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Last update on 25. Nov 2018 .
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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.

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 ´Predefined SRT/ACI´).
The corresponding syntax (see ´Search and Replace Tool (SRT)´, ´ARB Command Interpreter (ACI)´ and ´Regular Expressions (REG)´) is displayed in the 'ACI/SRT PROGRAM' subwindow. The displayed strings can be modified by typing to the subwindows.
 

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