* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
---!>
-<head>
-<title>Alignment Window Menus</title>
-</head>
-
-<body>
-<p><strong>Alignment Window Menus</strong></p>
- <li><strong>File</strong>
- <ul>
- <li><strong>Fetch Sequence</strong><br>
- <em>Shows a dialog window in which you can select known ids from
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
- the European Bioinformatics Institute. See <a
- href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
- <li><strong>Add Sequences</strong><em><br>
- Add sequences to the visible alignment from file, URL, or cut &
- paste window </em></li>
- <li><strong>Reload</strong><em><br>
- Reloads the alignment from the original file, if available.<br>
- <strong>Warning: This will delete any edits, analyses and
- colourings applied since the alignment was last saved, and cannot be
- undone.</strong></em></li>
- <li><strong>Save (Control S)</strong><em><br>
- Saves the alignment to the file it was loaded from (if available), in
- the same format, updating the original in place. </em></li>
- <li><strong>Save As (Control Shift S)<br>
- </strong><em>Save the alignment to local file. A file selection window
- will open, use the "Files of type:" selection box to
- determine which <a href="../io/index.html">alignment format</a> to
- save as.</em></li>
- <li><strong>Output to Textbox<br>
- </strong><em>The alignment will be displayed in plain text in a new
- window, which you can "Copy and Paste" using the pull down
- menu, or your standard operating system copy and paste keys. The
- output window also has a <strong>"New Window"</strong>
- button to import the (possibly edited) text as a new alignment.<br>
- Select the format of the text by selecting one of the following menu
- items.</em>
- <ul>
- <li><strong>FASTA</strong> <em></em></li>
- <li><strong>MSF</strong></li>
- <li><strong>CLUSTAL</strong></li>
- <li><strong>BLC</strong></li>
- <li><strong>PIR</strong></li>
- <li><strong>PFAM</strong></li>
- </ul>
- </li>
- <li><strong>Print (Control P)<br>
- </strong><em>Jalview will print the alignment using the current fonts and
- colours of your alignment. If the alignment has annotations visible,
- these will be printed below the alignment. If the alignment is wrapped
- the number of residues per line of your alignment will depend on the
- paper width or your alignment window width, whichever is the smaller.
- </em></li>
- <li><strong>Export Image</strong> <em><br>
- Creates an alignment graphic with the current view's annotation,
- alignment background colours and group colours. If the alignment is <a
- href="../features/wrap.html">wrapped</a>, the output will also be
- wrapped and will have the same visible residue width as the open
- alignment. </em>
- <ul>
- <li><strong>HTML<br>
- </strong><em>Create a <a href="../io/export.html">web page</a> from your
- alignment.</em></li>
- <li><strong>EPS<br>
- </strong><em>Create an <a href="../io/export.html">Encapsulated
- Postscript</a> file from your alignment.</em></li>
- <li><strong>PNG<br>
- </strong><em>Create a <a href="../io/export.html">Portable Network
- Graphics</a> file from your alignment.</em></li>
- </ul>
- </li>
- <li><strong>Export Features</strong><em><br>
- All features visible on the alignment can be saved to file or
- displayed in a textbox in either Jalview or GFF format</em></li>
- <li><strong>Export Annotations</strong><em><br>
- All annotations visible on the alignment can be saved to file or
- displayed in a textbox in Jalview annotations format. </em></li>
- <li><strong>Load Associated Tree<br>
- </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
- trees</a> stored in the Newick file format, and associate them with the
- alignment. Note: the ids of the tree file and your alignment MUST be
- the same.</em></li>
- <li><strong>Load Features / Annotations<br>
- </strong><em>Load files describing precalculated <a
- href="../features/featuresFormat.html">sequence features</a> or <a
- href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
- <li><strong>Close (Control W)</strong><br>
- <em>Close the alignment window. Make sure you have saved your
- alignment before you close - either as a Jalview project or by using
- the <strong>Save As</strong> menu.</em></li>
- </ul>
- </li>
- <li><strong>Edit</strong>
- <ul>
- <li><strong>Undo (Control Z)</strong><em><br>
- This will undo any edits you make to the alignment. This applies to
- insertion or deletion of gaps, cutting residues or sequences from the
- alignment or pasting sequences to the current alignment or sorting the
- alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
- adjustments to group sizes, or changes to the annotation panel. </em></li>
- <li><strong>Redo (Control Y)<br>
- </strong><em>Any actions which you undo can be redone using redo. </em></li>
- <li><strong>Cut (Control X)<br>
- </strong><em>This will make a copy of the currently selected residues
- before removing them from your alignment. Click on a sequence name if
- you wish to select a whole sequence. <br>
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
- <li><strong>Copy (Control C)</strong><br>
- <em>Copies the currently selected residues to the system
- clipboard - you can also do this by pressing <CTRL> and C
- (<APPLE> and C on MacOSX). <br>
- If you try to paste the clipboard contents to a text editor, you will
- see the format of the copied residues FASTA.</em></li>
- <li><strong>Paste </strong>
- <ul>
- <li><strong>To New Alignment (Control Shift V)<br>
- </strong><em>A new alignment window will be created from sequences
- previously copied or cut to the system clipboard. <br>
- Use <CTRL> and <SHIFT> and V(<APPLE> and
- <SHIFT;> and and V on MacOSX) to paste.</em></li>
- <li><strong>Add To This Alignment (Control V)<br>
- </strong><em>Copied sequences from another alignment window can be added
- to the current Jalview alignment. </em></li>
- </ul>
- </li>
- <li><strong>Delete (Backspace)<br>
- </strong><em>This will delete the currently selected residues without
- copying them to the clipboard. Like the other edit operations, this
- can be undone with <strong>Undo</strong>.</em></li>
- <li><strong>Remove Left (Control L)<br>
- </strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the left of the leftmost marked column. To mark a column,
- mouse click the scale bar above the alignment. Click again to unmark a
- column, or select "Deselect All" to deselect all columns.</em></li>
- <li><strong>Remove Right (Control R)<br>
- </strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the left of the leftmost marked column. To mark a column,
- mouse click the scale bar above the alignment. Click again to unmark a
- column, or select "Deselect All" to deselect all columns.</em></li>
- <li><strong>Remove Empty Columns (Control E)<br>
- </strong><em>All columns which only contain gap characters ("-",
- ".") will be deleted.<br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>. </em></li>
- <li><strong>Remove All Gaps (Control Shift E)</strong><br>
- <em>Gap characters ("-", ".") will be deleted
- from the selected area of the alignment. If no selection is made, ALL
- the gaps in the alignment will be removed.<br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>. </em></li>
- <li><strong>Remove Redundancy (Control D)<br>
- </strong><em>Selecting this option brings up a window asking you to select
- a threshold. If the percentage identity between any two sequences
- (under the current alignment) exceeds this value then one of the
- sequences (the shorter) is discarded. Press the "Apply"
- button to remove redundant sequences. The "Undo" button will
- undo the last redundancy deletion.</em></li>
- <li><strong>Pad Gaps<br>
- </strong><em>When selected, the alignment will be kept at minimal width
- (so there no empty columns before or after the first or last aligned
- residue) and all sequences will be padded with gap characters to the
- before and after their terminating residues.<br>
- This switch is useful when making a tree using unaligned sequences and
- when working with alignment analysis programs which require 'properly
- aligned sequences' to be all the same length.<br>
- You may set the default for <strong>Pad Gaps</strong> in the <a
- href="../features/preferences.html">preferences</a>. </em></li>
- </ul>
- </li>
- <li><strong>Select</strong>
- <ul>
- <li><strong><a href="../features/search.html">Find...
- (Control F)</a></strong><em><br>
- Opens the Find dialog box to search for residues, sequence name or
- residue position within the alignment and create new sequence features
- from the queries. </em></li>
- <li><strong>Select All (Control A)<br>
- </strong><em>Selects all the sequences and residues in the alignment. <br>
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select
- all.</em></li>
- <li><strong>Deselect All (Escape)<br>
- </strong><em>Removes the current selection box (red dashed box) from the
- alignment window. All selected sequences, residues and marked columns
- will be deselected. </em><em> <br>
- Use <ESCAPE> to deselect all.</em></li>
- <li><strong>Invert Sequence Selection (Control I)<br>
- </strong><em>Any sequence ids currently not selected will replace the
- current selection. </em></li>
- <li><strong>Invert Column Selection (Control Alt I)<br>
- </strong><em>Any columns currently not selected will replace the current
- column selection. </em></li>
- <li><strong>Undefine Groups (Control U)<br>
- </strong><em>The alignment will be reset with no defined groups.<br>
- <strong>WARNING</strong>: This cannot be undone.</em></li>
- <li><strong>Make Groups<br/></strong>
- <em>The currently selected groups of the alignment will be
- subdivided according to the contents of the currently selected region.
- <br/>Use this to subdivide an alignment based on the
- different combinations of residues observed at specific
- positions. (new in jalview 2.5)</em></li>
- </ul>
- </li>
- <li><strong>View</strong>
- <ul>
- <li><strong>New View (Control T)</strong><em><br>
- Creates a new view from the current alignment view. </em></li>
- <li><strong>Expand Views (X)</strong><em><br>
- Display each view associated with the alignment in its own alignment
- window, allowing several views to be displayed simultaneously. </em></li>
- <li><strong>Gather Views (G)</strong><em><br>
- Each view associated with the alignment will be displayed within its
- own tab on the current alignment window. </em></li>
- <li><strong>Show→(all Columns / Sequences / Sequences and Columns)</strong><em><br>
- All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
- <li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region )</strong><em><br>
- Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
- <li><strong>Automatic Scrolling<br>
- </strong><em>When selected, the view will automatically scroll to display the
- highlighted sequence position corresponding to the position under the mouse
- pointer in a linked alignment or structure view.</em>
- </li>
- <li><strong>Show Annotations<br>
- </strong><em>If this is selected the "Annotation Panel" will be
- displayed below the alignment. The default setting is to display the
- conservation calculation, quality calculation and consensus values as
- bar charts. </em></li>
- <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
- <ul><li>
- <strong>Apply to all groups<br></strong>
- When ticked, any modification to the current settings will be applied to all autocalculated annotation.
- </li>
- <li>
- <strong>Show Consensus Histogram<br></strong>
- Enable or disable the display of the histogram above the consensus sequence.
- </li>
- <li>
- <strong>Show Consensus Profile<br></strong>
- Enable or disable the display of the sequence logo above the consensus sequence.
- </li>
- <li>
- <strong>Group Conservation<br></strong>
- When ticked, display a conservation row for all groups (only available for protein alignments).
- </li>
- <li>
- <strong>Apply to all groups<br></strong>
- When ticked, display a consensus row for all groups.
- </li>
- </ul>
- </li>
- <li><strong>Show Sequence Features</strong><br>
- <em>Show or hide sequence features on this alignment.</em></li>
- <li><strong><a href="../features/featuresettings.html">Seqence
- Feature Settings...</a></strong><em><br>
- <em>Opens the Sequence Feature Settings dialog box to control the
- colour and display of sequence features on the alignment, and
- configure and retrieve features from DAS annotation servers.</em></li>
- <li><strong>Sequence ID Tooltip</strong><em> (application only)
- <br>This submenu's options allow the inclusion or exclusion of
- non-positional sequence features or database cross references
- from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
- <li><strong>Alignment Properties...<br/>
- </strong><em>Displays some simple statistics computed for the
- current alignment view and any named properties defined on the
- whole alignment.</em></li>
- <li><strong><a href="../features/overview.html">Overview
- Window</a><br>
- </strong><em>A scaled version of the alignment will be displayed in a
- small window. A red box will indicate the currently visible area of
- the alignment. Move the visible region using the mouse. </em></li>
- </ul>
- </li>
- <li><strong>Alignment Window Format Menu</strong>
- <ul>
- <li><strong>Font...<br>
- </strong><em>Opens the "Choose Font" dialog box, in order to
- change the font of the display and enable or disable 'smooth fonts'
- (anti-aliasing) for faster alignment rendering. </em></li>
- <li><strong>Wrap<br>
- </strong><em>When ticked, the alignment display is "<a
- href="../features/wrap.html">wrapped</a>" to the width of the
- alignment window. This is useful if your alignment has only a few
- sequences to view its full width at once.<br>
- Additional options for display of sequence numbering and scales are
- also visible in wrapped layout mode:<br>
- <ul>
- <li><strong>Scale Above</strong><br>
- Show the alignment column position scale.</li>
- <li><strong>Scale Left</strong><br>
- Show the sequence position for the first aligned residue in each row
- in the left column of the alignment.</li>
- <li><strong>Scale Right</strong><br>
- Show the sequence position for the last aligned residue in each row
- in the right-most column of the alignment.</li>
- <li><strong>Show Sequence Limits<br>
- </strong><em>If this box is selected the sequence name will have the start
- and end position of the sequence appended to the name, in the format
- NAME/START-END</em></li>
- <li><strong>Right Align Sequence ID<br>
- </strong><em>If this box is selected then the sequence names displayed in
- the sequence label area will be aligned against the left-hand edge of
- the alignment display, rather than the left-hand edge of the alignment
- window.</li>
- <li><strong>Show Hidden Markers<br>
- </strong><em>When this box is selected, positions in the alignment where
- rows and columns are hidden will be marked by blue arrows.</li>
- <li><strong>Boxes</strong><em><br>
- If this is selected the background of a residue will be coloured using
- the selected background colour. Useful if used in conjunction with
- "Colour Text." </em></li>
- <li><strong>Text<br>
- </strong><em>If this is selected the residues will be displayed using the
- standard 1 character amino acid alphabet.</em></li>
- <li><strong>Colour Text<br>
- </strong><em>If this is selected the residues will be coloured according
- to the background colour associated with that residue. The colour is
- slightly darker than background so the amino acid symbol remains
- visible. </em></li>
- <li><strong>Show Gaps<br>
- </strong><em>When this is selected, gap characters will be displayed as
- "." or "-". If unselected, then gap characters
- will appear as blank spaces. <br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>.</em></li>
- <li><strong>Centre Annotation Labels<br>
- </strong><em>Select this to center labels along an annotation row
- relative to their associated column (default is off, i.e. left-justified).</em></li>
- <li><strong>Show Unconserved<br>
- </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
- </em></li>
-
- </ul>
- <li><strong>Colour</strong>
- <ul>
- <li><strong>Apply Colour To All Groups<br>
- </strong><em>If this is selected, any changes made to the background
- colour will be applied to all currently defined groups.<br>
- </em></li>
- <li><strong><a href="../colourSchemes/textcolour.html">Colour
- Text...</a></strong><em><br>
- Opens the Colour Text dialog box to set a different text colour for
- light and dark background, and the intensity threshold for transition
- between them. </em></li>
- <li>Colour Scheme options: <strong>None, ClustalX,
- Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity,
- Helix Propensity, Strand Propensity, Turn Propensity, Buried Index,
- Nucleotide, User Defined<br>
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for a
- description of all colour schemes.</em><br>
- </li>
- <li><strong>By Conservation<br>
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
- by Conservation</a>.</em><br>
- </li>
- <li><strong>Modify Conservation Threshold<br>
- </strong><em>Use this to display the conservation threshold slider window.
- Useful if the window has been closed, or if the 'by conservation'
- option appears to be doing nothing!</em><br>
- </li>
- <li><strong>Above Identity Threshold<br>
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above
- Percentage Identity</a></em><strong>.<br>
- </strong></li>
- <li><strong>Modify Identity Threshold<br>
- </strong><em>Use this to set the threshold value for colouring above
- Identity. Useful if the window has been closed.<br>
- </em></li>
- <li><strong>By Annotation</strong><br>
- <em>Colours the alignment on a per-column value from a specified
- annotation. See <a href="../colourSchemes/annotationColouring.html">Annotation
- Colouring</a>.</em><br>
- </li>
- </ul>
- </li>
- <li><strong>Calculate</strong>
- <ul>
- <li><strong>Sort </strong>
- <ul>
- <li><strong>by ID</strong><em><br>
- This will sort the sequences according to sequence name. If the sort
- is repeated, the order of the sorted sequences will be inverted. </em></li>
- <li><strong>by Length</strong><em><br>
- This will sort the sequences according to their length (excluding gap characters). If the sort is
- repeated, the order of the sorted sequences will be inverted. </em></li>
- <li><strong>by Group</strong><strong><br>
- </strong><em>This will sort the sequences according to sequence name. If
- the sort is repeated, the order of the sorted sequences will be
- inverted. </em><strong></strong></li>
- <li><strong>by Pairwise Identity<br>
- </strong><em>This will sort the selected sequences by their percentage
- identity to the consensus sequence. The most similar sequence is put
- at the top. </em></li>
- <li><em>The <a href="../calculations/sorting.html">Sort
- menu</a> will have some additional options if you have just done a
- multiple alignment calculation, or opened a tree viewer window.</em><br>
- </li>
- </ul>
- </li>
- <li><strong>Calculate Tree </strong> <br>
- <em>Functions for calculating trees on the alignment or the
- currently selected region. See <a href="../calculations/tree.html">calculating
- trees</a>.</em>
- <ul>
- <li><strong>Average Distance Using % Identity</strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Neighbour Joining Using Blosum62<br>
- </strong></li>
- </ul>
- </li>
- <li><strong>Pairwise Alignments</strong><br>
- <em>Applies Smith and Waterman algorithm to selected sequences.
- See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
- </li>
- <li><strong>Principal Component Analysis</strong><br>
- <em>Shows a spatial clustering of the sequences based on the
- BLOSUM62 scores in the alignment. See <a
- href="../calculations/pca.html">Principal Component Analysis</a>.</em> <br>
- </li>
- <li><strong>Extract Scores ... (optional)</strong><br>
- <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
- When selected, these numbers are parsed into sequence associated annotation which can
- then be used to sort the alignment via the Sort by→Score menu.</em> <br>
- </li>
- <li><strong>Autocalculate Consensus</strong><br>
- <em>For large alignments it can be useful to deselect
- "Autocalculate Consensus" when editing. This prevents the
- sometimes lengthy calculations performed after each sequence edit.</em> <br>
- </li>
- </ul>
- </li>
- <li><strong>Web Service<br>
- </strong>
- <ul><li><strong>Fetch DB References</strong><br>
- <em>This will use any of the database services that Jalview is aware
- of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
- to verify the sequence and retrieve all database cross references and PDB ids
- associated with all or just the selected sequences in the alignment.</em><br>
- </li>
- </ul>
- <em>Selecting one of the following menu items starts a remote
- service on compute facilities at the University of Dundee. You need a
- continuous network connection in order to use these services through
- Jalview. </em>
- <ul>
- <li><strong>Alignment</strong>
- <ul>
- <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
- <em> Submits all, or just the currently selected sequences for
- alignment with clustal W.</em></li>
- <li><strong>ClustalW Multiple Sequence Alignment
- Realign</strong><br>
- <em> Submits the alignment or currently selected region for
- re-alignment with clustal W. Use this if you have added some new
- sequences to an existing alignment.</em></li>
- <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
- <em>Submits all, or just the currently selected region for
- alignment with MAFFT. </em></li>
- <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
- <em> Submits all, or just the currently selected sequences for
- alignment using Muscle. Do not use this if you are working with
- nucleic acid sequences.</em></li>
- </ul>
- </li>
- <li><strong>Secondary Structure Prediction</strong>
- <ul>
- <li><strong>JPred Secondary Structure Prediction</strong><br>
- <em>Secondary structure prediction by network consensus. The
- behaviour of this calculation depends on the current selection: </em></li>
- <li><em>If nothing is selected, and the displayed sequences
- appear to be aligned, then a JNet prediction will be run for the
- first sequence in the alignment, using the current alignment.
- Otherwise the first sequence will be submitted for prediction. </em></li>
- <li><em>If just one sequence (or a region on one sequence)
- has been selected, it will be submitted to the automatic JNet
- prediction server for homolog detection and prediction. </em></li>
- <li><em>If a set of sequences are selected, and they appear
- to be aligned, then the alignment will be used for a Jnet prediction
- on the <strong>first</strong> sequence in the set (that is, the one
- that appears first in the alignment window). </em></li>
- </ul>
- </li>
- </ul>
- </li>
-</ul>
-</body>
-</html>
+-->
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