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>
22 <div align="center"><strong>2.4.1</strong><br>
23 <em>Not Yet Released</em></div>
27 <li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li>
28 <li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
29 <li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
31 <li>URL links generated from description line for regular-expression based URL links (applet and application)
33 <li>Non-positional features displayed in sequence ID tooltip on applet
35 <li>Non-positional feature URL links are shown in link menu (applet and application)
37 <li>Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
39 <li>Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
41 <li>Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
43 <li>New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)</li>
44 <li>Order an alignment in order of average feature score or total feature count</li>
49 <li>Better handling of exceptions during sequence retrieval</li>
50 <li>URL links generated for all feature links (bugfix)</li>
51 <li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
52 <li>Added URL embedding instructions to features file documentation.</li>
53 <li>Sequences are now validated against EMBL database (broken in Version 2.4.0)</li>
54 <li>Codons containing ambiguous nucleotides translated as 'X' in peptide product</li>
55 <li>Sequence description lines properly shared via VAMSAS</li>
56 <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>
57 <li>Sequence fetcher fetches multiple records for all data sources</li>
64 <div align="center"><strong>2.4.0.b2</strong><br>
68 <ul><li>Experimental support for google analytics usage tracking.</li>
72 <ul><li>Fixed race condition in applet preventing startup in jre1.6.0u12+.</li>
79 <div align="center"><strong>2.4 bugfixes</strong><br>
86 <li>Sequences are now validated against EMBL database</li>
87 <li>Sequence fetcher fetches multiple records for all data sources</li>
93 <div align="center"><strong>2.4</strong><br>
97 <em>User Interface</em>
99 <li>Linked highlighting of codon and amino acid from translation
100 and protein products</li>
101 <li>Linked highlighting of structure associated with residue mapping to codon position</li>
102 <li>Sequence Fetcher provides example accession numbers and 'clear' button</li>
103 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
104 <li>Extract score function to parse whitespace separated numeric data in description line</li>
105 <li>Column labels in alignment annotation can be centred.</li>
106 <li>Tooltip for sequence associated annotation give name of sequence</li>
108 <em>Web Services and URL fetching</em>
110 <li>JPred3 web service</li>
111 <li>Prototype sequence search client (no public services available yet)</li>
112 <li>Fetch either seed alignment or full alignment from PFAM</li>
113 <li>URL Links created for matching database cross references as well as sequence ID</li>
114 <li>URL Links can be created using regular-expressions</li>
116 <em>Sequence Database Connectivity</em>
118 <li>Retrieval of cross-referenced sequences from other databases
120 <li>Generalised database reference retrieval and validation to
121 all fetchable databases</li>
122 <li>Fetch sequences from DAS sources supporting the sequence command</li>
124 <em>Import and Export</em>
125 <li>export annotation rows as CSV for spreadsheet import</li>
126 <li>Jalview projects record alignment dataset associations, EMBL
127 products, and cDNA sequence mappings</li>
128 <li>Sequence Group colour can be specified in Annotation File</li>
129 <li>Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme</li>
131 <em>VAMSAS Client capabilities (Experimental)</em>
133 <li>treenode binding for VAMSAS tree exchange</li>
134 <li>local editing and update of sequences in VAMSAS alignments
136 <li>Create new or select existing session to join</li>
137 <li>load and save of vamsas documents</li>
139 <em>Application command line</em>
141 <li>-tree parameter to open trees (introduced for passing from
143 <li>-fetchfrom command line argument to specify nicknames of
144 DAS servers to query for alignment features</li>
145 <li>-dasserver command line argument to add new servers that
146 are also automatically queried for features</li>
147 <li>-groovy command line argument executes a given groovy
148 script after all input data has been loaded and parsed</li>
150 <em>Applet-Application data exchange</em>
152 <li>Trees passed as applet parameters can be passed to
153 application (when using "View in full application")</li>
155 <em>Applet Parameters</em>
157 <li>feature group display control parameter</li>
158 <li>debug parameter</li>
159 <li>showbutton parameter</li>
161 <em>Applet API methods</em>
163 <li>newView public method</li>
164 <li>Window (current view) specific get/set public methods</li>
165 <li>Feature display control methods</li>
166 <li>get list of currently selected sequences</li>
168 <em>New Jalview distribution features</em>
170 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
171 <li>RELEASE file gives build properties for the latest Jalview
173 <li>Java 1.1 Applet build made easier and donotobfuscate
174 property controls execution of obfuscator</li>
175 <li>Build target for generating source distribution</li>
176 <li>Debug flag for javacc</li>
177 <li>.jalview_properties file is documented (slightly) in
178 jalview.bin.Cache</li>
179 <li>Continuous Build Integration for stable and development version of Application, Applet and source distribution</li>
185 <li>selected region output includes visible annotations (for
186 certain formats)</li>
187 <li>edit label/displaychar contains existing label/char for
189 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
190 <li>shorter peptide product names from EMBL records</li>
191 <li>Newick string generator makes compact representations</li>
192 <li>bootstrap values parsed correctly for tree files with
194 <li>pathological filechooser bug avoided by not allowing
195 filenames containing a ':'</li>
196 <li>Fixed exception when parsing GFF files containing global
197 sequence features</li>
198 <li>Alignment datasets are finalized only when number of
199 references from alignment sequences goes to zero</li>
200 <li>Close of tree branch colour box without colour selection
201 causes cascading exceptions</li>
202 <li>occasional negative imgwidth exceptions</li>
203 <li>better reporting of non-fatal warnings to user when file
205 <li>Save works when Jalview project is default format</li>
206 <li>Save as dialog opened if current alignment format is not a valid output format</li>
207 <li>Uniprot canonical names introduced for both das and vamsas</li>
208 <li>Histidine should be midblue (not pink!) in Zappo</li>
209 <li>error messages passed up and output when data read fails</li>
210 <li>edit undo recovers previous dataset sequence when sequence
212 <li>allow PDB files without pdb ID HEADER lines (like those
213 generated by MODELLER) to be read in properly</li>
214 <li>allow reading of JPred concise files as a normal filetype</li>
215 <li>Stockholm annotation parsing and alignment properties import fixed for PFAM records
217 <li>Structure view windows have correct name in Desktop window list</li>
218 <li>annotation consisting of sequence associated scores can be
219 read and written correctly to annotation file</li>
220 <li>Aligned cDNA translation to aligned peptide works correctly
222 <li>Fixed display of hidden sequence markers and non-italic font
223 for representatives in Applet</li>
224 <li>Applet Menus are always embedded in applet window on Macs.</li>
225 <li>Newly shown features appear at top of stack (in Applet)</li>
226 <li>Annotations added via parameter not drawn properly due to
227 null pointer exceptions</li>
228 <li>Secondary structure lines are drawn starting from first
229 column of alignment</li>
230 <li>Uniprot XML import updated for new schema release in July 2008</li>
231 <li>Sequence feature to sequence ID match for Features file is case-insensitive</li>
232 <li>Sequence features read from Features file appended to all sequences with matching IDs</li>
233 <li>PDB structure coloured correctly for associated views containing a sub-sequence</li>
234 <li>PDB files can be retrieved by applet from Jar files</li>
235 <li>feature and annotation file applet parameters referring to different directories are retrieved correctly</li>
236 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
237 <li>Fixed application hang whilst waiting for splash-screen version check to complete</li>
238 <li>Applet properly URLencodes input parameter values when passing them to the launchApp service</li>
239 <li>display name and local features preserved in results retrieved from web service</li>
240 <li>Visual delay indication for sequence retrieval and sequence fetcher initialisation</li>
241 <li>updated Application to use DAS 1.53e version of dasobert DAS client</li>
242 <li>Re-instated Full AMSA support and .amsa file association</li>
243 <li>Fixed parsing of JNet Concise annotation <em>sans</em> sequences</li>
249 <div align="center"><strong>2.3</strong><br>
254 <li>Jmol 11.0.2 integration</li>
255 <li>PDB views stored in Jalview XML files</li>
256 <li>Slide sequences</li>
257 <li>Edit sequence in place</li>
258 <li>EMBL CDS features</li>
259 <li>DAS Feature mapping</li>
260 <li>Feature ordering</li>
261 <li>Alignment Properties</li>
262 <li>Annotation Scores</li>
263 <li>Sort by scores</li>
264 <li>Feature/annotation editing in applet</li>
269 <li>Headless state operation in 2.2.1</li>
270 <li>Incorrect and unstable DNA pairwise alignment</li>
271 <li>Cut and paste of sequences with annotation</li>
272 <li>Feature group display state in XML</li>
273 <li>Feature ordering in XML</li>
274 <li>blc file iteration selection using filename # suffix</li>
275 <li>Stockholm alignment properties</li>
276 <li>Stockhom alignment secondary structure annotation</li>
277 <li>2.2.1 applet had no feature transparency</li>
278 <li>Number pad keys can be used in cursor mode</li>
279 <li>Structure Viewer mirror image resolved</li>
286 <div align="center"><strong>2.2.1</strong><br>
291 <li>Non standard characters can be read and displayed
292 <li>Annotations/Features can be imported/exported to the applet
294 <li>Applet allows editing of sequence/annotation/group name
296 <li>Preference setting to display sequence name in italics
297 <li>Annotation file format extended to allow Sequence_groups to
299 <li>Default opening of alignment overview panel can be specified
301 <li>PDB residue numbering annotation added to associated
307 <li>Applet crash under certain Linux OS with Java 1.6 installed
308 <li>Annotation file export / import bugs fixed
309 <li>PNG / EPS image output bugs fixed
315 <div align="center"><strong>2.2</strong><br>
320 <li>Multiple views on alignment
321 <li>Sequence feature editing
322 <li>"Reload" alignment
323 <li>"Save" to current filename
324 <li>Background dependent text colour
325 <li>Right align sequence ids
326 <li>User-defined lower case residue colours
329 <li>Menu item accelerator keys
330 <li>Control-V pastes to current alignment
331 <li>Cancel button for DAS Feature Fetching
332 <li>PCA and PDB Viewers zoom via mouse roller
333 <li>User-defined sub-tree colours and sub-tree selection
334 <li>'New Window' button on the 'Output to Text box'
339 <li>New memory efficient Undo/Redo System
340 <li>Optimised symbol lookups and conservation/consensus
342 <li>Region Conservation/Consensus recalculated after edits
343 <li>Fixed Remove Empty Columns Bug (empty columns at end of
345 <li>Slowed DAS Feature Fetching for increased robustness.
346 <li>Made angle brackets in ASCII feature descriptions display
348 <li>Re-instated Zoom function for PCA
349 <li>Sequence descriptions conserved in web service analysis
351 <li>Uniprot ID discoverer uses any word separated by ∣
352 <li>WsDbFetch query/result association resolved
353 <li>Tree leaf to sequence mapping improved
354 <li>Smooth fonts switch moved to FontChooser dialog box.
360 <div align="center"><strong>2.1.1</strong><br>
365 <li>Copy consensus sequence to clipboard</li>
370 <li>Image output - rightmost residues are rendered if sequence
371 id panel has been resized</li>
372 <li>Image output - all offscreen group boundaries are rendered</li>
373 <li>Annotation files with sequence references - all elements in
374 file are relative to sequence position</li>
375 <li>Mac Applet users can use Alt key for group editing</li>
381 <div align="center"><strong>2.1</strong><br>
386 <li>MAFFT Multiple Alignment in default Web Service list</li>
387 <li>DAS Feature fetching</li>
388 <li>Hide sequences and columns</li>
389 <li>Export Annotations and Features</li>
390 <li>GFF file reading / writing</li>
391 <li>Associate structures with sequences from local PDB files</li>
392 <li>Add sequences to exisiting alignment</li>
393 <li>Recently opened files / URL lists</li>
394 <li>Applet can launch the full application</li>
395 <li>Applet has transparency for features (Java 1.2 required)</li>
396 <li>Applet has user defined colours parameter</li>
397 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
402 <li>Redundancy Panel reinstalled in the Applet</li>
403 <li>Monospaced font - EPS / rescaling bug fixed</li>
404 <li>Annotation files with sequence references bug fixed</li>
410 <div align="center"><strong>2.08.1</strong><br>
415 <li>Change case of selected region from Popup menu</li>
416 <li>Choose to match case when searching</li>
417 <li>Middle mouse button and mouse movement can compress / expand
418 the visible width and height of the alignment</li>
423 <li>Annotation Panel displays complete JNet results</li>
429 <div align="center"><strong>2.08b</strong><br>
435 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
436 <li>Righthand label on wrapped alignments shows correct value</li>
442 <div align="center"><strong>2.08</strong><br>
447 <li>Editing can be locked to the selection area</li>
448 <li>Keyboard editing</li>
449 <li>Create sequence features from searches</li>
450 <li>Precalculated annotations can be loaded onto alignments</li>
451 <li>Features file allows grouping of features</li>
452 <li>Annotation Colouring scheme added</li>
453 <li>Smooth fonts off by default - Faster rendering</li>
454 <li>Choose to toggle Autocalculate Consensus On/Off</li>
459 <li>Drag & Drop fixed on Linux</li>
460 <li>Jalview Archive file faster to load/save, sequence
461 descriptions saved.</li>
467 <div align="center"><strong>2.07</strong><br>
472 <li>PDB Structure Viewer enhanced</li>
473 <li>Sequence Feature retrieval and display enhanced</li>
474 <li>Choose to output sequence start-end after sequence name for
476 <li>Sequence Fetcher WSDBFetch@EBI</li>
477 <li>Applet can read feature files, PDB files and can be used for
483 <li>HTML output writes groups and features</li>
484 <li>Group editing is Control and mouse click</li>
485 <li>File IO bugs</li>
491 <div align="center"><strong>2.06</strong><br>
496 <li>View annotations in wrapped mode</li>
497 <li>More options for PCA viewer</li>
502 <li>GUI bugs resolved</li>
503 <li>Runs with -nodisplay from command line</li>
509 <div align="center"><strong>2.05b</strong><br>
514 <li>Choose EPS export as lineart or text</li>
515 <li>Jar files are executable</li>
516 <li>Can read in Uracil - maps to unknown residue</li>
521 <li>Known OutOfMemory errors give warning message</li>
522 <li>Overview window calculated more efficiently</li>
523 <li>Several GUI bugs resolved</li>
529 <div align="center"><strong>2.05</strong><br>
534 <li>Edit and annotate in "Wrapped" view</li>
539 <li>Several GUI bugs resolved</li>
545 <div align="center"><strong>2.04</strong><br>
550 <li>Hold down mouse wheel & scroll to change font size</li>
555 <li>Improved JPred client reliability</li>
556 <li>Improved loading of Jalview files</li>
562 <div align="center"><strong>2.03</strong><br>
567 <li>Set Proxy server name and port in preferences</li>
568 <li>Multiple URL links from sequence ids</li>
569 <li>User Defined Colours can have a scheme name and added to
571 <li>Choose to ignore gaps in consensus calculation</li>
572 <li>Unix users can set default web browser</li>
573 <li>Runs without GUI for batch processing</li>
574 <li>Dynamically generated Web Service Menus</li>
579 <li>InstallAnywhere download for Sparc Solaris</li>
585 <div align="center"><strong>2.02</strong><br>
591 <li>Copy & Paste order of sequences maintains alignment
598 <div align="center"><strong>2.01</strong><br>
603 <li>Use delete key for deleting selection.</li>
604 <li>Use Mouse wheel to scroll sequences.</li>
605 <li>Help file updated to describe how to add alignment
607 <li>Version and build date written to build properties file.</li>
608 <li>InstallAnywhere installation will check for updates at
609 launch of Jalview.</li>
614 <li>Delete gaps bug fixed.</li>
615 <li>FileChooser sorts columns.</li>
616 <li>Can remove groups one by one.</li>
617 <li>Filechooser icons installed.</li>
618 <li>Finder ignores return character when searching. Return key
619 will initiate a search.<br>
626 <div align="center"><strong>2.0</strong><br>
631 <li>New codebase</li>