-<html>
-<head><title>Alignment Conservation Annotation</title></head>
-<body><p><strong>Alignment Conservation Annotation</strong></p>
-<p>This is an automatically calculated quantitative alignment
-annotation which measures the number of conserved physico-chemical
-properties conserved for each column of the alignment. Its calculation
-is based on the one used in
- the AMAS method of multiple sequence alignment analysis :<br>
-<ul>Livingstone
- C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
- for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
- No. 6 (745-756)).
-</ul>
-</p>
-<p>Conservation is measured as a numerical index reflecting the
-conservation of physico-chemical properties in the alignment:
-Identities score highest, and the next most conserved group contain
-substitutions to amino acids lying in the same physico-chemical
-class.</p>
-
-<p><em>Colouring an alignment by conservation</em><br>
-Conservation scores can be used to colour an alignment. This is
-explained further in the help page for <a
-href="../colourSchemes/conservation.html">conservation colouring</a>.
-</p>
-</body>
-</html>
+<html>\r
+<head><title>Alignment Conservation Annotation</title></head>\r
+<body><p><strong>Alignment Conservation Annotation</strong></p>\r
+<p>This is an automatically calculated quantitative alignment\r
+annotation which measures the number of conserved physico-chemical\r
+properties conserved for each column of the alignment. Its calculation\r
+is based on the one used in\r
+ the AMAS method of multiple sequence alignment analysis :<br>\r
+<ul>Livingstone\r
+ C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
+ for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>\r
+ No. 6 (745-756)).\r
+</ul>\r
+</p>\r
+<p>Conservation is measured as a numerical index reflecting the conservation of \r
+ <a href="../misc/aaproperties.html">physico-chemical \r
+ properties</a> in the alignment: Identities score highest, and the next most \r
+ conserved group contain substitutions to amino acids lying in the same physico-chemical \r
+ class.</p>\r
+\r
+<p><em>Colouring an alignment by conservation</em><br>\r
+Conservation scores can be used to colour an alignment. This is\r
+explained further in the help page for <a\r
+href="../colourSchemes/conservation.html">conservation colouring</a>.\r
+</p>\r
+</body>\r
+</html>\r
<head><title>Editing</title></head>\r
<body>\r
<p><strong>Editing</strong></p>\r
+<p><em>Jalview 2.08 Enhancements -</em> Editing can be restricted to the current \r
+ selection area. This allows the user to "Lock" the alignment either \r
+ side of the selection area. Any gap insertions or deletions will only affect \r
+ the current selection area. </p>\r
+<p><img src="editing.jpg" width="428" height="186" align="top"></p>\r
+<p>In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, \r
+ the same number of gaps will be inserted at position 116, (between M and L). \r
+</p>\r
+<p>Editing is possible via the keyboard by toggling the Cursor mode on / off with \r
+ F2. A full list of keyboard editing actions is found <a href="../keys.html">here</a>. \r
+</p>\r
+<p><strong>Tip:</strong> For large alignments, deselect "Calculate -> \r
+ Autocalculate Consensus" to prevent the alignment performing lengthy calculations \r
+ after every edit. </p>\r
<p><em>Inserting / removing gaps</em> - hold down the "Shift" key. Click\r
a residue with the mouse and drag the residue to the right to insert gaps or\r
to the left to remove gaps.<br>\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
+<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><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
+</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
-<html>
-<head>
-<title>Jalview Archives</title>
-</head>
-<body>
-
-<p><strong>Jalview Project Archives</strong>
-</p>
-
-<p>These are java archives of an XML file containing alignments, trees
-and Jalview display information. A data exchange standard is currently
-being developed, so there is no stable schema yet, but Jalview web
-services will soon make use of the same interchange format.</p>
-</body>
-</html>
+<html>\r
+<head>\r
+<title>Jalview Archives</title>\r
+</head>\r
+<body>\r
+\r
+<p><strong>Jalview Project Archives</strong>\r
+</p>\r
+\r
+<p>These are java archives of an XML file containing alignments, trees and Jalview \r
+ display information. A data exchange standard is currently being developed, \r
+ so there is no stable schema yet, but Jalview web services will soon make use \r
