-<html>\r
-<head>\r
-<title>Colour Schemes</title>\r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: "Courier New", Courier, mono;\r
- font-style: normal;\r
- font-size: medium;\r
-}\r
--->\r
-</style>\r
-</head>\r
-<body>\r
-<p><strong>Colour schemes</strong></p>\r
-<p>Jalview allows the user to set a background colour for the whole alignment\r
- and also set the colour of defined groups within the alignment. </p>\r
-<p>To change the background colour, simply select the colour from the "Colour"\r
- menu.</p>\r
-<p>To change the colour of a group, right click on any residue within a group\r
- and use the popup menu to define the group colour. </p>\r
-<p>At the top of the "Colour" menu the tick box "Apply Background \r
- Colour to all groups". This is automatically ticked as default and means \r
- the chosen colour will be applied to all existing groups. If you wish to maintain \r
- the colour scheme for defined groups, make sure you deselect this option before \r
- changing the background colour.</p>\r
- \r
-<div align="center"> \r
- <p> </p><table border="1">\r
- <tr> \r
- <td><table border="1">\r
- <tr> \r
- <td nowrap></td>\r
- <td>A</td>\r
- <td>R</td>\r
- <td>N</td>\r
- <td>D</td>\r
- <td>C</td>\r
- <td>Q</td>\r
- <td>E</td>\r
- <td>G</td>\r
- <td>H</td>\r
- <td>I</td>\r
- <td>L</td>\r
- <td>K</td>\r
- <td>M</td>\r
- <td>F</td>\r
- <td>P</td>\r
- <td>S</td>\r
- <td>T</td>\r
- <td>W</td>\r
- <td>Y</td>\r
- <td>V</td>\r
- <td>B</td>\r
- <td>X</td>\r
- <td>Z</td>\r
- </tr>\r
- <tr> \r
- <td height="24">Clustal</td>\r
- <td bgcolor="#80a0f0"></td>\r
- <td bgcolor="#f01505"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#c048c0"></td>\r
- <td bgcolor="#f08080"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#c048c0"></td>\r
- <td bgcolor="#f09048"></td>\r
- <td bgcolor="#15a4a4"></td>\r
- <td bgcolor="#80a0f0"></td>\r
- <td bgcolor="#80a0f0"></td>\r
- <td bgcolor="#f01505"></td>\r
- <td bgcolor="#80a0f0"></td>\r
- <td bgcolor="#80a0f0"></td>\r
- <td bgcolor="#ffff00"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#80a0f0"></td>\r
- <td bgcolor="#15a4a4"></td>\r
- <td bgcolor="#80a0f0"></td>\r
- <td></td>\r
- <td></td>\r
- <td></td>\r
- </tr>\r
- <tr> \r
- <td height="24">Zappo</td>\r
- <td bgcolor="#ffafaf"></td>\r
- <td bgcolor="#6464ff"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#ff0000"></td>\r
- <td bgcolor="#ffff00"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#ff0000"></td>\r
- <td bgcolor="#ff00ff"></td>\r
- <td bgcolor="#6464ff"></td>\r
- <td bgcolor="#ffafaf"></td>\r
- <td bgcolor="#ffafaf"></td>\r
- <td bgcolor="#6464ff"></td>\r
- <td bgcolor="#ffafaf"></td>\r
- <td bgcolor="#ffc800"></td>\r
- <td bgcolor="#ff00ff"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#ffc800"></td>\r
- <td bgcolor="#ffc800"></td>\r
- <td bgcolor="#ffafaf"></td>\r
- <td></td>\r
- <td></td>\r
- <td></td>\r
- </tr>\r
- <tr> \r
- <td>Taylor</td>\r
- <td bgcolor="#ccff00"></td>\r
- <td bgcolor="#0000ff"></td>\r
- <td bgcolor="#cc00ff"></td>\r
- <td bgcolor="#ff0000"></td>\r
- <td bgcolor="#ffff00"></td>\r
- <td bgcolor="#ff00cc"></td>\r
- <td bgcolor="#ff0066"></td>\r
- <td bgcolor="#ff9900"></td>\r
- <td bgcolor="#0066ff"></td>\r
- <td bgcolor="#66ff00"></td>\r
- <td bgcolor="#33ff00"></td>\r
- <td bgcolor="#6600ff"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#00ff66"></td>\r
- <td bgcolor="#ffcc00"></td>\r
- <td bgcolor="#ff3300"></td>\r
- <td bgcolor="#ff6600"></td>\r
- <td bgcolor="#00ccff"></td>\r
- <td bgcolor="#00ffcc"></td>\r
- <td bgcolor="#99ff00"></td>\r
- <td></td>\r
- <td></td>\r
- <td></td>\r
- </tr>\r
- <tr> \r
- <td>Hydrophobicity</td>\r
- <td bgcolor="#ad0052"></td>\r
- <td bgcolor="#0000ff"></td>\r
- <td bgcolor="#0c00f3"></td>\r
- <td bgcolor="#0c00f3"></td>\r
- <td bgcolor="#c2003d"></td>\r
- <td bgcolor="#0c00f3"></td>\r
- <td bgcolor="#0c00f3"></td>\r
- <td bgcolor="#6a0095"></td>\r
- <td bgcolor="#1500ea"></td>\r
- <td bgcolor="#ff0000"></td>\r
- <td bgcolor="#ea0015"></td>\r
- <td bgcolor="#0000ff"></td>\r
- <td bgcolor="#b0004f"></td>\r
- <td bgcolor="#cb0034"></td>\r
- <td bgcolor="#4600b9"></td>\r
- <td bgcolor="#5e00a1"></td>\r
- <td bgcolor="#61009e"></td>\r
- <td bgcolor="#5b00a4"></td>\r
- <td bgcolor="#4f00b0"></td>\r
- <td bgcolor="#f60009"></td>\r
- <td bgcolor="#0c00f3"></td>\r
- <td bgcolor="#680097"></td>\r
- <td bgcolor="#0c00f3"></td>\r
- </tr>\r
- <tr> \r
- <td>Helix Propensity</td>\r
- <td bgcolor="#e718e7"></td>\r
- <td bgcolor="#6f906f"></td>\r
- <td bgcolor="#1be41b"></td>\r
- <td bgcolor="#778877"></td>\r
- <td bgcolor="#23dc23"></td>\r
- <td bgcolor="#926d92"></td>\r
- <td bgcolor="#ff00ff"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#758a75"></td>\r
- <td bgcolor="#8a758a"></td>\r
- <td bgcolor="#ae51ae"></td>\r
- <td bgcolor="#a05fa0"></td>\r
- <td bgcolor="#ef10ef"></td>\r
- <td bgcolor="#986798"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#36c936"></td>\r
- <td bgcolor="#47b847"></td>\r
- <td bgcolor="#8a758a"></td>\r
- <td bgcolor="#21de21"></td>\r
- <td bgcolor="#857a85"></td>\r
- <td bgcolor="#49b649"></td>\r
- <td bgcolor="#758a75"></td>\r
- <td bgcolor="#c936c9"></td>\r
- </tr>\r
- <tr> \r
- <td nowrap>Strand Propensity</td>\r
- <td bgcolor="#5858a7"></td>\r
- <td bgcolor="#6b6b94"></td>\r
- <td bgcolor="#64649b"></td>\r
- <td bgcolor="#2121de"></td>\r
- <td bgcolor="#9d9d62"></td>\r
- <td bgcolor="#8c8c73"></td>\r
- <td bgcolor="#0000ff"></td>\r
- <td bgcolor="#4949b6"></td>\r
- <td bgcolor="#60609f"></td>\r
- <td bgcolor="#ecec13"></td>\r
- <td bgcolor="#b2b24d"></td>\r
- <td bgcolor="#4747b8"></td>\r
- <td bgcolor="#82827d"></td>\r
- <td bgcolor="#c2c23d"></td>\r
- <td bgcolor="#2323dc"></td>\r
- <td bgcolor="#4949b6"></td>\r
- <td bgcolor="#9d9d62"></td>\r
- <td bgcolor="#c0c03f"></td>\r
- <td bgcolor="#d3d32c"></td>\r
- <td bgcolor="#ffff00"></td>\r
- <td bgcolor="#4343bc"></td>\r
- <td bgcolor="#797986"></td>\r
- <td bgcolor="#4747b8"></td>\r
- </tr>\r
- <tr> \r
- <td>Turn Propensity</td>\r
- <td bgcolor="#2cd3d3"></td>\r
- <td bgcolor="#708f8f"></td>\r
- <td bgcolor="#ff0000"></td>\r
