3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Release History</title>
23 <p><strong>Release History</strong></p>
26 <td width="60" nowrap>
27 <div align="center"><em><strong>Release</strong></em></div>
30 <div align="center"><em><strong>New Features</strong></em></div>
33 <div align="center"><em><strong>Issues Resolved</strong></em></div>
39 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
40 <em>30/4/2010</em></div>
43 <em>New Capabilities</em>
45 <li>URL links generated from description line for
46 regular-expression based URL links (applet and application)
47 <li>Non-positional feature URL links are shown in link menu</li>
48 <li>Linked viewing of nucleic acid sequences and structures</li>
49 <li>Automatic Scrolling option in View menu to display the
50 currently highlighted region of an alignment.</li>
51 <li>Order an alignment by sequence length, or using the average score or total feature count for each sequence.</li>
52 <li>Shading features by score or associated description</li>
53 <li>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
54 <li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</li>
55 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
59 <li>Fetch DB References capabilities and UI expanded to support
60 retrieval from DAS sequence sources</li>
61 <li>Local DAS Sequence sources can be added via the command line
62 or via the Add local source dialog box.</li>
63 <li>DAS Dbref and DbxRef feature types are parsed as database
64 references and protein_name is parsed as description line (BioSapiens
66 <li>Enable or disable non-positional feature and database
67 references in sequence ID tooltip from View menu in application.</li>
68 <!-- <li>New hidden columns and rows and representatives capabilities
69 in annotations file (in progress - not yet fully implemented)</li> -->
70 <li>Group-associated consensus, sequence logos and conservation
72 <li>Symbol distributions for each column can be exported and
73 visualized as sequence logos</li>
74 <li>Optionally scale multi-character column labels to fit within
75 each column of annotation row<!-- todo for applet --></li>
76 <li>Optional automatic sort of associated alignment view when a
77 new tree is opened.</li>
78 <li>Jalview Java Console</li>
79 <li>Better placement of desktop window when moving between different screens.</li>
80 <li>New preference items for sequence ID tooltip and consensus
82 <li>Client to submit sequences and IDs to <a
83 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
84 <li><em>Vamsas Capabilities</em>
86 <li>Improved VAMSAS synchronization (jalview archive used to
87 preserve views, structures, and tree display settings)</li>
88 <li>Import of vamsas documents from disk or URL via command line</li>
89 <li>Sharing of selected regions between views and with other
90 VAMSAS applications (Experimental feature!)</li>
91 <li>Updated API to VAMSAS version 0.2</li>
97 <li>Middle button resizes annotation row height</li>
100 <li>sortByTree (true/false) - automatically sort the associated
101 alignment view by the tree when a new tree is opened.</li>
102 <li>showTreeBootstraps (true/false) - show or hide branch
103 bootstraps (default is to show them if available)</li>
104 <li>showTreeDistances (true/false) - show or hide branch lengths
105 (default is to show them if available)</li>
106 <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated
107 nodes should be highlighted in the tree view</li>
108 <li>heightScale and widthScale (1.0 or more) - increase the
109 height or width of a cell in the alignment grid relative to the
110 current font size.</li>
113 <li>Non-positional features displayed in sequence ID tooltip</li>
117 <li>Features format: graduated colour definitions and
118 specification of feature scores</li>
119 <li>Alignment Annotations format: new keywords for group
120 associated annotation (GROUP_REF) and annotation row display properties
121 (ROW_PROPERTIES)</li>
122 <li>XML formats extended to support graduated feature
123 colourschemes, group associated annotation, and profile visualization
128 <li>Source field in GFF files parsed as feature source rather
129 than description</li>
130 <li>Non-positional features are now included in sequence feature
