-Search.setIndex({docnames:["advanced","changelog","citations","client","develop","getting_started","included_tools","index","stats","va","war"],envversion:51,filenames:["advanced.rst","changelog.rst","citations.rst","client.rst","develop.rst","getting_started.rst","included_tools.rst","index.rst","stats.rst","va.rst","war.rst"],objects:{},objnames:{},objtypes:{},terms:{"0_17":0,"168h":8,"16th":7,"1st":7,"2nd":7,"378m":9,"512m":9,"6000m":0,"8cbe486":[1,6],"abstract":4,"boolean":4,"byte":[0,8],"case":[0,4,8,9],"class":[0,4],"default":[0,1,3,4,5,8,9],"enum":4,"export":0,"final":[0,4,5],"function":[0,3,5,7,10],"import":[2,4],"long":[0,4],"new":[0,1,3,5,7,9,10],"public":[4,7,10],"return":[0,1,4],"static":[0,4],"throw":4,"true":[0,4,8,10],"try":[0,10],"void":4,"while":4,Adding:7,DNS:9,For:[0,3,5,7,8,9,10],NOT:0,PBS:10,That:9,The:[0,1,3,5,7,8,9,10],Then:0,There:[0,4,8],These:[0,1,10],Use:4,Using:[0,3],aacon:[1,6],aaconw:[0,3],aamatrix:0,abandon:8,abil:4,abl:[0,1,3,4,8,9,10],about:[0,4,5,9,10],abov:[0,3,4,8,9,10],absolut:0,accept:[4,5,7,8],access:[0,1,3,5,7,9,10],accesslogvalv:0,accomplish:4,accord:0,accordingli:[0,4],account:[0,1,4],achiev:0,acid:[0,1,7],action:3,activ:0,actual:4,add:[4,9,10],added:[0,10],addit:[0,1,4],address:[0,9],adjust:0,admin:[8,9],administr:8,adminjabaw:9,advanc:[7,9],advantag:9,after:[0,4,8,9,10],again:0,against:[4,5],aim:4,alig:1,align:[0,1,2,3,5,7,9,10],all:[0,1,3,4,5,8,9,10],all_cluster_independent_test:4,all_cluster_independent_windows_only_test:4,allow:[0,1,2,3,5,8,9,10],allowlink:8,alon:5,alreadi:[0,10],also:[0,1,3,4,7,8,9],altern:[0,4,5,10],amazon:1,amd64:0,ami:1,amino:[0,1,7],amount:[0,8,9],analog:0,analysi:[0,1,2,5],analyt:[1,7],ani:[0,3,4,5,9,10],annot:4,anonym:0,anoth:[3,4,10],ant:[0,4],antiresourcelock:[8,10],anyon:[4,5],anyth:0,anywher:0,apach:[0,4,5,8,10],aparamet:3,apart:9,api:[1,3,7],app:5,appli:0,applianc:[7,8],applic:[0,1,3,7,9],appreci:0,appropri:[0,4],april:7,aptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqa:4,architectur:[0,5,10],archiv:[4,7,9],arg:4,argument:4,around:4,arraylist:4,artifact:7,ask:9,assum:[0,5,10],asynchron:[0,8],attempt:4,authent:[0,8],auto:9,autogener:0,autom:0,automat:[0,5,8,10],avail:[0,1,3,4,5,7,8,9,10],averag:0,avoid:[0,4,10],awstat:0,back:7,backward:1,balanc:7,bar:[3,4],barton:2,base:[0,8,9,10],basic:[0,3,4,10],batch:10,bear:9,becaus:[3,4,9],been:[1,3,4,8,9],befor:4,being:4,below:[0,1,3,4,5,8,9,10],benefit:7,besid:4,best:[0,9],better:[4,5,10],between:[0,4],bigger:0,bigmem:0,bin:[0,4],binari:[4,5,7,10],bind:0,bioinformat:[0,2,5,9],black:0,block:4,boot:[5,9],both:[0,1,3,5,10],bottom:[4,8],boundari:4,box:[0,9],bridg:9,brief:[5,7],browser:[0,5],btr304:2,bug:1,build:[0,7,10],bump:1,bundl:0,busi:0,button:5,bytearrayinputstream:4,calcul:[0,1,7,8,9],call:[0,1,3,4,10],caller:4,can:[0,3,4,5,8,9,10],cancel:[4,8],canceljob:4,cannot:[3,4,9],capac:10,catalina:[0,8,10],caution:4,cengin:0,chang:[0,1,3,4,5,8,9],changelog:7,charact:0,chase:0,check:[0,1,3,5,7,9,10],checker:0,chmod:0,choos:[0,5,9],chosen:0,chunk:4,chunkhold:4,citat:7,cite:2,clariti:3,classnam:0,clean:1,cli:[4,7],click:9,client:[0,1,7,9],client_help:4,clone:4,cloud:1,clustal:[1,3,4,6,8],clustalalignmentutil:4,clustalow:[0,3],clustalw2:0,clustalw:[0,1,3,4,6],clustalwsport:4,clustengin:0,cluster:[4,5,7,8,10],clusterengin:0,code:[0,3,7,10],coffe:[0,1,6],collect:[0,4,5,8],collector:8,color:0,column:8,come:[0,3,4,5,8,10],command:[0,7,9],comment:0,commerci:9,common:0,commun:[1,9],compar:1,compat:[1,4,5,10],compbio:[0,3,4],compil:[4,5,7,10],compilebin:[0,4,5],complain:0,complet:[0,5,7,8,10],compli:4,compliant:[0,3,5,10],complic:5,complil:4,complile_with_debug:4,compon:8,comput:[5,9],concern:5,condor:10,conf:[0,4,8,10],config:0,configur:[1,4,5,7,10],confirm:4,confus:4,connect:[0,5,7,9],conserv:[0,1,7],consid:8,consist:[4,5],consol:[3,9],constant:3,constraint:4,construct:4,constructor:4,consult:[8,10],consum:[3,5],contain:[0,1,4,5,8],content:[3,7,10],context:[0,3,5,8,10],contini:4,continu:2,contribut:[4,7],control:[3,4,5],convent:4,copi:[8,9],core:[0,9,10],correctli:0,correspond:[0,4],could:[0,1,3,4,10],couldn:0,coupl:0,cours:9,cpu:[0,9],crawler:8,creat:[0,4,8],credenti:9,css:0,current:[0,1,4,5,10],custom:[3,7],customalign:4,customsuit:4,customtest:4,dai:8,darlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttp:4,data:[0,4,5,9],databas:[0,4,8],datamodel:4,date:[0,3,8,10],deal:[1,9],dealt:10,debian:9,debug:[0,4],dec:7,decid:[0,4],dedic:1,defin:[1,3,4,7,8],definit:0,delet:1,demand:4,depend:[0,4,5,8,10],deploi:[0,4,5,8,9,10],deploy:[0,10],depth:0,describ:[0,4,8,10],descript:[0,1,4,8],descriptor:[0,10],design:[1,4],desktop:5,detail:[0,3,4,7,10],dev2:0,develop:[3,5,7],dhcp:9,did:0,differ:[0,3,4,9,10],directli:[0,4],directori:[0,1,4,5,7,10],disabl:[0,4,8],discoveri:4,disembl:[1,6],disemblw:[0,3],disk:[9,10],disord:[0,1,5,7],displai:[4,8,9],distribut:[0,1,7,9,10],distro:4,divers:1,dm_javadoc:0,doc:4,document:[0,1,3,4,5,10],doe:[0,4,8,9],doesn:5,doi:2,doing:[0,4],done:[0,1,3,