source: tags/ms_r16q4/HELP_SOURCE/oldhelp/searching.hlp

Last change on this file was 10842, checked in by westram, 11 years ago
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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4
5#Please insert subtopic references  (line starts with keyword SUB)
6#SUB    subtopic.hlp
7
8# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
9
10#************* Title of helpfile !! and start of real helpfile ********
11TITLE           Searching
12
13OCCURRENCE      ARB_NT/Species/Search and Query
14                ARB_NT/Genome/Search and Query
15
16DESCRIPTION     This describes the search feature in ARB.
17                When we talk about 'items' below, we mean e.g. 'species', 'genes', etc., depending
18                which search tool you are currently using.
19
20SECTION SEARCH FIELD
21
22                Each search expression applies either
23
24                     - to a specific item field (e.g. 'full_name') or
25                     - if you select the '[any field]' pseudo search field,
26                       all direct database subentries of the item are searched for the expression.
27                       This does NOT work for subcontainers (i.e. 'ali16s/data' is not searched).
28
29SECTION SEARCH EXPRESSION
30
31               - Each expression tries to match the complete field content,
32                 i.e. searching for 'test' will match only fields which
33                 exactly contain 'test' (not 'my test' or 'testing').
34
35               - If you search for '' (empty expression), all fields w/o data, i.e. all
36                 non-existing fields will be found.
37
38               - if you want to match all fields that contain some substring
39                 then use wildcards:
40
41                      - '*'
42
43                                will match any number of characters (including no characters).
44
45                      - '?'
46
47                                will match exactly one character
48
49                      If the whole search expression is '*', then it is handled like '?*' (which
50                      means 'at least one character'). So searching for '*' will report all
51                      existing fields.
52
53                      Examples:
54
55                        '*pseu*'        matches all fields with the substring 'pseu'
56                        'pyrococcus*'   matches all fields starting with 'pyrococcus'
57                        '*bact*ther*'   matches all fields with the substring 'bact' followed by 'ther'
58                                        (there may be many characters in-between or none, i.e. it as
59                                        well matches 'bactther')
60
61               - if the first character is '<' or '>' and the rest is a number,
62                 then a numerical comparison is done:
63
64                        - '<7'
65
66                          matches all fields containing a number smaller than 7
67
68                        - '>10'
69
70                          matches all fields containing a number greater than 10
71
72                        Be careful:
73
74                           Negating '<7' does NOT only match numbers greater or equal to seven. It as
75                           well finds all non-numeric contents. Use something like '>6.999' instead.
76
77               - if the first character is '/' then the following regular expression is used
78                 for the query (see LINK{reg.hlp}).
79
80               - if the first character is '|' then the following ACI expression is evaluated
81                 and the query hits, if the evaluation is not "0".
82                 See LINK{aci.hlp}.
83
84               - if the query string is completely empty, it hits if the selected field does
85                 not exist.
86
87SECTION SORTING RESULTS
88
89                Search results are displayed unsorted by default. You can sort them, by selecting
90                a different order with the sort radio button.
91                The available sort criteria are
92
93                    unsorted       display items like they are stored in database
94                    by value       sort by content of first query field
95                    by id          sort by unique item id (e.g. 'name' for species)
96                    by parent      sort by globally unique id of parent item (e.g. 'name' of organism for genes)
97                    by marked      sort marked before unmarked items
98                    by hit         sort by (and display) hit description (the hit description tells you
99                                   why an item was hit by query)
100                    reverse        reverts previously selected sort order
101
102                ARB remembers and uses all the sort criteria you apply.
103
104                Example: Selecting 'by id' will sort the items by their id (e.g. 'name'). If you
105                select 'by value' afterwards, ARB will sort items by the content of the first query
106                field - if the contents of some items are equal, it will still sort them by name.
107
108NOTES           Wildcarded or exact search always searches case insensitive.
109                Regular expression search always searches case sensitive.
110
111EXAMPLES        see LINK{sp_search.hlp}
112
113WARNINGS        Using ACI is a bit tricky here, cause you cannot see what happens.
114                Using 'trace(1)' somewhere in the ACI expression starts to print an
115                ACI trace to the console. Don't forget to use 'trace(0)' afterwards,
116                otherwise that may slow down ARB.
117
118BUGS            No bugs known
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