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

#Please insert subtopic references  (line starts with keyword SUB)
#SUB	export_format.hlp
SUB     arb_import.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		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