- <td bgcolor="#e81717"></td>\r
- <td bgcolor="#a85757"></td>\r
- <td bgcolor="#3fc0c0"></td>\r
- <td bgcolor="#778888"></td>\r
- <td bgcolor="#ff0000"></td>\r
- <td bgcolor="#708f8f"></td>\r
- <td bgcolor="#00ffff"></td>\r
- <td bgcolor="#1ce3e3"></td>\r
- <td bgcolor="#7e8181"></td>\r
- <td bgcolor="#1ee1e1"></td>\r
- <td bgcolor="#1ee1e1"></td>\r
- <td bgcolor="#f60909"></td>\r
- <td bgcolor="#e11e1e"></td>\r
- <td bgcolor="#738c8c"></td>\r
- <td bgcolor="#738c8c"></td>\r
- <td bgcolor="#9d6262"></td>\r
- <td bgcolor="#07f8f8"></td>\r
- <td bgcolor="#f30c0c"></td>\r
- <td bgcolor="#7c8383"></td>\r
- <td bgcolor="#5ba4a4"></td>\r
- </tr>\r
- <tr> \r
- <td>Buried Index</td>\r
- <td bgcolor="#00a35c"></td>\r
- <td bgcolor="#00fc03"></td>\r
- <td bgcolor="#00eb14"></td>\r
- <td bgcolor="#00eb14"></td>\r
- <td bgcolor="#0000ff"></td>\r
- <td bgcolor="#00f10e"></td>\r
- <td bgcolor="#00f10e"></td>\r
- <td bgcolor="#009d62"></td>\r
- <td bgcolor="#00d52a"></td>\r
- <td bgcolor="#0054ab"></td>\r
- <td bgcolor="#007b84"></td>\r
- <td bgcolor="#00ff00"></td>\r
- <td bgcolor="#009768"></td>\r
- <td bgcolor="#008778"></td>\r
- <td bgcolor="#00e01f"></td>\r
- <td bgcolor="#00d52a"></td>\r
- <td bgcolor="#00db24"></td>\r
- <td bgcolor="#00a857"></td>\r
- <td bgcolor="#00e619"></td>\r
- <td bgcolor="#005fa0"></td>\r
- <td bgcolor="#00eb14"></td>\r
- <td bgcolor="#00b649"></td>\r
- <td bgcolor="#00f10e"></td>\r
- </tr>\r
- </table></td>\r
- </tr>\r
- </table>\r
-</div>\r
-<p align="center"> </p>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Colour Schemes</title>
+<style type="text/css">
+<!--
+td {
+ font-family: "Courier New", Courier, mono;
+ font-style: normal;
+ font-size: medium;
+}
+-->
+</style>
+</head>
+<body>
+<p><strong>Colour schemes</strong></p>
+<p>Jalview allows the user to set a background colour for the whole
+alignment view or for each group defined on regions within it.</p>
+<p>To change the background colour, simply select the colour from
+the "Colour" menu.</p>
+<p>To change the colour of a group, right click on any residue
+within a group and use the popup menu to define the group colour.</p>
+<p>At the top of the "Colour" menu the tick box
+"Apply Background Colour to all groups". This is ticked by
+default so that a chosen colour scheme will be applied to all existing
+groups. If you wish to maintain the colour scheme for defined groups,
+make sure you deselect this option before changing the background
+colour.</p>
+<p>The <strong>"Colour→<a
+ href="../colourSchemes/textcolour.html">Colour Text...</a>"</strong> entry
+opens a dialog box to set a different text colour for light and dark
+background, and the intensity threshold for transition between them.</p>
+<p>The default colour schemes are summarised in the table below:
+<div align="center">
+<p> </p>
+<table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td>
+ <td>R</td>
+ <td>N</td>
+ <td>D</td>
+ <td>C</td>
+ <td>Q</td>
+ <td>E</td>
+ <td>G</td>
+ <td>H</td>
+ <td>I</td>
+ <td>L</td>
+ <td>K</td>
+ <td>M</td>
+ <td>F</td>
+ <td>P</td>
+ <td>S</td>
+ <td>T</td>
+ <td>W</td>
+ <td>Y</td>
+ <td>V</td>
+ <td>B</td>
+ <td>X</td>
+ <td>Z</td>
+ </tr>
+ <tr>
+ <td height="24">Clustal</td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f08080"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f09048"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Zappo</td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Taylor</td>
+ <td bgcolor="#ccff00"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#cc00ff"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#ff00cc"></td>
+ <td bgcolor="#ff0066"></td>
+ <td bgcolor="#ff9900"></td>
+ <td bgcolor="#0066ff"></td>
+ <td bgcolor="#66ff00"></td>
+ <td bgcolor="#33ff00"></td>
+ <td bgcolor="#6600ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff66"></td>
+ <td bgcolor="#ffcc00"></td>
+ <td bgcolor="#ff3300"></td>
+ <td bgcolor="#ff6600"></td>
+ <td bgcolor="#00ccff"></td>
+ <td bgcolor="#00ffcc"></td>
+ <td bgcolor="#99ff00"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Hydrophobicity</td>
+ <td bgcolor="#ad0052"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#c2003d"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#6a0095"></td>
+ <td bgcolor="#1500ea"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ea0015"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#b0004f"></td>
+ <td bgcolor="#cb0034"></td>
+ <td bgcolor="#4600b9"></td>
+ <td bgcolor="#5e00a1"></td>
+ <td bgcolor="#61009e"></td>
+ <td bgcolor="#5b00a4"></td>
+ <td bgcolor="#4f00b0"></td>
+ <td bgcolor="#f60009"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#680097"></td>
+ <td bgcolor="#0c00f3"></td>
+ </tr>
+ <tr>
+ <td>Helix Propensity</td>
+ <td bgcolor="#e718e7"></td>
+ <td bgcolor="#6f906f"></td>
+ <td bgcolor="#1be41b"></td>
+ <td bgcolor="#778877"></td>
+ <td bgcolor="#23dc23"></td>
+ <td bgcolor="#926d92"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#ae51ae"></td>
+ <td bgcolor="#a05fa0"></td>
+ <td bgcolor="#ef10ef"></td>
+ <td bgcolor="#986798"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#36c936"></td>
+ <td bgcolor="#47b847"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#21de21"></td>
+ <td bgcolor="#857a85"></td>
+ <td bgcolor="#49b649"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#c936c9"></td>
+ </tr>
+ <tr>
+ <td nowrap>Strand Propensity</td>
+ <td bgcolor="#5858a7"></td>
+ <td bgcolor="#6b6b94"></td>
+ <td bgcolor="#64649b"></td>
+ <td bgcolor="#2121de"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#8c8c73"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#60609f"></td>
+ <td bgcolor="#ecec13"></td>
+ <td bgcolor="#b2b24d"></td>
+ <td bgcolor="#4747b8"></td>
+ <td bgcolor="#82827d"></td>
+ <td bgcolor="#c2c23d"></td>
+ <td bgcolor="#2323dc"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#c0c03f"></td>
+ <td bgcolor="#d3d32c"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#4343bc"></td>
+ <td bgcolor="#797986"></td>
+ <td bgcolor="#4747b8"></td>
+ </tr>
+ <tr>
+ <td>Turn Propensity</td>
+ <td bgcolor="#2cd3d3"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#e81717"></td>
