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