3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ 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
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 <p><strong>Release History</strong></p>
29 <td width="60" nowrap>
31 <em><strong>Release</strong></em>
36 <em><strong>New Features</strong></em>
41 <em><strong>Issues Resolved</strong></em>
46 <td><div align="center">
47 <strong><a name="Jalview.2.9">2.9</a><br /> <em>9/9/2015</em></strong>
51 <li>Linked visualisation and analysis of DNA and Protein
54 <li>Translated cDNA alignments shown as split protein
55 and DNA alignment views</li>
56 <li>Codon consensus annotation for linked protein and
57 cDNA alignment views</li>
58 <li>Link cDNA or Protein product sequences by loading
59 them onto Protein or cDNA alignments</li>
60 <li>Reconstruct linked cDNA alignment from aligned
61 protein sequences</li>
64 <li>Jmol integration updated to Jmol v14.2.14</li>
65 <li>Import and export of Jalview alignment views as <a
66 href="">BioJSON</a></li>
67 <li>New alignment annotation file statements for
68 reference sequences and marking hidden columns</li>
69 <li>Reference sequence based alignment shading to
70 highlight variation</li>
71 <li>Select or hide columns according to alignment
73 <li>Find option for locating sequences by description</li>
74 <li>Conserved physicochemical properties shown in amino
75 acid conservation row</li>
76 <li>Alignments can be sorted by number of RNA helices</li>
77 </ul> <em>Application</em>
79 <li>New cDNA/Protein analysis capabilities
81 <li>Get Cross-References should open a Split Frame
82 view with cDNA/Protein</li>
83 <li>Detect when nucleotide sequences and protein
84 sequences are placed in the same alignment</li>
85 <li>Split cDNA/Protein views are saved in Jalview
90 <li>Use REST API to talk to Chimera</li>
91 <li>Selected regions in Chimera are highlighted in linked
94 <li>VARNA RNA viewer updated to v3.93</li>
95 <li>VARNA views are saved in Jalview Projects</li>
96 <li>Pseudoknots displayed as Jalview RNA annotation can
97 be shown in VARNA</li>
99 <li>Make groups for selection uses marked columns as well
100 as the active selected region</li>
102 <li>Calculate UPGMA and NJ trees using sequence feature
104 <li>New Export options
106 <li>New Export Settings dialog to control hidden
107 region export in flat file generation</li>
109 <li>Export alignment views for display with the <a
110 href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
112 <li>Export scrollable SVG in HTML page</li>
113 <li>Optional embedding of BioJSON data when exporting
114 alignment figures to HTML</li>
116 <li>3D structure retrieval and display
118 <li>Free text and structured queries with
119 the PDBe Search API</li>
120 <li>PDBe Search API based discovery and selection of
121 PDB structures for a sequence set</li>
125 <li>JPred4 employed for protein secondary structure
127 <li>Hide Insertions menu option to hide unaligned columns
128 for one or a group of sequences</li>
129 <li>Automatically hide insertions in alignments imported
130 from the JPred4 web server</li>
131 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
132 system on OSX<br />LGPL libraries courtesy of <a
133 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
135 <li>changed 'View nucleotide structure' submenu to 'View
136 VARNA 2D Structure'</li>
137 <li>change "View protein structure" menu option to "3D
140 </ul> <em>Applet</em>
142 <li>New layout for applet example pages</li>
143 <li>New parameters to enable SplitFrame view (file2,enableSplitFrame,
144 scaleProteinAsCdna)</li>
145 <li>New example demonstrating linked viewing of cDNA and
146 Protein alignments</li>
147 </ul> <em>Development and deployment</em>
149 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
150 <li>Include installation type and git revision in build
151 properties and console log output</li>
152 <li>Jalview Github organisation, and new github site for
153 storing BioJsMSA Templates</li>
154 <li>Jalview's unit tests now managed with TestNG</li></ul></td>
156 <!-- <em>General</em>
159 <!-- issues resolved --> <em>Application</em>
161 <li>Escape should close any open find dialogs</li>
162 <li>Typo in select-by-features status report</li>
163 <li>Consensus RNA secondary secondary structure
164 predictions are not highlighted in amber</li>
165 <li>Missing gap character in v2.7 example file means
166 alignment appears unaligned when pad-gaps is not enabled</li>
167 <li>First switch to RNA Helices colouring doesn't colour
168 associated structure views</li>
169 <li>ID width preference option is greyed out when auto
170 width checkbox not enabled</li>
171 <li>Stopped a warning dialog from being shown when
172 creating user defined colours</li>
173 <li>'View Mapping' in structure viewer shows sequence
174 mappings for just that viewer's sequences</li>
175 <li>Workaround for superposing PDB files containing
176 multiple models in Chimera</li>
177 <li>Report sequence position in status bar when hovering
178 over Jmol structure</li>
179 <li>Cannot output gaps as '.' symbols with Selection ->
180 output to text box</li>
181 <li>Flat file exports of alignments with hidden columns
182 have incorrect sequence start/end</li>
183 <li>'Aligning' a second chain to a Chimera structure from
185 <li>Colour schemes applied to structure viewers don't
186 work for nucleotide</li>
187 <li>Loading/cut'n'pasting an empty or invalid file leads
188 to a grey/invisible alignment window</li>
189 <li>Exported Jpred annotation from a sequence region
190 imports to different position</li>
191 <li>Space at beginning of sequence feature tooltips shown
192 on some platforms</li>
193 <li>Chimera viewer 'View | Show Chain' menu is not
195 <li>'New View' fails with a Null Pointer Exception in
196 console if Chimera has been opened</li>
197 <li>Mouseover to Chimera not working</li>
198 <li>Miscellaneous ENA XML feature qualifiers not
200 <li>NPE in annotation renderer after 'Extract Scores'</li>
201 <li>If two structures in one Chimera window, mouseover of
202 either sequence shows on first structure</li>
203 <li>'Show annotations' options should not make
204 non-positional annotations visible</li>
205 <li>Subsequence secondary structure annotation not shown
206 in right place after 'view flanking regions'</li>
207 <li>File Save As type unset when current file format is
209 <li>Save as '.jar' option removed for saving Jalview
211 <li>Colour by Sequence colouring in Chimera more
213 <li>Cannot 'add reference annotation' for a sequence in
214 several views on same alignment</li>
215 <li>Cannot show linked products for EMBL / ENA records</li>
216 <li>Jalview's tooltip wraps long texts containing no
218 </ul> <em>Applet</em>
219 <li>Jmol to JalviewLite mouseover/link not working</li>
220 <li>JalviewLite can't import sequences with ID descriptions
221 containing angle brackets</li>
223 </ul> <em>General</em>
225 <li>Cannot export and reimport RNA secondary structure
226 via jalview annotation file</li>
227 <li>Random helix colour palette for colour by annotation
228 with RNA secondary structure</li>
229 <li>Mouseover to cDNA from STOP residue in protein
230 translation doesn't work.</li>
231 <li>hints when using the select by annotation dialog box</li>
232 <li>Jmol alignment incorrect if PDB file has alternate CA
234 <li>FontChooser message dialog appears to hang after
235 choosing 1pt font</li>
236 <li>Peptide secondary structure incorrectly imported from
237 annotation file when annotation display text includes 'e' or
239 <li>Cannot set colour of new feature type whilst creating
241 <li>cDNA translation alignment should not be sequence
243 <li>'Show unconserved' doesn't work for lower case
245 <li>Nucleotide ambiguity codes involving R not recognised</li>
246 </ul> <em>Deployment and Documentation</em>
248 <li>Applet example pages appear different to the rest of
250 </ul> <em>Application Known issues</em>
252 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
253 <li>Misleading message appears after trying to delete
255 <li>Jalview icon not shown in dock after InstallAnywhere
256 version launches</li>
257 <li>Fetching EMBL reference for an RNA sequence results
258 fails with a sequence mismatch</li>
259 <li>Corrupted or unreadable alignment display when
260 scrolling alignment to right</li>
261 <li>ArrayIndexOutOfBoundsException thrown when remove
262 empty columns called on alignment with ragged gapped ends</li>
263 <li>auto calculated alignment annotation rows do not get
264 placed above or below non-autocalculated rows</li>
265 <li>Jalview dekstop becomes sluggish at full screen in
266 ultra-high resolution</li>
267 <li>Cannot disable consensus calculation independently of
268 quality and conservation</li>
269 <li>Mouseover highlighting between cDNA and protein can
270 become sluggish with more than one splitframe shown</li>
271 </ul> <em>Applet Known Issues</em>
273 <li>Core PDB parsing code requires Jmol</li>
274 <li>Sequence canvas panel goes white when alignment
275 window is being resized
281 <td width="60" nowrap>
283 <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
292 <ul><li>Reinstated the display of default example file on startup</li>
293 <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
299 <td><div align="center">
300 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
304 <li>Updated Java code signing certificate donated by Certum.PL.</li>
305 <li>Features and annotation preserved when performing pairwise
307 <li>RNA pseudoknot annotation can be
308 imported/exported/displayed</li>
309 <li>'colour by annotation' can colour by RNA and
310 protein secondary structure</li>
311 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