+ <td bgcolor="#a85757"></td>
+ <td bgcolor="#3fc0c0"></td>
+ <td bgcolor="#778888"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#00ffff"></td>
+ <td bgcolor="#1ce3e3"></td>
+ <td bgcolor="#7e8181"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#f60909"></td>
+ <td bgcolor="#e11e1e"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#9d6262"></td>
+ <td bgcolor="#07f8f8"></td>
+ <td bgcolor="#f30c0c"></td>
+ <td bgcolor="#7c8383"></td>
+ <td bgcolor="#5ba4a4"></td>
+ </tr>
+ <tr>
+ <td>Buried Index</td>
+ <td bgcolor="#00a35c"></td>
+ <td bgcolor="#00fc03"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#009d62"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#0054ab"></td>
+ <td bgcolor="#007b84"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#009768"></td>
+ <td bgcolor="#008778"></td>
+ <td bgcolor="#00e01f"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#00db24"></td>
+ <td bgcolor="#00a857"></td>
+ <td bgcolor="#00e619"></td>
+ <td bgcolor="#005fa0"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00b649"></td>
+ <td bgcolor="#00f10e"></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+</table>
+</div>
+<p align="center"> </p>
+</body>
+</html>
-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window Menus</strong></p>\r
-<ul>\r
- <li><strong>File</strong> \r
- <ul>\r
- <li><strong>Add Sequences</strong><em><br>\r
- Add sequences to the visible alignment from file, URL, or cut & paste \r
- window </em></li>\r
- <li><strong>Fetch Sequence</strong><br>\r
- <em>Shows a dialog window in which you can select known ids from Uniprot, \r
- EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
- Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence \r
- Fetcher</a></em>.</li>\r
- <li><strong>Save As<br>\r
- </strong><em>Save the alignment to local file. A file selection window \r
- will open, use the "Files of type:" selection box to determine \r
- which <a href="../io/index.html">alignment format</a> to save as.</em></li>\r
- <li><strong>Export</strong> <em><br>\r
- Creates an alignment graphic with the current annotation, alignment background \r
- colours and group colours. If the alignment is <a\r
- href="../features/wrap.html">wrapped</a>, the output will also be wrapped \r
- and will have the same visible residue width as the open alignment. </em> \r
- <ul>\r
- <li><strong>HTML<br>\r
- </strong><em>Create a <a href="../io/export.html">web page</a> from \r
- your alignment.</em></li>\r
- <li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/export.html">Encapsulated Postscript</a> \r
- file from your alignment.</em></li>\r
- <li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/export.html">Portable Network \r
- Graphics</a> file from your alignment.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Output to Textbox<br>\r
- </strong><em>The alignment will be displayed in plain text in a new window \r
- which you can "Copy and Paste" using the pull down menu, or \r
- your standard operating system copy and paste keys. <br>\r
- Select the format of the text by selecting one of the following menu items.</em> \r
- <ul>\r
- <li><strong>FASTA</strong> <em></em></li>\r
- <li><strong>MSF</strong></li>\r
- <li><strong>CLUSTAL</strong></li>\r
- <li><strong>BLC</strong></li>\r
- <li><strong>PIR</strong></li>\r
- <li><strong>PFAM</strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Print<br>\r
- </strong><em>Jalview will print the alignment using the current fonts \r
- and colours of your alignment. If the alignment has annotations visible, \r
- these will be printed below the alignment. If the alignment is wrapped \r
- the number of residues per line of your alignment will depend on the paper \r
- width or your alignment window width, whichever is the smaller. </em></li>\r
- <li><strong>Export Features</strong><em><br>\r
- All features visible on the alignment can be saved to file or displayed \r
- in a textbox in either Jalview or GFF format</em></li>\r
- <li><strong>Export Annotations</strong><em><br>\r
- All annotations visible on the alignment can be saved to file or displayed \r
- in a textbox in Jalview annotations format. </em></li>\r
- <li><strong>Load Associated Tree<br>\r
- </strong><em>Jalview can <a\r
- href="../calculations/treeviewer.html">view trees</a> stored in the Newick \r
- file format, and associate them with the alignment. Note: the ids of the \r
- tree file and your alignment MUST be the same.</em></li>\r
- <li><strong>Load Features / Annotations<br>\r
- </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence \r
- features</a> or <a href="../features/annotationsFormat.html">alignment \r
- annotations</a>.</em></li>\r
- <li><strong>Close</strong><br>\r
- <em>Close the alignment window. Make sure you have saved your alignment \r
- before you close - either as a Jalview project or by using the <strong>Save \r
- As</strong> menu.<br>\r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Edit</strong> \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 \r
- or pasting sequences to the current alignment or sorting the alignment. \r
- <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to \r
- group sizes, or changes to 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 \r
- before removing them from your alignment. Click on a sequence name if \r
- you wish to 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 \r
- can also do this by pressing <CTRL> and C (<APPLE> and C on \r
- MacOSX). <br>\r
- If you try to paste the clipboard contents to a text editor, you will \r
- see the format of the copied residues FASTA.</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 \r
- previously 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 \r
- added 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 \r
- copying them to the clipboard. Like the other edit operations, this can \r
- be undone with <strong>Undo</strong>.</em></li>\r
- <li><strong>Select All<br>\r
- </strong><em>Selects all the sequences and residues in the alignment. \r
- <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 \r
