<mapID target="webservice" url="html/webServices/index.html"/>\r
<mapID target="clustal" url="html/webServices/clustalw.html"/>\r
<mapID target="muscle" url="html/webServices/muscle.html"/>\r
+ <mapID target="mafft" url="html/webServices/mafft.html"/>\r
<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
<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="annotations.fileformat" url="html/features/annotationsFormat.html"/>\r
- <mapID target="features.fileformat" url="html/features/featuresFormat.html"/> \r
+ <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>\r
+ <mapID target="das.settings" url="html/features/dassettings.html"/>\r
<mapID target="edit" url="html/editing/index.html"/>\r
- <mapID target="edit.selareas" url="html/editing/selectionAreas.html"/>\r
<mapID target="jalarchive" url="html/features/jalarchive.html"/>\r
<mapID target="trees" url="html/calculations/tree.html"/>\r
<mapID target="sorting" url="html/calculations/sorting.html"/>\r
<mapID target="pca" url="html/calculations/pca.html"/>\r
<mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
<mapID target="redundancy" url="html/calculations/redundancy.html"/>\r
+ <mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>\r
\r
<mapID target="colours" url="html/colourSchemes/index.html" />\r
<mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>\r
<toc version="1.0">\r
<tocitem text="Jalview Documentation" target="home" expand="true" >\r
<tocitem text="What's new" target="new" expand="false">\r
- <tocitem text="Cursor Mode" target="cursor"/>\r
- <tocitem text="Selection Area Based Editing" target="edit.selareas"/>\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 text="Colour by Annotation Value" target="colours.annotation"/>\r
- <tocitem text="Modeller PIR File IO" target="io.modellerpir"/>\r
+ <tocitem text="MAFFT Alignment" target="mafft"/>\r
+ <tocitem text="DAS Feature Fetching" target="das.settings"/>\r
+ <tocitem text="Hide Regions" target="hiddenRegions"/> \r
</tocitem>\r
- <tocitem text="Release History" target="release"/>\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="Consensus" target="calcs.consensus"/>\r
- <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
- </tocitem>\r
- <tocitem text="Input / Output" target="io"/>\r
+ <tocitem text="Release History" target="release"/>\r
+ <tocitem text="Editing Alignments" target ="edit"/> \r
+ <tocitem text="Cursor Mode" target="cursor"/>\r
<tocitem text="Key Strokes" target="keys"/>\r
+ <tocitem text="Input / Output" target="io"/>\r
<tocitem text="Making figures" target="export"/>\r
- <tocitem text="Editing Alignments" target ="edit"/>\r
+ <tocitem text="Hidden Regions" target="hiddenRegions"/>\r
+ <tocitem text="Viewing PDB Files" target="viewingpdbs"/>\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 text="User Defined Sequence Features" target="search"/>\r
+ <tocitem text="DAS Features Settings" target="das.settings"/>\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
+ <tocitem text="MAFFT Alignment" target="mafft"/>\r
<tocitem text="JNet Prediction" target="jnet"/>\r
</tocitem>\r
<tocitem text="Colour Schemes" target="colours" expand="false">\r
<tocitem text="Pairwise Alignments" target="pairwise"/>\r
<tocitem text="Remove Redundancy" target="redundancy"/>\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="Consensus" target="calcs.consensus"/>\r
+ <tocitem text="Annotations File Format" target="annotations.fileformat"/>\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
contain only space characters ("-" or "." or " ")</p>\r
<p><em>Removing gaps</em> - Removes all gaps from the alignment. Gaps are "-"\r
or "." or " ".</p>\r
-<p><em>Set gap character</em> - Switches the gap character between "."\r
- and "-". If the "Render Gaps" option from the "View"\r
+<p><em>Set gap character</em> - Switches the gap character between "." \r
+ and "-". If the "Render Gaps" option from the "View" \r
menu is unticked all gaps will appear as blank spaces.</p>\r
<p> </p>\r
+<p><strong>Editing In Selection Areas</strong></p>\r
+<a href="index.html">Editing</a> can be restricted to the current selection area. \r
+This allows the user to "Lock" the alignment either side of the selection \r
+area. Any gap insertions or deletions will only affect the current selection area.\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><em>Locked selection area based editing was introduced in Jalview 2.08</em></p>\r
