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>
27 <strong>Release History</strong>
31 <td width="60" nowrap>
33 <em><strong>Release</strong></em>
38 <em><strong>New Features</strong></em>
43 <em><strong>Issues Resolved</strong></em>
48 <td><div align="center">
49 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
53 <li>Linked visualisation and analysis of DNA and Protein
56 <li>Translated cDNA alignments shown as split protein
57 and DNA alignment views</li>
58 <li>Codon consensus annotation for linked protein and
59 cDNA alignment views</li>
60 <li>Link cDNA or Protein product sequences by loading
61 them onto Protein or cDNA alignments</li>
62 <li>Reconstruct linked cDNA alignment from aligned
63 protein sequences</li>
66 <li>Jmol integration updated to Jmol v14.2.14</li>
67 <li>Import and export of Jalview alignment views as <a
68 href="features/bioJsonFormat.html">BioJSON</a></li>
69 <li>New alignment annotation file statements for
70 reference sequences and marking hidden columns</li>
71 <li>Reference sequence based alignment shading to
72 highlight variation</li>
73 <li>Select or hide columns according to alignment
75 <li>Find option for locating sequences by description</li>
76 <li>Conserved physicochemical properties shown in amino
77 acid conservation row</li>
78 <li>Alignments can be sorted by number of RNA helices</li>
79 </ul> <em>Application</em>
81 <li>New cDNA/Protein analysis capabilities
83 <li>Get Cross-References should open a Split Frame
84 view with cDNA/Protein</li>
85 <li>Detect when nucleotide sequences and protein
86 sequences are placed in the same alignment</li>
87 <li>Split cDNA/Protein views are saved in Jalview
92 <li>Use REST API to talk to Chimera</li>
93 <li>Selected regions in Chimera are highlighted in linked
96 <li>VARNA RNA viewer updated to v3.93</li>
97 <li>VARNA views are saved in Jalview Projects</li>
98 <li>Pseudoknots displayed as Jalview RNA annotation can
99 be shown in VARNA</li>
101 <li>Make groups for selection uses marked columns as well
102 as the active selected region</li>
104 <li>Calculate UPGMA and NJ trees using sequence feature
106 <li>New Export options
108 <li>New Export Settings dialog to control hidden
109 region export in flat file generation</li>
111 <li>Export alignment views for display with the <a
112 href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
114 <li>Export scrollable SVG in HTML page</li>
115 <li>Optional embedding of BioJSON data when exporting
116 alignment figures to HTML</li>
118 <li>3D structure retrieval and display
120 <li>Free text and structured queries with the PDBe
122 <li>PDBe Search API based discovery and selection of
123 PDB structures for a sequence set</li>
127 <li>JPred4 employed for protein secondary structure
129 <li>Hide Insertions menu option to hide unaligned columns
130 for one or a group of sequences</li>
131 <li>Automatically hide insertions in alignments imported
132 from the JPred4 web server</li>
133 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
134 system on OSX<br />LGPL libraries courtesy of <a
135 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
137 <li>changed 'View nucleotide structure' submenu to 'View
138 VARNA 2D Structure'</li>
139 <li>change "View protein structure" menu option to "3D
142 </ul> <em>Applet</em>
144 <li>New layout for applet example pages</li>
145 <li>New parameters to enable SplitFrame view
146 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
147 <li>New example demonstrating linked viewing of cDNA and
148 Protein alignments</li>
149 </ul> <em>Development and deployment</em>
151 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
152 <li>Include installation type and git revision in build
153 properties and console log output</li>
154 <li>Jalview Github organisation, and new github site for
155 storing BioJsMSA Templates</li>
156 <li>Jalview's unit tests now managed with TestNG</li>
159 <!-- <em>General</em>
161 </ul> --> <!-- issues resolved --> <em>Application</em>
163 <li>Escape should close any open find dialogs</li>
164 <li>Typo in select-by-features status report</li>
165 <li>Consensus RNA secondary secondary structure
166 predictions are not highlighted in amber</li>
167 <li>Missing gap character in v2.7 example file means
168 alignment appears unaligned when pad-gaps is not enabled</li>
169 <li>First switch to RNA Helices colouring doesn't colour
170 associated structure views</li>
171 <li>ID width preference option is greyed out when auto
172 width checkbox not enabled</li>
173 <li>Stopped a warning dialog from being shown when
174 creating user defined colours</li>
175 <li>'View Mapping' in structure viewer shows sequence
176 mappings for just that viewer's sequences</li>
177 <li>Workaround for superposing PDB files containing
178 multiple models in Chimera</li>
179 <li>Report sequence position in status bar when hovering
180 over Jmol structure</li>