- alignment window. All selected sequences, residues and marked columns \r
- will be deselected. </em><em> <br>\r
- Use <ESCAPE> to deselect all.</em></li>\r
- <li><strong>Invert Sequence Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the \r
- current selection. </em></li>\r
- <li><strong>Invert Column Selection<br>\r
- </strong><em>Any columns currently not selected will replace the current \r
- column 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 \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.</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.</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 \r
- the selected area of the alignment. If no selection is made, ALL the gaps \r
- in the 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 \r
- the current alignment) exceeds this value then one of the sequences (the \r
- shorter) is discarded. Press the "Apply" button to remove redundant \r
- sequences. The "Undo" button will undo the last redundancy deletion.</em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>When selected, the alignment will be kept at minimal width \r
- (so there no empty columns before or after the first or last aligned residue) \r
- and all sequences will be padded with gap characters to the before and \r
- after their terminating residues.<br>\r
- This switch is useful when making a tree using unaligned sequences and \r
- when working with alignment analysis programs which require 'properly \r
- aligned sequences' to be all the same length.<br>\r
- You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. \r
- </em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Search</strong> \r
- <ul>\r
- <li><strong>Find<br>\r
- </strong><em>Select this to <a href="../features/search.html">search</a> \r
- for residues, sequence name or residue position within the alignment and \r
- create new sequence features from the queries. <br>\r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>View</strong> \r
- <ul>\r
- <li><strong>Font<br>\r
- </strong><em>Change the font of the display from the "Choose Font" \r
- dialog box, which is shown when this item is selected. </em></li>\r
- <li><strong>Smooth Fonts</strong><em><br>\r
- If selected, the alignment will be drawn with anti-aliasing on which looks \r
- better, but performace is reduced. </em></li>\r
- <li><strong>Show (all Columns / Sequences)</strong><em><br>\r
- All hidden Columns / Sequences will be revealed. </em></li>\r
- <li><strong>Hide (all Columns / Sequences)</strong><em><br>\r
- Hides the all the currently selected Columns / Sequences</em></li>\r
- <li><strong>Wrap<br>\r
- </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>" \r
- to the width of the alignment window. This is useful if your alignment \r
- has only a few sequences to view its full width at once.<br>\r
- Options are available to show the residue numbering at the start and/or \r
- end of an alignment as well as showing the alignment position above each \r
- sequence row. <br>\r
- <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot \r
- be edited or have regions selected on it. </em></li>\r
- <li><strong>Show Full Sequence ID<br>\r
- </strong><em>If this box is selected the sequence name will have the start \r
- and end position of the sequence appended to the name, in the format NAME/START-END</em></li>\r
- <li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using \r
- the selected background colour. Useful if used in conjunction with "Colour \r
- Text." </em></li>\r
- <li><strong>Text<br>\r
- </strong><em>If this is selected the residues will be displayed using \r
- the standard 1 character amino acid alphabet.</em></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If this is selected the residues will be coloured according \r
- to the background colour associated with that residue. The colour is slightly \r
- darker than background so the amino acid symbol remains visible. </em></li>\r
- <li><strong>Show Gaps<br>\r
- </strong><em>When this is selected, gap characters will be displayed as \r
- "." or "-". If unselected, then gap characters will \r
- appear as blank spaces. <br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em></li>\r
- <li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will \r
- be displayed below the alignment. The default setting is to display the \r
- conservation calculation, quality calculation and consensus values as \r
- bar charts. </em></li>\r
- <li><strong>Fetch Sequence Features<br>\r
- </strong><em>If the sequence names are Swissprot entries Jalview will \r
- use the names to retrieve <a href="../features/seqfeatures.html">sequence \r
- features</a> from the EBI. Features which are 1 residue in length are \r
- coloured red, sequences longer than 1 residue are coloured blue. Move \r
- the mouse over a coloured feature to display the details of the feature. \r
- <br>\r
- Note: The retrieved information will update the sequence start and end \r
- labels if they are incorrect. </em></li>\r
- <li><strong>Show Sequence Features</strong><br>\r
- <em>Show or hide sequence features on this alignment.</em></li>\r
- <li><strong>Seqence Feature Settings...</strong><em><br>\r
- <em>Control the colour and display of sequence features on the alignment. \r
- See <a\r
- href="../features/featuresettings.html">Sequence Feature Settings</a>.</em></em></li>\r
- <li><strong><a href="../features/overview.html">Overview Window</a><br>\r
- </strong><em>A scaled version of the alignment will be displayed in a \r
- small window. A red box will indicate the currently visible area of the \r
- alignment. Move the visible region using the mouse. </em><strong> </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Colour</strong> \r
- <ul>\r
- <li><strong>Apply Colour To All Groups<br>\r
- </strong><em>If this is selected, any changes made to the background colour \r
- will be applied to all currently defined groups.</em></li>\r
- <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage \r
- Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, \r
- Turn Propensity, Buried Index, Nucleotide, User Defined<br>\r