131 and gff files (controlled via non-positional feature visibility in
133 <li>URL links generated for all feature links (bugfix)</li>
134 <li>Added URL embedding instructions to features file
136 <li>Codons containing ambiguous nucleotides translated as 'X' in
138 <li>Match case switch in find dialog box works for both sequence
139 ID and sequence string and query strings do not have to be in upper
140 case to match case-insensitively.</li>
141 <li>AMSA files only contain first column of multi-character
142 column annotation labels</li>
143 <li>Jalview Annotation File generation/parsing consistent with
144 documentation (e.g. Stockholm annotation can be exported and
146 <li>PDB files without embedded PDB IDs given a friendly name</li>
147 <li>Find incrementally searches ID string matches as well as
148 subsequence matches, and correctly reports total number of both.</li>
151 <li>Better handling of exceptions during sequence retrieval</li>
152 <li>Dasobert generated non-positional feature URL link text
153 excludes the start_end suffix</li>
154 <li>DAS feature and source retrieval buttons disabled when fetch
155 or registry operations in progress.</li>
156 <li>PDB files retrieved from URLs are cached properly</li>
157 <li>Sequence description lines properly shared via VAMSAS</li>
158 <li>Sequence fetcher fetches multiple records for all data
160 <li>Ensured that command line das feature retrieval completes
161 before alignment figures are generated.</li>
162 <li>Reduced time taken when opening file browser for first time.</li>
163 <li>isAligned check prior to calculating tree, PCA or submitting
164 an MSA to JNet now excludes hidden sequences.</li>
165 <li>User defined group colours properly recovered from Jalview projects.</li>
174 <div align="center"><strong>2.4.0.b2</strong><br>
179 <li>Experimental support for google analytics usage tracking.</li>
180 <li>Jalview privacy settings (user preferences and docs).</li>
185 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
186 <li>Exception when feature created from selection beyond length
188 <li>Allow synthetic PDB files to be imported gracefully</li>
189 <li>Sequence associated annotation rows associate with all
190 sequences with a given id</li>
191 <li>Find function matches case-insensitively for sequence ID
193 <li>Non-standard characters do not cause pairwise alignment to
194 fail with exception</li>
196 <em>Application Issues</em>
198 <li>Sequences are now validated against EMBL database</li>
199 <li>Sequence fetcher fetches multiple records for all data
202 <em>InstallAnywhere Issues</em>
204 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
205 installAnywhere mechanism)</li>
206 <li>Command line launching of JARs from InstallAnywhere version
207 (java class versioning error fixed)</li>
214 <div align="center"><strong>2.4</strong><br>
217 <td><em>User Interface</em>
219 <li>Linked highlighting of codon and amino acid from translation
220 and protein products</li>
221 <li>Linked highlighting of structure associated with residue
222 mapping to codon position</li>
223 <li>Sequence Fetcher provides example accession numbers and
225 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
226 <li>Extract score function to parse whitespace separated numeric
227 data in description line</li>
228 <li>Column labels in alignment annotation can be centred.</li>
229 <li>Tooltip for sequence associated annotation give name of
232 <em>Web Services and URL fetching</em>
234 <li>JPred3 web service</li>
235 <li>Prototype sequence search client (no public services
237 <li>Fetch either seed alignment or full alignment from PFAM</li>
238 <li>URL Links created for matching database cross references as
239 well as sequence ID</li>
240 <li>URL Links can be created using regular-expressions</li>
242 <em>Sequence Database Connectivity</em>
244 <li>Retrieval of cross-referenced sequences from other databases
246 <li>Generalised database reference retrieval and validation to
247 all fetchable databases</li>
248 <li>Fetch sequences from DAS sources supporting the sequence
251 <em>Import and Export</em>
252 <li>export annotation rows as CSV for spreadsheet import</li>
253 <li>Jalview projects record alignment dataset associations, EMBL
254 products, and cDNA sequence mappings</li>
