2 <head><title>Release History</title></head>
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4 <p><strong>Release History</strong> </p>
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7 <td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>
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8 <td ><div align="center"><em><strong>New Features</strong></em></div></td>
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9 <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>
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12 <td><div align="center"><strong>2.3</strong><br>
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15 <li>Jmol 11.0.2 integration</li>
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16 <li>PDB views stored in Jalview XML files</li>
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17 <li>Slide sequences</li>
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18 <li>Edit sequence in place</li>
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19 <li>EMBL CDS features</li>
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20 <li>DAS Feature mapping</li>
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21 <li>Feature ordering</li>
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22 <li>Alignment Properties</li>
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23 <li>Annotation Scores</li>
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24 <li>Sort by scores</li>
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25 <li>Feature/annotation editing in applet</li>
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28 <li>Headless state operation in 2.2.1</li>
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29 <li>Incorrect and unstable DNA pairwise alignment</li>
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30 <li>Cut and paste of sequences with annotation</li>
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31 <li>Feature group display state in XML</li>
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32 <li>Feature ordering in XML</li>
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33 <li>blc file iteration selection using filename # suffix</li>
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34 <li>Stockholm alignment properties</li>
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35 <li>Stockhom alignment secondary structure annotation</li>
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36 <li>2.2.1 applet had no feature transparency</li>
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37 <li>Number pad keys can be used in cursor mode</li>
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38 <li>Structure Viewer mirror image resolved</li>
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44 <td><div align="center"><strong>2.2.1</strong><br>
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47 <li>Non standard characters can be read and displayed
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48 <li>Annotations/Features can be imported/exported to the applet via textbox
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49 <li>Applet allows editing of sequence/annotation/group name & description
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50 <li>Preference setting to display sequence name in italics
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51 <li>Annotation file format extended to allow Sequence_groups
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53 <li>Default opening of alignment overview panel can be specified in
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55 <li>PDB residue numbering annotation added to associated sequences
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58 <li>Applet crash under certain Linux OS with Java 1.6 installed
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59 <li>Annotation file export / import bugs fixed
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60 <li>PNG / EPS image output bugs fixed</ul></td>
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63 <td><div align="center"><strong>2.2</strong><br>
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66 <li>Multiple views on alignment
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67 <li>Sequence feature editing
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68 <li>"Reload" alignment
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69 <li>"Save" to current filename
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70 <li>Background dependent text colour
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71 <li>Right align sequence ids
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72 <li>User-defined lower case residue colours
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75 <li>Menu item accelerator keys
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76 <li>Control-V pastes to current alignment
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77 <li>Cancel button for DAS Feature Fetching
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78 <li>PCA and PDB Viewers zoom via mouse roller
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79 <li>User-defined sub-tree colours and sub-tree selection
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80 <li>'New Window' button on the 'Output to Text box' </ul></td>
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82 <li>New memory efficient Undo/Redo System
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83 <li>Optimised symbol lookups and conservation/consensus calculations
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84 <li>Region Conservation/Consensus recalculated after edits
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85 <li>Fixed Remove Empty Columns Bug (empty columns at end of alignment)
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86 <li>Slowed DAS Feature Fetching for increased robustness.
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87 <li>Made angle brackets in ASCII feature descriptions display correctly
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88 <li>Re-instated Zoom function for PCA
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89 <li>Sequence descriptions conserved in web service analysis results
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90 <li>Uniprot ID discoverer uses any word separated by ∣
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91 <li>WsDbFetch query/result association resolved
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92 <li>Tree leaf to sequence mapping improved
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93 <li>Smooth fonts switch moved to FontChooser dialog box. </ul></td>
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96 <td> <div align="center"><strong>2.1.1</strong><br>
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99 <li>Copy consensus sequence to clipboard</li>
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102 <li>Image output - rightmost residues are rendered if sequence id panel
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103 has been resized</li>
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104 <li>Image output - all offscreen group boundaries are rendered </li>
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105 <li>Annotation files with sequence references - all elements in file are
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106 relative to sequence position</li>
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107 <li>Mac Applet users can use Alt key for group editing</li>
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111 <td><div align="center"><strong>2.1</strong><br>
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114 <li>MAFFT Multiple Alignment in default Web Service list</li>
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115 <li>DAS Feature fetching</li>
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116 <li>Hide sequences and columns</li>
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117 <li>Export Annotations and Features</li>
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118 <li>GFF file reading / writing</li>
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119 <li>Associate structures with sequences from local PDB files</li>
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120 <li>Add sequences to exisiting alignment</li>
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121 <li>Recently opened files / URL lists</li>
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122 <li>Applet can launch the full application</li>
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123 <li>Applet has transparency for features (Java 1.2 required)</li>
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124 <li>Applet has user defined colours parameter</li>
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125 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
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128 <li>Redundancy Panel reinstalled in the Applet</li>
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129 <li>Monospaced font - EPS / rescaling bug fixed</li>
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130 <li>Annotation files with sequence references bug fixed</li>
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134 <td><div align="center"><strong>2.08.1</strong><br>
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137 <li>Change case of selected region from Popup menu</li>
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138 <li>Choose to match case when searching</li>
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139 <li>Middle mouse button and mouse movement can compress / expand the visible
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140 width and height of the alignment</li>
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143 <li>Annotation Panel displays complete JNet results</li>
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147 <td><div align="center"><strong>2.08b</strong><br>
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151 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
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152 <li>Righthand label on wrapped alignments shows correct value</li>
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156 <td><div align="center"><strong>2.08</strong><br>
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159 <li>Editing can be locked to the selection area</li>
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160 <li>Keyboard editing</li>
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161 <li>Create sequence features from searches</li>
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162 <li>Precalculated annotations can be loaded onto alignments</li>
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163 <li>Features file allows grouping of features</li>
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164 <li>Annotation Colouring scheme added</li>
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165 <li>Smooth fonts off by default - Faster rendering</li>
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166 <li>Choose to toggle Autocalculate Consensus On/Off</li>
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169 <li>Drag & Drop fixed on Linux</li>
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170 <li>Jalview Archive file faster to load/save, sequence descriptions saved.
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175 <td><div align="center"><strong>2.07</strong><br>
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176 12/12/05</div></td>
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178 <li>PDB Structure Viewer enhanced</li>
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179 <li>Sequence Feature retrieval and display enhanced</li>
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180 <li>Choose to output sequence start-end after sequence name for file output</li>
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181 <li>Sequence Fetcher WSDBFetch@EBI</li>
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182 <li>Applet can read feature files, PDB files and can be used for HTML
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186 <li>HTML output writes groups and features</li>
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187 <li>Group editing is Control and mouse click</li>
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188 <li>File IO bugs</li>
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192 <td><div align="center"><strong>2.06</strong><br>
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195 <li>View annotations in wrapped mode</li>
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196 <li>More options for PCA viewer</li>
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199 <li>GUI bugs resolved</li>
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200 <li>Runs with -nodisplay from command line</li>
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204 <td height="63"> <div align="center"><strong>2.05b</strong><br>
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207 <li>Choose EPS export as lineart or text</li>
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208 <li>Jar files are executable</li>
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209 <li>Can read in Uracil - maps to unknown residue</li>
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212 <li>Known OutOfMemory errors give warning message</li>
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213 <li>Overview window calculated more efficiently</li>
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214 <li>Several GUI bugs resolved</li>
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218 <td><div align="center"><strong>2.05</strong><br>
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221 <li>Edit and annotate in "Wrapped" view</li>
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224 <li>Several GUI bugs resolved</li>
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228 <td><div align="center"><strong>2.04</strong><br>
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231 <li>Hold down mouse wheel & scroll to change font size</li>
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234 <li>Improved JPred client reliability</li>
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235 <li>Improved loading of Jalview files</li>
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239 <td> <div align="center"><strong>2.03</strong><br>
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242 <li>Set Proxy server name and port in preferences</li>
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243 <li>Multiple URL links from sequence ids</li>
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244 <li>User Defined Colours can have a scheme name and added to Colour Menu</li>
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245 <li>Choose to ignore gaps in consensus calculation</li>
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246 <li>Unix users can set default web browser</li>
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247 <li>Runs without GUI for batch processing</li>
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248 <li>Dynamically generated Web Service Menus</li>
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251 <li>InstallAnywhere download for Sparc Solaris</li>
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255 <td> <div align="center"><strong>2.02</strong><br>
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259 <li>Copy & Paste order of sequences maintains alignment order.</li>
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263 <td><div align="center"><strong>2.01</strong><br>
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266 <li>Use delete key for deleting selection.</li>
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267 <li>Use Mouse wheel to scroll sequences.</li>
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268 <li>Help file updated to describe how to add alignment annotations.</li>
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269 <li>Version and build date written to build properties file.</li>
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270 <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>
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273 <li>Delete gaps bug fixed.</li>
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274 <li>FileChooser sorts columns.</li>
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275 <li>Can remove groups one by one.</li>
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276 <li>Filechooser icons installed.</li>
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277 <li>Finder ignores return character when searching. Return key will initiate
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283 <td> <div align="center"><strong>2.0</strong><br>
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286 <li> New codebase</li>
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