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for \r
- a description of all colour schemes.</em></li>\r
- <li><strong>By Conservation<br>\r
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring \r
- by Conservation</a>.</em></li>\r
- <li><strong>Modify Conservation Threshold<br>\r
- </strong><em>Use this to display the conservation threshold slider window. \r
- Useful if the window has been closed, or if the 'by conservation' option \r
- appears to be doing nothing!</em></li>\r
- <li><strong>Above Identity Threshold<br>\r
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage \r
- Identity</a></em><strong>.</strong></li>\r
- <li><strong>Modify Identity Threshold<br>\r
- </strong><em>Use this to set the threshold value for colouring above Identity. \r
- Useful if the window has been closed. </em></li>\r
- <li><strong>By Annotation</strong><br>\r
- <em>Colours the alignment on a per-column value from a specified annotation. \r
- See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Calculate</strong> \r
- <ul>\r
- <li>Sort \r
- <ul>\r
- <li><strong>by ID</strong><em><br>\r
- This will sort the sequences according to sequence name. If the sort \r
- is repeated, the order of the sorted sequences will be inverted. </em></li>\r
- <li><strong>by Group</strong><strong><br>\r
- </strong><em>This will sort the sequences according to sequence name. \r
- If the sort is repeated, the order of the sorted sequences will be \r
- inverted. </em><strong></strong></li>\r
- <li><strong>by Pairwise Identity<br>\r
- </strong><em>This will sort the selected sequences by their percentage \r
- identity to the consensus sequence. The most similar sequence is put \r
- at the top. </em></li>\r
- <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will \r
- have some additional options if you have just done a multiple alignment \r
- calculation, or opened a tree viewer window.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Calculate Tree </strong> <br>\r
- <em>Functions for calculating trees on the alignment or the currently \r
- selected region. See <a\r
- href="../calculations/tree.html">calculating trees</a>.</em> \r
- <ul>\r
- <li><strong>Average Distance Using % Identity</strong></li>\r
- <li><strong>Neighbour Joining Using % Identity</strong></li>\r
- <li><strong>Average Distance Using Blosum62</strong></li>\r
- <li><strong>Neighbour Joining Using Blosum62</strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Pairwise Alignments</strong><br>\r
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise \r
- alignments</a>.</em></li>\r
- <li><strong>Principal Component Analysis</strong><br>\r
- <em>Shows a spatial clustering of the sequences based on the BLOSUM62 \r
- scores in the alignment. See <a href="../calculations/pca.html">Principal \r
- Component Analysis</a>.</em> </li>\r
- <li><strong>Translate cDNA</strong><br>\r
- <em>If you are viewing a cDNA alignment a very simple translation service \r
- is available. The translation ignores all gaps in the cDNA sequences. \r
- </em> <br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Web Service<br>\r
- </strong> <em>Selecting one of the following menu items starts a remote service \r
- on compute facilities at the University of Dundee. You need a continuous network \r
- connection in order to use these services through Jalview. </em> \r
- <ul>\r
- <li><strong>Alignment </strong> \r
- <ul>\r
- <li><strong>ClustalW Multiple Sequence Alignment</strong><br>\r
- <em> Submits all, or just the currently selected sequences for alignment \r
- with clustal W.</em></li>\r
- <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>\r
- <em> Submits the alignment or currently selected region for re-alignment \r
- with clustal W. Use this if you have added some new sequences to an \r
- existing alignment.</em></li>\r
- <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
- <em> Submits all, or jut the currently selected sequences for alignment \r
- using Muscle. Do not use this if you are working with nucleic acid \r
- sequences.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Secondary Structure Prediction</strong> \r
- <ul>\r
- <li><strong>JPred Secondary Structure Prediction</strong><br>\r
- <em>Secondary structure prediction by network consensus. The behaviour \r
- of this calculation depends on the current selection: </em></li>\r
- <li><em>If nothing is selected, and the displayed sequences appear to \r
- be aligned, then a JNet prediction will be run for the first sequence \r
- in the alignment, using the current alignment. Otherwise the first \r
- sequence will be submitted for prediction. </em></li>\r
- <li><em>If just one sequence (or a region on one sequence) has been \r
- selected, it will be submitted to the automatic JNet prediction server \r
- for homolog detection and prediction. </em></li>\r
- <li><em>If a set of sequences are selected, and they appear to be aligned, \r
- then the alignment will be used for a Jnet prediction on the <strong>first</strong> \r
- sequence selected in the set (that is, the one that was first clicked \r
- on). </em> </li>\r
- </ul>\r
- </li>\r
- </ul>\r
- </li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+<p><strong>Alignment Window Menus</strong></p>
+<ul>
+ <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. <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>
+ </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)</strong><em><br>
+ All hidden Columns / Sequences will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
+ Hides the all the currently selected Columns / Sequences</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>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><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>
+ </em></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>
+ </ul>
+ </li>
+ <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 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>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> <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>
<ul>
<li><strong><a href="../features/search.html">Find...
