3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 The Jalview Authors
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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <title>Release History</title>
24 <p><strong>Release History</strong></p>
27 <td width="60" nowrap>
28 <div align="center"><em><strong>Release</strong></em></div>
31 <div align="center"><em><strong>New Features</strong></em></div>
34 <div align="center"><em><strong>Issues Resolved</strong></em></div>
38 <td><div align="center">
39 <strong><a name="Jalview.2.8.1">2.8.1</a><br />
40 <em>20/5/2014</em></strong>
43 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
45 <li>Internationalisation of user interface (usually called i18n support) and
46 translation for Spanish locale</li>
47 <li>Define/Undefine group on current selection with
48 Ctrl-G/Shift Ctrl-G</li>
49 <li>Improved group creation/removal options in alignment/sequence Popup menu</li>
51 </ul> <em>Application</em>
53 <li>Interactive consensus RNA secondary structure prediction
54 VIENNA RNAAliFold JABA 2.1 service</li>
55 <li>Select columns containing particular features from Feature
57 <li>View all 'representative' PDB structures for selected
59 <li>Update Jalview project format:<ul><li>
60 Preserve sequence and annotation dataset (to store secondary structure annotation,etc)
61 </li><li>Per group and alignment annotation and RNA helix colouring</li></ul></li>
62 <li>New similarity measures for PCA and Tree calculation (PAM250) </li>
63 <li>Experimental support for retrieval and viewing of flanking
64 regions for an alignment</li>
68 </ul> <em>Other improvements</em>
69 <li>Sensible precision for symbol distribution percentages shown in logo tooltip.</li>
70 <li>Annotation panel height set according to amount of annotation when alignment first opened</li>
74 <!-- issues resolved --> <em>Application</em>
76 <li>logo keeps spinning and status remains at queued or
77 running after job is cancelled</li>
78 <li>cannot export features from alignments imported from Jalview/VAMSAS projects</li>
79 <li>buggy slider for web service parameters that take float
81 <li>Newly created RNA secondary structure line doesn't have
82 'display all symbols' flag set</li>
83 <li>T-COFFEE alignment score shading scheme and other annotation shading not saved in
85 <li>Local file cannot be loaded in freshly downloaded Jalview</li>
86 <li>??? unresolved ??? Jalview icon not shown on dock in
87 Mountain Lion/Webstart</li>
88 <li>Load file from desktop file browser fails</li>
89 <li>Occasional NPE thrown when calculating large trees</li>
90 <li>cannot reorder or slide sequences after dragging an
91 alignment onto desktop</li>
92 <li>Colour by annotation dialog throws NPE after using
93 'extract scores' function</li>
94 <li>Loading/cut'n'pasting an empty file leads to a grey
96 <li>Disorder thresholds rendered incorrectly after performing
97 iupred disorder prediction</li>
98 <li>Multiple group annotated consensus rows shown when
99 changing 'normalise logo' display setting</li>
100 <li>Annotation/RNA Helix colourschemes cannot be applied to alignment
101 with groups (2.8.0b1)</li>
102 <li>find shows blank dialog after 'finished searching' if nothing matches query</li>
103 <li>Null Pointer Exceptions raised when sorting by feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 --></li>
104 <li>Errors in Jmol console when structures in alignment don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol --></li>
105 <li>Not all working JABAWS services are shown in Jalview's menu</li>
106 <li>JAVAWS version of jalview fails to launch with 'invalid literal/length code'</li>
107 </ul> <em>Applet</em>
110 <li>Remove group option shown in applet when selection is not a group</li>
111 <li>Apply to all groups ticked but colourscheme changes don't
115 <li>Consensus sequence for alignments/groups with a single sequence were not calculated</li>
116 <li>annotation files that contain only groups imported as
117 annotation and junk sequences</li>
118 <li>Fasta files with sequences containing '*' incorrectly
119 recognised as PFAM or BLC</li>
120 <li>conservation/PID slider apply all groups option doesn't
121 affect background (2.8.0b1)
123 <li>redundancy highlighting is erratic at 0% and 100%</li>
124 <li>remove gapped columns fails for sequences with ragged
126 <li>AMSA annotation row with leading spaces is not registered correctly on import</li>
127 <li>Jalview crashes when selecting PCA analysis for certain alignments</li>
128 <li>Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting</li>
133 <td><div align="center">
134 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
139 <li>Trusted certificates for JalviewLite applet and
140 Jalview Desktop application<br />Certificate was donated by
141 <a href="https://www.certum.eu">Certum</a> to the Jalview
142 open source project).
