<html>
-<head><title>What's new ?</title></head>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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>What's new ?</title>
+</head>
<body>
-<p><strong>What's new ?</strong> </p>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ Jalview 2.8.2 is the first release produced by our new core
+ development team.<br /> It incorporates many minor improvements and
+ bug-fixes, and new features for working with 3D structure data,
+ shading alignments by secondary structure and generation of alignment
+ figures as Scalable Vector Graphics. <br />The majority of
+ improvements in this version of Jalview concern the desktop
+ application. As ever, the highlights are detailed below,
+ and the full list is given in the <a
+ href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
+ </p>
+ <p>
+ <strong>Annotation visualisation</strong> <br /> The alignment window
+ includes a new <em>Annotations</em> menu which provides controls for
+ the layout and display of sequence, group and alignment associated
+ annotation rows. It also now includes the <em>Autocalculated
+ Annotation</em> submenu (formerly located in the View menu), which
+ includes settings for the calculation and display of sequence
+ consensus, logos, and amino acid conservation for the alignment and
+ subgroups.
+ </p>
+ <p>
+ <strong>Sequence associated annotation</strong><br /> New controls
+ have also been added to the Sequence ID popup menu for the propagation
+ and display of sequence associated annotation such as secondary
+ structure assignments and disorder predictions. Annotation associated
+ with one or a group of sequence already shown on the alignment may be
+ shown or hidden, and any available annotation from 3D structure or
+ calculations performed in other Jalview windows can be copied to the
+ alignment
+ <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
+ The <strong>Colour by annotation</strong> function has also been
+ improved, allowing secondary structure annotation to be used to shade
+ sequences and alignment columns. Protein sequences can be coloured
+ according to the presence of a helix or sheet at each position, and
+ RNA sequences can be shaded according to each structure's stem/helix
+ pattern - which enables different RNA folding topologies to be quickly
+ identified.
+ </p>
+ <p>
+ <strong>3D Structural data analysis and display</strong><br />
+ Jalview now employs Jmol's PDB data API to retrieve secondary
+ structure assignments made by the DSSP algorithm. It can also employ
+ web services to obtain secondary structure assignments from RNA
+ structures. These assignments are shown as sequence associated
+ annotation for sequences which have cross-references to the PDB, or
+ have had PDB files associated with them via the <em>Structures</em>
+ submenu of the sequence ID popup menu. The extraction and display of
+ secondary structure and B-factor column annotation is controlled <em>via</em>
+ a new <strong>Structure</strong> tab in the Jalview Desktop's
+ Preferences dialog box.
+ </p>
+ <p>
+ <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
+ application can now be configured to employ UCSF Chimera for the
+ display of 3D structure data. UCSF Chimera is a python-based
+ high-performance molecular graphics and animation system developed by
+ the Resource for Biocomputing, Visualisation, and Informatics at the
+ University of California.<br />Jalview employs the 'StructureViz'
+ communication mechanism developed for Cytoscape by Morris et al.
+ (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
+ allows Jalview to send commands to Chimera, enabling structures to be
+ superimposed and shaded according to associated multiple aligmment
+ views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
+ would appreciate feedback ! Please send your comments to
+ jalview-discuss@jalview.org, and keep up to date with this feature's
+ development via http://issues.jalview.org/browse/JAL-1333.
+ </p>
+ <p>
+ <strong>Export of alignment figures as Scalable Vector
+ Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
+ supported by web browsers and graphics design programs, and allow
+ high-quality graphics for interactive exploration and publication.
+ Jalview now supports the generation of SVGs interactively (via the
+ Export) menu, and from the command line for server-side figure
+ generation.
+ </p>
-<p><strong>Jalview Version 2.2</strong></p>
-<p>Multiple views with different styles, colours, hidden regions for one alignment
-</p>
-<p>Easily add, amend and delete sequence features
-</p>
-<p>"Reload" alignment from File or URL to revert to original
-</p>
-<p>"Save" to current filename or "Save As" to new filename
-</p>
-<p>Set different text colour for dark or light background
-</p>
-<p>Right align sequence ids
-</p>
-<p>Set colour of lower case residues in a user defined colour scheme
-</p>
-<p>Menu Rearrangements: New <strong>Format</strong> for alignment layout and <strong>Select</strong> for region selection.
-</p>
-</p><p>Menu item accelerator keys added
-</p>
-<p>Control-V pastes sequences to active window, Control-Shift-V pastes to a new window.
-</p>
-<p>Raise/Minimise alignment and all associated windows from desktop window's <strong>window</strong> menu
-</p>
-<p>Select and colour whole branches of a tree</p>
-<p>'New Window' button on the 'Output to Text box' alignment output
-option to open a new alignment window after editing.</p>
-<p><strong>Issues Resolved</strong></p>
-</p>
-<p>
-Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system.
-</p>
-<p>Remove empty columns - if empty columns exist at the end of the
-alignment bug fixed.
-</p>
-<p>DAS feature fetching slowed down, doesn't overload DAS servers
-</p>
-<p>DAS feature fetching can be cancelled
-</p>
-<p>Correct display of > and < symbols for feature descriptions without explicit <html> tags.
-</p>
-<p>Zoom working in PCA viewer
-</p>
-<p>Sequence Descriptions retained after running a web service
-</p>
-<p> </p>
-<p>See the <a href="releases.html">Release History</a> page for details of all
- new features and resolved issues. </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff