<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>
+ <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.2.9">2.9</a><br /> <em>9/9/2015</em></strong>
+ <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
</div></td>
<td><em>General</em>
<ul>
</li>
<li>3D structure retrieval and display
<ul>
- <li>Free text and structured queries with
- the PDBe Search API</li>
+ <li>Free text and structured queries with the PDBe
+ Search API</li>
<li>PDBe Search API based discovery and selection of
PDB structures for a sequence set</li>
</ul>
</ul> <em>Applet</em>
<ul>
<li>New layout for applet example pages</li>
- <li>New parameters to enable SplitFrame view (file2,enableSplitFrame,
- scaleProteinAsCdna)</li>
+ <li>New parameters to enable SplitFrame view
+ (file2,enableSplitFrame, scaleProteinAsCdna)</li>
<li>New example demonstrating linked viewing of cDNA and
Protein alignments</li>
</ul> <em>Development and deployment</em>
<ul>
- <li>Java 1.7 minimum requirement for Jalview 2.9</li>
- <li>Include installation type and git revision in build
- properties and console log output</li>
- <li>Jalview Github organisation, and new github site for
- storing BioJsMSA Templates</li>
- <li>Jalview's unit tests now managed with TestNG</li></ul></td>
+ <li>Java 1.7 minimum requirement for Jalview 2.9</li>
+ <li>Include installation type and git revision in build
+ properties and console log output</li>
+ <li>Jalview Github organisation, and new github site for
+ storing BioJsMSA Templates</li>
+ <li>Jalview's unit tests now managed with TestNG</li>
+ </ul></td>
<td>
<!-- <em>General</em>
<ul>
- </ul> -->
- <!-- issues resolved --> <em>Application</em>
+ </ul> --> <!-- issues resolved --> <em>Application</em>
<ul>
<li>Escape should close any open find dialogs</li>
<li>Typo in select-by-features status report</li>
spaces</li>
</ul> <em>Applet</em>
<ul>
- <li>Jmol to JalviewLite mouseover/link not working</li>
- <li>JalviewLite can't import sequences with ID descriptions
- containing angle brackets</li>
+ <li>Jmol to JalviewLite mouseover/link not working</li>
+ <li>JalviewLite can't import sequences with ID
+ descriptions containing angle brackets</li>
</ul> <em>General</em>
<ul>
<li>Cannot export and reimport RNA secondary structure
<li>Core PDB parsing code requires Jmol</li>
<li>Sequence canvas panel goes white when alignment
window is being resized</li>
-
+
</ul>
</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>
- <li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
+ <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>
+ <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
+ post-hoc with 2.9 release</em>)
+ </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>
+ </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>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>
+ <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> <!-- <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>
+ <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>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>
+ <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>
- </td>
+ </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></td>
<td>
<ul>
<li>Trusted certificates for JalviewLite applet and
<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>
- <li>hide consensus histogram also hides conservation and
- quality histograms</li>
- </ul>
+ <li>hide consensus histogram also hides conservation and
+ quality histograms</li>
+ </ul>
</td>
</tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
- </div></td>
- <td><em>Application</em>
- <ul><li>Support for JABAWS 2.0 Services (AACon alignment
- conservation, protein disorder and Clustal Omega)</li>
- <li>JABAWS server status indicator in Web Services preferences
- </li>
- <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
- Jalview alignment window</li>
- <li>Updated Jalview build and deploy framework for OSX mountain
- lion, windows 7, and 8</li>
- <li>Nucleotide substitution matrix for PCA that supports RNA
- and ambiguity codes</li>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
+ </div></td>
+ <td><em>Application</em>
+ <ul>
+ <li>Support for JABAWS 2.0 Services (AACon alignment
+ conservation, protein disorder and Clustal Omega)</li>
+ <li>JABAWS server status indicator in Web Services
+ preferences</li>
+ <li>VARNA (http://varna.lri.fr) viewer for RNA structures
+ in Jalview alignment window</li>
+ <li>Updated Jalview build and deploy framework for OSX
+ mountain lion, windows 7, and 8</li>
+ <li>Nucleotide substitution matrix for PCA that supports
+ RNA and ambiguity codes</li>
- <li>Improved sequence database retrieval GUI</li>
- <li>Support fetching and database reference look up against
- multiple DAS sources (Fetch all from in 'fetch db refs')</li>
- <li>Jalview project improvements
- <ul>
- <li>Store and retrieve the 'belowAlignment' flag for
- annotation</li>
- <li>calcId attribute to group annotation rows on the
- alignment</li>
- <li>Store AACon calculation settings for a view in Jalview
- project</li>
+ <li>Improved sequence database retrieval GUI</li>
+ <li>Support fetching and database reference look up
+ against multiple DAS sources (Fetch all from in 'fetch db
+ refs')</li>
+ <li>Jalview project improvements
+ <ul>
+ <li>Store and retrieve the 'belowAlignment'
+ flag for annotation</li>
+ <li>calcId attribute to group annotation rows on the
+ alignment</li>
+ <li>Store AACon calculation settings for a view in
+ Jalview project</li>
- </ul>
- </li>
- <li>horizontal scrolling gesture support</li>
- <li>Visual progress indicator when PCA calculation is running</li>
- <li>Simpler JABA web services menus</li>
- <li>visual indication that web service results are still being
- retrieved from server</li>
- <li>Serialise the dialogs that are shown when Jalview starts up
- for first time</li>
- <li>Jalview user agent string for interacting with HTTP
- services</li>
- <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
- library</li>
- <li>Examples directory and Groovy library included in
- InstallAnywhere distribution</li>
- </ul> <em>Applet</em>
- <ul>
- <li>RNA alignment and secondary structure annotation
- visualization applet example</li>
- </ul> <em>General</em>
- <ul>
- <li>Normalise option for consensus sequence logo</li>
- <li>Reset button in PCA window to return dimensions to
- defaults</li>
- <li>Allow seqspace or Jalview variant of alignment PCA
- calculation</li>
- <li>PCA with either nucleic acid and protein substitution
- matrices
- <li>Allow windows containing HTML reports to be exported in
- HTML</li>
- <li>Interactive display and editing of RNA secondary structure
- contacts</li>
- <li>RNA Helix Alignment Colouring</li>
- <li>RNA base pair logo consensus</li>
- <li>Parse sequence associated secondary structure information
- in Stockholm files</li>
- <li>HTML Export database accessions and annotation information
- presented in tooltip for sequences</li>
- <li>Import secondary structure from LOCARNA clustalw style RNA
- alignment files</li>
- <li>import and visualise T-COFFEE quality scores for an
- alignment</li>
- <li>'colour by annotation' per sequence option to
- shade each sequence according to its associated alignment
- annotation</li>
- <li>New Jalview Logo</li>
- </ul> <em>Documentation and Development</em>
- <ul>
- <li>documentation for score matrices used in Jalview</li>
- <li>New Website!</li>
- </ul></td>
- <td><em>Application</em>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via
- wsdbfetch REST service</li>
- <li>Stop windows being moved outside desktop on OSX</li>
- <li>Filetype associations not installed for webstart launch</li>
- <li>Jalview does not always retrieve progress of a JABAWS job
- execution in full once it is complete</li>
- <li>revise SHMR RSBS definition to ensure alignment is
- uploaded via ali_file parameter</li>
- <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
- <li>View all structures superposed fails with exception</li>
- <li>Jnet job queues forever if a very short sequence is
- submitted for prediction</li>
- <li>Cut and paste menu not opened when mouse clicked on
- desktop window</li>
- <li>Putting fractional value into integer text box in
- alignment parameter dialog causes Jalview to hang</li>
- <li>Structure view highlighting doesn't work on windows 7
- </li>
- <li>View all structures fails with exception shown in
- structure view</li>
- <li>Characters in filename associated with PDBEntry not
- escaped in a platform independent way</li>
- <li>Jalview desktop fails to launch with exception when using
- proxy</li>
- <li>Tree calculation reports 'you must have 2 or more
- sequences selected' when selection is empty</li>
- <li>Jalview desktop fails to launch with jar signature failure
- when java web start temporary file caching is disabled</li>
- <li>DAS Sequence retrieval with range qualification results in
- sequence xref which includes range qualification</li>
- <li>Errors during processing of command line arguments cause
- progress bar (JAL-898) to be removed</li>
- <li>Replace comma for semi-colon option not disabled for DAS
- sources in sequence fetcher</li>
- <li>Cannot close news reader when JABAWS server warning dialog
- is shown</li>
- <li>Option widgets not updated to reflect user settings</li>
- <li>Edited sequence not submitted to web service</li>
- <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
- <li>InstallAnywhere installer doesn't unpack and run on
- OSX Mountain Lion</li>
- <li>Annotation panel not given a scroll bar when sequences
- with alignment annotation are pasted into the alignment</li>
- <li>Sequence associated annotation rows not associated when
- loaded from Jalview project</li>
- <li>Browser launch fails with NPE on java 1.7</li>
- <li>JABAWS alignment marked as finished when job was cancelled
- or job failed due to invalid input</li>
- <li>NPE with v2.7 example when clicking on Tree associated
- with all views</li>
- <li>Exceptions when copy/paste sequences with grouped
- annotation rows to new window</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Sequence features are momentarily displayed before they
- are hidden using hidefeaturegroups applet parameter</li>
- <li>loading features via javascript API automatically enables
- feature display</li>
- <li>scrollToColumnIn javascript API method doesn't work</li>
- </ul> <em>General</em>
- <ul>
- <li>Redundancy removal fails for rna alignment</li>
- <li>PCA calculation fails when sequence has been selected and
- then deselected</li>
- <li>PCA window shows grey box when first opened on OSX</li>
- <li>Letters coloured pink in sequence logo when alignment
- coloured with clustalx</li>
- <li>Choosing fonts without letter symbols defined causes
- exceptions and redraw errors</li>
