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 alignment.hlp |
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5 | UP security.hlp |
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6 | UP helix.hlp |
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7 | UP ecoliref.hlp |
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8 | UP configuration.hlp |
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9 | |
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10 | #Please insert subtopic references (line starts with keyword SUB) |
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11 | SUB man_arb_edit4.hlp |
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12 | SUB arb_edit4.hlp |
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13 | SUB e4_search.hlp |
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14 | SUB e4_replace.hlp |
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15 | SUB e4_block.hlp |
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16 | SUB nekey_map.hlp |
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17 | SUB helixsym.hlp |
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18 | SUB pfold.hlp |
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19 | |
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20 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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21 | |
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22 | #************* Title of helpfile !! and start of real helpfile ******** |
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23 | |
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24 | TITLE ARB_EDIT4 - Sequence primary and secondary structure editor |
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25 | |
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26 | OCCURRENCE ARB_NT/Sequence/Edit marked sequences |
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27 | |
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28 | DESCRIPTION The editor allows you to view and modify the sequences of 'marked |
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29 | species' or 'a selection of species' and 'SAI' (sequence associated |
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30 | information) stored in the data base. |
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31 | Potential secondary structure is automatically checked |
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32 | and the information can be displayed with the primary structure. |
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33 | In addition, an online column statistic may help you find |
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34 | sequence and alignment errors. |
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35 | |
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36 | The editor permanently communicates with the database and |
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37 | other ARB tools. Every change made by the editor is immediately |
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38 | exported to the database. All sequence changes made by other |
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39 | ARB tools are exported to the editor every 5 seconds. |
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40 | |
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41 | Multiple editors can be used synchronously. |
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42 | |
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43 | |
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44 | Display: |
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45 | |
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46 | First Column: Name of sequences or name of groups. |
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47 | Second C. Protection level and subtype of sequence. |
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48 | Last c. Sequence and secondary structure and more. |
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49 | |
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50 | Cursor: |
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51 | |
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52 | The cursor can be moved using the mouse or the arrow |
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53 | keys. The current cursor positions with respect to the |
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54 | alignment and the E. coli sequence (there has to be an |
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55 | 'SAI' entry: ECOLI) are indicated after the 'Position' |
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56 | and 'E.coli' prompts in the upper part of the |
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57 | 'ARB_EDIT4' window. |
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58 | |
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59 | These 3 positions and the IUPAC-display refer to the position |
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60 | RIGHT of the cursor. |
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61 | |
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62 | Position counting now starts with 1 (too many people were |
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63 | confused about position counting starting at position 0). |
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64 | |
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65 | Moving entries: |
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66 | |
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67 | To move an individual entry, position the cursor on the |
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68 | name, keep the left mouse button pressed, move the entry |
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69 | to the desired position, and release the button. |
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70 | |
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71 | Any entry can be fixed (keeps its position while |
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72 | scrolling vertically) at the top of the editing area by |
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73 | moving it somewhere above the double line (=top area). |
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74 | |
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75 | Undo/Redo: |
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76 | |
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77 | This undoes/redoes everything you did. |
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78 | |
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79 | Jump: |
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80 | |
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81 | If you selected a species in any other ARB component |
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82 | (i.e. in the Tree or in the Search Hitlist), you can |
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83 | jump to the selected species using this button. |
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84 | |
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85 | In general the editor will automatically jump to the |
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86 | selected species, unless the species is in a folded group. |
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87 | In this case all necessary groups will be unfolded. |
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88 | |
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89 | Get: |
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90 | |
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91 | If the species is already in the editor 'Get' does the |
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92 | same as 'Jump'. If the species is NOT loaded in the editor |
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93 | it will be inserted into the group 'More Sequences'. |
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94 | |
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95 | If you like to load several species into the editor, mark |
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96 | those species and use 'ARB_EDIT4/Edit/Load marked species' |
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97 | |
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98 | Editing: |
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99 | |
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100 | Protection: |
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101 | |
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102 | To perform editing, the protection level of the particular |
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103 | entry ('EDIT/Set protection of selected species') has to |
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104 | be set below or equal the global protection level |
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105 | (use the 'Protect' button on the menuboard). |
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106 | |
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107 | Note: There are two global protection levels: one in |
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108 | edit-mode and another one in align-mode. |
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109 | |
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110 | Modes: |
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111 | |
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112 | ARB_EDIT4 supports 2 modes: Align-mode and Edit-mode. |
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113 | To toggle between these two modes use the 'Align/Edit' |
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114 | button on the menuboard or press CTRL-E. |
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115 | |
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116 | Align-mode: |
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117 | |
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118 | Only gap symbols can be inserted ('-', '.' or |
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119 | 'Spc' key) or deleted ('Del' or 'Backspace' key) |
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120 | |
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121 | Sequence data cannot be modified - it only can be |
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122 | checked in this mode. Sequence check is performed |
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123 | by typing nucleotide (amino acid) symbols. |
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124 | Discrepancies between typed and existing symbols |
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125 | are indicated by beeping. |
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126 | |
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127 | Edit-mode: |
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128 | |
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129 | Edit-mode is divided into two submodes: Insert-mode |
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130 | and Replace-mode. Toggle between these submodes |
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131 | with the 'Insert/Replace' button on the menuboard |
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132 | or with CTRL-I. |
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133 | |
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134 | In Replace-mode inserted Nucleotides/gaps overwrite |
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135 | existing Nucleotides/gaps. |
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136 | In Insert-mode inserted Nucleotides/gaps do not |
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137 | overwrite, instead the whole sequence is shifted. |
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138 | |
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139 | Direction: |
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140 | |
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141 | ARB_EDIT4 should perform any editing function into both |
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142 | directions - forward and backward. To toggle the editing |
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143 | direction use the "5'->3'" button on the menuboard. |
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144 | |
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145 | Repeat editing functions: |
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146 | |
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147 | Nearly every editing function can be performed repeatedly |
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148 | by typing some digits before you perform the editing |
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149 | function. |
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150 | |
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151 | Example: '9-' inserts nine '-' |
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152 | |
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153 | If you need to insert digits, use the toggle in |
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154 | 'Properties/Options'. |
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155 | |
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156 | Key mapping: |
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157 | |
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158 | Nucleotide (amino acid) and gap symbols can be assigned |
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159 | to any of the letter and symbol keys by using the 'Key |
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160 | Mapping' facility ('Properties' menu). |
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161 | |
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162 | Moving nucleotide (amino acid) symbols: |
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163 | |
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164 | SHIFT + LEFT/RIGHT |
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165 | |
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166 | Push or pull a coherent sequence stretch next |
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167 | to the cursor. |
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168 | |
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169 | ALT + LEFT/RIGHT |
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170 | |
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171 | Move a single nucleotide (amino acid) symbol. |
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172 | |
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173 | If you move your cursor towards a gap, the next |
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174 | nucleotide (amino acid) symbol in movement |
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175 | direction is fetched and moved to the actual |
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176 | position. |
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177 | |
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178 | If you move your cursor towards a nucleotide |
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179 | (amino acid) symbol, it will jump aside the next |
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180 | nucleotide (amino acid) symbol. |
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181 | |
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182 | Other keys: |
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183 | |
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184 | CTRL+LEFT/RIGHT |
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185 | |
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186 | Jumps to the start of the next gap-region or non-gap-region. |
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187 | You may configure whether it always jumps over gap-regions. |
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188 | |
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189 | CTRL+UP/DOWN |
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190 | |
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191 | Like Ctrl-Left/Right, but vertical. |
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192 | |
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193 | HOME/END |
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194 | |
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195 | Jumps to the start/end of sequence. |
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196 | |
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197 | CTRL+HOME/END |
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198 | |
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199 | Jumps to the first/last sequence. |
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200 | |
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201 | Messages: |
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202 | |
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203 | Many (less serious) errors will not be announced by a popup |
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204 | window. Instead they appear at the small text window in the |
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205 | upper-right corner of the editor window. |
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206 | |
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207 | You can press one of the small buttons at the left side of this |
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208 | text window: |
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209 | |
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210 | - press the small lens to see more errors |
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211 | - press the small X to get rid of all errors |
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212 | |
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213 | EXAMPLES None |
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214 | |
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215 | NOTES You may use the META key instead of ALT (especially if there is no ALT key :) |
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216 | |
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217 | WARNINGS The key mappings may conflict with some window managers |
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218 | (eg. olvwm). Disable the CTRL-LEFT/RIGHT keys of the window |
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219 | manager. |
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220 | |
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221 | If you perform major database modifications such as |
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222 | |
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223 | - adding new SAIs |
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224 | |
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225 | you have to QUIT and restart the editor. |
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226 | |
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227 | BUGS - sometimes the editor crashes after aligning |
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228 | - some update problems (please report system and circumstances) |
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229 | (workaround: resize the editor window) |
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230 | |
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