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>
38 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
39 <em>14/6/2010</em></div>
44 <li>Alignment prettyprinter doesn't cope with long sequence IDs
46 <li>clustalx colourscheme colours Ds preferentially when both
47 D+E are present in over 50% of the column</li>
48 <li>nucleic acid structures retrieved from PDB do not import
50 <li>More columns get selected than were clicked on when a number
51 of columns are hidden</li>
52 <li>annotation label popup menu not providing correct
53 add/hide/show options when rows are hidden or none are present</li>
54 <li>Stockholm format shown in list of readable formats, and
55 parser copes better with alignments from RFAM.</li>
56 <li>CSV output of consensus only includes the percentage of all
57 symbols if sequence logo display is enabled</li>
62 <li>annotation panel disappears when annotation is
67 <li>Alignment view not redrawn properly when new alignment
68 opened where annotation panel is visible but no annotations are
69 present on alignment</li>
70 <li>pasted region containing hidden columns is incorrectly
71 displayed in new alignment window</li>
72 <li>Jalview slow to complete operations when stdout is flooded
73 (fix is to close the Jalview console)</li>
74 <li>typo in AlignmentFrame->View->Hide->all but
75 selected Rregions menu item.</li>
76 <li>inconsistent group submenu and Format submenu entry 'Un' or
78 <li>Sequence feature settings are being shared by multiple
79 distinct alignments</li>
80 <li>group annotation not recreated when tree partition is
82 <li>double click on group annotation to select sequences does
83 not propagate to associated trees</li>
84 <li>Mac OSX specific issues:
86 <li>exception raised when mouse clicked on desktop window
88 <li>Desktop menu placed on menu bar and application name set
90 <li>sequence feature settings not wide enough for the save
91 feature colourscheme button</li>
100 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
101 <em>30/4/2010</em></div>
104 <em>New Capabilities</em>
106 <li>URL links generated from description line for
107 regular-expression based URL links (applet and application)
108 <li>Non-positional feature URL links are shown in link menu</li>
109 <li>Linked viewing of nucleic acid sequences and structures</li>
110 <li>Automatic Scrolling option in View menu to display the
111 currently highlighted region of an alignment.</li>
112 <li>Order an alignment by sequence length, or using the average score or total feature count for each sequence.</li>
113 <li>Shading features by score or associated description</li>
114 <li>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
115 <li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</li>
116 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
120 <li>Fetch DB References capabilities and UI expanded to support
121 retrieval from DAS sequence sources</li>
122 <li>Local DAS Sequence sources can be added via the command line
123 or via the Add local source dialog box.</li>
124 <li>DAS Dbref and DbxRef feature types are parsed as database
125 references and protein_name is parsed as description line (BioSapiens
127 <li>Enable or disable non-positional feature and database
128 references in sequence ID tooltip from View menu in application.</li>
129 <!-- <li>New hidden columns and rows and representatives capabilities
130 in annotations file (in progress - not yet fully implemented)</li> -->
131 <li>Group-associated consensus, sequence logos and conservation
133 <li>Symbol distributions for each column can be exported and
134 visualized as sequence logos</li>
135 <li>Optionally scale multi-character column labels to fit within
136 each column of annotation row<!-- todo for applet --></li>
137 <li>Optional automatic sort of associated alignment view when a
138 new tree is opened.</li>
139 <li>Jalview Java Console</li>
140 <li>Better placement of desktop window when moving between different screens.</li>
141 <li>New preference items for sequence ID tooltip and consensus
143 <li>Client to submit sequences and IDs to <a
144 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
145 <li><em>Vamsas Capabilities</em>
147 <li>Improved VAMSAS synchronization (jalview archive used to
148 preserve views, structures, and tree display settings)</li>
149 <li>Import of vamsas documents from disk or URL via command line</li>
150 <li>Sharing of selected regions between views and with other
151 VAMSAS applications (Experimental feature!)</li>
152 <li>Updated API to VAMSAS version 0.2</li>
158 <li>Middle button resizes annotation row height</li>
161 <li>sortByTree (true/false) - automatically sort the associated
