| 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 arb_ntree.hlp |
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| 5 | UP arb_edit4.hlp |
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| 6 | UP mode_info.hlp |
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| 7 | UP security.hlp |
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| 8 | UP sp_search.hlp |
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| 9 | UP Protection.hlp |
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| 10 | |
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| 11 | #Please insert subtopic references (line starts with keyword SUB) |
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| 12 | SUB spaf_reorder.hlp |
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| 13 | SUB spaf_delete.hlp |
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| 14 | SUB spaf_create.hlp |
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| 15 | SUB spa_delete.hlp |
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| 16 | SUB spa_rename.hlp |
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| 17 | SUB spa_copy.hlp |
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| 18 | SUB spa_create.hlp |
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| 19 | SUB sp_sp_2_ext.hlp |
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| 20 | SUB scandb.hlp |
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| 21 | |
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| 22 | |
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| 23 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 24 | |
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| 25 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 26 | TITLE SPECIES INFORMATION |
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| 27 | |
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| 28 | OCCURRENCE ARB_NT/<INFO> button (top area; showing the short name of the selected species) |
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| 29 | ARB_NT/Species/Species Information |
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| 30 | ARB_NT/Species/Search (click into result list) |
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| 31 | ARB_NT/Info mode button (in the button bar on the left side) |
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| 32 | |
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| 33 | DESCRIPTION Displays species information stored within the 'fields' (see |
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| 34 | LINK{glossary.hlp}). |
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| 35 | |
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| 36 | The particular 'species' (see LINK{glossary.hlp}) |
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| 37 | can be 'marked' or 'unmarked' (see LINK{glossary.hlp}) |
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| 38 | by pressing the checkbox after the 'Marked?' prompt. |
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| 39 | |
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| 40 | Editing of 'field' entries is enabled or prevented by |
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| 41 | pressing the 'Edit enabled?' checkbox. |
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| 42 | |
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| 43 | The entries of a 'field' are modified by choosing it from |
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| 44 | the 'DATABASE FIELDS' subwindow and modifying the entries |
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| 45 | displayed in the 'Edit box' subwindow. |
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| 46 | |
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| 47 | NOTES The 'SEARCH & QUERY' window can be displayed by pressing the <SEARCH> |
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| 48 | button. |
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| 49 | |
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| 50 | For modification of 'field' entries, a protection level |
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| 51 | has to be selected from the Protection menu of the main |
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| 52 | window (ARB_NT/Protection) equal to or higher than that |
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| 53 | assigned to the selected 'field' |
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| 54 | |
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| 55 | Cut and paste of the window system can be used in the 'Edit |
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| 56 | box' subwindow. This provides is an easy way to export/import |
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| 57 | sequences. |
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| 58 | Use the left mouse button to mark (cut is done automatically). |
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| 59 | Then use the middle mouse button to paste. |
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| 60 | |
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| 61 | SECTION Locking information window to a specific species |
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| 62 | |
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| 63 | When you open this window it will always show the information of |
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| 64 | the currently selected species. That means if you select another species (in |
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| 65 | the tree or in the editor) this window will follow your selection and display |
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| 66 | the information of the newly selected species. |
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| 67 | |
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| 68 | By pressing the 'New window...' button you will open a second information |
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| 69 | window which will be LOCKED TO the currently selected species. |
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| 70 | That second information window will NOT FOLLOW the selected species (as the |
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| 71 | primary information window does). Instead of the 'New window...' button, it |
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| 72 | shows an 'Update' button. Pressing the 'Update' button will change the |
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| 73 | displayed species to the species currently selected. |
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| 74 | |
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| 75 | You can distinguish the two types of information windows by their window |
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| 76 | title: the LOCKED infowindow contains the name of the LOCKED species, the |
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| 77 | "normal" infowindow is entitled 'Species Information'. |
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| 78 | |
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| 79 | |
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| 80 | SECTION STANDARD ENTRIES |
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| 81 | |
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| 82 | The following database entries have a special meaning in ARB: |
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| 83 | |
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| 84 | name unique species ID (generated by ARB) |
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| 85 | full_name full species name (generated by the user) |
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| 86 | acc Accession number (automatically generated by ARB if missing) |
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| 87 | |
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| 88 | Entries relevant for DNA->AminoAcid encoding: |
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| 89 | |
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| 90 | codon_start contains the base inside the gene at which the |
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| 91 | first codon starts (valid: 1,2,3) |
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| 92 | if this entry is missing 1 is assumed |
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| 93 | transl_table the number of the translation table to be used |
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| 94 | (1 = Standard, ...) |
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| 95 | |
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| 96 | Commonly used database entries (e.g. by import/export): |
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| 97 | |
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| 98 | entry EMBL Genebank |
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| 99 | |
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| 100 | author RA REFERENCE/AUTHORS |
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| 101 | title RT REFERENCE/TITLE |
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| 102 | journal RL REFERENCE/JOURNAL |
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| 103 | refgrp RG REFERENCE/CONSRTM |
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| 104 | pubmed_id RX PUBMED REFERENCE/PUBMED |
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| 105 | medline_id RX MEDLINE REFERENCE/PUBMED |
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| 106 | version SV VERSION |
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| 107 | keywd KW KEYWORDS |
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| 108 | tax OC ORGANISM |
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| 109 | comment CC COMMENT |
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| 110 | |
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| 111 | description DE |
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| 112 | auth_comm RC |
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| 113 | nuc_rp RP |
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| 114 | db_xref DR |
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| 115 | date DT |
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| 116 | organelle OG |
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| 117 | definition DEFINITION |
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| 118 | |
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| 119 | EXAMPLES Update the 'full_name' 'Pseudomonas cepacia' to 'Comamonas |
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| 120 | cepacia': |
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| 121 | Select FIELDS: 'full_name' |
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| 122 | Move cursor into the 'Edit box' subwindow |
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| 123 | Delete: 'Pseudomonas' |
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| 124 | Type: 'Comamonas' |
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| 125 | |
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| 126 | WARNINGS It is recommended to reset the protection level after |
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| 127 | modifying entries to prevent unintentional modification |
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| 128 | or loss of data. |
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| 129 | |
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| 130 | BUGS No bugs known |
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