SearchingOCCURRENCE
ARB_NT/Species/Search and Query
ARB_NT/Genome/Search and Query
ARB_NT/Tree/Search groups..
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DESCRIPTION
This describes the search feature in ARB as used in the following search and query modules:
When we talk about 'items' below, we mean e.g. 'species', 'genes', 'taxonomic groups' etc., depending which search tool you are currently using.
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SEARCH FIELD
Each search expression applies either-
to a specific item field (e.g. 'full_name') or
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to some criterion calculated on the fly (e.g. amount of marked species inside a taxonomic group) or
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to any or all item fields, if you select one of the entries in "[...]".
The following special search fields may be available:-
"[any field]" reports a match if any direct field matches the expression.
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"[all fields]" reports a match if all direct fields match the expression.
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"[any recursive]" reports a match if any direct or hierarchical field matches the expression.
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"[all recursive]" reports a match if all direct and hierarchical fields match the expression.
Notes:
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search is much slower using one of the 'recursive' fields mostly because sequence data is searched as well.
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"[all fields]" is often used together with "not equal" (see below), making it equivalent to "no field matches expression".
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SEARCH OPERATORS
There are two kinds of search operators directly available for queries:
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the "equal" sign between the field and the match expression means that the selected field (or any field) should match the expression. Clicking on the sign inverts it into a "not equal" sign, which means the selected field shall not match the expression.
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the search operators at the beginning of the 2nd and 3rd line allow to connect the 3 search expressions available for each query. Possible values are 'and', 'or' or 'ign'.
More search operators are available to connect multiple (consecutive) queries:-
using 'Add species' provides a global OR operator (uniting the results of the preceeding and the next query),
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using 'Keep species' provides a global AND operator (intersecting the results of the preceeding and the next query) and
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using "that don't match the q." provides a global NOT operator for the next query
Results of queries can be transformed into a set of 'marked species' using "Mark listed unmark rest" and the marked species can be stored as ´Species selections (=editor configurations)´. Multiple stored configurations can be logically combined to new sets of marked species. To again create a query result from all marked species simply use "Search species ... that are marked".
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MATCH EXPRESSION SORTING RESULTS
Search results are displayed unsorted by default. You can sort them, by selecting a different order with the sort radio button.
The provided sort criteria depend on the kind of query. The following list shows the sort criteria available in ´Search Database for Species´:
unsorted display items like they are stored in database
by value sort by content of first query field
by number same as "by value", but sort numerically
(for string-type fields this sorts multiple columns of numbers)
by id sort by unique item id (e.g. 'name' for species)
by parent sort by globally unique id of parent item (e.g. 'name' of organism for genes)
by marked sort marked before unmarked items
by hit sort by (and display) hit description (the hit description tells you
why an item was hit by query)
reverse reverts previously selected sort order
ARB remembers and uses all the sort criteria you apply.
Example: Selecting 'by id' will sort the items by their id (e.g. 'name'). If you select 'by value' afterwards, ARB will sort items by the content of the first query field - if the contents of some items are equal, it will still sort them by name.
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NOTES
Wildcarded or exact search always searches case insensitive. Regular expression search always searches case sensitive.
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EXAMPLES WARNINGS
Using ACI is a bit tricky here, cause you cannot see what happens.
Using 'trace(1)' somewhere in the ACI expression starts to print an ACI trace to the console. To view the console refer to ´View ARB logs´.
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