<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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>
</td>
</tr>
<tr>
- <td>
- <div align="center">
- <strong><a name="Jalview2.7">2.7</a>
- </strong><br> <em>27/09/2011</em>
+ <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><em>Application</em>
+ <td>
+ <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <em>General</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:
+ <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>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>
+ <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>
- </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>
+ <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>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>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>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>
+ <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>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>
+ <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>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>
+ <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
+ 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>
+ <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>
+
+ <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>
<td>
<ul>
<li>Modeller PIR IO broken - cannot correctly import a pir
- file emitted by jalview</li>
+ 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
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
+ <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>
+ operation from the Jalview command line</li>
</ul>
</td>
<td>
href="webServices/index.html#envision2">Envision2</a> Workflows</li>
<li><em>Vamsas Capabilities</em>
<ul>
- <li>Improved VAMSAS synchronization (jalview archive used to
+ <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>
git://source.jalview.org / jalview.git / blobdiff