<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
<head>
<title>Release History</title>
</head>
<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br/><em>20/5/2014</em></strong>
+ </div>
+ </td>
+ <td> <!-- New features -->
+ <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <ul>
+ </ul> <em>Other improvements</em>
+ <ul>
+ </ul>
+ </td>
+ <td><!-- issues resolved -->
+ <ul>
+ </ul>
+ </td>
+ </tr>
<tr>
+ <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
+ Jalview Desktop application<br />Certificate was donated by
+ <a href="https://www.certum.eu">Certum</a> to the Jalview
+ open source project).
+ </li>
+ <li>Jalview SRS links replaced by Uniprot and EBI-search
+ </li>
+ <li>Output in Stockholm format</li>
+ <li>Allow import of data from gzipped files</li>
+ <li>Export/import group and sequence associated line
+ graph thresholds</li>
+ <li>Nucleotide substitution matrix that supports RNA and
+ ambiguity codes</li>
+ <li>Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred
+ works</li>
+ <li>Groovy scripting for headless jalview operation</li>
+ </ul> <em>Other improvements</em>
+ <ul>
+ <li>Upgrade desktop installer to InstallAnywhere 2013</li>
+ <li>COMBINE statement uses current SEQUENCE_REF and
+ GROUP_REF scope to group annotation rows</li>
+ <li>Support '' style escaping of quotes in Newick
+ files</li>
+ <li>Group options for JABAWS service by command line name</li>
+ <li>Empty tooltip shown for JABA service options with a
+ link but no description</li>
+ <li>Select primary source when selecting authority in
+ database fetcher GUI</li>
+ <li>Add .mfa to FASTA file extensions recognised by
+ Jalview</li>
+ <li>Annotation label tooltip text wrap</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Slow scrolling when lots of annotation rows are
+ displayed</li>
+ <li>Lots of NPE (and slowness) after creating RNA
+ secondary structure annotation line</li>
+ <li>Sequence database accessions not imported when
+ fetching alignments from Rfam</li>
+ <li>Incorrect SHMR submission for sequences with
+ identical IDs</li>
+ <li>View all structures does not always superpose
+ structures</li>
+ <li>Option widgets in service parameters not updated to
+ reflect user or preset settings</li>
+ <li>Null pointer exceptions for some services without
+ presets or adjustable parameters</li>
+ <li>Discover PDB IDs entry in structure menu doesn't
+ discover PDB xRefs</li>
+ <li>Exception encountered while trying to retrieve
+ features with DAS</li>
+ <li>Lowest value in annotation row isn't coloured
+ when colour by annotation (per sequence) is coloured</li>
+ <li>Keyboard mode P jumps to start of gapped region when
+ residue follows a gap</li>
+ <li>Jalview appears to hang importing an alignment with
+ Wrap as default or after enabling Wrap</li>
+ <li>'Right click to add annotations' message
+ shown in wrap mode when no annotations present</li>
+ <li>Disorder predictions fail with NPE if no automatic
+ annotation already exists on alignment</li>
+ <li>oninit javascript function should be called after
+ initialisation completes</li>
+ <li>Remove redundancy after disorder prediction corrupts
+ alignment window display</li>
+ <li>Example annotation file in documentation is invalid</li>
+ <li>Grouped line graph annotation rows are not exported
+ to annotation file</li>
+ <li>Multi-harmony analysis cannot be run when only two
+ groups created</li>
+ <li>Cannot create multiple groups of line graphs with
+ several 'combine' statements in annotation file</li>
+ <li>Pressing return several times causes Number Format
+ exceptions in keyboard mode</li>
+ <li>Multi-harmony (SHMMR) method doesn't submit
+ correct partitions for input data</li>
+ <li>Translation from DNA to Amino Acids fails</li>
+ <li>Jalview fail to load newick tree with quoted label</li>
+ <li>--headless flag isn't understood</li>
+ <li>ClassCastException when generating EPS in headless
+ mode</li>
+ <li>Adjusting sequence-associated shading threshold only
+ changes one row's threshold</li>
+ <li>Preferences and Feature settings panel panel
+ doesn't open</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>
+
+ <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>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>2.4</strong><br>
- Feb/2008</div>
+ <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>New VAMSAS capabilities in Jalview
+ <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>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>
+ <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>
- <li>Retrieval of cross-referenced sequences from other databases
- </li>
- <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>Linked highlighting of codon and amino acid from translation
- and protein products</li>
- <li>JPred3 web service</li>
- <li>Generalised database reference retrieval and validation to
- all fetchable databases</li>
- <li>Fetch sequences from DAS sources supporting the sequence command</li>
- <li>Sequence Fetcher GUI provides example accession numbers and 'clear' button</li>
- <li>Application command line
+ </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
+ 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>-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>
+ <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>
- <li>Trees passed as applet parameters can be passed to
- application (when using "View in full application")</li>
- <li>MemoryMonitor added as an option under Desktop's Tools menu
- </li>
- <li>allow reading of JPred concise files as a normal filetype</li>
- <li>sort sequences by named annotation scores</li>
- <li>Re-instated Full AMSA support and .amsa file association</li>
- <li>Stockholm annotation parsing and alignment properties import
- </li>
- <li>Applet Parameters
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
<ul>
- <li>feature group display control parameter</li>
- <li>debug parameter</li>
+ <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>Applet API methods
+ <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>newView public method</li>
- <li>Window (current view) specific get/set public methods</li>
- <li>Feature display control methods</li>
+ <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>
+
+ <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
<li>Debug flag for javacc</li>
<li>.jalview_properties file is documented (slightly) in
jalview.bin.Cache</li>
- <li>Group colour can be given as an RGB triplet which is used to colour all non-gap characters</li>
- <!-- <li>DAS Sequence Retrieval (in progress)</li> -->
+ <li>Continuous Build Integration for stable and development
+ version of Application, Applet and source distribution</li>
</ul>
+
</td>
<td>
<ul>
<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>
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>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>
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>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>
+ <td>
<div align="center"><strong>2.3</strong><br>
9/5/07</div>
</td>
git://source.jalview.org / jalview.git / blobdiff