162 alignment view by the tree when a new tree is opened.</li>
163 <li>showTreeBootstraps (true/false) - show or hide branch
164 bootstraps (default is to show them if available)</li>
165 <li>showTreeDistances (true/false) - show or hide branch lengths
166 (default is to show them if available)</li>
167 <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated
168 nodes should be highlighted in the tree view</li>
169 <li>heightScale and widthScale (1.0 or more) - increase the
170 height or width of a cell in the alignment grid relative to the
171 current font size.</li>
174 <li>Non-positional features displayed in sequence ID tooltip</li>
178 <li>Features format: graduated colour definitions and
179 specification of feature scores</li>
180 <li>Alignment Annotations format: new keywords for group
181 associated annotation (GROUP_REF) and annotation row display properties
182 (ROW_PROPERTIES)</li>
183 <li>XML formats extended to support graduated feature
184 colourschemes, group associated annotation, and profile visualization
189 <li>Source field in GFF files parsed as feature source rather
190 than description</li>
191 <li>Non-positional features are now included in sequence feature
192 and gff files (controlled via non-positional feature visibility in
194 <li>URL links generated for all feature links (bugfix)</li>
195 <li>Added URL embedding instructions to features file
197 <li>Codons containing ambiguous nucleotides translated as 'X' in
199 <li>Match case switch in find dialog box works for both sequence
200 ID and sequence string and query strings do not have to be in upper
201 case to match case-insensitively.</li>
202 <li>AMSA files only contain first column of multi-character
203 column annotation labels</li>
204 <li>Jalview Annotation File generation/parsing consistent with
205 documentation (e.g. Stockholm annotation can be exported and
207 <li>PDB files without embedded PDB IDs given a friendly name</li>
208 <li>Find incrementally searches ID string matches as well as
209 subsequence matches, and correctly reports total number of both.</li>
212 <li>Better handling of exceptions during sequence retrieval</li>
213 <li>Dasobert generated non-positional feature URL link text
214 excludes the start_end suffix</li>
215 <li>DAS feature and source retrieval buttons disabled when fetch
216 or registry operations in progress.</li>
217 <li>PDB files retrieved from URLs are cached properly</li>
218 <li>Sequence description lines properly shared via VAMSAS</li>
219 <li>Sequence fetcher fetches multiple records for all data
221 <li>Ensured that command line das feature retrieval completes
222 before alignment figures are generated.</li>
223 <li>Reduced time taken when opening file browser for first time.</li>
224 <li>isAligned check prior to calculating tree, PCA or submitting
225 an MSA to JNet now excludes hidden sequences.</li>
226 <li>User defined group colours properly recovered from Jalview projects.</li>
235 <div align="center"><strong>2.4.0.b2</strong><br>
240 <li>Experimental support for google analytics usage tracking.</li>
241 <li>Jalview privacy settings (user preferences and docs).</li>
246 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
247 <li>Exception when feature created from selection beyond length
249 <li>Allow synthetic PDB files to be imported gracefully</li>
250 <li>Sequence associated annotation rows associate with all
251 sequences with a given id</li>
252 <li>Find function matches case-insensitively for sequence ID
254 <li>Non-standard characters do not cause pairwise alignment to
255 fail with exception</li>
257 <em>Application Issues</em>
259 <li>Sequences are now validated against EMBL database</li>
260 <li>Sequence fetcher fetches multiple records for all data
263 <em>InstallAnywhere Issues</em>
265 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
266 installAnywhere mechanism)</li>
267 <li>Command line launching of JARs from InstallAnywhere version
268 (java class versioning error fixed)</li>
275 <div align="center"><strong>2.4</strong><br>
278 <td><em>User Interface</em>
280 <li>Linked highlighting of codon and amino acid from translation
281 and protein products</li>
282 <li>Linked highlighting of structure associated with residue
283 mapping to codon position</li>
284 <li>Sequence Fetcher provides example accession numbers and
286 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
287 <li>Extract score function to parse whitespace separated numeric
288 data in description line</li>
289 <li>Column labels in alignment annotation can be centred.</li>
290 <li>Tooltip for sequence associated annotation give name of
293 <em>Web Services and URL fetching</em>
295 <li>JPred3 web service</li>
