* 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/>.
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<head>
<title>What's new ?</title>
</head>
<body>
<p><strong>What's new ?</strong></p>
-<p><strong>Highlights in Jalview Version 2.4</strong></p>
+<p><strong>Highlights in Jalview Version 2.5</strong></p>
<ul>
- DNA and protein product highlighting<br>
- URL links generated with regular expressions<br>
- URL links for sequence database cross references<br>
- New sequence fetcher dialog and DAS Sequence Fetching<br>
- JPred Service upgraded to Jpred3<br>
- Memory monitor<br>
- PFAM full alignment retrieval<br>
- Generalised sequence database reference validation<br>
- DNA Protein Product sequence db traversal (Experimental)<br>
- VAMSAS Interoperation Client (Experimental)<br>
- export annotation rows as CSV for spreadsheet import<br>
- New application command line args and optional Groovy suport<br>
- New Applet API methods and parameters<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/>
+</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/>
</ul>
<p><strong>Issues Resolved (a select list)</strong></p>
<ul>
- Aligned cDNA translation to aligned peptide works correctly<br>
- selected region output includes visible annotations (for
- certain formats)<br>
- edit label/displaychar contains existing label/char for
- editing<br>
- Newick tree support improved for clustalW trees and preserving NHX style comments<br>
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'<br>
- Fixed exception when parsing GFF files containing global
- sequence features<br>
- Reference counting for alignment datasets<br>
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.<br>
- Save works when Jalview project is default format<br>
- Histidine should be midblue (not pink!) in Zappo<br>
- Undo recovers dataset sequence metadata when sequence
- regions are cut<br>
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly<br>
- Stockholm annotation parsing fixed and improved (PFAM records)<br>
- Re-instated Full AMSA support and .amsa file association (MyHits)<br>
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file<br>
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet<br>
- Applet Menus are always embedded in applet window on Macs.</br>
- Newly shown features appear at top of stack (in Applet)</br>
- Secondary structure lines are drawn starting from first
- column of alignment<br>
- Uniprot XML import updated for new schema release in July 2008<br>
- Sequence feature to sequence ID match for Features file is case-insensitive<br>
- Sequence features read from Features file appended to all sequences with matching IDs<br>
- PDB structure coloured correctly for associated views containing a sub-sequence<br>
- Display name and local features preserved in results retrieved from web service<br>
- Visual delay indication for sequence retrieval and sequence fetcher initialisation<br>
- Updated Application to use DAS 1.53e version of dasobert DAS client
+ <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/>
+ 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/>
+ </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>
</ul>
<p> </p>
git://source.jalview.org / jalview.git / blobdiff