-<html>\r
-<head><title>Release History</title></head>\r
-<body>\r
-<p><strong>Release History</strong> </p>\r
-<table border="1">\r
- <tr> \r
- <td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>\r
- <td ><div align="center"><em><strong>New Features</strong></em></div></td>\r
- <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.2.1</strong><br>\r
- 12/2/07</div></td>\r
- <td><ul>\r
- <li>Non standard characters can be read and displayed\r
- <li>Annotations/Features can be imported/exported to the applet via textbox\r
- <li>Applet allows editing of sequence/annotation/group name & description\r
- <li>Preference setting to display sequence name in italics\r
- <li>Annotation file format extended to allow Sequence_groups\r
- to be defined\r
- <li>Default opening of alignment overview panel can be specified in\r
- preferences\r
- <li>PDB residue numbering annotation added to associated sequences\r
- </ul></td>\r
- <td> <ul>\r
- <li>Applet crash under certain Linux OS with Java 1.6 installed\r
- <li>Annotation file export / import bugs fixed\r
- <li>PNG / EPS image output bugs fixed</ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.2</strong><br>\r
- 27/11/06</div></td>\r
- <td><ul>\r
- <li>Multiple views on alignment \r
- <li>Sequence feature editing \r
- <li>"Reload" alignment \r
- <li>"Save" to current filename \r
- <li>Background dependent text colour \r
- <li>Right align sequence ids \r
- <li>User-defined lower case residue colours \r
- <li>Format Menu \r
- <li>Select Menu \r
- <li>Menu item accelerator keys \r
- <li>Control-V pastes to current alignment \r
- <li>Cancel button for DAS Feature Fetching \r
- <li>PCA and PDB Viewers zoom via mouse roller \r
- <li>User-defined sub-tree colours and sub-tree selection \r
- <li>'New Window' button on the 'Output to Text box' </ul></td>\r
- <td> <ul>\r
- <li>New memory efficient Undo/Redo System \r
- <li>Optimised symbol lookups and conservation/consensus calculations \r
- <li>Region Conservation/Consensus recalculated after edits \r
- <li>Fixed Remove Empty Columns Bug (empty columns at end of alignment) \r
- <li>Slowed DAS Feature Fetching for increased robustness. \r
- <li>Made angle brackets in ASCII feature descriptions display correctly \r
- <li>Re-instated Zoom function for PCA \r
- <li>Sequence descriptions conserved in web service analysis results \r
- <li>Uniprot ID discoverer uses any word separated by ∣ \r
- <li>WsDbFetch query/result association resolved \r
- <li>Tree leaf to sequence mapping improved \r
- <li>Smooth fonts switch moved to FontChooser dialog box. </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.1.1</strong><br>\r
- 12/9/06</div></td>\r
- <td><ul>\r
- <li>Copy consensus sequence to clipboard</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Image output - rightmost residues are rendered if sequence id panel \r
- has been resized</li>\r
- <li>Image output - all offscreen group boundaries are rendered </li>\r
- <li>Annotation files with sequence references - all elements in file are \r
- relative to sequence position</li>\r
- <li>Mac Applet users can use Alt key for group editing</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.1</strong><br>\r
- 22/8/06</div></td>\r
- <td><ul>\r
- <li>MAFFT Multiple Alignment in default Web Service list</li>\r
- <li>DAS Feature fetching</li>\r
- <li>Hide sequences and columns</li>\r
- <li>Export Annotations and Features</li>\r
- <li>GFF file reading / writing</li>\r
- <li>Associate structures with sequences from local PDB files</li>\r
- <li>Add sequences to exisiting alignment</li>\r
- <li>Recently opened files / URL lists</li>\r
- <li>Applet can launch the full application</li>\r
- <li>Applet has transparency for features (Java 1.2 required)</li>\r
- <li>Applet has user defined colours parameter</li>\r
- <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Redundancy Panel reinstalled in the Applet</li>\r
- <li>Monospaced font - EPS / rescaling bug fixed</li>\r
- <li>Annotation files with sequence references bug fixed</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.08.1</strong><br>\r
- 2/5/06</div></td>\r
- <td><ul>\r
- <li>Change case of selected region from Popup menu</li>\r
- <li>Choose to match case when searching</li>\r
- <li>Middle mouse button and mouse movement can compress / expand the visible \r
- width and height of the alignment</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Annotation Panel displays complete JNet results</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.08b</strong><br>\r
- 18/4/06</div></td>\r
- <td> </td>\r
- <td><ul>\r
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>\r
- <li>Righthand label on wrapped alignments shows correct value</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.08</strong><br>\r
