
--- /dev/null
+++ b/binaries/src/jpred/tests/res_d16vpa_.hmm
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diff --git a/binaries/src/jpred/tests/res_d16vpa_.jnet b/binaries/src/jpred/tests/res_d16vpa_.jnet
new file mode 100644 (file)
index 0000000..a55c497
--- /dev/null
+++ b/binaries/src/jpred/tests/res_d16vpa_.jnet
@@ -0,0 +1,12 @@
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+JNETPROPC:0.9180,0.9303,0.9164,0.8871,0.8701,0.8544,0.8504,0.8382,0.8361,0.7921,0.6686,0.2123,0.1066,0.0724,0.0569,0.0561,0.0542,0.0608,0.0815,0.1254,0.2798,0.6569,0.8413,0.8972,0.8913,0.8730,0.8333,0.7020,0.2179,0.1104,0.0708,0.0544,0.0501,0.0463,0.0433,0.0404,0.0406,0.0489,0.0507,0.0605,0.0815,0.1306,0.2683,0.6411,0.8328,0.8767,0.8706,0.8425,0.8263,0.7564,0.6530,0.3826,0.3156,0.3714,0.5782,0.6085,0.3435,0.3881,0.7046,0.8492,0.8534,0.7354,0.2403,0.1078,0.0821,0.0760,0.0718,0.0681,0.0860,0.1344,0.2530,0.6131,0.8038,0.8612,0.8538,0.8317,0.8277,0.8213,0.8110,0.8105,0.8040,0.8040,0.8040,0.8040,0.8040,0.8040,0.8040,0.8129,0.8135,0.8105,0.8020,0.8138,0.8136,0.8133,0.7902,0.7466,0.5949,0.6924,0.7323,0.6712,0.2055,0.0885,0.0629,0.0517,0.0486,0.0535,0.0459,0.0458,0.0470,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0517,0.0480,0.0473,0.0489,0.0507,0.0605,0.0815,0.1306,0.2683,0.6411,0.8328,0.8862,0.8867,0.8670,0.8595,0.8195,0.6955,0.2274,0.1049,0.0708,0.0544,0.0501,0.0463,0.0459,0.0458,0.0470,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0565,0.0517,0.0480,0.0473,0.0489,0.0507,0.0605,0.0826,0.1353,0.2635,0.6387,0.8440,0.8821,0.8900,0.8548,0.7934,0.3300,0.2073,0.1362,0.1026,0.1006,0.1059,0.1528,0.2492,0.6780,0.8597,0.7946,0.5542,0.5679,0.3198,0.1705,0.1465,0.2348,0.6619,0.8451,0.8456,0.6821,0.2787,0.2872,0.6278,0.8293,0.8392,0.6733,0.2333,0.1131,0.1239,0.2676,0.6319,0.8095,0.8485,0.8434,0.8308,0.7893,0.7501,0.6551,0.3678,0.3499,0.4331,0.3053,0.3797,0.5618,0.5121,0.2493,0.2185,0.3274,0.6381,0.7840,0.9028,0.9110,0.6985,0.2206,0.1074,0.0925,0.1085,0.1886,0.3634,0.2478,0.3031,0.6527,0.8214,0.8270,0.8252,0.8108,0.6544,0.5316,0.6683,0.7669,0.8271,0.8295,0.8345,0.8369,0.8297,0.8268,0.7931,0.6686,0.2123,0.1049,0.0708,0.0544,0.0501,0.0445,0.0431,0.0426,0.0422,0.0480,0.0571,0.0684,0.1019,0.1898,0.4521,0.4635,0.7081,0.7965,0.8363,0.8466,0.8231,0.8178,0.8209,0.8032,0.8068,0.8028,0.7984,0.8011,0.8050,0.7992,0.8022,0.7809,0.6720,0.5492,0.6765,0.7610,0.8041,0.8125,0.8228,0.8298,0.8284,0.8379,0.8255,0.7919,0.5852,0.2151,0.1421,0.1534,0.1752,0.2069,0.3370,0.6099,0.7786,0.8582,0.8358,0.8253,0.7850,0.7255,0.6058,0.6916,0.7399,0.7972,0.8156,0.7868,0.7897,0.7991,0.8008,0.8324,0.8472,0.8882,0.9280,0.9424,

diff --git a/binaries/src/jpred/tests/res_d16vpa_.profile b/binaries/src/jpred/tests/res_d16vpa_.profile
new file mode 100644 (file)
index 0000000..8e097f6
--- /dev/null
+++ b/binaries/src/jpred/tests/res_d16vpa_.profile
@@ -0,0 +1,365 @@
+
+Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
+           A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V   A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
+    1 S    1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -2 -2 -1  4  1 -3 -2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.00    0.00
+    2 R   -1  6  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.00    0.00
+    3 M   -2 -2 -3 -4 -2 -2 -3 -4 -3  1  4 -2  5  0 -3 -2 -1 -2 -1  1    0   0   0   0   0   0   0   0   0   0  50   0  50   0   0   0   0   0   0   0  0.46 0.07
+    4 P   -1 -3 -3 -2 -3 -2 -2 -3 -3 -3 -4 -2 -3 -4  8 -1 -2 -4 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.20 0.13
+    5 S    1 -1  0 -1 -1  0 -1 -1 -1 -3 -3 -1 -2 -3 -1  5  1 -3 -2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0  0.63 0.13