181 <li>Cannot output gaps as '.' symbols with Selection ->
182 output to text box</li>
183 <li>Flat file exports of alignments with hidden columns
184 have incorrect sequence start/end</li>
185 <li>'Aligning' a second chain to a Chimera structure from
187 <li>Colour schemes applied to structure viewers don't
188 work for nucleotide</li>
189 <li>Loading/cut'n'pasting an empty or invalid file leads
190 to a grey/invisible alignment window</li>
191 <li>Exported Jpred annotation from a sequence region
192 imports to different position</li>
193 <li>Space at beginning of sequence feature tooltips shown
194 on some platforms</li>
195 <li>Chimera viewer 'View | Show Chain' menu is not
197 <li>'New View' fails with a Null Pointer Exception in
198 console if Chimera has been opened</li>
199 <li>Mouseover to Chimera not working</li>
200 <li>Miscellaneous ENA XML feature qualifiers not
202 <li>NPE in annotation renderer after 'Extract Scores'</li>
203 <li>If two structures in one Chimera window, mouseover of
204 either sequence shows on first structure</li>
205 <li>'Show annotations' options should not make
206 non-positional annotations visible</li>
207 <li>Subsequence secondary structure annotation not shown
208 in right place after 'view flanking regions'</li>
209 <li>File Save As type unset when current file format is
211 <li>Save as '.jar' option removed for saving Jalview
213 <li>Colour by Sequence colouring in Chimera more
215 <li>Cannot 'add reference annotation' for a sequence in
216 several views on same alignment</li>
217 <li>Cannot show linked products for EMBL / ENA records</li>
218 <li>Jalview's tooltip wraps long texts containing no
220 </ul> <em>Applet</em>
222 <li>Jmol to JalviewLite mouseover/link not working</li>
223 <li>JalviewLite can't import sequences with ID
224 descriptions containing angle brackets</li>
225 </ul> <em>General</em>
227 <li>Cannot export and reimport RNA secondary structure
228 via jalview annotation file</li>
229 <li>Random helix colour palette for colour by annotation
230 with RNA secondary structure</li>
231 <li>Mouseover to cDNA from STOP residue in protein
232 translation doesn't work.</li>
233 <li>hints when using the select by annotation dialog box</li>
234 <li>Jmol alignment incorrect if PDB file has alternate CA
236 <li>FontChooser message dialog appears to hang after
237 choosing 1pt font</li>
238 <li>Peptide secondary structure incorrectly imported from
239 annotation file when annotation display text includes 'e' or
241 <li>Cannot set colour of new feature type whilst creating
243 <li>cDNA translation alignment should not be sequence
245 <li>'Show unconserved' doesn't work for lower case
247 <li>Nucleotide ambiguity codes involving R not recognised</li>
248 </ul> <em>Deployment and Documentation</em>
250 <li>Applet example pages appear different to the rest of
252 </ul> <em>Application Known issues</em>
254 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
255 <li>Misleading message appears after trying to delete
257 <li>Jalview icon not shown in dock after InstallAnywhere
258 version launches</li>
259 <li>Fetching EMBL reference for an RNA sequence results
260 fails with a sequence mismatch</li>
261 <li>Corrupted or unreadable alignment display when
262 scrolling alignment to right</li>
263 <li>ArrayIndexOutOfBoundsException thrown when remove
264 empty columns called on alignment with ragged gapped ends</li>
265 <li>auto calculated alignment annotation rows do not get
266 placed above or below non-autocalculated rows</li>
267 <li>Jalview dekstop becomes sluggish at full screen in
268 ultra-high resolution</li>
269 <li>Cannot disable consensus calculation independently of
270 quality and conservation</li>
271 <li>Mouseover highlighting between cDNA and protein can
272 become sluggish with more than one splitframe shown</li>
273 </ul> <em>Applet Known Issues</em>
275 <li>Core PDB parsing code requires Jmol</li>
276 <li>Sequence canvas panel goes white when alignment
277 window is being resized</li>
283 <td width="60" nowrap>
285 <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br />
286 <em>15/12/2014</em></strong>
290 <div align="center"></div>
295 <li>Reinstated the display of default example file on
297 <li>All pairs shown in Jalview window when viewing
298 result of pairwise alignment</li>
304 <td><div align="center">
305 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
309 <li>Updated Java code signing certificate donated by
311 <li>Features and annotation preserved when performing
312 pairwise alignment</li>
313 <li>RNA pseudoknot annotation can be
314 imported/exported/displayed</li>
315 <li>'colour by annotation' can colour by RNA and
316 protein secondary structure</li>
317 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
318 post-hoc with 2.9 release</em>)
321 </ul> <em>Application</em>
323 <li>Extract and display secondary structure for sequences
