3 <title>Release History</title>
6 <p><strong>Release History</strong></p>
10 <div align="center"><em><strong>Release</strong></em></div>
13 <div align="center"><em><strong>New Features</strong></em></div>
16 <div align="center"><em><strong>Issues Resolved</strong></em></div>
21 <div align="center"><strong>2.4</strong><br>
26 <li>New VAMSAS capabilities in Jalview
28 <li>treenode binding for VAMSAS tree exchange</li>
29 <li>local editing and update of sequences in VAMSAS alignments
31 <li>Create new or select existing session to join</li>
32 <li>load and save of vamsas documents</li>
35 <li>Retrieval of cross-referenced sequences from other databases
37 <li>export annotation rows as CSV for spreadsheet import</li>
38 <li>Jalview projects record alignment dataset associations, EMBL
39 products, and cDNA sequence mappings</li>
40 <li>Linked highlighting of codon and amino acid from translation
41 and protein products</li>
42 <li>JPred3 web service</li>
43 <li>Generalised database reference retrieval and validation to
44 all fetchable databases</li>
45 <li>Application command line
47 <li>-tree parameter to open trees (introduced for passing from
49 <li>-fetchfrom command line argument to specify nicknames of
50 DAS servers to query for alignment features</li>
51 <li>-dasserver command line argument to add new servers that
52 are also automatically queried for features</li>
53 <li>-groovy command line argument executes a given groovy
54 script after all input data has been loaded and parsed</li>
57 <li>Trees passed as applet parameters can be passed to
58 application (when using "View in full application")</li>
59 <li>MemoryMonitor added as an option under Desktop's Tools menu
61 <li>allow reading of JPred concise files as a normal filetype</li>
62 <li>sort sequences by named annotation scores</li>
63 <li>Re-instated Full AMSA support and .amsa file association</li>
64 <li>Stockholm annotation parsing and alignment properties import
68 <li>feature group display control parameter</li>
69 <li>debug parameter</li>
72 <li>Applet API methods
74 <li>newView public method</li>
75 <li>Window (current view) specific get/set public methods</li>
76 <li>Feature display control methods</li>
80 <em>New Jalview distribution features</em>
82 <li>RELEASE file gives build properties for the latest Jalview
84 <li>Java 1.1 Applet build made easier and donotobfuscate
85 property controls execution of obfuscator</li>
86 <li>Build target for generating source distribution</li>
87 <li>Debug flag for javacc</li>
88 <li>.jalview_properties file is documented (slightly) in
89 jalview.bin.Cache</li>
94 <li>selected region output includes visible annotations (for
96 <li>edit label/displaychar contains existing label/char for
98 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
99 <li>shorter peptide product names from EMBL records</li>
100 <li>Newick string generator makes compact representations</li>
101 <li>bootstrap values parsed correctly for tree files with
103 <li>pathological filechooser bug avoided by not allowing
104 filenames containing a ':'</li>
105 <li>Fixed exception when parsing GFF files containing global
106 sequence features</li>
107 <li>Alignment datasets are finalized only when number of
108 references from alignment sequences goes to zero</li>
109 <li>Close of tree branch colour box without colour selection
110 causes cascading exceptions</li>
111 <li>occasional negative imgwidth exceptions</li>
112 <li>better reporting of non-fatal warnings to user when file
114 <li>Save works when Jalview project is default format</li>
115 <li>Uniprot canonical names introduced for both das and vamsas</li>
116 <li>Histidine should be midblue (not pink!) in Zappo</li>
117 <li>error messages passed up and output when data read fails</li>
118 <li>edit undo recovers previous dataset sequence when sequence
120 <li>allow PDB files without pdb ID HEADER lines (like those
121 generated by MODELLER) to be read in properly</li>
122 <li>annotation consisting of sequence associated scores can be
123 read and written correctly to annotation file</li>
124 <li>Aligned cDNA translation to aligned peptide works correctly
126 <li>Fixed display of hidden sequence markers and non-italic font
127 for representatives in Applet</li>
128 <li>Applet Menus are always embedded in applet window on Macs.</li>
129 <li>Newly shown features appear at top of stack (in Applet)</li>
130 <li>Annotations added via parameter not drawn properly due to
131 null pointer exceptions</li>
132 <li>Secondary structure lines are drawn starting from first
133 column of alignment</li>
139 <div align="center"><strong>2.3</strong><br>
144 <li>Jmol 11.0.2 integration</li>
145 <li>PDB views stored in Jalview XML files</li>
146 <li>Slide sequences</li>
147 <li>Edit sequence in place</li>
148 <li>EMBL CDS features</li>
149 <li>DAS Feature mapping</li>
150 <li>Feature ordering</li>
151 <li>Alignment Properties</li>
152 <li>Annotation Scores</li>
153 <li>Sort by scores</li>
154 <li>Feature/annotation editing in applet</li>
159 <li>Headless state operation in 2.2.1</li>
160 <li>Incorrect and unstable DNA pairwise alignment</li>
161 <li>Cut and paste of sequences with annotation</li>
162 <li>Feature group display state in XML</li>
163 <li>Feature ordering in XML</li>
164 <li>blc file iteration selection using filename # suffix</li>
165 <li>Stockholm alignment properties</li>
166 <li>Stockhom alignment secondary structure annotation</li>
167 <li>2.2.1 applet had no feature transparency</li>
168 <li>Number pad keys can be used in cursor mode</li>
169 <li>Structure Viewer mirror image resolved</li>
176 <div align="center"><strong>2.2.1</strong><br>
181 <li>Non standard characters can be read and displayed
182 <li>Annotations/Features can be imported/exported to the applet
184 <li>Applet allows editing of sequence/annotation/group name
186 <li>Preference setting to display sequence name in italics
187 <li>Annotation file format extended to allow Sequence_groups to
189 <li>Default opening of alignment overview panel can be specified
191 <li>PDB residue numbering annotation added to associated
197 <li>Applet crash under certain Linux OS with Java 1.6 installed
198 <li>Annotation file export / import bugs fixed
199 <li>PNG / EPS image output bugs fixed
205 <div align="center"><strong>2.2</strong><br>
210 <li>Multiple views on alignment
211 <li>Sequence feature editing
212 <li>"Reload" alignment
213 <li>"Save" to current filename
214 <li>Background dependent text colour
215 <li>Right align sequence ids
216 <li>User-defined lower case residue colours
219 <li>Menu item accelerator keys
220 <li>Control-V pastes to current alignment
221 <li>Cancel button for DAS Feature Fetching
222 <li>PCA and PDB Viewers zoom via mouse roller
223 <li>User-defined sub-tree colours and sub-tree selection
224 <li>'New Window' button on the 'Output to Text box'
229 <li>New memory efficient Undo/Redo System
230 <li>Optimised symbol lookups and conservation/consensus
232 <li>Region Conservation/Consensus recalculated after edits
233 <li>Fixed Remove Empty Columns Bug (empty columns at end of
235 <li>Slowed DAS Feature Fetching for increased robustness.
236 <li>Made angle brackets in ASCII feature descriptions display
238 <li>Re-instated Zoom function for PCA
239 <li>Sequence descriptions conserved in web service analysis
241 <li>Uniprot ID discoverer uses any word separated by ∣
242 <li>WsDbFetch query/result association resolved
243 <li>Tree leaf to sequence mapping improved
244 <li>Smooth fonts switch moved to FontChooser dialog box.
250 <div align="center"><strong>2.1.1</strong><br>
255 <li>Copy consensus sequence to clipboard</li>
260 <li>Image output - rightmost residues are rendered if sequence
261 id panel has been resized</li>
262 <li>Image output - all offscreen group boundaries are rendered</li>
263 <li>Annotation files with sequence references - all elements in
264 file are relative to sequence position</li>
265 <li>Mac Applet users can use Alt key for group editing</li>
271 <div align="center"><strong>2.1</strong><br>
276 <li>MAFFT Multiple Alignment in default Web Service list</li>
277 <li>DAS Feature fetching</li>
278 <li>Hide sequences and columns</li>
279 <li>Export Annotations and Features</li>
280 <li>GFF file reading / writing</li>
281 <li>Associate structures with sequences from local PDB files</li>
282 <li>Add sequences to exisiting alignment</li>
283 <li>Recently opened files / URL lists</li>
284 <li>Applet can launch the full application</li>
285 <li>Applet has transparency for features (Java 1.2 required)</li>
286 <li>Applet has user defined colours parameter</li>
287 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
292 <li>Redundancy Panel reinstalled in the Applet</li>
293 <li>Monospaced font - EPS / rescaling bug fixed</li>
294 <li>Annotation files with sequence references bug fixed</li>
300 <div align="center"><strong>2.08.1</strong><br>
305 <li>Change case of selected region from Popup menu</li>
306 <li>Choose to match case when searching</li>
307 <li>Middle mouse button and mouse movement can compress / expand
308 the visible width and height of the alignment</li>
313 <li>Annotation Panel displays complete JNet results</li>
319 <div align="center"><strong>2.08b</strong><br>
325 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
326 <li>Righthand label on wrapped alignments shows correct value</li>
332 <div align="center"><strong>2.08</strong><br>
337 <li>Editing can be locked to the selection area</li>
338 <li>Keyboard editing</li>
339 <li>Create sequence features from searches</li>
340 <li>Precalculated annotations can be loaded onto alignments</li>
341 <li>Features file allows grouping of features</li>
342 <li>Annotation Colouring scheme added</li>
343 <li>Smooth fonts off by default - Faster rendering</li>
344 <li>Choose to toggle Autocalculate Consensus On/Off</li>
349 <li>Drag & Drop fixed on Linux</li>
350 <li>Jalview Archive file faster to load/save, sequence
351 descriptions saved.</li>
357 <div align="center"><strong>2.07</strong><br>
362 <li>PDB Structure Viewer enhanced</li>
363 <li>Sequence Feature retrieval and display enhanced</li>
364 <li>Choose to output sequence start-end after sequence name for
366 <li>Sequence Fetcher WSDBFetch@EBI</li>
367 <li>Applet can read feature files, PDB files and can be used for
373 <li>HTML output writes groups and features</li>
374 <li>Group editing is Control and mouse click</li>
375 <li>File IO bugs</li>
381 <div align="center"><strong>2.06</strong><br>
386 <li>View annotations in wrapped mode</li>
387 <li>More options for PCA viewer</li>
392 <li>GUI bugs resolved</li>
393 <li>Runs with -nodisplay from command line</li>
399 <div align="center"><strong>2.05b</strong><br>
404 <li>Choose EPS export as lineart or text</li>
405 <li>Jar files are executable</li>
406 <li>Can read in Uracil - maps to unknown residue</li>
411 <li>Known OutOfMemory errors give warning message</li>
412 <li>Overview window calculated more efficiently</li>
413 <li>Several GUI bugs resolved</li>
419 <div align="center"><strong>2.05</strong><br>
424 <li>Edit and annotate in "Wrapped" view</li>
429 <li>Several GUI bugs resolved</li>
435 <div align="center"><strong>2.04</strong><br>
440 <li>Hold down mouse wheel & scroll to change font size</li>
445 <li>Improved JPred client reliability</li>
446 <li>Improved loading of Jalview files</li>
452 <div align="center"><strong>2.03</strong><br>
457 <li>Set Proxy server name and port in preferences</li>
458 <li>Multiple URL links from sequence ids</li>
459 <li>User Defined Colours can have a scheme name and added to
461 <li>Choose to ignore gaps in consensus calculation</li>
462 <li>Unix users can set default web browser</li>
463 <li>Runs without GUI for batch processing</li>
464 <li>Dynamically generated Web Service Menus</li>
469 <li>InstallAnywhere download for Sparc Solaris</li>
475 <div align="center"><strong>2.02</strong><br>
481 <li>Copy & Paste order of sequences maintains alignment
488 <div align="center"><strong>2.01</strong><br>
493 <li>Use delete key for deleting selection.</li>
494 <li>Use Mouse wheel to scroll sequences.</li>
495 <li>Help file updated to describe how to add alignment
497 <li>Version and build date written to build properties file.</li>
498 <li>InstallAnywhere installation will check for updates at
499 launch of Jalview.</li>
504 <li>Delete gaps bug fixed.</li>
505 <li>FileChooser sorts columns.</li>
506 <li>Can remove groups one by one.</li>
507 <li>Filechooser icons installed.</li>
508 <li>Finder ignores return character when searching. Return key
509 will initiate a search.<br>
516 <div align="center"><strong>2.0</strong><br>
521 <li>New codebase</li>