144 <li>Jalview SRS links replaced by Uniprot and EBI-search
146 <li>Output in Stockholm format</li>
147 <li>Allow import of data from gzipped files</li>
148 <li>Export/import group and sequence associated line
149 graph thresholds</li>
150 <li>Nucleotide substitution matrix that supports RNA and
152 <li>Allow disorder predictions to be made on the current
153 selection (or visible selection) in the same way that JPred
155 <li>Groovy scripting for headless jalview operation</li>
156 </ul> <em>Other improvements</em>
158 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
159 <li>COMBINE statement uses current SEQUENCE_REF and
160 GROUP_REF scope to group annotation rows</li>
161 <li>Support '' style escaping of quotes in Newick
163 <li>Group options for JABAWS service by command line name</li>
164 <li>Empty tooltip shown for JABA service options with a
165 link but no description</li>
166 <li>Select primary source when selecting authority in
167 database fetcher GUI</li>
168 <li>Add .mfa to FASTA file extensions recognised by
170 <li>Annotation label tooltip text wrap</li>
175 <li>Slow scrolling when lots of annotation rows are
177 <li>Lots of NPE (and slowness) after creating RNA
178 secondary structure annotation line</li>
179 <li>Sequence database accessions not imported when
180 fetching alignments from Rfam</li>
181 <li>Incorrect SHMR submission for sequences with
183 <li>View all structures does not always superpose
185 <li>Option widgets in service parameters not updated to
186 reflect user or preset settings</li>
187 <li>Null pointer exceptions for some services without
188 presets or adjustable parameters</li>
189 <li>Discover PDB IDs entry in structure menu doesn't
190 discover PDB xRefs</li>
191 <li>Exception encountered while trying to retrieve
192 features with DAS</li>
193 <li>Lowest value in annotation row isn't coloured
194 when colour by annotation (per sequence) is coloured</li>
195 <li>Keyboard mode P jumps to start of gapped region when
196 residue follows a gap</li>
197 <li>Jalview appears to hang importing an alignment with
198 Wrap as default or after enabling Wrap</li>
199 <li>'Right click to add annotations' message
200 shown in wrap mode when no annotations present</li>
201 <li>Disorder predictions fail with NPE if no automatic
202 annotation already exists on alignment</li>
203 <li>oninit javascript function should be called after
204 initialisation completes</li>
205 <li>Remove redundancy after disorder prediction corrupts
206 alignment window display</li>
207 <li>Example annotation file in documentation is invalid</li>
208 <li>Grouped line graph annotation rows are not exported
209 to annotation file</li>
210 <li>Multi-harmony analysis cannot be run when only two
212 <li>Cannot create multiple groups of line graphs with
213 several 'combine' statements in annotation file</li>
214 <li>Pressing return several times causes Number Format
215 exceptions in keyboard mode</li>
216 <li>Multi-harmony (SHMMR) method doesn't submit
217 correct partitions for input data</li>
218 <li>Translation from DNA to Amino Acids fails</li>
219 <li>Jalview fail to load newick tree with quoted label</li>
220 <li>--headless flag isn't understood</li>
221 <li>ClassCastException when generating EPS in headless
223 <li>Adjusting sequence-associated shading threshold only
224 changes one row's threshold</li>
225 <li>Preferences and Feature settings panel panel
226 doesn't open</li>
227 <li>hide consensus histogram also hides conservation and
228 quality histograms</li>
233 <td><div align="center">
234 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
236 <td><em>Application</em>
237 <ul><li>Support for JABAWS 2.0 Services (AACon alignment
238 conservation, protein disorder and Clustal Omega)</li>
239 <li>JABAWS server status indicator in Web Services preferences
241 <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
242 Jalview alignment window</li>
243 <li>Updated Jalview build and deploy framework for OSX mountain
244 lion, windows 7, and 8</li>
245 <li>Nucleotide substitution matrix for PCA that supports RNA
246 and ambiguity codes</li>
248 <li>Improved sequence database retrieval GUI</li>
249 <li>Support fetching and database reference look up against
250 multiple DAS sources (Fetch all from in 'fetch db refs')</li>
251 <li>Jalview project improvements
253 <li>Store and retrieve the 'belowAlignment' flag for
255 <li>calcId attribute to group annotation rows on the
257 <li>Store AACon calculation settings for a view in Jalview
262 <li>horizontal scrolling gesture support</li>
263 <li>Visual progress indicator when PCA calculation is running</li>
264 <li>Simpler JABA web services menus</li>
265 <li>visual indication that web service results are still being
266 retrieved from server</li>
267 <li>Serialise the dialogs that are shown when Jalview starts up
269 <li>Jalview user agent string for interacting with HTTP
271 <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
273 <li>Examples directory and Groovy library included in
274 InstallAnywhere distribution</li>
275 </ul> <em>Applet</em>
277 <li>RNA alignment and secondary structure annotation
278 visualization applet example</li>
279 </ul> <em>General</em>
281 <li>Normalise option for consensus sequence logo</li>
282 <li>Reset button in PCA window to return dimensions to
284 <li>Allow seqspace or Jalview variant of alignment PCA
286 <li>PCA with either nucleic acid and protein substitution
288 <li>Allow windows containing HTML reports to be exported in
290 <li>Interactive display and editing of RNA secondary structure
292 <li>RNA Helix Alignment Colouring</li>
293 <li>RNA base pair logo consensus</li>
294 <li>Parse sequence associated secondary structure information
295 in Stockholm files</li>
296 <li>HTML Export database accessions and annotation information
297 presented in tooltip for sequences</li>
298 <li>Import secondary structure from LOCARNA clustalw style RNA
300 <li>import and visualise T-COFFEE quality scores for an
302 <li>'colour by annotation' per sequence option to
303 shade each sequence according to its associated alignment
305 <li>New Jalview Logo</li>
306 </ul> <em>Documentation and Development</em>
308 <li>documentation for score matrices used in Jalview</li>
309 <li>New Website!</li>
311 <td><em>Application</em>
313 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
314 wsdbfetch REST service</li>
315 <li>Stop windows being moved outside desktop on OSX</li>
316 <li>Filetype associations not installed for webstart launch</li>
317 <li>Jalview does not always retrieve progress of a JABAWS job
318 execution in full once it is complete</li>
319 <li>revise SHMR RSBS definition to ensure alignment is
320 uploaded via ali_file parameter</li>
321 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
322 <li>View all structures superposed fails with exception</li>
323 <li>Jnet job queues forever if a very short sequence is
324 submitted for prediction</li>
325 <li>Cut and paste menu not opened when mouse clicked on
327 <li>Putting fractional value into integer text box in
328 alignment parameter dialog causes Jalview to hang</li>
329 <li>Structure view highlighting doesn't work on windows 7
331 <li>View all structures fails with exception shown in
333 <li>Characters in filename associated with PDBEntry not
334 escaped in a platform independent way</li>
335 <li>Jalview desktop fails to launch with exception when using
337 <li>Tree calculation reports 'you must have 2 or more
338 sequences selected' when selection is empty</li>
339 <li>Jalview desktop fails to launch with jar signature failure
340 when java web start temporary file caching is disabled</li>
341 <li>DAS Sequence retrieval with range qualification results in
342 sequence xref which includes range qualification</li>
343 <li>Errors during processing of command line arguments cause
344 progress bar (JAL-898) to be removed</li>
345 <li>Replace comma for semi-colon option not disabled for DAS
346 sources in sequence fetcher</li>
347 <li>Cannot close news reader when JABAWS server warning dialog
349 <li>Option widgets not updated to reflect user settings</li>
350 <li>Edited sequence not submitted to web service</li>
351 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
352 <li>InstallAnywhere installer doesn't unpack and run on
353 OSX Mountain Lion</li>
354 <li>Annotation panel not given a scroll bar when sequences
355 with alignment annotation are pasted into the alignment</li>
356 <li>Sequence associated annotation rows not associated when
357 loaded from Jalview project</li>
358 <li>Browser launch fails with NPE on java 1.7</li>
359 <li>JABAWS alignment marked as finished when job was cancelled
360 or job failed due to invalid input</li>
361 <li>NPE with v2.7 example when clicking on Tree associated
363 <li>Exceptions when copy/paste sequences with grouped
364 annotation rows to new window</li>
365 </ul> <em>Applet</em>
367 <li>Sequence features are momentarily displayed before they
368 are hidden using hidefeaturegroups applet parameter</li>
369 <li>loading features via javascript API automatically enables
371 <li>scrollToColumnIn javascript API method doesn't work</li>
372 </ul> <em>General</em>
374 <li>Redundancy removal fails for rna alignment</li>
375 <li>PCA calculation fails when sequence has been selected and
377 <li>PCA window shows grey box when first opened on OSX</li>
378 <li>Letters coloured pink in sequence logo when alignment
379 coloured with clustalx</li>
380 <li>Choosing fonts without letter symbols defined causes
381 exceptions and redraw errors</li>
382 <li>Initial PCA plot view is not same as manually reconfigured
384 <li>Grouped annotation graph label has incorrect line colour</li>
385 <li>Grouped annotation graph label display is corrupted for
392 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
395 <td><em>Application</em>
397 <li>Jalview Desktop News Reader</li>
398 <li>Tweaked default layout of web services menu</li>
399 <li>View/alignment association menu to enable user to easily
400 specify which alignment a multi-structure view takes its
401 colours/correspondences from</li>
402 <li>Allow properties file location to be specified as URL</li>
403 <li>Extend Jalview project to preserve associations between
404 many alignment views and a single Jmol display</li>
405 <li>Store annotation row height in Jalview project file</li>
406 <li>Annotation row column label formatting attributes stored
408 <li>Annotation row order for auto-calculated annotation rows
409 preserved in Jalview project file</li>
410 <li>Visual progress indication when Jalview state is saved
411 using Desktop window menu</li>
412 <li>Visual indication that command line arguments are still
414 <li>Groovy script execution from URL</li>
415 <li>Colour by annotation default min and max colours in
417 <li>Automatically associate PDB files dragged onto an
418 alignment with sequences that have high similarity and matching
420 <li>Update JGoogleAnalytics to latest release (0.3)</li>
421 <li>'view structures' option to open many structures
423 <li>Sort associated views menu option for tree panel</li>
424 <li>Group all JABA and non-JABA services for a particular
425 analysis function in its own submenu</li>
426 </ul> <em>Applet</em>
428 <li>Userdefined and autogenerated annotation rows for groups</li>
429 <li>Adjustment of alignment annotation pane height</li>
430 <li>Annotation scrollbar for annotation panel</li>
431 <li>Drag to reorder annotation rows in annotation panel</li>
432 <li>'automaticScrolling' parameter</li>
433 <li>Allow sequences with partial ID string matches to be
434 annotated from GFF/Jalview features files</li>
435 <li>Sequence logo annotation row in applet</li>
436 <li>Absolute paths relative to host server in applet
437 parameters are treated as such</li>
438 <li>New in the JalviewLite javascript API:
440 <li>JalviewLite.js javascript library</li>
441 <li>Javascript callbacks for
443 <li>Applet initialisation</li>
444 <li>Sequence/alignment mouse-overs and selections</li>
447 <li>scrollTo row and column alignment scrolling functions</li>
448 <li>Select sequence/alignment regions from javascript</li>
449 <li>javascript structure viewer harness to pass messages
450 between Jmol and Jalview when running as distinct applets</li>
451 <li>sortBy method</li>
452 <li>Set of applet and application examples shipped with
454 <li>New example to demonstrate JalviewLite and Jmol
455 javascript message exchange</li>
457 </ul> <em>General</em>
459 <li>Enable Jmol displays to be associated with multiple
460 multiple alignments</li>
461 <li>Option to automatically sort alignment with new tree</li>
462 <li>User configurable link to enable redirects to a
463 www.Jalview.org mirror</li>
464 <li>Jmol colours option for Jmol displays</li>
465 <li>Configurable newline string when writing alignment and
466 other flat files</li>
467 <li>Allow alignment annotation description lines to contain
469 </ul> <em>Documentation and Development</em>
471 <li>Add groovy test harness for bulk load testing to examples
473 <li>Groovy script to load and align a set of sequences using a
474 web service before displaying the result in the Jalview desktop</li>
