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 | UP sp_info.hlp |
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5 | |
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6 | #Please insert subtopic references (line starts with keyword SUB) |
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7 | #SUB subtopic.hlp |
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8 | |
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9 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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10 | |
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11 | #************* Title of helpfile !! and start of real helpfile ******** |
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12 | TITLE Node Display Setup (NDS) |
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13 | |
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14 | OCCURRENCE ARB_NT/Tree/NDS |
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15 | ARB_GENE_MAP/Properties/NDS |
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16 | |
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17 | NOTES Read this text carefully. You won't need this function, but |
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18 | it offers many many new possibilities. |
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19 | |
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20 | DESCRIPTION Extracts data from the database entries of every species and |
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21 | builds a user-readable string from that data. |
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22 | |
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23 | This string can be used in many different functions, especially |
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24 | to show the species information at the tips of the tree or |
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25 | to show gene information at the tips of the genes in the |
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26 | gene map. |
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27 | |
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28 | It allows you to show part of the sequences, the full_name, |
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29 | the accession numbers right in the tree. You may even |
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30 | generate tables with all kinds of useful information, like |
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31 | probe match results for a set of oligo probes. |
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32 | |
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33 | Choose the 'NDS' item from the 'ARB_NT/Tree' menu to |
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34 | display the 'NDS' window. |
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35 | |
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36 | Enable field extraction: |
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37 | |
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38 | Press the 'LEAF' and/or 'GRP.' checkbox to activate the display of |
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39 | the corresponding 'field' entry at leafs and/or groups |
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40 | of the tree shown in the tree display area of the 'ARB_NT' window. |
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41 | |
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42 | Select 'FIELD': |
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43 | |
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44 | The order of the data shown at the tree nodes |
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45 | (from left to right) corresponds to that in the 'NDS' |
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46 | window (top to bottom). To select a 'field' enter the field name |
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47 | by hand or press the respective <S> button and select it |
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48 | from the popup-list. |
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49 | |
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50 | Press <RESCAN> there to display all fields, if fields have been deleted |
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51 | from the list by 'Species Information/Delete hide fields'. |
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52 | |
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53 | Define number of characters: |
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54 | |
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55 | Type the number of characters (including blanks) to be |
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56 | displayed to the 'WIDTH' subwindow. |
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57 | |
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58 | Display SRT/ACI: |
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59 | |
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60 | The 'Search and replace Tool (SRT)' and the 'ARB Command |
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61 | Interpreter (ACI)' in combination with 'Nodes Display |
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62 | Setup (NDS)' allows information to be extracted and/or modified |
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63 | from the 'Field' entries, before being displayed at the tree nodes. |
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64 | |
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65 | Press the corresponding <SRT> button to display the |
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66 | 'SRT_ACI_SELECT' window and select a predefined procedure |
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67 | (see LINK{acisrt.hlp}). |
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68 | |
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69 | The corresponding syntax (see LINK{srt.hlp}, LINK{aci.hlp} and |
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70 | LINK{reg.hlp}) is displayed in the 'ACI SRT PROGRAM' subwindow. |
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71 | The displayed strings can be modified by typing to the subwindows. |
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72 | |
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73 | SECTION Sets of entries |
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74 | |
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75 | NDS configuration is done using 10 visible entries. |
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76 | Using the 'Entries XX - YY' button |
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77 | you can select which entry subset (of the overall 60 available entries) is shown in this window. |
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78 | |
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79 | For the resulting display information, you can use the next button to choose whether to |
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80 | |
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81 | 1. Use all entries (=default for backwards compatibility) or |
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82 | 2. Only use visible entries (recommended use) |
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83 | |
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84 | If you choose 1., any activated entry (out of 1-60) is used to create the resulting display information. |
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85 | Switching between entry subsets has no effect on result. |
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86 | |
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87 | If you choose 2., only the entries currently displayed in the NDS window are used to |
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88 | create the resulting display information. You may use the 'Entries ...' button |
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89 | to quickly switch between different display setups. |
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90 | |
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91 | NOTES Strings generated using 'SRT' or 'ACI' and displayed at the |
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92 | nodes are not stored in the database. You can use |
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93 | the 'Modify fields of listed species'-menuentry in the |
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94 | 'Search & Query' window to do this. |
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95 | |
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96 | The width of the output is limited to 4000 characters. |
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97 | |
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98 | EXAMPLES None |
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99 | |
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100 | WARNINGS The NDS setup is stored in the loaded ARB database. |
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101 | |
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102 | You can use the config-manager to store/restore the currently edited 10 entries |
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103 | into/from a named config. These configs will be stored in your account when |
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104 | you save properties. |
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105 | Such stored configs can be used to copy the NDS (e.g. from 'Entries 1-10' to 'Entries 11-20' |
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106 | or from one ARB database to another). |
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107 | |
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108 | BUGS None |
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109 | |
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