(Control F)</a></strong><em><br>
- Opens the Find dialog box to perform regular expression searches on the
- aligned sequences and their IDs and create new features.
+ 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.
<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>
-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window Calculate Menu</strong></p>\r
-<ul>\r
- <li><strong>Sort </strong> \r
- <ul>\r
- <li><strong>by ID</strong><em><br>\r
- This will sort the sequences according to sequence name. If the sort is \r
- repeated, the order of the sorted sequences will be inverted. </em></li>\r
- <li><strong>by Group</strong><strong><br>\r
- </strong><em>This will sort the sequences according to sequence name. \r
- If the sort is repeated, the order of the sorted sequences will be inverted. \r
- </em><strong></strong></li>\r
- <li><strong>by Pairwise Identity<br>\r
- </strong><em>This will sort the selected sequences by their percentage \r
- identity to the consensus sequence. The most similar sequence is put at \r
- the top. </em></li>\r
- <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have \r
- some additional options if you have just done a multiple alignment calculation, \r
- or opened a tree viewer window.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Calculate Tree </strong> <br>\r
- <em>Functions for calculating trees on the alignment or the currently selected \r
- region. See <a\r
- href="../calculations/tree.html">calculating trees</a>.</em> \r
- <ul>\r
- <li><strong>Average Distance Using % Identity</strong></li>\r
- <li><strong>Neighbour Joining Using % Identity</strong></li>\r
- <li><strong>Average Distance Using Blosum62</strong></li>\r
- <li><strong>Neighbour Joining Using Blosum62<br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Pairwise Alignments</strong><br>\r
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise \r
- alignments</a>.</em><br>\r
- </li>\r
- <li><strong>Principal Component Analysis</strong><br>\r
- <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores \r
- in the alignment. See <a href="../calculations/pca.html">Principal Component \r
- Analysis</a>.</em> <br>\r
- </li>\r
- <li><strong>Autocalculate Consensus</strong><br>\r
- <em>For large alignments it can be useful to deselect "Autocalculate \r
- Consensus" when editing. This prevents lengthy calculations which are \r
- performed after each sequence edit.</em> <br>\r
- </li>\r
-</ul>\r
- </body>\r
-</html>\r
+<html>
+<head><title>Alignment Window Menus</title></head>
+
+<body>
+<p><strong>Alignment Window Calculate Menu</strong></p>
+<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 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>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>
+ </body>
+</html>
</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>
- <strong> </strong>
</ul>
<p> </p>
</body>
-<html>\r
-<head><title>Desktop Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Desktop Menus</strong></p>\r
-<ul>\r
- <li><strong>File</strong><em> </em> \r
- <ul>\r
- <li><strong>Input Alignment from</strong><em> (See more on <a href="../io/index.html">file \r
- formats</a>) </em> \r
- <ul>\r
- <li><strong>File</strong><br>\r
- <em>open file(s) on your local file system</em></li>\r
- <li><strong>URL</strong><br>\r
- <em>open a file from a website. The URL MUST start with http://</em></li>\r
- <li><strong>Textbox</strong><br>\r
- <em>copy and paste an alignment into a text window</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Fetch Sequence<br>\r
- </strong><em>Shows a dialog window in which you can select known ids from \r
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by \r
- the European Bioinformatics Institute.</em></li>\r
- <li><strong>Save Project</strong><br>\r
- <em>Saves all currently open alignment windows with their current view \r
- settings and any associated trees, as a <a href="../features/jalarchive.html">Jalview \r
- Archive</a> (which has a .jar extension).</em></li>\r
- <li><strong>Load Project</strong><br>\r
- <em>Loads Jalview archives <strong>only</strong>.</em></li>\r
- <li><strong>Quit</strong><br>\r
- <em>Close Jalview. Warning - any annotations you have made on alignments \r
- will be lost unless you Save your work before quitting.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Tools </strong> \r
- <ul>\r
- <li><strong><a href="../features/preferences.html">Preferences<br>\r
- </a></strong><em>Change the default visual settings for opening new alignment \r
- windows.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Help </strong> \r
- <ul>\r
- <li><strong>About<br>\r
- </strong><em>Displays the version and creation date of the application, \r
- as well as acknowledgements and a citation reference. </em></li>\r
- <li><strong>Documentation<br>\r
- </strong><em>Displays help files as a browseable, searchable set of pages \r
- with a table of contents. </em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Window<br>\r
- </strong><em>Each time a new window is added to the Jalview Desktop a new \r
- menu item will be added to the "Window" menu. If you are working \r
- with several alignments, trees or other types of windows use the "Window" \r
- menu to bring your window of choice to the top of the pile if it has been \r
- hidden by other windows. </em></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Desktop Menus</title>
+</head>
+
+<body>
+<p><strong>Desktop Menus</strong></p>
+<ul>
+ <li><em> <strong>File</strong></em>
+ <ul>
+ <li><strong>Input Alignment from</strong><em> (See more on <a
+ href="../io/index.html">file formats</a>) </em>
+ <ul>
+ <li><strong>File (Control O)</strong><br>
+ <em>open file(s) on your local file system</em></li>
+ <li><strong>URL</strong><br>
+ <em>open a file from a website. The URL MUST start with http://</em></li>
+ <li><strong>Textbox</strong><br>
+ <em>copy and paste an alignment into a text window</em></li>
+ </ul>
+ </li>
+ <li><strong>Fetch Sequence<br>
+ </strong><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.</em></li>
+ <li><strong>Save Project</strong><br>
+ <em>Saves all currently open alignment windows with their current
+ view settings and any associated trees, as a <a
+ href="../features/jalarchive.html">Jalview Archive</a> (which has a
+ .jar extension).</em></li>
+ <li><strong>Load Project</strong><br>
+ <em>Loads Jalview archives <strong>only</strong>.</em></li>
+ <li><strong>Quit</strong><br>
+ <em>Close Jalview. <br><strong>Note - any annotation you have made on
+ alignments will be lost unless you Save your work before quitting.<br></em><br>
+ </li>
+ </ul>
+ </li>
+ <li><strong>Tools </strong>
+ <ul>
+ <li><strong><a href="../features/preferences.html">Preferences<br>
+ </a></strong><em>Change the default visual settings for opening new alignment
+ windows.</em><strong><br>
+ </strong></li>
+ </ul>
+ </li>
+ <li><strong>Help </strong>
+ <ul>
+ <li><strong>About<br>
+ </strong><em>Displays the version and creation date of the application, as
+ well as acknowledgements and a citation reference. </em></li>
+ <li><strong>Documentation<br>
+ </strong><em>Displays help files as a browseable, searchable set of pages
+ with a table of contents. </em><strong><br>
+ </strong></li>
+ </ul>
+ </li>
+ <li><strong>Window</strong><br>
+ <em>Each time a new window is added to the Jalview Desktop a
+ corresponding menu item will be added to the "Window" menu
+ that will bring the window to the top of the pile when it is selected.