475 <li>Restructured javascript and applet api documentation</li>
476 <li>Ant target to publish example html files with applet
478 <li>Netbeans project for building Jalview from source</li>
479 <li>ant task to create online javadoc for Jalview source</li>
481 <td><em>Application</em>
483 <li>User defined colourscheme throws exception when current
484 built in colourscheme is saved as new scheme</li>
485 <li>AlignFrame->Save in application pops up save dialog for
486 valid filename/format</li>
487 <li>Cannot view associated structure for Uniprot sequence</li>
488 <li>PDB file association breaks for Uniprot sequence P37173</li>
489 <li>Associate PDB from file dialog does not tell you which
490 sequence is to be associated with the file</li>
491 <li>Find All raises null pointer exception when query only
492 matches sequence IDs</li>
493 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
494 <li>Jalview project with Jmol views created with Jalview 2.4
495 cannot be loaded</li>
496 <li>Filetype associations not installed for webstart launch</li>
497 <li>Two or more chains in a single PDB file associated with
498 sequences in different alignments do not get coloured by their
499 associated sequence</li>
500 <li>Visibility status of autocalculated annotation row not
501 preserved when project is loaded</li>
502 <li>Annotation row height and visibility attributes not stored
503 in Jalview project</li>
504 <li>Tree bootstraps are not preserved when saved as a Jalview
506 <li>Envision2 workflow tooltips are corrupted</li>
507 <li>Enabling show group conservation also enables colour by
509 <li>Duplicate group associated conservation or consensus
510 created on new view</li>
511 <li>Annotation scrollbar not displayed after 'show all
512 hidden annotation rows' option selected</li>
513 <li>Alignment quality not updated after alignment annotation
514 row is hidden then shown</li>
515 <li>Preserve colouring of structures coloured by sequences in
516 pre Jalview 2.7 projects</li>
517 <li>Web service job parameter dialog is not laid out properly
519 <li>Web services menu not refreshed after 'reset
520 services' button is pressed in preferences</li>
521 <li>Annotation off by one in Jalview v2_3 example project</li>
522 <li>Structures imported from file and saved in project get
523 name like jalview_pdb1234.txt when reloaded</li>
524 <li>Jalview does not always retrieve progress of a JABAWS job
525 execution in full once it is complete</li>
526 </ul> <em>Applet</em>
528 <li>Alignment height set incorrectly when lots of annotation
529 rows are displayed</li>
530 <li>Relative URLs in feature HTML text not resolved to
532 <li>View follows highlighting does not work for positions in
534 <li><= shown as = in tooltip</li>
535 <li>Export features raises exception when no features exist</li>
536 <li>Separator string used for serialising lists of IDs for
537 javascript api is modified when separator string provided as
539 <li>Null pointer exception when selecting tree leaves for
540 alignment with no existing selection</li>
541 <li>Relative URLs for datasources assumed to be relative to
542 applet's codebase</li>
543 <li>Status bar not updated after finished searching and search
544 wraps around to first result</li>
545 <li>StructureSelectionManager instance shared between several
546 Jalview applets causes race conditions and memory leaks</li>
547 <li>Hover tooltip and mouseover of position on structure not
548 sent from Jmol in applet</li>
549 <li>Certain sequences of javascript method calls to applet API
550 fatally hang browser</li>
551 </ul> <em>General</em>
553 <li>View follows structure mouseover scrolls beyond position
554 with wrapped view and hidden regions</li>
555 <li>Find sequence position moves to wrong residue with/without
557 <li>Sequence length given in alignment properties window is
559 <li>InvalidNumberFormat exceptions thrown when trying to
560 import PDB like structure files</li>
561 <li>Positional search results are only highlighted between
562 user-supplied sequence start/end bounds</li>
563 <li>End attribute of sequence is not validated</li>
564 <li>Find dialog only finds first sequence containing a given
565 sequence position</li>
566 <li>Sequence numbering not preserved in MSF alignment output</li>
567 <li>Jalview PDB file reader does not extract sequence from
568 nucleotide chains correctly</li>
569 <li>Structure colours not updated when tree partition changed
571 <li>Sequence associated secondary structure not correctly
572 parsed in interleaved stockholm</li>
573 <li>Colour by annotation dialog does not restore current state
575 <li>Hiding (nearly) all sequences doesn't work properly</li>
576 <li>Sequences containing lowercase letters are not properly
577 associated with their pdb files</li>
578 </ul> <em>Documentation and Development</em>
580 <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
587 <strong><a name="Jalview2.6.1">2.6.1</a>
588 </strong><br> <em>15/11/2010</em>
590 <td><em>Application</em>
592 <li>New warning dialog when the Jalview Desktop cannot contact
594 <li>JABA service parameters for a preset are shown in service
596 <li>JABA Service menu entries reworded</li>
600 <li>Modeller PIR IO broken - cannot correctly import a pir
601 file emitted by Jalview</li>
602 <li>Existing feature settings transferred to new alignment
603 view created from cut'n'paste</li>
604 <li>Improved test for mixed amino/nucleotide chains when
605 parsing PDB files</li>
606 <li>Consensus and conservation annotation rows occasionally
607 become blank for all new windows</li>
608 <li>Exception raised when right clicking above sequences in
609 wrapped view mode</li>
610 </ul> <em>Application</em>
612 <li>multiple multiply aligned structure views cause cpu usage
613 to hit 100% and computer to hang</li>
614 <li>Web Service parameter layout breaks for long user
616 <li>Jaba service discovery hangs desktop if Jaba server is
622 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
623 <em>26/9/2010</em></div>
625 <td><em>Application</em>
627 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
628 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
629 <li>Web Services preference tab</li>
630 <li>Analysis parameters dialog box and user defined preferences</li>
631 <li>Improved speed and layout of Envision2 service menu</li>
632 <li>Superpose structures using associated sequence alignment</li>
633 <li>Export coordinates and projection as CSV from PCA viewer</li>
637 <li>enable javascript: execution by the applet via the link out
642 <li>Updated the Jmol Jalview interface to work with Jmol series
644 <li>The Jalview Desktop and JalviewLite applet now require Java
646 <li>Allow Jalview feature colour specification for GFF sequence
647 annotation files</li>
648 <li>New 'colour by label' keword in Jalview feature file type
649 colour specification</li>
650 <li>New Jalview Desktop Groovy API method that allows a script
651 to check if it being run in an interactive session or in a batch
652 operation from the Jalview command line</li>
657 <li>clustalx colourscheme colours Ds preferentially when both
658 D+E are present in over 50% of the column</li>
663 <li>typo in AlignmentFrame->View->Hide->all but
664 selected Regions menu item</li>
665 <li>sequence fetcher replaces ',' for ';' when the ',' is part
666 of a valid accession ID</li>
667 <li>fatal OOM if object retrieved by sequence fetcher runs out
669 <li>unhandled Out of Memory Error when viewing pca analysis
671 <li>InstallAnywhere builds fail to launch on OS X java 10.5
672 update 4 (due to apple Java 1.6 update)</li>
673 <li>Installanywhere Jalview silently fails to launch</li>
677 <li>Jalview.getFeatureGroups() raises an
678 ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
684 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
685 <em>14/6/2010</em></div>
690 <li>Alignment prettyprinter doesn't cope with long sequence IDs
692 <li>clustalx colourscheme colours Ds preferentially when both
693 D+E are present in over 50% of the column</li>
694 <li>nucleic acid structures retrieved from PDB do not import
696 <li>More columns get selected than were clicked on when a number
697 of columns are hidden</li>
698 <li>annotation label popup menu not providing correct
699 add/hide/show options when rows are hidden or none are present</li>
700 <li>Stockholm format shown in list of readable formats, and
701 parser copes better with alignments from RFAM.</li>
702 <li>CSV output of consensus only includes the percentage of all
703 symbols if sequence logo display is enabled</li>
708 <li>annotation panel disappears when annotation is
713 <li>Alignment view not redrawn properly when new alignment
714 opened where annotation panel is visible but no annotations are
715 present on alignment</li>
716 <li>pasted region containing hidden columns is incorrectly
717 displayed in new alignment window</li>
718 <li>Jalview slow to complete operations when stdout is flooded
719 (fix is to close the Jalview console)</li>
720 <li>typo in AlignmentFrame->View->Hide->all but
721 selected Rregions menu item.</li>
722 <li>inconsistent group submenu and Format submenu entry 'Un' or
724 <li>Sequence feature settings are being shared by multiple
725 distinct alignments</li>
726 <li>group annotation not recreated when tree partition is
728 <li>double click on group annotation to select sequences does
729 not propagate to associated trees</li>
730 <li>Mac OSX specific issues:
732 <li>exception raised when mouse clicked on desktop window
734 <li>Desktop menu placed on menu bar and application name set
736 <li>sequence feature settings not wide enough for the save
737 feature colourscheme button</li>
746 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
747 <em>30/4/2010</em></div>
749 <td><em>New Capabilities</em>
751 <li>URL links generated from description line for
752 regular-expression based URL links (applet and application)
753 <li>Non-positional feature URL links are shown in link menu</li>
754 <li>Linked viewing of nucleic acid sequences and structures</li>
755 <li>Automatic Scrolling option in View menu to display the
756 currently highlighted region of an alignment.</li>
757 <li>Order an alignment by sequence length, or using the average
758 score or total feature count for each sequence.</li>
759 <li>Shading features by score or associated description</li>
760 <li>Subdivide alignment and groups based on identity of selected
761 subsequence (Make Groups from Selection).</li>
762 <li>New hide/show options including Shift+Control+H to hide
763 everything but the currently selected region.</li>
764 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
768 <li>Fetch DB References capabilities and UI expanded to support
769 retrieval from DAS sequence sources</li>
770 <li>Local DAS Sequence sources can be added via the command line
771 or via the Add local source dialog box.</li>
772 <li>DAS Dbref and DbxRef feature types are parsed as database
773 references and protein_name is parsed as description line (BioSapiens
775 <li>Enable or disable non-positional feature and database
776 references in sequence ID tooltip from View menu in application.</li>
777 <!-- <li>New hidden columns and rows and representatives capabilities
778 in annotations file (in progress - not yet fully implemented)</li> -->
779 <li>Group-associated consensus, sequence logos and conservation
781 <li>Symbol distributions for each column can be exported and
782 visualized as sequence logos</li>
783 <li>Optionally scale multi-character column labels to fit within
784 each column of annotation row<!-- todo for applet --></li>
785 <li>Optional automatic sort of associated alignment view when a
786 new tree is opened.</li>
787 <li>Jalview Java Console</li>
788 <li>Better placement of desktop window when moving between
789 different screens.</li>
790 <li>New preference items for sequence ID tooltip and consensus
792 <li>Client to submit sequences and IDs to <a
793 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
794 <li><em>Vamsas Capabilities</em>
796 <li>Improved VAMSAS synchronization (Jalview archive used to
797 preserve views, structures, and tree display settings)</li>
798 <li>Import of vamsas documents from disk or URL via command
800 <li>Sharing of selected regions between views and with other
801 VAMSAS applications (Experimental feature!)</li>
802 <li>Updated API to VAMSAS version 0.2</li>
808 <li>Middle button resizes annotation row height</li>
811 <li>sortByTree (true/false) - automatically sort the associated
812 alignment view by the tree when a new tree is opened.</li>
813 <li>showTreeBootstraps (true/false) - show or hide branch
814 bootstraps (default is to show them if available)</li>
815 <li>showTreeDistances (true/false) - show or hide branch
816 lengths (default is to show them if available)</li>
817 <li>showUnlinkedTreeNodes (true/false) - indicate if
818 unassociated nodes should be highlighted in the tree view</li>
819 <li>heightScale and widthScale (1.0 or more) - increase the
820 height or width of a cell in the alignment grid relative to the
821 current font size.</li>
