1 | #Please insert up references in the next lines (line starts with keyword UP) |
---|
2 | UP arb.hlp |
---|
3 | UP 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 ******** |
---|
11 | TITLE Searching |
---|
12 | |
---|
13 | OCCURRENCE ARB_NT/Species/Search and Query |
---|
14 | ARB_NT/Genome/Search and Query |
---|
15 | |
---|
16 | DESCRIPTION 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 | |
---|
20 | SECTION 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 | |
---|
29 | SECTION 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 | |
---|
87 | SECTION 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 | |
---|
108 | NOTES Wildcarded or exact search always searches case insensitive. |
---|
109 | Regular expression search always searches case sensitive. |
---|
110 | |
---|
111 | EXAMPLES see LINK{sp_search.hlp} |
---|
112 | |
---|
113 | WARNINGS 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 | |
---|
118 | BUGS No bugs known |
---|