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.</li>
58 <li>annotation panel disappears when annotation is
63 <li>Alignment view not redrawn properly when new alignment
64 opened where annotation panel is visible but no annotations are
65 present on alignment</li>
66 <li>pasted region containing hidden columns is incorrectly
67 displayed in new alignment window</li>
68 <li>Jalview slow to complete operations when stdout is flooded
69 (fix is to close the Jalview console)</li>
70 <li>CSV output of consensus only includes the percentage of all
71 symbols if sequence logo display is enabled</li>
72 <li>typo in AlignmentFrame->View->Hide->all but
73 selected Rregions menu item.</li>
74 <li>inconsistent group submenu and Format submenu entry 'Un' or
76 <li>Sequence feature settings are being shared by multiple
77 distinct alignments</li>
78 <li>group annotation not recreated when tree partition is
80 <li>double click on group annotation to select sequences does
81 not propagate to associated trees</li>
82 <li>Mac OSX specific issues:
84 <li>exception raised when mouse clicked on desktop window
86 <li>Desktop menu placed on menu bar and application name set
88 <li>sequence feature settings not wide enough for the save
89 feature colourscheme button</li>
98 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
99 <em>30/4/2010</em></div>
101 <td><em>New Capabilities</em>
103 <li>URL links generated from description line for
104 regular-expression based URL links (applet and application)
105 <li>Non-positional feature URL links are shown in link menu</li>
106 <li>Linked viewing of nucleic acid sequences and structures</li>
107 <li>Automatic Scrolling option in View menu to display the
108 currently highlighted region of an alignment.</li>
109 <li>Order an alignment by sequence length, or using the average
110 score or total feature count for each sequence.</li>
111 <li>Shading features by score or associated description</li>
112 <li>Subdivide alignment and groups based on identity of selected
113 subsequence (Make Groups from Selection).</li>
114 <li>New hide/show options including Shift+Control+H to hide
115 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
141 different screens.</li>
142 <li>New preference items for sequence ID tooltip and consensus
144 <li>Client to submit sequences and IDs to <a
145 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
146 <li><em>Vamsas Capabilities</em>
148 <li>Improved VAMSAS synchronization (jalview archive used to
149 preserve views, structures, and tree display settings)</li>
150 <li>Import of vamsas documents from disk or URL via command
152 <li>Sharing of selected regions between views and with other
153 VAMSAS applications (Experimental feature!)</li>
154 <li>Updated API to VAMSAS version 0.2</li>
160 <li>Middle button resizes annotation row height</li>
163 <li>sortByTree (true/false) - automatically sort the associated
164 alignment view by the tree when a new tree is opened.</li>
165 <li>showTreeBootstraps (true/false) - show or hide branch
166 bootstraps (default is to show them if available)</li>
167 <li>showTreeDistances (true/false) - show or hide branch
168 lengths (default is to show them if available)</li>
169 <li>showUnlinkedTreeNodes (true/false) - indicate if
170 unassociated nodes should be highlighted in the tree view</li>
171 <li>heightScale and widthScale (1.0 or more) - increase the
172 height or width of a cell in the alignment grid relative to the
173 current font size.</li>
176 <li>Non-positional features displayed in sequence ID tooltip</li>
180 <li>Features format: graduated colour definitions and
181 specification of feature scores</li>
182 <li>Alignment Annotations format: new keywords for group
183 associated annotation (GROUP_REF) and annotation row display
184 properties (ROW_PROPERTIES)</li>
185 <li>XML formats extended to support graduated feature
186 colourschemes, group associated annotation, and profile visualization
191 <li>Source field in GFF files parsed as feature source rather
192 than description</li>
193 <li>Non-positional features are now included in sequence feature
194 and gff files (controlled via non-positional feature visibility in
196 <li>URL links generated for all feature links (bugfix)</li>
197 <li>Added URL embedding instructions to features file
199 <li>Codons containing ambiguous nucleotides translated as 'X' in
201 <li>Match case switch in find dialog box works for both sequence
202 ID and sequence string and query strings do not have to be in upper
203 case to match case-insensitively.</li>
204 <li>AMSA files only contain first column of multi-character
205 column annotation labels</li>
206 <li>Jalview Annotation File generation/parsing consistent with
207 documentation (e.g. Stockholm annotation can be exported and
209 <li>PDB files without embedded PDB IDs given a friendly name</li>
210 <li>Find incrementally searches ID string matches as well as
211 subsequence matches, and correctly reports total number of both.</li>
214 <li>Better handling of exceptions during sequence retrieval</li>
215 <li>Dasobert generated non-positional feature URL link text
216 excludes the start_end suffix</li>
217 <li>DAS feature and source retrieval buttons disabled when
218 fetch or registry operations in progress.</li>
219 <li>PDB files retrieved from URLs are cached properly</li>
220 <li>Sequence description lines properly shared via VAMSAS</li>
221 <li>Sequence fetcher fetches multiple records for all data
223 <li>Ensured that command line das feature retrieval completes
224 before alignment figures are generated.</li>
225 <li>Reduced time taken when opening file browser for first
227 <li>isAligned check prior to calculating tree, PCA or
228 submitting an MSA to JNet now excludes hidden sequences.</li>
229 <li>User defined group colours properly recovered from Jalview
239 <div align="center"><strong>2.4.0.b2</strong><br>
244 <li>Experimental support for google analytics usage tracking.</li>
245 <li>Jalview privacy settings (user preferences and docs).</li>
250 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
251 <li>Exception when feature created from selection beyond length
253 <li>Allow synthetic PDB files to be imported gracefully</li>
254 <li>Sequence associated annotation rows associate with all
255 sequences with a given id</li>
256 <li>Find function matches case-insensitively for sequence ID
258 <li>Non-standard characters do not cause pairwise alignment to
259 fail with exception</li>
261 <em>Application Issues</em>
263 <li>Sequences are now validated against EMBL database</li>
264 <li>Sequence fetcher fetches multiple records for all data
267 <em>InstallAnywhere Issues</em>
269 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
270 installAnywhere mechanism)</li>
271 <li>Command line launching of JARs from InstallAnywhere version
272 (java class versioning error fixed)</li>
279 <div align="center"><strong>2.4</strong><br>
282 <td><em>User Interface</em>
284 <li>Linked highlighting of codon and amino acid from translation
285 and protein products</li>
286 <li>Linked highlighting of structure associated with residue
287 mapping to codon position</li>
288 <li>Sequence Fetcher provides example accession numbers and
290 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
291 <li>Extract score function to parse whitespace separated numeric
292 data in description line</li>
293 <li>Column labels in alignment annotation can be centred.</li>
294 <li>Tooltip for sequence associated annotation give name of
297 <em>Web Services and URL fetching</em>
299 <li>JPred3 web service</li>
300 <li>Prototype sequence search client (no public services
302 <li>Fetch either seed alignment or full alignment from PFAM</li>
303 <li>URL Links created for matching database cross references as
304 well as sequence ID</li>
305 <li>URL Links can be created using regular-expressions</li>
307 <em>Sequence Database Connectivity</em>
309 <li>Retrieval of cross-referenced sequences from other databases
311 <li>Generalised database reference retrieval and validation to
312 all fetchable databases</li>
313 <li>Fetch sequences from DAS sources supporting the sequence
316 <em>Import and Export</em>
317 <li>export annotation rows as CSV for spreadsheet import</li>
318 <li>Jalview projects record alignment dataset associations, EMBL
319 products, and cDNA sequence mappings</li>
320 <li>Sequence Group colour can be specified in Annotation File</li>