324 with 3D structures</li>
325 <li>Support for parsing RNAML</li>
326 <li>Annotations menu for layout
328 <li>sort sequence annotation rows by alignment</li>
329 <li>place sequence annotation above/below alignment
332 <li>Output in Stockholm format</li>
333 <li>Internationalisation: improved Spanish (es)
335 <li>Structure viewer preferences tab</li>
336 <li>Disorder and Secondary Structure annotation tracks
337 shared between alignments</li>
338 <li>UCSF Chimera launch and linked highlighting from
340 <li>Show/hide all sequence associated annotation rows for
341 all or current selection</li>
342 <li>disorder and secondary structure predictions
343 available as dataset annotation</li>
344 <li>Per-sequence rna helices colouring</li>
347 <li>Sequence database accessions imported when fetching
348 alignments from Rfam</li>
349 <li>update VARNA version to 3.91</li>
351 <li>New groovy scripts for exporting aligned positions,
352 conservation values, and calculating sum of pairs scores.</li>
353 <li>Command line argument to set default JABAWS server</li>
354 <li>include installation type in build properties and
355 console log output</li>
356 <li>Updated Jalview project format to preserve dataset
360 <!-- issues resolved --> <em>Application</em>
362 <li>Distinguish alignment and sequence associated RNA
363 structure in structure->view->VARNA</li>
364 <li>Raise dialog box if user deletes all sequences in an
366 <li>Pressing F1 results in documentation opening twice</li>
367 <li>Sequence feature tooltip is wrapped</li>
368 <li>Double click on sequence associated annotation
369 selects only first column</li>
370 <li>Redundancy removal doesn't result in unlinked
371 leaves shown in tree</li>
372 <li>Undos after several redundancy removals don't undo
374 <li>Hide sequence doesn't hide associated annotation</li>
375 <li>User defined colours dialog box too big to fit on
376 screen and buttons not visible</li>
377 <li>author list isn't updated if already written to
378 Jalview properties</li>
379 <li>Popup menu won't open after retrieving sequence
381 <li>File open window for associate PDB doesn't open</li>
382 <li>Left-then-right click on a sequence id opens a
383 browser search window</li>
384 <li>Cannot open sequence feature shading/sort popup menu
385 in feature settings dialog</li>
386 <li>better tooltip placement for some areas of Jalview
388 <li>Allow addition of JABAWS Server which doesn't
390 <li>Web services parameters dialog box is too large to
392 <li>Muscle nucleotide alignment preset obscured by
394 <li>JABAWS preset submenus don't contain newly
395 defined user preset</li>
396 <li>MSA web services warns user if they were launched
397 with invalid input</li>
398 <li>Jalview cannot contact DAS Registy when running on
401 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
402 'Superpose with' submenu not shown when new view
406 </ul> <!-- <em>Applet</em>
408 </ul> <em>General</em>
410 </ul>--> <em>Deployment and Documentation</em>
412 <li>2G and 1G options in launchApp have no effect on
413 memory allocation</li>
414 <li>launchApp service doesn't automatically open
415 www.jalview.org/examples/exampleFile.jar if no file is given</li>
417 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
418 InstallAnywhere reports cannot find valid JVM when Java
421 </ul> <em>Application Known issues</em>
424 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
425 corrupted or unreadable alignment display when scrolling
429 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
430 retrieval fails but progress bar continues for DAS retrieval
431 with large number of ID
434 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
435 flatfile output of visible region has incorrect sequence
439 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
440 rna structure consensus doesn't update when secondary
441 structure tracks are rearranged
444 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
445 invalid rna structure positional highlighting does not
446 highlight position of invalid base pairs
449 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
450 out of memory errors are not raised when saving Jalview
451 project from alignment window file menu
454 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
455 Switching to RNA Helices colouring doesn't propagate to
459 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
460 colour by RNA Helices not enabled when user created
461 annotation added to alignment
464 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
465 Jalview icon not shown on dock in Mountain Lion/Webstart
467 </ul> <em>Applet Known Issues</em>
470 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
471 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
474 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
475 Jalview and Jmol example not compatible with IE9
