*
* 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>
git://source.jalview.org / jalview.git / blobdiff