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UP	arb.hlp
UP	glossary.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE		Searching

OCCURRENCE	ARB_NT/Species/Search and Query
                ARB_NT/Genome/Search and Query

DESCRIPTION     This describes the search feature in ARB.
                When we talk about 'items' below, we mean e.g. 'species', 'genes', etc., depending
                which search tool you are currently using.

SECTION SEARCH FIELD

                Each search expression applies either

                     - to a specific item field (e.g. 'full_name') or 
                     - if you select the '[any field]' pseudo search field,
                       all direct database subentries of the item are searched for the expression.
                       This does NOT work for subcontainers (i.e. 'ali16s/data' is not searched).

SECTION SEARCH EXPRESSION

               - Each expression tries to match the complete field content,
                 i.e. searching for 'test' will match only fields which 
                 exactly contain 'test' (not 'my test' or 'testing').

               - If you search for '' (empty expression), all fields w/o data, i.e. all
                 non-existing fields will be found.

               - if you want to match all fields that contain some substring
                 then use wildcards:

                      - '*'     will match any number of characters (including no characters).
                      - '?'     will match exactly one character

                      If the whole search expression is '*', then it is handled like '?*' (which
                      means 'at least one character'). So searching for '*' will report all
                      existing fields.

                      Examples:

                        '*pseu*'        matches all fields with the substring 'pseu'
                        'pyrococcus*'   matches all fields starting with 'pyrococcus'
                        '*bact*ther*'   matches all fields with the substring 'bact' followed by 'ther'
                                        (there may be many characters in-between or none, i.e. it as
                                        well matches 'bactther')

               - if the first character is '<' or '>' and the rest is a number,
                 then a numerical comparison is done:

                        - '<7'       matches all fields containing a number smaller than 7
                        - '>10'      matches all fields containing a number greater than 10

                        Be careful:
                           Negating '<7' does NOT only match numbers greater or equal to seven. It as
                           well finds all non-numeric contents. Use something like '>6.999' instead.

               - if the first character is '/' then the following regular expression is used
                 for the query (see LINK{reg.hlp}).

               - if the first character is '|' then the following ACI expression is evaluated
                 and the query hits, if the evaluation is not "0".
                 See LINK{aci.hlp}.

               - if the query string is completely empty, it hits if the selected field does
                 not exist.

SECTION SORTING RESULTS

                Search results are displayed unsorted by default. You can sort them, by selecting
                a different order with the sort radio button.
                The available sort criteria are

                    unsorted       display items like they are stored in database
                    by value       sort by content of first query field
                    by id          sort by unique item id (e.g. 'name' for species)
                    by parent      sort by globally unique id of parent item (e.g. 'name' of organism for genes)
                    by marked      sort marked before unmarked items
                    by hit         sort by (and display) hit description (the hit description tells you
                                   why an item was hit by query)
                    reverse        reverts previously selected sort order

                ARB remembers and uses all the sort criteria you apply.

                Example: Selecting 'by id' will sort the items by their id (e.g. 'name'). If you
                select 'by value' afterwards, ARB will sort items by the content of the first query
                field - if the contents of some items are equal, it will still sort them by name.

NOTES		Wildcarded or exact search always searches case insensitive.
                Regular expression search always searches case sensitive.

EXAMPLES	see LINK{sp_search.hlp}

WARNINGS	Using ACI is a bit tricky here, cause you cannot see what happens.
                Using 'trace(1)' somewhere in the ACI expression starts to print an
                ACI trace to the console. Don't forget to use 'trace(0)' afterwards,
                otherwise that may slow down ARB.

BUGS		No bugs known