\r
<body>\r
<p><strong>Alignment Window Edit Menu</strong></p>\r
+<strong>Edit</strong> \r
<ul>\r
- <li><strong>Edit</strong></li>\r
+ <li><strong>Undo</strong><em><br>\r
+ This will undo any edits you make to the alignment. This applies to insertion \r
+ or deletion of gaps, cutting residues or sequences from the alignment or pasting \r
+ sequences to the current alignment or sorting the alignment. <strong>NOTE:</strong> \r
+ It DOES NOT undo colour changes, adjustments to group sizes, or changes to \r
+ the annotation panel. </em></li>\r
+ <li><strong>Redo<br>\r
+ </strong><em>Any actions which you undo can be redone using redo. </em></li>\r
+ <li><strong>Cut<br>\r
+ </strong><em>This will make a copy of the currently selected residues before \r
+ removing them from your alignment. Click on a sequence name if you wish to \r
+ select a whole sequence. <br>\r
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>\r
+ <li><strong>Copy</strong><br>\r
+ <em>Copies the currently selected residues to the system clipboard - you can \r
+ also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX). \r
+ <br>\r
+ If you try to paste the clipboard contents to a text editor, you will see \r
+ the format of the copied residues is a tab separated list</em><br>\r
+ NAME START_RES END_RES SEQUENCE </li>\r
+ <li><strong>Paste </strong> \r
+ <ul>\r
+ <li><strong>To New Alignment<br>\r
+ </strong><em>A new alignment window will be created from sequences previously \r
+ copied or cut to the system clipboard. <br>\r
+ Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>\r
+ <li><strong>Add To This Alignment<br>\r
+ </strong><em>Copied sequences from another alignment window can be added \r
+ to the current Jalview alignment. </em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Delete<br>\r
+ </strong><em>This will delete the currently selected residues without copying \r
+ them to the clipboard. Like the other edit operations, this can be undone \r
+ with <strong>Undo</strong>.</em></li>\r
+ <li><strong>Select All<br>\r
+ </strong><em>Selects all the sequences and residues in the alignment. <br>\r
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>\r
+ <li><strong>Deselect All<br>\r
+ </strong><em>Removes the current selection box (red dashed box) from the alignment \r
+ window. All selected sequences, residues and marked columns will be deselected. \r
+ </em><em> <br>\r
+ Use <ESCAPE> to deselect all.</em></li>\r
+ <li><strong>Invert Selection<br>\r
+ </strong><em>Any sequence ids currently not selected will replace the current \r
+ selection. </em></li>\r
+ <li><strong>Undefine Groups<br>\r
+ </strong><em>The alignment will be reset with no defined groups.<br>\r
+ <strong>WARNING</strong>: This cannot be undone.</em></li>\r
+ <li><strong>Remove Left<br>\r
+ </strong><em>If the alignment has marked columns, the alignment will be trimmed \r
+ to the left of the leftmost marked column. To mark a column, mouse click the \r
+ scale bar above the alignment. Click again to unmark a column, or select "Deselect \r
+ All" to deselect all columns.</em></li>\r
+ <li><strong>Remove Right<br>\r
+ </strong><em>If the alignment has marked columns, the alignment will be trimmed \r
+ to the left of the leftmost marked column. To mark a column, mouse click the \r
+ scale bar above the alignment. Click again to unmark a column, or select "Deselect \r
+ All" to deselect all columns.</em></li>\r
+ <li><strong>Remove Empty Columns<br>\r
+ </strong><em>All columns which only contain gap characters ("-", \r
+ ".") will be deleted.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ </em></li>\r
+ <li><strong>Remove All Gaps</strong><br>\r
+ <em>Gap characters ("-", ".") will be deleted from the \r
+ selected area of the alignment. If no selection is made, ALL the gaps in the \r
+ alignment will be removed.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ </em> </li>\r
+ <li><strong>Remove Redundancy<br>\r
+ </strong><em>Selecting this option brings up a window asking you to select \r
+ a threshold. If the percentage identity between any two sequences (under the \r
+ current alignment) exceeds this value then one of the sequences (the shorter) \r
+ is discarded. Press the "Apply" button to remove redundant sequences. \r
+ The "Undo" button will undo the last redundancy deletion.</em></li>\r
+ <li><strong>Pad Gaps<br>\r
+ </strong><em>Adds gaps to the end of all the sequences so they are all the \r
+ same length. This is useful for making a tree using unaligned sequences.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ </em></li>\r
</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Undo</strong><em><br>\r
- This will undo any edits you make to the alignment. This applies to insertion\r
- or deletion of gaps, cutting residues or sequences from the alignment or\r
- pasting sequences to the current alignment or sorting the\r
- alignment. <strong>NOTE:</strong> It DOES NOT undo colour\r
- changes, adjustments to group sizes, or changes to the annotation panel. <br>\r
- </em></li>\r
- <li><strong>Redo<br>\r
- </strong><em>Any actions which you undo can be redone using redo. <br>\r
- </em></li>\r
- <li><strong>Cut<br>\r
- </strong><em>This will make a copy of the currently selected residues before\r
- removing them from your alignment. Click on a sequence name if you wish\r
- to select a whole sequence. <br>\r
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.<br>\r
- </em></li>\r
- <li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system\r
- clipboard - you can also do this by pressing <CTRL> and C\r
- (<APPLE> and C on MacOSX). <br>\r
- If you try to paste the clipboard contents to a text editor, you will see\r
- the format of the copied residues is a tab separated list:<br>\r
-<pre>\r
-NAME START_RES END_RES SEQUENCE\r
-</pre><br>\r
- </em></li>\r
- <li><strong>Paste</strong>\r
- <ul>\r
- <li><strong>To New Alignment<br>\r
- </strong><em>A new alignment window will be created from sequences previously\r
- copied or cut to the system clipboard. <br>\r
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>\r
- <li><strong>Add To This Alignment<br>\r
- </strong><em>Copied sequences from another alignment window can be added\r
- to the current Jalview alignment. <br>\r
- </em><strong> </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues\r
- without copying them to the clipboard. Like the other edit\r
- operations, this can be undone with <strong>Undo</strong>.<br>\r
- </em></li>\r
- <li><strong>Select All<br>\r
- </strong><em>Selects all the sequences and residues in the alignment. <br>\r
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.<br>\r
- </em></li>\r
- <li><strong>Deselect All<br>\r
- </strong><em>Removes the current selection box (red dashed box) from the\r
- alignment window. All selected sequences, residues and marked columns will\r
- be deselected. </em><em> <br>\r
- Use <ESCAPE> to deselect all.<br>\r
- </em></li>\r
- <li><strong>Invert Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the current\r
- selection. <br>\r
- </em><strong> </strong></li>\r
- <li><strong>Undefine Groups<br>\r
- </strong><em>The alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:\r
- This cannot be undone.<br>\r
- </em></li>\r
- <li><strong>Remove Left<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be\r
- trimmed to the left of the leftmost marked column. To mark a column, mouse\r
- click the scale bar above the alignment. Click again to unmark a column,\r
- or select "Deselect All" to deselect all columns.<br>\r
- </em></li>\r
- <li><strong>Remove Right<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be\r
- trimmed to the left of the leftmost marked column. To mark a column, mouse\r
- click the scale bar above the alignment. Click again to unmark a column,\r
- or select "Deselect All" to deselect all columns.<br>\r
- </em></li>\r
- <li><strong>Remove Empty Columns<br>\r
- </strong><em>All columns which only contain gap characters ("-",\r
- ".") will be deleted.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
- </em><em><br>\r
- </em></li>\r
- <li><strong>Remove All Gaps</strong><br>\r
- <em><strong>All</strong> gap characters ("-", ".") will be deleted from\r
- the alignment.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
- <br>\r
- </em> </li>\r
- <li><strong>Remove Redundancy<br>\r
- </strong><em>Selecting this option brings up a window asking you to select\r
- a threshold. If the percentage identity between any two sequences\r
- (under the current alignment) exceeds this\r
- value then one of the sequences (the shorter) is discarded. Press the "Apply"\r
- button to remove redundant sequences. The "Undo" button will undo the last\r
- redundancy deletion.<br>\r
- </em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>Adds gaps to the end of all the sequences so they\r
- are all the same length. This is useful for making a tree using\r
- unaligned sequences.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
- </em></li>\r
- </ul>\r
-</blockquote>\r
+ <blockquote> </blockquote>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff