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-<head><title>What's new ?</title></head>
+<head>
+<title>What's new ?</title>
+</head>
<body>
-<p><strong>What's new ?</strong> </p>
-<p>If you are reading this then you will already have seen some of the recent changes
- made to Jalview.<br>
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window. </p>
-<p>If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:</p>
+<p><strong>What's new ?</strong></p>
+<p><strong>Highlights in Jalview Version 2.4</strong></p>
<ul>
- <li>Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.</li>
- <li>To insert or edit the gaps in one sequence in alignment, the
- "Shift" key must be held down when dragging the mouse.</li>
- <li>To insert or edit gaps for a group of sequences, the
- "Alt" key (or in X windows the "Control"
- key) must be held down.</li>
- <li>Selecting colour schemes in the colour menu either sets just the
- "background" colourscheme for the alignment, or - when
- the tickbox "Apply colour to all groups" is ticked,
- applies the scheme to the background and all groups defined on the alignment.</li>
- <li>Use the right mouse button (apple and click on the Mac) whilst
- the pointer is within the selection area to access the "define" region menu to
- define a new region, give it a name, and change its colourscheme and display
- properties.</li>
- <li>Conservation is automatically updated whenever the alignment is edited</li>
- <li>There is no "quick draw" option</li>
- <li>Edits can be undone, and redone!</li>
+ 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>
</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>
+
+<p> </p>
+<p>See the <a href="releases.html">Release History</a> page for
+details of all new features and resolved issues.</p>
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git://source.jalview.org / jalview.git / blobdiff