+ of the same interchange format.</p>\r
+<p>For those who want to know...<br>\r
+ Jalview uses java classes automatically created using <a href="http://www.castor.org">Castor</a>. \r
+ Jalview 2.08 uses descriptor classes which significantly increase the speed \r
+ of marshalling / unmarshalling java objects into XML. Files created prior to \r
+ Jalview 2.08 can still be read in, but they will be saved in the new format. \r
+</p>\r
+</body>\r
+</html>\r
<p><em>Full Sequence ID</em> - If selected the ID panel will display the name of a sequence \r
plus the start and end residues in the format name/start-end. If not selected, \r
the displayed ID will be the name of the sequence.</p>\r
-<p><em>Font</em> - The default font name, size and style can be set for a new alignment \r
- window. </p>\r
+<p><em>Font</em> - The default font name, size and style can be set for a new \r
+ alignment window. </p>\r
+<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering \r
+ of the alignment.</p>\r
<p><em>Gap Symbol</em> - The default gap symbol may be set to either "-" or "."</p>\r
<p><em>Colour</em> - The default colour scheme for a new alignment window. If \r
the chosen option is "User Defined" then the last User Defined Colour \r
<p><strong>Search</strong></p>\r
<p>The search box is displayed by pressing Control and F or\r
selecting "Find..." from the "Search" menu.</p>\r
-<img src="search.gif">\r
-<p>"Find next" will find the next occurence of the specified\r
- and adjust the alignment window view to show it, and "Find\r
- all" highlights all matches for a pattern. The "Create new\r
- group" is a quick way to highlight and group residues matching\r
- the specified search pattern throughout the alignment.</p> \r
+<img src="search.gif" width="339" height="111">\r
+<p>"Find next" will find the next occurence of the specified and adjust \r
+ the alignment window view to show it, and "Find all" highlights all \r
+ matches for a pattern. The "New Feature" is a quick way to highlight \r
+ and group residues matching the specified search pattern throughout the alignment. \r
+ If "New Feature" is selected, the feature can be given a name from \r
+ a popup input box. Use the "Feature Settings" under the "View" \r
+ menu to change the visibility and colour of the new sequence feature.</p> \r
<ul>\r
<li>The search uses regular expressions. (understands a mixture of\r
posix and perl style regex - see below for a summary)</li>\r
<html>\r
<head><title>Sequence Features</title></head>\r
<body>\r
-<p><strong>View→Sequence Features</strong></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>Jalview will attempt to retrieve sequence features from Uniprot files using \r
the EBI dbFetch web service using the given sequence names. A 100% match with \r
the Uniprot record is required to view the Sequence Features.</p>\r
-<p>More information about the feature is given in a tooltip, which is\r
- viewed by moving the mouse pointer over a sequence feature. The\r
- description associated with the feature will then be displayed in a small\r
- label near the pointer.</p>\r
+<p>More information about the feature is given in a tooltip, which is viewed by \r
+ moving the mouse pointer over a sequence feature. The description associated \r
+ with the feature will then be displayed in a small label near the pointer.</p>\r
+<p><strong>View→Show Sequence Features</strong></p>\r
+<p>Select whether to view the sequence features added to this alignment or not.</p>\r
<p><strong>View→Feature Settings...</strong>\r
<p>Once sequence features have been loaded onto an alignment features can be hidden \r
or have their rendering priority changed using the Feature Settings dialog. \r
sequence and a Uniprot record was identified, but the sequence name\r
must be manually changed (by right clicking on the sequence ID and selecting\r
<strong>Sequence→Edit Name</strong>), before Jalview will show its sequence\r
- features.<ul>\r
- <li>remember to save your alignment if you have updated any of the\r
- sequence IDs!\r
- </li>\r
- </ul></p>\r
+ features.\r
+<ul>\r
+ <li>remember to save your alignment if you have updated any of the sequence \r
+ IDs! </li>\r
+</ul>\r
+<p>Precalculated Sequence Features may be added to an alignment from the command \r
+ line, drag and drop, or from the "File->Load Features / Annotations" \r
+ menu item. See the <a href="featuresFormat.html">Features File Format</a> for \r
+ more details.</p>\r
</body>\r
</html>\r
<p>Control 'F' - Launches the search window. </p>\r
<p>Up Arrow - Moves selected sequence(s) up the alignment</p>\r
<p>Down Arrow - Moves selected sequence(s) down the alignment.</p>\r
+<p>F1 - Show Help Documentation</p>\r
+<p>F2 - Toggle Cursor mode on / off</p>\r
+<p>With Cursor mode on....</p>\r
+<ul>\r
+ <li>Cursor keys - Move cursor around the alignment.</li>\r
+</ul>\r
+<ul>\r
+ <li>Space - Insert a gap at the cursor position. <br>\r
+ To insert 12 spaces at the current cursor, type 12 before pressing Space.<br>\r
+ To group insert, hold control or shift together with space.</li>\r
+</ul>\r
+<ul>\r
+ <li>Delete - Delete a gap at the cursor position.<br>\r
+ To delete 12 spaces at the current cursor, type 12 before pressing Delete.<br>\r
+ To group delete, hold down control or shift together with Delete.</li>\r
+</ul>\r
+<ul>\r
+ <li>S - Type a number x then press 'S' to jump to sequence x.</li>\r
+</ul>\r
+<ul>\r
+ <li>C - Type a number x then press 'C' to jump to column x.</li>\r
+</ul>\r
+<ul>\r
+ <li>P - Type a number x then press 'P' to jump to position x in current sequence.</li>\r
+</ul>\r
+<ul>\r
+ <li>Q - Define the top left corner of the selection area</li>\r
+</ul>\r
+<ul>\r
+ <li>M - Define the bottom right corner of the selection area</li>\r
+</ul>\r
+<p> </p>\r
<p> </p>\r
</body>\r
</html>\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>Jalview load 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<br>\r
</strong><em>Close the alignment window. Make sure you have saved your \r
alignment before you close - either as a Jalview project or by using the \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
<ul>\r
<li><strong>Colour</strong></li>\r
</ul>\r
-<blockquote>\r
+<blockquote> \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
+ </strong><em>If this is selected, any changes made to the background colour \r
will be applied to all currently defined groups.<br>\r
</em></li>\r
- <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,\r
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried\r
- Index, Nucleotide, User Defined<br>\r
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for\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><br>\r
</li>\r
<li><strong>By Conservation<br>\r
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring \r
by Conservation</a>.</em><br>\r
</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\r
- conservation' option appears to be doing nothing!</em><br></li>\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><br>\r
+ </li>\r
<li><strong>Above Identity Threshold<br>\r
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage \r
Identity</a></em><strong>.<br>\r
</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
+ </strong><em>Use this to set the threshold value for colouring above Identity. \r
+ Useful if the window has been closed.<br>\r
+ </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
</blockquote>\r
</body>\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. <br>\r
+ dialog box, which is shown when this item is selected. Select a "Monospaced" \r
+ font for fast rendering of your alignment. The checkbox labelled "Monospaced" \r
+ indicates whether the chosen font uses characters all of the same width.<br>\r
+ </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.<br>\r
</em></li>\r
<li><strong>Wrap<br>\r
</strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>" \r
<li><strong>Seqence Settings </strong><em><br>\r
<em>If features have been added to the alignment then the priority of rendering \r
the features can be altered so that overlapping features can be displayed \r
- or hidden. See <a href="features/seqfeatures.html">Sequence Features</a>.</em><br>\r
+ or hidden. See <a href="../features/seqfeatures.html">Sequence Features</a>.</em><br>\r
</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 small \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<br>\r
- </strong><em>You may edit the name of each sequence. A window will be \r
- displayed asking for a new sequence name to be entered. Press OK to accept \r
- your edit.</em><strong><br>\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><strong><br>\r
</strong></li>\r
<li><strong>View PDB Structure<br>\r
</strong><em>\r
<p><strong>Release History</strong> </p>\r
<table border="1">\r
<tr> \r
- <td><div align="center"><em><strong>Release</strong></em></div></td>\r
- <td><div align="center"><em><strong>New Features</strong></em></div></td>\r
- <td><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
+ <td width="71"><div align="center"><em><strong>Release</strong></em></div></td>\r
+ <td width="343"><div align="center"><em><strong>New Features</strong></em></div></td>\r
+ <td width="358"><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.08</strong><br>\r
+ 6/4/06</div></td>\r
+ <td><ul>\r
+ <li>Editing can be locked to selection area</li>\r
+ <li>Keyboard editing</li>\r
+ <li>Create sequence features from Searches</li>\r
+ <li>Precalculated annotations can be loaded onto alignments</li>\r
+ <li>Features file allows grouping of features</li>\r
+ <li>Annotation Colouring scheme added</li>\r
+ <li>Smooth fonts off by default - Faster rendering</li>\r
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Drag & Drop fixed on Linux</li>\r
+ <li>Jalview Archive file faster to load/save, sequence descriptions saved. \r
+ </li>\r
+ </ul></td>\r
</tr>\r
<tr> \r
<td><div align="center"><strong>2.07</strong><br>\r
</ul></td>\r
</tr>\r
<tr> \r
- <td height="63">\r
-<div align="center"><strong>2.05b</strong><br>\r
+ <td height="63"> <div align="center"><strong>2.05b</strong><br>\r
15/9/05</div></td>\r
<td><ul>\r
<li>Choose EPS export as lineart or text</li>\r
<head><title>What's new ?</title></head>\r
<body>\r
<p><strong>What's new ?</strong> </p>\r
-<p>Jalview Version 2.07 </p>\r
-<p><a href="features/seqfetch.html">Sequence Fetcher</a> has been added to quickly\r
- retrieve sequences with known ids from several databases.</p>\r
-<p><a href="features/seqfeatures.html">Sequence Features enhanced</a> to allow\r
- the user to display all features of a Uniprot file on the alignment and subsequently\r
- colour, hide or show overlapping features. </p>\r
-<p><a href="io/fileformats.html">Choose to omit /start-end from sequences when\r
- saving files.</a> This is important for saving files to be used by some programs\r
- which cannot read the original Jalview sequence output with the appended /start-end.</p>\r
-<p><a href="features/pdbviewer.html">PDB structure viewer enhanced</a>. Mapping\r
- between sequence and structure has been enhanced, colours on the alignment are\r
- reflected in the structure viewer.</p>\r
-<p><a href="http://www.jalview.org/examples/applets.html">Jalview Applet can read\r
- in feature files, PDB files be used as input to HTML form</a> See the website\r
- to find out the new parameters available for the Applet Version of Jalview.</p>\r
-<p> </p>\r
+<p>Jalview Version 2.08</p>\r
+<p> <a href="editing/index.html">Editing</a> can be locked to selection area. \r
+ Any edits made within the locked area do not affect the rest of the alignment.</p>\r
+<p> Keyboard editing - press F2 to toggle Cursor mode 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
+ Previously results from searches were added as alignment positions, which was \r
+ wrong. Now the search results are saved as sequence features and their visibility \r
+ and colour can be modified using the <a href="features/seqfeatures.html">Sequence \r
+ Feature Settings</a> window.</p>\r
+<p> Precalculated annotations can be loaded onto alignments. The <a href="features/annotationsFormat.html">Annotation \r
+ File</a> format is a tab delimited set of values.</p>\r
+<p> <a href="features/featuresFormat.html">Features file</a> allows grouping of \r
+ features. The <a href="features/seqfeatures.html">Sequence Feature Settings</a> \r
+ window then makes it very easy to set the visibility of groups of features. \r
+</p>\r
+<p> <a href="colourSchemes/annotationColouring.html">Annotation Colouring</a> \r
+ scheme added. A new colour scheme which colours columns on a per-column value.</p>\r
+<p> Smooth fonts off by default - Faster rendering. Toggle on / off from the View \r
+ menu, or can be set in Preferences.</p>\r
+<p> Choose to toggle Autocalculate Consensus On/Off from the Calculate menu.<br>\r
+</p>\r
<p><strong>Issues Resolved</strong></p>\r
-<p>Group Editing is possible with Control and mouse click. Alt key and mouse press\r
- does not work as this translates as the middle mouse button, which since 2.04\r
- is now used to scroll the alignment and change the font size. </p>\r
-<p>HTML export now writes groups and features which were previously missing.</p>\r
-<p> </p>\r
+<p> Drag & Drop fixed on Linux</p>\r
+<p> Jalview Archive file faster to load/save, sequence descriptions saved.<br>\r
+</p>\r
<p>See the <a href="releases.html">Release History</a> page for details of all\r
new features and resolved issues. </p>\r
</body>\r
git://source.jalview.org / jalview.git / commitdiff
