2 <head><title>Alignment Window Menus</title></head>
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5 <p><strong>Alignment Window Edit Menu</strong></p>
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6 <strong>Edit</strong>
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8 <li><strong>Undo</strong><em><br>
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9 This will undo any edits you make to the alignment. This applies to insertion
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10 or deletion of gaps, cutting residues or sequences from the alignment or pasting
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11 sequences to the current alignment or sorting the alignment. <strong>NOTE:</strong>
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12 It DOES NOT undo colour changes, adjustments to group sizes, or changes to
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13 the annotation panel. </em></li>
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14 <li><strong>Redo<br>
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15 </strong><em>Any actions which you undo can be redone using redo. </em></li>
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17 </strong><em>This will make a copy of the currently selected residues before
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18 removing them from your alignment. Click on a sequence name if you wish to
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19 select a whole sequence. <br>
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20 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
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21 <li><strong>Copy</strong><br>
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22 <em>Copies the currently selected residues to the system clipboard - you can
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23 also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX).
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25 If you try to paste the clipboard contents to a text editor, you will see
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26 the format of the copied residues FASTA.</em></li>
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27 <li><strong>Paste </strong>
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29 <li><strong>To New Alignment<br>
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30 </strong><em>A new alignment window will be created from sequences previously
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31 copied or cut to the system clipboard. <br>
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32 Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>
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33 <li><strong>Add To This Alignment<br>
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34 </strong><em>Copied sequences from another alignment window can be added
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35 to the current Jalview alignment. </em></li>
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38 <li><strong>Delete<br>
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39 </strong><em>This will delete the currently selected residues without copying
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40 them to the clipboard. Like the other edit operations, this can be undone
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41 with <strong>Undo</strong>.</em></li>
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42 <li><strong>Select All<br>
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43 </strong><em>Selects all the sequences and residues in the alignment. <br>
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44 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>
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45 <li><strong>Deselect All<br>
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46 </strong><em>Removes the current selection box (red dashed box) from the alignment
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47 window. All selected sequences, residues and marked columns will be deselected.
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49 Use <ESCAPE> to deselect all.</em></li>
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50 <li><strong>Invert Sequence Selection<br>
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51 </strong><em>Any sequence ids currently not selected will replace the current
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52 selection. </em></li>
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53 <li><strong>Invert Column Selection<br>
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54 </strong><em>Any columns currently not selected will replace the current column
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55 selection. </em></li>
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56 <li><strong>Undefine Groups<br>
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57 </strong><em>The alignment will be reset with no defined groups.<br>
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58 <strong>WARNING</strong>: This cannot be undone.</em></li>
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59 <li><strong>Remove Left<br>
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60 </strong><em>If the alignment has marked columns, the alignment will be trimmed
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61 to the left of the leftmost marked column. To mark a column, mouse click the
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62 scale bar above the alignment. Click again to unmark a column, or select "Deselect
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63 All" to deselect all columns.</em></li>
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64 <li><strong>Remove Right<br>
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65 </strong><em>If the alignment has marked columns, the alignment will be trimmed
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66 to the left of the leftmost marked column. To mark a column, mouse click the
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67 scale bar above the alignment. Click again to unmark a column, or select "Deselect
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68 All" to deselect all columns.</em></li>
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69 <li><strong>Remove Empty Columns<br>
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70 </strong><em>All columns which only contain gap characters ("-",
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71 ".") will be deleted.<br>
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72 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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74 <li><strong>Remove All Gaps</strong><br>
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75 <em>Gap characters ("-", ".") will be deleted from the
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76 selected area of the alignment. If no selection is made, ALL the gaps in the
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77 alignment will be removed.<br>
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78 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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80 <li><strong>Remove Redundancy<br>
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81 </strong><em>Selecting this option brings up a window asking you to select
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82 a threshold. If the percentage identity between any two sequences (under the
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83 current alignment) exceeds this value then one of the sequences (the shorter)
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84 is discarded. Press the "Apply" button to remove redundant sequences.
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85 The "Undo" button will undo the last redundancy deletion.</em></li>
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86 <li><strong>Pad Gaps<br>
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87 </strong><em>When selected, the alignment will be kept at minimal width (so
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88 there no empty columns before or after the first or last aligned residue)
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89 and all sequences will be padded with gap characters to the before and after
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90 their terminating residues.<br>
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91 This switch is useful when making a tree using unaligned sequences and when
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92 working with alignment analysis programs which require 'properly aligned sequences'
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93 to be all the same length.<br>
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94 You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>.
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git://source.jalview.org / jalview.git / blob