source: trunk/HELP_SOURCE/source/props_nds.hlp

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UP      arb.hlp
UP      glossary.hlp
UP      sp_info.hlp

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#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           Node Display Setup (NDS)

OCCURRENCE      ARB_NT/Tree/NDS
                ARB_GENE_MAP/Properties/NDS

NOTES           Read this text carefully. You won't need this function, but
                it offers many many new possibilities.

DESCRIPTION     Extracts data from the database entries of every species and
                builds a user-readable string from that data.

                This string can be used in many different functions, especially
                to show the species information at the tips of the tree or
                to show gene information at the tips of the genes in the
                gene map.

                It allows you to show part of the sequences, the full_name,
                the accession numbers right in the tree. You may even
                generate tables with all kinds of useful information, like
                probe match results for a set of oligo probes.

                Choose the 'NDS' item from the 'ARB_NT/Tree' menu to
                display the 'NDS' window.

                The order of the data shown at the tree nodes (from left
                to right) corresponds to the order in the 'NDS' window (top to bottom).

                Enable field extraction:

                        Check the 'LEAF' and/or 'GRP.' checkbox to activate the display of
                        the corresponding 'field' entry at leafs and/or groups
                        of the tree shown in the tree display area of the 'ARB_NT' window.

                Select 'FIELD':

                        To select a 'field' click the field name
                        button and select a fieldname from the popup list.

                        At each leaf ARB will display the content of that field as it is stored
                        in the species at leaf.
                        If an ACI/SRT (see below) is specified, it will be applied
                        to the field content and the result will be displayed.

                        If a species has no content stored for the selected field,
                        ARB will silently skip that entry from display.
                        No ACI expression will get applied in that case.

                        If you like to unconditionally apply the ACI/SRT expression,
                        select '<no field>' here.

                        Selecting a field for group entries does not make sense anymore (old ARB versions
                        made use of that). Groups may contain several fields (e.g. 'group_name', 'grouped', ...),
                        but to access these fields you have to use the ACI command 'readdb'.

                        Normally it is recommended to select '<no field>' for groups and
                        to use the 'taxonomy' ACI command to
                        retrieve (hierarchical) information about taxonomy.

                Define number of characters:

                        Specify the (maximum) number of characters (including blanks)
                        allowed to be displayed in the 'WIDTH' subwindow.
                        If the result is longer, it will be truncated.

                        To avoid truncation insert zero.

                Display ACI/SRT:

                        If an ACI/SRT expression is specified,
                        the found field content (or an empty string if no field was selected)
                        will get modified by that expression, before it will be displayed at the tree nodes.

                        Several predefined expressions are available via the <S> button in front of
                        the ACI/SRT field (see LINK{acisrt.hlp}).

                        The corresponding syntax (see LINK{srt.hlp}, LINK{aci.hlp} and
                        LINK{reg.hlp}) is displayed in the 'ACI/SRT PROGRAM' subwindow.
                        The displayed strings can be modified by typing to the subwindows.

SECTION         Sets of entries

                NDS configuration is done using 10 visible entries. 
                Using the 'Entries XX - YY' button
                you can select which entry subset (of the overall 60 available entries) is shown in this window.
                
                For the resulting display information, you can use the next button to choose whether to

                        1. Use all entries (=default for backwards compatibility) or
                        2. Only use visible entries (recommended use)

                If you choose 1., any activated entry (out of 1-60) is used to create the resulting display information.
                Switching between entry subsets has no effect on result.

                If you choose 2., only the entries currently displayed in the NDS window are used to 
                create the resulting display information. You may use the 'Entries ...' button
                to quickly switch between different display setups.

NOTES           Strings generated using 'SRT' or 'ACI' and displayed at the
                nodes are not stored in the database. You can use
                the 'Modify fields of listed species'-menuentry in the
                'Search & Query' window to do this.

                The width of the output is limited to 4000 characters.

EXAMPLES        None

WARNINGS        The NDS setup is stored in the loaded ARB database.

                You can use the config-manager to store/restore the currently edited 10 entries
                into/from a named config. These configs will be stored in your account when
                you save properties.
                Such stored configs can be used to copy the NDS (e.g. from 'Entries 1-10' to 'Entries 11-20'
                or from one ARB database to another).

BUGS            None