- <li>Initial PCA plot view is not same as manually reconfigured
- view</li>
- <li>Grouped annotation graph label has incorrect line colour</li>
- <li>Grouped annotation graph label display is corrupted for
- lots of labels</li>
- </ul>
- </tr>
- <tr>
- <td>
- <div align="center">
- <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
- </div>
- </td>
- <td><em>Application</em>
- <ul>
- <li>Jalview Desktop News Reader</li>
- <li>Tweaked default layout of web services menu</li>
- <li>View/alignment association menu to enable user to easily
- specify which alignment a multi-structure view takes its
- colours/correspondences from</li>
- <li>Allow properties file location to be specified as URL</li>
- <li>Extend Jalview project to preserve associations between
- many alignment views and a single Jmol display</li>
- <li>Store annotation row height in Jalview project file</li>
- <li>Annotation row column label formatting attributes stored
- in project file</li>
- <li>Annotation row order for auto-calculated annotation rows
- preserved in Jalview project file</li>
- <li>Visual progress indication when Jalview state is saved
- using Desktop window menu</li>
- <li>Visual indication that command line arguments are still
- being processed</li>
- <li>Groovy script execution from URL</li>
- <li>Colour by annotation default min and max colours in
- preferences</li>
- <li>Automatically associate PDB files dragged onto an
- alignment with sequences that have high similarity and matching
- IDs</li>
- <li>Update JGoogleAnalytics to latest release (0.3)</li>
- <li>'view structures' option to open many structures
- in same window</li>
- <li>Sort associated views menu option for tree panel</li>
- <li>Group all JABA and non-JABA services for a particular
- analysis function in its own submenu</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Userdefined and autogenerated annotation rows for groups</li>
- <li>Adjustment of alignment annotation pane height</li>
- <li>Annotation scrollbar for annotation panel</li>
- <li>Drag to reorder annotation rows in annotation panel</li>
- <li>'automaticScrolling' parameter</li>
- <li>Allow sequences with partial ID string matches to be
- annotated from GFF/Jalview features files</li>
- <li>Sequence logo annotation row in applet</li>
- <li>Absolute paths relative to host server in applet
- parameters are treated as such</li>
- <li>New in the JalviewLite javascript API:
- <ul>
- <li>JalviewLite.js javascript library</li>
- <li>Javascript callbacks for
- <ul>
- <li>Applet initialisation</li>
- <li>Sequence/alignment mouse-overs and selections</li>
+ </ul>
+ </li>
+ <li>horizontal scrolling gesture support</li>
+ <li>Visual progress indicator when PCA calculation is
+ running</li>
+ <li>Simpler JABA web services menus</li>
+ <li>visual indication that web service results are still
+ being retrieved from server</li>
+ <li>Serialise the dialogs that are shown when Jalview
+ starts up for first time</li>
+ <li>Jalview user agent string for interacting with HTTP
+ services</li>
+ <li>DAS 1.6 and DAS 2.0 source support using new JDAS
+ client library</li>
+ <li>Examples directory and Groovy library included in
+ InstallAnywhere distribution</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>RNA alignment and secondary structure annotation
+ visualization applet example</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>Normalise option for consensus sequence logo</li>
+ <li>Reset button in PCA window to return dimensions to
+ defaults</li>
+ <li>Allow seqspace or Jalview variant of alignment PCA
+ calculation</li>
+ <li>PCA with either nucleic acid and protein substitution
+ matrices
+ <li>Allow windows containing HTML reports to be exported
+ in HTML</li>
+ <li>Interactive display and editing of RNA secondary
+ structure contacts</li>
+ <li>RNA Helix Alignment Colouring</li>
+ <li>RNA base pair logo consensus</li>
+ <li>Parse sequence associated secondary structure
+ information in Stockholm files</li>
+ <li>HTML Export database accessions and annotation
+ information presented in tooltip for sequences</li>
+ <li>Import secondary structure from LOCARNA clustalw
+ style RNA alignment files</li>
+ <li>import and visualise T-COFFEE quality scores for an
+ alignment</li>
+ <li>'colour by annotation' per sequence option to
+ shade each sequence according to its associated alignment
+ annotation</li>
+ <li>New Jalview Logo</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>documentation for score matrices used in Jalview</li>
+ <li>New Website!</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>PDB, Unprot and EMBL (ENA) databases retrieved via
+ wsdbfetch REST service</li>
+ <li>Stop windows being moved outside desktop on OSX</li>
+ <li>Filetype associations not installed for webstart
+ launch</li>
+ <li>Jalview does not always retrieve progress of a JABAWS
+ job execution in full once it is complete</li>
+ <li>revise SHMR RSBS definition to ensure alignment is
+ uploaded via ali_file parameter</li>
+ <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
+ <li>View all structures superposed fails with exception</li>
+ <li>Jnet job queues forever if a very short sequence is
+ submitted for prediction</li>
+ <li>Cut and paste menu not opened when mouse clicked on
+ desktop window</li>
+ <li>Putting fractional value into integer text box in
+ alignment parameter dialog causes Jalview to hang</li>
+ <li>Structure view highlighting doesn't work on
+ windows 7</li>
+ <li>View all structures fails with exception shown in
+ structure view</li>
+ <li>Characters in filename associated with PDBEntry not
+ escaped in a platform independent way</li>
+ <li>Jalview desktop fails to launch with exception when
+ using proxy</li>
+ <li>Tree calculation reports 'you must have 2 or more
+ sequences selected' when selection is empty</li>
+ <li>Jalview desktop fails to launch with jar signature
+ failure when java web start temporary file caching is
+ disabled</li>
+ <li>DAS Sequence retrieval with range qualification
+ results in sequence xref which includes range qualification</li>
+ <li>Errors during processing of command line arguments
+ cause progress bar (JAL-898) to be removed</li>
+ <li>Replace comma for semi-colon option not disabled for
+ DAS sources in sequence fetcher</li>
+ <li>Cannot close news reader when JABAWS server warning
+ dialog is shown</li>
+ <li>Option widgets not updated to reflect user settings</li>
+ <li>Edited sequence not submitted to web service</li>
+ <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
+ <li>InstallAnywhere installer doesn't unpack and run
+ on OSX Mountain Lion</li>
+ <li>Annotation panel not given a scroll bar when
+ sequences with alignment annotation are pasted into the
+ alignment</li>
+ <li>Sequence associated annotation rows not associated
+ when loaded from Jalview project</li>
+ <li>Browser launch fails with NPE on java 1.7</li>
+ <li>JABAWS alignment marked as finished when job was
+ cancelled or job failed due to invalid input</li>
+ <li>NPE with v2.7 example when clicking on Tree
+ associated with all views</li>
+ <li>Exceptions when copy/paste sequences with grouped
+ annotation rows to new window</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Sequence features are momentarily displayed before
+ they are hidden using hidefeaturegroups applet parameter</li>
+ <li>loading features via javascript API automatically
+ enables feature display</li>
+ <li>scrollToColumnIn javascript API method doesn't
+ work</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>Redundancy removal fails for rna alignment</li>
+ <li>PCA calculation fails when sequence has been selected
+ and then deselected</li>
+ <li>PCA window shows grey box when first opened on OSX</li>
+ <li>Letters coloured pink in sequence logo when alignment
+ coloured with clustalx</li>
+ <li>Choosing fonts without letter symbols defined causes
+ exceptions and redraw errors</li>
+ <li>Initial PCA plot view is not same as manually
+ reconfigured view</li>
+ <li>Grouped annotation graph label has incorrect line
+ colour</li>
+ <li>Grouped annotation graph label display is corrupted
+ for lots of labels</li>
</ul>
- </li>
- <li>scrollTo row and column alignment scrolling functions</li>
- <li>Select sequence/alignment regions from javascript</li>
- <li>javascript structure viewer harness to pass messages
- between Jmol and Jalview when running as distinct applets</li>
- <li>sortBy method</li>
- <li>Set of applet and application examples shipped with
- documentation</li>
- <li>New example to demonstrate JalviewLite and Jmol
- javascript message exchange</li>
- </ul>
- </ul> <em>General</em>
- <ul>
- <li>Enable Jmol displays to be associated with multiple
- multiple alignments</li>
- <li>Option to automatically sort alignment with new tree</li>
- <li>User configurable link to enable redirects to a
- www.Jalview.org mirror</li>
- <li>Jmol colours option for Jmol displays</li>
- <li>Configurable newline string when writing alignment and
- other flat files</li>
- <li>Allow alignment annotation description lines to contain
- html tags</li>
- </ul> <em>Documentation and Development</em>
- <ul>
- <li>Add groovy test harness for bulk load testing to examples
- </li>
- <li>Groovy script to load and align a set of sequences using a
- web service before displaying the result in the Jalview desktop</li>
- <li>Restructured javascript and applet api documentation</li>
- <li>Ant target to publish example html files with applet
- archive</li>
- <li>Netbeans project for building Jalview from source</li>
- <li>ant task to create online javadoc for Jalview source</li>
- </ul></td>
- <td><em>Application</em>
- <ul>
- <li>User defined colourscheme throws exception when current
- built in colourscheme is saved as new scheme</li>
- <li>AlignFrame->Save in application pops up save dialog for
- valid filename/format</li>
- <li>Cannot view associated structure for Uniprot sequence</li>
- <li>PDB file association breaks for Uniprot sequence P37173</li>
- <li>Associate PDB from file dialog does not tell you which
- sequence is to be associated with the file</li>
- <li>Find All raises null pointer exception when query only
- matches sequence IDs</li>
- <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
- <li>Jalview project with Jmol views created with Jalview 2.4
- cannot be loaded</li>
- <li>Filetype associations not installed for webstart launch</li>
- <li>Two or more chains in a single PDB file associated with
- sequences in different alignments do not get coloured by their
- associated sequence</li>
- <li>Visibility status of autocalculated annotation row not
- preserved when project is loaded</li>
- <li>Annotation row height and visibility attributes not stored
- in Jalview project</li>
- <li>Tree bootstraps are not preserved when saved as a Jalview
- project</li>
- <li>Envision2 workflow tooltips are corrupted</li>
- <li>Enabling show group conservation also enables colour by
- conservation</li>
- <li>Duplicate group associated conservation or consensus
- created on new view</li>
- <li>Annotation scrollbar not displayed after 'show all
- hidden annotation rows' option selected</li>
- <li>Alignment quality not updated after alignment annotation
- row is hidden then shown</li>
- <li>Preserve colouring of structures coloured by sequences in
- pre Jalview 2.7 projects</li>
- <li>Web service job parameter dialog is not laid out properly
- </li>
- <li>Web services menu not refreshed after 'reset
- services' button is pressed in preferences</li>
- <li>Annotation off by one in Jalview v2_3 example project</li>
- <li>Structures imported from file and saved in project get
- name like jalview_pdb1234.txt when reloaded</li>
- <li>Jalview does not always retrieve progress of a JABAWS job
- execution in full once it is complete</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Alignment height set incorrectly when lots of annotation
- rows are displayed</li>
- <li>Relative URLs in feature HTML text not resolved to
- codebase</li>
- <li>View follows highlighting does not work for positions in
- sequences</li>
- <li><= shown as = in tooltip</li>
- <li>Export features raises exception when no features exist</li>
- <li>Separator string used for serialising lists of IDs for
- javascript api is modified when separator string provided as
- parameter</li>
- <li>Null pointer exception when selecting tree leaves for
- alignment with no existing selection</li>
- <li>Relative URLs for datasources assumed to be relative to
- applet's codebase</li>
- <li>Status bar not updated after finished searching and search
- wraps around to first result</li>
- <li>StructureSelectionManager instance shared between several
- Jalview applets causes race conditions and memory leaks</li>
- <li>Hover tooltip and mouseover of position on structure not
- sent from Jmol in applet</li>
- <li>Certain sequences of javascript method calls to applet API
- fatally hang browser</li>
- </ul> <em>General</em>
- <ul>
- <li>View follows structure mouseover scrolls beyond position
- with wrapped view and hidden regions</li>
- <li>Find sequence position moves to wrong residue with/without
- hidden columns</li>
- <li>Sequence length given in alignment properties window is
- off by 1</li>
- <li>InvalidNumberFormat exceptions thrown when trying to
- import PDB like structure files</li>
- <li>Positional search results are only highlighted between
- user-supplied sequence start/end bounds</li>
- <li>End attribute of sequence is not validated</li>
- <li>Find dialog only finds first sequence containing a given
- sequence position</li>
- <li>Sequence numbering not preserved in MSF alignment output</li>
- <li>Jalview PDB file reader does not extract sequence from
- nucleotide chains correctly</li>
- <li>Structure colours not updated when tree partition changed
- in alignment</li>
- <li>Sequence associated secondary structure not correctly
- parsed in interleaved stockholm</li>
- <li>Colour by annotation dialog does not restore current state
- </li>
- <li>Hiding (nearly) all sequences doesn't work properly</li>
- <li>Sequences containing lowercase letters are not properly
- associated with their pdb files</li>
- </ul> <em>Documentation and Development</em>
- <ul>
- <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
- tool</li>
- </ul></td>
- </tr>
- <tr>
- <td>
- <div align="center">
- <strong><a name="Jalview2.6.1">2.6.1</a>
- </strong><br> <em>15/11/2010</em>
- </div></td>
- <td><em>Application</em>
- <ul>
- <li>New warning dialog when the Jalview Desktop cannot contact
- web services</li>
- <li>JABA service parameters for a preset are shown in service
- job window</li>
- <li>JABA Service menu entries reworded</li>
- </ul></td>
- <td>
- <ul>
- <li>Modeller PIR IO broken - cannot correctly import a pir
- file emitted by Jalview</li>
- <li>Existing feature settings transferred to new alignment
- view created from cut'n'paste</li>
- <li>Improved test for mixed amino/nucleotide chains when
- parsing PDB files</li>
- <li>Consensus and conservation annotation rows occasionally
- become blank for all new windows</li>
- <li>Exception raised when right clicking above sequences in
- wrapped view mode</li>
- </ul> <em>Application</em>
- <ul>
- <li>multiple multiply aligned structure views cause cpu usage
- to hit 100% and computer to hang</li>
- <li>Web Service parameter layout breaks for long user
- parameter names</li>
- <li>Jaba service discovery hangs desktop if Jaba server is
- down</li>
- </ul></td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
- <em>26/9/2010</em></div>
- </td>
- <td><em>Application</em>
- <ul>
- <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
- <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
- <li>Web Services preference tab</li>
- <li>Analysis parameters dialog box and user defined preferences</li>
- <li>Improved speed and layout of Envision2 service menu</li>
- <li>Superpose structures using associated sequence alignment</li>
- <li>Export coordinates and projection as CSV from PCA viewer</li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>enable javascript: execution by the applet via the link out
- mechanism</li>
- </ul>
- <em>Other</em>
- <ul>
- <li>Updated the Jmol Jalview interface to work with Jmol series
- 12</li>
- <li>The Jalview Desktop and JalviewLite applet now require Java
- 1.5</li>
- <li>Allow Jalview feature colour specification for GFF sequence
- annotation files</li>
- <li>New 'colour by label' keword in Jalview feature file type
- colour specification</li>
- <li>New Jalview Desktop Groovy API method that allows a script
- to check if it being run in an interactive session or in a batch
- operation from the Jalview command line</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>clustalx colourscheme colours Ds preferentially when both
- D+E are present in over 50% of the column</li>
- </ul>
-
- <em>Application</em>
- <ul>
- <li>typo in AlignmentFrame->View->Hide->all but
- selected Regions menu item</li>
- <li>sequence fetcher replaces ',' for ';' when the ',' is part
- of a valid accession ID</li>
- <li>fatal OOM if object retrieved by sequence fetcher runs out
- of memory</li>
- <li>unhandled Out of Memory Error when viewing pca analysis
- results</li>
- <li>InstallAnywhere builds fail to launch on OS X java 10.5
- update 4 (due to apple Java 1.6 update)</li>
- <li>Installanywhere Jalview silently fails to launch</li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>Jalview.getFeatureGroups() raises an
- ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
- <em>14/6/2010</em></div>
- </td>
- <td></td>
- <td>
- <ul>
- <li>Alignment prettyprinter doesn't cope with long sequence IDs
- </li>
- <li>clustalx colourscheme colours Ds preferentially when both
- D+E are present in over 50% of the column</li>
- <li>nucleic acid structures retrieved from PDB do not import
- correctly</li>
- <li>More columns get selected than were clicked on when a number
- of columns are hidden</li>
- <li>annotation label popup menu not providing correct
- add/hide/show options when rows are hidden or none are present</li>
- <li>Stockholm format shown in list of readable formats, and
- parser copes better with alignments from RFAM.</li>
- <li>CSV output of consensus only includes the percentage of all
- symbols if sequence logo display is enabled</li>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>Jalview Desktop News Reader</li>
+ <li>Tweaked default layout of web services menu</li>
+ <li>View/alignment association menu to enable user to
+ easily specify which alignment a multi-structure view takes
+ its colours/correspondences from</li>
+ <li>Allow properties file location to be specified as URL</li>
+ <li>Extend Jalview project to preserve associations
+ between many alignment views and a single Jmol display</li>
+ <li>Store annotation row height in Jalview project file</li>
+ <li>Annotation row column label formatting attributes
+ stored in project file</li>
+ <li>Annotation row order for auto-calculated annotation
+ rows preserved in Jalview project file</li>
+ <li>Visual progress indication when Jalview state is
+ saved using Desktop window menu</li>
+ <li>Visual indication that command line arguments are
+ still being processed</li>
+ <li>Groovy script execution from URL</li>
+ <li>Colour by annotation default min and max colours in
+ preferences</li>
+ <li>Automatically associate PDB files dragged onto an
+ alignment with sequences that have high similarity and
+ matching IDs</li>
+ <li>Update JGoogleAnalytics to latest release (0.3)</li>
+ <li>'view structures' option to open many
+ structures in same window</li>
+ <li>Sort associated views menu option for tree panel</li>
+ <li>Group all JABA and non-JABA services for a particular
+ analysis function in its own submenu</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Userdefined and autogenerated annotation rows for
+ groups</li>
+ <li>Adjustment of alignment annotation pane height</li>
+ <li>Annotation scrollbar for annotation panel</li>
+ <li>Drag to reorder annotation rows in annotation panel</li>
+ <li>'automaticScrolling' parameter</li>
+ <li>Allow sequences with partial ID string matches to be
+ annotated from GFF/Jalview features files</li>
+ <li>Sequence logo annotation row in applet</li>
+ <li>Absolute paths relative to host server in applet
+ parameters are treated as such</li>
+ <li>New in the JalviewLite javascript API:
+ <ul>
+ <li>JalviewLite.js javascript library</li>
+ <li>Javascript callbacks for
+ <ul>
+ <li>Applet initialisation</li>
+ <li>Sequence/alignment mouse-overs and selections</li>
+ </ul>
+ </li>
+ <li>scrollTo row and column alignment scrolling
+ functions</li>
+ <li>Select sequence/alignment regions from javascript</li>
+ <li>javascript structure viewer harness to pass
+ messages between Jmol and Jalview when running as
+ distinct applets</li>
+ <li>sortBy method</li>
+ <li>Set of applet and application examples shipped
+ with documentation</li>
+ <li>New example to demonstrate JalviewLite and Jmol
+ javascript message exchange</li>
+ </ul>
+ </ul> <em>General</em>
+ <ul>
+ <li>Enable Jmol displays to be associated with multiple
+ multiple alignments</li>
+ <li>Option to automatically sort alignment with new tree</li>
+ <li>User configurable link to enable redirects to a
+ www.Jalview.org mirror</li>
+ <li>Jmol colours option for Jmol displays</li>
+ <li>Configurable newline string when writing alignment
+ and other flat files</li>
+ <li>Allow alignment annotation description lines to
+ contain html tags</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>Add groovy test harness for bulk load testing to
+ examples</li>
+ <li>Groovy script to load and align a set of sequences
+ using a web service before displaying the result in the
+ Jalview desktop</li>
+ <li>Restructured javascript and applet api documentation</li>
+ <li>Ant target to publish example html files with applet
+ archive</li>
+ <li>Netbeans project for building Jalview from source</li>
+ <li>ant task to create online javadoc for Jalview source</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>User defined colourscheme throws exception when
+ current built in colourscheme is saved as new scheme</li>
+ <li>AlignFrame->Save in application pops up save
+ dialog for valid filename/format</li>
+ <li>Cannot view associated structure for Uniprot sequence</li>
+ <li>PDB file association breaks for Uniprot sequence
+ P37173</li>
+ <li>Associate PDB from file dialog does not tell you
+ which sequence is to be associated with the file</li>
+ <li>Find All raises null pointer exception when query
+ only matches sequence IDs</li>
+ <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
+ <li>Jalview project with Jmol views created with Jalview
+ 2.4 cannot be loaded</li>
+ <li>Filetype associations not installed for webstart
+ launch</li>
+ <li>Two or more chains in a single PDB file associated
+ with sequences in different alignments do not get coloured
+ by their associated sequence</li>
+ <li>Visibility status of autocalculated annotation row
+ not preserved when project is loaded</li>
+ <li>Annotation row height and visibility attributes not
+ stored in Jalview project</li>
+ <li>Tree bootstraps are not preserved when saved as a
+ Jalview project</li>
+ <li>Envision2 workflow tooltips are corrupted</li>
+ <li>Enabling show group conservation also enables colour
+ by conservation</li>
+ <li>Duplicate group associated conservation or consensus
+ created on new view</li>
+ <li>Annotation scrollbar not displayed after 'show
+ all hidden annotation rows' option selected</li>
+ <li>Alignment quality not updated after alignment
+ annotation row is hidden then shown</li>
+ <li>Preserve colouring of structures coloured by
+ sequences in pre Jalview 2.7 projects</li>
+ <li>Web service job parameter dialog is not laid out
+ properly</li>
+ <li>Web services menu not refreshed after 'reset
+ services' button is pressed in preferences</li>
+ <li>Annotation off by one in Jalview v2_3 example project</li>
+ <li>Structures imported from file and saved in project
+ get name like jalview_pdb1234.txt when reloaded</li>
+ <li>Jalview does not always retrieve progress of a JABAWS
+ job execution in full once it is complete</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Alignment height set incorrectly when lots of
+ annotation rows are displayed</li>
+ <li>Relative URLs in feature HTML text not resolved to
+ codebase</li>
+ <li>View follows highlighting does not work for positions
+ in sequences</li>
+ <li><= shown as = in tooltip</li>
+ <li>Export features raises exception when no features
+ exist</li>
+ <li>Separator string used for serialising lists of IDs
+ for javascript api is modified when separator string
+ provided as parameter</li>
+ <li>Null pointer exception when selecting tree leaves for
+ alignment with no existing selection</li>
+ <li>Relative URLs for datasources assumed to be relative
+ to applet's codebase</li>
+ <li>Status bar not updated after finished searching and
+ search wraps around to first result</li>
+ <li>StructureSelectionManager instance shared between
+ several Jalview applets causes race conditions and memory
+ leaks</li>
+ <li>Hover tooltip and mouseover of position on structure
+ not sent from Jmol in applet</li>
+ <li>Certain sequences of javascript method calls to
+ applet API fatally hang browser</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>View follows structure mouseover scrolls beyond
+ position with wrapped view and hidden regions</li>
+ <li>Find sequence position moves to wrong residue
+ with/without hidden columns</li>
+ <li>Sequence length given in alignment properties window
+ is off by 1</li>
+ <li>InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files</li>
+ <li>Positional search results are only highlighted
+ between user-supplied sequence start/end bounds</li>
+ <li>End attribute of sequence is not validated</li>
+ <li>Find dialog only finds first sequence containing a
+ given sequence position</li>
+ <li>Sequence numbering not preserved in MSF alignment
+ output</li>
+ <li>Jalview PDB file reader does not extract sequence
+ from nucleotide chains correctly</li>
+ <li>Structure colours not updated when tree partition
+ changed in alignment</li>
+ <li>Sequence associated secondary structure not correctly
+ parsed in interleaved stockholm</li>
+ <li>Colour by annotation dialog does not restore current
+ state</li>
+ <li>Hiding (nearly) all sequences doesn't work
+ properly</li>
+ <li>Sequences containing lowercase letters are not
+ properly associated with their pdb files</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>schemas/JalviewWsParamSet.xsd corrupted by
+ ApplyCopyright tool</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>New warning dialog when the Jalview Desktop cannot
+ contact web services</li>
+ <li>JABA service parameters for a preset are shown in
+ service job window</li>
+ <li>JABA Service menu entries reworded</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>Modeller PIR IO broken - cannot correctly import a
+ pir file emitted by Jalview</li>
+ <li>Existing feature settings transferred to new
+ alignment view created from cut'n'paste</li>
+ <li>Improved test for mixed amino/nucleotide chains when
+ parsing PDB files</li>
+ <li>Consensus and conservation annotation rows
+ occasionally become blank for all new windows</li>
+ <li>Exception raised when right clicking above sequences
+ in wrapped view mode</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>multiple multiply aligned structure views cause cpu
+ usage to hit 100% and computer to hang</li>
+ <li>Web Service parameter layout breaks for long user
+ parameter names</li>
+ <li>Jaba service discovery hangs desktop if Jaba server
+ is down</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
+ <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
+ (JABAWS)
+ </li>
+ <li>Web Services preference tab</li>
+ <li>Analysis parameters dialog box and user defined
+ preferences</li>
+ <li>Improved speed and layout of Envision2 service menu</li>
+ <li>Superpose structures using associated sequence
+ alignment</li>
+ <li>Export coordinates and projection as CSV from PCA
+ viewer</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>enable javascript: execution by the applet via the
+ link out mechanism</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Updated the Jmol Jalview interface to work with Jmol
+ series 12</li>
+ <li>The Jalview Desktop and JalviewLite applet now
+ require Java 1.5</li>
+ <li>Allow Jalview feature colour specification for GFF
+ sequence annotation files</li>
+ <li>New 'colour by label' keword in Jalview feature file
+ type colour specification</li>
+ <li>New Jalview Desktop Groovy API method that allows a
+ script to check if it being run in an interactive session or
+ in a batch operation from the Jalview command line</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Regions menu item</li>
+ <li>sequence fetcher replaces ',' for ';' when the ',' is
+ part of a valid accession ID</li>
+ <li>fatal OOM if object retrieved by sequence fetcher
+ runs out of memory</li>
+ <li>unhandled Out of Memory Error when viewing pca
+ analysis results</li>
+ <li>InstallAnywhere builds fail to launch on OS X java
+ 10.5 update 4 (due to apple Java 1.6 update)</li>
+ <li>Installanywhere Jalview silently fails to launch</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Jalview.getFeatureGroups() raises an
+ ArrayIndexOutOfBoundsException if no feature groups are
+ defined.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
+ </div>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li>Alignment prettyprinter doesn't cope with long
+ sequence IDs</li>
+ <li>clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column</li>
+ <li>nucleic acid structures retrieved from PDB do not
+ import correctly</li>
+ <li>More columns get selected than were clicked on when a
+ number of columns are hidden</li>
+ <li>annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are
+ present</li>
+ <li>Stockholm format shown in list of readable formats,
+ and parser copes better with alignments from RFAM.</li>
+ <li>CSV output of consensus only includes the percentage
+ of all symbols if sequence logo display is enabled</li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>annotation panel disappears when annotation is
- hidden/removed</li>
- </ul>
- <em>Application</em>
- <ul>
- <li>Alignment view not redrawn properly when new alignment
- opened where annotation panel is visible but no annotations are
- present on alignment</li>
- <li>pasted region containing hidden columns is incorrectly
- displayed in new alignment window</li>
- <li>Jalview slow to complete operations when stdout is flooded
- (fix is to close the Jalview console)</li>
- <li>typo in AlignmentFrame->View->Hide->all but
- selected Rregions menu item.</li>
- <li>inconsistent group submenu and Format submenu entry 'Un' or
- 'Non'conserved</li>
- <li>Sequence feature settings are being shared by multiple
- distinct alignments</li>
- <li>group annotation not recreated when tree partition is
- changed</li>
- <li>double click on group annotation to select sequences does
- not propagate to associated trees</li>
- <li>Mac OSX specific issues:
- <ul>
- <li>exception raised when mouse clicked on desktop window
- background</li>
- <li>Desktop menu placed on menu bar and application name set
- correctly</li>
- <li>sequence feature settings not wide enough for the save
- feature colourscheme button</li>
- </ul>
- </li>
- </ul>
- </td>
- </tr>
- <tr>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>annotation panel disappears when annotation is
+ hidden/removed</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Alignment view not redrawn properly when new
+ alignment opened where annotation panel is visible but no
+ annotations are present on alignment</li>
+ <li>pasted region containing hidden columns is
+ incorrectly displayed in new alignment window</li>
+ <li>Jalview slow to complete operations when stdout is
+ flooded (fix is to close the Jalview console)</li>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.</li>
+ <li>inconsistent group submenu and Format submenu entry
+ 'Un' or 'Non'conserved</li>
+ <li>Sequence feature settings are being shared by
+ multiple distinct alignments</li>
+ <li>group annotation not recreated when tree partition is
+ changed</li>
+ <li>double click on group annotation to select sequences
+ does not propagate to associated trees</li>
+ <li>Mac OSX specific issues:
+ <ul>
+ <li>exception raised when mouse clicked on desktop
+ window background</li>
+ <li>Desktop menu placed on menu bar and application
+ name set correctly</li>
+ <li>sequence feature settings not wide enough for the
+ save feature colourscheme button</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
- <td>
- <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
- <em>30/4/2010</em></div>
- </td>
- <td><em>New Capabilities</em>
- <ul>
- <li>URL links generated from description line for
- regular-expression based URL links (applet and application)
- <li>Non-positional feature URL links are shown in link menu</li>
- <li>Linked viewing of nucleic acid sequences and structures</li>
- <li>Automatic Scrolling option in View menu to display the
- currently highlighted region of an alignment.</li>
- <li>Order an alignment by sequence length, or using the average
- score or total feature count for each sequence.</li>
- <li>Shading features by score or associated description</li>
- <li>Subdivide alignment and groups based on identity of selected
- subsequence (Make Groups from Selection).</li>
- <li>New hide/show options including Shift+Control+H to hide
- everything but the currently selected region.</li>
- <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
- </ul>
- <em>Application</em>
- <ul>
- <li>Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources</li>
- <li>Local DAS Sequence sources can be added via the command line
- or via the Add local source dialog box.</li>
- <li>DAS Dbref and DbxRef feature types are parsed as database
- references and protein_name is parsed as description line (BioSapiens
- terms).</li>
- <li>Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.</li>
- <!-- <li>New hidden columns and rows and representatives capabilities
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
+ </div>
+ </td>
+ <td><em>New Capabilities</em>
+ <ul>
+ <li>URL links generated from description line for
+ regular-expression based URL links (applet and application)
+
+ <li>Non-positional feature URL links are shown in link
+ menu</li>
+ <li>Linked viewing of nucleic acid sequences and
+ structures</li>
+ <li>Automatic Scrolling option in View menu to display
+ the currently highlighted region of an alignment.</li>
+ <li>Order an alignment by sequence length, or using the
+ average score or total feature count for each sequence.</li>
+ <li>Shading features by score or associated description</li>
+ <li>Subdivide alignment and groups based on identity of
+ selected subsequence (Make Groups from Selection).</li>
+ <li>New hide/show options including Shift+Control+H to
+ hide everything but the currently selected region.</li>
+ <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
+ </ul> <em>Application</em>
+ <ul>
+ <li>Fetch DB References capabilities and UI expanded to
+ support retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the
+ command line or via the Add local source dialog box.</li>
+ <li>DAS Dbref and DbxRef feature types are parsed as
+ database references and protein_name is parsed as
+ description line (BioSapiens terms).</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in
+ application.</li>
+ <!-- <li>New hidden columns and rows and representatives capabilities
in annotations file (in progress - not yet fully implemented)</li> -->
- <li>Group-associated consensus, sequence logos and conservation
- plots</li>
- <li>Symbol distributions for each column can be exported and
- visualized as sequence logos</li>
- <li>Optionally scale multi-character column labels to fit within
- each column of annotation row<!-- todo for applet --></li>
- <li>Optional automatic sort of associated alignment view when a
- new tree is opened.</li>
- <li>Jalview Java Console</li>
- <li>Better placement of desktop window when moving between
- different screens.</li>
- <li>New preference items for sequence ID tooltip and consensus
- annotation</li>
- <li>Client to submit sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a> Workflows</li>
- <li><em>Vamsas Capabilities</em>
- <ul>
- <li>Improved VAMSAS synchronization (Jalview archive used to
- preserve views, structures, and tree display settings)</li>
- <li>Import of vamsas documents from disk or URL via command
- line</li>
- <li>Sharing of selected regions between views and with other
- VAMSAS applications (Experimental feature!)</li>
- <li>Updated API to VAMSAS version 0.2</li>
- </ul>
- </li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>Middle button resizes annotation row height</li>
- <li>New Parameters
- <ul>
- <li>sortByTree (true/false) - automatically sort the associated
- alignment view by the tree when a new tree is opened.</li>
- <li>showTreeBootstraps (true/false) - show or hide branch
- bootstraps (default is to show them if available)</li>
- <li>showTreeDistances (true/false) - show or hide branch
- lengths (default is to show them if available)</li>
- <li>showUnlinkedTreeNodes (true/false) - indicate if
- unassociated nodes should be highlighted in the tree view</li>
- <li>heightScale and widthScale (1.0 or more) - increase the
- height or width of a cell in the alignment grid relative to the
- current font size.</li>
- </ul>
- </li>
- <li>Non-positional features displayed in sequence ID tooltip</li>
- </ul>
- <em>Other</em>
- <ul>
- <li>Features format: graduated colour definitions and
- specification of feature scores</li>
- <li>Alignment Annotations format: new keywords for group
- associated annotation (GROUP_REF) and annotation row display
- properties (ROW_PROPERTIES)</li>
- <li>XML formats extended to support graduated feature
- colourschemes, group associated annotation, and profile visualization
- settings.</li>
- </td>
- <td>
- <ul>
- <li>Source field in GFF files parsed as feature source rather
- than description</li>
- <li>Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).</li>
- <li>URL links generated for all feature links (bugfix)</li>
- <li>Added URL embedding instructions to features file
- documentation.</li>
- <li>Codons containing ambiguous nucleotides translated as 'X' in
- peptide product</li>
- <li>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.</li>
- <li>AMSA files only contain first column of multi-character
- column annotation labels</li>
- <li>Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)</li>
- <li>PDB files without embedded PDB IDs given a friendly name</li>
- <li>Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.</li>
- <li>Application:
- <ul>
- <li>Better handling of exceptions during sequence retrieval</li>
- <li>Dasobert generated non-positional feature URL link text
- excludes the start_end suffix</li>
- <li>DAS feature and source retrieval buttons disabled when
- fetch or registry operations in progress.</li>
- <li>PDB files retrieved from URLs are cached properly</li>
- <li>Sequence description lines properly shared via VAMSAS</li>
- <li>Sequence fetcher fetches multiple records for all data
- sources</li>
- <li>Ensured that command line das feature retrieval completes
- before alignment figures are generated.</li>
- <li>Reduced time taken when opening file browser for first
- time.</li>
- <li>isAligned check prior to calculating tree, PCA or
- submitting an MSA to JNet now excludes hidden sequences.</li>
- <li>User defined group colours properly recovered from Jalview
- projects.</li>
- </ul>
- </li>
- </ul>
- </td>
-
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.4.0.b2</strong><br>
- 28/10/2009</div>
- </td>
- <td>
- <ul>
- <li>Experimental support for google analytics usage tracking.</li>
- <li>Jalview privacy settings (user preferences and docs).</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
- <li>Exception when feature created from selection beyond length
- of sequence.</li>
- <li>Allow synthetic PDB files to be imported gracefully</li>
- <li>Sequence associated annotation rows associate with all
- sequences with a given id</li>
- <li>Find function matches case-insensitively for sequence ID
- string searches</li>
- <li>Non-standard characters do not cause pairwise alignment to
- fail with exception</li>
- </ul>
- <em>Application Issues</em>
- <ul>
- <li>Sequences are now validated against EMBL database</li>
- <li>Sequence fetcher fetches multiple records for all data
- sources</li>
- </ul>
- <em>InstallAnywhere Issues</em>
- <ul>
- <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
- installAnywhere mechanism)</li>
- <li>Command line launching of JARs from InstallAnywhere version
- (java class versioning error fixed)</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
+ <li>Group-associated consensus, sequence logos and
+ conservation plots</li>
+ <li>Symbol distributions for each column can be exported
+ and visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit
+ within each column of annotation row<!-- todo for applet -->
+ </li>
+ <li>Optional automatic sort of associated alignment view
+ when a new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving
+ between different screens.</li>
+ <li>New preference items for sequence ID tooltip and
+ consensus annotation</li>
+ <li>Client to submit sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a>
+ Workflows
+ </li>
+ <li><em>Vamsas Capabilities</em>
+ <ul>
+ <li>Improved VAMSAS synchronization (Jalview archive
+ used to preserve views, structures, and tree display
+ settings)</li>
+ <li>Import of vamsas documents from disk or URL via
+ command line</li>
+ <li>Sharing of selected regions between views and
+ with other VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul></li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the
+ associated alignment view by the tree when a new tree is
+ opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide
+ branch bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide
+ branch lengths (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if
+ unassociated nodes should be highlighted in the tree
+ view</li>
+ <li>heightScale and widthScale (1.0 or more) -
+ increase the height or width of a cell in the alignment
+ grid relative to the current font size.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID
+ tooltip</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display
+ properties (ROW_PROPERTIES)</li>
+ <li>XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile
+ visualization settings.</li></td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source
+ rather than description</li>
+ <li>Non-positional features are now included in sequence
+ feature and gff files (controlled via non-positional feature
+ visibility in tooltip).</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as
+ 'X' in peptide product</li>
+ <li>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.</li>
+ <li>AMSA files only contain first column of
+ multi-character column annotation labels</li>
+ <li>Jalview Annotation File generation/parsing consistent
+ with documentation (e.g. Stockholm annotation can be
+ exported and re-imported)</li>
+ <li>PDB files without embedded PDB IDs given a friendly
+ name</li>
+ <li>Find incrementally searches ID string matches as well
+ as subsequence matches, and correctly reports total number
+ of both.</li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence
+ retrieval</li>
+ <li>Dasobert generated non-positional feature URL
+ link text excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled
+ when fetch or registry operations in progress.</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via
+ VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ <li>Ensured that command line das feature retrieval
+ completes before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for
+ first time.</li>
+ <li>isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered
+ from Jalview projects.</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
- <div align="center"><strong>2.4</strong><br>
- 27/8/2008</div>
- </td>
- <td><em>User Interface</em>
- <ul>
- <li>Linked highlighting of codon and amino acid from translation
- and protein products</li>
- <li>Linked highlighting of structure associated with residue
- mapping to codon position</li>
- <li>Sequence Fetcher provides example accession numbers and
- 'clear' button</li>
- <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
- <li>Extract score function to parse whitespace separated numeric
- data in description line</li>
- <li>Column labels in alignment annotation can be centred.</li>
- <li>Tooltip for sequence associated annotation give name of
- sequence</li>
- </ul>
- <em>Web Services and URL fetching</em>
- <ul>
- <li>JPred3 web service</li>
- <li>Prototype sequence search client (no public services
- available yet)</li>
- <li>Fetch either seed alignment or full alignment from PFAM</li>
- <li>URL Links created for matching database cross references as
- well as sequence ID</li>
- <li>URL Links can be created using regular-expressions</li>
- </ul>
- <em>Sequence Database Connectivity</em>
- <ul>
- <li>Retrieval of cross-referenced sequences from other databases
- </li>
- <li>Generalised database reference retrieval and validation to
- all fetchable databases</li>
- <li>Fetch sequences from DAS sources supporting the sequence
- command</li>
- </ul>
- <em>Import and Export</em>
- <li>export annotation rows as CSV for spreadsheet import</li>
- <li>Jalview projects record alignment dataset associations, EMBL
- products, and cDNA sequence mappings</li>
- <li>Sequence Group colour can be specified in Annotation File</li>
- <li>Ad-hoc colouring of group in Annotation File using RGB
- triplet as name of colourscheme</li>
- </ul>
- <em>VAMSAS Client capabilities (Experimental)</em>
- <ul>
- <li>treenode binding for VAMSAS tree exchange</li>
- <li>local editing and update of sequences in VAMSAS alignments
- (experimental)</li>
- <li>Create new or select existing session to join</li>
- <li>load and save of vamsas documents</li>
- </ul>
- <em>Application command line</em>
- <ul>
- <li>-tree parameter to open trees (introduced for passing from
- applet)</li>
- <li>-fetchfrom command line argument to specify nicknames of DAS
- servers to query for alignment features</li>
- <li>-dasserver command line argument to add new servers that are
- also automatically queried for features</li>
- <li>-groovy command line argument executes a given groovy script
- after all input data has been loaded and parsed</li>
- </ul>
- <em>Applet-Application data exchange</em>
- <ul>
- <li>Trees passed as applet parameters can be passed to
- application (when using "View in full application")</li>
- </ul>
- <em>Applet Parameters</em>
- <ul>
- <li>feature group display control parameter</li>
- <li>debug parameter</li>
- <li>showbutton parameter</li>
- </ul>
- <em>Applet API methods</em>
- <ul>
- <li>newView public method</li>
- <li>Window (current view) specific get/set public methods</li>
- <li>Feature display control methods</li>
- <li>get list of currently selected sequences</li>
- </ul>
- <em>New Jalview distribution features</em>
- <ul>
- <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
- <li>RELEASE file gives build properties for the latest Jalview
- release.</li>
- <li>Java 1.1 Applet build made easier and donotobfuscate
- property controls execution of obfuscator</li>
- <li>Build target for generating source distribution</li>
- <li>Debug flag for javacc</li>
- <li>.jalview_properties file is documented (slightly) in
- jalview.bin.Cache</li>
- <li>Continuous Build Integration for stable and development
- version of Application, Applet and source distribution</li>
- </ul>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.4.0.b2</strong><br> 28/10/2009
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Experimental support for google analytics usage
+ tracking.</li>
+ <li>Jalview privacy settings (user preferences and docs).</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Race condition in applet preventing startup in
+ jre1.6.0u12+.</li>
+ <li>Exception when feature created from selection beyond
+ length of sequence.</li>
+ <li>Allow synthetic PDB files to be imported gracefully</li>
+ <li>Sequence associated annotation rows associate with
+ all sequences with a given id</li>
+ <li>Find function matches case-insensitively for sequence
+ ID string searches</li>
+ <li>Non-standard characters do not cause pairwise
+ alignment to fail with exception</li>
+ </ul> <em>Application Issues</em>
+ <ul>
+ <li>Sequences are now validated against EMBL database</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ </ul> <em>InstallAnywhere Issues</em>
+ <ul>
+ <li>Dock icon works for Mac OS X java (Mac 1.6 update
+ issue with installAnywhere mechanism)</li>
+ <li>Command line launching of JARs from InstallAnywhere
+ version (java class versioning error fixed)</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
- </td>
- <td>
- <ul>
- <li>selected region output includes visible annotations (for
- certain formats)</li>
- <li>edit label/displaychar contains existing label/char for
- editing</li>
- <li>update PDBEntries when DBRefEntries change (vamsas)</li>
- <li>shorter peptide product names from EMBL records</li>
- <li>Newick string generator makes compact representations</li>
- <li>bootstrap values parsed correctly for tree files with
- comments</li>
- <li>pathological filechooser bug avoided by not allowing
- filenames containing a ':'</li>
- <li>Fixed exception when parsing GFF files containing global
- sequence features</li>
- <li>Alignment datasets are finalized only when number of
- references from alignment sequences goes to zero</li>
- <li>Close of tree branch colour box without colour selection
- causes cascading exceptions</li>
- <li>occasional negative imgwidth exceptions</li>
- <li>better reporting of non-fatal warnings to user when file
- parsing fails.</li>
- <li>Save works when Jalview project is default format</li>
- <li>Save as dialog opened if current alignment format is not a
- valid output format</li>
- <li>Uniprot canonical names introduced for both das and vamsas</li>
- <li>Histidine should be midblue (not pink!) in Zappo</li>
- <li>error messages passed up and output when data read fails</li>
- <li>edit undo recovers previous dataset sequence when sequence
- is edited</li>
- <li>allow PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) to be read in properly</li>
- <li>allow reading of JPred concise files as a normal filetype</li>
- <li>Stockholm annotation parsing and alignment properties import
- fixed for PFAM records</li>
- <li>Structure view windows have correct name in Desktop window
- list</li>
- <li>annotation consisting of sequence associated scores can be
- read and written correctly to annotation file</li>
- <li>Aligned cDNA translation to aligned peptide works correctly</li>
- <li>Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet</li>
- <li>Applet Menus are always embedded in applet window on Macs.</li>
- <li>Newly shown features appear at top of stack (in Applet)</li>
- <li>Annotations added via parameter not drawn properly due to
- null pointer exceptions</li>
- <li>Secondary structure lines are drawn starting from first
- column of alignment</li>
- <li>Uniprot XML import updated for new schema release in July
- 2008</li>
- <li>Sequence feature to sequence ID match for Features file is
- case-insensitive</li>
- <li>Sequence features read from Features file appended to all
- sequences with matching IDs</li>
- <li>PDB structure coloured correctly for associated views
- containing a sub-sequence</li>
- <li>PDB files can be retrieved by applet from Jar files</li>
- <li>feature and annotation file applet parameters referring to
- different directories are retrieved correctly</li>
- <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
- <li>Fixed application hang whilst waiting for splash-screen
- version check to complete</li>
- <li>Applet properly URLencodes input parameter values when
- passing them to the launchApp service</li>
- <li>display name and local features preserved in results
- retrieved from web service</li>
- <li>Visual delay indication for sequence retrieval and sequence
- fetcher initialisation</li>
- <li>updated Application to use DAS 1.53e version of dasobert DAS
- client</li>
- <li>Re-instated Full AMSA support and .amsa file association</li>
- <li>Fixed parsing of JNet Concise annotation <em>sans</em>
- sequences</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.3</strong><br>
- 9/5/07</div>
- </td>
- <td>
- <ul>
- <li>Jmol 11.0.2 integration</li>
- <li>PDB views stored in Jalview XML files</li>
- <li>Slide sequences</li>
- <li>Edit sequence in place</li>
- <li>EMBL CDS features</li>
- <li>DAS Feature mapping</li>
- <li>Feature ordering</li>
- <li>Alignment Properties</li>
- <li>Annotation Scores</li>
- <li>Sort by scores</li>
- <li>Feature/annotation editing in applet</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Headless state operation in 2.2.1</li>
- <li>Incorrect and unstable DNA pairwise alignment</li>
- <li>Cut and paste of sequences with annotation</li>
- <li>Feature group display state in XML</li>
- <li>Feature ordering in XML</li>
- <li>blc file iteration selection using filename # suffix</li>
- <li>Stockholm alignment properties</li>
- <li>Stockhom alignment secondary structure annotation</li>
- <li>2.2.1 applet had no feature transparency</li>
- <li>Number pad keys can be used in cursor mode</li>
- <li>Structure Viewer mirror image resolved</li>
- </ul>
- </td>
+ <div align="center">
+ <strong>2.4</strong><br> 27/8/2008
+ </div>
+ </td>
+ <td><em>User Interface</em>
+ <ul>
+ <li>Linked highlighting of codon and amino acid from
+ translation and protein products</li>
+ <li>Linked highlighting of structure associated with
+ residue mapping to codon position</li>
+ <li>Sequence Fetcher provides example accession numbers
+ and 'clear' button</li>
+ <li>MemoryMonitor added as an option under Desktop's
+ Tools menu</li>
+ <li>Extract score function to parse whitespace separated
+ numeric data in description line</li>
+ <li>Column labels in alignment annotation can be centred.</li>
+ <li>Tooltip for sequence associated annotation give name
+ of sequence</li>
+ </ul> <em>Web Services and URL fetching</em>
+ <ul>
+ <li>JPred3 web service</li>
+ <li>Prototype sequence search client (no public services
+ available yet)</li>
+ <li>Fetch either seed alignment or full alignment from
+ PFAM</li>
+ <li>URL Links created for matching database cross
+ references as well as sequence ID</li>
+ <li>URL Links can be created using regular-expressions</li>
+ </ul> <em>Sequence Database Connectivity</em>
+ <ul>
+ <li>Retrieval of cross-referenced sequences from other
+ databases</li>
+ <li>Generalised database reference retrieval and
+ validation to all fetchable databases</li>
+ <li>Fetch sequences from DAS sources supporting the
+ sequence command</li>
+ </ul> <em>Import and Export</em>
+ <li>export annotation rows as CSV for spreadsheet import</li>
+ <li>Jalview projects record alignment dataset associations,
+ EMBL products, and cDNA sequence mappings</li>
+ <li>Sequence Group colour can be specified in Annotation
+ File</li>
+ <li>Ad-hoc colouring of group in Annotation File using RGB
+ triplet as name of colourscheme</li>
+ </ul> <em>VAMSAS Client capabilities (Experimental)</em>
+ <ul>
+ <li>treenode binding for VAMSAS tree exchange</li>
+ <li>local editing and update of sequences in VAMSAS
+ alignments (experimental)</li>
+ <li>Create new or select existing session to join</li>
+ <li>load and save of vamsas documents</li>
+ </ul> <em>Application command line</em>
+ <ul>
+ <li>-tree parameter to open trees (introduced for passing
+ from applet)</li>
+ <li>-fetchfrom command line argument to specify nicknames
+ of DAS servers to query for alignment features</li>
+ <li>-dasserver command line argument to add new servers
+ that are also automatically queried for features</li>
+ <li>-groovy command line argument executes a given groovy
+ script after all input data has been loaded and parsed</li>
+ </ul> <em>Applet-Application data exchange</em>
+ <ul>
+ <li>Trees passed as applet parameters can be passed to
+ application (when using "View in full
+ application")</li>
+ </ul> <em>Applet Parameters</em>
+ <ul>
+ <li>feature group display control parameter</li>
+ <li>debug parameter</li>
+ <li>showbutton parameter</li>
+ </ul> <em>Applet API methods</em>
+ <ul>
+ <li>newView public method</li>
+ <li>Window (current view) specific get/set public methods</li>
+ <li>Feature display control methods</li>
+ <li>get list of currently selected sequences</li>
+ </ul> <em>New Jalview distribution features</em>
+ <ul>
+ <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <li>RELEASE file gives build properties for the latest
+ Jalview release.</li>
+ <li>Java 1.1 Applet build made easier and donotobfuscate
+ property controls execution of obfuscator</li>
+ <li>Build target for generating source distribution</li>
+ <li>Debug flag for javacc</li>
+ <li>.jalview_properties file is documented (slightly) in
+ jalview.bin.Cache</li>
+ <li>Continuous Build Integration for stable and
+ development version of Application, Applet and source
+ distribution</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>selected region output includes visible annotations
+ (for certain formats)</li>
+ <li>edit label/displaychar contains existing label/char
+ for editing</li>
+ <li>update PDBEntries when DBRefEntries change (vamsas)</li>
+ <li>shorter peptide product names from EMBL records</li>
+ <li>Newick string generator makes compact representations</li>
+ <li>bootstrap values parsed correctly for tree files with
+ comments</li>
+ <li>pathological filechooser bug avoided by not allowing
+ filenames containing a ':'</li>
+ <li>Fixed exception when parsing GFF files containing
+ global sequence features</li>
+ <li>Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero</li>
+ <li>Close of tree branch colour box without colour
+ selection causes cascading exceptions</li>
+ <li>occasional negative imgwidth exceptions</li>
+ <li>better reporting of non-fatal warnings to user when
+ file parsing fails.</li>
+ <li>Save works when Jalview project is default format</li>
+ <li>Save as dialog opened if current alignment format is
+ not a valid output format</li>
+ <li>Uniprot canonical names introduced for both das and
+ vamsas</li>
+ <li>Histidine should be midblue (not pink!) in Zappo</li>
+ <li>error messages passed up and output when data read
+ fails</li>
+ <li>edit undo recovers previous dataset sequence when
+ sequence is edited</li>
+ <li>allow PDB files without pdb ID HEADER lines (like
+ those generated by MODELLER) to be read in properly</li>
+ <li>allow reading of JPred concise files as a normal
+ filetype</li>
+ <li>Stockholm annotation parsing and alignment properties
+ import fixed for PFAM records</li>
+ <li>Structure view windows have correct name in Desktop
+ window list</li>
+ <li>annotation consisting of sequence associated scores
+ can be read and written correctly to annotation file</li>
+ <li>Aligned cDNA translation to aligned peptide works
+ correctly</li>
+ <li>Fixed display of hidden sequence markers and
+ non-italic font for representatives in Applet</li>
+ <li>Applet Menus are always embedded in applet window on
+ Macs.</li>
+ <li>Newly shown features appear at top of stack (in
+ Applet)</li>
+ <li>Annotations added via parameter not drawn properly
+ due to null pointer exceptions</li>
+ <li>Secondary structure lines are drawn starting from
+ first column of alignment</li>
+ <li>Uniprot XML import updated for new schema release in
+ July 2008</li>
+ <li>Sequence feature to sequence ID match for Features
+ file is case-insensitive</li>
+ <li>Sequence features read from Features file appended to
+ all sequences with matching IDs</li>
+ <li>PDB structure coloured correctly for associated views
+ containing a sub-sequence</li>
+ <li>PDB files can be retrieved by applet from Jar files</li>
+ <li>feature and annotation file applet parameters
+ referring to different directories are retrieved correctly</li>
+ <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
+ <li>Fixed application hang whilst waiting for
+ splash-screen version check to complete</li>
+ <li>Applet properly URLencodes input parameter values
+ when passing them to the launchApp service</li>
+ <li>display name and local features preserved in results
+ retrieved from web service</li>
+ <li>Visual delay indication for sequence retrieval and
+ sequence fetcher initialisation</li>
+ <li>updated Application to use DAS 1.53e version of
+ dasobert DAS client</li>
+ <li>Re-instated Full AMSA support and .amsa file
+ association</li>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ sequences
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.3</strong><br> 9/5/07
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Jmol 11.0.2 integration</li>
+ <li>PDB views stored in Jalview XML files</li>
+ <li>Slide sequences</li>
+ <li>Edit sequence in place</li>
+ <li>EMBL CDS features</li>
+ <li>DAS Feature mapping</li>
+ <li>Feature ordering</li>
+ <li>Alignment Properties</li>
+ <li>Annotation Scores</li>
+ <li>Sort by scores</li>
+ <li>Feature/annotation editing in applet</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Headless state operation in 2.2.1</li>
+ <li>Incorrect and unstable DNA pairwise alignment</li>
+ <li>Cut and paste of sequences with annotation</li>
+ <li>Feature group display state in XML</li>
+ <li>Feature ordering in XML</li>
+ <li>blc file iteration selection using filename # suffix</li>
+ <li>Stockholm alignment properties</li>
+ <li>Stockhom alignment secondary structure annotation</li>
+ <li>2.2.1 applet had no feature transparency</li>
+ <li>Number pad keys can be used in cursor mode</li>
+ <li>Structure Viewer mirror image resolved</li>
+ </ul>
+ </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.2.1</strong><br>
- 12/2/07</div>
- </td>
- <td>
- <ul>
- <li>Non standard characters can be read and displayed
- <li>Annotations/Features can be imported/exported to the applet
- via textbox
- <li>Applet allows editing of sequence/annotation/group name
- & description
- <li>Preference setting to display sequence name in italics
- <li>Annotation file format extended to allow Sequence_groups to
- be defined
- <li>Default opening of alignment overview panel can be specified
- in preferences
- <li>PDB residue numbering annotation added to associated
- sequences
- </ul>
- </td>
- <td>
- <ul>
- <li>Applet crash under certain Linux OS with Java 1.6 installed
- <li>Annotation file export / import bugs fixed
- <li>PNG / EPS image output bugs fixed
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.2</strong><br>
- 27/11/06</div>
- </td>
- <td>
- <ul>
- <li>Multiple views on alignment
- <li>Sequence feature editing
- <li>"Reload" alignment
- <li>"Save" to current filename
- <li>Background dependent text colour
- <li>Right align sequence ids
- <li>User-defined lower case residue colours
- <li>Format Menu
- <li>Select Menu
- <li>Menu item accelerator keys
- <li>Control-V pastes to current alignment
- <li>Cancel button for DAS Feature Fetching
- <li>PCA and PDB Viewers zoom via mouse roller
- <li>User-defined sub-tree colours and sub-tree selection
- <li>'New Window' button on the 'Output to Text box'
- </ul>
- </td>
- <td>
- <ul>
- <li>New memory efficient Undo/Redo System
- <li>Optimised symbol lookups and conservation/consensus
- calculations
- <li>Region Conservation/Consensus recalculated after edits
- <li>Fixed Remove Empty Columns Bug (empty columns at end of
- alignment)
- <li>Slowed DAS Feature Fetching for increased robustness.
- <li>Made angle brackets in ASCII feature descriptions display
- correctly
- <li>Re-instated Zoom function for PCA
- <li>Sequence descriptions conserved in web service analysis
- results
- <li>Uniprot ID discoverer uses any word separated by ∣
- <li>WsDbFetch query/result association resolved
- <li>Tree leaf to sequence mapping improved
- <li>Smooth fonts switch moved to FontChooser dialog box.
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.1.1</strong><br>
- 12/9/06</div>
- </td>
- <td>
- <ul>
- <li>Copy consensus sequence to clipboard</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Image output - rightmost residues are rendered if sequence
- id panel has been resized</li>
- <li>Image output - all offscreen group boundaries are rendered</li>
- <li>Annotation files with sequence references - all elements in
- file are relative to sequence position</li>
- <li>Mac Applet users can use Alt key for group editing</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.1</strong><br>
- 22/8/06</div>
- </td>
- <td>
- <ul>
- <li>MAFFT Multiple Alignment in default Web Service list</li>
- <li>DAS Feature fetching</li>
- <li>Hide sequences and columns</li>
- <li>Export Annotations and Features</li>
- <li>GFF file reading / writing</li>
- <li>Associate structures with sequences from local PDB files</li>
- <li>Add sequences to exisiting alignment</li>
- <li>Recently opened files / URL lists</li>
- <li>Applet can launch the full application</li>
- <li>Applet has transparency for features (Java 1.2 required)</li>
- <li>Applet has user defined colours parameter</li>
- <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Redundancy Panel reinstalled in the Applet</li>
- <li>Monospaced font - EPS / rescaling bug fixed</li>
- <li>Annotation files with sequence references bug fixed</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08.1</strong><br>
- 2/5/06</div>
- </td>
- <td>
- <ul>
- <li>Change case of selected region from Popup menu</li>
- <li>Choose to match case when searching</li>
- <li>Middle mouse button and mouse movement can compress / expand
- the visible width and height of the alignment</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Annotation Panel displays complete JNet results</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08b</strong><br>
- 18/4/06</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
- <li>Righthand label on wrapped alignments shows correct value</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08</strong><br>
- 10/4/06</div>
- </td>
- <td>
- <ul>
- <li>Editing can be locked to the selection area</li>
- <li>Keyboard editing</li>
- <li>Create sequence features from searches</li>
- <li>Precalculated annotations can be loaded onto alignments</li>
- <li>Features file allows grouping of features</li>
- <li>Annotation Colouring scheme added</li>
- <li>Smooth fonts off by default - Faster rendering</li>
- <li>Choose to toggle Autocalculate Consensus On/Off</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Drag & Drop fixed on Linux</li>
- <li>Jalview Archive file faster to load/save, sequence
- descriptions saved.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.07</strong><br>
- 12/12/05</div>
- </td>
- <td>
- <ul>
- <li>PDB Structure Viewer enhanced</li>
- <li>Sequence Feature retrieval and display enhanced</li>
- <li>Choose to output sequence start-end after sequence name for
- file output</li>
- <li>Sequence Fetcher WSDBFetch@EBI</li>
- <li>Applet can read feature files, PDB files and can be used for
- HTML form input</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>HTML output writes groups and features</li>
- <li>Group editing is Control and mouse click</li>
- <li>File IO bugs</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.06</strong><br>
- 28/9/05</div>
- </td>
- <td>
- <ul>
- <li>View annotations in wrapped mode</li>
- <li>More options for PCA viewer</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>GUI bugs resolved</li>
- <li>Runs with -nodisplay from command line</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td height="63">
- <div align="center"><strong>2.05b</strong><br>
- 15/9/05</div>
- </td>
- <td>
- <ul>
- <li>Choose EPS export as lineart or text</li>
- <li>Jar files are executable</li>
- <li>Can read in Uracil - maps to unknown residue</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Known OutOfMemory errors give warning message</li>
- <li>Overview window calculated more efficiently</li>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.05</strong><br>
- 30/8/05</div>
- </td>
- <td>
- <ul>
- <li>Edit and annotate in "Wrapped" view</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.04</strong><br>
- 24/8/05</div>
- </td>
- <td>
- <ul>
- <li>Hold down mouse wheel & scroll to change font size</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Improved JPred client reliability</li>
- <li>Improved loading of Jalview files</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.03</strong><br>
- 18/8/05</div>
- </td>
- <td>
- <ul>
- <li>Set Proxy server name and port in preferences</li>
- <li>Multiple URL links from sequence ids</li>
- <li>User Defined Colours can have a scheme name and added to
- Colour Menu</li>
- <li>Choose to ignore gaps in consensus calculation</li>
- <li>Unix users can set default web browser</li>
- <li>Runs without GUI for batch processing</li>
- <li>Dynamically generated Web Service Menus</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>InstallAnywhere download for Sparc Solaris</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.02</strong><br>
- 18/7/05</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Copy & Paste order of sequences maintains alignment
- order.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.01</strong><br>
- 12/7/05</div>
- </td>
- <td>
- <ul>
- <li>Use delete key for deleting selection.</li>
- <li>Use Mouse wheel to scroll sequences.</li>
- <li>Help file updated to describe how to add alignment
- annotations.</li>
- <li>Version and build date written to build properties file.</li>
- <li>InstallAnywhere installation will check for updates at
- launch of Jalview.</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Delete gaps bug fixed.</li>
- <li>FileChooser sorts columns.</li>
- <li>Can remove groups one by one.</li>
- <li>Filechooser icons installed.</li>
- <li>Finder ignores return character when searching. Return key
- will initiate a search.<br>
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.0</strong><br>
- 20/6/05</div>
- </td>
- <td>
- <ul>
- <li>New codebase</li>
- </ul>
- </td>
- <td> </td>
- </tr>
-</table>
-<p> </p>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.2.1</strong><br> 12/2/07
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Non standard characters can be read and displayed
+ <li>Annotations/Features can be imported/exported to the
+ applet via textbox
+ <li>Applet allows editing of sequence/annotation/group
+ name & description
+ <li>Preference setting to display sequence name in
+ italics
+ <li>Annotation file format extended to allow
+ Sequence_groups to be defined
+ <li>Default opening of alignment overview panel can be
+ specified in preferences
+ <li>PDB residue numbering annotation added to associated
+ sequences
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Applet crash under certain Linux OS with Java 1.6
+ installed
+ <li>Annotation file export / import bugs fixed
+ <li>PNG / EPS image output bugs fixed
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.2</strong><br> 27/11/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Multiple views on alignment
+ <li>Sequence feature editing
+ <li>"Reload" alignment
+ <li>"Save" to current filename
+ <li>Background dependent text colour
+ <li>Right align sequence ids
+ <li>User-defined lower case residue colours
+ <li>Format Menu
+ <li>Select Menu
+ <li>Menu item accelerator keys
+ <li>Control-V pastes to current alignment
+ <li>Cancel button for DAS Feature Fetching
+ <li>PCA and PDB Viewers zoom via mouse roller
+ <li>User-defined sub-tree colours and sub-tree selection
+
+ <li>'New Window' button on the 'Output to Text box'
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>New memory efficient Undo/Redo System
+ <li>Optimised symbol lookups and conservation/consensus
+ calculations
+ <li>Region Conservation/Consensus recalculated after
+ edits
+ <li>Fixed Remove Empty Columns Bug (empty columns at end
+ of alignment)
+ <li>Slowed DAS Feature Fetching for increased robustness.
+
+ <li>Made angle brackets in ASCII feature descriptions
+ display correctly
+ <li>Re-instated Zoom function for PCA
+ <li>Sequence descriptions conserved in web service
+ analysis results
+ <li>Uniprot ID discoverer uses any word separated by
+ ∣
+ <li>WsDbFetch query/result association resolved
+ <li>Tree leaf to sequence mapping improved
+ <li>Smooth fonts switch moved to FontChooser dialog box.
+
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.1.1</strong><br> 12/9/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Copy consensus sequence to clipboard</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Image output - rightmost residues are rendered if
+ sequence id panel has been resized</li>
+ <li>Image output - all offscreen group boundaries are
+ rendered</li>
+ <li>Annotation files with sequence references - all
+ elements in file are relative to sequence position</li>
+ <li>Mac Applet users can use Alt key for group editing</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.1</strong><br> 22/8/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>MAFFT Multiple Alignment in default Web Service list</li>
+ <li>DAS Feature fetching</li>
+ <li>Hide sequences and columns</li>
+ <li>Export Annotations and Features</li>
+ <li>GFF file reading / writing</li>
+ <li>Associate structures with sequences from local PDB
+ files</li>
+ <li>Add sequences to exisiting alignment</li>
+ <li>Recently opened files / URL lists</li>
+ <li>Applet can launch the full application</li>
+ <li>Applet has transparency for features (Java 1.2
+ required)</li>
+ <li>Applet has user defined colours parameter</li>
+ <li>Applet can load sequences from parameter
+ "sequence<em>x</em>"
+ </li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Redundancy Panel reinstalled in the Applet</li>
+ <li>Monospaced font - EPS / rescaling bug fixed</li>
+ <li>Annotation files with sequence references bug fixed</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.08.1</strong><br> 2/5/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Change case of selected region from Popup menu</li>
+ <li>Choose to match case when searching</li>
+ <li>Middle mouse button and mouse movement can compress /
+ expand the visible width and height of the alignment</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Annotation Panel displays complete JNet results</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.08b</strong><br> 18/4/06
+ </div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>Righthand label on wrapped alignments shows correct
+ value</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.08</strong><br> 10/4/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Editing can be locked to the selection area</li>
+ <li>Keyboard editing</li>
+ <li>Create sequence features from searches</li>
+ <li>Precalculated annotations can be loaded onto
+ alignments</li>
+ <li>Features file allows grouping of features</li>
+ <li>Annotation Colouring scheme added</li>
+ <li>Smooth fonts off by default - Faster rendering</li>
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Drag & Drop fixed on Linux</li>
+ <li>Jalview Archive file faster to load/save, sequence
+ descriptions saved.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.07</strong><br> 12/12/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>PDB Structure Viewer enhanced</li>
+ <li>Sequence Feature retrieval and display enhanced</li>
+ <li>Choose to output sequence start-end after sequence
+ name for file output</li>
+ <li>Sequence Fetcher WSDBFetch@EBI</li>
+ <li>Applet can read feature files, PDB files and can be
+ used for HTML form input</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>HTML output writes groups and features</li>
+ <li>Group editing is Control and mouse click</li>
+ <li>File IO bugs</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.06</strong><br> 28/9/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>View annotations in wrapped mode</li>
+ <li>More options for PCA viewer</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>GUI bugs resolved</li>
+ <li>Runs with -nodisplay from command line</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td height="63">
+ <div align="center">
+ <strong>2.05b</strong><br> 15/9/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Choose EPS export as lineart or text</li>
+ <li>Jar files are executable</li>
+ <li>Can read in Uracil - maps to unknown residue</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Known OutOfMemory errors give warning message</li>
+ <li>Overview window calculated more efficiently</li>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.05</strong><br> 30/8/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Edit and annotate in "Wrapped" view</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.04</strong><br> 24/8/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Hold down mouse wheel & scroll to change font
+ size</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Improved JPred client reliability</li>
+ <li>Improved loading of Jalview files</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.03</strong><br> 18/8/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Set Proxy server name and port in preferences</li>
+ <li>Multiple URL links from sequence ids</li>
+ <li>User Defined Colours can have a scheme name and added
+ to Colour Menu</li>
+ <li>Choose to ignore gaps in consensus calculation</li>
+ <li>Unix users can set default web browser</li>
+ <li>Runs without GUI for batch processing</li>
+ <li>Dynamically generated Web Service Menus</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>InstallAnywhere download for Sparc Solaris</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.02</strong><br> 18/7/05
+ </div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Copy & Paste order of sequences maintains
+ alignment order.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.01</strong><br> 12/7/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Use delete key for deleting selection.</li>
+ <li>Use Mouse wheel to scroll sequences.</li>
+ <li>Help file updated to describe how to add alignment
+ annotations.</li>
+ <li>Version and build date written to build properties
+ file.</li>
+ <li>InstallAnywhere installation will check for updates
+ at launch of Jalview.</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Delete gaps bug fixed.</li>
+ <li>FileChooser sorts columns.</li>
+ <li>Can remove groups one by one.</li>
+ <li>Filechooser icons installed.</li>
+ <li>Finder ignores return character when searching.
+ Return key will initiate a search.<br>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.0</strong><br> 20/6/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>New codebase</li>
+ </ul>
+ </td>
+ <td> </td>
+ </tr>
+ </table>
+ <p> </p>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff