#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp
UP      arb_merge_workflow.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB     del_list.hlp
SUB     write_field_list.hlp
SUB     mod_field_list.hlp
SUB     mg_xfer_field_of_listed.hlp
SUB     mg_xfer_field_of_sel.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE           Compare and Transfer Species Entries

OCCURRENCE      ARB_MERGE/Transfer species

DESCRIPTION     Allows
                        * database searching,
                        * comparison of the two databases,
                        * transferring data from left to right
                        * realigning sequences to new alignment

        Database Searching:

                To perform database searching within the individual databases
                use the left or right part of the 'TRANSFER SPECIES' window for
                source and target database (DB), respectively.

                The database is scanned for 'species' (see LINK{glossary.hlp})
                which contain (or do not contain) the search string within the
                specified 'field' (see LINK{glossary.hlp}). The corresponding
                'species' and the respective 'field' entries are listed in the
                'HIT LIST' subwindow. The number of hits is displayed after the
                'Hits:' prompt.

                Define whether matching or non matching species should be
                listed by pressing the appropriate combination of left
                and right buttons in the 'QUERY TYPE' area. Performing
                multiple searches, define whether the list of 'species'
                should be replaced by the new results, whether newly
                found 'species' should be removed from or appended
                to the existing list.

                Select a 'field' from the 'Fields' subwindow.

                Type the search string to the 'Search string' subwindow.

                Press the 'RUN QUERY' button of the results area.

                See also LINK{searching.hlp} and LINK{search_equal_fields.hlp}.

        Data Transfer:

                Transfer will always happen from source to target species
                (i.e. from left to right side).

                Select the transfer mode:
                 * "whole species" will copy all fields,
                 * "single field" will copy one single field (selectable, allows to append data) and
                 * "using FTS" will use the "field transfer set" selected below (see LINK{xferset.hlp}).

                Select the transfer scope:
                 * "selected species" will copy (from) the selected species into
                   a new species or to the species selected in the right-side
                   hitlist.
                 * "listed species" will copy all species listed in the left-side hitlist.

                Click the 'Transfer species' button in the window center to transfer
                according to selected transfer-type and -scope.

                See LINK{save.hlp} for howto save the modified database(s).

SECTION         Adapt Alignment

                ARB Merge tries to keep the alignment correct. Normally people
                have inserted new gaps in either the left or right database.
                By entering the ID(s) of some reference species in the input
                box in the upper center of the TRANSFER SPECIES window, the
                program will try to find those species in both databases,
                create a column reference list, and realign all transferred
                sequences.

                To enable this feature, enable the 'Adapt alignment' toggle.

SECTION         Overwritten data

                This section describes when and what data will be overwritten
                and when data gets mixed into existing data.

                In "whole species" transfer mode
                 * any existing species (with the same ID, i.e. 'name') will be deleted and
                 * a full copy of each source species will be created.

                The "single field" and "using FTS" transfer modes
                 * will copy from the selected source species to the selected target species
                   when "selected species" scope is used or
                 * will copy from each listed species to (a new or already existing) target species
                   with the same ID.

                Some fields are handled special:
                 * the 'name' entry will always be transferred when missing at target.
                 * the 'acc' entry will be transferred when missing at target (and when "using FTS" mode).
                 * all transferred 'ali_*/data' entries will be targeted by alignment adaption (see section above).

NOTES           None


EXAMPLES        For examples for database searching see LINK{sp_search.hlp}.


WARNINGS        The data will always be transferred from the source DB to
                the target DB.
                If you want to align sequences during transfer, it is recommended
                that the left database has fewer gaps than the right one.

                If there are entries (for selected data) in both databases,
                those in the target DB will be overwritten!


BUGS            No bugs known