#Please insert up references in the next lines (line starts with keyword UP)
UP	sp_search.hlp
UP	gene_search.hlp
UP	security.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB	tags.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		MODIFY FIELDS OF LISTED SPECIES/GENES

OCCURRENCE	ARB_NT/Species/Search/More Functions/Modify fields of listed
		ARB_NT/Genes/Search/More Functions/Modify fields of listed
		ARB_NT/Tree/NDS

DESCRIPTION	Finds and replaces substrings within fields/tagged subfields of
		all listed species/genes. The entries within the selected
		fields of all listed species/genes can be modified either
		individually or	globally.

		Three different languages can be used to modify an entry:

		SRT:	indicated by a leading ':' character
		ACI:	indicated by a leading '|' character
		REG:	indicated by sourrounding '/' characters

	Details:

		REG: Simple Regular Expressions (not for beginners)

			'/Search RegExpr/Replace String/'  or
			'/Search RegExpr/'

			(see LINK{reg.hlp} for more details)

		SRT: Replaces substrings

                        Syntax: ':old_string=new_string' (see LINK{srt.hlp} for more details)

                        Example: remove all spaces with SRT ': ='

			Different search/replace commands can be performed
			simultaneously and have to be separated by ':'

                                      ':search1=replace1:search2=replace2:  ...  :searchn=replacen'.

			'*' and '?' are wild cards for multiple and single
                        characters, respectively.

		ACI: More sophisticated string manipulations

                     Read LINK{aci.hlp} for more information.

SECTION Options

                * 'Use Tags' allows to tag entries or modify only tagged parts of entries. See LINK{tags.hlp} for details.
                * 'Double Pars' causes the result of the 'Command' to be interpreted and executed as command once again (special; in doubt don't use)
                * 'Create missing target fields' with type=STRING if checked. Bail out with error otherwise.
                * 'Accept conversion errors':
                  - if checked, accepts modifications like writing "hello" to a numeric field (which will be written as '0')
                  - otherwise arb will abort with an error in such cases (Note that writing "4711" to numeric fields will work w/o error)

NOTES		You may add new commands by editing one of the files:

			$ARBHOME/lib/sellists/mod_fields.sellst

			$ARBHOME/lib/sellists/mod_gene_fields.sellst

		You should save this file to another location when
		installing new versions of ARB or it will be overwritten.

		A better way is to create your own list(s). All list
		matching 'mod_fields*.sellst' will be loaded, where
		'mod_fields.sellst' is loaded.

                If you have created any scripts which might be useful for
                other ARB users send them to LINK{devel@arb-home.de}.

EXAMPLES	':p?r=p?1w'	 replaces 	par to paw
						pbr to pbw
						pcr to pcw ...

		':p??r=p?2?1r'	 swaps the two letters between p and r

		':a*=b*1'        replaces only the first 'a' by 'b'

		':?* *=?1. *2'	 Replaces the first word by its first
				 letter + '.'

		':\:=\n'	 replaces all ':' by <newline>

		':*=*1 *(key1)'	 appends the database field <key1>

		':*=*1 *(key1|nothing found)'
				appends the database field <key1>
				if <key1> does not contain entries
				append 'nothing  found'

		1. Global modification: Replace 'spec.' by 'sp.' within
			the field full_name of all listed species:

			Press:		'MODIFY FIELDS OF LISTED SPECIES'
			Select Field:	'full_name'
			Type Command:	':spec.=sp.'
			Press:		'GO'

		2. Individual modification: Append the particular entries
			of fields 'title' and 'journal' to that of the
			fields 'author' of all listed species if there
			are any entries:

			Press:		'MODIFY FIELDS OF LISTED SPECIES'
			Select Field:	'author'
			Type Command:	':*=*1 *(title) *(journal)'
			Press:		'GO'

NOTE		Undo does work.

WARNINGS	Be careful if search or replace string contain
		special characters (such as ':').

BUGS		No bugs known