313 </ul> <em>Application</em>
315 <li>Extract and display secondary structure for sequences with
317 <li>Support for parsing RNAML</li>
318 <li>Annotations menu for layout
320 <li>sort sequence annotation rows by alignment</li>
321 <li>place sequence annotation above/below alignment
324 <li>Output in Stockholm format</li>
325 <li>Internationalisation: improved Spanish (es) translation</li>
326 <li>Structure viewer preferences tab</li>
327 <li>Disorder and Secondary Structure annotation tracks shared
328 between alignments</li>
329 <li>UCSF Chimera launch and linked highlighting from Jalview</li>
330 <li>Show/hide all sequence associated annotation rows for all
331 or current selection</li>
332 <li>disorder and secondary structure predictions available as
333 dataset annotation</li>
334 <li>Per-sequence rna helices colouring</li>
337 <li>Sequence database accessions imported when fetching
338 alignments from Rfam</li>
339 <li>update VARNA version to 3.91</li>
341 <li>New groovy scripts for exporting aligned positions,
342 conservation values, and calculating sum of pairs scores.</li>
343 <li>Command line argument to set default JABAWS server</li>
344 <li>include installation type in build properties and console
346 <li>Updated Jalview project format to preserve dataset annotation</li>
349 <!-- issues resolved --> <em>Application</em>
351 <li>Distinguish alignment and sequence associated RNA
352 structure in structure->view->VARNA</li>
353 <li>Raise dialog box if user deletes all sequences in an
355 <li>Pressing F1 results in documentation opening twice</li>
356 <li>Sequence feature tooltip is wrapped</li>
357 <li>Double click on sequence associated annotation selects
358 only first column</li>
359 <li>Redundancy removal doesn't result in unlinked leaves
361 <li>Undos after several redundancy removals don't undo
363 <li>Hide sequence doesn't hide associated annotation</li>
364 <li>User defined colours dialog box too big to fit on screen
365 and buttons not visible</li>
366 <li>author list isn't updated if already written to Jalview
368 <li>Popup menu won't open after retrieving sequence from
370 <li>File open window for associate PDB doesn't open</li>
371 <li>Left-then-right click on a sequence id opens a browser
373 <li>Cannot open sequence feature shading/sort popup menu in
374 feature settings dialog</li>
375 <li>better tooltip placement for some areas of Jalview desktop</li>
376 <li>Allow addition of JABAWS Server which doesn't pass
378 <li>Web services parameters dialog box is too large to fit on
380 <li>Muscle nucleotide alignment preset obscured by tooltip</li>
381 <li>JABAWS preset submenus don't contain newly defined
383 <li>MSA web services warns user if they were launched with
385 <li>Jalview cannot contact DAS Registy when running on Java 8</li>
387 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
388 'Superpose with' submenu not shown when new view created
391 </ul> <!-- <em>Applet</em>
393 </ul> <em>General</em>
395 </ul>--> <em>Deployment and Documentation</em>
397 <li>2G and 1G options in launchApp have no effect on memory
399 <li>launchApp service doesn't automatically open
400 www.jalview.org/examples/exampleFile.jar if no file is given</li>
402 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
403 InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
406 </ul> <em>Application Known issues</em>
409 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
410 corrupted or unreadable alignment display when scrolling alignment
414 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
415 retrieval fails but progress bar continues for DAS retrieval with
419 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
420 flatfile output of visible region has incorrect sequence start/end
423 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
424 rna structure consensus doesn't update when secondary
425 structure tracks are rearranged
428 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
429 invalid rna structure positional highlighting does not highlight
430 position of invalid base pairs
433 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
434 out of memory errors are not raised when saving Jalview project
435 from alignment window file menu
438 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
439 Switching to RNA Helices colouring doesn't propagate to
443 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
444 colour by RNA Helices not enabled when user created annotation
448 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
449 Jalview icon not shown on dock in Mountain Lion/Webstart
451 </ul> <em>Applet Known Issues</em>
454 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
455 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
458 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
459 Jalview and Jmol example not compatible with IE9
462 <li>Sort by annotation score doesn't reverse order when
468 <td><div align="center">
469 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
472 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
475 <li>Internationalisation of user interface (usually called
476 i18n support) and translation for Spanish locale</li>
477 <li>Define/Undefine group on current selection with
478 Ctrl-G/Shift Ctrl-G</li>
479 <li>Improved group creation/removal options in
480 alignment/sequence Popup menu</li>
481 <li>Sensible precision for symbol distribution percentages
482 shown in logo tooltip.</li>
483 <li>Annotation panel height set according to amount of
484 annotation when alignment first opened</li>
485 </ul> <em>Application</em>
487 <li>Interactive consensus RNA secondary structure prediction
488 VIENNA RNAAliFold JABA 2.1 service</li>
489 <li>Select columns containing particular features from Feature
491 <li>View all 'representative' PDB structures for selected
493 <li>Update Jalview project format:
495 <li>New file extension for Jalview projects '.jvp'</li>
496 <li>Preserve sequence and annotation dataset (to store
497 secondary structure annotation,etc)</li>
498 <li>Per group and alignment annotation and RNA helix
502 <li>New similarity measures for PCA and Tree calculation
504 <li>Experimental support for retrieval and viewing of flanking
505 regions for an alignment</li>
509 <!-- issues resolved --> <em>Application</em>
511 <li>logo keeps spinning and status remains at queued or
512 running after job is cancelled</li>
513 <li>cannot export features from alignments imported from
514 Jalview/VAMSAS projects</li>
515 <li>Buggy slider for web service parameters that take float
517 <li>Newly created RNA secondary structure line doesn't have
518 'display all symbols' flag set</li>
519 <li>T-COFFEE alignment score shading scheme and other
520 annotation shading not saved in Jalview project</li>
521 <li>Local file cannot be loaded in freshly downloaded Jalview</li>
522 <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
523 <li>Load file from desktop file browser fails</li>
524 <li>Occasional NPE thrown when calculating large trees</li>
525 <li>Cannot reorder or slide sequences after dragging an
526 alignment onto desktop</li>
527 <li>Colour by annotation dialog throws NPE after using
528 'extract scores' function</li>
529 <li>Loading/cut'n'pasting an empty file leads to a grey
530 alignment window</li>
531 <li>Disorder thresholds rendered incorrectly after performing
532 IUPred disorder prediction</li>
533 <li>Multiple group annotated consensus rows shown when
534 changing 'normalise logo' display setting</li>
535 <li>Find shows blank dialog after 'finished searching' if
536 nothing matches query</li>
537 <li>Null Pointer Exceptions raised when sorting by feature
538 with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
540 <li>Errors in Jmol console when structures in alignment don't
541 overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
543 <li>Not all working JABAWS services are shown in Jalview's
545 <li>JAVAWS version of Jalview fails to launch with 'invalid
546 literal/length code'</li>
547 <li>Annotation/RNA Helix colourschemes cannot be applied to
548 alignment with groups (actually fixed in 2.8.0b1)</li>
549 <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
551 </ul> <em>Applet</em>
553 <li>Remove group option is shown even when selection is not a
555 <li>Apply to all groups ticked but colourscheme changes don't
557 <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
558 <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
559 <li>Increased font size for dropdown menus on OSX and embedded windows</li>
562 <li>Consensus sequence for alignments/groups with a single
563 sequence were not calculated</li>
564 <li>annotation files that contain only groups imported as
565 annotation and junk sequences</li>
566 <li>Fasta files with sequences containing '*' incorrectly
567 recognised as PFAM or BLC</li>
568 <li>conservation/PID slider apply all groups option doesn't
569 affect background (2.8.0b1)
571 <li>redundancy highlighting is erratic at 0% and 100%</li>
572 <li>Remove gapped columns fails for sequences with ragged
574 <li>AMSA annotation row with leading spaces is not registered
575 correctly on import</li>
576 <li>Jalview crashes when selecting PCA analysis for certain
578 <li>Opening the colour by annotation dialog for an existing
579 annotation based 'use original colours' colourscheme loses
580 original colours setting</li>
585 <td><div align="center">
586 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
591 <li>Trusted certificates for JalviewLite applet and
592 Jalview Desktop application<br />Certificate was donated by
593 <a href="https://www.certum.eu">Certum</a> to the Jalview
594 open source project).
596 <li>Jalview SRS links replaced by Uniprot and EBI-search
598 <li>Output in Stockholm format</li>
599 <li>Allow import of data from gzipped files</li>
600 <li>Export/import group and sequence associated line
601 graph thresholds</li>
602 <li>Nucleotide substitution matrix that supports RNA and
604 <li>Allow disorder predictions to be made on the current
605 selection (or visible selection) in the same way that JPred
607 <li>Groovy scripting for headless Jalview operation</li>
608 </ul> <em>Other improvements</em>
610 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
611 <li>COMBINE statement uses current SEQUENCE_REF and
612 GROUP_REF scope to group annotation rows</li>
613 <li>Support '' style escaping of quotes in Newick
615 <li>Group options for JABAWS service by command line name</li>
616 <li>Empty tooltip shown for JABA service options with a
617 link but no description</li>
618 <li>Select primary source when selecting authority in
619 database fetcher GUI</li>
620 <li>Add .mfa to FASTA file extensions recognised by
622 <li>Annotation label tooltip text wrap</li>
627 <li>Slow scrolling when lots of annotation rows are
629 <li>Lots of NPE (and slowness) after creating RNA
630 secondary structure annotation line</li>
631 <li>Sequence database accessions not imported when
632 fetching alignments from Rfam</li>
633 <li>Incorrect SHMR submission for sequences with
635 <li>View all structures does not always superpose
637 <li>Option widgets in service parameters not updated to
638 reflect user or preset settings</li>
639 <li>Null pointer exceptions for some services without
640 presets or adjustable parameters</li>
641 <li>Discover PDB IDs entry in structure menu doesn't
642 discover PDB xRefs</li>
643 <li>Exception encountered while trying to retrieve
644 features with DAS</li>
645 <li>Lowest value in annotation row isn't coloured
646 when colour by annotation (per sequence) is coloured</li>
647 <li>Keyboard mode P jumps to start of gapped region when
648 residue follows a gap</li>
649 <li>Jalview appears to hang importing an alignment with
650 Wrap as default or after enabling Wrap</li>
651 <li>'Right click to add annotations' message
652 shown in wrap mode when no annotations present</li>
653 <li>Disorder predictions fail with NPE if no automatic
654 annotation already exists on alignment</li>
655 <li>oninit javascript function should be called after
656 initialisation completes</li>
657 <li>Remove redundancy after disorder prediction corrupts
658 alignment window display</li>
659 <li>Example annotation file in documentation is invalid</li>
660 <li>Grouped line graph annotation rows are not exported
661 to annotation file</li>
662 <li>Multi-harmony analysis cannot be run when only two
664 <li>Cannot create multiple groups of line graphs with
665 several 'combine' statements in annotation file</li>
666 <li>Pressing return several times causes Number Format
667 exceptions in keyboard mode</li>
668 <li>Multi-harmony (SHMMR) method doesn't submit
669 correct partitions for input data</li>
670 <li>Translation from DNA to Amino Acids fails</li>
671 <li>Jalview fail to load newick tree with quoted label</li>
672 <li>--headless flag isn't understood</li>
673 <li>ClassCastException when generating EPS in headless
675 <li>Adjusting sequence-associated shading threshold only
676 changes one row's threshold</li>
677 <li>Preferences and Feature settings panel panel
678 doesn't open</li>
679 <li>hide consensus histogram also hides conservation and
680 quality histograms</li>
685 <td><div align="center">
686 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
688 <td><em>Application</em>
689 <ul><li>Support for JABAWS 2.0 Services (AACon alignment
690 conservation, protein disorder and Clustal Omega)</li>
691 <li>JABAWS server status indicator in Web Services preferences
693 <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
694 Jalview alignment window</li>
695 <li>Updated Jalview build and deploy framework for OSX mountain
696 lion, windows 7, and 8</li>
697 <li>Nucleotide substitution matrix for PCA that supports RNA
698 and ambiguity codes</li>
700 <li>Improved sequence database retrieval GUI</li>
701 <li>Support fetching and database reference look up against
702 multiple DAS sources (Fetch all from in 'fetch db refs')</li>
703 <li>Jalview project improvements
705 <li>Store and retrieve the 'belowAlignment' flag for
707 <li>calcId attribute to group annotation rows on the
709 <li>Store AACon calculation settings for a view in Jalview
714 <li>horizontal scrolling gesture support</li>
715 <li>Visual progress indicator when PCA calculation is running</li>
716 <li>Simpler JABA web services menus</li>
717 <li>visual indication that web service results are still being
718 retrieved from server</li>
719 <li>Serialise the dialogs that are shown when Jalview starts up
721 <li>Jalview user agent string for interacting with HTTP
723 <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
725 <li>Examples directory and Groovy library included in
726 InstallAnywhere distribution</li>
727 </ul> <em>Applet</em>
729 <li>RNA alignment and secondary structure annotation
730 visualization applet example</li>
731 </ul> <em>General</em>
733 <li>Normalise option for consensus sequence logo</li>
734 <li>Reset button in PCA window to return dimensions to
736 <li>Allow seqspace or Jalview variant of alignment PCA
738 <li>PCA with either nucleic acid and protein substitution
740 <li>Allow windows containing HTML reports to be exported in
742 <li>Interactive display and editing of RNA secondary structure
744 <li>RNA Helix Alignment Colouring</li>
745 <li>RNA base pair logo consensus</li>
746 <li>Parse sequence associated secondary structure information
747 in Stockholm files</li>
748 <li>HTML Export database accessions and annotation information
749 presented in tooltip for sequences</li>
750 <li>Import secondary structure from LOCARNA clustalw style RNA
752 <li>import and visualise T-COFFEE quality scores for an
754 <li>'colour by annotation' per sequence option to
755 shade each sequence according to its associated alignment
757 <li>New Jalview Logo</li>
758 </ul> <em>Documentation and Development</em>
760 <li>documentation for score matrices used in Jalview</li>
761 <li>New Website!</li>
763 <td><em>Application</em>
765 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
766 wsdbfetch REST service</li>
767 <li>Stop windows being moved outside desktop on OSX</li>
768 <li>Filetype associations not installed for webstart launch</li>
769 <li>Jalview does not always retrieve progress of a JABAWS job
770 execution in full once it is complete</li>
771 <li>revise SHMR RSBS definition to ensure alignment is
772 uploaded via ali_file parameter</li>
773 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
774 <li>View all structures superposed fails with exception</li>
775 <li>Jnet job queues forever if a very short sequence is
776 submitted for prediction</li>
777 <li>Cut and paste menu not opened when mouse clicked on
779 <li>Putting fractional value into integer text box in
780 alignment parameter dialog causes Jalview to hang</li>
781 <li>Structure view highlighting doesn't work on windows 7
783 <li>View all structures fails with exception shown in
785 <li>Characters in filename associated with PDBEntry not
786 escaped in a platform independent way</li>
787 <li>Jalview desktop fails to launch with exception when using
789 <li>Tree calculation reports 'you must have 2 or more
790 sequences selected' when selection is empty</li>
791 <li>Jalview desktop fails to launch with jar signature failure
792 when java web start temporary file caching is disabled</li>
793 <li>DAS Sequence retrieval with range qualification results in
794 sequence xref which includes range qualification</li>
795 <li>Errors during processing of command line arguments cause
796 progress bar (JAL-898) to be removed</li>
797 <li>Replace comma for semi-colon option not disabled for DAS
798 sources in sequence fetcher</li>