478 <li>Sort by annotation score doesn't reverse order
484 <td><div align="center">
485 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
488 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
491 <li>Internationalisation of user interface (usually
492 called i18n support) and translation for Spanish locale</li>
493 <li>Define/Undefine group on current selection with
494 Ctrl-G/Shift Ctrl-G</li>
495 <li>Improved group creation/removal options in
496 alignment/sequence Popup menu</li>
497 <li>Sensible precision for symbol distribution
498 percentages shown in logo tooltip.</li>
499 <li>Annotation panel height set according to amount of
500 annotation when alignment first opened</li>
501 </ul> <em>Application</em>
503 <li>Interactive consensus RNA secondary structure
504 prediction VIENNA RNAAliFold JABA 2.1 service</li>
505 <li>Select columns containing particular features from
506 Feature Settings dialog</li>
507 <li>View all 'representative' PDB structures for selected
509 <li>Update Jalview project format:
511 <li>New file extension for Jalview projects '.jvp'</li>
512 <li>Preserve sequence and annotation dataset (to
513 store secondary structure annotation,etc)</li>
514 <li>Per group and alignment annotation and RNA helix
518 <li>New similarity measures for PCA and Tree calculation
520 <li>Experimental support for retrieval and viewing of
521 flanking regions for an alignment</li>
525 <!-- issues resolved --> <em>Application</em>
527 <li>logo keeps spinning and status remains at queued or
528 running after job is cancelled</li>
529 <li>cannot export features from alignments imported from
530 Jalview/VAMSAS projects</li>
531 <li>Buggy slider for web service parameters that take
533 <li>Newly created RNA secondary structure line doesn't
534 have 'display all symbols' flag set</li>
535 <li>T-COFFEE alignment score shading scheme and other
536 annotation shading not saved in Jalview project</li>
537 <li>Local file cannot be loaded in freshly downloaded
539 <li>Jalview icon not shown on dock in Mountain
541 <li>Load file from desktop file browser fails</li>
542 <li>Occasional NPE thrown when calculating large trees</li>
543 <li>Cannot reorder or slide sequences after dragging an
544 alignment onto desktop</li>
545 <li>Colour by annotation dialog throws NPE after using
546 'extract scores' function</li>
547 <li>Loading/cut'n'pasting an empty file leads to a grey
548 alignment window</li>
549 <li>Disorder thresholds rendered incorrectly after
550 performing IUPred disorder prediction</li>
551 <li>Multiple group annotated consensus rows shown when
552 changing 'normalise logo' display setting</li>
553 <li>Find shows blank dialog after 'finished searching' if
554 nothing matches query</li>
555 <li>Null Pointer Exceptions raised when sorting by
556 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
558 <li>Errors in Jmol console when structures in alignment
559 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
561 <li>Not all working JABAWS services are shown in
563 <li>JAVAWS version of Jalview fails to launch with
564 'invalid literal/length code'</li>
565 <li>Annotation/RNA Helix colourschemes cannot be applied
566 to alignment with groups (actually fixed in 2.8.0b1)</li>
567 <li>RNA Helices and T-Coffee Scores available as default
570 </ul> <em>Applet</em>
572 <li>Remove group option is shown even when selection is
574 <li>Apply to all groups ticked but colourscheme changes
575 don't affect groups</li>
576 <li>Documented RNA Helices and T-Coffee Scores as valid
577 colourscheme name</li>
578 <li>Annotation labels drawn on sequence IDs when
579 Annotation panel is not displayed</li>
580 <li>Increased font size for dropdown menus on OSX and
581 embedded windows</li>
584 <li>Consensus sequence for alignments/groups with a
585 single sequence were not calculated</li>
586 <li>annotation files that contain only groups imported as
587 annotation and junk sequences</li>
588 <li>Fasta files with sequences containing '*' incorrectly
589 recognised as PFAM or BLC</li>
590 <li>conservation/PID slider apply all groups option
591 doesn't affect background (2.8.0b1)
593 <li>redundancy highlighting is erratic at 0% and 100%</li>
594 <li>Remove gapped columns fails for sequences with ragged
596 <li>AMSA annotation row with leading spaces is not
597 registered correctly on import</li>
598 <li>Jalview crashes when selecting PCA analysis for
599 certain alignments</li>
600 <li>Opening the colour by annotation dialog for an
601 existing annotation based 'use original colours'
602 colourscheme loses original colours setting</li>
607 <td><div align="center">
608 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
609 <em>30/1/2014</em></strong>
613 <li>Trusted certificates for JalviewLite applet and
614 Jalview Desktop application<br />Certificate was donated by
615 <a href="https://www.certum.eu">Certum</a> to the Jalview
616 open source project).
618 <li>Jalview SRS links replaced by Uniprot and EBI-search
620 <li>Output in Stockholm format</li>
621 <li>Allow import of data from gzipped files</li>
622 <li>Export/import group and sequence associated line
623 graph thresholds</li>
624 <li>Nucleotide substitution matrix that supports RNA and
626 <li>Allow disorder predictions to be made on the current
627 selection (or visible selection) in the same way that JPred
629 <li>Groovy scripting for headless Jalview operation</li>
630 </ul> <em>Other improvements</em>
632 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
633 <li>COMBINE statement uses current SEQUENCE_REF and
634 GROUP_REF scope to group annotation rows</li>
635 <li>Support '' style escaping of quotes in Newick
637 <li>Group options for JABAWS service by command line name</li>
638 <li>Empty tooltip shown for JABA service options with a
639 link but no description</li>
640 <li>Select primary source when selecting authority in
641 database fetcher GUI</li>
642 <li>Add .mfa to FASTA file extensions recognised by
644 <li>Annotation label tooltip text wrap</li>
649 <li>Slow scrolling when lots of annotation rows are
651 <li>Lots of NPE (and slowness) after creating RNA
652 secondary structure annotation line</li>
653 <li>Sequence database accessions not imported when
654 fetching alignments from Rfam</li>
655 <li>Incorrect SHMR submission for sequences with
657 <li>View all structures does not always superpose
659 <li>Option widgets in service parameters not updated to
660 reflect user or preset settings</li>
661 <li>Null pointer exceptions for some services without
662 presets or adjustable parameters</li>
663 <li>Discover PDB IDs entry in structure menu doesn't
664 discover PDB xRefs</li>
665 <li>Exception encountered while trying to retrieve
666 features with DAS</li>
667 <li>Lowest value in annotation row isn't coloured
668 when colour by annotation (per sequence) is coloured</li>
669 <li>Keyboard mode P jumps to start of gapped region when
670 residue follows a gap</li>
671 <li>Jalview appears to hang importing an alignment with
672 Wrap as default or after enabling Wrap</li>
673 <li>'Right click to add annotations' message
674 shown in wrap mode when no annotations present</li>
675 <li>Disorder predictions fail with NPE if no automatic
676 annotation already exists on alignment</li>
677 <li>oninit javascript function should be called after
678 initialisation completes</li>
679 <li>Remove redundancy after disorder prediction corrupts
680 alignment window display</li>
681 <li>Example annotation file in documentation is invalid</li>
682 <li>Grouped line graph annotation rows are not exported
683 to annotation file</li>
684 <li>Multi-harmony analysis cannot be run when only two
686 <li>Cannot create multiple groups of line graphs with
687 several 'combine' statements in annotation file</li>
688 <li>Pressing return several times causes Number Format
689 exceptions in keyboard mode</li>
690 <li>Multi-harmony (SHMMR) method doesn't submit
691 correct partitions for input data</li>
692 <li>Translation from DNA to Amino Acids fails</li>
693 <li>Jalview fail to load newick tree with quoted label</li>
694 <li>--headless flag isn't understood</li>
695 <li>ClassCastException when generating EPS in headless
697 <li>Adjusting sequence-associated shading threshold only
698 changes one row's threshold</li>
699 <li>Preferences and Feature settings panel panel
700 doesn't open</li>
701 <li>hide consensus histogram also hides conservation and
702 quality histograms</li>
707 <td><div align="center">
708 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
710 <td><em>Application</em>
712 <li>Support for JABAWS 2.0 Services (AACon alignment
713 conservation, protein disorder and Clustal Omega)</li>
714 <li>JABAWS server status indicator in Web Services
716 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
717 in Jalview alignment window</li>
718 <li>Updated Jalview build and deploy framework for OSX
719 mountain lion, windows 7, and 8</li>
720 <li>Nucleotide substitution matrix for PCA that supports
721 RNA and ambiguity codes</li>
723 <li>Improved sequence database retrieval GUI</li>
724 <li>Support fetching and database reference look up
725 against multiple DAS sources (Fetch all from in 'fetch db
727 <li>Jalview project improvements
729 <li>Store and retrieve the 'belowAlignment'
730 flag for annotation</li>
731 <li>calcId attribute to group annotation rows on the
733 <li>Store AACon calculation settings for a view in
738 <li>horizontal scrolling gesture support</li>
739 <li>Visual progress indicator when PCA calculation is
741 <li>Simpler JABA web services menus</li>
742 <li>visual indication that web service results are still
743 being retrieved from server</li>
744 <li>Serialise the dialogs that are shown when Jalview
745 starts up for first time</li>
746 <li>Jalview user agent string for interacting with HTTP
748 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
750 <li>Examples directory and Groovy library included in
751 InstallAnywhere distribution</li>
752 </ul> <em>Applet</em>
754 <li>RNA alignment and secondary structure annotation
755 visualization applet example</li>
756 </ul> <em>General</em>
758 <li>Normalise option for consensus sequence logo</li>
759 <li>Reset button in PCA window to return dimensions to
761 <li>Allow seqspace or Jalview variant of alignment PCA
763 <li>PCA with either nucleic acid and protein substitution
765 <li>Allow windows containing HTML reports to be exported
767 <li>Interactive display and editing of RNA secondary
768 structure contacts</li>
769 <li>RNA Helix Alignment Colouring</li>
770 <li>RNA base pair logo consensus</li>
771 <li>Parse sequence associated secondary structure
772 information in Stockholm files</li>
773 <li>HTML Export database accessions and annotation
774 information presented in tooltip for sequences</li>
775 <li>Import secondary structure from LOCARNA clustalw
776 style RNA alignment files</li>
777 <li>import and visualise T-COFFEE quality scores for an
779 <li>'colour by annotation' per sequence option to
780 shade each sequence according to its associated alignment
782 <li>New Jalview Logo</li>
783 </ul> <em>Documentation and Development</em>
785 <li>documentation for score matrices used in Jalview</li>
786 <li>New Website!</li>
788 <td><em>Application</em>
790 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
791 wsdbfetch REST service</li>
792 <li>Stop windows being moved outside desktop on OSX</li>
793 <li>Filetype associations not installed for webstart
795 <li>Jalview does not always retrieve progress of a JABAWS
796 job execution in full once it is complete</li>
797 <li>revise SHMR RSBS definition to ensure alignment is
798 uploaded via ali_file parameter</li>
799 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
800 <li>View all structures superposed fails with exception</li>
801 <li>Jnet job queues forever if a very short sequence is
802 submitted for prediction</li>
803 <li>Cut and paste menu not opened when mouse clicked on
805 <li>Putting fractional value into integer text box in
806 alignment parameter dialog causes Jalview to hang</li>
807 <li>Structure view highlighting doesn't work on
809 <li>View all structures fails with exception shown in
811 <li>Characters in filename associated with PDBEntry not
812 escaped in a platform independent way</li>
813 <li>Jalview desktop fails to launch with exception when
815 <li>Tree calculation reports 'you must have 2 or more
816 sequences selected' when selection is empty</li>
817 <li>Jalview desktop fails to launch with jar signature
818 failure when java web start temporary file caching is
820 <li>DAS Sequence retrieval with range qualification
821 results in sequence xref which includes range qualification</li>
822 <li>Errors during processing of command line arguments
823 cause progress bar (JAL-898) to be removed</li>
824 <li>Replace comma for semi-colon option not disabled for
825 DAS sources in sequence fetcher</li>
826 <li>Cannot close news reader when JABAWS server warning
828 <li>Option widgets not updated to reflect user settings</li>
829 <li>Edited sequence not submitted to web service</li>
830 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
831 <li>InstallAnywhere installer doesn't unpack and run
832 on OSX Mountain Lion</li>
833 <li>Annotation panel not given a scroll bar when
834 sequences with alignment annotation are pasted into the
836 <li>Sequence associated annotation rows not associated
837 when loaded from Jalview project</li>
838 <li>Browser launch fails with NPE on java 1.7</li>
839 <li>JABAWS alignment marked as finished when job was
840 cancelled or job failed due to invalid input</li>
841 <li>NPE with v2.7 example when clicking on Tree
842 associated with all views</li>
843 <li>Exceptions when copy/paste sequences with grouped
844 annotation rows to new window</li>
845 </ul> <em>Applet</em>
847 <li>Sequence features are momentarily displayed before
848 they are hidden using hidefeaturegroups applet parameter</li>
849 <li>loading features via javascript API automatically
850 enables feature display</li>
851 <li>scrollToColumnIn javascript API method doesn't
853 </ul> <em>General</em>
855 <li>Redundancy removal fails for rna alignment</li>
856 <li>PCA calculation fails when sequence has been selected
857 and then deselected</li>
858 <li>PCA window shows grey box when first opened on OSX</li>
859 <li>Letters coloured pink in sequence logo when alignment
860 coloured with clustalx</li>
861 <li>Choosing fonts without letter symbols defined causes
862 exceptions and redraw errors</li>
863 <li>Initial PCA plot view is not same as manually
864 reconfigured view</li>
865 <li>Grouped annotation graph label has incorrect line
867 <li>Grouped annotation graph label display is corrupted
868 for lots of labels</li>
874 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
877 <td><em>Application</em>
879 <li>Jalview Desktop News Reader</li>
880 <li>Tweaked default layout of web services menu</li>
881 <li>View/alignment association menu to enable user to
882 easily specify which alignment a multi-structure view takes
883 its colours/correspondences from</li>
884 <li>Allow properties file location to be specified as URL</li>
885 <li>Extend Jalview project to preserve associations
886 between many alignment views and a single Jmol display</li>
887 <li>Store annotation row height in Jalview project file</li>
888 <li>Annotation row column label formatting attributes
889 stored in project file</li>
890 <li>Annotation row order for auto-calculated annotation