- 10/4/06</div></td>\r
- <td><ul>\r
- <li>Editing can be locked to the selection area</li>\r
- <li>Keyboard editing</li>\r
- <li>Create sequence features from searches</li>\r
- <li>Precalculated annotations can be loaded onto alignments</li>\r
- <li>Features file allows grouping of features</li>\r
- <li>Annotation Colouring scheme added</li>\r
- <li>Smooth fonts off by default - Faster rendering</li>\r
- <li>Choose to toggle Autocalculate Consensus On/Off</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Drag & Drop fixed on Linux</li>\r
- <li>Jalview Archive file faster to load/save, sequence descriptions saved. \r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.07</strong><br>\r
- 12/12/05</div></td>\r
- <td><ul>\r
- <li>PDB Structure Viewer enhanced</li>\r
- <li>Sequence Feature retrieval and display enhanced</li>\r
- <li>Choose to output sequence start-end after sequence name for file output</li>\r
- <li>Sequence Fetcher WSDBFetch@EBI</li>\r
- <li>Applet can read feature files, PDB files and can be used for HTML \r
- form input</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>HTML output writes groups and features</li>\r
- <li>Group editing is Control and mouse click</li>\r
- <li>File IO bugs</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.06</strong><br>\r
- 28/9/05</div></td>\r
- <td><ul>\r
- <li>View annotations in wrapped mode</li>\r
- <li>More options for PCA viewer</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>GUI bugs resolved</li>\r
- <li>Runs with -nodisplay from command line</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td height="63"> <div align="center"><strong>2.05b</strong><br>\r
- 15/9/05</div></td>\r
- <td><ul>\r
- <li>Choose EPS export as lineart or text</li>\r
- <li>Jar files are executable</li>\r
- <li>Can read in Uracil - maps to unknown residue</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Known OutOfMemory errors give warning message</li>\r
- <li>Overview window calculated more efficiently</li>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.05</strong><br>\r
- 30/8/05</div></td>\r
- <td><ul>\r
- <li>Edit and annotate in "Wrapped" view</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.04</strong><br>\r
- 24/8/05</div></td>\r
- <td><ul>\r
- <li>Hold down mouse wheel & scroll to change font size</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Improved JPred client reliability</li>\r
- <li>Improved loading of Jalview files</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.03</strong><br>\r
- 18/8/05</div></td>\r
- <td><ul>\r
- <li>Set Proxy server name and port in preferences</li>\r
- <li>Multiple URL links from sequence ids</li>\r
- <li>User Defined Colours can have a scheme name and added to Colour Menu</li>\r
- <li>Choose to ignore gaps in consensus calculation</li>\r
- <li>Unix users can set default web browser</li>\r
- <li>Runs without GUI for batch processing</li>\r
- <li>Dynamically generated Web Service Menus</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>InstallAnywhere download for Sparc Solaris</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.02</strong><br>\r
- 18/7/05</div></td>\r
- <td> </td>\r
- <td><ul>\r
- <li>Copy & Paste order of sequences maintains alignment order.</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.01</strong><br>\r
- 12/7/05</div></td>\r
- <td><ul>\r
- <li>Use delete key for deleting selection.</li>\r
- <li>Use Mouse wheel to scroll sequences.</li>\r
- <li>Help file updated to describe how to add alignment annotations.</li>\r
- <li>Version and build date written to build properties file.</li>\r
- <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Delete gaps bug fixed.</li>\r
- <li>FileChooser sorts columns.</li>\r
- <li>Can remove groups one by one.</li>\r
- <li>Filechooser icons installed.</li>\r
- <li>Finder ignores return character when searching. Return key will initiate \r
- a search.<br>\r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.0</strong><br>\r
- 20/6/05</div></td>\r
- <td ><ul>\r
- <li> New codebase</li>\r
- </ul></td>\r
- <td > </td>\r
- </tr>\r
-</table>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Release History</title></head>
+<body>
+<p><strong>Release History</strong> </p>
+<table border="1">
+ <tr>
+ <td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>
+ <td ><div align="center"><em><strong>New Features</strong></em></div></td>
+ <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.3</strong><br>
+ 2/5/07</div></td>
+ <td><ul>
+ <li>Jmol 11 integration</li>
+ <li>PDB views in Jalview XML</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>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.2.1</strong><br>
+ 12/2/07</div></td>
+ <td><ul>
+ <li>Non standard characters can be read and displayed
+ <li>Annotations/Features can be imported/exported to the applet via textbox
+ <li>Applet allows editing of sequence/annotation/group name & description
+ <li>Preference setting to display sequence name in italics
+ <li>Annotation file format extended to allow Sequence_groups
+ to be defined
+ <li>Default opening of alignment overview panel can be specified in
+ preferences
+ <li>PDB residue numbering annotation added to associated sequences
+ </ul></td>
+ <td> <ul>
+ <li>Applet crash under certain Linux OS with Java 1.6 installed
+ <li>Annotation file export / import bugs fixed
+ <li>PNG / EPS image output bugs fixed</ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.2</strong><br>
+ 27/11/06</div></td>
+ <td><ul>
+ <li>Multiple views on alignment
+ <li>Sequence feature editing
+ <li>"Reload" alignment
+ <li>"Save" to current filename
+ <li>Background dependent text colour
+ <li>Right align sequence ids
+ <li>User-defined lower case residue colours
+ <li>Format Menu
+ <li>Select Menu
+ <li>Menu item accelerator keys
+ <li>Control-V pastes to current alignment
+ <li>Cancel button for DAS Feature Fetching
+ <li>PCA and PDB Viewers zoom via mouse roller
+ <li>User-defined sub-tree colours and sub-tree selection
+ <li>'New Window' button on the 'Output to Text box' </ul></td>
+ <td> <ul>
+ <li>New memory efficient Undo/Redo System
+ <li>Optimised symbol lookups and conservation/consensus calculations
+ <li>Region Conservation/Consensus recalculated after edits
+ <li>Fixed Remove Empty Columns Bug (empty columns at end of alignment)
+ <li>Slowed DAS Feature Fetching for increased robustness.
+ <li>Made angle brackets in ASCII feature descriptions display correctly
+ <li>Re-instated Zoom function for PCA
+ <li>Sequence descriptions conserved in web service analysis results
+ <li>Uniprot ID discoverer uses any word separated by ∣
+ <li>WsDbFetch query/result association resolved
+ <li>Tree leaf to sequence mapping improved
+ <li>Smooth fonts switch moved to FontChooser dialog box. </ul></td>
+ </tr>
+ <tr>
+ <td> <div align="center"><strong>2.1.1</strong><br>
+ 12/9/06</div></td>
+ <td><ul>
+ <li>Copy consensus sequence to clipboard</li>
+ </ul></td>
+ <td><ul>
+ <li>Image output - rightmost residues are rendered if sequence id panel
+ has been resized</li>
+ <li>Image output - all offscreen group boundaries are rendered </li>
+ <li>Annotation files with sequence references - all elements in file are
+ relative to sequence position</li>
+ <li>Mac Applet users can use Alt key for group editing</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.1</strong><br>
+ 22/8/06</div></td>
+ <td><ul>
+ <li>MAFFT Multiple Alignment in default Web Service list</li>
+ <li>DAS Feature fetching</li>
+ <li>Hide sequences and columns</li>
+ <li>Export Annotations and Features</li>
+ <li>GFF file reading / writing</li>
+ <li>Associate structures with sequences from local PDB files</li>
+ <li>Add sequences to exisiting alignment</li>
+ <li>Recently opened files / URL lists</li>
+ <li>Applet can launch the full application</li>
+ <li>Applet has transparency for features (Java 1.2 required)</li>
+ <li>Applet has user defined colours parameter</li>
+ <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
+ </ul></td>
+ <td><ul>
+ <li>Redundancy Panel reinstalled in the Applet</li>
+ <li>Monospaced font - EPS / rescaling bug fixed</li>
+ <li>Annotation files with sequence references bug fixed</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.08.1</strong><br>
+ 2/5/06</div></td>
+ <td><ul>
+ <li>Change case of selected region from Popup menu</li>
+ <li>Choose to match case when searching</li>
+ <li>Middle mouse button and mouse movement can compress / expand the visible
+ width and height of the alignment</li>
+ </ul></td>
+ <td><ul>
+ <li>Annotation Panel displays complete JNet results</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.08b</strong><br>
+ 18/4/06</div></td>
+ <td> </td>
+ <td><ul>
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>Righthand label on wrapped alignments shows correct value</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.08</strong><br>
+ 10/4/06</div></td>
+ <td><ul>
+ <li>Editing can be locked to the selection area</li>
+ <li>Keyboard editing</li>
+ <li>Create sequence features from searches</li>
+ <li>Precalculated annotations can be loaded onto alignments</li>
+ <li>Features file allows grouping of features</li>
+ <li>Annotation Colouring scheme added</li>
+ <li>Smooth fonts off by default - Faster rendering</li>
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ </ul></td>
+ <td><ul>
+ <li>Drag & Drop fixed on Linux</li>
+ <li>Jalview Archive file faster to load/save, sequence descriptions saved.