799 <li>Cannot close news reader when JABAWS server warning dialog
801 <li>Option widgets not updated to reflect user settings</li>
802 <li>Edited sequence not submitted to web service</li>
803 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
804 <li>InstallAnywhere installer doesn't unpack and run on
805 OSX Mountain Lion</li>
806 <li>Annotation panel not given a scroll bar when sequences
807 with alignment annotation are pasted into the alignment</li>
808 <li>Sequence associated annotation rows not associated when
809 loaded from Jalview project</li>
810 <li>Browser launch fails with NPE on java 1.7</li>
811 <li>JABAWS alignment marked as finished when job was cancelled
812 or job failed due to invalid input</li>
813 <li>NPE with v2.7 example when clicking on Tree associated
815 <li>Exceptions when copy/paste sequences with grouped
816 annotation rows to new window</li>
817 </ul> <em>Applet</em>
819 <li>Sequence features are momentarily displayed before they
820 are hidden using hidefeaturegroups applet parameter</li>
821 <li>loading features via javascript API automatically enables
823 <li>scrollToColumnIn javascript API method doesn't work</li>
824 </ul> <em>General</em>
826 <li>Redundancy removal fails for rna alignment</li>
827 <li>PCA calculation fails when sequence has been selected and
829 <li>PCA window shows grey box when first opened on OSX</li>
830 <li>Letters coloured pink in sequence logo when alignment
831 coloured with clustalx</li>
832 <li>Choosing fonts without letter symbols defined causes
833 exceptions and redraw errors</li>
834 <li>Initial PCA plot view is not same as manually reconfigured
836 <li>Grouped annotation graph label has incorrect line colour</li>
837 <li>Grouped annotation graph label display is corrupted for
844 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
847 <td><em>Application</em>
849 <li>Jalview Desktop News Reader</li>
850 <li>Tweaked default layout of web services menu</li>
851 <li>View/alignment association menu to enable user to easily
852 specify which alignment a multi-structure view takes its
853 colours/correspondences from</li>
854 <li>Allow properties file location to be specified as URL</li>
855 <li>Extend Jalview project to preserve associations between
856 many alignment views and a single Jmol display</li>
857 <li>Store annotation row height in Jalview project file</li>
858 <li>Annotation row column label formatting attributes stored
860 <li>Annotation row order for auto-calculated annotation rows
861 preserved in Jalview project file</li>
862 <li>Visual progress indication when Jalview state is saved
863 using Desktop window menu</li>
864 <li>Visual indication that command line arguments are still
866 <li>Groovy script execution from URL</li>
867 <li>Colour by annotation default min and max colours in
869 <li>Automatically associate PDB files dragged onto an
870 alignment with sequences that have high similarity and matching
872 <li>Update JGoogleAnalytics to latest release (0.3)</li>
873 <li>'view structures' option to open many structures
875 <li>Sort associated views menu option for tree panel</li>
876 <li>Group all JABA and non-JABA services for a particular
877 analysis function in its own submenu</li>
878 </ul> <em>Applet</em>
880 <li>Userdefined and autogenerated annotation rows for groups</li>
881 <li>Adjustment of alignment annotation pane height</li>
882 <li>Annotation scrollbar for annotation panel</li>
883 <li>Drag to reorder annotation rows in annotation panel</li>
884 <li>'automaticScrolling' parameter</li>
885 <li>Allow sequences with partial ID string matches to be
886 annotated from GFF/Jalview features files</li>
887 <li>Sequence logo annotation row in applet</li>
888 <li>Absolute paths relative to host server in applet
889 parameters are treated as such</li>
890 <li>New in the JalviewLite javascript API:
892 <li>JalviewLite.js javascript library</li>
893 <li>Javascript callbacks for
895 <li>Applet initialisation</li>
896 <li>Sequence/alignment mouse-overs and selections</li>
899 <li>scrollTo row and column alignment scrolling functions</li>
900 <li>Select sequence/alignment regions from javascript</li>
901 <li>javascript structure viewer harness to pass messages
902 between Jmol and Jalview when running as distinct applets</li>
903 <li>sortBy method</li>
904 <li>Set of applet and application examples shipped with
906 <li>New example to demonstrate JalviewLite and Jmol
907 javascript message exchange</li>
909 </ul> <em>General</em>
911 <li>Enable Jmol displays to be associated with multiple
912 multiple alignments</li>
913 <li>Option to automatically sort alignment with new tree</li>
914 <li>User configurable link to enable redirects to a
915 www.Jalview.org mirror</li>
916 <li>Jmol colours option for Jmol displays</li>
917 <li>Configurable newline string when writing alignment and
918 other flat files</li>
919 <li>Allow alignment annotation description lines to contain
921 </ul> <em>Documentation and Development</em>
923 <li>Add groovy test harness for bulk load testing to examples
925 <li>Groovy script to load and align a set of sequences using a
926 web service before displaying the result in the Jalview desktop</li>
927 <li>Restructured javascript and applet api documentation</li>
928 <li>Ant target to publish example html files with applet
930 <li>Netbeans project for building Jalview from source</li>
931 <li>ant task to create online javadoc for Jalview source</li>
933 <td><em>Application</em>
935 <li>User defined colourscheme throws exception when current
936 built in colourscheme is saved as new scheme</li>
937 <li>AlignFrame->Save in application pops up save dialog for
938 valid filename/format</li>
939 <li>Cannot view associated structure for Uniprot sequence</li>
940 <li>PDB file association breaks for Uniprot sequence P37173</li>
941 <li>Associate PDB from file dialog does not tell you which
942 sequence is to be associated with the file</li>
943 <li>Find All raises null pointer exception when query only
944 matches sequence IDs</li>
945 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
946 <li>Jalview project with Jmol views created with Jalview 2.4
947 cannot be loaded</li>
948 <li>Filetype associations not installed for webstart launch</li>
949 <li>Two or more chains in a single PDB file associated with
950 sequences in different alignments do not get coloured by their
951 associated sequence</li>
952 <li>Visibility status of autocalculated annotation row not
953 preserved when project is loaded</li>
954 <li>Annotation row height and visibility attributes not stored
955 in Jalview project</li>
956 <li>Tree bootstraps are not preserved when saved as a Jalview
958 <li>Envision2 workflow tooltips are corrupted</li>
959 <li>Enabling show group conservation also enables colour by
961 <li>Duplicate group associated conservation or consensus
962 created on new view</li>
963 <li>Annotation scrollbar not displayed after 'show all
964 hidden annotation rows' option selected</li>
965 <li>Alignment quality not updated after alignment annotation
966 row is hidden then shown</li>
967 <li>Preserve colouring of structures coloured by sequences in
968 pre Jalview 2.7 projects</li>
969 <li>Web service job parameter dialog is not laid out properly
971 <li>Web services menu not refreshed after 'reset
972 services' button is pressed in preferences</li>
973 <li>Annotation off by one in Jalview v2_3 example project</li>
974 <li>Structures imported from file and saved in project get
975 name like jalview_pdb1234.txt when reloaded</li>
976 <li>Jalview does not always retrieve progress of a JABAWS job
977 execution in full once it is complete</li>
978 </ul> <em>Applet</em>
980 <li>Alignment height set incorrectly when lots of annotation
981 rows are displayed</li>
982 <li>Relative URLs in feature HTML text not resolved to
984 <li>View follows highlighting does not work for positions in
986 <li><= shown as = in tooltip</li>
987 <li>Export features raises exception when no features exist</li>
