</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>
+ </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>CSV output of consensus only includes the percentage of all
+ symbols if sequence logo display is enabled</li>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.</li>
+ <li>inconsistent group submenu and Format submenu entry 'Un' or
+ 'Non'conserved</li>
+ <li>Sequence feature settings are being shared by multiple
+ distinct alignments</li>
+ <li>group annotation not recreated when tree partition is
+ changed</li>
+ <li>double click on group annotation to select sequences does
+ not propagate to associated trees</li>
+ <li>Mac OSX specific issues:
+ <ul>
+ <li>exception raised when mouse clicked on desktop window
+ background</li>
+ <li>Desktop menu placed on menu bar and application name set
+ correctly</li>
+ <li>sequence feature settings not wide enough for the save
+ feature colourscheme button</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
<td>
<div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
<em>30/4/2010</em></div>
</td>
- <td>
- <em>New Capabilities</em>
+ <td><em>New Capabilities</em>
<ul>
<li>URL links generated from description line for
regular-expression based URL links (applet and application)
<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>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>
+ <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
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the command line
+ or via the Add local source dialog box.</li>
+ <li>DAS Dbref and DbxRef feature types are parsed as database
+ references and protein_name is parsed as description line (BioSapiens
+ terms).</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.</li>
+ <!-- <li>New hidden columns and rows and representatives capabilities
in annotations file (in progress - not yet fully implemented)</li> -->
- <li>Group-associated consensus, sequence logos and conservation
- plots</li>
- <li>Symbol distributions for each column can be exported and
- visualized as sequence logos</li>
- <li>Optionally scale multi-character column labels to fit within
- each column of annotation row<!-- todo for applet --></li>
- <li>Optional automatic sort of associated alignment view when a
- new tree is opened.</li>
- <li>Jalview Java Console</li>
- <li>Better placement of desktop window when moving between different screens.</li>
- <li>New preference items for sequence ID tooltip and consensus
- annotation</li>
- <li>Client to submit sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a> Workflows</li>
- <li><em>Vamsas Capabilities</em>
- <ul>
- <li>Improved VAMSAS synchronization (jalview archive used to
- preserve views, structures, and tree display settings)</li>
- <li>Import of vamsas documents from disk or URL via command line</li>
- <li>Sharing of selected regions between views and with other
- VAMSAS applications (Experimental feature!)</li>
- <li>Updated API to VAMSAS version 0.2</li>
- </ul>
- </li>
-</ul>
-<em>Applet</em>
-<ul>
- <li>Middle button resizes annotation row height</li>
- <li>New Parameters
- <ul>
- <li>sortByTree (true/false) - automatically sort the associated
- alignment view by the tree when a new tree is opened.</li>
- <li>showTreeBootstraps (true/false) - show or hide branch
- bootstraps (default is to show them if available)</li>
- <li>showTreeDistances (true/false) - show or hide branch lengths
- (default is to show them if available)</li>
- <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated
- nodes should be highlighted in the tree view</li>
- <li>heightScale and widthScale (1.0 or more) - increase the
- height or width of a cell in the alignment grid relative to the
- current font size.</li>
- </ul>
- </li>
- <li>Non-positional features displayed in sequence ID tooltip</li>
-</ul>
-<em>Other</em>
-<ul>
- <li>Features format: graduated colour definitions and
- specification of feature scores</li>
- <li>Alignment Annotations format: new keywords for group
- associated annotation (GROUP_REF) and annotation row display properties
- (ROW_PROPERTIES)</li>
- <li>XML formats extended to support graduated feature
- colourschemes, group associated annotation, and profile visualization
- settings.</li>
- </td>
- <td>
- <ul>
- <li>Source field in GFF files parsed as feature source rather
- than description</li>
- <li>Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).</li>
- <li>URL links generated for all feature links (bugfix)</li>
- <li>Added URL embedding instructions to features file
- documentation.</li>
- <li>Codons containing ambiguous nucleotides translated as 'X' in
- peptide product</li>
- <li>Match case switch in find dialog box works for both sequence
- ID and sequence string and query strings do not have to be in upper
- case to match case-insensitively.</li>
- <li>AMSA files only contain first column of multi-character
- column annotation labels</li>
- <li>Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)</li>
- <li>PDB files without embedded PDB IDs given a friendly name</li>
- <li>Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.</li>
- <li>Application:
- <ul>
- <li>Better handling of exceptions during sequence retrieval</li>
- <li>Dasobert generated non-positional feature URL link text
- excludes the start_end suffix</li>
- <li>DAS feature and source retrieval buttons disabled when fetch
- or registry operations in progress.</li>
- <li>PDB files retrieved from URLs are cached properly</li>
- <li>Sequence description lines properly shared via VAMSAS</li>
- <li>Sequence fetcher fetches multiple records for all data
- sources</li>
- <li>Ensured that command line das feature retrieval completes
- before alignment figures are generated.</li>
- <li>Reduced time taken when opening file browser for first time.</li>
- <li>isAligned check prior to calculating tree, PCA or submitting
- an MSA to JNet now excludes hidden sequences.</li>
- <li>User defined group colours properly recovered from Jalview projects.</li>
- </ul>
- </li>
- </ul>
- </td>
+ <li>Group-associated consensus, sequence logos and conservation
+ plots</li>
+ <li>Symbol distributions for each column can be exported and
+ visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit within
+ each column of annotation row<!-- todo for applet --></li>
+ <li>Optional automatic sort of associated alignment view when a
+ new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving between
+ different screens.</li>
+ <li>New preference items for sequence ID tooltip and consensus
+ annotation</li>
+ <li>Client to submit sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a> Workflows</li>
+ <li><em>Vamsas Capabilities</em>
+ <ul>
+ <li>Improved VAMSAS synchronization (jalview archive used to
+ preserve views, structures, and tree display settings)</li>
+ <li>Import of vamsas documents from disk or URL via command
+ line</li>
+ <li>Sharing of selected regions between views and with other
+ VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul>
+ </li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the associated
+ alignment view by the tree when a new tree is opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide branch
+ bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide branch
+ lengths (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if
+ unassociated nodes should be highlighted in the tree view</li>
+ <li>heightScale and widthScale (1.0 or more) - increase the
+ height or width of a cell in the alignment grid relative to the
+ current font size.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID tooltip</li>
+ </ul>
+ <em>Other</em>
+ <ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display
+ properties (ROW_PROPERTIES)</li>
+ <li>XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile visualization
+ settings.</li>
+ </td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source rather
+ than description</li>
+ <li>Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product</li>
+ <li>Match case switch in find dialog box works for both sequence
+ ID and sequence string and query strings do not have to be in upper
+ case to match case-insensitively.</li>
+ <li>AMSA files only contain first column of multi-character
+ column annotation labels</li>
+ <li>Jalview Annotation File generation/parsing consistent with
+ documentation (e.g. Stockholm annotation can be exported and
+ re-imported)</li>
+ <li>PDB files without embedded PDB IDs given a friendly name</li>
+ <li>Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.</li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence retrieval</li>
+ <li>Dasobert generated non-positional feature URL link text
+ excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled when
+ fetch or registry operations in progress.</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all data
+ sources</li>
+ <li>Ensured that command line das feature retrieval completes
+ before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for first
+ time.</li>
+ <li>isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered from Jalview
+ projects.</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
</tr>
<tr>
<li>Sequence Group colour can be specified in Annotation File</li>
<li>Ad-hoc colouring of group in Annotation File using RGB
triplet as name of colourscheme</li>
-</ul>
-<em>VAMSAS Client capabilities (Experimental)</em>
-<ul>
- <li>treenode binding for VAMSAS tree exchange</li>
- <li>local editing and update of sequences in VAMSAS alignments
- (experimental)</li>
- <li>Create new or select existing session to join</li>
- <li>load and save of vamsas documents</li>
-</ul>
-<em>Application command line</em>
-<ul>
- <li>-tree parameter to open trees (introduced for passing from
- applet)</li>
- <li>-fetchfrom command line argument to specify nicknames of DAS
- servers to query for alignment features</li>
- <li>-dasserver command line argument to add new servers that are
- also automatically queried for features</li>
- <li>-groovy command line argument executes a given groovy script
- after all input data has been loaded and parsed</li>
-</ul>
-<em>Applet-Application data exchange</em>
-<ul>
- <li>Trees passed as applet parameters can be passed to application
- (when using "View in full application")</li>
-</ul>
-<em>Applet Parameters</em>
-<ul>
- <li>feature group display control parameter</li>
- <li>debug parameter</li>
- <li>showbutton parameter</li>
-</ul>
-<em>Applet API methods</em>
-<ul>
- <li>newView public method</li>
- <li>Window (current view) specific get/set public methods</li>
- <li>Feature display control methods</li>
- <li>get list of currently selected sequences</li>
-</ul>
-<em>New Jalview distribution features</em>
-<ul>
- <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
- <li>RELEASE file gives build properties for the latest Jalview
- release.</li>
- <li>Java 1.1 Applet build made easier and donotobfuscate property
- controls execution of obfuscator</li>
- <li>Build target for generating source distribution</li>
- <li>Debug flag for javacc</li>
- <li>.jalview_properties file is documented (slightly) in
- jalview.bin.Cache</li>
- <li>Continuous Build Integration for stable and development
- version of Application, Applet and source distribution</li>
-</ul>
+ </ul>
+ <em>VAMSAS Client capabilities (Experimental)</em>
+ <ul>
+ <li>treenode binding for VAMSAS tree exchange</li>
+ <li>local editing and update of sequences in VAMSAS alignments
+ (experimental)</li>
+ <li>Create new or select existing session to join</li>
+ <li>load and save of vamsas documents</li>
+ </ul>
+ <em>Application command line</em>
+ <ul>
+ <li>-tree parameter to open trees (introduced for passing from
+ applet)</li>
+ <li>-fetchfrom command line argument to specify nicknames of DAS
+ servers to query for alignment features</li>
+ <li>-dasserver command line argument to add new servers that are
+ also automatically queried for features</li>
+ <li>-groovy command line argument executes a given groovy script
+ after all input data has been loaded and parsed</li>
+ </ul>
+ <em>Applet-Application data exchange</em>
+ <ul>
+ <li>Trees passed as applet parameters can be passed to
+ application (when using "View in full application")</li>
+ </ul>
+ <em>Applet Parameters</em>
+ <ul>
+ <li>feature group display control parameter</li>
+ <li>debug parameter</li>
+ <li>showbutton parameter</li>
+ </ul>
+ <em>Applet API methods</em>
+ <ul>
+ <li>newView public method</li>
+ <li>Window (current view) specific get/set public methods</li>
+ <li>Feature display control methods</li>
+ <li>get list of currently selected sequences</li>
+ </ul>
+ <em>New Jalview distribution features</em>
+ <ul>
+ <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <li>RELEASE file gives build properties for the latest Jalview
+ release.</li>
+ <li>Java 1.1 Applet build made easier and donotobfuscate
+ property controls execution of obfuscator</li>
+ <li>Build target for generating source distribution</li>
+ <li>Debug flag for javacc</li>
+ <li>.jalview_properties file is documented (slightly) in
+ jalview.bin.Cache</li>
+ <li>Continuous Build Integration for stable and development
+ version of Application, Applet and source distribution</li>
+ </ul>
-</td>
-<td>
-<ul>
- <li>selected region output includes visible annotations (for
- certain formats)</li>
- <li>edit label/displaychar contains existing label/char for
- editing</li>
- <li>update PDBEntries when DBRefEntries change (vamsas)</li>
- <li>shorter peptide product names from EMBL records</li>
- <li>Newick string generator makes compact representations</li>
- <li>bootstrap values parsed correctly for tree files with comments</li>
- <li>pathological filechooser bug avoided by not allowing filenames
- containing a ':'</li>
- <li>Fixed exception when parsing GFF files containing global
- sequence features</li>
- <li>Alignment datasets are finalized only when number of
- references from alignment sequences goes to zero</li>
- <li>Close of tree branch colour box without colour selection
- causes cascading exceptions</li>
- <li>occasional negative imgwidth exceptions</li>
- <li>better reporting of non-fatal warnings to user when file
- parsing fails.</li>
- <li>Save works when Jalview project is default format</li>
- <li>Save as dialog opened if current alignment format is not a
- valid output format</li>
- <li>Uniprot canonical names introduced for both das and vamsas</li>
- <li>Histidine should be midblue (not pink!) in Zappo</li>
- <li>error messages passed up and output when data read fails</li>
- <li>edit undo recovers previous dataset sequence when sequence is
- edited</li>
- <li>allow PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) to be read in properly</li>
- <li>allow reading of JPred concise files as a normal filetype</li>
- <li>Stockholm annotation parsing and alignment properties import
- fixed for PFAM records</li>
- <li>Structure view windows have correct name in Desktop window
- list</li>
- <li>annotation consisting of sequence associated scores can be
- read and written correctly to annotation file</li>
- <li>Aligned cDNA translation to aligned peptide works correctly</li>
- <li>Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet</li>
- <li>Applet Menus are always embedded in applet window on Macs.</li>
- <li>Newly shown features appear at top of stack (in Applet)</li>
- <li>Annotations added via parameter not drawn properly due to null
- pointer exceptions</li>
- <li>Secondary structure lines are drawn starting from first column
- of alignment</li>
- <li>Uniprot XML import updated for new schema release in July 2008</li>
- <li>Sequence feature to sequence ID match for Features file is
- case-insensitive</li>
- <li>Sequence features read from Features file appended to all
- sequences with matching IDs</li>
- <li>PDB structure coloured correctly for associated views
- containing a sub-sequence</li>
- <li>PDB files can be retrieved by applet from Jar files</li>
- <li>feature and annotation file applet parameters referring to
- different directories are retrieved correctly</li>
- <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
- <li>Fixed application hang whilst waiting for splash-screen
- version check to complete</li>
- <li>Applet properly URLencodes input parameter values when passing
- them to the launchApp service</li>
- <li>display name and local features preserved in results retrieved
- from web service</li>
- <li>Visual delay indication for sequence retrieval and sequence
- fetcher initialisation</li>
- <li>updated Application to use DAS 1.53e version of dasobert DAS
- client</li>
- <li>Re-instated Full AMSA support and .amsa file association</li>
- <li>Fixed parsing of JNet Concise annotation <em>sans</em>
- sequences</li>
-</ul>
-</td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.3</strong><br>
- 9/5/07</div>
- </td>
- <td>
- <ul>
- <li>Jmol 11.0.2 integration</li>
- <li>PDB views stored in Jalview XML files</li>
- <li>Slide sequences</li>
- <li>Edit sequence in place</li>
- <li>EMBL CDS features</li>
- <li>DAS Feature mapping</li>
- <li>Feature ordering</li>
- <li>Alignment Properties</li>
- <li>Annotation Scores</li>
- <li>Sort by scores</li>
- <li>Feature/annotation editing in applet</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Headless state operation in 2.2.1</li>
- <li>Incorrect and unstable DNA pairwise alignment</li>
- <li>Cut and paste of sequences with annotation</li>
- <li>Feature group display state in XML</li>
- <li>Feature ordering in XML</li>
- <li>blc file iteration selection using filename # suffix</li>
- <li>Stockholm alignment properties</li>
- <li>Stockhom alignment secondary structure annotation</li>
- <li>2.2.1 applet had no feature transparency</li>
- <li>Number pad keys can be used in cursor mode</li>
- <li>Structure Viewer mirror image resolved</li>
- </ul>
- </td>
+ </td>
+ <td>
+ <ul>
+ <li>selected region output includes visible annotations (for
+ certain formats)</li>
+ <li>edit label/displaychar contains existing label/char for
+ editing</li>
+ <li>update PDBEntries when DBRefEntries change (vamsas)</li>
+ <li>shorter peptide product names from EMBL records</li>
+ <li>Newick string generator makes compact representations</li>
+ <li>bootstrap values parsed correctly for tree files with
+ comments</li>
+ <li>pathological filechooser bug avoided by not allowing
+ filenames containing a ':'</li>
+ <li>Fixed exception when parsing GFF files containing global
+ sequence features</li>
+ <li>Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero</li>
+ <li>Close of tree branch colour box without colour selection
+ causes cascading exceptions</li>
+ <li>occasional negative imgwidth exceptions</li>
+ <li>better reporting of non-fatal warnings to user when file
+ parsing fails.</li>
+ <li>Save works when Jalview project is default format</li>
+ <li>Save as dialog opened if current alignment format is not a
+ valid output format</li>
+ <li>Uniprot canonical names introduced for both das and vamsas</li>
+ <li>Histidine should be midblue (not pink!) in Zappo</li>
+ <li>error messages passed up and output when data read fails</li>
+ <li>edit undo recovers previous dataset sequence when sequence
+ is edited</li>
+ <li>allow PDB files without pdb ID HEADER lines (like those
+ generated by MODELLER) to be read in properly</li>
+ <li>allow reading of JPred concise files as a normal filetype</li>
+ <li>Stockholm annotation parsing and alignment properties import
+ fixed for PFAM records</li>
+ <li>Structure view windows have correct name in Desktop window
+ list</li>
+ <li>annotation consisting of sequence associated scores can be
+ read and written correctly to annotation file</li>
+ <li>Aligned cDNA translation to aligned peptide works correctly</li>
+ <li>Fixed display of hidden sequence markers and non-italic font
+ for representatives in Applet</li>
+ <li>Applet Menus are always embedded in applet window on Macs.</li>
+ <li>Newly shown features appear at top of stack (in Applet)</li>
+ <li>Annotations added via parameter not drawn properly due to
+ null pointer exceptions</li>
+ <li>Secondary structure lines are drawn starting from first
+ column of alignment</li>
+ <li>Uniprot XML import updated for new schema release in July
+ 2008</li>
+ <li>Sequence feature to sequence ID match for Features file is
+ case-insensitive</li>
+ <li>Sequence features read from Features file appended to all
+ sequences with matching IDs</li>
+ <li>PDB structure coloured correctly for associated views
+ containing a sub-sequence</li>
+ <li>PDB files can be retrieved by applet from Jar files</li>
+ <li>feature and annotation file applet parameters referring to
+ different directories are retrieved correctly</li>
+ <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
+ <li>Fixed application hang whilst waiting for splash-screen
+ version check to complete</li>
+ <li>Applet properly URLencodes input parameter values when
+ passing them to the launchApp service</li>
+ <li>display name and local features preserved in results
+ retrieved from web service</li>
+ <li>Visual delay indication for sequence retrieval and sequence
+ fetcher initialisation</li>
+ <li>updated Application to use DAS 1.53e version of dasobert DAS
+ client</li>
+ <li>Re-instated Full AMSA support and .amsa file association</li>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ sequences</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.3</strong><br>
+ 9/5/07</div>
+ </td>
+ <td>
+ <ul>
+ <li>Jmol 11.0.2 integration</li>
+ <li>PDB views stored in Jalview XML files</li>
+ <li>Slide sequences</li>
+ <li>Edit sequence in place</li>
+ <li>EMBL CDS features</li>
+ <li>DAS Feature mapping</li>
+ <li>Feature ordering</li>
+ <li>Alignment Properties</li>
+ <li>Annotation Scores</li>
+ <li>Sort by scores</li>
+ <li>Feature/annotation editing in applet</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Headless state operation in 2.2.1</li>
+ <li>Incorrect and unstable DNA pairwise alignment</li>
+ <li>Cut and paste of sequences with annotation</li>
+ <li>Feature group display state in XML</li>
+ <li>Feature ordering in XML</li>
+ <li>blc file iteration selection using filename # suffix</li>
+ <li>Stockholm alignment properties</li>
+ <li>Stockhom alignment secondary structure annotation</li>
+ <li>2.2.1 applet had no feature transparency</li>
+ <li>Number pad keys can be used in cursor mode</li>
+ <li>Structure Viewer mirror image resolved</li>
+ </ul>
+ </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.2.1</strong><br>
- 12/2/07</div>
- </td>
- <td>
- <ul>
- <li>Non standard characters can be read and displayed
- <li>Annotations/Features can be imported/exported to the applet
- via textbox
- <li>Applet allows editing of sequence/annotation/group name &
- description
- <li>Preference setting to display sequence name in italics
- <li>Annotation file format extended to allow Sequence_groups to
- be defined
- <li>Default opening of alignment overview panel can be specified
- in preferences
- <li>PDB residue numbering annotation added to associated
- sequences
- </ul>
- </td>
- <td>
- <ul>
- <li>Applet crash under certain Linux OS with Java 1.6 installed
- <li>Annotation file export / import bugs fixed
- <li>PNG / EPS image output bugs fixed
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.2</strong><br>
- 27/11/06</div>
- </td>
- <td>
- <ul>
- <li>Multiple views on alignment
- <li>Sequence feature editing
- <li>"Reload" alignment
- <li>"Save" to current filename
- <li>Background dependent text colour
- <li>Right align sequence ids
- <li>User-defined lower case residue colours
- <li>Format Menu
- <li>Select Menu
- <li>Menu item accelerator keys
- <li>Control-V pastes to current alignment
- <li>Cancel button for DAS Feature Fetching
- <li>PCA and PDB Viewers zoom via mouse roller
- <li>User-defined sub-tree colours and sub-tree selection
- <li>'New Window' button on the 'Output to Text box'
- </ul>
- </td>
- <td>
- <ul>
- <li>New memory efficient Undo/Redo System
- <li>Optimised symbol lookups and conservation/consensus
- calculations
- <li>Region Conservation/Consensus recalculated after edits
- <li>Fixed Remove Empty Columns Bug (empty columns at end of
- alignment)
- <li>Slowed DAS Feature Fetching for increased robustness.
- <li>Made angle brackets in ASCII feature descriptions display
- correctly
- <li>Re-instated Zoom function for PCA
- <li>Sequence descriptions conserved in web service analysis
- results
- <li>Uniprot ID discoverer uses any word separated by ∣
- <li>WsDbFetch query/result association resolved
- <li>Tree leaf to sequence mapping improved
- <li>Smooth fonts switch moved to FontChooser dialog box.
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.1.1</strong><br>
- 12/9/06</div>
- </td>
- <td>
- <ul>
- <li>Copy consensus sequence to clipboard</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Image output - rightmost residues are rendered if sequence id
- panel has been resized</li>
- <li>Image output - all offscreen group boundaries are rendered</li>
- <li>Annotation files with sequence references - all elements in
- file are relative to sequence position</li>
- <li>Mac Applet users can use Alt key for group editing</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.1</strong><br>
- 22/8/06</div>
- </td>
- <td>
- <ul>
- <li>MAFFT Multiple Alignment in default Web Service list</li>
- <li>DAS Feature fetching</li>
- <li>Hide sequences and columns</li>
- <li>Export Annotations and Features</li>
- <li>GFF file reading / writing</li>
- <li>Associate structures with sequences from local PDB files</li>
- <li>Add sequences to exisiting alignment</li>
- <li>Recently opened files / URL lists</li>
- <li>Applet can launch the full application</li>
- <li>Applet has transparency for features (Java 1.2 required)</li>
- <li>Applet has user defined colours parameter</li>
- <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Redundancy Panel reinstalled in the Applet</li>
- <li>Monospaced font - EPS / rescaling bug fixed</li>
- <li>Annotation files with sequence references bug fixed</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.08.1</strong><br>
- 2/5/06</div>
- </td>
- <td>
- <ul>
- <li>Change case of selected region from Popup menu</li>
- <li>Choose to match case when searching</li>
- <li>Middle mouse button and mouse movement can compress / expand
- the visible width and height of the alignment</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Annotation Panel displays complete JNet results</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.08b</strong><br>
- 18/4/06</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
- <li>Righthand label on wrapped alignments shows correct value</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.08</strong><br>
- 10/4/06</div>
- </td>
- <td>
- <ul>
- <li>Editing can be locked to the selection area</li>
- <li>Keyboard editing</li>
- <li>Create sequence features from searches</li>
- <li>Precalculated annotations can be loaded onto alignments</li>
- <li>Features file allows grouping of features</li>
- <li>Annotation Colouring scheme added</li>
- <li>Smooth fonts off by default - Faster rendering</li>
- <li>Choose to toggle Autocalculate Consensus On/Off</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Drag & Drop fixed on Linux</li>
- <li>Jalview Archive file faster to load/save, sequence
- descriptions saved.</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.07</strong><br>
- 12/12/05</div>
- </td>
- <td>
- <ul>
- <li>PDB Structure Viewer enhanced</li>
- <li>Sequence Feature retrieval and display enhanced</li>
- <li>Choose to output sequence start-end after sequence name for
- file output</li>
- <li>Sequence Fetcher WSDBFetch@EBI</li>
- <li>Applet can read feature files, PDB files and can be used for
- HTML form input</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>HTML output writes groups and features</li>
- <li>Group editing is Control and mouse click</li>
- <li>File IO bugs</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.06</strong><br>
- 28/9/05</div>
- </td>
- <td>
- <ul>
- <li>View annotations in wrapped mode</li>
- <li>More options for PCA viewer</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>GUI bugs resolved</li>
- <li>Runs with -nodisplay from command line</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td height="63">
- <div align="center"><strong>2.05b</strong><br>
- 15/9/05</div>
- </td>
- <td>
- <ul>
- <li>Choose EPS export as lineart or text</li>
- <li>Jar files are executable</li>
- <li>Can read in Uracil - maps to unknown residue</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Known OutOfMemory errors give warning message</li>
- <li>Overview window calculated more efficiently</li>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.05</strong><br>
- 30/8/05</div>
- </td>
- <td>
- <ul>
- <li>Edit and annotate in "Wrapped" view</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.04</strong><br>
- 24/8/05</div>
- </td>
- <td>
- <ul>
- <li>Hold down mouse wheel & scroll to change font size</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Improved JPred client reliability</li>
- <li>Improved loading of Jalview files</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.03</strong><br>
- 18/8/05</div>
- </td>
- <td>
- <ul>
- <li>Set Proxy server name and port in preferences</li>
- <li>Multiple URL links from sequence ids</li>
- <li>User Defined Colours can have a scheme name and added to
- Colour Menu</li>
- <li>Choose to ignore gaps in consensus calculation</li>
- <li>Unix users can set default web browser</li>
- <li>Runs without GUI for batch processing</li>
- <li>Dynamically generated Web Service Menus</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>InstallAnywhere download for Sparc Solaris</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.02</strong><br>
- 18/7/05</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Copy & Paste order of sequences maintains alignment
- order.</li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.01</strong><br>
- 12/7/05</div>
- </td>
- <td>
- <ul>
- <li>Use delete key for deleting selection.</li>
- <li>Use Mouse wheel to scroll sequences.</li>
- <li>Help file updated to describe how to add alignment
- annotations.</li>
- <li>Version and build date written to build properties file.</li>
- <li>InstallAnywhere installation will check for updates at launch
- of Jalview.</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Delete gaps bug fixed.</li>
- <li>FileChooser sorts columns.</li>
- <li>Can remove groups one by one.</li>
- <li>Filechooser icons installed.</li>
- <li>Finder ignores return character when searching. Return key
- will initiate a search.<br>
- </li>
- </ul>
- </td>
-</tr>
-<tr>
- <td>
- <div align="center"><strong>2.0</strong><br>
- 20/6/05</div>
- </td>
- <td>
- <ul>
- <li>New codebase</li>
- </ul>
- </td>
- <td> </td>
-</tr>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.2.1</strong><br>
+ 12/2/07</div>
+ </td>
+ <td>
+ <ul>
+ <li>Non standard characters can be read and displayed
+ <li>Annotations/Features can be imported/exported to the applet
+ via textbox
+ <li>Applet allows editing of sequence/annotation/group name
+ & description
+ <li>Preference setting to display sequence name in italics
+ <li>Annotation file format extended to allow Sequence_groups to
+ be defined
+ <li>Default opening of alignment overview panel can be specified
+ in preferences
+ <li>PDB residue numbering annotation added to associated
+ sequences
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Applet crash under certain Linux OS with Java 1.6 installed
+ <li>Annotation file export / import bugs fixed
+ <li>PNG / EPS image output bugs fixed
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.2</strong><br>
+ 27/11/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Multiple views on alignment
+ <li>Sequence feature editing
+ <li>"Reload" alignment
+ <li>"Save" to current filename
+ <li>Background dependent text colour
+ <li>Right align sequence ids
+ <li>User-defined lower case residue colours
+ <li>Format Menu
+ <li>Select Menu
+ <li>Menu item accelerator keys
+ <li>Control-V pastes to current alignment
+ <li>Cancel button for DAS Feature Fetching
+ <li>PCA and PDB Viewers zoom via mouse roller
+ <li>User-defined sub-tree colours and sub-tree selection
+ <li>'New Window' button on the 'Output to Text box'
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>New memory efficient Undo/Redo System
+ <li>Optimised symbol lookups and conservation/consensus
+ calculations
+ <li>Region Conservation/Consensus recalculated after edits
+ <li>Fixed Remove Empty Columns Bug (empty columns at end of
+ alignment)
+ <li>Slowed DAS Feature Fetching for increased robustness.
+ <li>Made angle brackets in ASCII feature descriptions display
+ correctly
+ <li>Re-instated Zoom function for PCA
+ <li>Sequence descriptions conserved in web service analysis
+ results
+ <li>Uniprot ID discoverer uses any word separated by ∣
+ <li>WsDbFetch query/result association resolved
+ <li>Tree leaf to sequence mapping improved
+ <li>Smooth fonts switch moved to FontChooser dialog box.
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.1.1</strong><br>
+ 12/9/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Copy consensus sequence to clipboard</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Image output - rightmost residues are rendered if sequence
+ id panel has been resized</li>
+ <li>Image output - all offscreen group boundaries are rendered</li>
+ <li>Annotation files with sequence references - all elements in
+ file are relative to sequence position</li>
+ <li>Mac Applet users can use Alt key for group editing</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.1</strong><br>
+ 22/8/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>MAFFT Multiple Alignment in default Web Service list</li>
+ <li>DAS Feature fetching</li>
+ <li>Hide sequences and columns</li>
+ <li>Export Annotations and Features</li>
+ <li>GFF file reading / writing</li>
+ <li>Associate structures with sequences from local PDB files</li>
+ <li>Add sequences to exisiting alignment</li>
+ <li>Recently opened files / URL lists</li>
+ <li>Applet can launch the full application</li>
+ <li>Applet has transparency for features (Java 1.2 required)</li>
+ <li>Applet has user defined colours parameter</li>
+ <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Redundancy Panel reinstalled in the Applet</li>
+ <li>Monospaced font - EPS / rescaling bug fixed</li>
+ <li>Annotation files with sequence references bug fixed</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.08.1</strong><br>
+ 2/5/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Change case of selected region from Popup menu</li>
+ <li>Choose to match case when searching</li>
+ <li>Middle mouse button and mouse movement can compress / expand
+ the visible width and height of the alignment</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Annotation Panel displays complete JNet results</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.08b</strong><br>
+ 18/4/06</div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>Righthand label on wrapped alignments shows correct value</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.08</strong><br>
+ 10/4/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Editing can be locked to the selection area</li>
+ <li>Keyboard editing</li>
+ <li>Create sequence features from searches</li>
+ <li>Precalculated annotations can be loaded onto alignments</li>
+ <li>Features file allows grouping of features</li>
+ <li>Annotation Colouring scheme added</li>
+ <li>Smooth fonts off by default - Faster rendering</li>
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Drag & Drop fixed on Linux</li>
+ <li>Jalview Archive file faster to load/save, sequence
+ descriptions saved.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.07</strong><br>
+ 12/12/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>PDB Structure Viewer enhanced</li>
+ <li>Sequence Feature retrieval and display enhanced</li>
+ <li>Choose to output sequence start-end after sequence name for
+ file output</li>
+ <li>Sequence Fetcher WSDBFetch@EBI</li>
+ <li>Applet can read feature files, PDB files and can be used for
+ HTML form input</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>HTML output writes groups and features</li>
+ <li>Group editing is Control and mouse click</li>
+ <li>File IO bugs</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.06</strong><br>
+ 28/9/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>View annotations in wrapped mode</li>
+ <li>More options for PCA viewer</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>GUI bugs resolved</li>
+ <li>Runs with -nodisplay from command line</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td height="63">
+ <div align="center"><strong>2.05b</strong><br>
+ 15/9/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Choose EPS export as lineart or text</li>
+ <li>Jar files are executable</li>
+ <li>Can read in Uracil - maps to unknown residue</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Known OutOfMemory errors give warning message</li>
+ <li>Overview window calculated more efficiently</li>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.05</strong><br>
+ 30/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Edit and annotate in "Wrapped" view</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.04</strong><br>
+ 24/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Hold down mouse wheel & scroll to change font size</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Improved JPred client reliability</li>
+ <li>Improved loading of Jalview files</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.03</strong><br>
+ 18/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Set Proxy server name and port in preferences</li>
+ <li>Multiple URL links from sequence ids</li>
+ <li>User Defined Colours can have a scheme name and added to
+ Colour Menu</li>
+ <li>Choose to ignore gaps in consensus calculation</li>
+ <li>Unix users can set default web browser</li>
+ <li>Runs without GUI for batch processing</li>
+ <li>Dynamically generated Web Service Menus</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>InstallAnywhere download for Sparc Solaris</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.02</strong><br>
+ 18/7/05</div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Copy & Paste order of sequences maintains alignment
+ order.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.01</strong><br>
+ 12/7/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Use delete key for deleting selection.</li>
+ <li>Use Mouse wheel to scroll sequences.</li>
+ <li>Help file updated to describe how to add alignment
+ annotations.</li>
+ <li>Version and build date written to build properties file.</li>
+ <li>InstallAnywhere installation will check for updates at
+ launch of Jalview.</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Delete gaps bug fixed.</li>
+ <li>FileChooser sorts columns.</li>
+ <li>Can remove groups one by one.</li>
+ <li>Filechooser icons installed.</li>
+ <li>Finder ignores return character when searching. Return key
+ will initiate a search.<br>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.0</strong><br>
+ 20/6/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>New codebase</li>
+ </ul>
+ </td>
+ <td> </td>
+ </tr>
</table>
<p> </p>
</body>
git://source.jalview.org / jalview.git / commitdiff