296 <li>Prototype sequence search client (no public services
298 <li>Fetch either seed alignment or full alignment from PFAM</li>
299 <li>URL Links created for matching database cross references as
300 well as sequence ID</li>
301 <li>URL Links can be created using regular-expressions</li>
303 <em>Sequence Database Connectivity</em>
305 <li>Retrieval of cross-referenced sequences from other databases
307 <li>Generalised database reference retrieval and validation to
308 all fetchable databases</li>
309 <li>Fetch sequences from DAS sources supporting the sequence
312 <em>Import and Export</em>
313 <li>export annotation rows as CSV for spreadsheet import</li>
314 <li>Jalview projects record alignment dataset associations, EMBL
315 products, and cDNA sequence mappings</li>
316 <li>Sequence Group colour can be specified in Annotation File</li>
317 <li>Ad-hoc colouring of group in Annotation File using RGB
318 triplet as name of colourscheme</li>
320 <em>VAMSAS Client capabilities (Experimental)</em>
322 <li>treenode binding for VAMSAS tree exchange</li>
323 <li>local editing and update of sequences in VAMSAS alignments
325 <li>Create new or select existing session to join</li>
326 <li>load and save of vamsas documents</li>
328 <em>Application command line</em>
330 <li>-tree parameter to open trees (introduced for passing from
332 <li>-fetchfrom command line argument to specify nicknames of DAS
333 servers to query for alignment features</li>
334 <li>-dasserver command line argument to add new servers that are
335 also automatically queried for features</li>
336 <li>-groovy command line argument executes a given groovy script
337 after all input data has been loaded and parsed</li>
339 <em>Applet-Application data exchange</em>
341 <li>Trees passed as applet parameters can be passed to application
342 (when using "View in full application")</li>
344 <em>Applet Parameters</em>
346 <li>feature group display control parameter</li>
347 <li>debug parameter</li>
348 <li>showbutton parameter</li>
350 <em>Applet API methods</em>
352 <li>newView public method</li>
353 <li>Window (current view) specific get/set public methods</li>
354 <li>Feature display control methods</li>
355 <li>get list of currently selected sequences</li>
357 <em>New Jalview distribution features</em>
359 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
360 <li>RELEASE file gives build properties for the latest Jalview
362 <li>Java 1.1 Applet build made easier and donotobfuscate property
363 controls execution of obfuscator</li>
364 <li>Build target for generating source distribution</li>
365 <li>Debug flag for javacc</li>
366 <li>.jalview_properties file is documented (slightly) in
367 jalview.bin.Cache</li>
368 <li>Continuous Build Integration for stable and development
369 version of Application, Applet and source distribution</li>
375 <li>selected region output includes visible annotations (for
376 certain formats)</li>
377 <li>edit label/displaychar contains existing label/char for
379 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
380 <li>shorter peptide product names from EMBL records</li>
381 <li>Newick string generator makes compact representations</li>
382 <li>bootstrap values parsed correctly for tree files with comments</li>
383 <li>pathological filechooser bug avoided by not allowing filenames
384 containing a ':'</li>
385 <li>Fixed exception when parsing GFF files containing global
386 sequence features</li>
387 <li>Alignment datasets are finalized only when number of
388 references from alignment sequences goes to zero</li>
389 <li>Close of tree branch colour box without colour selection
390 causes cascading exceptions</li>
391 <li>occasional negative imgwidth exceptions</li>
392 <li>better reporting of non-fatal warnings to user when file
394 <li>Save works when Jalview project is default format</li>
395 <li>Save as dialog opened if current alignment format is not a
396 valid output format</li>
397 <li>Uniprot canonical names introduced for both das and vamsas</li>
398 <li>Histidine should be midblue (not pink!) in Zappo</li>
399 <li>error messages passed up and output when data read fails</li>
400 <li>edit undo recovers previous dataset sequence when sequence is
402 <li>allow PDB files without pdb ID HEADER lines (like those
403 generated by MODELLER) to be read in properly</li>
404 <li>allow reading of JPred concise files as a normal filetype</li>
405 <li>Stockholm annotation parsing and alignment properties import
406 fixed for PFAM records</li>
407 <li>Structure view windows have correct name in Desktop window
409 <li>annotation consisting of sequence associated scores can be
410 read and written correctly to annotation file</li>