+<p> </p>\r
</body>\r
</html>\r
-<html>
-<head>
-<title>Sequence Feature Settings Dialog Box</title>
-</head>
-<body>
-<p><strong>Sequence Feature Settings Dialog Box</strong></p>
-<p>Select <strong>View→Feature Settings...</strong> menu entry in
-an alignment window to open the feature settings dialog box, which
-allows you to precisely control the presence and appearance of
-sequence features for the current alignment.</p>
-<center><img src="appFeatureSettings.gif" align="center"><br>Sequence Feature
- Settings for the Jalview Application</img></center>
-<p>The top section of the dialog box lists all the sequence feature
- groups, along with a tickbox for each that controls whether its
- features are displayed. The table in the middle lists all the
- features in the currently selected groups, along with their display
- colour and whether they are currently being displayed (only the
- ticked features and groups are displayed). <strong><em>You can change the
- colour used for a feature in the associated alignment by clicking on
- its colour box.</em></strong></p>
-<p><strong>Transparency and Feature Ordering</strong></p><p>
- It is important to realise that sequence features are often not
- distinct and often overlap (for example, a metal binding site
- feature may be attached to one position along a stretch of sequence
- marked with a secondary structure feature).</p>
-<p>The ordering of the sequence features in the dialog box list is the
- order used by jalview for rendering sequence features. A feature at
- the bottom of the list is rendered <em>below</em> a feature higher
- up in the list.<br><em><strong>You can change the order of a feature
- by dragging it up and down the list with the
- mouse</strong></em>.</p>
-<p>
- The <strong><em>transparency slider setting</em></strong> (currently only available
- in the application version) controls the visibility of features
- rendered below other features. Reducing the transparency will mean
- that features at the top of the list can obscure features lower
- down, and increasing it allows the user to 'see through' the upper
- layers of a set of features.</p>
-<p><strong><em>You can save all features, with their current colours and visibility
- in a Jalview format file. </em></strong>
-</p>
-</body>
-</html>
+<html>\r
+<head>\r
+<title>Sequence Feature Settings Dialog Box</title>\r
+</head>\r
+<body>\r
+<p><strong>Sequence Feature Settings Dialog Box</strong></p>\r
+<p>Select <strong>View→Feature Settings...</strong> menu entry in\r
+an alignment window to open the feature settings dialog box, which\r
+allows you to precisely control the presence and appearance of\r
+sequence features for the current alignment.</p>\r
+<center>\r
+ <img src="featureSettings.gif" width="432" height="327"> <br>\r
+ Sequence Feature\r
+ Settings for the Jalview Application</img></center>\r
+<p>The top section of the dialog box lists all the sequence feature\r
+ groups, along with a tickbox for each that controls whether its\r
+ features are displayed. The table in the middle lists all the\r
+ features in the currently selected groups, along with their display\r
+ colour and whether they are currently being displayed (only the\r
+ ticked features and groups are displayed). <strong><em>You can change the\r
+ colour used for a feature in the associated alignment by clicking on\r
+ its colour box.</em></strong></p>\r
+<p><strong>Transparency and Feature Ordering</strong></p><p>\r
+ It is important to realise that sequence features are often not\r
+ distinct and often overlap (for example, a metal binding site\r
+ feature may be attached to one position along a stretch of sequence\r
+ marked with a secondary structure feature).</p>\r
+<p>The ordering of the sequence features in the dialog box list is the\r
+ order used by jalview for rendering sequence features. A feature at\r
+ the bottom of the list is rendered <em>below</em> a feature higher\r
+ up in the list.<br><em><strong>You can change the order of a feature\r
+ by dragging it up and down the list with the\r
+ mouse</strong></em>.</p>\r
+<p>\r
+ The <strong><em>transparency slider setting</em></strong> (currently only available\r
+ in the application version) controls the visibility of features\r
+ rendered below other features. Reducing the transparency will mean\r
+ that features at the top of the list can obscure features lower\r
+ down, and increasing it allows the user to 'see through' the upper\r
+ layers of a set of features.</p>\r
+<p><strong><em>You can save all features, with their current colours and visibility \r
+ in a Jalview format file. </em></strong>\r
+</p>\r
+</body>\r
+</html>\r
diagrams and publications.</em>\r
</li></ul>\r
\r
-<p><em>Tips for working with EPS Files</em></p><li>The EPS file generated by jalview contains vector\r
- graphics which are directly editable in graphics applications such as\r
- Adobe Illustrator.</li>\r
+<p><em>Tips for working with EPS Files</em></p>\r
+<li>The EPS file generated by jalview contains vector graphics which are directly \r
+ editable in graphics applications such as Adobe Illustrator.</li>\r
+<li>EPS files can be produced as "Text" or "Lineart". Use \r
+ "Text" if you want the final document to be MUCH smaller in diskspace \r
+ and be able to search, edit and select text. Use "Lineart" if you \r
+ want an exact image of the alignment as displayed in Jalview. This is useful \r
+ if a 3rd Party EPS viewer does not have the same Font which the EPS file was \r
+ created with.</li>\r
<li>When importing an EPS into to a Microsoft office document, a snapshot image of the\r
file will be displayed which often looks blurred. Right-click the\r
image and choose "Edit image." to convert it to word\r
<head><title>What's new ?</title></head>\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 <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
- Previously, the regions of sequences highlighted as the result of\r
- searches were added as new regions in the alignment. Now, the sequence region\r
- selected by a search can be used to define named sequences features\r
- attached to the sequence, rather than the alignment.\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 features <em>en masse</em>) and user defined\r
- feature colours as well as transparency controls, using the <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
- enhanced. Precalculated symbolic and quantitative annotations (text labels,\r
- secondary structure symbols and multiple scalar graphs) can now be\r
- loaded onto alignments via the <a\r
- href="features/annotationsFormat.html">Annotation\r
- File</a>. Additionally, the <a\r
- href="colourSchemes/annotationColouring.html">Annotation\r
- Colouring</a> dialog box allows an alignment to be coloured based on\r
- any of the graphed quantities with which it is annotated.</p>\r
-<p>Rendering speed has been improved by disabling anti-aliasing via\r
- the <strong>Smooth Fonts</strong>\r
- option in the <strong>View \r
- menu</strong> (its default set in <strong>Preferences</strong>). In addition, response\r
- times when editing alignments can be reduced by turning off the automatic\r
- calculation of amino acid property Consensus (which has been\r
- reintroduced to the <strong>Calculate</strong> menu as <strong>Autocalculate Consensus</strong>).<br>\r
-</p>\r
+<p>Jalview Version 2.1</p>\r
+<p>The multiple sequence alignment program <a href="webServices/mafft.html">MAFFT</a> \r
+ is available from the default Web Service list.</p>\r
+<p>The sequence feature retrieval system using DBFetch from EBI has been replaced \r
+ with <a href="features/dassettings.html">DAS Feature fetching</a> capabilities.</p>\r
+<p><a href="features/hiddenRegions.html">Hide sequences and columns</a></p>\r
+<p>Export Annotations and Features</p>\r
+<p>GFF file reading / writing</p>\r
+<p>Associate structures with sequences from local PDB files</p>\r
+<p>Add sequences to exisiting alignment</p>\r
+<p>Recently opened files / URL lists</p>\r
+<p>Applet can launch the full application</p>\r
+<p>Applet has transparency for features (Java 1.2 required)</p>\r
+<p>Applet has user defined colours parameter</p>\r
+<p> </p>\r
<p><strong>Issues Resolved</strong></p>\r
-<ul>\r
-<li>Drag & Drop now works on common Linux desktops (at least KDE\r
-and Gnome)</li>\r
-<li>Jalview XML Archive Input/Output is now faster (using an\r
-internal Jalview schema), and sequence description strings are now\r
-preserved in the archive.</li>\r
-<li>Jalview can now correctly read and write <a\r
-href="io/modellerpir.html">MODELLER style\r
-PIR</a> files.\r
-</li>\r
-</ul>\r
+<p>Redundancy Panel reinstalled in the Applet</p>\r
+<p>Monospaced font - EPS / rescaling bug fixed</p>\r
+<p>Annotation files with sequence references bug fixed</p>\r
+<p> </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
