-#-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
-# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
-#
-# 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/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
history</a> for the bugs that this release resolves.</p>
<p><strong>Highlights in Jalview Version 2.5</strong></p>
<ul>
- Linked viewing of nucleic acid sequences and structures
- <br />
- Automatic Scrolling option in View menu to display the currently
- highlighted region of an alignment.
- <br />
- Order an alignment by sequence length, or using the average score or
- total feature count for each sequence.
- <br />
- Shading features by score or associated description
- <br />
- Subdivide alignment and groups based on identity of selected
- subsequence (Make Groups from Selection).
- <br />
- New hide/show options including Shift+Control+H to hide everything but
- the currently selected region.
- <br />
+ Linked viewing of nucleic acid sequences and structures<br/>
+ Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.<br/>
+ Order an alignment by sequence length, or using the average score or total feature count for each sequence.<br/>
+ Shading features by score or associated description<br/>
+ Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).<br/>
+ New hide/show options including Shift+Control+H to hide everything but the currently selected region.<br/>
</ul>
<em>Jalview Desktop:</em>
<ul>
- Fetch DB References capabilities and UI expanded to support retrieval
- from DAS sequence sources
- <br />
- Enable or disable non-positional feature and database references in
- sequence ID tooltip from View menu in application.
- <br />
- Group-associated consensus, sequence logos and conservation plots
- <br />
- Symbol distributions for each column can be exported and visualized as
- sequence logos
- <br />
- Jalview Java Console
- <br />
- New webservice for submitting sequences and IDs to
- <a href="webServices/index.html#envision2">Envision2</a>
- Workflows
- <br />
- Improved VAMSAS synchronization and sharing of selections.
- <br />
+ Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources<br/>
+ Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.<br/>
+ Group-associated consensus, sequence logos and conservation
+ plots<br/>
+ Symbol distributions for each column can be exported and
+ visualized as sequence logos<br/>
+ Jalview Java Console<br/>
+ New webservice for submitting sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a> Workflows<br/>
+ Improved VAMSAS synchronization and sharing of selections.<br/>
</ul>
<em>JalviewLite:</em>
<ul>
- Middle button resizes annotation row height
- <br />
- New Parameters - including default tree display settings.
- <br />
- Non-positional features displayed in ID tooltip
- <br />
+ Middle button resizes annotation row height<br/>
+ New Parameters - including default tree display settings.<br/>
+ Non-positional features displayed in ID tooltip<br/>
</ul>
<p><strong>Issues Resolved (a select list)</strong></p>
<ul>
<ul>
- Source field in GFF files parsed as feature source rather than
- description
- <br />
- Non-positional features are now included in sequence feature and gff
- files (controlled via non-positional feature visibility in tooltip).
- <br />
- URL links generated for all feature links (bugfix)
- <br />
- Codons containing ambiguous nucleotides translated as 'X' in peptide
- product
- <br />
- Match case switch in find dialog box works for both sequence ID and
- sequence string and query strings do not have to be in upper case to
- match case-insensitively.
- <br />
+ Source field in GFF files parsed as feature source rather
+ than description<br/>
+ Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).<br/>
+ URL links generated for all feature links (bugfix)<br/>
+ Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product<br/>
+ Match case switch in find dialog box works for both sequence
+ ID and sequence string and query strings do not have to be in upper
+ case to match case-insensitively.<br/>
Jalview Annotation File generation/parsing consistent with
documentation (e.g. Stockholm annotation can be exported and
- re-imported)
- <br />
- Find incrementally searches ID string matches as well as subsequence
- matches, and correctly reports total number of both.
- <br />
+ re-imported)<br/>
+ Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.<br/>
</ul>
<em>Desktop Issues</em>
<ul>
- Better handling of exceptions during sequence retrieval
- <br />
- PDB files retrieved from URLs are cached properly
- <br />
- Sequence description lines properly shared via VAMSAS
- <br />
- Sequence fetcher fetches multiple records for all data sources
- <br />
- Ensured that command line das feature retrieval completes before
- alignment figures are generated.
- <br />
- Reduced time taken when opening file browser for first time.
- <br />
- User defined group colours properly recovered from Jalview projects.
- <br />
- </ul>
+ Better handling of exceptions during sequence retrieval<br/>
+ PDB files retrieved from URLs are cached properly<br/>
+ Sequence description lines properly shared via VAMSAS<br/>
+ Sequence fetcher fetches multiple records for all data
+ sources<br/>
+ Ensured that command line das feature retrieval completes
+ before alignment figures are generated.<br/>
+ Reduced time taken when opening file browser for first time.<br/>
+ User defined group colours properly recovered from Jalview projects.<br/>
+ </ul>
</ul>
<p> </p>
git://source.jalview.org / jalview.git / blobdiff