+ <ul>
+ <li><strong>Close All</strong><br>
+ Close all alignment and analysis windows.<br><strong>Note: This will erase all alignments from memory, and cannot be undone!</strong></li>
+ <li><strong>Raise Associated Windows</strong><br>
+ Bring all windows associated with the current alignment to the top of the pile.
+ </li>
+ <li><strong>Minimise Associated Windows</strong><br>
+ Hide all windows related to the current alignment behind icons on the Jalview Desktop.
+ </ul>
+ </em></li>
+ </ul>
+</body>
+</html>
-<html>\r
-<head><title>Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Menus</strong></p>\r
-<p>Menus are used in 3 places in Jalview - the "Desktop Menu", the "Alignment \r
- Menu" and the "Popup Menu".</p>\r
-<p>The <a href="desktopMenu.html">Desktop Menu</a> is always visible and is the \r
- starting point for loading new alignments.</p>\r
-<p>The <a href="alignmentMenu.html">Alignment Menu</a> is visible once and alignment \r
- has been opened.</p>\r
-<p>The <a href="popupMenu.html">Popup Menu</a> is made visible by clicking with \r
- the right mouse button on a sequence or the name of a sequence in an alignment \r
- window. </p>\r
-\r
-</body>\r
-</html>\r
+<html>
+<head><title>Menus</title></head>
+
+<body>
+<p><strong>Menus</strong></p>
+<p>Menus are used in 3 places in Jalview - the "Desktop Menu", the "Alignment
+ Menu" and the "Popup Menu".</p>
+<p>The <a href="desktopMenu.html">Desktop Menu</a> is always visible and is the
+ starting point for loading new alignments.</p>
+<p>The <a href="alignmentMenu.html">Alignment Menu</a> is visible once and alignment
+ has been opened.</p>
+<p>The <a href="popupMenu.html">Popup Menu</a> is made visible by clicking with
+ the right mouse button on a sequence or the name of a sequence in an alignment
+ window. </p>
+ <p>The <a href="alwannotations.html">Annotations Menu</a> is opened by right-clicking on an annotation row label.</p>
+
+</body>
+</html>
-<html>\r
-<head><title>Popup Menu</title></head>\r
-\r
-<body>\r
-<p><strong>Popup Menu</strong><br>\r
- <em>This menu is visible when right clicking either within a selected region \r
- on the alignment or on a selected sequence name. It may not be\r
- accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>\r
-<ul>\r
- <li><strong>Selection</strong> \r
- <ul>\r
- <li><strong>Edit </strong> \r
- <ul>\r
- <li><strong>Copy</strong><br>\r
- <em>Copys the selected region. In the applet version, the copied sequences \r
- are not available to the system clipboard.</em> </li>\r
- <li><strong>Cut<br>\r
- </strong><em>Cuts the selected region from the alignment. In the applet \r
- version, the copied sequences are not available to the system clipboard.</em> \r
- </li>\r
- <li><strong>To Upper Case</strong><em><strong><br>\r
- </strong><em>Changes the case of selected region to lower case.</em> \r
- </em></li>\r
- <li><strong>To Lower Case<br>\r
- </strong><em>Changes the case of selected region to upper case.</em><strong> \r
- </strong></li>\r
- <li><strong>Toggle Case</strong><br>\r
- <em>Switches the case of all residues within the selected region.</em> \r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Output to Textbox<br>\r
- </strong><em>The selection area will be output to a a text window in the \r
- selected alignment format. </em></li>\r
- <li><strong>Group<br>\r
- </strong><em>This will display a window asking for the name of the currently \r
- selected group. Click OK to set the name, cancel to use the default group \r
- name. </em></li>\r
- <li><strong>Remove Group<br>\r
- </strong><em>This will undefine the selected group. </em><strong> </strong></li>\r
- <li><strong>Group Colour<br>\r
- </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> \r
- of the group.</em><strong> </strong></li>\r
- <li><strong>Boxes<br>\r
- </strong><em>If selected the background of a residue within the selected \r
- group will be coloured according to the assigned colour scheme.</em><strong> \r
- </strong></li>\r
- <li><strong> Text<br>\r
- </strong><em>If selected the selected group will display text. </em></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If selected the selected group will display text in a colour \r
- slightly darker than the background colour of that residue.</em></li>\r
- <li><strong>Border Colour <br>\r
- </strong><em>Selecting this will display a "Colour Chooser" \r
- window. Select a colour than press OK to set the border colour of a group.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Sequence Id<br>\r
- </strong><em>This menu is only visible if you right-click on a sequence name. \r
- </em> \r
- <ul>\r
- <li><strong>Edit Name/Description<br>\r
- </strong><em>You may edit the name and description of each sequence. A \r
- window will be displayed asking for a new sequence name and sequence description \r
- to be entered. Press OK to accept your edit. To save sequence descriptions, \r
- you must save in Fasta, PIR or Jalview File format.</em></li>\r
- <li><strong>Associate Structure with Sequence</strong> \r
- <ul>\r
- <li><strong>From File<br>\r
- </strong><em>Load a PDB file from local disk which will be associated \r
- with this sequence. This file will be used if the user subsequently \r
- clicks on "View PDB Structure" menu item.</em></li>\r
- <li><strong>Enter PDB id<br>\r
- </strong><em>Enter the PDB id from an input window. This PDB id will \r
- be used by the service WSDBFetch, provided by the EBI, to fetch the \r
- PDB file if the user subsequently clicks on "View PDB Structure" \r
- menu item. </em></li>\r
- <li><strong>Discover PDB ids<br>\r
- </strong><em>This will use the service WSDBFetch, provided by the \r
- EBI, to retrieve all PDB ids associated with the sequences in the \r
- alignment if the sequences have valid Uniprot names or accession ids. \r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>View PDB Structure<br>\r
- </strong><em> If the sequence has an associated PDB file added by one \r
- of the methods described above, Jalview will display a 3D interactive \r
- viewer of the file.<br>\r
- This entry is only present if the sequence has an <a href="../features/viewingpdbs.html">associated \r
- PDB structure</a>. </em></li>\r
- <li><strong>Represent Group With (Sequence Id)</strong><br>\r
- <em>All sequences in the current selection group will be hidden, apart \r
- from (Sequence Id). Any edits performed on the visible representative \r
- sequence will be propagated to the hidden sequences. </em></li>\r
- <li><strong>Link</strong><br>\r
- <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> \r
- Connections tab.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Hide Sequences</strong><br>\r
- <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> \r
- Connections tab. It is only displayed when you right click (Apple click) on \r
- a sequence id. </em><strong><br>\r
- <br>\r
- </strong></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Popup Menu</title>
+</head>
+
+<body>
+<p><strong>Popup Menu</strong><br>
+<em>This menu is visible when right clicking either within a
+selected region on the alignment or on a selected sequence name. It may
+not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
+<ul>
+ <li><strong>Selection</strong>
+ <ul>
+ <li><strong>Edit </strong>
+ <ul>
+ <li><strong>Copy</strong><br>
+ <em>Copys the selected region. In the applet version, the copied
+ sequences are not available to the system clipboard.</em></li>
+ <li><strong>Cut<br>
+ </strong><em>Cuts the selected region from the alignment. In the applet
+ version, the copied sequences are not available to the system
+ clipboard.</em></li>
+ <li><strong>To Upper Case</strong><em><strong><br>
+ </strong><em>Changes the case of selected region to lower case.</em> </em></li>
+ <li><strong>To Lower Case<br>
+ </strong><em>Changes the case of selected region to upper case.</em><strong>
+ </strong></li>
+ <li><strong>Toggle Case</strong><br>
+ <em>Switches the case of all residues within the selected
+ region.</em></li>
+ </ul>
+ </li>
+ <li><strong>Output to Textbox<br>
+ </strong><em>The selection area will be output to a a text window in the
+ selected alignment format. </em></li>
+ <li><strong><a href="../features/creatinFeatures.html">Create
+ Sequence Feature...</a></strong><br>
+ <em>Opens the dialog box for creating sequence features over the
+ currently selected region on each selected sequence.</em></li>
+ <li><strong>Group</strong><br>
+ <em>Group Operations</em>
+ <ul>
+ <li><strong>Group</strong><em>This will display a window
+ asking for the name of the currently selected group. Click OK to set
+ the name, cancel to use the default group name. </em></li>
+ <li><strong>Remove Group<br>
+ </strong><em>This will undefine the selected group. </em><strong> </strong></li>
+ <li><strong>Group Colour<br>
+ </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> of
+ the group.</em><strong> </strong></li>
+ <li><strong>Boxes<br>
+ </strong><em>If selected the background of a residue within the selected
+ group will be coloured according to the assigned colour scheme.</em><strong>
+ </strong></li>
+ <li><strong>Text<br>
+ </strong><em>If selected the selected group will display text. </em></li>
+ <li><strong>Colour Text<br>
+ </strong><em>If selected the selected group will display text in a colour
+ slightly darker than the background colour of that residue.</em></li>
+ <li><strong>Border Colour <br>
+ </strong><em>Selecting this will display a "Colour Chooser"
+ window. Select a colour than press OK to set the border colour of a
+ group.</em></li>
+ </ul>
+ </li>
+ </ul>
+ </li>
+ <li><strong>Sequence Id<br>
+ </strong><em>This menu is only visible if you right-click on a sequence
+ name. </em>
+ <ul>
+ <li><strong>Edit Name/Description<br>
+ </strong><em>You may edit the name and description of each sequence. A
+ window will be displayed asking for a new sequence name and sequence
+ description to be entered. Press OK to accept your edit. To save
+ sequence descriptions, you must save in Fasta, PIR or Jalview File
+ format.</em></li>
+ <li><strong>Associate Structure with Sequence</strong>
+ <ul>
+ <li><strong>From File<br>
+ </strong><em>Load a PDB file from local disk which will be associated
+ with this sequence. This file will be used if the user subsequently
+ clicks on "View PDB Structure" menu item.</em></li>
+ <li><strong>Enter PDB id<br>
+ </strong><em>Enter the PDB id from an input window. This PDB id will be
+ used by the service WSDBFetch, provided by the EBI, to fetch the PDB
+ file if the user subsequently clicks on "View PDB
+ Structure" menu item. </em></li>
+ <li><strong>Discover PDB ids<br>
+ </strong><em>This will use the service WSDBFetch, provided by the EBI, to
+ retrieve all PDB ids associated with the sequences in the alignment
+ if the sequences have valid Uniprot names or accession ids. </em></li>
+ </ul>
+ </li>
+ <li><strong>View PDB Structure<br>
+ </strong><em> If the sequence has an associated PDB file added by one of
+ the methods described above, Jalview will display a 3D interactive
+ viewer of the file.<br>
+ This entry is only present if the sequence has an <a
+ href="../features/viewingpdbs.html">associated PDB structure</a>. </em></li>
+ <li><strong>Represent Group With (Sequence Id)</strong><br>
+ <em>All sequences in the current selection group will be hidden,
+ apart from (Sequence Id). Any edits performed on the visible
+ representative sequence will be propagated to the hidden sequences. </em></li>
+ <li><strong>Link</strong><br>
+ <em>This menu item lists all links which have been set up in the
+ <a href="../features/preferences.html">Preferences</a> Connections
+ tab.</em><strong><br>
+ </strong></li>
+ </ul>
+ </li>
+ <li><strong>Hide Sequences</strong><br>
+ <em>This menu item lists all links which have been set up in the <a
+ href="../features/preferences.html">Preferences</a> Connections tab.
+ It is only displayed when you right click (Apple click) on a sequence
+ id. </em><strong><br>
+ <br>
+ </strong></li>
+</ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff