The people listed below are 'The Jalview Authors', who collectively
own the copyright to the Jalview source code and permit it to be released under GPL.
-This is the authoritative list. It was correct on 6th Oct 2016.
+This is the authoritative list. It was correct on 23rd November 2016.
If you are releasing a version of Jalview, please make sure any
statement of authorship in the GUI reflects the list shown here.
In particular, check the resources/authors.props file !
Jim Procter
-Andrew Waterhouse
Mungo Carstairs
Tochukwu 'Charles' Ofoegbu
+Kira Mourao
+Andrew Waterhouse
Jan Engelhardt
Lauren Lui
Anne Menard
When a selection is highlighted in a Jalview window, use the
<em>Select→Select Highlighted Region</em> or press <em>B</em>
to add the mapped positions to the alignment window's column
- selection.
+ selection.<br /> <em>Hint: Use your machine's 'switch
+ application' key combination (Alt-Tab on Windows and Linux,
+ Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview
+ before pressing 'B' to select highlighted regions.</em>
</p>
<p>
Basic screen operations (see <a
<strong>Selecting regions from Search Results</strong>
</p>
<p>
- Press 'B' or select the <em>Select Highlighted Columns</em> option
- from the alignment window's select menu to add columns containing
+ Press 'B' or use the <em>Select Highlighted Columns</em> option from
+ the alignment window's select menu to add columns containing
highlighted search results to the alignment window's column
- selection.
+ selection. Alt-'B' will add all but the highlighted columns, and
+ Ctrl (or Cmd) -B will toggle the column selection for the
+ highlighted region.
</p>
<p>
</tr>
<tr><td><strong>B</strong></td>
<td>Both</td>
- <td>Mark the currently highlighted columns</td>
+ <td>Add highlighted columns to current column selection</td>
</tr>
<tr><td><strong>Alt 'B'</strong></td>
<td>Both</td>
- <td>Mark all but the currently highlighted columns</td>
+ <td>Add all but the currently highlighted columns to current selection</td>
</tr>
<tr><td><strong>Control 'B'</strong></td>
<td>Both</td>
- <td>Toggle the marks on the currently highlighted
- columns (or all others if Alt is pressed)</td>
+ <td>Toggle the column selection marks for the currently highlighted
+ columns (or all others if Alt is also pressed)</td>
</tr>
<tr>
<td><strong>H</strong></td>
<em>Application</em>
<ul>
<li>
- <!-- JAL-1723 -->Sequence ID tool tips have been tamed
- (databases sorted alphabetically, abridged ID sets)
+ <!-- JAL-1723 -->Sequence ID tool tip presents abridged
+ set of database cross-references, sorted alphabetically
</li>
<li>
<!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
from database cross references. Users with custom links
- will receive a warning dialog asking them to update their
- preferences.
+ will receive a <a href="webServices/urllinks.html#warning">warning
+ dialog</a> asking them to update their preferences.
</li>
<li>
<!-- JAL-2287-->Cancel button and escape listener on
Chimera session
</li>
<li>
- <!-- JAL-2320-->Jalview's chimera control window closes if
+ <!-- JAL-2320-->Jalview's Chimera control window closes if
the Chimera it is connected to is shut down
</li>
<li>
- <!-- JAL-2281-->Custom URL links for database
- cross-references are matched to database name regardless
- of case
- </li>
- <li>
- <!-- JAL-1738-->Select highlighted columns menu item and
- keystroke (B) to mark columns containing highlighted
- regions from structure selections or results of a Find
- operation
+ <!-- JAL-1738-->New keystroke (B) and Select highlighted
+ columns menu item to mark columns containing
+ highlighted regions (e.g. from structure selections or results
+ of a Find operation)
</li>
<li>
<!-- JAL-2284-->Command line option for batch-generation
of HTML pages rendering alignment data with the BioJS
MSAviewer
</li>
-
-
</ul>
- <em>Applet</em>
+<!-- --> <em>Applet</em>
<ul>
- </ul>
+ </ul> -->
<em>Build and deployment</em>
<ul>
<li>Updated Jalview's Certum code signing certificate
than a range in linked structure views, and treated
correctly when selecting and computing trees from features
</li>
+ <li>
+ <!-- JAL-2281-->Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+ </li>
</ul>
<em>Application</em>
lysozyme results in a PDB Client error dialog box
</li>
</ul>
+ <!--
<em>Applet</em>
<ul>
- </ul>
+ </ul> -->
<em>Build and deployment</em>
<ul>
<li>
the sequence ID for the sequence (<em>since Jalview 2.10.1</em>).
</p>
<p>
- If Jalview opens a project with links which include $SEQUENCE_ID$ tokens, it will present
- the user with a warning message, as these links may need to be updated to use $DB_ACCESSION$, if
- they were added before Jalview 2.10.1. The message lists the links which should be reviewed.
- The warning can be turned off completely via a checkbox in the message dialog.
+ <strong><a name="warning">Warning dialog about updating
+ your configured URL links</a></strong><br /> In the desktop
+ prior to Jalview 2.10.1, the only way to configure custom links for
+ a particular database cross-reference for a sequence was to give it
+ a name that
+ <em>exactly</em> matched the database source, and a regular
+ expression for filtering out any spurious matches generated when the
+ custom linked was tested against the Sequence's ID string. Since the
+ introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$
+ will not be used for database cross-reference accession strings, and
+ if you have custom links configured, Jalview will raise a warning
+ message so let you know that you may need to update your links to
+ use $DB_ACCESSION$.
