// default setting ---------------------   // lines start with "//" or "#" are recognized as comments.
                                           // text following "//" in the line is also recognized as comments.
                                           // blank lines (including spaces) are ignored.
                                           
>default                                   // the block starts with ">default" (default block) defines the base 
                                           // settings of all the other blocks (search block) starts with other ">".
                                           // The parameters defined in the default block is applied for each search
                                           // unless the parameters are overwrite in the search block.
                                           
marginMass            = 1                  // mass tolerance for searching.
                                           // the value should be less than 10 ppm for ExactMassDB(-HR2),
                                           // and 2 dalton for the other databases.
                                           // if exceeds, searching will be skipped.
                                           
isPpmMarginMass       = true               // true: marginMass is recognized as ppm, 
                                           // false: marginMass is treated as dalton
                                           
isEnabledRatio13c     = true               // if true, filtering by 13C/12C ratio is performed
marginRatio13c        = 5                  // % tolerance for 13C/12C filtering
// databases --------------------------
searchDbExactmass     = false              // if true, enables search for ExactMassDB
searchDbExactmass_hr2 = false              // if true, enables search for ExactMassDB-HR2
searchDbKnapsack      = false              // if true, enables search for KNApSAcK
searchDbKegg          = false              // if true, enables search for KEGG
searchDbPubchem       = false              // if true, enables search for PubChem
searchDbKomics        = false              // if true, enables search for KomicMarket
searchDbFlavViewer    = false              // if true, enables search for Flavonoid Viewer (by Dr. Arita)
searchDbLipidMaps     = false              // if true, enables search for LipidMAPS
searchDbPep1000       = false              // if true, enables search for Pep1000
searchDbHmdb          = false              // if true, enables search for HMDB
// filter options ---------------------
isOnlyPhosphate       = false              // if true, all P atoms are assumed to be included in phosphate
restrictAtomNumC      = false              // if true, restrictions of atom numbers (min and max) for C is enabled
restrictAtomNumN      = true               // if true, restrictions of atom numbers (min and max) for N is enabled 
restrictAtomNumS      = true               // if true, restrictions of atom numbers (min and max) for S is enabled 
restrictAtomNumP      = true               // if true, restrictions of atom numbers (min and max) for P is enabled 
restrictAtomNumX1     = false              // if true, restrictions of atom numbers (min and max) for X1 is enabled 
labelAtomX1           =                    // The chemical symbol of the restrictions for atom X1 (e.g. Cl)
minAtomNumC           = 0                  // minimum number of atom C contained in the formula
minAtomNumN           = 0                  // minimum number of atom N contained in the formula
minAtomNumS           = 0                  // minimum number of atom S contained in the formula
minAtomNumP           = 0                  // minimum number of atom P contained in the formula
minAtomNumX1          = 0                  // minimum number of atom X1 contained in the formula
maxAtomNumC           = 100                // maximum number of atom C contained in the formula
maxAtomNumN           = 5                  // maximum number of atom N contained in the formula
maxAtomNumS           = 5                  // maximum number of atom S contained in the formula
maxAtomNumP           = 5                  // maximum number of atom P contained in the formula
maxAtomNumX1          = 10                 // maximum number of atom X1 contained in the formula
showOnlyAglyconForFlavonoidViewer = false  // if true, only aglycons for Flavonoid Viewer entries will be shown
applyAtomRestrictionOnlyForExmass = false  // if true, the restrictions for the atom numbers are applied only for the
                                           // results from ExactMassDB(-HR2)
// network setting --------------------
networkProxyEnabled    = false             // trun it true if network proxy setting is required in your organization.
networkProxyServerName = your.proxy.server // the name of the proxy server
networkProxyPort       = 8080              // the port number 
                                           // please ask the network administrator of your organization for the details.
// adduct setting ---------------------
adduct_ifMulti = auto                      // this is for the peaks to which multiple candiates of adduct are assigned.
                                           // auto: searches are performed with all of the candidate adducts.
                                           
//adduct_ifMulti =                         // if blank or comment out, skip searching
//adduct_ifMulti = 1, 2, 3, 4, 9           // searches will be performed with defined indices of the adducts.
                                           // the indices are same as the index numbers in the ionizationMode.txt file
                                           // that start by zero.
                                           
//adduct_ifMulti = auto, 1, 2, 3, 4, 9     // a mixed description is allowed.

//adduct_force = 9                         // this setting forces the search with the adduct defined by the index
                                           // index number in the ionizationMode.txt file.
                                           // if the parameter enables, the normal searching according to the assigned
                                           // adduct for each peak is omitted.
                                           
//adduct_force = 1, 9                      // multiple adducts can be defined.


// search block settings ------------- //
>clear	true                               // a search block starts with ">", following a short title, <tab>, 
                                           // and a switch (true/false).
                                           // the short title will be used as memo.

                                           
do_clearResults = true                     // parameters starts with "do_" are for only search blocks.
                                           // do_clearResults is enabled, the search results already exists are removed
                                           // before the searching of this block.
                                           
>All 1 ppm	false                          // if false is set after the <tab>, the search block will be skipped.
marginMass            = 1
searchDbKnapsack      = true
searchDbKegg          = true
searchDbLipidMaps     = true
searchDbFlavViewer    = true
searchDbHmdb          = true
searchDbPubchem       = true
searchDbExactmass_hr2 = true
searchDbPep1000       = true

>Compound DBs 1 ppm	true
marginMass         = 1
searchDbKnapsack   = true
searchDbKegg       = true
searchDbLipidMaps  = true
searchDbFlavViewer = true
searchDbHmdb       = true                  // if no search result are obtained in this block, the search process will 
                                           // continue to the next search block.
                                           
>Formula Predisction 1 ppm	true           // when search results already exists, the search block will be skipped 
                                           // unless "do_addResults" or "do_mergeResults" parameter is enabled.
marginMass            = 1
searchDbExactmass_hr2 = true

>Compound DBs 5 ppm	true
marginMass         = 5
searchDbKnapsack   = true
searchDbKegg       = true
searchDbLipidMaps  = true
searchDbFlavViewer = true
searchDbHmdb       = true
do_mergeResults    = true                  // if true, the search for this search block is forced.
                                           // the search results are merged at the end of the existing results.
                                           // the records already exists are omitted from merging.
>Peptide	true
marginMass         = 3
searchDbPep1000    = true
do_addResults      = true                  // if true, the search for this search block is forced.
                                           // the search results are added anyway after the existing results.
                                           // therefore, it will be a cause of redundancy of search results.
                                           // but the process is faster than that of merging.
                                           // please use it when the redundancy will be logically avoidable,
                                           // in such cases that the new target databases are selected in this block.

>Formula Prediction 1ppm	true
marginMass            = 1
searchDbExactmass_hr2 = true
restrictAtomNumN      = true
restrictAtomNumS      = true
do_mergeResults       = true
do_sortResults        = true               // if true, the search results are sorted by absolute value of delta ppm
                                           // after searching in this block.