4,8],doubt:0,download:[0,1,3,4,5,7],dpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi:4,drive:9,drmaa:[0,5,10],drop:[1,5,10],due:[1,8],dunde:[0,4,5],durat:4,dure:8,each:[0,1,4,8],eas:1,easi:[4,5],easier:9,easiest:[0,4,5],ec2:1,eclips:4,edit:[0,4,9],edu:3,eight:4,either:[0,3,5],elect:5,elimin:5,elsewher:0,empti:8,enabl:[0,1,5,8,9,10],encod:[0,8,10],encourag:[1,4],end:0,engin:[1,4,7,8,10],ensur:4,enter:[4,5],enumer:4,env:0,environ:[4,7,9,10],environment:4,equal:3,equip:0,error:[0,4,8],especi:0,etc:[0,3,4],evalu:0,even:0,everi:[4,8],everyth:0,exact:0,exactli:[0,3,4],examin:0,exampl:[0,5,7,8,10],excerpt:4,excess:[0,4],exclud:[4,8],exec_nam:0,exectu:4,execut:[1,3,4,5,7,10],executablenam:4,executablenameparamat:0,executionstatist:[0,4],exist:[0,1],expand:9,expend:4,experi:[0,10],explanatori:4,explicit:10,explicitli:0,exploit:0,extend:4,extract:1,fail:[0,1,4,10],failur:[4,8],fals:[0,8,10],fasta34:0,fasta:[0,1,3,4],fasta_4_mafft:0,fastalist:4,fastaparttre:3,fastasequ:4,faster:[0,9],fastest:0,fatal:0,favorit:3,favour:1,featur:4,feb:0,februari:8,femdgfaddfgallqalarrhgwlgi:4,few:[0,4,8],field:4,file:[3,5,7,8,9,10],fileinputstream:4,filenam:4,filenotfoundexcept:4,fileoutputstream:4,find:[0,4],fine:[4,9],finish:[4,8],first:[0,4,8,9],five:4,fix:1,flag:[4,10],flexibl:10,folder:[4,9,10],follow:[0,4,8,10],foo:4,foobar:3,foofriend:3,forget:0,format:[3,4],found:[0,4,8,10],four:[1,4],framework:4,free:9,freeli:9,friend:4,friendli:5,from:[0,1,3,5,6,7,8,9,10],full:[0,3,4],full_javadoc:0,fulli:[0,1],fund:[0,2],further:[0,2,4,8],furthermor:0,fusion:[5,9],futur:5,gap:4,gapopen:4,gapopenpenalti:4,gcc:0,gener:[0,1,4,8,10],geoffrei:2,get:[0,1,4,7],getargu:4,getbyt:4,getfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi:4,getjobstatu:4,getlimit:4,getport:4,getpreset:4,getpresetbynam:4,getresult:4,getrunneropt:4,git:[4,7],gitweb:4,give:10,given:[0,4,5,10],globplot:6,globplotw:[0,3],globu:10,glprob:[1,6],glprobsw:0,gnu:5,going:[0,4],good:[0,5],googl:[1,7],googleanalyt:1,got:0,graphic:5,greater:[0,1],greatli:0,grid:10,gridwai:10,gridwar:0,group:[0,4,5,10],guid:[5,7],h_cpu:0,h_vmem:0,hand:4,handi:[0,3,4],handl:[3,4,10],hard:[4,9],hardwar:5,has:[0,1,3,4,5,8,9,10],hash:0,have:[0,1,4,5,7,8,9,10],health:0,heavi:9,heavili:[0,9],help:[0,1,2,4,5,8,9],here:[0,3,4,7,8,10],hierarchi:4,higher:3,hold:4,holder:4,home:[0,4],homepag:7,host:[0,3,4,9,10],host_and_context:3,hotloop:1,hour:8,how:[0,3,4,5],howev:[0,4,9,10],hptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhg:4,html:0,http:[0,3,4,5,9,10],httpcoderesponseservicestatu:0,huge:0,i386:0,idea:0,identif:1,identifi:4,idl:[0,4],idllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvl:4,ignor:3,imag:[0,1,9],impati:5,implement:[4,6,10],improv:[1,2],includ:[0,1,3,4,5,7],incompat:1,incomplet:8,incorpor:5,increas:0,independ:[0,3,4,10],index:0,indic:[8,9],individu:[0,8],inf:[0,4,5],influenc:0,info:[0,9],inform:[0,1,3,4,5,8,9,10],infrastructur:5,initi:[0,4,8],input:[0,3,4,8],inputfil:3,inputs:8,insert:4,insid:0,instal:[0,1,4,5,7],instanc:[0,3,4,10],instead:[0,4,5],institut:5,instruct:[3,5],integr:1,interest:5,interfac:[4,5],intern:7,internet:[5,9],interoper:[3,5],interruptedexcept:4,intranet:5,introduc:1,involv:4,ioexcept:4,ipv4:9,ipv6:9,iscancel:8,iscollect:8,isfinish:8,isol:4,issu:[4,7],its:[0,3,4,5,10],itself:0,iupr:6,iupredw:[0,3],jaba:[0,3,4,5,8,10],jabaw:[1,2,3,10],jabaws_serv:0,jalview:[1,4,7,9],jame:2,jan:8,januari:8,jar:[0,3,4,5],java:[0,2,3,4,5,6,9,10],java_hom:0,java_opt:0,javadoc:[0,4],javascript:0,javax:4,jax:4,jaxb:4,jaxw:4,jdk1:0,jdk:0,job:[1,3,4,5,7,10],jobid:[4,8],jobsout:[0,4],jobstatu:4,jobsubmissionexcept:4,jobtempl:0,jpred:1,jpredalig:1,jpredw:1,jre:0,jronn:[1,6],jronnw:[0,3],jsp:0,jul:7,junit:4,just:[0,3,5,9,10],jvm:[0,4],jws2:0,jws2client:4,keep:[4,9,10],kei:[3,8],keyboard:9,know:[0,4,10],known:[0,5],lab:[0,5,10],languag:[0,3,4,5],laptop:5,larg:[0,5,9],larger:9,last:8,later:[1,4,8],latest:1,latter:0,launch:5,layer:4,ld_library_path:[0,4],least:[0,5],leav:[0,4],length:0,let:[0,3,4,8,9,10],letter:0,level:[0,4],lfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavala:4,lib:[0,5],librari:[0,1,3,4,5,10],life:4,lightweight:0,like:[0,3,4,5,9],limit:[1,3,4,7,9,10],limitexceededexcept:4,limitsmanag:4,line:[0,7,9],link:[0,4,8],linux:[0,4,5,9,10],list:[0,1,3,4,5,7],littl:[0,4],llnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrpl:4,load:[4,7],local:[4,5,7,8,9,10],localengineexecutionlimit:0,localhost:[0,5,8,10],localhost_access_log:0,locat:[0,4,8,9],log4j:0,log:[7,8],logdir:0,login:[8,9],long_test:4,longer:[1,4],look:[0,4,7],lowercas:4,lrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgaf:4,lsf:10,lx24:0,mac:[1,5,9,10],machin:[0,1,3,4,5,9,10],made:[4,8],mafft:[1,3,4,6,7],mafft_binari:0,mafftlimit:0,mafftparamet:0,mafftpreset:0,mafftw:[0,3],mai:[0,4,8,9,10],main:[0,4,5,8],make:[0,4,5,8,9,10],man_serverwar:0,manag:10,mani:[0,10],manipul:3,manner:5,manoeuvr:4,manual:[9,10],map:4,marker:4,match:4,matric:0,matrix:4,matter:3,maximum:[0,5,8],maxruntim:8,mayb:8,mean:[0,1,3,4,5,8,9],memori:[0,9,10],mention:4,menu:[0,5,9],messag:[0,9],meta:4,metadata:4,method:[0,1,4,5],mgdttagemavqrglalhq:3,mgdttagemavqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrah:4,might:[0,4,5,9,10],min:[3,4],mind:9,minimum:9,minor:1,minut:[4,8],miss:0,mode:4,model:[0,4],modifi:[0,4],monitor:[0,4],month:8,monthli:8,more:[0,1,3,4,5,8,9,10],most:[3,5,8,9],mostli:4,move:9,msa:4,msaprob:[1,6],msaprobsw:0,msaw:4,mtadgprellqlraav:3,mtadgprellqlraavrhrpqdfvawl:3,mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgr:4,mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrv:4,multi:8,multipl:[0,1,2,4,5,7],muscl:[0,6],musclew:[0,3],must:[0,1,10],myhost:[0,3],mylabserv:3,myuni:3,name:[0,3,4,5,8,9,10],namespac:4,nat:9,nativ:[0,3,4],natur:8,navig:[0,8],necessari:[4,10],necessarili:8,need:[0,3,4,5,8,9,10],net:4,network:9,never:[0,1,8],newer:1,next:[3,4],nine:4,node:[0,10],nofft:3,non:0,none:9,normal:0,noscor:3,note:[3,4,8],noth:[4,9],notic:4,now:[1,3,4],nput:3,nucleotid:0,number:[0,1,4,8,10],object:[1,4],obtain:[4,7],obvious:10,oct:7,off:3,offer:[0,1,4,9],offici:10,often:0,older:10,omega:[1,6],onc:[0,4,5,9],one:[0,1,3,4,5,8,9,10],ones:0,onli:[0,3,4,8,9,10],open:[0,3,4,5,7,9],oper:[0,5,9,10],oppos:8,optim:0,option:[0,1,3,4,5,8,9],optionlist:4,oracl:[9,10],order:[0,8],org:[0,4],organ:5,orient:[0,4],other:[0,3,4,5,8,9,10],otherwis:[0,10],our:[0,1,4,7],out:[0,3,4,8,10],output:[0,3,4],outputfil:3,outsid:[0,8,9],outstream:4,over:[3,5,9],overhead:0,overload:10,overview:[0,7],ovf:9,own:[0,3,5],packag:[0,1,3,4,5],page:[0,1,3,4,5,7,8,9],pam300:4,panel:5,parallel:[9,10],paramet:[0,1,3,7],parameterinputfil:3,parser:4,part:[0,3,4,5,8],parti:10,particular:[0,4,8,10],pass:[0,4],password:[8,9],path:[0,1,3,4,5,10],path_to_jar_fil:3,pattern:0,paus:4,pbspro:10,pdf:7,peer:1,per:8,perfectli:10,perform:[0,4,5],period:[1,4,8],pertain:4,peter:[2,8],pipedexecut:4,plai:9,plain:[4,8],platform:[4,9,10],player:[5,9],pleas:[0,3,4,8,9,10],plugin:4,point:[0,3,4,5,8,9,10],port:[0,4],portabl:4,posix:0,possibl:[8,9,10],post:0,power:[0,9],powerpc:10,pqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhad:4,pre:[1,4,7,9,10],predict:[0,1,5,7],prefer:[0,5,9],prefix:0,prepar:[7,9],preprocess:8,present:8,preset:[0,3,7],presetalign:4,presetman:4,presetmanag:4,presetnam:[3,4],press:5,prevent:[0,4,10],previou:4,print:3,println:4,privaci:5,privat:[0,4,5,9,10],privileg:[7,10],prm:3,probabl:0,probcon:[0,6],probconsw:[0,3],problem:[0,4],procedur:[4,10],procerror:8,process:[0,1,3,4,8],procoutput:8,procter:2,produc:[0,8],product:[0,9],profil:[0,4],prog_doc:0,program:[0,1,3,5,7,9,10],programmat:3,prohibit:0,project:[1,2,7],prolong:4,proper:1,properti:[0,1,4,8],protein:[0,1,5,7],protocol:0,provid:[0,1,3,4,5,9],proxi:4,publicli:[4,5],publish:0,pullexecstatist:4,purpos:0,put:[0,4,10],pvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgv:4,qllpeepyitaqllnavaqgvgavepfaflsedasaaesvrplaptrvrskgplrvgfvsngfga:4,qname:4,qpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgea:4,qualifi:4,qualifiednam:4,qualifiedservicenam:4,queer:0,queri:0,quickstart:5,rais:0,ram:[0,9],rang:5,rather:9,read:[0,4,5,7,10],readfasta:4,readi:5,real:4,reason:0,rebuild:4,rebuilt:4,recent:0,recheck:4,recommend:[0,1,3,4,5,9,10],recompil:[4,7,10],reconfigur:9,record:[1,4,8],redirect:0,reduc:[0,10],refer:[0,4,9],reflect:1,refus:10,regist:4,reject:0,rel:0,relat:[0,4],releas:7,rem465:1,remot:0,remov:[0,10],repeat:0,replac:[0,1,4,8],report:[0,4,7],repositori:[0,4],repres:4,request:[4,7,8,10],requir:[0,1,4,5,9,10],rerun_failed_test:4,reserv:0,reset:4,resid:[0,10],resili:10,resolut:0,resolvehost:0,resourc:[0,4,9],respect:[0,8],respond:0,respons:0,rest:[1,10],restart:[0,8,10],restructuredtext:4,result:[0,4,8],resultnotavailableexcept:4,results:8,retre:3,retriev:[0,4,8],reus:[4,7],review:0,right:10,rlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwl:4,rna:[0,7],rnaalifold:6,rnaalifoldw:[0,1],rnastructscoremanag:1,role:8,rolenam:8,ronn:6,root:[4,9,10],rout:9,row:8,rule:0,run:[0,1,3,4,5,8,9,10],run_cluster_dependent_test:4,runner:4,runnerconfig:[4,8],runtest:4,runtim:[8,10],rwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqg:4,sai:9,same:[0,3,4,5,8,9,10],satisfi:4,scientif:1,score:1,scoremanag:1,screen:[0,9],screenshot:8,script:[0,3,4,5,10],search:0,second:[4,8],secondari:[0,1,7],section:[0,4,8],secur:[1,5],see:[0,3,4,5,8,9],select:5,self:4,semicolon:0,send:[5,10],sensit:5,sent:0,separ:[0,3,10],sequenc:[0,1,2,3,5,7],sequenceannot:4,sequencelist:4,sequenceutil:4,sequenti:4,serial:4,serv:[0,4,10],server:[3,4,7,9,10],server_url:0,servic:[0,1,2,3,5,7,8,9,10],servicenam:[0,3],servicestatu:0,servlet:[1,10],set:[0,3,4,8,9,10],setenv:0,setexecflag:[0,4],setexecutableflag:4,setnativespecif:0,setup:5,setvalu:4,seven:4,sever:[0,1,4,5],sftp:9,sge:0,sge_root:0,sgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgc:4,share:10,shell:9,ship:5,shot:9,should:[0,1,4,5,8,9,10],show:[3,8],shown:[3,5],side:4,sign:[1,3],signific:0,silent:4,similar:[4,9],similarli:9,simpl:[0,4,5],simplest:8,simpli:[0,4,5,9,10],simplifi:[0,1],sinc:[0,4,10],singl:[5,9,10],site:[3,10],six:4,size:[5,7,8],skeletalexecut:4,sleep:4,slightli:5,small:[0,10],smaller:0,soap:[0,3,4,5],softwar:[3,4,5],some:[0,1,4],someth:4,sometim:[4,8,10],soon:[5,8,9],sourc:[0,3,5,7,10],space:[4,10],special:4,specif:[0,3,4,10],specifi:[0,3,8],speed:[0,4],sphinx:1,split:4,squeez:9,src:[0,4,5],ssh:9,stabil:4,stage:4,stand:5,standalon:9,standard:[0,1,4,8],standlon:9,start:[0,7,8,9],startup:0,stat:8,statist:[0,1,4,7],statpag:[0,4],statu:[0,1,5,7],step:0,still:10,stlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmd:4,stop:1,storag:0,store:[0,4],stori:8,straight:0,straightforward:5,stream:8,string:[1,4],structur:[0,1,7],stub:4,subfold:4,submiss:0,submit:[0,4,5,8],substitut:0,successfulli:0,suffici:[4,9,10],suffix:0,suggest:[0,4,5],suit:[0,4,5,9],suitabl:0,summari:8,sun:[0,4,10],suppli:[0,1,4,10],support:[0,1,3,4,5,9,10],sure:[0,4,8,10],swap:1,symbol:[0,1,8],system:[4,5,7,8,9,10],tabl:[0,8],take:[0,4,9],task:[0,4,5,9,10],tcoffeew:[0,3],tell:0,temp:4,templat:7,temporari:[0,4,8],ten:4,tend:4,termin:0,test:[3,5,7,9,10],testcas:4,testng:4,testoutput:0,testsrc:4,text:[4,8],than:[0,1,4,9,10],thei:[0,4,5,9],them:[0,3,4,5,9,10],thi:[0,1,3,4,5,7,8,9,10],thin:4,third:[4,10],though:4,thread:[0,1,4,10],three:[0,4],through:[4,5],thu:[0,4],thw:0,time:[0,4,8,9],timestamp:8,tip:0,titl:8,tmp:0,togeth:[3,4],tomcat:[0,1,5,7,9,10],tomcat_dir:0,tomcat_root:[0,8],tomcatroot:10,too:[0,5,10],tool:[0,4,5,7,9],top:4,tostr:4,total:8,trace:0,tracker:[4,7],treat:0,trim:3,troshin:2,troubleshoot:7,tune:9,turnkei:[5,9],tvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfd:4,two:[0,1,4,10],txt:[0,4,8],type:[0,4,5],uncom:0,undeploi:10,undeploy:10,under:[0,4,5],underneath:4,uniqu:8,unit:7,univers:[0,4,5],unix:[5,8],unless:9,unlik:[5,9],unpack:[5,9,10],unsupportedruntimeexcept:4,until:[0,4],updat:[0,1,4],upon:[0,4],upper:4,url:[0,3,4,5,9,10],us_intl:9,usag:7,use:[0,1,2,3,4,5,8,9,10],used:[0,1,3,4,9,10],useful:[0,3,4],user:[0,1,5,8,9,10],usernam:8,uses:[0,4,5,9,10],using:[0,3,4,5,8,10],utf:[8,10],util:[0,4],valid:7,valu:[0,3,4],valv:0,variabl:[4,7],variou:0,veri:[0,1,4,5],version:[0,3,5,6,7,8,9,10],vgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptgl:4,via:[3,5,9],viennarna:6,view:[4,7],violat:4,virtial:9,virtual:[0,7,8],virtualbox:[1,9],visial:0,visit:5,visual:[1,8],visualis:8,vm_ip:9,vmware:[1,5,9],vmx:9,vrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaq:4,vwmare:9,wai:[0,3,4,5,8,9],wait:[0,4],want:[0,3,4,5,7,9],war:[1,4,7,8,9],warn:0,wast:0,watch:4,web:[0,1,2,3,7,9],webal:0,webapp:[0,5,10],webapplicationpath:0,webmean:9,webservic:[0,4,5],websit:[1,4],weight:4,welcom:3,well:[0,4,5,10],were:[1,4,8,10],what:[0,5,9],whatev:[0,4],when:[0,2,8,9],whenev:4,where:[0,3,4,5,8,9],wherea:0,whether:[4,8,9],which:[0,1,3,4,5,8,9,10],who:[0,4,5,9],whole:[0,8],whose:8,why:0,wide:5,window:[0,4,5,9,10],wish:0,within:[0,1,4,8],without:[0,4,9,10],work:[2,4,5,7,9,10],would:[0,3,4,5,9],wrap:4,wrapper:4,write:[3,5,7],writeclustalalign:4,written:0,wrongparameterexcept:4,wsbuild:4,wsdl:[4,7],wsimport:[0,4],www:[0,4,10],x86:[0,10],xincgc:0,xml:[0,4,8,10],xms512m:0,xmx1024m:0,xxx:0,xxxlimit:0,xxxparamet:[0,4],xxxpreset:0,yesterdai:3,you:[0,2,3,4,5,7,8,9,10],your:[3,5,7,8,9,10],your_jaba_context_nam:0,your_jabaws_server_url:0,yourself:[0,5],yvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsykln:4,zip:10},titles:["Advanced Usage","Changelog","Citations","Command Line Client (CLI)","For Developers","Getting Started","Included Tools","Welcome to JABAWS’s documentation!","Usage Statistics","Virtual Appliance (VA)","Web Application Archive (WAR)"],titleterms:{"16th":1,"1st":1,"2nd":1,"function":4,"new":4,"public":5,Adding:4,For:4,The:4,accept:0,access:[4,8],acid:6,advanc:0,align:[4,6],amino:6,analyt:0,api:4,applianc:[5,9],applic:[5,8,10],april:1,archiv:[5,10],artifact:4,balanc:0,benefit:5,binari:0,brief:4,build:4,calcul:4,changelog:1,check:4,citat:2,cli:[3,5],client:[3,4,5],cluster:0,code:4,command:[3,4,5],compil:0,complet:4,configur:[0,8,9],connect:4,conserv:6,content:[0,8],custom:4,dec:1,defin:0,detail:8,develop:4,directori:8,disord:6,distribut:[4,5],document:7,engin:0,environ:0,exampl:[3,4],execut:[0,8],file:[0,4],from:4,get:5,googl:0,guid:4,includ:6,instal:[3,9,10],intern:0,jabaw:[0,4,5,7,8,9],jalview:5,job:[0,8],jul:1,limit:0,line:[3,4,5],list:8,load:0,local:0,log:0,mafft:0,multipl:6,obtain:0,oct:1,overview:4,paramet:4,pre:0,predict:6,prepar:4,preset:4,privileg:8,program:4,project:4,protein:6,recompil:0,releas:1,request:0,reus:0,rna:6,secondari:6,sequenc:[4,6],server:[0,5,8],servic:4,size:0,sourc:4,start:5,statist:8,statu:4,structur:[4,6],system:0,templat:4,test:[0,4],tomcat:8,tool:6,troubleshoot:10,unit:4,usag:[0,3,8,9,10],valid:0,variabl:0,version:1,view:8,virtual:[5,9],war:[0,5,10],web:[4,5,8,10],welcom:7,work:0,write:4,wsdl:0,your:[0,4]}})
\ No newline at end of file
+Search.setIndex({docnames:["advanced","changelog","citations","client","develop","getting_started","included_tools","index","stats","va","war"],envversion:51,filenames:["advanced.rst","changelog.rst","citations.rst","client.rst","develop.rst","getting_started.rst","included_tools.rst","index.rst","stats.rst","va.rst","war.rst"],objects:{},objnames:{},objtypes:{},terms:{"0_17":0,"168h":8,"16th":7,"1st":7,"2nd":7,"378m":9,"512m":9,"6000m":0,"8cbe486":[1,6],"abstract":4,"boolean":4,"byte":[0,8],"case":[0,4,8,9],"class":[0,4],"default":[0,1,3,4,5,8,9],"enum":4,"export":0,"final":[0,4,5],"function":[0,3,5,7,10],"import":[2,4],"long":[0,4],"new":[0,1,3,5,7,9,10],"public":[4,7,10],"return":[0,1,4],"static":[0,4],"throw":4,"true":[0,4,8,10],"try":[0,10],"void":4,"while":4,Adding:7,DNS:9,For:[0,3,5,7,8,9,10],NOT:0,PBS:10,That:9,The:[0,1,3,5,7,8,9,10],Then:0,There:[0,4,8],These:[0,1,10],Use:4,Using:[0,3],aacon:[1,6],aaconw:[0,3],aamatrix:0,abandon:8,abil:4,abl:[0,1,3,4,8,9,10],about:[0,4,5,9,10],abov:[0,3,4,8,9,10],absolut:0,accept:[4,5,7,8],access:[0,1,3,5,7,9,10],accesslogvalv:0,accomplish:4,accord:0,accordingli:[0,4],account:[0,1,4],achiev:0,acid:[0,1,7],action:3,activ:0,actual:4,add:[4,9,10],added:[0,10],addit:[0,1,4],address:[0,9],adjust:0,admin:[8,9],administr:8,advanc:[7,9],advantag:9,after:[0,4,8,9,10],again:0,against:[4,5],aim:4,alig:1,align:[0,1,2,3,5,7,9,10],all:[0,1,3,4,5,8,9,10],all_cluster_independent_test:4,all_cluster_independent_windows_only_test:4,allow:[0,1,2,3,5,8,9,10],allowlink:8,alon:5,alreadi:[0,10],also:[0,1,3,4,7,8,9],altern:[0,4,5,10],amazon:1,amd64:0,ami:1,amino:[0,1,7],amount:[0,8,9],analog:0,analysi:[0,1,2,5],analyt:[1,7],ani:[0,3,4,5,9,10],annot:4,anonym:0,anoth:[3,4,10],ant:[0,4],antiresourcelock:[8,10],anyon:[4,5],anyth:0,anywher:0,apach:[0,4,5,8,10],aparamet:3,apart:9,api:[1,3,7],app:5,appli:0,applianc:[7,8],applic:[0,1,3,7,9],appreci:0,appropri:[0,4],april:7,aptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqa:4,architectur:[0,5,10],archiv:[4,7,9],arg:4,argument:4,around:4,arraylist:4,artifact:7,ask:9,assum:[0,5,10],asynchron:[0,8],attempt:4,authent:[0,8],auto:9,autogener:0,autom:0,automat:[0,5,8,10],avail:[0,1,3,4,5,7,8,9,10],averag:0,avoid:[0,4,10],awstat:0,back:7,backward:1,balanc:7,bar:[3,4],barton:2,base:[0,8,9,10],basic:[0,3,4,10],batch:10,bear:9,becaus:[3,4,9],been:[1,3,4,8,9],befor:4,being:4,below:[0,1,3,4,5,8,9,10],benefit:7,besid:4,best:[0,9],better:[4,5,10],between:[0,4],bigger:0,bigmem:0,bin:[0,4],binari:[4,5,7,10],bind:0,bioinformat:[0,2,5,9],black:0,block:4,boot:[5,9],both:[0,1,3,5,10],bottom:[4,8],boundari:4,box:[0,9],bridg:9,brief:[5,7],browser:[0,5],btr304:2,bug:1,build:[0,7,10],bump:1,bundl:0,busi:0,button:5,bytearrayinputstream:4,calcul:[0,1,7,8,9],call:[0,1,3,4,10],caller:4,can:[0,3,4,5,8,9,10],cancel:[4,8],canceljob:4,cannot:[3,4,9],capac:10,catalina:[0,8,10],caution:4,cengin:0,chang:[0,1,3,4,5,8,9],changelog:7,charact:0,chase:0,check:[0,1,3,5,7,9,10],checker:0,chmod:0,choos:[0,5,9],chosen:0,chunk:4,chunkhold:4,citat:7,cite:2,clariti:3,classnam:0,clean:1,cli:[4,7],click:9,client:[0,1,7,9],client_help:4,clone:4,cloud:1,clustal:[1,3,4,6,8],clustalalignmentutil:4,clustalow:[0,3],clustalw2:0,clustalw:[0,1,3,4,6],clustalwsport:4,clustengin:0,cluster:[4,5,7,8,10],clusterengin:0,code:[0,3,7,10],coffe:[0,1,6],collect:[0,4,5,8],collector:8,color:0,column:8,come:[0,3,4,5,8,10],command:[0,7,9],comment:0,commerci:9,common:0,commun:[1,9],compar:1,compat:[1,4,5,10],compbio:[0,3,4],compil:[4,5,7,10],compilebin:[0,4,5],complain:0,complet:[0,5,7,8,10],compli:4,compliant:[0,3,5,10],complic:5,complil:4,complile_with_debug:4,compon:8,comput:[5,9],concern:5,condor:10,conf:[0,4,8,10],config:0,configur:[1,4,5,7,10],confirm:4,confus:4,connect:[0,5,7,9],conserv:[0,1,7],consid:8,consist:[4,5],consol:[3,9],constant:3,constraint:4,construct:4,constructor:4,consult:[8,10],consum:[3,5],contain:[0,1,4,5,8],content:[3,7,10],context:[0,3,5,8,10],contini:4,continu:2,contribut:[4,7],control:[3,4,5],convent:4,copi:[8,9],core:[0,9,10],correctli:0,correspond:[0,4],could:[0,1,3,4,10],couldn:0,coupl:0,cours:9,cpu:[0,9],crawler:8,creat:[0,4,8],credenti:9,css:0,current:[0,1,4,5,10],custom:[3,7],customalign:4,customsuit:4,customtest:4,dai:8,darlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttp:4,data:[0,4,5,9],databas:[0,4,8],datamodel:4,date:[0,3,8,10],deal:[1,9],dealt:10,debian:9,debug:[0,4],dec:7,decid:[0,4],dedic:1,defin:[1,3,4,7,8],definit:0,delet:1,demand:4,depend:[0,4,5,8,10],deploi:[0,4,5,8,9,10],deploy:[0,10],depth:0,describ:[0,4,8,10],descript:[0,1,4,8],descriptor:[0,10],design:[1,4],desktop:5,detail:[0,3,4,7,10],dev2:0,develop:[3,5,7],dhcp:9,did:0,differ:[0,3,4,9,10],directli:[0,4],directori:[0,1,4,5,7,10],disabl:[0,4,8],discoveri:4,disembl:[1,6],disemblw:[0,3],disk:[9,10],disord:[0,1,5,7],displai:[4,8,9],distribut:[0,1,7,9,10],distro:4,divers:1,dm_javadoc:0,doc:4,document:[0,1,3,4,5,10],doe:[0,4,8,9],doesn:5,doi:2,doing:[0,4],done:[0,1,3,4,8],doubt:0,download:[0,1,3,4,5,7],dpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi:4,drive:9,drmaa:[0,5,10],drop:[1,5,10],due:[1,8],dunde:[0,4,5],durat:4,dure:8,each:[0,1,4,8],eas:1,easi:[4,5],easier:9,easiest:[0,4,5],ec2:1,eclips:4,edit:[0,4,9],edu:3,eight:4,either:[0,3,5],elect:5,elimin:5,elsewher:0,empti:8,enabl:[0,1,5,8,9,10],encod:[0,8,10],encourag:[1,4],end:0,engin:[1,4,7,8,10],ensur:4,enter:[4,5],enumer:4,env:0,environ:[4,7,9,10],environment:4,equal:3,equip:0,error:[0,4,8],especi:0,etc:[0,3,4],evalu:0,even:0,everi:[4,8],everyth:0,exact:0,exactli:[0,3,4],examin:0,exampl:[0,5,7,8,10],excerpt:4,excess:[0,4],exclud:[4,8],exec_nam:0,exectu:4,execut:[1,3,4,5,7,10],executablenam:4,executablenameparamat:0,executionstatist:[0,4],exist:[0,1],expand:9,expend:4,experi:[0,10],explanatori:4,explicit:10,explicitli:0,exploit:0,extend:4,extract:1,fail:[0,1,4,10],failur:[4,8],fals:[0,8,10],fasta34:0,fasta:[0,1,3,4],fasta_4_mafft:0,fastalist:4,fastaparttre:3,fastasequ:4,faster:[0,9],fastest:0,fatal:0,favorit:3,favour:1,featur:4,feb:0,februari:8,femdgfaddfgallqalarrhgwlgi:4,few:[0,4,8],field:4,file:[3,5,7,8,9,10],fileinputstream:4,filenam:4,filenotfoundexcept:4,fileoutputstream:4,find:[0,4],fine:[4,9],finish:[4,8],first:[0,4,8,9],five:4,fix:1,flag:[4,10],flexibl:10,folder:[4,9,10],follow:[0,4,8,10],foo:4,foobar:3,foofriend:3,forget:0,format:[3,4],found:[0,4,8,10],four:[1,4],framework:4,free:9,freeli:9,friend:4,friendli:5,from:[0,1,3,5,6,7,8,9,10],full:[0,3,4],full_javadoc:0,fulli:[0,1],fund:[0,2],further:[0,2,4,8],furthermor:0,fusion:[5,9],futur:5,gap:4,gapopen:4,gapopenpenalti:4,gcc:0,gener:[0,1,4,8,10],geoffrei:2,get:[0,1,4,7],getargu:4,getbyt:4,getfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi:4,getjobstatu:4,getlimit:4,getport:4,getpreset:4,getpresetbynam:4,getresult:4,getrunneropt:4,git:[4,7],gitweb:4,give:10,given:[0,4,5,10],globplot:6,globplotw:[0,3],globu:10,glprob:[1,6],glprobsw:0,gnu:[5,9],going:[0,4],good:[0,5],googl:[1,7],googleanalyt:1,got:0,graphic:5,greater:[0,1],greatli:0,grid:10,gridwai:10,gridwar:0,group:[0,4,5,10],guid:[5,7],h_cpu:0,h_vmem:0,hand:4,handi:[0,3,4],handl:[3,4,10],hard:[4,9],hardwar:5,has:[0,1,3,4,5,8,9,10],hash:0,have:[0,1,4,5,7,8,9,10],health:0,heavi:9,heavili:[0,9],help:[0,1,2,4,5,8,9],here:[0,3,4,7,8,10],hierarchi:4,higher:3,hold:4,holder:4,home:[0,4],homepag:7,host:[0,3,4,9,10],host_and_context:3,hotloop:1,hour:8,how:[0,3,4,5],howev:[0,4,9,10],hptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhg:4,html:0,http:[0,3,4,5,9,10],httpcoderesponseservicestatu:0,huge:0,i386:0,idea:0,identif:1,identifi:4,idl:[0,4],idllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvl:4,ignor:3,imag:[0,1,9],impati:5,implement:[4,6,10],improv:[1,2],includ:[0,1,3,4,5,7],incompat:1,incomplet:8,incorpor:5,increas:0,independ:[0,3,4,10],index:0,indic:[8,9],individu:[0,8],inf:[0,4,5],influenc:0,info:[0,9],inform:[0,1,3,4,5,8,9,10],infrastructur:5,initi:[0,4,8],input:[0,3,4,8],inputfil:3,inputs:8,insert:4,insid:0,instal:[0,1,4,5,7],instanc:[0,3,4,10],instead:[0,4,5],institut:5,instruct:[3,5],integr:1,interest:5,interfac:[4,5],intern:7,internet:[5,9],interoper:[3,5],interruptedexcept:4,intranet:5,introduc:1,involv:4,ioexcept:4,ipv4:9,ipv6:9,iscancel:8,iscollect:8,isfinish:8,isol:4,issu:[4,7],its:[0,3,4,5,10],itself:0,iupr:6,iupredw:[0,3],jaba:[0,3,4,5,8,10],jabaw:[1,2,3,10],jabaws_serv:0,jabawsadmin1:9,jabawsadmin2:9,jalview:[1,4,7,9],jame:2,jan:8,januari:8,jar:[0,3,4,5],java:[0,2,3,4,5,6,9,10],java_hom:0,java_opt:0,javadoc:[0,4],javascript:0,javax:4,jax:4,jaxb:4,jaxw:4,jdk1:0,jdk:0,jessi:9,job:[1,3,4,5,7,10],jobid:[4,8],jobsout:[0,4],jobstatu:4,jobsubmissionexcept:4,jobtempl:0,jpred:1,jpredalig:1,jpredw:1,jre:0,jronn:[1,6],jronnw:[0,3],jsp:0,jul:7,junit:4,just:[0,3,5,9,10],jvm:[0,4],jws2:0,jws2client:4,keep:[4,9,10],kei:[3,8],keyboard:9,know:[0,4,10],known:[0,5],lab:[0,5,10],languag:[0,3,4,5],laptop:5,larg:[0,5,9],larger:9,last:8,later:[1,4,8],latest:1,latter:0,launch:5,layer:4,ld_library_path:[0,4],least:[0,5],leav:[0,4],length:0,let:[0,3,4,8,9,10],letter:0,level:[0,4],lfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavala:4,lib:[0,5],librari:[0,1,3,4,5,10],life:4,lightweight:0,like:[0,3,4,5,9],limit:[1,3,4,7,9,10],limitexceededexcept:4,limitsmanag:4,line:[0,7,9],link:[0,4,8],linux:[0,4,5,9,10],list:[0,1,3,4,5,7],littl:[0,4],llnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrpl:4,load:[4,7],local:[4,5,7,8,9,10],localengineexecutionlimit:0,localhost:[0,5,8,10],localhost_access_log:0,locat:[0,4,8,9],log4j:0,log:[7,8],logdir:0,login:[8,9],long_test:4,longer:[1,4],look:[0,4,7],lowercas:4,lrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgaf:4,lsf:10,lx24:0,mac:[1,5,9,10],machin:[0,1,3,4,5,9,10],made:[4,8],mafft:[1,3,4,6,7],mafft_binari:0,mafftlimit:0,mafftparamet:0,mafftpreset:0,mafftw:[0,3],mai:[0,4,8,9,10],main:[0,4,5,8],make:[0,4,5,8,9,10],man_serverwar:0,manag:10,mani:[0,10],manipul:3,manner:5,manoeuvr:4,manual:[9,10],map:4,marker:4,match:4,matric:0,matrix:4,matter:3,maximum:[0,5,8],maxruntim:8,mayb:8,mean:[0,1,3,4,5,8,9],memori:[0,9,10],mention:4,menu:[0,5,9],messag:[0,9],meta:4,metadata:4,method:[0,1,4,5],mgdttagemavqrglalhq:3,mgdttagemavqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrah:4,might:[0,4,5,9,10],min:[3,4],mind:9,minimum:9,minor:1,minut:[4,8],miss:0,mode:4,model:[0,4],modifi:[0,4],monitor:[0,4],month:8,monthli:8,more:[0,1,3,4,5,8,9,10],most:[3,5,8,9],mostli:4,move:9,msa:4,msaprob:[1,6],msaprobsw:0,msaw:4,mtadgprellqlraav:3,mtadgprellqlraavrhrpqdfvawl:3,mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgr:4,mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrv:4,multi:8,multipl:[0,1,2,4,5,7],muscl:[0,6],musclew:[0,3],must:[0,1,10],myhost:[0,3],mylabserv:3,mysql:9,myuni:3,name:[0,3,4,5,8,9,10],namespac:4,nat:9,nativ:[0,3,4],natur:8,navig:[0,8],necessari:[4,10],necessarili:8,need:[0,3,4,5,8,9,10],net:4,network:9,never:[0,1,8],newer:1,next:[3,4],nine:4,node:[0,10],nofft:3,non:0,none:9,normal:0,noscor:3,note:[3,4,8],noth:[4,9],notic:4,now:[1,3,4],nput:3,nucleotid:0,number:[0,1,4,8,10],object:[1,4],obtain:[4,7],obvious:10,oct:7,off:3,offer:[0,1,4,9],offici:10,often:0,older:10,omega:[1,6],onc:[0,4,5,9],one:[0,1,3,4,5,8,9,10],ones:0,onli:[0,3,4,8,9,10],open:[0,3,4,5,7,9],oper:[0,5,9,10],oppos:8,optim:0,option:[0,1,3,4,5,8,9],optionlist:4,oracl:[9,10],order:[0,8],org:[0,4],organ:5,orient:[0,4],other:[0,3,4,5,8,9,10],otherwis:[0,10],our:[0,1,4,7],out:[0,3,4,8,10],output:[0,3,4],outputfil:3,outsid:[0,8,9],outstream:4,over:[3,5,9],overhead:0,overload:10,overview:[0,7],ovf:9,own:[0,3,5],packag:[0,1,3,4,5],page:[0,1,3,4,5,7,8,9],pam300:4,panel:5,parallel:[9,10],paramet:[0,1,3,7],parameterinputfil:3,parser:4,part:[0,3,4,5,8],parti:10,particular:[0,4,8,10],pass:[0,4],password:[8,9],path:[0,1,3,4,5,10],path_to_jar_fil:3,pattern:0,paus:4,pbspro:10,pdf:7,peer:1,per:8,perfectli:10,perform:[0,4,5],period:[1,4,8],pertain:4,peter:[2,8],pipedexecut:4,plai:9,plain:[4,8],platform:[4,9,10],player:[5,9],pleas:[0,3,4,8,9,10],plugin:4,point:[0,3,4,5,8,9,10],port:[0,4],portabl:4,posix:0,possibl:[8,9,10],post:0,power:[0,9],powerpc:10,pqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhad:4,pre:[1,4,7,9,10],predict:[0,1,5,7],prefer:[0,5,9],prefix:0,prepar:[7,9],preprocess:8,present:8,preset:[0,3,7],presetalign:4,presetman:4,presetmanag:4,presetnam:[3,4],press:5,prevent:[0,4,10],previou:4,print:3,println:4,privaci:5,privat:[0,4,5,9,10],privileg:[7,10],prm:3,probabl:0,probcon:[0,6],probconsw:[0,3],problem:[0,4],procedur:[4,10],procerror:8,process:[0,1,3,4,8],procoutput:8,procter:2,produc:[0,8],product:[0,9],profil:[0,4],prog_doc:0,program:[0,1,3,5,7,9,10],programmat:3,prohibit:0,project:[1,2,7],prolong:4,proper:1,properti:[0,1,4,8],protein:[0,1,5,7],protocol:0,provid:[0,1,3,4,5,9],proxi:4,publicli:[4,5],publish:0,pullexecstatist:4,purpos:0,put:[0,4,10],pvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgv:4,qllpeepyitaqllnavaqgvgavepfaflsedasaaesvrplaptrvrskgplrvgfvsngfga:4,qname:4,qpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgea:4,qualifi:4,qualifiednam:4,qualifiedservicenam:4,queer:0,queri:0,quickstart:5,rais:0,ram:[0,9],rang:5,rather:9,read:[0,4,5,7,10],readfasta:4,readi:5,real:4,reason:0,rebuild:4,rebuilt:4,recent:0,recheck:4,recommend:[0,1,3,4,5,9,10],recompil:[4,7,10],reconfigur:9,record:[1,4,8],redirect:0,reduc:[0,10],refer:[0,4,9],reflect:1,refus:10,regist:4,reject:0,rel:0,relat:[0,4],releas:7,rem465:1,remot:0,remov:[0,10],repeat:0,replac:[0,1,4,8],report:[0,4,7],repositori:[0,4],repres:4,request:[4,7,8,10],requir:[0,1,4,5,9,10],rerun_failed_test:4,reserv:0,reset:4,resid:[0,10],resili:10,resolut:0,resolvehost:0,resourc:[0,4,9],respect:[0,8],respond:0,respons:0,rest:[1,10],restart:[0,8,10],restructuredtext:4,result:[0,4,8],resultnotavailableexcept:4,results:8,retre:3,retriev:[0,4,8],reus:[4,7],review:0,right:10,rlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwl:4,rna:[0,7],rnaalifold:6,rnaalifoldw:[0,1],rnastructscoremanag:1,role:8,rolenam:8,ronn:6,root:[4,9,10],rout:9,row:8,rule:0,run:[0,1,3,4,5,8,9,10],run_cluster_dependent_test:4,runner:4,runnerconfig:[4,8],runtest:4,runtim:[8,10],rwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqg:4,sai:9,same:[0,3,4,5,8,9,10],satisfi:4,scientif:1,score:1,scoremanag:1,screen:[0,9],screenshot:8,script:[0,3,4,5,10],search:0,second:[4,8],secondari:[0,1,7],section:[0,4,8],secur:[1,5],see:[0,3,4,5,8,9],select:5,self:4,semicolon:0,send:[5,10],sensit:5,sent:0,separ:[0,3,10],sequenc:[0,1,2,3,5,7],sequenceannot:4,sequencelist:4,sequenceutil:4,sequenti:4,serial:4,serv:[0,4,10],server:[3,4,7,9,10],server_url:0,servic:[0,1,2,3,5,7,8,9,10],servicenam:[0,3],servicestatu:0,servlet:[1,10],set:[0,3,4,8,9,10],setenv:0,setexecflag:[0,4],setexecutableflag:4,setnativespecif:0,setup:5,setvalu:4,seven:4,sever:[0,1,4,5],sftp:9,sge:0,sge_root:0,sgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgc:4,share:10,shell:9,ship:5,shot:9,should:[0,1,4,5,8,9,10],show:[3,8],shown:[3,5],side:4,sign:[1,3],signific:0,silent:4,similar:[4,9],similarli:9,simpl:[0,4,5],simplest:8,simpli:[0,4,5,9,10],simplifi:[0,1],sinc:[0,4,10],singl:[5,9,10],site:[3,10],six:4,size:[5,7,8],skeletalexecut:4,sleep:4,slightli:5,small:[0,10],smaller:0,soap:[0,3,4,5],softwar:[3,4,5],some:[0,1,4],someth:4,sometim:[4,8,10],soon:8,sourc:[0,3,5,7,10],space:[4,10],special:4,specif:[0,3,4,10],specifi:[0,3,8],speed:[0,4],sphinx:1,split:4,src:[0,4,5],ssh:9,stabil:4,stage:4,stand:5,standalon:9,standard:[0,1,4,8],standlon:9,start:[0,7,8,9],startup:0,stat:8,statist:[0,1,4,7],statpag:[0,4],statu:[0,1,5,7],step:0,still:10,stlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmd:4,stop:1,storag:0,store:[0,4],stori:8,straight:0,straightforward:5,stream:8,string:[1,4],structur:[0,1,7],stub:4,subfold:4,submiss:0,submit:[0,4,5,8],substitut:0,successfulli:0,suffici:[4,9,10],suffix:0,suggest:[0,4,5],suit:[0,4,5,9],suitabl:0,summari:8,sun:[0,4,10],suppli:[0,1,4,10],support:[0,1,3,4,5,9,10],sure:[0,4,8,10],swap:1,symbol:[0,1,8],system:[4,5,7,8,9,10],tabl:[0,8],take:[0,4,9],task:[0,4,5,9,10],tcoffeew:[0,3],tell:0,temp:4,templat:7,temporari:[0,4,8],ten:4,tend:4,termin:0,test:[3,5,7,9,10],testcas:4,testng:4,testoutput:0,testsrc:4,text:[4,8],than:[0,1,4,9,10],thei:[0,4,5,9],them:[0,3,4,5,9,10],thi:[0,1,3,4,5,7,8,9,10],thin:4,third:[4,10],though:4,thread:[0,1,4,10],three:[0,4],through:[4,5],thu:[0,4],thw:0,time:[0,4,8,9],timestamp:8,tip:0,titl:8,tmp:0,togeth:[3,4],tomcat:[0,1,5,7,9,10],tomcat_dir:0,tomcat_root:[0,8],tomcatroot:10,too:[0,5,10],tool:[0,4,5,7,9],top:4,tostr:4,total:8,trace:0,tracker:[4,7],treat:0,trim:3,troshin:2,troubleshoot:7,tune:9,turnkei:[5,9],tvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfd:4,two:[0,1,4,10],txt:[0,4,8],type:[0,4,5],uncom:0,undeploi:10,undeploy:10,under:[0,4,5],underneath:4,uniqu:8,unit:7,univers:[0,4,5],unix:[5,8],unless:9,unlik:[5,9],unpack:[5,9,10],unsupportedruntimeexcept:4,until:[0,4],updat:[0,1,4],upon:[0,4],upper:4,url:[0,3,4,5,9,10],us_intl:9,usag:7,use:[0,1,2,3,4,5,8,9,10],used:[0,1,3,4,9,10],useful:[0,3,4],user:[0,1,5,8,9,10],usernam:8,uses:[0,4,5,9,10],using:[0,3,4,5,8,10],utf:[8,10],util:[0,4],valid:7,valu:[0,3,4],valv:0,variabl:[4,7],variou:0,veri:[0,1,4,5],version:[0,3,5,6,7,8,9,10],vgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptgl:4,via:[3,5,9],viennarna:6,view:[4,7],violat:4,virtial:9,virtual:[0,7,8],virtualbox:[1,9],visial:0,visit:5,visual:[1,8],visualis:8,vm_ip:9,vmware:[1,5,9],vmx:9,vrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaq:4,vwmare:9,wai:[0,3,4,5,8,9],wait:[0,4],want:[0,3,4,5,7,9],war:[1,4,7,8,9],warn:0,wast:0,watch:4,web:[0,1,2,3,7,9],webal:0,webapp:[0,5,10],webapplicationpath:0,webmean:9,webservic:[0,4,5],websit:[1,4],weight:4,welcom:3,well:[0,4,5,10],were:[1,4,8,10],what:[0,5,9],whatev:[0,4],when:[0,2,8,9],whenev:4,where:[0,3,4,5,8,9],wherea:0,whether:[4,8,9],which:[0,1,3,4,5,8,9,10],who:[0,4,5,9],whole:[0,8],whose:8,why:0,wide:5,window:[0,4,5,9,10],wish:0,within:[0,1,4,8],without:[0,4,9,10],work:[2,4,5,7,9,10],would:[0,3,4,5,9],wrap:4,wrapper:4,write:[3,5,7],writeclustalalign:4,written:0,wrongparameterexcept:4,wsbuild:4,wsdl:[4,7],wsimport:[0,4],www:[0,4,10],x86:[0,10],xincgc:0,xml:[0,4,8,10],xms512m:0,xmx1024m:0,xxx:0,xxxlimit:0,xxxparamet:[0,4],xxxpreset:0,yesterdai:3,you:[0,2,3,4,5,7,8,9,10],your:[3,5,7,8,9,10],your_jaba_context_nam:0,your_jabaws_server_url:0,yourself:[0,5],yvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsykln:4,zip:10},titles:["Advanced Usage","Changelog","Citations","Command Line Client (CLI)","For Developers","Getting Started","Included Tools","Welcome to JABAWS’s documentation!","Usage Statistics","Virtual Appliance (VA)","Web Application Archive (WAR)"],titleterms:{"16th":1,"1st":1,"2nd":1,"function":4,"new":4,"public":5,Adding:4,For:4,The:4,accept:0,access:[4,8],acid:6,advanc:0,align:[4,6],amino:6,analyt:0,api:4,applianc:[5,9],applic:[5,8,10],april:1,archiv:[5,10],artifact:4,balanc:0,benefit:5,binari:0,brief:4,build:4,calcul:4,changelog:1,check:4,citat:2,cli:[3,5],client:[3,4,5],cluster:0,code:4,command:[3,4,5],compil:0,complet:4,configur:[0,8,9],connect:4,conserv:6,content:[0,8],custom:4,dec:1,defin:0,detail:8,develop:4,directori:8,disord:6,distribut:[4,5],document:7,engin:0,environ:0,exampl:[3,4],execut:[0,8],file:[0,4],from:4,get:5,googl:0,guid:4,includ:6,instal:[3,9,10],intern:0,jabaw:[0,4,5,7,8,9],jalview:5,job:[0,8],jul:1,limit:0,line:[3,4,5],list:8,load:0,local:0,log:0,mafft:0,multipl:6,obtain:0,oct:1,overview:4,paramet:4,pre:0,predict:6,prepar:4,preset:4,privileg:8,program:4,project:4,protein:6,recompil:0,releas:1,request:0,reus:0,rna:6,secondari:6,sequenc:[4,6],server:[0,5,8],servic:4,size:0,sourc:4,start:5,statist:8,statu:4,structur:[4,6],system:0,templat:4,test:[0,4],tomcat:8,tool:6,troubleshoot:10,unit:4,usag:[0,3,8,9,10],valid:0,variabl:0,version:1,view:8,virtual:[5,9],war:[0,5,10],web:[4,5,8,10],welcom:7,work:0,write:4,wsdl:0,your:[0,4]}})
\ No newline at end of file
git://source.jalview.org / jabaws.git / commitdiff