<mapID target="wrap" url="html/features/wrap.html"/>\r
<mapID target="overview" url="html/features/overview.html"/>\r
<mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
+ <mapID target="alannotation" url="html/features/annotation.html"/>\r
\r
<mapID target="webservice" url="html/webServices/index.html"/>\r
<mapID target="clustal" url="html/webServices/clustalw.html"/>\r
<mapID target="alwCalc" url="html/menus/alwcalculate.html"/>\r
\r
<mapID target="popMenu" url="html/menus/popupMenu.html"/>\r
+ <mapID target="annotMenus" url="html/menus/alwannotations.html"/>\r
\r
\r
<mapID target="aminoAcids" url="html/misc/aminoAcids.html" />\r
<tocitem text="Wrap Alignment" target="wrap"/>\r
<tocitem text="Overview Window" target ="overview"/>\r
<tocitem text="Sequence Features" target ="seqfeatures"/>\r
+ <tocitem text="Alignment Annotations" target ="alannotation"/>\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="Editing Alignments" 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="Edit Menu" target="alwEdit"/> \r
<tocitem text="Colour Menu" target="alwColour"/>\r
<tocitem text="Calculation Menu" target="alwCalc"/>\r
- </tocitem>\r
+ <tocitem text="Annotation Menus" target="annotMenus"/>\r
<tocitem text="Popup Menu" target="popMenu"/>\r
+ </tocitem>\r
+\r
</tocitem>\r
</tocitem>\r
<tocitem text="Useful information" expand="false">\r
--- /dev/null
+<html>\r
+<head><title>Alignment Annotation</title></head>\r
+<body>\r
+<p><strong>Alignment Annotation</strong></p>\r
+\r
+<p>In addition to the definition of groups, Jalview also allows you to\r
+mark particular columns of an alignment and add symbols and text in\r
+the annotation area shown below the alignment (which may be hidden if\r
+<strong>View→Show Annotation</strong> is not ticked).\r
+</p>\r
+\r
+<p>\r
+Annotation rows are added using the <strong>Annotation Label</strong>\r
+menu, which is obtained by clicking anywhere on the annotation row labels\r
+area (below the sequence ID area).\r
+</p><ul>\r
+<li>Add New Row<br>\r
+<em>Adds a new, named annotation row (a dialog box will pop up for you\r
+to enter the label for the new row). </em>\r
+</li><li>Hide Row<br>\r
+<em>Hides the annotation row whose label was clicked in order to bring\r
+up the menu.</em>\r
+</li><li>Delete Row<br>\r
+<em>Deletes the annotation row whose label was clicked in order to bring\r
+up the menu.</em>\r
+</li><li>Show All Hidden Rows<br>\r
+<em>Shows all hidden annotation rows.</em>\r
+</li><li>Show Values in Text Box<br>\r
+<em>Opens a text box with a list of comma-separated values\r
+corresponding to the annotation (numerical or otherwise) at each\r
+position in the row. This is useful to export alignment quality\r
+measurements for further analysis.</em>\r
+</li>\r
+</ul>\r
+<p>\r
+<strong>Editing Label and secondary structure Annotation</strong></p>\r
+<p>\r
+Use the <strong>left mouse button</strong> to select a position along the row that are to\r
+be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination\r
+with the left-click will select more than one position, or a range of\r
+positions on the alignment.\r
+</p>\r
+<p>Once the desired position has been selected, use the <strong>right mouse\r
+button</strong> to open the <strong>annotation menu</strong>:</p>\r
+<ul>\r
+<li>Helix<br><em>Mark selected positions with a helix glyph (a red\r
+oval), and optional text label (see below). A\r
+dialog box will open for you to enter the text. Consecutive ovals\r
+will be rendered as an unbroken red line.</em>\r
+</li>\r
+<li>Sheet<br><em>Mark selected positions with a sheet glyph (a green\r
+arrow oriented from left to right), and optional text label (see\r
+below). A dialog box will open for you to enter the text. Consecutive\r
+arrows will be joined together to form a single green arrow.</em>\r
+</li>\r
+<li>Label<br><em>Set the text label at the selected positions. A\r
+dialog box will open for you to enter the text. If\r
+more that one consecutive position is marked with the same label, only\r
+the first position's label will be rendered.</em>\r
+</li>\r
+<li>Colour<br><em>Changes the colour of the annotation text label.</em>\r
+</li>\r
+<li>Remove Annotation<br><em>Blanks any annotation at the selected positions on\r
+the row. Note: <strong>This cannot be undone</strong></em>\r
+</li>\r
+</ul>\r
+<p>\r
+Annotation is stored and retrieved using <a\r
+href="../features/jalarchive.html">Jalview Archives</a>. Quantitative\r
+annnotation is also possible, but currently only possible with the\r
+JNet web service, or by creating your own Jalview Archive (which\r
+contains XML conforming to the Jalview-Vamsas XML schema).\r
+</p>\r
+<p><em>Current Limitations</em></p>\r
+\r
+<p>In the current version of Jalview, reordering of the annotation\r
+rows is not possible. If you save \r
+your annotation as a Jalview file, however, it will be reloaded with user \r
+annotations at the top (nearest the alignment), above any of the\r
+automatically generated Conservation, Quality or consensus\r
+annotations.</p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>
+<head>
+<title>Annotation Panel Menus</title>
+</head>
+<body>
+<p><strong>Annotation Panel Menus</strong></p>
+<ul>
+<li>
+<strong>Annotation Label Popup Menu</strong><br>
+<em>This menu is opened by clicking anywhere on the annotation row labels
+area (below the sequence ID area).</em>
+<ul>
+<li><strong>
+Add New Row</strong><br>
+<em>Adds a new, named annotation row (a dialog box will pop up for you
+to enter the label for the new row). </em>
+</li><li><strong>Hide Row</strong><br>
+<em>Hides the annotation row whose label was clicked in order to bring
+up the menu.</em>
+</li><li><strong>Delete Row</strong><br>
+<em>Deletes the annotation row whose label was clicked in order to bring
+up the menu.</em>
+</li><li><strong>Show All Hidden Rows</strong><br>
+<em>Shows all hidden annotation rows.</em>
+</li><li><strong>Show Values in Text Box</strong><br>
+<em>Opens a text box with a list of comma-separated values
+corresponding to the annotation (numerical or otherwise) at each
+position in the row. This is useful to export alignment quality
+measurements for further analysis.</em>
+</li>
+</ul>
+</li>
+<li><strong>Annotation Popup Menu<br></strong><em>This menu is opened when
+right-clicking on the selected positions of an annotation.</em>
+<ul>
+<li><strong>Helix</strong><br><em>Mark selected positions with a helix glyph (a red
+oval), and optional text label (see below). Consecutive ovals
+will be rendered as an unbroken red line.</em>
+</li>
+<li><strong>Sheet</strong><br><em>Mark selected positions with a sheet glyph (a green
+arrow oriented from left to right), and optional text label (see
+below). Consecutive arrows will be joined together to form a single
+green arrow.</em>
+</li>
+<li><strong>Label</strong><br><em>Sets the text label at the selected positions. If
+more that one consecutive position is marked with the same label, only
+the first position's label will be rendered.</em>
+</li>
+<li><strong>Colour</strong><br><em>Changes the colour of the annotation text label.</em>
+</li>
+<li><strong>Remove Annotation</strong><br><em>Blanks any annotation at the selected positions on
+the row. Note: <strong>This cannot be undone</strong></em>
+</li>
+</ul>
+</li>
+</ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff