source: branches/lib/HELP_SOURCE/source/sp_info.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 5.3 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_ntree.hlp
5UP      arb_edit4.hlp
6UP      mode_info.hlp
7UP      security.hlp
8UP      sp_search.hlp
9UP      Protection.hlp
10
11#       sub topics:
12SUB     spaf_reorder.hlp
13SUB     spaf_delete.hlp
14SUB     spaf_create.hlp
15SUB     spa_delete.hlp
16SUB     spa_rename.hlp
17SUB     spa_copy.hlp
18SUB     spa_create.hlp
19SUB     sp_sp_2_ext.hlp
20SUB     scandb.hlp
21
22
23# format described in ../help.readme
24
25
26TITLE           SPECIES INFORMATION
27
28OCCURRENCE      ARB_NT/<INFO> button (top area; showing the short name of the selected species)
29                ARB_NT/Species/Species Information
30                ARB_NT/Species/Search/Info button
31                ARB_NT/Info mode button (in the button bar on the left side)
32                ARB_EDIT4/Info mode button
33                ARB_PARSIMONY/Info mode button
34
35DESCRIPTION     Displays species information stored within the 'fields' (see
36                LINK{glossary.hlp}).
37
38                The particular 'species' (see LINK{glossary.hlp})
39                can be 'marked' or 'unmarked' (see LINK{glossary.hlp})
40                by pressing the checkbox after the 'Marked?' prompt.
41
42                Editing of 'field' entries is enabled or prevented by
43                pressing the 'Edit enabled?' checkbox.
44
45                The entries of a 'field' are modified by choosing it from
46                the 'DATABASE FIELDS' subwindow and modifying the entries
47                displayed in the 'Edit box' subwindow.
48
49NOTES           The 'SEARCH & QUERY' window can be displayed by pressing the <SEARCH>
50                button.
51
52                For modification of 'field' entries, a protection level
53                has to be selected from the Protection menu of the main
54                window (ARB_NT/Protection) equal to or higher than that
55                assigned to the selected 'field'
56
57                LINK{copyNpaste.hlp} can be used in the 'Edit box' subwindow.
58                This provides is easy way to manually export/import (sequence) data.
59
60SECTION         Locking information window to a specific species
61
62                When you open this window it will always show the information of
63                the currently LINK{selected.hlp}. That means if you select another species (in
64                the tree or in the editor) this window will follow your selection and display
65                the information of the newly selected species.
66
67                By pressing the 'Lock view' button you will open a second information
68                window which will be LOCKED TO the currently selected species.
69                That second information window will NOT FOLLOW the selected species (as the
70                primary information window does). Instead of the 'Lock view' button, it
71                shows an 'Update' button. Pressing the 'Update' button will change the
72                displayed species to the species currently selected.
73
74                You can distinguish the two types of information windows by their window
75                title and by the color of the area showing the ID of the selected species.
76
77
78SECTION         STANDARD ENTRIES
79
80                The following database entries have a special meaning in ARB:
81
82                name            unique species ID (generated by ARB)
83                full_name       full species name (generated by the user)
84                acc             Accession number (automatically generated by ARB if missing)
85
86                Entries relevant for DNA->AminoAcid encoding:
87
88                codon_start     contains the base inside the gene at which the
89                                first codon starts (valid: 1,2,3)
90                                if this entry is missing 1 is assumed
91                transl_table    the number of the translation table to be used
92                                (1 = Standard, ...)
93
94                Commonly used database entries (e.g. by import/export):
95
96                entry           EMBL           Genebank
97
98                author          RA             REFERENCE/AUTHORS
99                title           RT             REFERENCE/TITLE
100                journal         RL             REFERENCE/JOURNAL
101                refgrp          RG             REFERENCE/CONSRTM
102                pubmed_id       RX PUBMED      REFERENCE/PUBMED
103                medline_id      RX MEDLINE     REFERENCE/PUBMED
104                version         SV             VERSION
105                keywd           KW             KEYWORDS
106                tax             OC             ORGANISM
107                comment         CC             COMMENT
108
109                description     DE
110                auth_comm       RC
111                nuc_rp          RP
112                db_xref         DR             DBLINK
113                date            DT
114                organelle       OG
115                definition                     DEFINITION
116
117EXAMPLES        Update the 'full_name' 'Pseudomonas cepacia' to 'Comamonas
118                cepacia':
119                        Select FIELDS:  'full_name'
120                        Move cursor into the 'Edit box' subwindow
121                        Delete:         'Pseudomonas'
122                        Type:           'Comamonas'
123
124WARNINGS        It is recommended to reset the protection level after
125                modifying entries to prevent unintentional modification
126                or loss of data.
127
128BUGS            No bugs known
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