988 <li>Separator string used for serialising lists of IDs for
989 javascript api is modified when separator string provided as
991 <li>Null pointer exception when selecting tree leaves for
992 alignment with no existing selection</li>
993 <li>Relative URLs for datasources assumed to be relative to
994 applet's codebase</li>
995 <li>Status bar not updated after finished searching and search
996 wraps around to first result</li>
997 <li>StructureSelectionManager instance shared between several
998 Jalview applets causes race conditions and memory leaks</li>
999 <li>Hover tooltip and mouseover of position on structure not
1000 sent from Jmol in applet</li>
1001 <li>Certain sequences of javascript method calls to applet API
1002 fatally hang browser</li>
1003 </ul> <em>General</em>
1005 <li>View follows structure mouseover scrolls beyond position
1006 with wrapped view and hidden regions</li>
1007 <li>Find sequence position moves to wrong residue with/without
1009 <li>Sequence length given in alignment properties window is
1011 <li>InvalidNumberFormat exceptions thrown when trying to
1012 import PDB like structure files</li>
1013 <li>Positional search results are only highlighted between
1014 user-supplied sequence start/end bounds</li>
1015 <li>End attribute of sequence is not validated</li>
1016 <li>Find dialog only finds first sequence containing a given
1017 sequence position</li>
1018 <li>Sequence numbering not preserved in MSF alignment output</li>
1019 <li>Jalview PDB file reader does not extract sequence from
1020 nucleotide chains correctly</li>
1021 <li>Structure colours not updated when tree partition changed
1023 <li>Sequence associated secondary structure not correctly
1024 parsed in interleaved stockholm</li>
1025 <li>Colour by annotation dialog does not restore current state
1027 <li>Hiding (nearly) all sequences doesn't work properly</li>
1028 <li>Sequences containing lowercase letters are not properly
1029 associated with their pdb files</li>
1030 </ul> <em>Documentation and Development</em>
1032 <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
1038 <div align="center">
1039 <strong><a name="Jalview2.6.1">2.6.1</a>
1040 </strong><br> <em>15/11/2010</em>
1042 <td><em>Application</em>
1044 <li>New warning dialog when the Jalview Desktop cannot contact
1046 <li>JABA service parameters for a preset are shown in service
1048 <li>JABA Service menu entries reworded</li>
1052 <li>Modeller PIR IO broken - cannot correctly import a pir
1053 file emitted by Jalview</li>
1054 <li>Existing feature settings transferred to new alignment
1055 view created from cut'n'paste</li>
1056 <li>Improved test for mixed amino/nucleotide chains when
1057 parsing PDB files</li>
1058 <li>Consensus and conservation annotation rows occasionally
1059 become blank for all new windows</li>
1060 <li>Exception raised when right clicking above sequences in
1061 wrapped view mode</li>
1062 </ul> <em>Application</em>
1064 <li>multiple multiply aligned structure views cause cpu usage
1065 to hit 100% and computer to hang</li>
1066 <li>Web Service parameter layout breaks for long user
1067 parameter names</li>
1068 <li>Jaba service discovery hangs desktop if Jaba server is
1074 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
1075 <em>26/9/2010</em></div>
1077 <td><em>Application</em>
1079 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1080 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
1081 <li>Web Services preference tab</li>
1082 <li>Analysis parameters dialog box and user defined preferences</li>
1083 <li>Improved speed and layout of Envision2 service menu</li>
1084 <li>Superpose structures using associated sequence alignment</li>
1085 <li>Export coordinates and projection as CSV from PCA viewer</li>
1089 <li>enable javascript: execution by the applet via the link out
1094 <li>Updated the Jmol Jalview interface to work with Jmol series
1096 <li>The Jalview Desktop and JalviewLite applet now require Java
1098 <li>Allow Jalview feature colour specification for GFF sequence
1099 annotation files</li>
1100 <li>New 'colour by label' keword in Jalview feature file type
1101 colour specification</li>
1102 <li>New Jalview Desktop Groovy API method that allows a script
1103 to check if it being run in an interactive session or in a batch
1104 operation from the Jalview command line</li>
1109 <li>clustalx colourscheme colours Ds preferentially when both
1110 D+E are present in over 50% of the column</li>
1113 <em>Application</em>
1115 <li>typo in AlignmentFrame->View->Hide->all but
1116 selected Regions menu item</li>
1117 <li>sequence fetcher replaces ',' for ';' when the ',' is part
1118 of a valid accession ID</li>
1119 <li>fatal OOM if object retrieved by sequence fetcher runs out
1121 <li>unhandled Out of Memory Error when viewing pca analysis
1123 <li>InstallAnywhere builds fail to launch on OS X java 10.5
1124 update 4 (due to apple Java 1.6 update)</li>
1125 <li>Installanywhere Jalview silently fails to launch</li>
1129 <li>Jalview.getFeatureGroups() raises an
1130 ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
1136 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
1137 <em>14/6/2010</em></div>
1142 <li>Alignment prettyprinter doesn't cope with long sequence IDs
1144 <li>clustalx colourscheme colours Ds preferentially when both
1145 D+E are present in over 50% of the column</li>
1146 <li>nucleic acid structures retrieved from PDB do not import
1148 <li>More columns get selected than were clicked on when a number
1149 of columns are hidden</li>
1150 <li>annotation label popup menu not providing correct
1151 add/hide/show options when rows are hidden or none are present</li>
1152 <li>Stockholm format shown in list of readable formats, and
1153 parser copes better with alignments from RFAM.</li>
1154 <li>CSV output of consensus only includes the percentage of all
1155 symbols if sequence logo display is enabled</li>
1160 <li>annotation panel disappears when annotation is
1163 <em>Application</em>
1165 <li>Alignment view not redrawn properly when new alignment
1166 opened where annotation panel is visible but no annotations are
1167 present on alignment</li>
1168 <li>pasted region containing hidden columns is incorrectly
1169 displayed in new alignment window</li>
1170 <li>Jalview slow to complete operations when stdout is flooded
1171 (fix is to close the Jalview console)</li>
1172 <li>typo in AlignmentFrame->View->Hide->all but
1173 selected Rregions menu item.</li>
1174 <li>inconsistent group submenu and Format submenu entry 'Un' or
1176 <li>Sequence feature settings are being shared by multiple
1177 distinct alignments</li>
1178 <li>group annotation not recreated when tree partition is
1180 <li>double click on group annotation to select sequences does
1181 not propagate to associated trees</li>
1182 <li>Mac OSX specific issues:
1184 <li>exception raised when mouse clicked on desktop window
1186 <li>Desktop menu placed on menu bar and application name set
1188 <li>sequence feature settings not wide enough for the save
1189 feature colourscheme button</li>
1198 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
1199 <em>30/4/2010</em></div>
1201 <td><em>New Capabilities</em>
1203 <li>URL links generated from description line for
1204 regular-expression based URL links (applet and application)
1205 <li>Non-positional feature URL links are shown in link menu</li>
1206 <li>Linked viewing of nucleic acid sequences and structures</li>
1207 <li>Automatic Scrolling option in View menu to display the
1208 currently highlighted region of an alignment.</li>
1209 <li>Order an alignment by sequence length, or using the average
1210 score or total feature count for each sequence.</li>
1211 <li>Shading features by score or associated description</li>
1212 <li>Subdivide alignment and groups based on identity of selected
1213 subsequence (Make Groups from Selection).</li>
1214 <li>New hide/show options including Shift+Control+H to hide
1215 everything but the currently selected region.</li>
1216 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1218 <em>Application</em>
1220 <li>Fetch DB References capabilities and UI expanded to support
1221 retrieval from DAS sequence sources</li>
1222 <li>Local DAS Sequence sources can be added via the command line
1223 or via the Add local source dialog box.</li>
1224 <li>DAS Dbref and DbxRef feature types are parsed as database
1225 references and protein_name is parsed as description line (BioSapiens
1227 <li>Enable or disable non-positional feature and database
1228 references in sequence ID tooltip from View menu in application.</li>
1229 <!-- <li>New hidden columns and rows and representatives capabilities
1230 in annotations file (in progress - not yet fully implemented)</li> -->
1231 <li>Group-associated consensus, sequence logos and conservation
1233 <li>Symbol distributions for each column can be exported and
1234 visualized as sequence logos</li>
1235 <li>Optionally scale multi-character column labels to fit within
1236 each column of annotation row<!-- todo for applet --></li>
1237 <li>Optional automatic sort of associated alignment view when a
1238 new tree is opened.</li>
1239 <li>Jalview Java Console</li>
1240 <li>Better placement of desktop window when moving between
1241 different screens.</li>
1242 <li>New preference items for sequence ID tooltip and consensus
1244 <li>Client to submit sequences and IDs to <a
1245 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
1246 <li><em>Vamsas Capabilities</em>
1248 <li>Improved VAMSAS synchronization (Jalview archive used to
1249 preserve views, structures, and tree display settings)</li>
1250 <li>Import of vamsas documents from disk or URL via command
1252 <li>Sharing of selected regions between views and with other
1253 VAMSAS applications (Experimental feature!)</li>
1254 <li>Updated API to VAMSAS version 0.2</li>
1260 <li>Middle button resizes annotation row height</li>
1263 <li>sortByTree (true/false) - automatically sort the associated
1264 alignment view by the tree when a new tree is opened.</li>
1265 <li>showTreeBootstraps (true/false) - show or hide branch
1266 bootstraps (default is to show them if available)</li>
1267 <li>showTreeDistances (true/false) - show or hide branch
1268 lengths (default is to show them if available)</li>
1269 <li>showUnlinkedTreeNodes (true/false) - indicate if
1270 unassociated nodes should be highlighted in the tree view</li>
1271 <li>heightScale and widthScale (1.0 or more) - increase the
1272 height or width of a cell in the alignment grid relative to the
1273 current font size.</li>
1276 <li>Non-positional features displayed in sequence ID tooltip</li>
1280 <li>Features format: graduated colour definitions and
1281 specification of feature scores</li>
1282 <li>Alignment Annotations format: new keywords for group
1283 associated annotation (GROUP_REF) and annotation row display
1284 properties (ROW_PROPERTIES)</li>
1285 <li>XML formats extended to support graduated feature
1286 colourschemes, group associated annotation, and profile visualization
1291 <li>Source field in GFF files parsed as feature source rather
1292 than description</li>
1293 <li>Non-positional features are now included in sequence feature
1294 and gff files (controlled via non-positional feature visibility in
1296 <li>URL links generated for all feature links (bugfix)</li>
1297 <li>Added URL embedding instructions to features file
1299 <li>Codons containing ambiguous nucleotides translated as 'X' in
1300 peptide product</li>
1301 <li>Match case switch in find dialog box works for both sequence
1302 ID and sequence string and query strings do not have to be in upper
1303 case to match case-insensitively.</li>
1304 <li>AMSA files only contain first column of multi-character
1305 column annotation labels</li>
1306 <li>Jalview Annotation File generation/parsing consistent with
1307 documentation (e.g. Stockholm annotation can be exported and
1309 <li>PDB files without embedded PDB IDs given a friendly name</li>
1310 <li>Find incrementally searches ID string matches as well as
1311 subsequence matches, and correctly reports total number of both.</li>
1314 <li>Better handling of exceptions during sequence retrieval</li>
1315 <li>Dasobert generated non-positional feature URL link text
1316 excludes the start_end suffix</li>
1317 <li>DAS feature and source retrieval buttons disabled when
1318 fetch or registry operations in progress.</li>
1319 <li>PDB files retrieved from URLs are cached properly</li>
1320 <li>Sequence description lines properly shared via VAMSAS</li>
1321 <li>Sequence fetcher fetches multiple records for all data
1323 <li>Ensured that command line das feature retrieval completes
1324 before alignment figures are generated.</li>
1325 <li>Reduced time taken when opening file browser for first
1327 <li>isAligned check prior to calculating tree, PCA or
1328 submitting an MSA to JNet now excludes hidden sequences.</li>
1329 <li>User defined group colours properly recovered from Jalview
1339 <div align="center"><strong>2.4.0.b2</strong><br>
1344 <li>Experimental support for google analytics usage tracking.</li>
1345 <li>Jalview privacy settings (user preferences and docs).</li>
1350 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
1351 <li>Exception when feature created from selection beyond length
1353 <li>Allow synthetic PDB files to be imported gracefully</li>
1354 <li>Sequence associated annotation rows associate with all
1355 sequences with a given id</li>
1356 <li>Find function matches case-insensitively for sequence ID
1357 string searches</li>
1358 <li>Non-standard characters do not cause pairwise alignment to
1359 fail with exception</li>
1361 <em>Application Issues</em>
1363 <li>Sequences are now validated against EMBL database</li>
1364 <li>Sequence fetcher fetches multiple records for all data
1367 <em>InstallAnywhere Issues</em>
1369 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
1370 installAnywhere mechanism)</li>
1371 <li>Command line launching of JARs from InstallAnywhere version
1372 (java class versioning error fixed)</li>
1379 <div align="center"><strong>2.4</strong><br>
1382 <td><em>User Interface</em>
1384 <li>Linked highlighting of codon and amino acid from translation
1385 and protein products</li>
1386 <li>Linked highlighting of structure associated with residue
1387 mapping to codon position</li>
1388 <li>Sequence Fetcher provides example accession numbers and
1390 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
1391 <li>Extract score function to parse whitespace separated numeric
1392 data in description line</li>
1393 <li>Column labels in alignment annotation can be centred.</li>
1394 <li>Tooltip for sequence associated annotation give name of
1397 <em>Web Services and URL fetching</em>
1399 <li>JPred3 web service</li>
1400 <li>Prototype sequence search client (no public services
1402 <li>Fetch either seed alignment or full alignment from PFAM</li>
1403 <li>URL Links created for matching database cross references as
1404 well as sequence ID</li>
1405 <li>URL Links can be created using regular-expressions</li>
1407 <em>Sequence Database Connectivity</em>
1409 <li>Retrieval of cross-referenced sequences from other databases
1411 <li>Generalised database reference retrieval and validation to
1412 all fetchable databases</li>
1413 <li>Fetch sequences from DAS sources supporting the sequence
1416 <em>Import and Export</em>
1417 <li>export annotation rows as CSV for spreadsheet import</li>
1418 <li>Jalview projects record alignment dataset associations, EMBL
1419 products, and cDNA sequence mappings</li>
1420 <li>Sequence Group colour can be specified in Annotation File</li>
1421 <li>Ad-hoc colouring of group in Annotation File using RGB
1422 triplet as name of colourscheme</li>
1424 <em>VAMSAS Client capabilities (Experimental)</em>
1426 <li>treenode binding for VAMSAS tree exchange</li>
1427 <li>local editing and update of sequences in VAMSAS alignments
1429 <li>Create new or select existing session to join</li>
1430 <li>load and save of vamsas documents</li>
1432 <em>Application command line</em>
1434 <li>-tree parameter to open trees (introduced for passing from
1436 <li>-fetchfrom command line argument to specify nicknames of DAS
1437 servers to query for alignment features</li>
1438 <li>-dasserver command line argument to add new servers that are
1439 also automatically queried for features</li>
1440 <li>-groovy command line argument executes a given groovy script
1441 after all input data has been loaded and parsed</li>
1443 <em>Applet-Application data exchange</em>
1445 <li>Trees passed as applet parameters can be passed to
1446 application (when using "View in full application")</li>
1448 <em>Applet Parameters</em>
1450 <li>feature group display control parameter</li>
1451 <li>debug parameter</li>
1452 <li>showbutton parameter</li>
1454 <em>Applet API methods</em>
1456 <li>newView public method</li>
1457 <li>Window (current view) specific get/set public methods</li>
1458 <li>Feature display control methods</li>
1459 <li>get list of currently selected sequences</li>
1461 <em>New Jalview distribution features</em>
1463 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1464 <li>RELEASE file gives build properties for the latest Jalview
1466 <li>Java 1.1 Applet build made easier and donotobfuscate
1467 property controls execution of obfuscator</li>
1468 <li>Build target for generating source distribution</li>
1469 <li>Debug flag for javacc</li>
1470 <li>.jalview_properties file is documented (slightly) in
1471 jalview.bin.Cache</li>
1472 <li>Continuous Build Integration for stable and development
1473 version of Application, Applet and source distribution</li>
1479 <li>selected region output includes visible annotations (for
1480 certain formats)</li>
1481 <li>edit label/displaychar contains existing label/char for
1483 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1484 <li>shorter peptide product names from EMBL records</li>
1485 <li>Newick string generator makes compact representations</li>
1486 <li>bootstrap values parsed correctly for tree files with
1488 <li>pathological filechooser bug avoided by not allowing
1489 filenames containing a ':'</li>
1490 <li>Fixed exception when parsing GFF files containing global
1491 sequence features</li>
1492 <li>Alignment datasets are finalized only when number of
1493 references from alignment sequences goes to zero</li>
1494 <li>Close of tree branch colour box without colour selection
1495 causes cascading exceptions</li>
1496 <li>occasional negative imgwidth exceptions</li>
1497 <li>better reporting of non-fatal warnings to user when file
1499 <li>Save works when Jalview project is default format</li>
1500 <li>Save as dialog opened if current alignment format is not a
1501 valid output format</li>
1502 <li>Uniprot canonical names introduced for both das and vamsas</li>
1503 <li>Histidine should be midblue (not pink!) in Zappo</li>
1504 <li>error messages passed up and output when data read fails</li>
1505 <li>edit undo recovers previous dataset sequence when sequence
1507 <li>allow PDB files without pdb ID HEADER lines (like those
1508 generated by MODELLER) to be read in properly</li>
1509 <li>allow reading of JPred concise files as a normal filetype</li>
1510 <li>Stockholm annotation parsing and alignment properties import
1511 fixed for PFAM records</li>
1512 <li>Structure view windows have correct name in Desktop window
1514 <li>annotation consisting of sequence associated scores can be
1515 read and written correctly to annotation file</li>
1516 <li>Aligned cDNA translation to aligned peptide works correctly</li>
1517 <li>Fixed display of hidden sequence markers and non-italic font
1518 for representatives in Applet</li>
1519 <li>Applet Menus are always embedded in applet window on Macs.</li>
1520 <li>Newly shown features appear at top of stack (in Applet)</li>
1521 <li>Annotations added via parameter not drawn properly due to
1522 null pointer exceptions</li>
1523 <li>Secondary structure lines are drawn starting from first
1524 column of alignment</li>
1525 <li>Uniprot XML import updated for new schema release in July
1527 <li>Sequence feature to sequence ID match for Features file is
1528 case-insensitive</li>
1529 <li>Sequence features read from Features file appended to all
1530 sequences with matching IDs</li>
1531 <li>PDB structure coloured correctly for associated views
1532 containing a sub-sequence</li>
1533 <li>PDB files can be retrieved by applet from Jar files</li>
1534 <li>feature and annotation file applet parameters referring to
1535 different directories are retrieved correctly</li>
1536 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1537 <li>Fixed application hang whilst waiting for splash-screen
1538 version check to complete</li>
1539 <li>Applet properly URLencodes input parameter values when
1540 passing them to the launchApp service</li>
1541 <li>display name and local features preserved in results
1542 retrieved from web service</li>
1543 <li>Visual delay indication for sequence retrieval and sequence
1544 fetcher initialisation</li>
1545 <li>updated Application to use DAS 1.53e version of dasobert DAS
1547 <li>Re-instated Full AMSA support and .amsa file association</li>
1548 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1555 <div align="center"><strong>2.3</strong><br>
1560 <li>Jmol 11.0.2 integration</li>
1561 <li>PDB views stored in Jalview XML files</li>
1562 <li>Slide sequences</li>
1563 <li>Edit sequence in place</li>
1564 <li>EMBL CDS features</li>
1565 <li>DAS Feature mapping</li>
1566 <li>Feature ordering</li>
1567 <li>Alignment Properties</li>
1568 <li>Annotation Scores</li>
1569 <li>Sort by scores</li>
1570 <li>Feature/annotation editing in applet</li>
1575 <li>Headless state operation in 2.2.1</li>
1576 <li>Incorrect and unstable DNA pairwise alignment</li>
1577 <li>Cut and paste of sequences with annotation</li>
1578 <li>Feature group display state in XML</li>
1579 <li>Feature ordering in XML</li>
1580 <li>blc file iteration selection using filename # suffix</li>
1581 <li>Stockholm alignment properties</li>
1582 <li>Stockhom alignment secondary structure annotation</li>
1583 <li>2.2.1 applet had no feature transparency</li>
1584 <li>Number pad keys can be used in cursor mode</li>
1585 <li>Structure Viewer mirror image resolved</li>
1592 <div align="center"><strong>2.2.1</strong><br>
1597 <li>Non standard characters can be read and displayed
1598 <li>Annotations/Features can be imported/exported to the applet
1600 <li>Applet allows editing of sequence/annotation/group name
1602 <li>Preference setting to display sequence name in italics
1603 <li>Annotation file format extended to allow Sequence_groups to
1605 <li>Default opening of alignment overview panel can be specified
1607 <li>PDB residue numbering annotation added to associated
1613 <li>Applet crash under certain Linux OS with Java 1.6 installed
1614 <li>Annotation file export / import bugs fixed
1615 <li>PNG / EPS image output bugs fixed
1621 <div align="center"><strong>2.2</strong><br>
1626 <li>Multiple views on alignment
1627 <li>Sequence feature editing
1628 <li>"Reload" alignment
1629 <li>"Save" to current filename
1630 <li>Background dependent text colour
1631 <li>Right align sequence ids
1632 <li>User-defined lower case residue colours
1635 <li>Menu item accelerator keys
1636 <li>Control-V pastes to current alignment
1637 <li>Cancel button for DAS Feature Fetching
1638 <li>PCA and PDB Viewers zoom via mouse roller
1639 <li>User-defined sub-tree colours and sub-tree selection
1640 <li>'New Window' button on the 'Output to Text box'
1645 <li>New memory efficient Undo/Redo System
1646 <li>Optimised symbol lookups and conservation/consensus
1648 <li>Region Conservation/Consensus recalculated after edits
1649 <li>Fixed Remove Empty Columns Bug (empty columns at end of
1651 <li>Slowed DAS Feature Fetching for increased robustness.