+    6 P   -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -5  8 -2 -2 -5 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.29 0.21
+    7 P   -2 -2 -2 -1 -4 -1  2 -3 -2 -4 -4 -1 -3 -5  8 -1 -2 -4 -4 -3    0   0   0   0   0   0  19   0   0   0   0   0   0   0  81   0   0   0   0   0  1.76 0.21
+    8 M    1  3 -2 -3 -3  0 -1 -2 -2 -2 -1  3  4 -2 -3 -1 -2  7 -1 -2   19  17   0   0   0   0   0   0   0   0   0  27  20   0   0   0   0  17   0   0  0.46 0.21
+    9 P    2 -2 -2 -2 -1 -2 -2 -2 -2  0 -1 -2 -1 -2  4 -1 -1 -3 -2  3   28   1   1   1   0   1   1   1   0   1   2   1   0   1  21   1   1   0   1  35  0.36 0.17
+   10 V    4 -2 -2 -3 -1 -2 -2 -1 -3 -1 -2 -2 -1 -3 -2  0  2 -3 -2  2   66   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  13   0   0  20  0.44 0.21
+   11 P    0 -2  0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3  4  5  1 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0  20  80   0   0   0   0  0.73 0.21
+   12 P   -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  9 -2 -2 -5 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.35 0.27
+   13 A    3 -2  2  2 -2 -1 -1  1 -2 -3 -3  1 -2 -4 -2  1  1 -4 -3 -2   40   0  12  11   0   0   0   7   0   0   0  11   0   0   0  10   7   0   0   0  0.36 0.30
+   14 A    4 -3 -3 -3 -2 -2 -2 -2 -3  1  1 -2 -1 -2 -2  1 -1 -4 -3  1   56   0   0   0   0   0   0   0   0  11  12   0   0   0   0  10   0   0   0  11  0.40 0.30
+   15 L   -3 -3 -5 -5 -2 -3 -4 -5 -4  1  6 -4  1 -1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0  0.95 0.36
+   16 F    1 -3 -3 -4 -3 -3 -3 -4  0  0 -2 -3 -2  4 -4 -2 -2  0  7 -2   15   0   0   0   0   0   0   0   0   7   0   0   0  15   0   0   0   0  62   0  0.98 0.39
+   17 N   -2  0  3  1 -4  5  2 -3 -1 -4 -4  3 -2 -4 -3 -1  1 -4 -3 -4    0   0  20   8   0  32  12   0   0   0   0  21   0   0   0   0   8   0   0   0  0.61 0.41
+   18 R   -3  6  3 -2 -5  3 -1 -3 -1 -4 -4  1 -3 -4 -3 -1 -2 -4 -3 -4    0  64  21   0   0  15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.97 0.41
+   19 L    1 -3 -4 -5 -2 -3 -4 -4 -4  0  5 -3  4 -1 -4 -3 -2 -3 -2  0   14   0   0   0   0   0   0   0   0   0  74   0  12   0   0   0   0   0   0   0  0.72 0.41
+   20 L   -3 -3 -4 -4 -3  3 -2 -5 -3  4  4 -2  0 -1 -4 -3 -2 -3 -2  0    0   0   0   0   0  21   0   0   0  30  49   0   0   0   0   0   0   0   0   0  0.59 0.41
+   21 D    1  1  1  3 -3 -1  0  0  3 -3 -1 -1 -2 -4 -3  1  2 -4 -3 -3   17   8   7  20   0   0   6   5   8   0   8   0   0   0   0   7  14   0   0   0  0.26 0.41
+   22 D   -2 -2 -1  5 -5  0  6 -3 -2 -5 -5 -1 -4 -5 -3 -1 -2 -5 -4 -4    0   0   0  39   0   0  61   0   0   0   0   0   0   0   0   0   0   0   0   0  1.12 0.43
+   23 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  1  6 -4  1 -1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0  1.04 0.43
+   24 G    0 -2  1  4 -4  2 -1  4  2 -5 -5 -2 -3 -4 -3 -1 -2 -4 -3 -4    6   0   6  28   0  14   0  39   7   0   0   0   0   0   0   0   0   0   0   0  0.68 0.43
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+  355 F   -2 -3 -3 -4 -3 -4 -4 -3 -1  0  0 -3  0  7 -4 -3 -2  1  3 -1    0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0  0.74 0.01
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+
+                      K         Lambda
+Standard Ungapped    0.1374     0.3234
+Standard Gapped      0.0410     0.2670
+PSI Ungapped         0.1702     0.3177
+PSI Gapped           0.0521     0.2670

diff --git a/binaries/src/jpred/tests/res_d16vpa_.pssm b/binaries/src/jpred/tests/res_d16vpa_.pssm
new file mode 100644 (file)
index 0000000..8b8db6a
--- /dev/null
+++ b/binaries/src/jpred/tests/res_d16vpa_.pssm
@@ -0,0 +1,356 @@
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diff --git a/binaries/src/jpred/tests/res_d16vpa_.res b/binaries/src/jpred/tests/res_d16vpa_.res
