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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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<head>
<title>Alignment Window Menus</title>
</head>
<body>
- <p>
- <strong>Alignment Window Menus</strong>
- </p>
- <ul>
+ <!-- NOTE: THIS PAGE COLLECTS TOGETHER THE INDIVIDUAL ALIGNMENT WINDOW MENU PAGES - DON"T EDIT INDIVIDUAL ENTRIES HERE! -->
+ <p>
+ <strong>Alignment Window Menus</strong>
+ </p>
+ <ul>
<li><strong>File</strong>
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows a
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>
+ <li><strong>FASTA</strong> </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>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>Phylip</strong></li>
+ <li><strong>JSON</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
+<li><strong>Page Setup ...</strong><br>
+ <em>Open the printing system's Page Setup dialog box, to
+ control page size, layout and orientation.</em></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>
+ <li><strong>SVG<br>
+ </strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
+ <li><strong>BioJS<br>
+ </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </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>
<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
+ 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
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
+ before you close - either from the Desktop's <strong>Save Project</strong> File menu option, or by using the <strong>Save
As</strong> menu.</em>
</li>
</ul></li>
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
+ the alignment will be kept at minimal width (so there are 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
+ sequences will be padded with gap characters 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
</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>Create Group (Control G)<br></strong>
- <em>Create a group containing the currently selected sequences.</em></li>
+ <li><a href="../features/search.html"><strong>Find... (Control F)</strong></a><br>
+ <em>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><strong>Select All (Control A)</strong><strong><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></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>Create Group (Control G)<br></strong>
+ <em>Create a group containing the currently selected sequences.</em></li>
<li><strong>Remove Group (Shift Control G)<br></strong>
- <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
- <li><strong>Make Groups for selection<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>
- <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>
+ <em>Ungroup the currently selected sequence group.</em></li>
+ <li><strong>Make Groups for selection<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 at marked columns.
+ </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><a
+ href="../features/columnFilterByAnnotation.html">Select/Hide Columns by Annotation</a></strong> <br />
+ <em>Select or Hide columns in the alignment according to
+ secondary structure, labels and values shown in alignment
+ annotation rows. </em></li>
</ul></li>
<li><strong>View</strong>
<ul>
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><em>Settings
- for the display of autocalculated annotation.</em>
- <ul>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, any modification to the current settings will be applied
- to all autocalculated annotation.</em></li>
- <li><strong>Show Consensus Histogram<br> </strong><em>
- Enable or disable the display of the histogram above the
- consensus sequence.</em></li>
- <li><strong>Show Consensus Logo<br> </strong><em> Enable
- or disable the display of the Consensus Logo above the consensus
- sequence.</em></li>
- <li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.</em></li>
- <li><strong>Group Conservation<br> </strong><em> When
- ticked, display a conservation row for all groups (only available
- for protein alignments).</em></li>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, display a consensus row for all groups.</em></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
+ <li><strong><a href="../features/featuresettings.html">Sequence
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
using the mouse. </em>
</li>
</ul></li>
+ <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+ <ul>
+ <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>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for example, Consensus,
+ or secondary structure prediction from alignment).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
+ or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
+ (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+ allowing you to make a manual ordering of the annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br> </strong><em>Settings
+ for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em>
+ Show autocalculated annotations above sequence-specific annotations.
+ Note this also applies to other annotations for the alignment, for example secondary
+ structure prediction from alignment.</em></li>
+ <li><strong>Show last<br></strong><em>
+ Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br> </strong><em> When
+ ticked, any modification to the current settings will be applied
+ to all autocalculated annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br> </strong><em>
+ Enable or disable the display of the histogram above the
+ consensus sequence.</em></li>
+ <li><strong>Show Consensus Logo<br> </strong><em> Enable
+ or disable the display of the Consensus Logo above the consensus
+ sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.</em></li>
+ <li><strong>Group Conservation<br> </strong><em> When
+ ticked, display a conservation row for all groups (only available
+ for protein alignments).</em></li>
+ <li><strong>Group Consensus<br> </strong><em> When
+ ticked, display a consensus row for all groups.</em></li>
+ </ul>
+ </li>
+ </ul>
+ </li>
<li><strong>Alignment Window Format Menu</strong>
<ul>
<li><strong>Font...<br> </strong><em>Opens the
</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>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>Neighbour Joining Using PAM250 </strong></li>
+ <li><strong>Neighbour Joining Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Neighbour Joining Using Blosum62 </strong></li>
+ <li><strong>Neighbour Joining Using % Identity</strong></li>
+ <li><strong>Average Distance Using PAM250 </strong></li>
+ <li><strong>Average Distance Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Average Distance Using Blosum62</strong></li>
+ <li><strong>Average Distance Using % Identity</strong></li>
+ </ul> <strong>Note: Since Version 2.8.1, a number of
+ additional similarity measures for tree calculation are
+ provided in this menu.</strong></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
+ a spatial clustering of the sequences based on similarity scores calculated with
+ the alignment. See <a href="../calculations/pca.html">Principal
Component Analysis</a>.</em> <br>
</li>
<li><strong>Extract Scores ... (optional)</strong><br> <em>This
<li><strong>Sort With New Tree</strong><br> <em>When
enabled, Jalview will automatically sort the alignment when a new
tree is calculated or loaded onto it.</em> <br></li>
- </ul></li>
+ <li><strong>Show Flanking Regions</strong><br> <em>Opens
+ a new alignment window showing any additional sequence data either
+ side of the current alignment. Useful in conjunction with 'Fetch
+ Database References' when the 'Trim Retrieved Sequences' option is
+ disabled to retrieve full length sequences for a set of aligned
+ peptides. </em></li>
+ </ul></li>
<li><strong>Web Service Menu</strong><br /> <em>This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
<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. <br />'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.</em><br></li>
+ submenu contains options for accessing 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 sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+ <ul>
+ <li>'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated with
+ sequences in the alignment. <br> <strong>Note: Disabling this
+ could cause out of memory errors when working with genomic
+ sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<</li>
+ </ul> Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em><br></li>
</ul>
<p>Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or
git://source.jalview.org / jalview.git / blobdiff