824 <li>Non-positional features displayed in sequence ID tooltip</li>
828 <li>Features format: graduated colour definitions and
829 specification of feature scores</li>
830 <li>Alignment Annotations format: new keywords for group
831 associated annotation (GROUP_REF) and annotation row display
832 properties (ROW_PROPERTIES)</li>
833 <li>XML formats extended to support graduated feature
834 colourschemes, group associated annotation, and profile visualization
839 <li>Source field in GFF files parsed as feature source rather
840 than description</li>
841 <li>Non-positional features are now included in sequence feature
842 and gff files (controlled via non-positional feature visibility in
844 <li>URL links generated for all feature links (bugfix)</li>
845 <li>Added URL embedding instructions to features file
847 <li>Codons containing ambiguous nucleotides translated as 'X' in
849 <li>Match case switch in find dialog box works for both sequence
850 ID and sequence string and query strings do not have to be in upper
851 case to match case-insensitively.</li>
852 <li>AMSA files only contain first column of multi-character
853 column annotation labels</li>
854 <li>Jalview Annotation File generation/parsing consistent with
855 documentation (e.g. Stockholm annotation can be exported and
857 <li>PDB files without embedded PDB IDs given a friendly name</li>
858 <li>Find incrementally searches ID string matches as well as
859 subsequence matches, and correctly reports total number of both.</li>
862 <li>Better handling of exceptions during sequence retrieval</li>
863 <li>Dasobert generated non-positional feature URL link text
864 excludes the start_end suffix</li>
865 <li>DAS feature and source retrieval buttons disabled when
866 fetch or registry operations in progress.</li>
867 <li>PDB files retrieved from URLs are cached properly</li>
868 <li>Sequence description lines properly shared via VAMSAS</li>
869 <li>Sequence fetcher fetches multiple records for all data
871 <li>Ensured that command line das feature retrieval completes
872 before alignment figures are generated.</li>
873 <li>Reduced time taken when opening file browser for first
875 <li>isAligned check prior to calculating tree, PCA or
876 submitting an MSA to JNet now excludes hidden sequences.</li>
877 <li>User defined group colours properly recovered from Jalview
887 <div align="center"><strong>2.4.0.b2</strong><br>
892 <li>Experimental support for google analytics usage tracking.</li>
893 <li>Jalview privacy settings (user preferences and docs).</li>
898 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
899 <li>Exception when feature created from selection beyond length
901 <li>Allow synthetic PDB files to be imported gracefully</li>
902 <li>Sequence associated annotation rows associate with all
903 sequences with a given id</li>
904 <li>Find function matches case-insensitively for sequence ID
906 <li>Non-standard characters do not cause pairwise alignment to
907 fail with exception</li>
909 <em>Application Issues</em>
911 <li>Sequences are now validated against EMBL database</li>
912 <li>Sequence fetcher fetches multiple records for all data
915 <em>InstallAnywhere Issues</em>
917 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
918 installAnywhere mechanism)</li>
919 <li>Command line launching of JARs from InstallAnywhere version
920 (java class versioning error fixed)</li>
927 <div align="center"><strong>2.4</strong><br>
930 <td><em>User Interface</em>
932 <li>Linked highlighting of codon and amino acid from translation
933 and protein products</li>
934 <li>Linked highlighting of structure associated with residue
935 mapping to codon position</li>
936 <li>Sequence Fetcher provides example accession numbers and
938 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
939 <li>Extract score function to parse whitespace separated numeric
940 data in description line</li>
941 <li>Column labels in alignment annotation can be centred.</li>
942 <li>Tooltip for sequence associated annotation give name of
945 <em>Web Services and URL fetching</em>
947 <li>JPred3 web service</li>
948 <li>Prototype sequence search client (no public services
950 <li>Fetch either seed alignment or full alignment from PFAM</li>
951 <li>URL Links created for matching database cross references as
952 well as sequence ID</li>
953 <li>URL Links can be created using regular-expressions</li>
955 <em>Sequence Database Connectivity</em>
957 <li>Retrieval of cross-referenced sequences from other databases
959 <li>Generalised database reference retrieval and validation to
960 all fetchable databases</li>
961 <li>Fetch sequences from DAS sources supporting the sequence
964 <em>Import and Export</em>
965 <li>export annotation rows as CSV for spreadsheet import</li>
966 <li>Jalview projects record alignment dataset associations, EMBL
967 products, and cDNA sequence mappings</li>
968 <li>Sequence Group colour can be specified in Annotation File</li>
969 <li>Ad-hoc colouring of group in Annotation File using RGB
970 triplet as name of colourscheme</li>
972 <em>VAMSAS Client capabilities (Experimental)</em>
974 <li>treenode binding for VAMSAS tree exchange</li>
975 <li>local editing and update of sequences in VAMSAS alignments
977 <li>Create new or select existing session to join</li>
978 <li>load and save of vamsas documents</li>
980 <em>Application command line</em>
982 <li>-tree parameter to open trees (introduced for passing from
984 <li>-fetchfrom command line argument to specify nicknames of DAS
985 servers to query for alignment features</li>
986 <li>-dasserver command line argument to add new servers that are
987 also automatically queried for features</li>
988 <li>-groovy command line argument executes a given groovy script
989 after all input data has been loaded and parsed</li>
991 <em>Applet-Application data exchange</em>
993 <li>Trees passed as applet parameters can be passed to
994 application (when using "View in full application")</li>
996 <em>Applet Parameters</em>
998 <li>feature group display control parameter</li>
999 <li>debug parameter</li>
1000 <li>showbutton parameter</li>
1002 <em>Applet API methods</em>
1004 <li>newView public method</li>
1005 <li>Window (current view) specific get/set public methods</li>
1006 <li>Feature display control methods</li>
1007 <li>get list of currently selected sequences</li>
1009 <em>New Jalview distribution features</em>
1011 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1012 <li>RELEASE file gives build properties for the latest Jalview
1014 <li>Java 1.1 Applet build made easier and donotobfuscate
1015 property controls execution of obfuscator</li>
1016 <li>Build target for generating source distribution</li>
1017 <li>Debug flag for javacc</li>
1018 <li>.jalview_properties file is documented (slightly) in
1019 jalview.bin.Cache</li>
1020 <li>Continuous Build Integration for stable and development
1021 version of Application, Applet and source distribution</li>
1027 <li>selected region output includes visible annotations (for
1028 certain formats)</li>
1029 <li>edit label/displaychar contains existing label/char for
1031 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1032 <li>shorter peptide product names from EMBL records</li>
1033 <li>Newick string generator makes compact representations</li>
1034 <li>bootstrap values parsed correctly for tree files with
1036 <li>pathological filechooser bug avoided by not allowing
1037 filenames containing a ':'</li>
1038 <li>Fixed exception when parsing GFF files containing global
1039 sequence features</li>
1040 <li>Alignment datasets are finalized only when number of
1041 references from alignment sequences goes to zero</li>
1042 <li>Close of tree branch colour box without colour selection
1043 causes cascading exceptions</li>
1044 <li>occasional negative imgwidth exceptions</li>
1045 <li>better reporting of non-fatal warnings to user when file
1047 <li>Save works when Jalview project is default format</li>
1048 <li>Save as dialog opened if current alignment format is not a
1049 valid output format</li>
1050 <li>Uniprot canonical names introduced for both das and vamsas</li>
1051 <li>Histidine should be midblue (not pink!) in Zappo</li>
1052 <li>error messages passed up and output when data read fails</li>
1053 <li>edit undo recovers previous dataset sequence when sequence
1055 <li>allow PDB files without pdb ID HEADER lines (like those
1056 generated by MODELLER) to be read in properly</li>
1057 <li>allow reading of JPred concise files as a normal filetype</li>
1058 <li>Stockholm annotation parsing and alignment properties import
1059 fixed for PFAM records</li>
1060 <li>Structure view windows have correct name in Desktop window
1062 <li>annotation consisting of sequence associated scores can be
1063 read and written correctly to annotation file</li>
1064 <li>Aligned cDNA translation to aligned peptide works correctly</li>
1065 <li>Fixed display of hidden sequence markers and non-italic font
1066 for representatives in Applet</li>
1067 <li>Applet Menus are always embedded in applet window on Macs.</li>
1068 <li>Newly shown features appear at top of stack (in Applet)</li>
1069 <li>Annotations added via parameter not drawn properly due to
1070 null pointer exceptions</li>
1071 <li>Secondary structure lines are drawn starting from first
1072 column of alignment</li>
1073 <li>Uniprot XML import updated for new schema release in July
1075 <li>Sequence feature to sequence ID match for Features file is
1076 case-insensitive</li>
1077 <li>Sequence features read from Features file appended to all
1078 sequences with matching IDs</li>
1079 <li>PDB structure coloured correctly for associated views
1080 containing a sub-sequence</li>
1081 <li>PDB files can be retrieved by applet from Jar files</li>
1082 <li>feature and annotation file applet parameters referring to
1083 different directories are retrieved correctly</li>
1084 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1085 <li>Fixed application hang whilst waiting for splash-screen
1086 version check to complete</li>
1087 <li>Applet properly URLencodes input parameter values when
1088 passing them to the launchApp service</li>
1089 <li>display name and local features preserved in results
1090 retrieved from web service</li>
1091 <li>Visual delay indication for sequence retrieval and sequence
1092 fetcher initialisation</li>
1093 <li>updated Application to use DAS 1.53e version of dasobert DAS
1095 <li>Re-instated Full AMSA support and .amsa file association</li>
1096 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1103 <div align="center"><strong>2.3</strong><br>
1108 <li>Jmol 11.0.2 integration</li>
1109 <li>PDB views stored in Jalview XML files</li>
1110 <li>Slide sequences</li>
1111 <li>Edit sequence in place</li>
1112 <li>EMBL CDS features</li>
1113 <li>DAS Feature mapping</li>
1114 <li>Feature ordering</li>
1115 <li>Alignment Properties</li>
1116 <li>Annotation Scores</li>
1117 <li>Sort by scores</li>
1118 <li>Feature/annotation editing in applet</li>
1123 <li>Headless state operation in 2.2.1</li>
1124 <li>Incorrect and unstable DNA pairwise alignment</li>
1125 <li>Cut and paste of sequences with annotation</li>
1126 <li>Feature group display state in XML</li>
1127 <li>Feature ordering in XML</li>
1128 <li>blc file iteration selection using filename # suffix</li>
1129 <li>Stockholm alignment properties</li>
1130 <li>Stockhom alignment secondary structure annotation</li>
1131 <li>2.2.1 applet had no feature transparency</li>
1132 <li>Number pad keys can be used in cursor mode</li>
1133 <li>Structure Viewer mirror image resolved</li>
1140 <div align="center"><strong>2.2.1</strong><br>
1145 <li>Non standard characters can be read and displayed
1146 <li>Annotations/Features can be imported/exported to the applet
1148 <li>Applet allows editing of sequence/annotation/group name
1150 <li>Preference setting to display sequence name in italics
1151 <li>Annotation file format extended to allow Sequence_groups to
1153 <li>Default opening of alignment overview panel can be specified
1155 <li>PDB residue numbering annotation added to associated
1161 <li>Applet crash under certain Linux OS with Java 1.6 installed
1162 <li>Annotation file export / import bugs fixed
1163 <li>PNG / EPS image output bugs fixed
1169 <div align="center"><strong>2.2</strong><br>
1174 <li>Multiple views on alignment
1175 <li>Sequence feature editing
1176 <li>"Reload" alignment
1177 <li>"Save" to current filename
1178 <li>Background dependent text colour
1179 <li>Right align sequence ids
1180 <li>User-defined lower case residue colours
1183 <li>Menu item accelerator keys
1184 <li>Control-V pastes to current alignment
1185 <li>Cancel button for DAS Feature Fetching
1186 <li>PCA and PDB Viewers zoom via mouse roller
1187 <li>User-defined sub-tree colours and sub-tree selection
1188 <li>'New Window' button on the 'Output to Text box'
1193 <li>New memory efficient Undo/Redo System
1194 <li>Optimised symbol lookups and conservation/consensus
1196 <li>Region Conservation/Consensus recalculated after edits
1197 <li>Fixed Remove Empty Columns Bug (empty columns at end of
1199 <li>Slowed DAS Feature Fetching for increased robustness.
1200 <li>Made angle brackets in ASCII feature descriptions display
1202 <li>Re-instated Zoom function for PCA
1203 <li>Sequence descriptions conserved in web service analysis
1205 <li>Uniprot ID discoverer uses any word separated by ∣
1206 <li>WsDbFetch query/result association resolved
1207 <li>Tree leaf to sequence mapping improved
1208 <li>Smooth fonts switch moved to FontChooser dialog box.
1214 <div align="center"><strong>2.1.1</strong><br>
1219 <li>Copy consensus sequence to clipboard</li>
1224 <li>Image output - rightmost residues are rendered if sequence
1225 id panel has been resized</li>
1226 <li>Image output - all offscreen group boundaries are rendered</li>
1227 <li>Annotation files with sequence references - all elements in
1228 file are relative to sequence position</li>
1229 <li>Mac Applet users can use Alt key for group editing</li>
1235 <div align="center"><strong>2.1</strong><br>
1240 <li>MAFFT Multiple Alignment in default Web Service list</li>
1241 <li>DAS Feature fetching</li>
1242 <li>Hide sequences and columns</li>
1243 <li>Export Annotations and Features</li>
1244 <li>GFF file reading / writing</li>
1245 <li>Associate structures with sequences from local PDB files</li>
1246 <li>Add sequences to exisiting alignment</li>
1247 <li>Recently opened files / URL lists</li>
1248 <li>Applet can launch the full application</li>
1249 <li>Applet has transparency for features (Java 1.2 required)</li>
1250 <li>Applet has user defined colours parameter</li>
1251 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
1256 <li>Redundancy Panel reinstalled in the Applet</li>
1257 <li>Monospaced font - EPS / rescaling bug fixed</li>
1258 <li>Annotation files with sequence references bug fixed</li>
1264 <div align="center"><strong>2.08.1</strong><br>
1269 <li>Change case of selected region from Popup menu</li>
1270 <li>Choose to match case when searching</li>
1271 <li>Middle mouse button and mouse movement can compress / expand
1272 the visible width and height of the alignment</li>
1277 <li>Annotation Panel displays complete JNet results</li>
1283 <div align="center"><strong>2.08b</strong><br>
1289 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1290 <li>Righthand label on wrapped alignments shows correct value</li>
1296 <div align="center"><strong>2.08</strong><br>
1301 <li>Editing can be locked to the selection area</li>
1302 <li>Keyboard editing</li>
1303 <li>Create sequence features from searches</li>
1304 <li>Precalculated annotations can be loaded onto alignments</li>
1305 <li>Features file allows grouping of features</li>
1306 <li>Annotation Colouring scheme added</li>
1307 <li>Smooth fonts off by default - Faster rendering</li>
1308 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1313 <li>Drag & Drop fixed on Linux</li>
1314 <li>Jalview Archive file faster to load/save, sequence
1315 descriptions saved.</li>
1321 <div align="center"><strong>2.07</strong><br>
1326 <li>PDB Structure Viewer enhanced</li>
1327 <li>Sequence Feature retrieval and display enhanced</li>
1328 <li>Choose to output sequence start-end after sequence name for
1330 <li>Sequence Fetcher WSDBFetch@EBI</li>
1331 <li>Applet can read feature files, PDB files and can be used for
1332 HTML form input</li>
1337 <li>HTML output writes groups and features</li>
1338 <li>Group editing is Control and mouse click</li>
1339 <li>File IO bugs</li>
1345 <div align="center"><strong>2.06</strong><br>
1350 <li>View annotations in wrapped mode</li>
1351 <li>More options for PCA viewer</li>
1356 <li>GUI bugs resolved</li>
1357 <li>Runs with -nodisplay from command line</li>
1363 <div align="center"><strong>2.05b</strong><br>
1368 <li>Choose EPS export as lineart or text</li>
1369 <li>Jar files are executable</li>
1370 <li>Can read in Uracil - maps to unknown residue</li>
1375 <li>Known OutOfMemory errors give warning message</li>
1376 <li>Overview window calculated more efficiently</li>
1377 <li>Several GUI bugs resolved</li>
1383 <div align="center"><strong>2.05</strong><br>
1388 <li>Edit and annotate in "Wrapped" view</li>
1393 <li>Several GUI bugs resolved</li>
1399 <div align="center"><strong>2.04</strong><br>
1404 <li>Hold down mouse wheel & scroll to change font size</li>
1409 <li>Improved JPred client reliability</li>
1410 <li>Improved loading of Jalview files</li>
1416 <div align="center"><strong>2.03</strong><br>
1421 <li>Set Proxy server name and port in preferences</li>
1422 <li>Multiple URL links from sequence ids</li>
1423 <li>User Defined Colours can have a scheme name and added to
1425 <li>Choose to ignore gaps in consensus calculation</li>
1426 <li>Unix users can set default web browser</li>
1427 <li>Runs without GUI for batch processing</li>
1428 <li>Dynamically generated Web Service Menus</li>
1433 <li>InstallAnywhere download for Sparc Solaris</li>
1439 <div align="center"><strong>2.02</strong><br>
1445 <li>Copy & Paste order of sequences maintains alignment
1452 <div align="center"><strong>2.01</strong><br>
1457 <li>Use delete key for deleting selection.</li>
1458 <li>Use Mouse wheel to scroll sequences.</li>
1459 <li>Help file updated to describe how to add alignment
1461 <li>Version and build date written to build properties file.</li>
1462 <li>InstallAnywhere installation will check for updates at
1463 launch of Jalview.</li>
1468 <li>Delete gaps bug fixed.</li>
1469 <li>FileChooser sorts columns.</li>
1470 <li>Can remove groups one by one.</li>
1471 <li>Filechooser icons installed.</li>
1472 <li>Finder ignores return character when searching. Return key
1473 will initiate a search.<br>
1480 <div align="center"><strong>2.0</strong><br>
1485 <li>New codebase</li>