-<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 mark particular \r
- columns of an alignment and add symbols and text in the annotation area shown \r
- below the alignment (which may be hidden if <strong>View→Show Annotation</strong> \r
- is not ticked). </p>\r
-<p>As of Jalview 2.08 precalculated annotations can be added to alignments from \r
- the command line, drag and drop, or from the "File-> Load Features / \r
- Annotations" menu item. See the <a href="annotationsFormat.html">Annotations \r
- File Format</a> for more details.</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>\r
-<ul>\r
- <li>Add New Row<br>\r
- <em>Adds a new, named annotation row (a dialog box will pop up for you to \r
- enter the label for the new row). </em> </li>\r
- <li>Hide Row<br>\r
- <em>Hides the annotation row whose label was clicked in order to bring up \r
- the menu.</em> </li>\r
- <li>Delete Row<br>\r
- <em>Deletes the annotation row whose label was clicked in order to bring up \r
- the menu.</em> </li>\r
- <li>Show All Hidden Rows<br>\r
- <em>Shows all hidden annotation rows.</em> </li>\r
- <li>Show Values in Text Box<br>\r
- <em>Opens a text box with a list of comma-separated values corresponding to \r
- the annotation (numerical or otherwise) at each position in the row. This \r
- is useful to export alignment quality 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
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Alignment Annotation</title>
+</head>
+<body>
+ <p>
+ <strong>Alignment Annotation</strong>
+ </p>
+
+ <p>
+ In addition to the definition of groups and sequence features,
+ Jalview can display symbols and graphs under the columns of an
+ alignment. These annotation tracks are displayed in the annotation
+ area below the alignment. The annotation area's visibility is
+ controlled with the <strong>View→Show Annotation</strong>
+ option.
+ </p>
+ <p>
+ <strong>Types of annotation</strong>
+ <ul>
+ <li><a name="seqannots"><strong>Sequence
+ associated annotation.</strong></a><br />Data displayed on sequence
+ annotation rows are associated with the positions of a sequence.
+ Often this is 'Reference annotation' such as secondary structure
+ information derived from 3D structure data, or from the results of
+ sequence based prediction of <a href="../webServices/jnet.html">secondary
+ structure</a> and <a href="../webServices/proteinDisorder.html">disorder</a>.
+ If reference annotation is available for a the currently selected
+ sequences, it can be shown by selecting the <strong>Add
+ Reference Annotation</strong> option in the sequence or selection popup
+ menu.</li>
+ <li><strong>Group associated annotation.</strong><br />Data can
+ be associated with groups defined on the alignment. If sequence
+ groups are defined, <a href="../calculations/conservation.html">Conservation</a>
+ and <a href="../calculations/consensus.html">Consensus</a>
+ annotation can be enabled for each group from the <a
+ href="../menus/alwannotation.html">Annotations menu</a>, or can be
+ imported from a Jalview <a href="annotationsFormat.html">Annotations
+ file</a>.</li>
+ <li><strong>Alignment associated annotation.</strong><br />Annotation
+ rows associated with columns on the alignment are simply
+ 'alignment annotation'. Controls allow you to <a href="#iaannot">interactively
+ create alignment annotation</a> to add labels and symbols to
+ alignment columns. Jalview's consensus, conservation and quality
+ calculations also create histogram and sequence logo annotations
+ on the alignment.</li>
+ </ul>
+ <p>
+ <strong>Importing and exporting annotation</strong><br />
+ Annotations on an alignment view are saved in Jalview project files.
+ You can also load <a href="annotationsFormat.html">Annotations
+ Files</a> in order to add any kind of quantitative and symbolic
+ annotations to an alignment. To see an example, use the <strong>Export
+ Features/Annotation</strong> option from an alignment window's File menu.
+ </p>
+ <p>
+ <strong>Layout and display controls</strong><br /> Individual and
+ groups of annotation rows can be shown or hidden using the pop-up
+ menu obtained by right-clicking the label. You can also reorder them
+ by dragging the label to a new position with the left mouse button.
+ The <strong>Annotations</strong> menu provides settings controlling
+ the ordering and display of sequence, group and alignment associated
+ annotation. The <strong>Colour by annotation</strong> option in the
+ colour menu allows annotation to be used to <a
+ href="../colourSchemes/annotationColouring.html">shade the
+ alignment</a>. Annotations can also be used to <a
+ href="../features/columnFilterByAnnotation.html">select or
+ hide columns</a> via the dialog opened from the <strong>Selection</strong>
+ menu.
+ </p>
+ <p>
+ <strong>Sequence Highlighting and Selection from Annotation</strong>
+ </p>
+ <p>
+ A <strong>single click</strong> on the label of an annotation row
+ associated with sequences and sequence groups will cause the
+ associated sequences to be highlighted in the alignment view. <strong>Double
+ clicking</strong> the label will select the associated sequences, replacing
+ any existing selection. Like with other kinds of selection, <strong>shift
+ double-click</strong> will add associated sequences, and <strong>Ctrl
+ (Mac CMD) double-click</strong> will toggle inclusion of associated
+ sequences in the selection.
+ <p>
+ <strong>Interactive Alignment Annotation</strong>
+ </p>
+ <p>
+ <a name="iaannot"> Annotation rows</a> are added using the <strong>Annotation
+ Label</strong> menu, which is obtained by clicking anywhere on the
+ annotation row labels area (below the sequence ID area).
+ </p>
+ <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>Edit Label/Description</strong><br> <em>This
+ opens a dialog where you can change the name (displayed label),
+ or the description (as shown on the label tooltip) of the
+ clicked annotation. </em></li>
+ <li><strong>Hide This Row</strong><br> <em>Hides the
+ annotation row whose label was clicked in order to bring up the
+ menu.</em></li>
+ <li><strong>Hide All <em><label></em></strong><br> <em>Hides
+ all annotation rows whose label matches the one clicked. (This
+ option is only shown for annotations that relate to individual
+ sequences, not for whole alignment annotations. Since Jalview
+ 2.8.2.)</em></li>
+ <li><strong>Delete This 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>Export Annotation</strong> <em>(Application
+ only)</em><br> <em>Annotations can be saved to file or
+ output to a text window in either the Jalview annotations format
+ or as a spreadsheet style set of comma separated values (CSV). </em>
+ </li>
+ <li><strong>Show Values in Text Box</strong> <em>(applet
+ only)</em><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>
+ <li><strong>Scale Label To Column</strong><em>(introduced
+ in 2.5)</em><br> <em>Selecting this toggles whether column
+ labels will be shrunk to fit within each column, or displayed
+ using the view's standard font size.</em></li>
+ </ul>
+ <p>
+ <strong>Editing labels and secondary structure annotation
+ rows</strong>
+ </p>
+ <p>
+ Use the <strong>left mouse button</strong> to select a position
+ along the row that are to be annotated - these regions will be
+ coloured red. Press <strong>Control</strong> or <strong>shift</strong>
+ in combination with the left-click to either select an additional
+ position, or a range of positions on the alignment.
+ </p>
+ <p>
+ Once positions have been selected, use the <strong>right
+ mouse button</strong> and select one of the following from the <strong>annotation
+ menu</strong>:
+ </p>
+ <ul>
+ <li>Helix<br> <em>Marks selected positions with a
+ helix glyph (a red oval), and optional text label (see below). A
+ dialog box will open for you to enter the text. Consecutive
+ ovals will be rendered as an unbroken red line.</em>
+ </li>
+ <li>Sheet<br> <em>Marks selected positions with a
+ sheet glyph (a green arrow oriented from left to right), and
+ optional text label (see below). A dialog box will open for you
+ to enter the text. Consecutive arrows will be joined together to
+ form a single green arrow.</em>
+ </li>
+ <li><a name="rna">RNA Helix</a> (only shown when working with
+ nucleotide sequences)<br> <em>Marks selected positions
+ as participating in a base pair either upstream or downstream.
+ When the dialog box opens, enter a '(' to indicate these bases
+ pair with columns upstream (to right), and ')' to indicate this
+ region pairs with bases to the left of the highlighted columns.
+ Other kinds of base-pair annotation are also supported (e.g. 'A'
+ and 'a', or '<' and '>'), and Jalview will suggest an
+ appropriate symbol based on the closest unmatched parenthesis to
+ the left.<br />If any brackets do not match up, then an orange
+ square will highlight the first position where a bracket was
+ found not to match.
+ </em></li>
+ <li>Label<br> <em>Set the text label at the selected
+ positions. A dialog box will open for you to enter the text. If
+ more than one consecutive position is marked with the same
+ label, only the first position's label will be rendered.</em>
+ </li>
+ <li>Colour<br> <em>Changes the colour of the
+ annotation text label.</em>
+ </li>
+ <li>Remove Annotation<br> <em>Blanks any annotation
+ at the selected positions on the row. Note: <strong>This
+ cannot be undone</strong>
+ </em>
+ </li>
+ </ul>
+ <p>
+ User defined annotation is stored and retrieved using <a
+ href="../features/jalarchive.html">Jalview Archives</a>.
+ </p>
+ <p>
+ <em>Current Limitations</em>
+ </p>
+ <p>
+ The Jalview user interface does not support interactive creation and
+ editing of quantitative annotation (histograms and line graphs), or
+ to create annotation associated with a specific sequence or group.
+ It is also incapable of annotation grouping or changing the style of
+ existing annotation (e.g. to change between line or bar charts, or
+ to make multiple line graphs). These annotation capabilities are
+ only possible by the import of an <a href="annotationsFormat.html">Annotation
+ file</a>.<br>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff