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>
48 <li>Better handling of exceptions during sequence retrieval</li>
49 <li>URL links generated for all feature links (bugfix)</li>
50 <li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
51 <li>Added URL embedding instructions to features file documentation.</li>
52 <li>Sequences are now validated against EMBL database (broken in Version 2.4.0)</li>
53 <li>Codons containing ambiguous nucleotides translated as 'X' in peptide product</li>
54 <li>Sequence description lines properly shared via VAMSAS</li>
55 <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>
62 <div align="center"><strong>2.4</strong><br>
66 <em>User Interface</em>
68 <li>Linked highlighting of codon and amino acid from translation
69 and protein products</li>
70 <li>Linked highlighting of structure associated with residue mapping to codon position</li>
71 <li>Sequence Fetcher provides example accession numbers and 'clear' button</li>
72 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
73 <li>Extract score function to parse whitespace separated numeric data in description line</li>
74 <li>Column labels in alignment annotation can be centred.</li>
75 <li>Tooltip for sequence associated annotation give name of sequence</li>
77 <em>Web Services and URL fetching</em>
79 <li>JPred3 web service</li>
80 <li>Prototype sequence search client (no public services available yet)</li>
81 <li>Fetch either seed alignment or full alignment from PFAM</li>
82 <li>URL Links created for matching database cross references as well as sequence ID</li>
83 <li>URL Links can be created using regular-expressions</li>
85 <em>Sequence Database Connectivity</em>
87 <li>Retrieval of cross-referenced sequences from other databases
89 <li>Generalised database reference retrieval and validation to
90 all fetchable databases</li>
91 <li>Fetch sequences from DAS sources supporting the sequence command</li>
93 <em>Import and Export</em>
94 <li>export annotation rows as CSV for spreadsheet import</li>
95 <li>Jalview projects record alignment dataset associations, EMBL
96 products, and cDNA sequence mappings</li>
97 <li>Sequence Group colour can be specified in Annotation File</li>
98 <li>Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme</li>
100 <em>VAMSAS Client capabilities (Experimental)</em>
102 <li>treenode binding for VAMSAS tree exchange</li>
103 <li>local editing and update of sequences in VAMSAS alignments
105 <li>Create new or select existing session to join</li>
106 <li>load and save of vamsas documents</li>
108 <em>Application command line</em>
110 <li>-tree parameter to open trees (introduced for passing from
112 <li>-fetchfrom command line argument to specify nicknames of
113 DAS servers to query for alignment features</li>
114 <li>-dasserver command line argument to add new servers that
115 are also automatically queried for features</li>
116 <li>-groovy command line argument executes a given groovy
117 script after all input data has been loaded and parsed</li>
119 <em>Applet-Application data exchange</em>
121 <li>Trees passed as applet parameters can be passed to
122 application (when using "View in full application")</li>
124 <em>Applet Parameters</em>
126 <li>feature group display control parameter</li>
127 <li>debug parameter</li>
128 <li>showbutton parameter</li>
130 <em>Applet API methods</em>
132 <li>newView public method</li>
133 <li>Window (current view) specific get/set public methods</li>
134 <li>Feature display control methods</li>
135 <li>get list of currently selected sequences</li>
137 <em>New Jalview distribution features</em>
139 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
140 <li>RELEASE file gives build properties for the latest Jalview
142 <li>Java 1.1 Applet build made easier and donotobfuscate
143 property controls execution of obfuscator</li>
144 <li>Build target for generating source distribution</li>
145 <li>Debug flag for javacc</li>
146 <li>.jalview_properties file is documented (slightly) in
147 jalview.bin.Cache</li>
148 <li>Continuous Build Integration for stable and development version of Application, Applet and source distribution</li>
154 <li>selected region output includes visible annotations (for
155 certain formats)</li>
156 <li>edit label/displaychar contains existing label/char for
158 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
159 <li>shorter peptide product names from EMBL records</li>
160 <li>Newick string generator makes compact representations</li>
161 <li>bootstrap values parsed correctly for tree files with
163 <li>pathological filechooser bug avoided by not allowing
164 filenames containing a ':'</li>
165 <li>Fixed exception when parsing GFF files containing global
166 sequence features</li>
167 <li>Alignment datasets are finalized only when number of
168 references from alignment sequences goes to zero</li>
169 <li>Close of tree branch colour box without colour selection
170 causes cascading exceptions</li>
171 <li>occasional negative imgwidth exceptions</li>
172 <li>better reporting of non-fatal warnings to user when file
174 <li>Save works when Jalview project is default format</li>
175 <li>Save as dialog opened if current alignment format is not a valid output format</li>
176 <li>Uniprot canonical names introduced for both das and vamsas</li>
177 <li>Histidine should be midblue (not pink!) in Zappo</li>
178 <li>error messages passed up and output when data read fails</li>
179 <li>edit undo recovers previous dataset sequence when sequence
181 <li>allow PDB files without pdb ID HEADER lines (like those
182 generated by MODELLER) to be read in properly</li>
183 <li>allow reading of JPred concise files as a normal filetype</li>
184 <li>Stockholm annotation parsing and alignment properties import fixed for PFAM records
186 <li>Structure view windows have correct name in Desktop window list</li>
187 <li>annotation consisting of sequence associated scores can be
188 read and written correctly to annotation file</li>
189 <li>Aligned cDNA translation to aligned peptide works correctly
191 <li>Fixed display of hidden sequence markers and non-italic font
192 for representatives in Applet</li>
193 <li>Applet Menus are always embedded in applet window on Macs.</li>
194 <li>Newly shown features appear at top of stack (in Applet)</li>
195 <li>Annotations added via parameter not drawn properly due to
196 null pointer exceptions</li>
197 <li>Secondary structure lines are drawn starting from first
198 column of alignment</li>
199 <li>Uniprot XML import updated for new schema release in July 2008</li>
200 <li>Sequence feature to sequence ID match for Features file is case-insensitive</li>
201 <li>Sequence features read from Features file appended to all sequences with matching IDs</li>
202 <li>PDB structure coloured correctly for associated views containing a sub-sequence</li>
203 <li>PDB files can be retrieved by applet from Jar files</li>
204 <li>feature and annotation file applet parameters referring to different directories are retrieved correctly</li>
205 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
206 <li>Fixed application hang whilst waiting for splash-screen version check to complete</li>
207 <li>Applet properly URLencodes input parameter values when passing them to the launchApp service</li>
208 <li>display name and local features preserved in results retrieved from web service</li>
209 <li>Visual delay indication for sequence retrieval and sequence fetcher initialisation</li>
210 <li>updated Application to use DAS 1.53e version of dasobert DAS client</li>
211 <li>Re-instated Full AMSA support and .amsa file association</li>
212 <li>Fixed parsing of JNet Concise annotation <em>sans</em> sequences</li>
218 <div align="center"><strong>2.3</strong><br>
223 <li>Jmol 11.0.2 integration</li>
224 <li>PDB views stored in Jalview XML files</li>
225 <li>Slide sequences</li>
226 <li>Edit sequence in place</li>
227 <li>EMBL CDS features</li>
228 <li>DAS Feature mapping</li>
229 <li>Feature ordering</li>
230 <li>Alignment Properties</li>
231 <li>Annotation Scores</li>
232 <li>Sort by scores</li>
233 <li>Feature/annotation editing in applet</li>
238 <li>Headless state operation in 2.2.1</li>
239 <li>Incorrect and unstable DNA pairwise alignment</li>
240 <li>Cut and paste of sequences with annotation</li>
241 <li>Feature group display state in XML</li>
242 <li>Feature ordering in XML</li>
243 <li>blc file iteration selection using filename # suffix</li>
244 <li>Stockholm alignment properties</li>
245 <li>Stockhom alignment secondary structure annotation</li>
246 <li>2.2.1 applet had no feature transparency</li>
247 <li>Number pad keys can be used in cursor mode</li>
248 <li>Structure Viewer mirror image resolved</li>
255 <div align="center"><strong>2.2.1</strong><br>
260 <li>Non standard characters can be read and displayed
261 <li>Annotations/Features can be imported/exported to the applet
263 <li>Applet allows editing of sequence/annotation/group name
265 <li>Preference setting to display sequence name in italics
266 <li>Annotation file format extended to allow Sequence_groups to
268 <li>Default opening of alignment overview panel can be specified
270 <li>PDB residue numbering annotation added to associated
276 <li>Applet crash under certain Linux OS with Java 1.6 installed
277 <li>Annotation file export / import bugs fixed
278 <li>PNG / EPS image output bugs fixed
284 <div align="center"><strong>2.2</strong><br>
289 <li>Multiple views on alignment
290 <li>Sequence feature editing
291 <li>"Reload" alignment
292 <li>"Save" to current filename
293 <li>Background dependent text colour
294 <li>Right align sequence ids
295 <li>User-defined lower case residue colours
298 <li>Menu item accelerator keys
299 <li>Control-V pastes to current alignment
300 <li>Cancel button for DAS Feature Fetching
301 <li>PCA and PDB Viewers zoom via mouse roller
302 <li>User-defined sub-tree colours and sub-tree selection
303 <li>'New Window' button on the 'Output to Text box'
308 <li>New memory efficient Undo/Redo System
309 <li>Optimised symbol lookups and conservation/consensus
311 <li>Region Conservation/Consensus recalculated after edits
312 <li>Fixed Remove Empty Columns Bug (empty columns at end of
314 <li>Slowed DAS Feature Fetching for increased robustness.
315 <li>Made angle brackets in ASCII feature descriptions display
317 <li>Re-instated Zoom function for PCA
318 <li>Sequence descriptions conserved in web service analysis
320 <li>Uniprot ID discoverer uses any word separated by ∣
321 <li>WsDbFetch query/result association resolved
322 <li>Tree leaf to sequence mapping improved
323 <li>Smooth fonts switch moved to FontChooser dialog box.
329 <div align="center"><strong>2.1.1</strong><br>
334 <li>Copy consensus sequence to clipboard</li>
339 <li>Image output - rightmost residues are rendered if sequence
340 id panel has been resized</li>
341 <li>Image output - all offscreen group boundaries are rendered</li>
342 <li>Annotation files with sequence references - all elements in
343 file are relative to sequence position</li>
344 <li>Mac Applet users can use Alt key for group editing</li>
350 <div align="center"><strong>2.1</strong><br>
355 <li>MAFFT Multiple Alignment in default Web Service list</li>
356 <li>DAS Feature fetching</li>
357 <li>Hide sequences and columns</li>
358 <li>Export Annotations and Features</li>
359 <li>GFF file reading / writing</li>
360 <li>Associate structures with sequences from local PDB files</li>
361 <li>Add sequences to exisiting alignment</li>
362 <li>Recently opened files / URL lists</li>
363 <li>Applet can launch the full application</li>
364 <li>Applet has transparency for features (Java 1.2 required)</li>
365 <li>Applet has user defined colours parameter</li>
366 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
371 <li>Redundancy Panel reinstalled in the Applet</li>
372 <li>Monospaced font - EPS / rescaling bug fixed</li>
373 <li>Annotation files with sequence references bug fixed</li>
379 <div align="center"><strong>2.08.1</strong><br>
384 <li>Change case of selected region from Popup menu</li>
385 <li>Choose to match case when searching</li>
386 <li>Middle mouse button and mouse movement can compress / expand
387 the visible width and height of the alignment</li>
392 <li>Annotation Panel displays complete JNet results</li>
398 <div align="center"><strong>2.08b</strong><br>
404 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
405 <li>Righthand label on wrapped alignments shows correct value</li>
411 <div align="center"><strong>2.08</strong><br>
416 <li>Editing can be locked to the selection area</li>
417 <li>Keyboard editing</li>
418 <li>Create sequence features from searches</li>
419 <li>Precalculated annotations can be loaded onto alignments</li>
420 <li>Features file allows grouping of features</li>
421 <li>Annotation Colouring scheme added</li>
422 <li>Smooth fonts off by default - Faster rendering</li>
423 <li>Choose to toggle Autocalculate Consensus On/Off</li>
428 <li>Drag & Drop fixed on Linux</li>
429 <li>Jalview Archive file faster to load/save, sequence
430 descriptions saved.</li>
436 <div align="center"><strong>2.07</strong><br>
441 <li>PDB Structure Viewer enhanced</li>
442 <li>Sequence Feature retrieval and display enhanced</li>
443 <li>Choose to output sequence start-end after sequence name for
445 <li>Sequence Fetcher WSDBFetch@EBI</li>
446 <li>Applet can read feature files, PDB files and can be used for
452 <li>HTML output writes groups and features</li>
453 <li>Group editing is Control and mouse click</li>
454 <li>File IO bugs</li>
460 <div align="center"><strong>2.06</strong><br>
465 <li>View annotations in wrapped mode</li>
466 <li>More options for PCA viewer</li>
471 <li>GUI bugs resolved</li>
472 <li>Runs with -nodisplay from command line</li>
478 <div align="center"><strong>2.05b</strong><br>
483 <li>Choose EPS export as lineart or text</li>
484 <li>Jar files are executable</li>
485 <li>Can read in Uracil - maps to unknown residue</li>
490 <li>Known OutOfMemory errors give warning message</li>
491 <li>Overview window calculated more efficiently</li>
492 <li>Several GUI bugs resolved</li>
498 <div align="center"><strong>2.05</strong><br>
503 <li>Edit and annotate in "Wrapped" view</li>
508 <li>Several GUI bugs resolved</li>
514 <div align="center"><strong>2.04</strong><br>
519 <li>Hold down mouse wheel & scroll to change font size</li>
524 <li>Improved JPred client reliability</li>
525 <li>Improved loading of Jalview files</li>
531 <div align="center"><strong>2.03</strong><br>
536 <li>Set Proxy server name and port in preferences</li>
537 <li>Multiple URL links from sequence ids</li>
538 <li>User Defined Colours can have a scheme name and added to
540 <li>Choose to ignore gaps in consensus calculation</li>
541 <li>Unix users can set default web browser</li>
542 <li>Runs without GUI for batch processing</li>
543 <li>Dynamically generated Web Service Menus</li>
548 <li>InstallAnywhere download for Sparc Solaris</li>
554 <div align="center"><strong>2.02</strong><br>
560 <li>Copy & Paste order of sequences maintains alignment
567 <div align="center"><strong>2.01</strong><br>
572 <li>Use delete key for deleting selection.</li>
573 <li>Use Mouse wheel to scroll sequences.</li>
574 <li>Help file updated to describe how to add alignment
576 <li>Version and build date written to build properties file.</li>
577 <li>InstallAnywhere installation will check for updates at
578 launch of Jalview.</li>
583 <li>Delete gaps bug fixed.</li>
584 <li>FileChooser sorts columns.</li>
585 <li>Can remove groups one by one.</li>
586 <li>Filechooser icons installed.</li>
587 <li>Finder ignores return character when searching. Return key
588 will initiate a search.<br>
595 <div align="center"><strong>2.0</strong><br>
600 <li>New codebase</li>