<mapID target="jnet" url="html/webServices/jnet.html"/>\r
<mapID target="seqfetch" url="html/features/seqfetch.html"/>\r
<mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
+ <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>\r
<mapID target="pdbviewer" url="html/features/pdbviewer.html"/>\r
<mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>\r
<mapID target="preferences" url="html/features/preferences.html"/> \r
target="editInSelArea"/>\r
<tocitem text="User Defined Sequence Features" target="search"/>\r
<tocitem text="Sequence Feature Groups" target="seqfeatures"/>\r
+ <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
<tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>\r
<tocitem text="Annotations File" target="annotations.fileformat"/>\r
</tocitem>\r
<tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
<tocitem text="Conservation" target="calcs.alconserv"/>\r
<tocitem text="Quality" target="calcs.alquality"/>\r
+ <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
</tocitem>\r
<tocitem text="Input / Output" target="io"/>\r
<tocitem text="Key Strokes" target="keys"/>\r
<tocitem text="Making figures" target="export"/>\r
<tocitem text="Editing Alignments" target ="edit"/>\r
- <tocitem text="Sequence Features" target="seqfeatures"/>\r
+ <tocitem text="Sequence Features" target="seqfeatures" expand="false">\r
+ <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
+ <tocitem text="Sequence Features File" target="features.fileformat"/>\r
+ </tocitem>\r
<tocitem text="Web Services" target="webservice" expand="false">\r
<tocitem text="Clustal Alignment" target="clustal"/>\r
<tocitem text="Muscle Alignment" target="muscle"/>\r
<body>\r
<p><strong>Alignment Annotation</strong></p>\r
\r
-<p>In addition to the definition of groups and sequence features, Jalview also \r
- allows you to mark particular columns of an alignment and add symbols and text \r
+<p>In addition to the definition of groups and sequence features,\r
+ Jalview can display symbols and graphs under the columns of an\r
+ alignment, and allow you to mark particular columns of an alignment and add symbols and text \r
in the annotation area shown below the alignment (which may be hidden if <strong>View→Show \r
Annotation</strong> 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
+<p>Web services can also add annotation to an alignment (see the\r
+ <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic\r
+ annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations \r
+ File</a> for more details.</p>\r
\r
<p>\r
Annotation rows are added using the <strong>Annotation Label</strong>\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
+User defined annotation is stored and retrieved using <a\r
+href="../features/jalarchive.html">Jalview Archives</a>.\r
</p>\r
<p><em>Current Limitations</em></p>\r
\r
placed at the <em>startIndex</em>'th column.</p><p>Sequence associations\r
are turned off for subsequent annotation definitions by:\r
<strong><pre>SEQUENCE_REF	ALIGNMENT</pre></strong></p>\r
-<p><em>LINE_GRAPH</em> type annotations can be given a colour,\r
- combined onto the same vertical axis, and have abscissa (lines of\r
- constant value - <em>so they are horizontal</em>) at particular\r
- values using the following lines (respectively):<!--</p>\r
-<p><font size="3" face="Courier New, Courier, mono">-->\r
-<strong><pre>COLOUR	graph name	colour\r
-COMBINE	graph 1 name	graph 2 name\r
-GRAPHLINE	graph name	value	label	colour</pre></strong></p>\r
-<p>An example Annotation file is given below:</p>\r
-<p><font size="3" face="Courier New, Courier, mono">#Comment lines follow the hash symbol<br>\r
- JALVIEW_ANNOTATION<br>\r
- SEQUENCE_REF FER1_MESCR 5<br>\r
- BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\r
- LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2<br>\r
- LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2<br>\r
- BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>\r
- NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>\r
- NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">COLOUR	Bar Graph 2	blue<br>\r
- COLOUR	Red Values	255,0,0<br>\r
- COLOUR	Green Values	green<br>\r
- COLOUR	Purple Letters	151,52,228<br>\r
- COMBINE	Green Values	Red Values</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">GRAPHLINE	Red Values	2.6	threshold	black \r
- </font><br>\r
-</p>\r
-<p><br>\r
-</p>\r
+<p><em>LINE_GRAPH</em> type annotations can be given a colour\r
+ (specified as 24 bit RGB triplet in hexadecimal or comma separated values),\r
+ combined onto the same vertical axis, and have ordinate lines (horizontal\r
+ lines at a particular vertical axis value) using the following\r
+ commands (respectively):\r
+<strong><pre>COLOUR	<em>graph_name</em>	<em>colour</em>\r
+COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>\r
+GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em></pre></strong>\r
+<p>An example Annotation file is given below:\r
+<pre>#Comment lines follow the hash symbol\r
+JALVIEW_ANNOTATION\r
+SEQUENCE_REF	FER1_MESCR	5\r
+BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+\r
+LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2\r
+LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2\r
+BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4\r
+NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||\r
+NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n\r
+COLOUR	Bar Graph 2	blue\r
+COLOUR	Red Values	255,0,0\r
+COLOUR	Green Values	green\r
+COLOUR	Purple Letters	151,52,228\r
+COMBINE	Green Values	Red Values\r
+GRAPHLINE	Red Values	2.6	threshold	black\r
+</pre></p>\r
</body>\r
</html>\r
<p><strong>Sequence Features</strong></p>\r
<p>Jalview can colour parts of a sequence based on the presence of\r
sequence features - which may be retrieved from database records (such\r
-as Uniprot), the result of <a href="../search.html">sequence motif\r
-searches</a> or simply read from a <a href="featuresFormat.html">sequence features file</a>.</p>\r
+as Uniprot), the result of <a href="search.html">sequence motif\r
+searches</a> or simply read from a <a\r
+href="featuresFormat.html">sequence features file</a>.</p>\r
+<p><strong>Sequence Feature Groups</strong></p>\r
+<p>Since Jalview 2.08, sequence features assigned to a sequence can be\r
+organised into groups, which may indicate that the features were all retrieved\r
+from the same database (such as Uniprot features), or generated by the\r
+same analysis process (as might be specified in a <a\r
+href="featuresFormat.html">sequence features file</a>).</p>\r
+<p><strong>Sequence Feature Inheritance</strong></p>\r
+<p>Since Jalview 2.07, sequence features are <em>global</em> to a set of\r
+sequences appearing (independently or together) in many different\r
+alignments. Practically, this means features loaded onto one alignment\r
+can be viewed in any alignments involving the same sequences. The same\r
+sequence appears in different alignments when a new alignment is\r
+generated by submitting an existing set of sequences to one of the\r
+alignment or prediction web services, and when sequences are copied\r
+and pasted into other alignment windows.</p>\r
<p><strong>View→Fetch Sequence Features</strong></p>\r
<p>When this option is selected, sequence features extracted from the <a href="http://www.ebi.uniprot.org/">Uniprot</a> \r
record for each sequence are displayed on the alignment.</p>\r
<p>Toggle the display of sequence features in this alignment.</p>\r
<p><strong>View→Feature Settings...</strong>\r
<p>Once sequence features have been loaded, their display can be fully\r
- controlled using the alignment window's Feature Settings dialog box\r
- :</p>\r
-<img src="appFeatureSettings.gif" align="left"/>\r
-\r
-<p> features can be hidden \r
- or have their rendering priority changed using the Feature Settings dialog. \r
- This displays all the features loaded, the colour and whether to display the \r
- feature or not. You can easily change the colour by clicking the colour box.<br>\r
- It is important to realise that the order in which features are drawn to the \r
- alignment may result in overlapping features being hidden. Features at the foot \r
- of the table are rendered first. Therefore features higher up the table will \r
- be drawn over the top of lower featrues. You can change the order of the feature \r
- priority by dragging the feature with your mouse. <br>\r
- Use the transparency setting as another way to visualise overlapping features. \r
-<p><strong><em>You can save all features, with their current colours and visibility \r
- in a Jalview format file. </em></strong>\r
+ controlled using the alignment window's <a\r
+ href="featuresettings.html">Sequence Feature Settings</a> dialog\r
+ box. Feature colour schemes and display parameters are unique to a\r
+ particular alignment, so it is possible to colour the same sequence\r
+ features differently in different alignment views.</p>\r
<p><strong>The Sequence Identification Process</strong>\r
\r
</p>\r
<tr>\r
<td><strong>Control 'F'</strong></td><td>Both</td><td>Launches the search\r
window</td></tr>\r
-<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a numeric parameter [p] for a cursor movement or edit command</td></tr>\r
+</table>\r
+<p>The compound commands available in the Cursor mode are summarised\r
+below. Single letter commands can be prefixed by digits to specify a repetition\r
+number, and some more complex commands take one or more numeric\r
+parameters (prefixing the command key and separated by commas).</p>\r
+<table border=1><tr><td><strong>Compound\r
+Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>\r
+<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a\r
+numeric parameter (<strong>[p]</strong>) or repetition number for a cursor movement or edit\r
+command.</td></tr>\r
<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or more numeric parameters ([p1],[p2]) for a command.</td></tr>\r
-<tr><td><strong>[p1],[p2]Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (p1) and row (p2) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>\r
+<tr><td><strong>[p1],[p2]<br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (p1) and row (p2) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>\r
<tr><td><strong>[p1]S</strong></td><td>Cursor</td><td>Jump to the p1'th sequence in the alignment.</td></tr>\r
<tr><td><strong>[p1]P</strong></td><td>Cursor</td><td>Jump to p1'th amino acid in current sequence.</td></tr>\r
<tr><td><strong>[p1]C</strong></td><td>Cursor</td><td>Jump to p1'th column in the alignment.</td></tr>\r
<tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>\r
<tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>\r
-<tr><td><strong>[p1]Space</strong></td><td>Cursor</td><td>Inserts p1 gaps at the current position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
-<tr><td><strong>[p1]Delete</strong></td><td>Cursor</td><td>Remove p1 gaps at the cursor position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
+<tr><td><strong>[p1]<br>Space</strong></td><td>Cursor</td><td>Inserts p1 gaps at the current position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
+<tr><td><strong>[p1]<br>Delete</strong></td><td>Cursor</td><td>Remove p1 gaps at the cursor position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
</table>\r
<p> </p>\r
<p> </p>\r
<body>\r
<p><strong>What's new ?</strong> </p>\r
<p>Jalview Version 2.08</p>\r
-<p> <a href="editing/index.html">Editing</a> can be locked to the selection area. \r
- Any edits made within the locked area do not affect the rest of the alignment.</p>\r
+<p><a href="editing/index.html">Editing</a> can be <a href="editing/selectionAreas.html">locked to the\r
+ selection area</a> so that any edits made within the locked area do\r
+ not unexpectedly shift other parts of the alignment.</p>\r
<p> Keyboard editing - press F2 to toggle <a href="features/cursorMode.html">cursor mode</a> On / Off. For a full list \r
of keyboard controls, look <a href="keys.html">here</a>.</p>\r
<p> <a href="features/search.html">Create sequence features from searches</a>. \r
</p>\r
<p>Sequence feature display and rendering has also been enhanced, with\r
the addition of sequence feature groups (which can be used to show\r
- or hide a set of feature types <em>en masse</em>) and user defined\r
+ or hide a set of features <em>en masse</em>) and user defined\r
feature colours as well as transparency controls, using the <a\r
- href="features/seqfeatures.html">Sequence Feature Settings</a>\r
+ href="features/featuresettings.html">Sequence Feature Settings</a>\r
window. The <a href="features/featuresFormat.html">Features file</a>\r
has also been extended to accomodate these enhancements.</p>\r
<p>Alignment annotation and colouring is also considerably\r
git://source.jalview.org / jalview.git / commitdiff