</head>
<body>
<p><strong>What's new ?</strong></p>
+<p>Jalview 2.5.1 is a bug fix release for the 2.5 version of
+Jalview. See the <a href="releases.html#Jalview2.5.1">release
+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