- </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>