source: trunk/HELP_SOURCE/source/searching.hlp

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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                ARB_NT/Tree/Search groups..
16
17DESCRIPTION     This describes the search feature in ARB as used in the following
18                search and query modules:
19                       * LINK{sp_search.hlp}
20                       * LINK{group_search.hlp}
21                       * LINK{gene_search.hlp}
22
23                When we talk about 'items' below, we mean e.g. 'species', 'genes', 'taxonomic groups'
24                etc., depending which search tool you are currently using.
25
26
27SECTION SEARCH FIELD
28
29                Each search expression applies either
30
31                     - to a specific item field (e.g. 'full_name') or
32                     - to some criterion calculated on the fly (e.g. amount of marked species inside a taxonomic group) or
33                     - to any or all item fields, if you select one of the entries in "[...]".
34
35                The following special search fields may be available:
36
37                     * "[any field]" reports a match if any direct field matches the expression.
38                     * "[all fields]" reports a match if all direct fields match the expression.
39                     * "[any recursive]" reports a match if any direct or hierarchical field matches the expression.
40                     * "[all recursive]" reports a match if all direct and hierarchical fields match the expression.
41
42                     Notes:
43
44                        * search is much slower using one of the 'recursive' fields mostly
45                          because sequence data is searched as well.
46                        * "[all fields]" is often used together with "not equal" (see below),
47                          making it equivalent to "no field matches expression".
48
49SECTION SEARCH OPERATORS
50
51               There are two kinds of search operators directly available for queries:
52
53               1. the "equal" sign between the field and the match expression means that
54                  the selected field (or any field) should match the expression.
55                  Clicking on the sign inverts it into a "not equal" sign, which means
56                  the selected field shall not match the expression.
57
58               2. the search operators at the beginning of the 2nd and 3rd line
59                  allow to connect the 3 search expressions available for each query.
60                  Possible values are 'and', 'or' or 'ign'.
61
62                  - 'ign' stands for "ignore" (the rest of the line will be ignored)
63                  - selecting 'and' means the preceeding and the expression behind have to match
64                  - selecting 'or' means the preceeding or the expression behind have to match
65
66                  There is no operator precedence, i.e.
67                  - "1st and 2nd or 3rd" is interpreted as "(1st and 2nd) or 3rd" AND
68                  - "1st or 2nd and 3rd" is interpreted as "(1st or 2nd) and 3rd"
69
70               More search operators are available to connect multiple (consecutive) queries:
71
72                  - using 'Add species' provides a global OR operator (uniting the results
73                    of the preceeding and the next query),
74                  - using 'Keep species' provides a global AND operator (intersecting the results
75                    of the preceeding and the next query) and
76                  - using "that don't match the q." provides a global NOT operator for the next query
77
78               Results of queries can be transformed into a set of 'marked species'
79               using "Mark listed unmark rest" and the marked species can be stored
80               as LINK{species_configs.hlp}. Multiple stored configurations can be
81               logically combined to new sets of marked species.
82               To again create a query result from all marked species simply use
83               "Search species ... that are marked".
84
85
86SECTION MATCH EXPRESSION
87
88               - Each expression tries to match the complete field content
89                 (or the result of the underlaying calculation),
90                 i.e. searching for 'test' will match only fields which
91                 exactly contain 'test' (not 'my test' or 'testing').
92
93               - If you search for '' (empty expression), all fields w/o data, i.e. all
94                 non-existing fields will be found.
95
96               - if you want to match all fields that contain some substring
97                 then use wildcards:
98
99                      - '*'
100
101                                will match any number of characters (including no characters).
102
103                      - '?'
104
105                                will match exactly one character
106
107                      If the whole search expression is '*', then it is handled like '?*' (which
108                      means 'at least one character'). That means searching for '*' will match any
109                      non-empty field.
110
111                      Examples:
112
113                        '*pseu*'        matches all fields with the substring 'pseu'
114                        'pyrococcus*'   matches all fields starting with 'pyrococcus'
115                        '*bact*ther*'   matches all fields with the substring 'bact' followed by 'ther'
116                                        (there may be many characters in-between or none,
117                                        i.e. it does match 'bactther' as well as 'Corynebacterium diphtheriae')
118
119               - if the first character is '<' or '>' and the rest is a number,
120                 then a numerical comparison is performed:
121
122                        - '<7'
123
124                          matches all fields containing a number smaller than 7
125
126                        - '>10'
127
128                          matches all fields containing a number greater than 10
129
130                        Be careful:
131
132                           Negating '<7' does NOT only match numbers greater or equal to seven. It as
133                           well finds all non-numeric contents. Use something like '>6.999' instead.
134
135               - if the first character is '/' then the following regular expression is used
136                 for the query (see LINK{reg.hlp}).
137
138               - if the first character is '|' then the following ACI expression is evaluated
139                 and the query hits, if the evaluation is not "0".
140                 See LINK{aci.hlp}.
141
142               - if the query string is completely empty, it hits if the selected field does
143                 not exist (or if a calculation produces no/empty result).
144
145SECTION SORTING RESULTS
146
147                Search results are displayed unsorted by default. You can sort them, by selecting
148                a different order with the sort radio button.
149
150                The provided sort criteria depend on the kind of query. The following list shows
151                the sort criteria available in LINK{sp_search.hlp}:
152
153                    unsorted       display items like they are stored in database
154                    by value       sort by content of first query field
155                    by number      same as "by value", but sort numerically
156                                   (for string-type fields this sorts multiple columns of numbers)
157                    by id          sort by unique item id (e.g. 'name' for species)
158                    by parent      sort by globally unique id of parent item (e.g. 'name' of organism for genes)
159                    by marked      sort marked before unmarked items
160                    by hit         sort by (and display) hit description (the hit description tells you
161                                   why an item was hit by query)
162                    reverse        reverts previously selected sort order
163
164                ARB remembers and uses all the sort criteria you apply.
165
166                Example: Selecting 'by id' will sort the items by their id (e.g. 'name'). If you
167                select 'by value' afterwards, ARB will sort items by the content of the first query
168                field - if the contents of some items are equal, it will still sort them by name.
169
170NOTES           Wildcarded or exact search always searches case insensitive.
171                Regular expression search always searches case sensitive.
172
173EXAMPLES        see LINK{sp_search.hlp}
174
175WARNINGS        Using ACI is a bit tricky here, cause you cannot see what happens.
176
177                Using 'trace(1)' somewhere in the ACI expression starts to print an
178                ACI trace to the console. To view the console refer to LINK{console.hlp}.
179
180BUGS            No bugs known
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