321 <li>Ad-hoc colouring of group in Annotation File using RGB
322 triplet as name of colourscheme</li>
324 <em>VAMSAS Client capabilities (Experimental)</em>
326 <li>treenode binding for VAMSAS tree exchange</li>
327 <li>local editing and update of sequences in VAMSAS alignments
329 <li>Create new or select existing session to join</li>
330 <li>load and save of vamsas documents</li>
332 <em>Application command line</em>
334 <li>-tree parameter to open trees (introduced for passing from
336 <li>-fetchfrom command line argument to specify nicknames of DAS
337 servers to query for alignment features</li>
338 <li>-dasserver command line argument to add new servers that are
339 also automatically queried for features</li>
340 <li>-groovy command line argument executes a given groovy script
341 after all input data has been loaded and parsed</li>
343 <em>Applet-Application data exchange</em>
345 <li>Trees passed as applet parameters can be passed to
346 application (when using "View in full application")</li>
348 <em>Applet Parameters</em>
350 <li>feature group display control parameter</li>
351 <li>debug parameter</li>
352 <li>showbutton parameter</li>
354 <em>Applet API methods</em>
356 <li>newView public method</li>
357 <li>Window (current view) specific get/set public methods</li>
358 <li>Feature display control methods</li>
359 <li>get list of currently selected sequences</li>
361 <em>New Jalview distribution features</em>
363 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
364 <li>RELEASE file gives build properties for the latest Jalview
366 <li>Java 1.1 Applet build made easier and donotobfuscate
367 property controls execution of obfuscator</li>
368 <li>Build target for generating source distribution</li>
369 <li>Debug flag for javacc</li>
370 <li>.jalview_properties file is documented (slightly) in
371 jalview.bin.Cache</li>
372 <li>Continuous Build Integration for stable and development
373 version of Application, Applet and source distribution</li>
379 <li>selected region output includes visible annotations (for
380 certain formats)</li>
381 <li>edit label/displaychar contains existing label/char for
383 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
384 <li>shorter peptide product names from EMBL records</li>
385 <li>Newick string generator makes compact representations</li>
386 <li>bootstrap values parsed correctly for tree files with
388 <li>pathological filechooser bug avoided by not allowing
389 filenames containing a ':'</li>
390 <li>Fixed exception when parsing GFF files containing global
391 sequence features</li>
392 <li>Alignment datasets are finalized only when number of
393 references from alignment sequences goes to zero</li>
394 <li>Close of tree branch colour box without colour selection
395 causes cascading exceptions</li>
396 <li>occasional negative imgwidth exceptions</li>
397 <li>better reporting of non-fatal warnings to user when file
399 <li>Save works when Jalview project is default format</li>
400 <li>Save as dialog opened if current alignment format is not a
401 valid output format</li>
402 <li>Uniprot canonical names introduced for both das and vamsas</li>
403 <li>Histidine should be midblue (not pink!) in Zappo</li>
404 <li>error messages passed up and output when data read fails</li>
405 <li>edit undo recovers previous dataset sequence when sequence
407 <li>allow PDB files without pdb ID HEADER lines (like those
408 generated by MODELLER) to be read in properly</li>
409 <li>allow reading of JPred concise files as a normal filetype</li>
410 <li>Stockholm annotation parsing and alignment properties import
411 fixed for PFAM records</li>
412 <li>Structure view windows have correct name in Desktop window
414 <li>annotation consisting of sequence associated scores can be
415 read and written correctly to annotation file</li>
416 <li>Aligned cDNA translation to aligned peptide works correctly</li>
417 <li>Fixed display of hidden sequence markers and non-italic font
418 for representatives in Applet</li>
419 <li>Applet Menus are always embedded in applet window on Macs.</li>
420 <li>Newly shown features appear at top of stack (in Applet)</li>
421 <li>Annotations added via parameter not drawn properly due to
422 null pointer exceptions</li>
