\r
<mapID target="webservice" url="html/webServices/index.html"/>\r
<mapID target="clustal" url="html/webServices/clustal.html"/>\r
+ <mapID target="muscle" url="html/webServices/muscle.html"/>\r
+ <mapID target="jnet" url="html/webServices/jnet.html"/>\r
\r
<mapID target="io" url="html/io/index.html"/>\r
+ <mapID target="export" url="html/io/export.html"/>\r
<mapID target="alformats" url="html/io/fileformats.html"/>\r
<mapID target="edit" url="html/editing/index.html"/>\r
<mapID target="jalarchive" url="html/features/jalarchive.html"/>\r
<mapID target="menus" url="html/menus/index.html"/>\r
<mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>\r
<mapID target="alMenu" url="html/menus/alignmentMenu.html"/>\r
+ <mapID target="alwFile" url="html/menus/alwfile.html"/>\r
+ <mapID target="alwEdit" url="html/menus/alwedit.html"/>\r
+ <mapID target="alwColour" url="html/menus/alwcolour.html"/>\r
+ <mapID target="alwCalc" url="html/menus/alwcalculate.html"/>\r
+\r
<mapID target="popMenu" url="html/menus/popupMenu.html"/>\r
\r
\r
<tocitem text="Sequence Features" target ="seqfeatures"/>\r
</tocitem>\r
<tocitem text="Input /Output" target="io"/>\r
+ <tocitem text="Making figures" target="export"/>\r
<tocitem text="Editing Alignment" target ="edit"/>\r
<tocitem text="Web Services" target="webservice" expand="false">\r
<tocitem text="Clustal Alignment" target="clustal"/>\r
+ <tocitem text="Muscle Alignment" target="muscle"/>\r
+ <tocitem text="JNet Prediction" target="jnet"/>\r
</tocitem>\r
<tocitem text="Colour Schemes" target="colours" expand="false">\r
<tocitem text="ClustalX" target="colours.clustal"/>\r
</tocitem>\r
<tocitem text="Window Menus" target="menus" expand="false">\r
<tocitem text="Desktop Window" target="desktopMenu"/>\r
- <tocitem text="Alignment Window" target="alMenu"/>\r
+ <tocitem text="Alignment Window" target="alMenu">\r
+ <tocitem text="File Menu" target="alwFile"/>\r
+ <tocitem text="Edit Menu" target="alwEdit"/> \r
+ <tocitem text="Colour Menu" target="alwColour"/>\r
+ <tocitem text="Calculation Menu" target="alwCalc"/>\r
+ </tocitem>\r
<tocitem text="Popup Menu" target="popMenu"/>\r
</tocitem>\r
</tocitem>\r
<p><strong>Sorting Sequences</strong></p>
<p>Any group of selected sequences may be reordered by pressing the
up or down arrow keys. The whole alignment may also be reordered by
-the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
+the use of the functions in the Sort menu (<strong>Calculate→Sort</strong>):
</p>
<ul>
<li><p><strong>Sort by ID</strong></p>
order the sequences corresponding to those leaves in the
alignment.<br>
If a tree has been calculated from or associated with the current
-alignment, its name will appear in the submenu <em>Sort->By Tree Order</em>.</p><p>
+alignment, its name will appear in the submenu <strong>Sort→By Tree Order</strong>.</p><p>
</li>
<li><p><strong>Sort by alignment ordering</strong></p>
<p>Multiple alignment methods often order the sequences in their
<body>\r
<p><strong>Calculation of trees from alignments</strong></p>\r
<p>Trees are calculated on either the complete alignment, or just the\r
-currently selected group of sequences. There are four different\r
-calculations, using one of two distance measures and constructing the\r
-tree from one of two algorithms :\r
+currently selected group of sequences, using the functions in the\r
+<strong>Calculate→Calculate tree</strong> submenu. There are\r
+four different calculations, using one of two distance measures and\r
+constructing the tree from one of two algorithms :\r
</p>\r
<p><strong>Distance Measures</strong></p>\r
<p>Trees are calculated on the basis of a measure of similarity\r
<title>Exporting alignments as artwork</title>
</head>
<body>
-<p><strong>Export<a name="export"></a></strong></p>
+<p><strong>Exporting alignments as graphics and lineart<a name="export"></a></strong></p>
<p>The alignment view can be printed using
<strong>File→Print</strong>, or exported in a number of ways via the
<strong>File→Export</strong> menu:
<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of\r
these file formats.</p>\r
<p>Additionally, annotated whole sets of alignments and trees can be\r
-read from a Jalview\r
-(jar) format file using <strong>Desktop→Load Project</strong>. </p>\r
+read from a <a href="../features/jalarchive.html">Jalview (jar)\r
+format</a> file using <strong>Desktop→Load\r
+Project</strong>. </p>\r
<p>Use the <strong>Desktop→Input Alignment</strong> menu to read in files from:</p>\r
<ul>\r
<li><strong>From File</strong>: the local file system</li>\r
Submits all, or jut the currently selected sequences for\r
alignment using Muscle. Do not use this if you are working with\r
nucleic acid sequences.</em><br>\r
- <li><strong>JPred</strong><br><em>\r
+ <li><strong>JNet</strong><br><em>\r
Secondary structure prediction by network consensus. The\r
behaviour of this calculation depends on the current selection:\r
<ul>\r
<body>\r
<p><strong>Web services</strong></p>\r
<p>A variety of web services are available from the Alignment window's\r
- <strong>Calculations→Web Service→</strong> menu.\r
+ <strong>Calculations→Web Service</strong> menu.\r
</p>\r
<p>Jalview's distributed computations are SOAP based services exposing\r
protein sequence alignment and secondary structure prediction programs. These services actually run\r
Dundee, and are maintained by the Barton group.\r
</p>\r
<p><strong>Web Service Dialog Box</strong></p>\r
-<img src=""> \r
+<img src="clwqueued.gif">\r
<p>\r
- This dialog box is displayed when a web service job is submitted.\r
+ This dialog box is displayed when a web service job\r
+ is submitted. It gives the name of the service and\r
+ any method citation information, and monitors the\r
+ progress of the calculation. The cancel button will\r
+ permanently cancel the job, but this is only\r
+ possible for some services.\r
</p>\r
<p>Current services:\r
<ul>\r
git://source.jalview.org / jalview.git / commitdiff
