! Syntax Highlighting Patterns for the NEXUS sequence format ! ! by Markus Goeker XII/2006 ! made in NEdit 5.5 ! ! INSTALLATION ! ! Load these patterns by starting nedit with: ! ! nedit -import ! ! Then, check that the patterns were loaded correctly, and choose Save Defaults ! from the Preferences menu. The new patterns will now be incorporated into ! your own .nedit file, so the next time you start NEdit, you will no longer ! need to use -import. ! ! These patterns were written to make editing data and batch files for PAUP* ! easier. They include all command and command options of the NEXUS blocks ! described in the PAUP* 4b10 manual. ! ! These comments will not appear in your ~/.nedit ! nedit.highlightPatterns: Nexus:10:0{\n\ header:"^#NEXUS[ \\t]*$":::Flag::\n\ Comment:"\\[":"\\]"::Comment::\n\ command end:";":::Keyword::\n\ block delimiter:"<(?ibegin)>[\\s\\n\\r]+\\w+[\\s\\n\\r]*;|<(?iend|endblock)>[\\s\\n\\r]*;":::Preprocessor1::\n\ command in taxa or characters or data block:"<(?icharlabels|charstatelabels|dimensions|eliminate|format|matrix|statelabels|taxlabels|translate|tree)>":::Keyword::\n\ command in paup block:"<(?iagree|alltrees|ancstates|assume|bandb|basefreqs|bootstrap|cd|charpartition|charset|cleartrees|condense|constraints|contree|cstatus|ctype|delete|deroottrees|describetrees|dscores|dset|edit|exclude|execute|export|exset|factory|filter|fstatus|gammaplot|generatetrees|gettrees|help|hompart|hsearch|include|ingroup|jackknife|lake|leave|loadconstr|log|lscores|lset|matrixrep|mprsets|nj|outgroup|pairdiff|permute|pscores|pset|puzzle|quit|randtrees|rateset|reconstruct|restore|revfilter|reweight|roottrees|saveassum|savedist|savetrees|set|showanc|showcharparts|showconstr|showdist|showmatrix|showratesets|showtaxparts|showtrees|showusertypes|sorttrees|stardecomp|surfcheck|taxpartition|taxset|time|tonexus|treedist|treeinfo|treewts|tstatus|typeset|undelete|upgma|usertype|weights|wts|wtset)>":::Keyword::\n\ paup default command:"<(?idefaults)>|\\*":::Warning::\n\ command in assumptions or sets or codons block:"<(?iancstates|charpartition|charset|codonposset|exset|options|taxpartition|taxset|typeset|usertype|wtset)>":::Keyword::\n\ command option in taxa or characters or data or distances or trees block:"<(?idatatype|diagonal|equate|gap|interleave|labels|matchchar|missing|nchar|newtaxa|nodiagonal|nolabels|notokens|ntax|respectcase|symbols|tokens|transpose|triangle)>":::Storage Type::\n\ command option in paup block:"<(?iabortrep|adams|addseq|adjustapplim|all|allblocks|alldiglab|allowpunct|allprobs|allsitesmean|allswap|always|ancstates|apolist|append|approxlim|asbackbone|autoclose|autoinc|background|basefreq|basewt|best|binary|bionj|bootreps|breakties|brlenepsil|brlens|bseed|categlikes|charsperline|checkevts|chglist|chuckscore|ci|class|cleartrees|clock|cmcolwid|cmcstatus|cmlabels|cmshoweq|collapse|condense|conlevel|constraints|converse|criterion|cutoffpct|datatype|dcollapse|defaultmode|deldupes|deleted|delta|diagnose|diagonal|displayout|distance|dstatus|duptrees|enforce|errorbeep|errorstop|estfreq|exactn|excluded|exset|fd|fdclasses|fdfile|fdonly|fdtype|file|first|fit|flock|flushlog|format|from|fromfile|fromtree|full|fvalue|gapmode|gapsymbol|gfit|gk|goloboff|gpeewee|grpa|grpb|grpc|grpd|grpfreq|guninf|hi|hold|homoplasy|identsymbol|includeanc|increase|index|indices|initbrlen|initseeds|interleaved|jseed|keep|keepall|keybeep|khtest|labelnode|lcollapse|le50|lessresolv|limitperrep|linebreaks|logiter|longfmt|majrule|maxdecimals|maxpass|maxscore|maxtrees|means|metric|minforfit|minmemreq|minscore|missdist|misssymbol|mldistforls|mode|model|monitor|mprsets|mstaxa|mstaxahennig|multrees|nbest|ncat|nchar|nchuck|ndecimals|negbrlen|nonbinary|nonparamtest|notifybeep|npuzzles|nreps|nst|ntrees|numge|numle|objective|opt|ordphylip|outroot|paramclock|parsapprox|partition|patristic|pause|pctdelete|percent|permdel|pinvar|plot|power|prune|pseed|querybeep|randomize|range|rates|rc|rclass|rearrlimit|recon|reconlimit|reftax|removefreq|replace|reprate|resample|retain|reverse|ri|rmatrix|root|rooted|rootmethod|rseed|rstatus|savebootp|savereps|scorefile|sd|search|second|seed|semigraph|semistrict|setstorecmd|shape|shortfmt|showabbrev|showall|showexcluded|showqmatrix|showtaxnum|showtree|shtest|single|sitelikes|siterates|sorttrees|spectdist|start|startvals|status|steepest|stepmatrix|stop|storeaswts|storebrlens|storetreewts|strict|subst|sumtabonly|swap|tabspaces|tailkh|taxa|taxablk|taxlabels|tcompress|test|testdetails|the|tieseed|timelimit|tl|to|tofile|torder|total|tratio|treefile|treenum|trees|triangle|truncate|typeset|undefined|undefmult|unordphylip|unrooted|upbound|useapprox|useapproxl|usenonmin|userbrlens|usetreewts|variant|visnotify|warnblkname|warnredef|warnreset|warnroot|warntree|warntsave|wts|wtset|xout|zerolentest)>":::Storage Type::\n\ command option in assumptions or sets or codons block:"<(?icstree|deftype|gapmode|notokens|polytcount|standard|stepmatrix|tokens|vector)>":::Storage Type::\n\ option type in taxa or characters or data or distances or trees block:"<(?iboth|dna|left|lower|no|nucleotide|protein|right|rna|standard|upper|yes)>":::Text Arg2::\n\ option type in paup block:"<(?iabs|acctran|addseq|agd1|agreement|all|allow|allquart|allstates|alphabet|altnexus|ambequal|arbitrary|asis|asterisk|auto|bandb|barchart|beep|bincode|both|brlens|choose4|ci|cladogram|closest|compare2|constant|crude|current|custom|deltran|distance|dna|doswindows|eliminate|empirical|equal|equiprobable|estimate|exclude|f81|f84|faststep|flashonly|following|fourgrps|freqpars|full|fullopt|furthest|gamma|gcg|gtr|hennig|hennig86|heuristic|hide|histogram|hky|hky85|ignore|include|infer|infinity|ingroup|internal|jac|jc|joint|k2p|k3p|keep|kmaxmini|left|likelihood|logdet|lower|ls|lsfit|lundberg|macintosh|marginal|markovian|maxbrlen|maximum|maxmini|mdrambaut|me|mean|median|mega|midpoint|minbrlen|minf|minimum|minlength|missing|ml|monophyl|msg|native|neili|newstate|nexus|nj|nni|no|nodelabels|none|normal|nowarn|nucleotide|obsonly|onecolumn|option|outgroup|p|paraphyl|parsapprox|parsimony|partition|phylip|phylogram|pir|polymorph|polytomy|previous|prohibit|prompt|proportional|protein|ptp|rambaut|random|range|rateset|rc|rell|repeatcnt|restsite|ri|right|rogers|setabsval|sets|setzero|show|showalert|silent|simple|sitespec|splittimes|spr|standard|stepwise|sumonly|symdiff|systematic|tabtext|tajnei|tamnei|tbr|terminal|text|thorne|threeplus1|ti|total|tptp|tratio|trees|truncate|tv|twicemax|uncertain|unix|unmodified|upgma|upholt|upper|user|var|variable|warn|yes)>":::Text Arg2::\n\ option type in assumptions or sets or codons block:"<(?idollo|dollo.dn|dollo.up|indel|irrev|irrev.dn|irrev.up|maxsteps|minsteps|missing|newstate|ord|unord)>":::Text Arg2::\n\ dna sequence:"<(?i[acgtry]+)>":::String2::\n\ String1:"""":""""::String::\n\ String2:"'":"'"::String1::\n\ command structuring:"[/=,:(){}-]":::Text Arg::\n\ Number:"<([0-9]+(\\.[0-9]+)?([Ee]-?[0-9]+)?)>":::Numeric Const::\n\ missing data:"\\?":::Text Comment::\n\ }\n\ nedit.languageModes: Nexus:.nex .nxs .paup::::::