411 <li>Aligned cDNA translation to aligned peptide works correctly</li>
412 <li>Fixed display of hidden sequence markers and non-italic font
413 for representatives in Applet</li>
414 <li>Applet Menus are always embedded in applet window on Macs.</li>
415 <li>Newly shown features appear at top of stack (in Applet)</li>
416 <li>Annotations added via parameter not drawn properly due to null
417 pointer exceptions</li>
418 <li>Secondary structure lines are drawn starting from first column
420 <li>Uniprot XML import updated for new schema release in July 2008</li>
421 <li>Sequence feature to sequence ID match for Features file is
422 case-insensitive</li>
423 <li>Sequence features read from Features file appended to all
424 sequences with matching IDs</li>
425 <li>PDB structure coloured correctly for associated views
426 containing a sub-sequence</li>
427 <li>PDB files can be retrieved by applet from Jar files</li>
428 <li>feature and annotation file applet parameters referring to
429 different directories are retrieved correctly</li>
430 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
431 <li>Fixed application hang whilst waiting for splash-screen
432 version check to complete</li>
433 <li>Applet properly URLencodes input parameter values when passing
434 them to the launchApp service</li>
435 <li>display name and local features preserved in results retrieved
436 from web service</li>
437 <li>Visual delay indication for sequence retrieval and sequence
438 fetcher initialisation</li>
439 <li>updated Application to use DAS 1.53e version of dasobert DAS
441 <li>Re-instated Full AMSA support and .amsa file association</li>
442 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
449 <div align="center"><strong>2.3</strong><br>
454 <li>Jmol 11.0.2 integration</li>
455 <li>PDB views stored in Jalview XML files</li>
456 <li>Slide sequences</li>
457 <li>Edit sequence in place</li>
458 <li>EMBL CDS features</li>
459 <li>DAS Feature mapping</li>
460 <li>Feature ordering</li>
461 <li>Alignment Properties</li>
462 <li>Annotation Scores</li>
463 <li>Sort by scores</li>
464 <li>Feature/annotation editing in applet</li>
469 <li>Headless state operation in 2.2.1</li>
470 <li>Incorrect and unstable DNA pairwise alignment</li>
471 <li>Cut and paste of sequences with annotation</li>
472 <li>Feature group display state in XML</li>
473 <li>Feature ordering in XML</li>
474 <li>blc file iteration selection using filename # suffix</li>
475 <li>Stockholm alignment properties</li>
476 <li>Stockhom alignment secondary structure annotation</li>
477 <li>2.2.1 applet had no feature transparency</li>
478 <li>Number pad keys can be used in cursor mode</li>
479 <li>Structure Viewer mirror image resolved</li>
486 <div align="center"><strong>2.2.1</strong><br>
491 <li>Non standard characters can be read and displayed
492 <li>Annotations/Features can be imported/exported to the applet
494 <li>Applet allows editing of sequence/annotation/group name &
496 <li>Preference setting to display sequence name in italics
497 <li>Annotation file format extended to allow Sequence_groups to
499 <li>Default opening of alignment overview panel can be specified
501 <li>PDB residue numbering annotation added to associated
507 <li>Applet crash under certain Linux OS with Java 1.6 installed
508 <li>Annotation file export / import bugs fixed
509 <li>PNG / EPS image output bugs fixed
515 <div align="center"><strong>2.2</strong><br>
520 <li>Multiple views on alignment
521 <li>Sequence feature editing
522 <li>"Reload" alignment
523 <li>"Save" to current filename
524 <li>Background dependent text colour
525 <li>Right align sequence ids
526 <li>User-defined lower case residue colours
529 <li>Menu item accelerator keys
530 <li>Control-V pastes to current alignment
531 <li>Cancel button for DAS Feature Fetching
532 <li>PCA and PDB Viewers zoom via mouse roller
533 <li>User-defined sub-tree colours and sub-tree selection
534 <li>'New Window' button on the 'Output to Text box'
539 <li>New memory efficient Undo/Redo System
540 <li>Optimised symbol lookups and conservation/consensus
542 <li>Region Conservation/Consensus recalculated after edits
543 <li>Fixed Remove Empty Columns Bug (empty columns at end of
545 <li>Slowed DAS Feature Fetching for increased robustness.
546 <li>Made angle brackets in ASCII feature descriptions display
548 <li>Re-instated Zoom function for PCA
549 <li>Sequence descriptions conserved in web service analysis
551 <li>Uniprot ID discoverer uses any word separated by ∣
552 <li>WsDbFetch query/result association resolved
553 <li>Tree leaf to sequence mapping improved
554 <li>Smooth fonts switch moved to FontChooser dialog box.
560 <div align="center"><strong>2.1.1</strong><br>
565 <li>Copy consensus sequence to clipboard</li>
570 <li>Image output - rightmost residues are rendered if sequence id
571 panel has been resized</li>
572 <li>Image output - all offscreen group boundaries are rendered</li>
573 <li>Annotation files with sequence references - all elements in
574 file are relative to sequence position</li>
575 <li>Mac Applet users can use Alt key for group editing</li>
581 <div align="center"><strong>2.1</strong><br>
586 <li>MAFFT Multiple Alignment in default Web Service list</li>
587 <li>DAS Feature fetching</li>
588 <li>Hide sequences and columns</li>
589 <li>Export Annotations and Features</li>
590 <li>GFF file reading / writing</li>
591 <li>Associate structures with sequences from local PDB files</li>
592 <li>Add sequences to exisiting alignment</li>
593 <li>Recently opened files / URL lists</li>
594 <li>Applet can launch the full application</li>
595 <li>Applet has transparency for features (Java 1.2 required)</li>
596 <li>Applet has user defined colours parameter</li>
597 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
602 <li>Redundancy Panel reinstalled in the Applet</li>
603 <li>Monospaced font - EPS / rescaling bug fixed</li>
604 <li>Annotation files with sequence references bug fixed</li>
610 <div align="center"><strong>2.08.1</strong><br>
615 <li>Change case of selected region from Popup menu</li>
616 <li>Choose to match case when searching</li>
617 <li>Middle mouse button and mouse movement can compress / expand
618 the visible width and height of the alignment</li>
623 <li>Annotation Panel displays complete JNet results</li>
629 <div align="center"><strong>2.08b</strong><br>
635 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
636 <li>Righthand label on wrapped alignments shows correct value</li>
642 <div align="center"><strong>2.08</strong><br>
647 <li>Editing can be locked to the selection area</li>
648 <li>Keyboard editing</li>
649 <li>Create sequence features from searches</li>
650 <li>Precalculated annotations can be loaded onto alignments</li>
651 <li>Features file allows grouping of features</li>
652 <li>Annotation Colouring scheme added</li>
653 <li>Smooth fonts off by default - Faster rendering</li>
654 <li>Choose to toggle Autocalculate Consensus On/Off</li>
659 <li>Drag & Drop fixed on Linux</li>
660 <li>Jalview Archive file faster to load/save, sequence
661 descriptions saved.</li>
667 <div align="center"><strong>2.07</strong><br>
672 <li>PDB Structure Viewer enhanced</li>
673 <li>Sequence Feature retrieval and display enhanced</li>
674 <li>Choose to output sequence start-end after sequence name for
676 <li>Sequence Fetcher WSDBFetch@EBI</li>
677 <li>Applet can read feature files, PDB files and can be used for
683 <li>HTML output writes groups and features</li>
684 <li>Group editing is Control and mouse click</li>
685 <li>File IO bugs</li>
691 <div align="center"><strong>2.06</strong><br>
696 <li>View annotations in wrapped mode</li>
697 <li>More options for PCA viewer</li>
702 <li>GUI bugs resolved</li>
703 <li>Runs with -nodisplay from command line</li>
709 <div align="center"><strong>2.05b</strong><br>
714 <li>Choose EPS export as lineart or text</li>
715 <li>Jar files are executable</li>
716 <li>Can read in Uracil - maps to unknown residue</li>
721 <li>Known OutOfMemory errors give warning message</li>
722 <li>Overview window calculated more efficiently</li>
723 <li>Several GUI bugs resolved</li>
729 <div align="center"><strong>2.05</strong><br>
734 <li>Edit and annotate in "Wrapped" view</li>
739 <li>Several GUI bugs resolved</li>
745 <div align="center"><strong>2.04</strong><br>
750 <li>Hold down mouse wheel & scroll to change font size</li>
755 <li>Improved JPred client reliability</li>
756 <li>Improved loading of Jalview files</li>
762 <div align="center"><strong>2.03</strong><br>
767 <li>Set Proxy server name and port in preferences</li>
768 <li>Multiple URL links from sequence ids</li>
769 <li>User Defined Colours can have a scheme name and added to
771 <li>Choose to ignore gaps in consensus calculation</li>
772 <li>Unix users can set default web browser</li>
773 <li>Runs without GUI for batch processing</li>
774 <li>Dynamically generated Web Service Menus</li>
779 <li>InstallAnywhere download for Sparc Solaris</li>
785 <div align="center"><strong>2.02</strong><br>
791 <li>Copy & Paste order of sequences maintains alignment
798 <div align="center"><strong>2.01</strong><br>
803 <li>Use delete key for deleting selection.</li>
804 <li>Use Mouse wheel to scroll sequences.</li>
805 <li>Help file updated to describe how to add alignment
807 <li>Version and build date written to build properties file.</li>
808 <li>InstallAnywhere installation will check for updates at launch
814 <li>Delete gaps bug fixed.</li>
815 <li>FileChooser sorts columns.</li>
816 <li>Can remove groups one by one.</li>
817 <li>Filechooser icons installed.</li>
818 <li>Finder ignores return character when searching. Return key
819 will initiate a search.<br>
826 <div align="center"><strong>2.0</strong><br>
831 <li>New codebase</li>