423 <li>Secondary structure lines are drawn starting from first
424 column of alignment</li>
425 <li>Uniprot XML import updated for new schema release in July
427 <li>Sequence feature to sequence ID match for Features file is
428 case-insensitive</li>
429 <li>Sequence features read from Features file appended to all
430 sequences with matching IDs</li>
431 <li>PDB structure coloured correctly for associated views
432 containing a sub-sequence</li>
433 <li>PDB files can be retrieved by applet from Jar files</li>
434 <li>feature and annotation file applet parameters referring to
435 different directories are retrieved correctly</li>
436 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
437 <li>Fixed application hang whilst waiting for splash-screen
438 version check to complete</li>
439 <li>Applet properly URLencodes input parameter values when
440 passing them to the launchApp service</li>
441 <li>display name and local features preserved in results
442 retrieved from web service</li>
443 <li>Visual delay indication for sequence retrieval and sequence
444 fetcher initialisation</li>
445 <li>updated Application to use DAS 1.53e version of dasobert DAS
447 <li>Re-instated Full AMSA support and .amsa file association</li>
448 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
455 <div align="center"><strong>2.3</strong><br>
460 <li>Jmol 11.0.2 integration</li>
461 <li>PDB views stored in Jalview XML files</li>
462 <li>Slide sequences</li>
463 <li>Edit sequence in place</li>
464 <li>EMBL CDS features</li>
465 <li>DAS Feature mapping</li>
466 <li>Feature ordering</li>
467 <li>Alignment Properties</li>
468 <li>Annotation Scores</li>
469 <li>Sort by scores</li>
470 <li>Feature/annotation editing in applet</li>
475 <li>Headless state operation in 2.2.1</li>
476 <li>Incorrect and unstable DNA pairwise alignment</li>
477 <li>Cut and paste of sequences with annotation</li>
478 <li>Feature group display state in XML</li>
479 <li>Feature ordering in XML</li>
480 <li>blc file iteration selection using filename # suffix</li>
481 <li>Stockholm alignment properties</li>
482 <li>Stockhom alignment secondary structure annotation</li>
483 <li>2.2.1 applet had no feature transparency</li>
484 <li>Number pad keys can be used in cursor mode</li>
485 <li>Structure Viewer mirror image resolved</li>
492 <div align="center"><strong>2.2.1</strong><br>
497 <li>Non standard characters can be read and displayed
498 <li>Annotations/Features can be imported/exported to the applet
500 <li>Applet allows editing of sequence/annotation/group name
502 <li>Preference setting to display sequence name in italics
503 <li>Annotation file format extended to allow Sequence_groups to
505 <li>Default opening of alignment overview panel can be specified
507 <li>PDB residue numbering annotation added to associated
513 <li>Applet crash under certain Linux OS with Java 1.6 installed
514 <li>Annotation file export / import bugs fixed
515 <li>PNG / EPS image output bugs fixed
521 <div align="center"><strong>2.2</strong><br>
526 <li>Multiple views on alignment
527 <li>Sequence feature editing
528 <li>"Reload" alignment
529 <li>"Save" to current filename
530 <li>Background dependent text colour
531 <li>Right align sequence ids
532 <li>User-defined lower case residue colours
535 <li>Menu item accelerator keys
536 <li>Control-V pastes to current alignment
537 <li>Cancel button for DAS Feature Fetching
538 <li>PCA and PDB Viewers zoom via mouse roller
539 <li>User-defined sub-tree colours and sub-tree selection
540 <li>'New Window' button on the 'Output to Text box'
545 <li>New memory efficient Undo/Redo System
546 <li>Optimised symbol lookups and conservation/consensus
548 <li>Region Conservation/Consensus recalculated after edits
549 <li>Fixed Remove Empty Columns Bug (empty columns at end of
551 <li>Slowed DAS Feature Fetching for increased robustness.
552 <li>Made angle brackets in ASCII feature descriptions display
554 <li>Re-instated Zoom function for PCA
555 <li>Sequence descriptions conserved in web service analysis
557 <li>Uniprot ID discoverer uses any word separated by ∣
558 <li>WsDbFetch query/result association resolved
559 <li>Tree leaf to sequence mapping improved
560 <li>Smooth fonts switch moved to FontChooser dialog box.
566 <div align="center"><strong>2.1.1</strong><br>
571 <li>Copy consensus sequence to clipboard</li>
576 <li>Image output - rightmost residues are rendered if sequence
577 id panel has been resized</li>
578 <li>Image output - all offscreen group boundaries are rendered</li>
579 <li>Annotation files with sequence references - all elements in
580 file are relative to sequence position</li>
581 <li>Mac Applet users can use Alt key for group editing</li>
587 <div align="center"><strong>2.1</strong><br>
592 <li>MAFFT Multiple Alignment in default Web Service list</li>
593 <li>DAS Feature fetching</li>
594 <li>Hide sequences and columns</li>
595 <li>Export Annotations and Features</li>
596 <li>GFF file reading / writing</li>
597 <li>Associate structures with sequences from local PDB files</li>
598 <li>Add sequences to exisiting alignment</li>
599 <li>Recently opened files / URL lists</li>
600 <li>Applet can launch the full application</li>
601 <li>Applet has transparency for features (Java 1.2 required)</li>
602 <li>Applet has user defined colours parameter</li>
603 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
608 <li>Redundancy Panel reinstalled in the Applet</li>
609 <li>Monospaced font - EPS / rescaling bug fixed</li>
610 <li>Annotation files with sequence references bug fixed</li>
616 <div align="center"><strong>2.08.1</strong><br>
621 <li>Change case of selected region from Popup menu</li>
622 <li>Choose to match case when searching</li>
623 <li>Middle mouse button and mouse movement can compress / expand
624 the visible width and height of the alignment</li>
629 <li>Annotation Panel displays complete JNet results</li>
635 <div align="center"><strong>2.08b</strong><br>
641 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
642 <li>Righthand label on wrapped alignments shows correct value</li>
648 <div align="center"><strong>2.08</strong><br>
653 <li>Editing can be locked to the selection area</li>
654 <li>Keyboard editing</li>
655 <li>Create sequence features from searches</li>
656 <li>Precalculated annotations can be loaded onto alignments</li>
657 <li>Features file allows grouping of features</li>
658 <li>Annotation Colouring scheme added</li>
659 <li>Smooth fonts off by default - Faster rendering</li>
660 <li>Choose to toggle Autocalculate Consensus On/Off</li>
665 <li>Drag & Drop fixed on Linux</li>
666 <li>Jalview Archive file faster to load/save, sequence
667 descriptions saved.</li>
673 <div align="center"><strong>2.07</strong><br>
678 <li>PDB Structure Viewer enhanced</li>
679 <li>Sequence Feature retrieval and display enhanced</li>
680 <li>Choose to output sequence start-end after sequence name for
682 <li>Sequence Fetcher WSDBFetch@EBI</li>
683 <li>Applet can read feature files, PDB files and can be used for
689 <li>HTML output writes groups and features</li>
690 <li>Group editing is Control and mouse click</li>
691 <li>File IO bugs</li>
697 <div align="center"><strong>2.06</strong><br>
702 <li>View annotations in wrapped mode</li>
703 <li>More options for PCA viewer</li>
708 <li>GUI bugs resolved</li>
709 <li>Runs with -nodisplay from command line</li>
715 <div align="center"><strong>2.05b</strong><br>
720 <li>Choose EPS export as lineart or text</li>
721 <li>Jar files are executable</li>
722 <li>Can read in Uracil - maps to unknown residue</li>
727 <li>Known OutOfMemory errors give warning message</li>
728 <li>Overview window calculated more efficiently</li>
729 <li>Several GUI bugs resolved</li>
735 <div align="center"><strong>2.05</strong><br>
740 <li>Edit and annotate in "Wrapped" view</li>
745 <li>Several GUI bugs resolved</li>
751 <div align="center"><strong>2.04</strong><br>
756 <li>Hold down mouse wheel & scroll to change font size</li>
761 <li>Improved JPred client reliability</li>
762 <li>Improved loading of Jalview files</li>
768 <div align="center"><strong>2.03</strong><br>
773 <li>Set Proxy server name and port in preferences</li>
774 <li>Multiple URL links from sequence ids</li>
775 <li>User Defined Colours can have a scheme name and added to
777 <li>Choose to ignore gaps in consensus calculation</li>
778 <li>Unix users can set default web browser</li>
779 <li>Runs without GUI for batch processing</li>
780 <li>Dynamically generated Web Service Menus</li>
785 <li>InstallAnywhere download for Sparc Solaris</li>
791 <div align="center"><strong>2.02</strong><br>
797 <li>Copy & Paste order of sequences maintains alignment
804 <div align="center"><strong>2.01</strong><br>
809 <li>Use delete key for deleting selection.</li>
810 <li>Use Mouse wheel to scroll sequences.</li>
811 <li>Help file updated to describe how to add alignment
813 <li>Version and build date written to build properties file.</li>
814 <li>InstallAnywhere installation will check for updates at
815 launch of Jalview.</li>
820 <li>Delete gaps bug fixed.</li>
821 <li>FileChooser sorts columns.</li>
822 <li>Can remove groups one by one.</li>
823 <li>Filechooser icons installed.</li>
824 <li>Finder ignores return character when searching. Return key
825 will initiate a search.<br>
832 <div align="center"><strong>2.0</strong><br>
837 <li>New codebase</li>