new file mode 100644 (file)
index 0000000..55507ce
--- /dev/null
+++ b/binaries/src/jpred/tests/res_d16vpa_.res
@@ -0,0 +1,114 @@
+>jnetpred
+-----------HHHHHHHHHH-------HHHHHHHHHHHHHHH-------------EE----HHHHHHHHH-
+------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------EEEEEEE---
+H-HHEE----EE----EEEE--------HHHHH--HHH-----EEEEE---------E----------HHHH
+HHHHHHHHHHHH------------------------------HHHHH---------------------
+>JNETSOL25
+--------B-BB-BBB--BB--B-B--B--BB-BB--B-BBBBBBBBBB--BBBBB-BBBBBB--BB-BB--
+-BB---BBBB-B-B---B--BB-----B--BB--B--BB---B-BBB--BB-BBB-BBBBBB-BB---B---
+B--B-B------B--BB-BBB---BB-BBB-BBBBBBBBBBBBBBBBBBBBBBB-B-----BBBBB-B-B--
+---B-BBBBBBBBBBBBBBB---BB-B--B--B-BBB--B-BBBBBB-BB------BB--B-B-B-BBBBBB
+BBBBBBBBBB-BBB-B--------B--BBBBB----BBBBBBBBBBB-BB---BB--B-BBB--B---
+>JNETSOL5
+--------------BB--B--------B--BB--B------BB-BB------B--B-BB------B---B--
+---------B-----------------B--BB--B-------B------B--BB--BB-BBB--B---B---
+-----B----------B---B-------B--BB-BB-B---B-BB--BB--B---------BB--B-B----
+---B-BBB-B-BB--BBB-B-------------------B-B-BB-B-B------------------B-B-B
+-B---B---B-B-----------------------------B--BBB---------------------
+>JNETSOL0
+------------------B-------------------------B--------------------B------
+---------------------------------------------------------B-B----B-------
+-------------------------------------B---B--B--B------------------------
+-----B-----------------------------------------------------------------B
+--------------------------------------------------------------------
+>JNETHMM
+-----------HHHHHHHHHH-------HHHHHHHHHHHHHHH--------HHH---E----HHHHHHHHH-
+----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------EEEEEEE---
+---EEE----EE----EEEE--------HHHHH--HH------EEEEEEEE-----------------HHHH
+HHHHHHHHHHHH-----------------------------HHHHHH---------------------
+>JNETPSSM
+-----------HHHHHHHHHH-------HHHHHHHHHH-----------------EEE----HHHHHHHHH-
+------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
+---------HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----EEEEEEE--H
+HHHHHHHE---EE---EEEE---------H----HHHHH----HHHHHH-------EEE----------HHH
+HHHHHHHHHHH-H-----------------------------HEEEE-----------------EE--
+>QUERY
+SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA
+YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL
+HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES
+WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG
+YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL
+>UniRef90_Q00028
+-----PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD
+SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ
+LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ
+RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG
+FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA--------------
+>UniRef90_Q8B635
+-----PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN
+SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS
+IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH
+RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG
+FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA--------------
+>UniRef90_Q9E205
+-----PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS
+ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS
+SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE
+NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG
+FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS--------------
+>UniRef90_Q88530
+--LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE
+NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L
+NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ
+GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG
+YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS--------------
+>UniRef90_B4XS08
+------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S
+EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG
+VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ
+YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG
+FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP-------------
+>UniRef90_P09265
+---PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S
+TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT
+TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE
+RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG
+FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE-----------
+>UniRef90_Q2QBC8
+------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA
+HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL
+HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ
+ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG
+YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL-------------------
+>UniRef90_Q90603
+---------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK
+NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD
+LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ
+ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV
+YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD----------------
+>UniRef90_O89246
+--------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE
+EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP
+SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ
+LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA
+YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR----
+>UniRef90_Q5PP87
+----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA
+PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD
+-------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ
+ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG
+YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG----------------------------
+>UniRef90_Q65819
+----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL
+AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T
+AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ
+RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG
+FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS---------------
+>UniRef90_O56869
+-RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS
+GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV
+GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES
+-QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA
+YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP-------------

diff --git a/binaries/src/jpred/tests/todo.bash b/binaries/src/jpred/tests/todo.bash
index 5a757ba..030ea8a 100755 (executable)
--- a/binaries/src/jpred/tests/todo.bash
+++ b/binaries/src/jpred/tests/todo.bash
@@ -21,9 +21,9 @@ ln -s /data/UNIREFdb databases
 
 
 ####################################################################################################
-../jpred.pl -seq d16vpa_.fas     -o res_d16vpa_ -dbname ported_db -ncpu 4 -debug
-../jpred.pl -seq SCOP175B_nr.seq -o res_SCOP175B_nr -dbname ported_db -ncpu 4 -debug
-../jpred.pl -seq T-state1.fas    -o res_T-state1.res -dbname ported_db -ncpu 4 -debug
-../jpred.pl -seq T-state2.fas    -o res_T-state2.res -dbname ported_db -ncpu 4 -debug
+../jpred.pl -seq d16vpa_.fas -o res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq SCOP175B_nr.seq -o res_SCOP175B_nr -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq T-state1.fas    -o res_T-state1.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq T-state2.fas    -o res_T-state2.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
 
 ./webscripts/fasta2concise < d16vpa_.res.align > d16vpa_.res.align.csv