!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! $Source: /kappa1/srs4_0/odd/RCS/parameter.sdl,v $ ! $Revision: 1.18 $ ! $Date: 1995/02/02 16:42:54 $ ! $Author: etzold $ ! !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! functions for checking !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #function /id=%F_ISNEWSET /name="QryCheckNam" /args="(char *)" /module=QUERY #function /id=%F_CHECKQS /name="QryParse" /args="(char *)" /module=QUERY #function /id=%F_CHECKFIELDQUERY /name="QryParse" /args="(char *)"/module=QUERY #function /id=%F_CHECKEXPR /name="QryCheck" /args="(char *)" /module=QUERY #function /id=%F_CHECKQUERY /name="QryCheck" /args="(char *)" /module=QUERY #function /id=%F_CHECKINFILE /name="FilTestR" /args="(char *)" #function /id=%F_CHECKOUTFILE /name="FilTestW" /args="(char *)" #function /id=%F_CHECKOUTDIR /name="FilTestDirW" /args="(char *)" #function /id=%F_CHECKFIELDLIST /name="LibParSetFields" /args="(char *)" #function /id=%F_CHECKLIBLIST /name="LibParSetLibs" /args="(char *)" #function /id=%F_CHECKLINKLIBLIST /name="LibParSetLinkLibs" /args="(char *)" #function /id=%F_SETENVIRONMENT /name="LibSetEnvironment" /args="(char *)" #partable ! /parfiles="~/.srsparam","sys$login:srsparam.dat","$SRSETC/.srsparam", ! "SRSETC:.srsparam" { ! !format of output ! #parameter /id=%PAR_SEQFORMAT /name="seqFormat" /type=string /comment="format of sequence output file" /str=asis ! was 'fasta', dgg #parameter /super=@PAR_SEQFORMAT /str=gcg /state=value #parameter /super=@PAR_SEQFORMAT /str=pir /state=value !nbrf/pir format #parameter /super=@PAR_SEQFORMAT /str=embl /state=value #parameter /super=@PAR_SEQFORMAT /str=fasta /state=value #parameter /super=@PAR_SEQFORMAT /str=asis /state=value ! dgg, leave format as is #parameter /super=@PAR_SEQFORMAT /str=genbank /state=value ! dgg #parameter /super=@PAR_SEQFORMAT /str=codata /state=value ! dgg #parameter /name="printText" /type=bool /num=0 /comment="copy complete text (annotation) part of entry" #parameter /name="printData" /type=bool /num=0 /comment="copy data (eg, sequence) part of entry" #parameter /name="fieldList" /type=string /parType=@PART_FIELDLIST /comment="include fields in entry list " #parameter /name="doQueryReport" /type=bool /num=0 /comment="write a report about the query" #parameter /name="doOnlyQueryReport" /type=bool /num=0 /comment="report only what would have been found" #parameter /name="printMinOccur" /type=number /num=0 /comment="print only words that occur number of times" #parameter /name="listFOSN" /type=bool /num=1 /comment="produces a FOSN (File Of Sequence Names)" #parameter /name=printToFile /type=bool /num=0 /comment="print resultant entries to file(s)" #parameter /name="fosnWithPos" /type=bool /num=0 /comment="output FOSN includes sequence feature locations" ! dgg addition #parameter /name="listFSE" /type=string /str="" /comment="produce a File of Sequence Entries" ! !file and directory names ! #parameter /name=indexDirName /type=string /str="SRSINX:" /comment="directory with the indices" #parameter /name=tempDirName /type=string /str="SRSTEMP:" /comment="name of temporary files directory" ! dgg #parameter /name=outDirName /type=string /str="SRSINX:" /comment="name of output directory" #parameter /name=etcDir /type=string /str="SRSETC:" /comment="path of script that prepares SRS environment" #parameter /name=updateScriptName /type=string /str="" /comment="File name of output script file." #parameter /name=environment /type=string /partype=@PART_ENVIRONMENT /comment="Name of the library environment" /str=unix ! !query options ! #parameter /name="setName" /type=string /partype=@PART_SETNAME #parameter /name="makeWild" /type=bool /partype=@PART_BOOLEAN /num=0 /comment="appends a wildcard to each search word" #parameter /name="linkToLibs" /type=bool /partype=@PART_BOOLEAN /num=0 /comment="links a single entry to selected libraries" #parameter /name="linkToSet" /type=bool /partype=@PART_BOOLEAN /num=0 /comment="links result of query to selected libraries" #parameter /name="libList" /type=string /parType=@PART_LIBLIST /comment="select libraries of group" #parameter /name="linkLibList" /type=string /parType=@PART_LINKLIBLIST /comment="list of libraries to be linked to" #parameter /name="queryFileName" /type=string /comment="name of file containing a list of queries" ! !others ! #parameter /name="printLibInfo" /type=bool /num=0 /comment="prints info about specified library" #parameter /name="printLibs" /type=bool /num=0 /comment="prints a list of all active libraries" #parameter /name="linkTable" /type=string /comment="print link table of entries found by query to selected libs" #parameter /name="getStartupInfo" /type=bool /partype=@PART_BOOLEAN /comment="Startup info for client programs." ! !options for retrieval of sequence features ! #parameter /name="shiftbeginpos" /type=number /comment="shift feature begin position" #parameter /name="shiftendpos" /type=number /comment="shift feature end position" #parameter /name="isshiftbeginrelend" /type=bool /num=0 /comment="shift of feature begin is relative to end pos" #parameter /name="isshiftendrelbegin" /type=bool /comment="shift of feature end is relative to begin pos" #parameter /name="takeuncompletefeature" /type=bool /comment="accecpt incomplete features" /num=1 #parameter /name="takeuncompleteshiftfeature" /type=bool /comment="accecpt incomplete shifted features" ! !building indices ! #parameter /name=showWarnings /num=0 /type=bool /comment="display warnings caused by errors in the databank" #parameter /name=compress /type=bool /comment="compresses indices built previously" #parameter /name=touchIndex /type=bool /comment="touch index" #parameter /name=relocateLib /type=bool /comment="relocate library, ie, build a new IDX file" #parameter /name=buildIndex /num=1 /type=bool /comment="build all or selected search indices for library" #parameter /name=parseTest /type=bool /comment="display only extracted values" #parameter /name=readLink /type=bool /comment="read library and process link information" #parameter /name=indexLink /type=bool /comment="build a link using two indices" #parameter /name=releaseName /type=string /comment="assign a release name to a set of indices" ! !checking and maintaining indices ! #parameter /name=procIndexSize /type=number /num=15000 /comment="total index size (kb) to be processed in one go" #parameter /name=checkLibList /type=string /comment="list of libraries to be checked - else all libraries" #parameter /name=notCheckLibList /type=string /comment="list of libraries to be exclued from checking" #parameter /name=srsEnvHeader /type=bool /comment="produces 'srsenv.h' defining all SRS env variables" ! !options for WWW programs ! #parameter /name=getOddFile /type=string /comment="The name of the ODD file that contains the databank description." #parameter /name=dontShowOrig /type=bool /comment="don't list the query..only links to it" #parameter /name=userId /type=string /comment="user ID, or file, name associated with a WWW session" #parameter /name=visitIndexValue /type=string /comment="visit the set of entries belonging to an index value" #parameter /name=queryManager /type=bool /comment="activates query manager" #parameter /name=setListPar /type=bool /comment="allows to set parameters for viewing a set" #parameter /name=printHelpTopic /type=string /comment="prints specified help topic" #parameter /name=queryCombine /type=bool /comment="executes query that was specified in the query manager" #parameter /name=topPage /type=bool /comment="revisists top page" #parameter /name=doRepeat /type=bool /comment="revisits query form with same input as before" #parameter /name=doHyperTextLinks /type=bool /comment="revisits query form with same input as before" #parameter /name=doQueryForm /type=bool /comment="present the query form" #parameter /name=doQuery /type=bool /comment="do the query" #parameter /name=libInfo /type=string /comment="print some info about library" #parameter /name=linkInfo /type=bool /comment="print some info about link between 2 libraries" #parameter /name=listSetNumber /type=number /comment="number (in history) of set to be listed" #parameter /name=viewSetNumber /type=number /comment="number (in history) of set to be viewed" #parameter /name=listQuery /type=string /comment="query of set to be listed" #parameter /name=doBlastSearch /type=bool /comment="perform a search with Blast and index results" #parameter /name=prepBlastSearch /type=bool /comment="collect user input for a search with Blast" #parameter /name=listEntriesChunkSize /type=number /num=50 /comment="number of entries to be listed in one go" #parameter /name=listEntriesStartN /type=number /comment="number of first entry in set to be listed" #parameter /name=viewEntriesChunkSize /type=number /num=10 /comment="number of entries to be viewed in one go" #parameter /name=viewEntriesStartN /type=number /comment="number of first entry in set to be viewed" #parameter /name="maxValN" /type=number /num=0 /comment="print only words that occur number of times" #parameter /name=getMessage /type=bool /comment="get a message from user" #parameter /name=sendMessage /type=bool /comment="send a user message to the messages file" #parameter /name=subEntryN /type=number /comment="number of subentry to be accessed" #parameter /name=translateSequence /type=bool /comment="print the translation product instead of DNA sequence" #parameter /name=linkLibSelect /type=bool /comment="display a table with all possible links" #parameter /name=linkToLibs /type=bool /comment="link set/entry to other libraries" #parameter /name=printLinkTable /type=bool /comment="print a link table" #parameter /name=printNetwork /type=bool /comment="print a network in tabular form." ! !trembl options ! #parameter /name=tremblInFile /type=string /comment="Optional input file name. The file extension and format must be the same as of the specified library." #parameter /name=findAccNoCommand /type=string /comment="The command with which to obtain a sequence file from an accession number. Put a '%%s' where the accession number should be placed within the command (eg, 'findacc %%s')." #parameter /name=inputSeqFile /type=string /comment="Name of the file obtained by the above command; again a '%%s' must be placed in lieu of the accession number (eg, '%%s.seq')." #parameter /name=libName /type=string /comment="Name of the input library. If you specify a file name then this specifies the format of the file." ! !reflink ! #parameter /name=readLib /type=string /comment="name of library to be read for references" #parameter /name=searchLib /type=string /str=medline /comment="name of library to be searched for references" #parameter /name=journalListFile /type=string /comment="name of journal list to be read/written" /comment="name of library to be searched for references" #parameter /name=doJournalList /type=bool /comment="make a new journal list" #parameter /name=doMergeJournalLists /type=bool /comment="merge two journal lists to one" #parameter /name=doRefLink /type=bool /comment="link the two libraries using their references" #parameter /name=doRefLinkFile /type=bool /comment="write a text file with all links found" !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! parameter type objects !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #partype /id=%PART_SETNAME /name="setName" /max=20 /min=0 /check=@F_ISNEWSET /charset="a-zA-Z0-9_" #partype /id=%PART_BOOLEAN /name="boolean" /max=3 /min=0 /charset="yYnN01oOfFjJ" #partype /name="fieldQuery" /max=200 /min=0 /check=@F_CHECKFIELDQUERY /charset="a-zA-Z0-9\-_$[]().;*?&|!'" #partype /name="inFileName" /max=200 /min=0 /check=@F_CHECKINFILE /charset="a-zA-Z0-9\-_$[]().;*?&|!'" #partype /name="outFileName" /max=200 /min=0 /check=@F_CHECKOUTFILE /charset="a-zA-Z0-9\-_$[]().;*?&|!'" #partype /name="query" /max=200 /min=0 /check=@F_CHECKOUTDIR /charset="a-zA-Z0-9\-_$[]().;*?&|!'" #partype /id=%PART_FIELDLIST /name="fieldList" /check=@F_CHECKFIELDLIST /charset="a-zA-Z0-9 " #partype /id=%PART_LIBLIST /name="libList" /check=@F_CHECKLIBLIST /charset="a-zA-Z0-9_\- " #partype /id=%PART_LINKLIBLIST /name="libList" /check=@F_CHECKLINKLIBLIST /charset="a-zA-Z0-9_\- " #partype /id=%PART_ENVIRONMENT /name="env" /check=@F_SETENVIRONMENT /charset="a-zA-Z0-9_\- " }