255 <li>Sequence Group colour can be specified in Annotation File</li>
256 <li>Ad-hoc colouring of group in Annotation File using RGB
257 triplet as name of colourscheme</li>
259 <em>VAMSAS Client capabilities (Experimental)</em>
261 <li>treenode binding for VAMSAS tree exchange</li>
262 <li>local editing and update of sequences in VAMSAS alignments
264 <li>Create new or select existing session to join</li>
265 <li>load and save of vamsas documents</li>
267 <em>Application command line</em>
269 <li>-tree parameter to open trees (introduced for passing from
271 <li>-fetchfrom command line argument to specify nicknames of DAS
272 servers to query for alignment features</li>
273 <li>-dasserver command line argument to add new servers that are
274 also automatically queried for features</li>
275 <li>-groovy command line argument executes a given groovy script
276 after all input data has been loaded and parsed</li>
278 <em>Applet-Application data exchange</em>
280 <li>Trees passed as applet parameters can be passed to application
281 (when using "View in full application")</li>
283 <em>Applet Parameters</em>
285 <li>feature group display control parameter</li>
286 <li>debug parameter</li>
287 <li>showbutton parameter</li>
289 <em>Applet API methods</em>
291 <li>newView public method</li>
292 <li>Window (current view) specific get/set public methods</li>
293 <li>Feature display control methods</li>
294 <li>get list of currently selected sequences</li>
296 <em>New Jalview distribution features</em>
298 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
299 <li>RELEASE file gives build properties for the latest Jalview
301 <li>Java 1.1 Applet build made easier and donotobfuscate property
302 controls execution of obfuscator</li>
303 <li>Build target for generating source distribution</li>
304 <li>Debug flag for javacc</li>
305 <li>.jalview_properties file is documented (slightly) in
306 jalview.bin.Cache</li>
307 <li>Continuous Build Integration for stable and development
308 version of Application, Applet and source distribution</li>
314 <li>selected region output includes visible annotations (for
315 certain formats)</li>
316 <li>edit label/displaychar contains existing label/char for
318 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
319 <li>shorter peptide product names from EMBL records</li>
320 <li>Newick string generator makes compact representations</li>
321 <li>bootstrap values parsed correctly for tree files with comments</li>
322 <li>pathological filechooser bug avoided by not allowing filenames
323 containing a ':'</li>
324 <li>Fixed exception when parsing GFF files containing global
325 sequence features</li>
326 <li>Alignment datasets are finalized only when number of
327 references from alignment sequences goes to zero</li>
328 <li>Close of tree branch colour box without colour selection
329 causes cascading exceptions</li>
330 <li>occasional negative imgwidth exceptions</li>
331 <li>better reporting of non-fatal warnings to user when file
333 <li>Save works when Jalview project is default format</li>
334 <li>Save as dialog opened if current alignment format is not a
335 valid output format</li>
336 <li>Uniprot canonical names introduced for both das and vamsas</li>
337 <li>Histidine should be midblue (not pink!) in Zappo</li>
338 <li>error messages passed up and output when data read fails</li>
339 <li>edit undo recovers previous dataset sequence when sequence is
341 <li>allow PDB files without pdb ID HEADER lines (like those
342 generated by MODELLER) to be read in properly</li>
343 <li>allow reading of JPred concise files as a normal filetype</li>
344 <li>Stockholm annotation parsing and alignment properties import
345 fixed for PFAM records</li>
346 <li>Structure view windows have correct name in Desktop window
348 <li>annotation consisting of sequence associated scores can be
349 read and written correctly to annotation file</li>
350 <li>Aligned cDNA translation to aligned peptide works correctly</li>
351 <li>Fixed display of hidden sequence markers and non-italic font
352 for representatives in Applet</li>
353 <li>Applet Menus are always embedded in applet window on Macs.</li>
354 <li>Newly shown features appear at top of stack (in Applet)</li>
355 <li>Annotations added via parameter not drawn properly due to null