</p>
<p>
<strong>Regular Expression Substitution</strong><br> A url may
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.0b1 ?</strong>
+ <strong>What's new in Jalview 2.10.1 ?</strong>
</p>
<p>
- Jalview 2.10.0b1 is a patch release for 2.10, the next major release
- in the Jalview 2 series. Full details are in the <a
- href="releases.html#Jalview.2.10.0b1">Jalview 2.10b1 Release
- Notes</a>, but the highlights are below.
+ Jalview 2.10.1 was released on 24th November 2016. Full details are
+ in the <a href="releases.html#Jalview.2.10.1">Jalview 2.10.1
+ Release Notes</a>, but the highlights are below. This is also the
+ first release to include contributions from Kira Mourão, who
+ joined Jalview's core development team in October 2016.
</p>
<ul>
- <li>Drag and drop reinstated for the Jalview desktop on
- Windows, Linux and older OSX systems.</li>
- <li>Problems loading local PDB files have been fixed</li>
- <li>Conservation shading can be disabled for PID and consensus
- based colour scheme</li>
- </ul>
- <p><em>Major highlights of the 2.10.0 Release</em></p>
- <ul>
- <li><strong>Ensembl sequence fetcher</strong><br />Annotated
- Genes, transcripts and proteins can be retrieved via Jalview's new
- <a href="features/ensemblsequencefetcher.html">Ensembl REST
- client</a>. Support for import of Ensembl data allows:
- <ul>
- <li><strong>Aligned locus view</strong><br />Transcripts
- retrieved for a gene identifier via the Ensembl or
- EnsemblGenomes sequence databases are automatically aligned to
- their reference genome, and introns hidden from the view.</li>
- <li><strong>Sequence variant data</strong><br />Jalview
- propagates variant annotation on genomic regions onto
- transcripts and protein products, complete with associated
- metadata such as clinical significance.</li>
- </ul></li>
- <li><strong>Ensembl and ENA 'show cross-references'
- support</strong><br />The Calculations menu's <strong>'Show
- cross-references'</strong> now offers Ensembl as well as EMBLCDS and
- Uniprot when CDS/Protein mapping data is available for download or
- display. This allows variant annotation to be added directly to an
- alignment of UniProt sequences.</li>
- <li><strong>Working with structures</strong>
- <ul>
- <li><strong>More accurate structure mappings</strong><br />
- Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
- to <a href="features/siftsmapping.html">match structures
- to UniProt sequences</a>, even for structures containing
- multiple copies of a sequence.</li>
- <li><strong>Import structures as mmCIF</strong><br />Jalview
- now downloads data from the EMBL-EBI's PDBe site as <a
- href="features/mmcif.html">mmCIF</a>. This allows very large
- structures to be imported, such as the HIV virus capsid
- assembly.</li>
- <li><strong>Chimera users will need to upgrade to
- 1.11.1</strong><br />If you use Chimera to view structures
- downloaded by Jalview 2.10, you will need to make sure you are
- running the latest version of <a href="features/chimera.html">Chimera</a>.</li>
- </ul></li>
- <li><strong>UniProt Free Text Search</strong><br />The new
- search dialog for UniProt allows you to browse and retrieve
- sequences with free-text search, or structured queries.</li>
- <li><strong>Reference sequence alignment view</strong><br />
- Jalview 2.9 introduced support for reference sequences. In 2.10,
- when a reference sequence is defined for the alignment, the
- alignment column ruler is now numbered according to the reference
- sequence. The reference sequence for alignment views can also be
- saved and restored from Jalview projects.</li>
+ <li><strong>More memory efficient</strong><br />We've slimmed
+ down the consensus analysis data structures used by Jalview so
+ even wider alignments can be worked with.</li>
+ <li><strong>Select highlighted region</strong><br />Press 'B'
+ or use the new menu option in the alignment window's Select menu
+ to mark columns containing highlighted regions generated from
+ structure selections, mouse-overs, or resulting from a
+ Find operation.</li>
+ <li><strong>New custom link mechanism for opening URLs
+ for database cross references.</strong><br /> If you have customised URL
+ links in your Jalview preferences, then you may already have seen
+ the <a href="webServices/urllinks.html">Update your links
+ warning dialog.</a></li>
+ <li><strong>New command line export option for BioJS
+ MSAviewer</strong><br />A number of small bugs with the HTML export
+ functions from the Jalview desktop were also fixed.</li>
+ <li><strong>Small but significant changes to the
+ physicochemical properties and consensus calculations</strong><br />Threonine
+ is no longer considered a non-hydrophobic residue in the protein
+ conservation calculation, and minor bugs addressed in PID and
+ consensus colouring.</li>
</ul>
</body>
YEAR=2016
-AUTHORS=J Procter, M Carstairs, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
-AUTHORFNAMES=Jim Procter, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+AUTHORS=J Procter, M Carstairs, TC Ofoegbu, K Mourao, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTHORFNAMES=Jim Procter, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Kira Mourao, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
\ No newline at end of file
action.calculate = Calculate
action.select_all = Select all
action.select_highlighted_columns = Select Highlighted Columns
-tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-B to toggle, and Alt-B to mark all but highlighted columns
+tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns
action.deselect_all = Deselect all
action.invert_selection = Invert selection
action.using_jmol = Using Jmol
action.colour = Color
action.calculate = Calcular
action.select_all = Seleccionar Todo
+action.select_highlighted_columns = Seleccionar columnas resaltadas
+tooltip.select_highlighted_columns = Presione B para marcar las columnas resaltadas, Ctrl (o Cmd)-B para cambiarlas, y Alt-B para marcar todas menos las columnas resaltadas
action.deselect_all = Deseleccionar Todo
action.invert_selection = Invertir selección
action.using_jmol = Usar Jmol
git://source.jalview.org / jalview.git / commitdiff