+ </li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.07</strong><br>
+ 12/12/05</div></td>
+ <td><ul>
+ <li>PDB Structure Viewer enhanced</li>
+ <li>Sequence Feature retrieval and display enhanced</li>
+ <li>Choose to output sequence start-end after sequence name for file output</li>
+ <li>Sequence Fetcher WSDBFetch@EBI</li>
+ <li>Applet can read feature files, PDB files and can be used for HTML
+ form input</li>
+ </ul></td>
+ <td><ul>
+ <li>HTML output writes groups and features</li>
+ <li>Group editing is Control and mouse click</li>
+ <li>File IO bugs</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.06</strong><br>
+ 28/9/05</div></td>
+ <td><ul>
+ <li>View annotations in wrapped mode</li>
+ <li>More options for PCA viewer</li>
+ </ul></td>
+ <td><ul>
+ <li>GUI bugs resolved</li>
+ <li>Runs with -nodisplay from command line</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td height="63"> <div align="center"><strong>2.05b</strong><br>
+ 15/9/05</div></td>
+ <td><ul>
+ <li>Choose EPS export as lineart or text</li>
+ <li>Jar files are executable</li>
+ <li>Can read in Uracil - maps to unknown residue</li>
+ </ul></td>
+ <td><ul>
+ <li>Known OutOfMemory errors give warning message</li>
+ <li>Overview window calculated more efficiently</li>
+ <li>Several GUI bugs resolved</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.05</strong><br>
+ 30/8/05</div></td>
+ <td><ul>
+ <li>Edit and annotate in "Wrapped" view</li>
+ </ul></td>
+ <td><ul>
+ <li>Several GUI bugs resolved</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.04</strong><br>
+ 24/8/05</div></td>
+ <td><ul>
+ <li>Hold down mouse wheel & scroll to change font size</li>
+ </ul></td>
+ <td><ul>
+ <li>Improved JPred client reliability</li>
+ <li>Improved loading of Jalview files</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td> <div align="center"><strong>2.03</strong><br>
+ 18/8/05</div></td>
+ <td><ul>
+ <li>Set Proxy server name and port in preferences</li>
+ <li>Multiple URL links from sequence ids</li>
+ <li>User Defined Colours can have a scheme name and added to Colour Menu</li>
+ <li>Choose to ignore gaps in consensus calculation</li>
+ <li>Unix users can set default web browser</li>
+ <li>Runs without GUI for batch processing</li>
+ <li>Dynamically generated Web Service Menus</li>
+ </ul></td>
+ <td><ul>
+ <li>InstallAnywhere download for Sparc Solaris</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td> <div align="center"><strong>2.02</strong><br>
+ 18/7/05</div></td>
+ <td> </td>
+ <td><ul>
+ <li>Copy & Paste order of sequences maintains alignment order.</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.01</strong><br>
+ 12/7/05</div></td>
+ <td><ul>
+ <li>Use delete key for deleting selection.</li>
+ <li>Use Mouse wheel to scroll sequences.</li>
+ <li>Help file updated to describe how to add alignment annotations.</li>
+ <li>Version and build date written to build properties file.</li>
+ <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>
+ </ul></td>
+ <td><ul>
+ <li>Delete gaps bug fixed.</li>
+ <li>FileChooser sorts columns.</li>
+ <li>Can remove groups one by one.</li>
+ <li>Filechooser icons installed.</li>
+ <li>Finder ignores return character when searching. Return key will initiate
+ a search.<br>
+ </li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td> <div align="center"><strong>2.0</strong><br>
+ 20/6/05</div></td>
+ <td ><ul>
+ <li> New codebase</li>
+ </ul></td>
+ <td > </td>
+ </tr>
+</table>
+<p> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff