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Last update on 25. Nov 2018 .
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Species flags

OCCURRENCE

ARB_EDIT4/Properties/Select species flags

 

DESCRIPTION

This module allows to show clickable flags between the species name and the sequence display area.

These flags display the values of selected database fields interpreted as bool (ie. "on"/"off") and by clicking them, you are able to toggle the values of these database fields (between 0 and 1).

The following list shows how different field contents are mapped to flag states:

Field content                       Flag state
---------------------------------------------
field missing                       off
'0'                                 off
integer<>0                          on
non-numeric text                    off
floating point [0.0 .. 0.5[         off
floating point [0.5 .. inf]         on

You can display up to 5 database fields at the same time.

The setup of displayed flags is stored together with your database (not inside edit4-properties). This means: if you save your database while flags are shown in EDIT4, another user will see these flags after opening the editor on that database. You can use the config-manager icon to store the current setup inside properties and to restore it for a different database.

The size of the clickable boxes depends on the size of the space available, which is determined by other settings, eg.

  • by the size of several fonts,
  • by the lengths of the customized flag abbreviations or
  • by sequence-sequence-spacing.

 

NOTES

To display more than just a bool value use ´ARB_EDIT4: Node Display Setup (NDS)´ with an ACI like

readdb(name);" | ";readdb(nuc)

Flags work for SAIs as well.

 

EXAMPLES

Example workflow using species flags:

Imagine your goal is to check and probably correct the alignment of several species.

  1. use ´Search Database for Species´ to query those species for which you like to check the alignment (e.g. by searching for low qualities reported by ´Calculate sequence quality´)
  2. use ´Write to fields of Listed´ to write '1' into the field 'tocheck' for queried species
  3. load these species into the editor and configure to show the following fields as flags:
    • 'tocheck'
    • 'bad_alignment' (new field)
    • 'bad_sequence' (new field)

    The latter two fields should not exist for this use case to work as intended.
  4. Go through your sequences and decide for each
    • whether the sequence data has sufficient quality (if not -> check 'bad_sequence')
    • whether the sequence alignment needs to be improved (if yes -> check 'bad alignment')

    After each decision made, clear the 'tocheck' flag of that sequence.
    (when done with all sequences, you might want to remove the 'tocheck' field from the database)
  5. Use Search to find all species with 'bad_sequence' set to 1 and mark these species. Either remove them from your tree(s) or completely remove them from the database.
    (now the 'bad_sequence' field is obsolete and may be removed)
  6. Restart the editor with all species which have 'bad_alignment' set to 1 (plus all species needed to fix their alignment).
    Change flag setup to show the following flags:
    • 'bad_alignment'
    • 'fixed' (new field)

  7. Go through the alignment, fix the alignment of every species which has 'bad_alignment' set and set the 'fixed' flag to mark your progress.

(now all flags entries may be removed)

 

WARNINGS

None

 

BUGS

No bugs known