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

#Please insert subtopic references  (line starts with keyword SUB)
#SUB	subtopic.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		Search and highlight sequence patterns

OCCURRENCE	ARB_EDIT4/View/Search
                ARB_EDIT4/<extended top area>/<search fields and buttons>

DESCRIPTION	ARB_EDIT4 supports searching and highlighting sequence patterns.

                It supports 9 different pattern types, which will each be displayed
                in it's own color. Pattern types are e.g. "User1", "Probe",
                "Primer (global)", ...

                Basic controls for each search pattern are available in the
                extended top-area of ARB_EDIT4 (to extend the top-area click the
                'MORE' button): there you may jump to the next/previous occurrence of
                each pattern type, toggle pattern type display and open the detailed
                search parameter dialog for each pattern type.

SECTION         Detailed search parameters (one window for each pattern type)

		Search patterns

			In the text field you can enter multiple search patterns.
			Different patterns are separated by newlines or commas.

			'?' is treated as single letter wildcard

			'#' is an end-of-line comment

				Text written behind # will not be used for search.
				Instead this text will be displayed in the message
				window when you position your cursor on a found
				pattern.

                Mark species with matches

                        Marks all species that match any of the current search patterns
                        (does not change marks of any other species).

		Last/Next

			Jumps to the last/next occurrence of any of the given patterns.
			You can repeat your last search by pressing <CTRL-S> while focus
                        is inside sequence view.

                        In the extended top-area of ARB_EDIT4 there are global NEXT/LAST
                        buttons. They jump to the next match of ANY of all 9 pattern types.

		Show?

			If checked, the found parts are shown in different
			background colors (defined at Properties/Data Search)

                        See NOTES below for overlap priority.

		Open folded?

			If checked, the Last/Next-Button will open folded groups,
			to jump to the next occurrence. Otherwise search will jump
			over folded groups.

		Auto jump?

			If checked, the cursor will automatically jump to the
			nearest occurrence, if you change the search pattern or
			other search parameters.

		Ignore gaps in sequence?

			If checked, gaps in sequence will be ignored.
			(ACGU will find A-CG-U, AC---GU, ...)

		Ignore gaps in pattern?

			If checked, gaps in the search pattern will be ignored.
			(A-CG-U, AC---GU, ... will find ACGU)

		Treat T and U as match?

			If checked, T and U will be treated as equal.
			(ACGU will find ACGT and vice versa)

		Ignore case?

			If checked, a and A, c and C, ... are treated as
			equal (aCGu will find ACGU, AcgU, acgu, ...)

		Search for complement?

			If checked, search will go as well for complemented
			patterns.

		Search for reverse?

			If checked, search will go as well for reversed patterns.

		Exact!

			If checked, search will only go for the given combination
			of 'complement' and 'reverse'.

			Example: If 'Exact', 'complement' and 'reverse' are checked,
				 search will go only for complemented AND reversed
				 patterns.

		Allowed mismatches

			Defines the minimum and maximum allowed number of
			non-matching base characters.

SECTION         Store/restore search patterns

                There are two ways to store/restore search patterns:

                      * using the LINK{prop_configs.hlp} icon
                      * using the SAVE and LOAD buttons

                The latter is obsoleted and is only supported for compatibility.

                Both store/restore all search parameters described above and
                both provide the possibility to exchange the search parameters between
                databases/users by saving/loading them to/from files and to move
                search parameters between different pattern types.

NOTES		Highlighted search patterns are drawn on top of
                other conditions determining background color (see LINK{e4_background_priority.hlp}).

                If the results from different pattern types overlap, patterns are
                prioritized as listed in the 'View/Search' submenu,
                i.e. "User1" is painted above "Primer (global)" and hence parts of
                the latter may be invisible.

                The hits may also be highlighted in ARB_SECEDIT (see LINK{sec_display.hlp}).

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known