356 pointer exceptions</li>
357 <li>Secondary structure lines are drawn starting from first column
359 <li>Uniprot XML import updated for new schema release in July 2008</li>
360 <li>Sequence feature to sequence ID match for Features file is
361 case-insensitive</li>
362 <li>Sequence features read from Features file appended to all
363 sequences with matching IDs</li>
364 <li>PDB structure coloured correctly for associated views
365 containing a sub-sequence</li>
366 <li>PDB files can be retrieved by applet from Jar files</li>
367 <li>feature and annotation file applet parameters referring to
368 different directories are retrieved correctly</li>
369 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
370 <li>Fixed application hang whilst waiting for splash-screen
371 version check to complete</li>
372 <li>Applet properly URLencodes input parameter values when passing
373 them to the launchApp service</li>
374 <li>display name and local features preserved in results retrieved
375 from web service</li>
376 <li>Visual delay indication for sequence retrieval and sequence
377 fetcher initialisation</li>
378 <li>updated Application to use DAS 1.53e version of dasobert DAS
380 <li>Re-instated Full AMSA support and .amsa file association</li>
381 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
388 <div align="center"><strong>2.3</strong><br>
393 <li>Jmol 11.0.2 integration</li>
394 <li>PDB views stored in Jalview XML files</li>
395 <li>Slide sequences</li>
396 <li>Edit sequence in place</li>
397 <li>EMBL CDS features</li>
398 <li>DAS Feature mapping</li>
399 <li>Feature ordering</li>
400 <li>Alignment Properties</li>
401 <li>Annotation Scores</li>
402 <li>Sort by scores</li>
403 <li>Feature/annotation editing in applet</li>
408 <li>Headless state operation in 2.2.1</li>
409 <li>Incorrect and unstable DNA pairwise alignment</li>
410 <li>Cut and paste of sequences with annotation</li>
411 <li>Feature group display state in XML</li>
412 <li>Feature ordering in XML</li>
413 <li>blc file iteration selection using filename # suffix</li>
414 <li>Stockholm alignment properties</li>
415 <li>Stockhom alignment secondary structure annotation</li>
416 <li>2.2.1 applet had no feature transparency</li>
417 <li>Number pad keys can be used in cursor mode</li>
418 <li>Structure Viewer mirror image resolved</li>
425 <div align="center"><strong>2.2.1</strong><br>
430 <li>Non standard characters can be read and displayed
431 <li>Annotations/Features can be imported/exported to the applet
433 <li>Applet allows editing of sequence/annotation/group name &
435 <li>Preference setting to display sequence name in italics
436 <li>Annotation file format extended to allow Sequence_groups to
438 <li>Default opening of alignment overview panel can be specified
440 <li>PDB residue numbering annotation added to associated
446 <li>Applet crash under certain Linux OS with Java 1.6 installed
447 <li>Annotation file export / import bugs fixed
448 <li>PNG / EPS image output bugs fixed
454 <div align="center"><strong>2.2</strong><br>
459 <li>Multiple views on alignment
460 <li>Sequence feature editing
461 <li>"Reload" alignment
462 <li>"Save" to current filename
463 <li>Background dependent text colour
464 <li>Right align sequence ids
465 <li>User-defined lower case residue colours
468 <li>Menu item accelerator keys
469 <li>Control-V pastes to current alignment
470 <li>Cancel button for DAS Feature Fetching
471 <li>PCA and PDB Viewers zoom via mouse roller
472 <li>User-defined sub-tree colours and sub-tree selection
473 <li>'New Window' button on the 'Output to Text box'
478 <li>New memory efficient Undo/Redo System
479 <li>Optimised symbol lookups and conservation/consensus
481 <li>Region Conservation/Consensus recalculated after edits
482 <li>Fixed Remove Empty Columns Bug (empty columns at end of
484 <li>Slowed DAS Feature Fetching for increased robustness.
485 <li>Made angle brackets in ASCII feature descriptions display
487 <li>Re-instated Zoom function for PCA
488 <li>Sequence descriptions conserved in web service analysis
490 <li>Uniprot ID discoverer uses any word separated by ∣
491 <li>WsDbFetch query/result association resolved
492 <li>Tree leaf to sequence mapping improved
493 <li>Smooth fonts switch moved to FontChooser dialog box.
499 <div align="center"><strong>2.1.1</strong><br>
504 <li>Copy consensus sequence to clipboard</li>
509 <li>Image output - rightmost residues are rendered if sequence id
510 panel has been resized</li>
511 <li>Image output - all offscreen group boundaries are rendered</li>
512 <li>Annotation files with sequence references - all elements in
513 file are relative to sequence position</li>
514 <li>Mac Applet users can use Alt key for group editing</li>
520 <div align="center"><strong>2.1</strong><br>
525 <li>MAFFT Multiple Alignment in default Web Service list</li>
526 <li>DAS Feature fetching</li>
527 <li>Hide sequences and columns</li>
528 <li>Export Annotations and Features</li>
529 <li>GFF file reading / writing</li>
530 <li>Associate structures with sequences from local PDB files</li>
531 <li>Add sequences to exisiting alignment</li>
532 <li>Recently opened files / URL lists</li>
533 <li>Applet can launch the full application</li>
534 <li>Applet has transparency for features (Java 1.2 required)</li>
535 <li>Applet has user defined colours parameter</li>
536 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
541 <li>Redundancy Panel reinstalled in the Applet</li>
542 <li>Monospaced font - EPS / rescaling bug fixed</li>
543 <li>Annotation files with sequence references bug fixed</li>
549 <div align="center"><strong>2.08.1</strong><br>
554 <li>Change case of selected region from Popup menu</li>
555 <li>Choose to match case when searching</li>
556 <li>Middle mouse button and mouse movement can compress / expand
557 the visible width and height of the alignment</li>
562 <li>Annotation Panel displays complete JNet results</li>
568 <div align="center"><strong>2.08b</strong><br>
574 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
575 <li>Righthand label on wrapped alignments shows correct value</li>
581 <div align="center"><strong>2.08</strong><br>
586 <li>Editing can be locked to the selection area</li>
587 <li>Keyboard editing</li>
588 <li>Create sequence features from searches</li>
589 <li>Precalculated annotations can be loaded onto alignments</li>
590 <li>Features file allows grouping of features</li>
591 <li>Annotation Colouring scheme added</li>
592 <li>Smooth fonts off by default - Faster rendering</li>
593 <li>Choose to toggle Autocalculate Consensus On/Off</li>
598 <li>Drag & Drop fixed on Linux</li>
599 <li>Jalview Archive file faster to load/save, sequence
600 descriptions saved.</li>
606 <div align="center"><strong>2.07</strong><br>
611 <li>PDB Structure Viewer enhanced</li>
612 <li>Sequence Feature retrieval and display enhanced</li>
613 <li>Choose to output sequence start-end after sequence name for
615 <li>Sequence Fetcher WSDBFetch@EBI</li>
616 <li>Applet can read feature files, PDB files and can be used for
622 <li>HTML output writes groups and features</li>
623 <li>Group editing is Control and mouse click</li>
624 <li>File IO bugs</li>
630 <div align="center"><strong>2.06</strong><br>
635 <li>View annotations in wrapped mode</li>
636 <li>More options for PCA viewer</li>
641 <li>GUI bugs resolved</li>
642 <li>Runs with -nodisplay from command line</li>
648 <div align="center"><strong>2.05b</strong><br>
653 <li>Choose EPS export as lineart or text</li>
654 <li>Jar files are executable</li>
655 <li>Can read in Uracil - maps to unknown residue</li>
660 <li>Known OutOfMemory errors give warning message</li>
661 <li>Overview window calculated more efficiently</li>
662 <li>Several GUI bugs resolved</li>
668 <div align="center"><strong>2.05</strong><br>
673 <li>Edit and annotate in "Wrapped" view</li>
678 <li>Several GUI bugs resolved</li>
684 <div align="center"><strong>2.04</strong><br>
689 <li>Hold down mouse wheel & scroll to change font size</li>
694 <li>Improved JPred client reliability</li>
695 <li>Improved loading of Jalview files</li>
701 <div align="center"><strong>2.03</strong><br>
706 <li>Set Proxy server name and port in preferences</li>
707 <li>Multiple URL links from sequence ids</li>
708 <li>User Defined Colours can have a scheme name and added to
710 <li>Choose to ignore gaps in consensus calculation</li>
711 <li>Unix users can set default web browser</li>
712 <li>Runs without GUI for batch processing</li>
713 <li>Dynamically generated Web Service Menus</li>
718 <li>InstallAnywhere download for Sparc Solaris</li>
724 <div align="center"><strong>2.02</strong><br>
730 <li>Copy & Paste order of sequences maintains alignment
737 <div align="center"><strong>2.01</strong><br>
742 <li>Use delete key for deleting selection.</li>
743 <li>Use Mouse wheel to scroll sequences.</li>
744 <li>Help file updated to describe how to add alignment
746 <li>Version and build date written to build properties file.</li>
747 <li>InstallAnywhere installation will check for updates at launch
753 <li>Delete gaps bug fixed.</li>
754 <li>FileChooser sorts columns.</li>
755 <li>Can remove groups one by one.</li>
756 <li>Filechooser icons installed.</li>
757 <li>Finder ignores return character when searching. Return key
758 will initiate a search.<br>
765 <div align="center"><strong>2.0</strong><br>
770 <li>New codebase</li>