</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
<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>
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>
</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>
</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>
- <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>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>
git://source.jalview.org / jalview.git / blobdiff