<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Release History</title>
</head>
<body>
<p><strong>Release History</strong></p>
<table border="1">
- <tr>
- <td width="60" nowrap>
- <div align="center"><em><strong>Release</strong></em></div>
- </td>
- <td>
- <div align="center"><em><strong>New Features</strong></em></div>
- </td>
- <td>
- <div align="center"><em><strong>Issues Resolved</strong></em></div>
- </td>
- </tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview.2.8.1">2.8.1</a><br/><em>20/5/2014</em></strong>
- </div>
- </td>
- <td> <!-- New features -->
- <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
- <ul>
- </ul> <em>Other improvements</em>
- <ul>
- </ul>
- </td>
- <td><!-- issues resolved -->
- <ul>
- </ul>
- </td>
- </tr>
- <tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <em><strong>Release</strong></em>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <em><strong>New Features</strong></em>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <em><strong>Issues Resolved</strong></em>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <ul><li>Reinstated the display of default example file on startup</li>
+ <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
+ </div></td>
+ <td><em>General</em>
+ <ul>
+ <li>Updated Java code signing certificate donated by Certum.PL.</li>
+ <li>Features and annotation preserved when performing pairwise
+ alignment</li>
+ <li>RNA pseudoknot annotation can be
+ imported/exported/displayed</li>
+ <li>'colour by annotation' can colour by RNA and
+ protein secondary structure</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Extract and display secondary structure for sequences with
+ 3D structures</li>
+ <li>Support for parsing RNAML</li>
+ <li>Annotations menu for layout
+ <ul>
+ <li>sort sequence annotation rows by alignment</li>
+ <li>place sequence annotation above/below alignment
+ annotation</li>
+ </ul>
+ <li>Output in Stockholm format</li>
+ <li>Internationalisation: improved Spanish (es) translation</li>
+ <li>Structure viewer preferences tab</li>
+ <li>Disorder and Secondary Structure annotation tracks shared
+ between alignments</li>
+ <li>UCSF Chimera launch and linked highlighting from Jalview</li>
+ <li>Show/hide all sequence associated annotation rows for all
+ or current selection</li>
+ <li>disorder and secondary structure predictions available as
+ dataset annotation</li>
+ <li>Per-sequence rna helices colouring</li>
+
+
+ <li>Sequence database accessions imported when fetching
+ alignments from Rfam</li>
+ <li>update VARNA version to 3.91</li>
+
+ <li>New groovy scripts for exporting aligned positions,
+ conservation values, and calculating sum of pairs scores.</li>
+ <li>Command line argument to set default JABAWS server</li>
+ <li>include installation type in build properties and console
+ log output</li>
+ <li>Updated Jalview project format to preserve dataset annotation</li>
+ </ul></td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>Distinguish alignment and sequence associated RNA
+ structure in structure->view->VARNA</li>
+ <li>Raise dialog box if user deletes all sequences in an
+ alignment</li>
+ <li>Pressing F1 results in documentation opening twice</li>
+ <li>Sequence feature tooltip is wrapped</li>
+ <li>Double click on sequence associated annotation selects
+ only first column</li>
+ <li>Redundancy removal doesn't result in unlinked leaves
+ shown in tree</li>
+ <li>Undos after several redundancy removals don't undo
+ properly</li>
+ <li>Hide sequence doesn't hide associated annotation</li>
+ <li>User defined colours dialog box too big to fit on screen
+ and buttons not visible</li>
+ <li>author list isn't updated if already written to jalview
+ properties</li>
+ <li>Popup menu won't open after retrieving sequence from
+ database</li>
+ <li>File open window for associate PDB doesn't open</li>
+ <li>Left-then-right click on a sequence id opens a browser
+ search window</li>
+ <li>Cannot open sequence feature shading/sort popup menu in
+ feature settings dialog</li>
+ <li>better tooltip placement for some areas of Jalview desktop</li>
+ <li>Allow addition of JABAWS Server which doesn't pass
+ validation</li>
+ <li>Web services parameters dialog box is too large to fit on
+ screen</li>
+ <li>Muscle nucleotide alignment preset obscured by tooltip</li>
+ <li>JABAWS preset submenus don't contain newly defined
+ user preset</li>
+ <li>MSA web services warns user if they were launched with
+ invalid input</li>
+ <li>Jalview cannot contact DAS Registy when running on Java 8</li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
+ 'Superpose with' submenu not shown when new view created
+ </li>
+
+ </ul> <!-- <em>Applet</em>
+ <ul>
+ </ul> <em>General</em>
+ <ul>
+ </ul>--> <em>Deployment and Documentation</em>
+ <ul>
+ <li>2G and 1G options in launchApp have no effect on memory
+ allocation</li>
+ <li>launchApp service doesn't automatically open
+ www.jalview.org/examples/exampleFile.jar if no file is given</li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
+ InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
+ available
+ </li>
+ </ul> <em>Application Known issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
+ corrupted or unreadable alignment display when scrolling alignment
+ to right
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
+ retrieval fails but progress bar continues for DAS retrieval with
+ large number of ID
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
+ flatfile output of visible region has incorrect sequence start/end
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
+ rna structure consensus doesn't update when secondary
+ structure tracks are rearranged
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
+ invalid rna structure positional highlighting does not highlight
+ position of invalid base pairs
+ </li>
+ <li>
+ <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
+ out of memory errors are not raised when saving jalview project
+ from alignment window file menu
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
+ colour by RNA Helices not enabled when user created annotation
+ added to alignment
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+ </li>
+ </ul> <em>Applet Known Issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
+ Jalview and Jmol example not compatible with IE9
+ </li>
+
+ <li>Sort by annotation score doesn't reverse order when
+ selected</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
+ </div></td>
+ <td>
+ <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <em>General</em>
+ <ul>
+ <li>Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale</li>
+ <li>Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G</li>
+ <li>Improved group creation/removal options in
+ alignment/sequence Popup menu</li>
+ <li>Sensible precision for symbol distribution percentages
+ shown in logo tooltip.</li>
+ <li>Annotation panel height set according to amount of
+ annotation when alignment first opened</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Interactive consensus RNA secondary structure prediction
+ VIENNA RNAAliFold JABA 2.1 service</li>
+ <li>Select columns containing particular features from Feature
+ Settings dialog</li>
+ <li>View all 'representative' PDB structures for selected
+ sequences</li>
+ <li>Update Jalview project format:
+ <ul>
+ <li>New file extension for Jalview projects '.jvp'</li>
+ <li>Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)</li>
+ <li>Per group and alignment annotation and RNA helix
+ colouring</li>
+ </ul>
+ </li>
+ <li>New similarity measures for PCA and Tree calculation
+ (PAM250)</li>
+ <li>Experimental support for retrieval and viewing of flanking
+ regions for an alignment</li>
+ </ul>
+ </td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>logo keeps spinning and status remains at queued or
+ running after job is cancelled</li>
+ <li>cannot export features from alignments imported from
+ Jalview/VAMSAS projects</li>
+ <li>Buggy slider for web service parameters that take float
+ values</li>
+ <li>Newly created RNA secondary structure line doesn't have
+ 'display all symbols' flag set</li>
+ <li>T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in jalview project</li>
+ <li>Local file cannot be loaded in freshly downloaded Jalview</li>
+ <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
+ <li>Load file from desktop file browser fails</li>
+ <li>Occasional NPE thrown when calculating large trees</li>
+ <li>Cannot reorder or slide sequences after dragging an
+ alignment onto desktop</li>
+ <li>Colour by annotation dialog throws NPE after using
+ 'extract scores' function</li>
+ <li>Loading/cut'n'pasting an empty file leads to a grey
+ alignment window</li>
+ <li>Disorder thresholds rendered incorrectly after performing
+ IUPred disorder prediction</li>
+ <li>Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting</li>
+ <li>Find shows blank dialog after 'finished searching' if
+ nothing matches query</li>
+ <li>Null Pointer Exceptions raised when sorting by feature
+ with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
+ </li>
+ <li>Errors in Jmol console when structures in alignment don't
+ overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
+ </li>
+ <li>Not all working JABAWS services are shown in Jalview's
+ menu</li>
+ <li>JAVAWS version of jalview fails to launch with 'invalid
+ literal/length code'</li>
+ <li>Annotation/RNA Helix colourschemes cannot be applied to
+ alignment with groups (actually fixed in 2.8.0b1)</li>
+ <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Remove group option is shown even when selection is not a
+ group</li>
+ <li>Apply to all groups ticked but colourscheme changes don't
+ affect groups</li>
+ <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
+ <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
+ <li>Increased font size for dropdown menus on OSX and embedded windows</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Consensus sequence for alignments/groups with a single
+ sequence were not calculated</li>
+ <li>annotation files that contain only groups imported as
+ annotation and junk sequences</li>
+ <li>Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC</li>
+ <li>conservation/PID slider apply all groups option doesn't
+ affect background (2.8.0b1)
+ <li></li>
+ <li>redundancy highlighting is erratic at 0% and 100%</li>
+ <li>Remove gapped columns fails for sequences with ragged
+ trailing gaps</li>
+ <li>AMSA annotation row with leading spaces is not registered
+ correctly on import</li>
+ <li>Jalview crashes when selecting PCA analysis for certain
+ alignments</li>
+ <li>Opening the colour by annotation dialog for an existing
+ annotation based 'use original colours' colourscheme loses
+ original colours setting</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
<td><div align="center">
<strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
</div>
<li>ClassCastException when generating EPS in headless
mode</li>
<li>Adjusting sequence-associated shading threshold only
- changes one row's threshold</li>
+ changes one row's threshold</li>
<li>Preferences and Feature settings panel panel
doesn't open</li>
- </ul>
+ <li>hide consensus histogram also hides conservation and
+ quality histograms</li>
+ </ul>
</td>
</tr>
<tr>
git://source.jalview.org / jalview.git / blobdiff