source: branches/lib/HELP_SOURCE/source/arb_export.hlp

#       main topics:
UP      arb.hlp
UP      glossary.hlp
UP      mark.hlp
UP      nt_align_select.hlp

#       sub topics:
SUB     arb_import.hlp

# format described in ../help.readme


TITLE           Export Selected Species and Sequences

OCCURRENCE      ARB_NT/File/Export/Export to external format

DESCRIPTION
                Exports the selected 'alignment' of some or all 'species' in
                various formats.

                Select a format from the format list.

                Select a field transfer set (FTS) if you like to select or modify
                the data to be exported.

                Choose whether to export all or only marked species.

                Choose a filter to export only selected columns.

                Select a compression method:
                       - 'none' preserves the alignment information
                       - 'vertical gaps' removes all columns containing only gaps
                       - 'all gaps' completely remove the alignment information

                Check 'Cut stop codon' to cut off the sequence at the stop codon.

                Define whether the data should be written to one or to multiple
                        files by clicking on the checkbox after the 'Should the
                        data be written to multiple files:' prompt. In the
                        multiple file mode, each 'species' is written to its own
                        file.

                Define an output file name by selecting from the 'Directories
                        and Files' subwindow or by typing it to the 'Output File
                        Name' subwindow. In the multiple file mode, the
                        resulting filenames are created by appending the
                        'species name' to the specified output filename
                        separated by underscores (filename_species name).

                Press the <GO> button


SECTION         Export filters

                Default export filters available for all users are stored in
                directory $ARBHOME/lib/export/*.eft.

                ARB reads the selected format and replaces all references to
                species fields by the value of the referred field.
                See LINK{export_format.hlp} for more information.

                Specifying a FTS will (virtually) modify the contents of fields
                used in the export filter.
                Note: this will NOT affect the fields original content, it just
                is a temporary change, visible only to the export filter.

                    Simple example: if the export filter accesses the field 'author' and
                    you use some arb database where the author is stored
                    in the field 'autref', you may create a FTS containing one simple
                    forwarding rule "autref -> author".

                    The content of field 'autref' will be exported
                    whenever 'author' is accessed (but your database will
                    not get modified).

                    This FTS can be used with any export form that uses 'author'.


SECTION         Custom export filters

                You may create and store your own private export filters in
                directory '~/.arb_prop/filter'.
                See LINK{export_format.hlp} for information
                about the export filter definition language.

                Press the 'Test' button to modify and test the selected filter
                (see LINK{export_test.hlp}).

NOTES           None

EXAMPLES        None

BUGS            No bugs known