1652 <li>Made angle brackets in ASCII feature descriptions display
1654 <li>Re-instated Zoom function for PCA
1655 <li>Sequence descriptions conserved in web service analysis
1657 <li>Uniprot ID discoverer uses any word separated by ∣
1658 <li>WsDbFetch query/result association resolved
1659 <li>Tree leaf to sequence mapping improved
1660 <li>Smooth fonts switch moved to FontChooser dialog box.
1666 <div align="center"><strong>2.1.1</strong><br>
1671 <li>Copy consensus sequence to clipboard</li>
1676 <li>Image output - rightmost residues are rendered if sequence
1677 id panel has been resized</li>
1678 <li>Image output - all offscreen group boundaries are rendered</li>
1679 <li>Annotation files with sequence references - all elements in
1680 file are relative to sequence position</li>
1681 <li>Mac Applet users can use Alt key for group editing</li>
1687 <div align="center"><strong>2.1</strong><br>
1692 <li>MAFFT Multiple Alignment in default Web Service list</li>
1693 <li>DAS Feature fetching</li>
1694 <li>Hide sequences and columns</li>
1695 <li>Export Annotations and Features</li>
1696 <li>GFF file reading / writing</li>
1697 <li>Associate structures with sequences from local PDB files</li>
1698 <li>Add sequences to exisiting alignment</li>
1699 <li>Recently opened files / URL lists</li>
1700 <li>Applet can launch the full application</li>
1701 <li>Applet has transparency for features (Java 1.2 required)</li>
1702 <li>Applet has user defined colours parameter</li>
1703 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
1708 <li>Redundancy Panel reinstalled in the Applet</li>
1709 <li>Monospaced font - EPS / rescaling bug fixed</li>
1710 <li>Annotation files with sequence references bug fixed</li>
1716 <div align="center"><strong>2.08.1</strong><br>
1721 <li>Change case of selected region from Popup menu</li>
1722 <li>Choose to match case when searching</li>
1723 <li>Middle mouse button and mouse movement can compress / expand
1724 the visible width and height of the alignment</li>
1729 <li>Annotation Panel displays complete JNet results</li>
1735 <div align="center"><strong>2.08b</strong><br>
1741 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1742 <li>Righthand label on wrapped alignments shows correct value</li>
1748 <div align="center"><strong>2.08</strong><br>
1753 <li>Editing can be locked to the selection area</li>
1754 <li>Keyboard editing</li>
1755 <li>Create sequence features from searches</li>
1756 <li>Precalculated annotations can be loaded onto alignments</li>
1757 <li>Features file allows grouping of features</li>
1758 <li>Annotation Colouring scheme added</li>
1759 <li>Smooth fonts off by default - Faster rendering</li>
1760 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1765 <li>Drag & Drop fixed on Linux</li>
1766 <li>Jalview Archive file faster to load/save, sequence
1767 descriptions saved.</li>
1773 <div align="center"><strong>2.07</strong><br>
1778 <li>PDB Structure Viewer enhanced</li>
1779 <li>Sequence Feature retrieval and display enhanced</li>
1780 <li>Choose to output sequence start-end after sequence name for
1782 <li>Sequence Fetcher WSDBFetch@EBI</li>
1783 <li>Applet can read feature files, PDB files and can be used for
1784 HTML form input</li>
1789 <li>HTML output writes groups and features</li>
1790 <li>Group editing is Control and mouse click</li>
1791 <li>File IO bugs</li>
1797 <div align="center"><strong>2.06</strong><br>
1802 <li>View annotations in wrapped mode</li>
1803 <li>More options for PCA viewer</li>
1808 <li>GUI bugs resolved</li>
1809 <li>Runs with -nodisplay from command line</li>
1815 <div align="center"><strong>2.05b</strong><br>
1820 <li>Choose EPS export as lineart or text</li>
1821 <li>Jar files are executable</li>
1822 <li>Can read in Uracil - maps to unknown residue</li>
1827 <li>Known OutOfMemory errors give warning message</li>
1828 <li>Overview window calculated more efficiently</li>
1829 <li>Several GUI bugs resolved</li>
1835 <div align="center"><strong>2.05</strong><br>
1840 <li>Edit and annotate in "Wrapped" view</li>
1845 <li>Several GUI bugs resolved</li>
1851 <div align="center"><strong>2.04</strong><br>
1856 <li>Hold down mouse wheel & scroll to change font size</li>
1861 <li>Improved JPred client reliability</li>
1862 <li>Improved loading of Jalview files</li>
1868 <div align="center"><strong>2.03</strong><br>
1873 <li>Set Proxy server name and port in preferences</li>
1874 <li>Multiple URL links from sequence ids</li>
1875 <li>User Defined Colours can have a scheme name and added to
1877 <li>Choose to ignore gaps in consensus calculation</li>
1878 <li>Unix users can set default web browser</li>
1879 <li>Runs without GUI for batch processing</li>
1880 <li>Dynamically generated Web Service Menus</li>
1885 <li>InstallAnywhere download for Sparc Solaris</li>
1891 <div align="center"><strong>2.02</strong><br>
1897 <li>Copy & Paste order of sequences maintains alignment
1904 <div align="center"><strong>2.01</strong><br>
1909 <li>Use delete key for deleting selection.</li>
1910 <li>Use Mouse wheel to scroll sequences.</li>
1911 <li>Help file updated to describe how to add alignment
1913 <li>Version and build date written to build properties file.</li>
1914 <li>InstallAnywhere installation will check for updates at
1915 launch of Jalview.</li>
1920 <li>Delete gaps bug fixed.</li>
1921 <li>FileChooser sorts columns.</li>
1922 <li>Can remove groups one by one.</li>
1923 <li>Filechooser icons installed.</li>
1924 <li>Finder ignores return character when searching. Return key
1925 will initiate a search.<br>
1932 <div align="center"><strong>2.0</strong><br>
1937 <li>New codebase</li>