891 rows preserved in Jalview project file</li>
892 <li>Visual progress indication when Jalview state is
893 saved using Desktop window menu</li>
894 <li>Visual indication that command line arguments are
895 still being processed</li>
896 <li>Groovy script execution from URL</li>
897 <li>Colour by annotation default min and max colours in
899 <li>Automatically associate PDB files dragged onto an
900 alignment with sequences that have high similarity and
902 <li>Update JGoogleAnalytics to latest release (0.3)</li>
903 <li>'view structures' option to open many
904 structures in same window</li>
905 <li>Sort associated views menu option for tree panel</li>
906 <li>Group all JABA and non-JABA services for a particular
907 analysis function in its own submenu</li>
908 </ul> <em>Applet</em>
910 <li>Userdefined and autogenerated annotation rows for
912 <li>Adjustment of alignment annotation pane height</li>
913 <li>Annotation scrollbar for annotation panel</li>
914 <li>Drag to reorder annotation rows in annotation panel</li>
915 <li>'automaticScrolling' parameter</li>
916 <li>Allow sequences with partial ID string matches to be
917 annotated from GFF/Jalview features files</li>
918 <li>Sequence logo annotation row in applet</li>
919 <li>Absolute paths relative to host server in applet
920 parameters are treated as such</li>
921 <li>New in the JalviewLite javascript API:
923 <li>JalviewLite.js javascript library</li>
924 <li>Javascript callbacks for
926 <li>Applet initialisation</li>
927 <li>Sequence/alignment mouse-overs and selections</li>
930 <li>scrollTo row and column alignment scrolling
932 <li>Select sequence/alignment regions from javascript</li>
933 <li>javascript structure viewer harness to pass
934 messages between Jmol and Jalview when running as
935 distinct applets</li>
936 <li>sortBy method</li>
937 <li>Set of applet and application examples shipped
938 with documentation</li>
939 <li>New example to demonstrate JalviewLite and Jmol
940 javascript message exchange</li>
942 </ul> <em>General</em>
944 <li>Enable Jmol displays to be associated with multiple
945 multiple alignments</li>
946 <li>Option to automatically sort alignment with new tree</li>
947 <li>User configurable link to enable redirects to a
948 www.Jalview.org mirror</li>
949 <li>Jmol colours option for Jmol displays</li>
950 <li>Configurable newline string when writing alignment
951 and other flat files</li>
952 <li>Allow alignment annotation description lines to
953 contain html tags</li>
954 </ul> <em>Documentation and Development</em>
956 <li>Add groovy test harness for bulk load testing to
958 <li>Groovy script to load and align a set of sequences
959 using a web service before displaying the result in the
961 <li>Restructured javascript and applet api documentation</li>
962 <li>Ant target to publish example html files with applet
964 <li>Netbeans project for building Jalview from source</li>
965 <li>ant task to create online javadoc for Jalview source</li>
967 <td><em>Application</em>
969 <li>User defined colourscheme throws exception when
970 current built in colourscheme is saved as new scheme</li>
971 <li>AlignFrame->Save in application pops up save
972 dialog for valid filename/format</li>
973 <li>Cannot view associated structure for Uniprot sequence</li>
974 <li>PDB file association breaks for Uniprot sequence
976 <li>Associate PDB from file dialog does not tell you
977 which sequence is to be associated with the file</li>
978 <li>Find All raises null pointer exception when query
979 only matches sequence IDs</li>
980 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
981 <li>Jalview project with Jmol views created with Jalview
982 2.4 cannot be loaded</li>
983 <li>Filetype associations not installed for webstart
985 <li>Two or more chains in a single PDB file associated
986 with sequences in different alignments do not get coloured
987 by their associated sequence</li>
988 <li>Visibility status of autocalculated annotation row
989 not preserved when project is loaded</li>
990 <li>Annotation row height and visibility attributes not
991 stored in Jalview project</li>
992 <li>Tree bootstraps are not preserved when saved as a
994 <li>Envision2 workflow tooltips are corrupted</li>
995 <li>Enabling show group conservation also enables colour
997 <li>Duplicate group associated conservation or consensus
998 created on new view</li>
999 <li>Annotation scrollbar not displayed after 'show
1000 all hidden annotation rows' option selected</li>
1001 <li>Alignment quality not updated after alignment
1002 annotation row is hidden then shown</li>
1003 <li>Preserve colouring of structures coloured by
1004 sequences in pre Jalview 2.7 projects</li>
1005 <li>Web service job parameter dialog is not laid out
1007 <li>Web services menu not refreshed after 'reset
1008 services' button is pressed in preferences</li>
1009 <li>Annotation off by one in Jalview v2_3 example project</li>
1010 <li>Structures imported from file and saved in project
1011 get name like jalview_pdb1234.txt when reloaded</li>
1012 <li>Jalview does not always retrieve progress of a JABAWS
1013 job execution in full once it is complete</li>
1014 </ul> <em>Applet</em>
1016 <li>Alignment height set incorrectly when lots of
1017 annotation rows are displayed</li>
1018 <li>Relative URLs in feature HTML text not resolved to
1020 <li>View follows highlighting does not work for positions
1022 <li><= shown as = in tooltip</li>
1023 <li>Export features raises exception when no features
1025 <li>Separator string used for serialising lists of IDs
1026 for javascript api is modified when separator string
1027 provided as parameter</li>
1028 <li>Null pointer exception when selecting tree leaves for
1029 alignment with no existing selection</li>
1030 <li>Relative URLs for datasources assumed to be relative
1031 to applet's codebase</li>
1032 <li>Status bar not updated after finished searching and
1033 search wraps around to first result</li>
1034 <li>StructureSelectionManager instance shared between
1035 several Jalview applets causes race conditions and memory
1037 <li>Hover tooltip and mouseover of position on structure
1038 not sent from Jmol in applet</li>
1039 <li>Certain sequences of javascript method calls to
1040 applet API fatally hang browser</li>
1041 </ul> <em>General</em>
1043 <li>View follows structure mouseover scrolls beyond
1044 position with wrapped view and hidden regions</li>
1045 <li>Find sequence position moves to wrong residue
1046 with/without hidden columns</li>
1047 <li>Sequence length given in alignment properties window
1049 <li>InvalidNumberFormat exceptions thrown when trying to
1050 import PDB like structure files</li>
1051 <li>Positional search results are only highlighted
1052 between user-supplied sequence start/end bounds</li>
1053 <li>End attribute of sequence is not validated</li>
1054 <li>Find dialog only finds first sequence containing a
1055 given sequence position</li>
1056 <li>Sequence numbering not preserved in MSF alignment
1058 <li>Jalview PDB file reader does not extract sequence
1059 from nucleotide chains correctly</li>
1060 <li>Structure colours not updated when tree partition
1061 changed in alignment</li>
1062 <li>Sequence associated secondary structure not correctly
1063 parsed in interleaved stockholm</li>
1064 <li>Colour by annotation dialog does not restore current
1066 <li>Hiding (nearly) all sequences doesn't work
1068 <li>Sequences containing lowercase letters are not
1069 properly associated with their pdb files</li>
1070 </ul> <em>Documentation and Development</em>
1072 <li>schemas/JalviewWsParamSet.xsd corrupted by
1073 ApplyCopyright tool</li>
1078 <div align="center">
1079 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1082 <td><em>Application</em>
1084 <li>New warning dialog when the Jalview Desktop cannot
1085 contact web services</li>
1086 <li>JABA service parameters for a preset are shown in
1087 service job window</li>
1088 <li>JABA Service menu entries reworded</li>
1092 <li>Modeller PIR IO broken - cannot correctly import a
1093 pir file emitted by Jalview</li>
1094 <li>Existing feature settings transferred to new
1095 alignment view created from cut'n'paste</li>
1096 <li>Improved test for mixed amino/nucleotide chains when
1097 parsing PDB files</li>
1098 <li>Consensus and conservation annotation rows
1099 occasionally become blank for all new windows</li>
1100 <li>Exception raised when right clicking above sequences
1101 in wrapped view mode</li>
1102 </ul> <em>Application</em>
1104 <li>multiple multiply aligned structure views cause cpu
1105 usage to hit 100% and computer to hang</li>
1106 <li>Web Service parameter layout breaks for long user
1107 parameter names</li>
1108 <li>Jaba service discovery hangs desktop if Jaba server
1115 <div align="center">
1116 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1119 <td><em>Application</em>
1121 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1122 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1125 <li>Web Services preference tab</li>
1126 <li>Analysis parameters dialog box and user defined
1128 <li>Improved speed and layout of Envision2 service menu</li>
1129 <li>Superpose structures using associated sequence
1131 <li>Export coordinates and projection as CSV from PCA
1133 </ul> <em>Applet</em>
1135 <li>enable javascript: execution by the applet via the
1136 link out mechanism</li>
1137 </ul> <em>Other</em>
1139 <li>Updated the Jmol Jalview interface to work with Jmol
1141 <li>The Jalview Desktop and JalviewLite applet now
1142 require Java 1.5</li>
1143 <li>Allow Jalview feature colour specification for GFF
1144 sequence annotation files</li>
1145 <li>New 'colour by label' keword in Jalview feature file
1146 type colour specification</li>
1147 <li>New Jalview Desktop Groovy API method that allows a
1148 script to check if it being run in an interactive session or
1149 in a batch operation from the Jalview command line</li>
1153 <li>clustalx colourscheme colours Ds preferentially when
1154 both D+E are present in over 50% of the column</li>
1155 </ul> <em>Application</em>
1157 <li>typo in AlignmentFrame->View->Hide->all but
1158 selected Regions menu item</li>
1159 <li>sequence fetcher replaces ',' for ';' when the ',' is
1160 part of a valid accession ID</li>
1161 <li>fatal OOM if object retrieved by sequence fetcher
1162 runs out of memory</li>
1163 <li>unhandled Out of Memory Error when viewing pca
1164 analysis results</li>
1165 <li>InstallAnywhere builds fail to launch on OS X java
1166 10.5 update 4 (due to apple Java 1.6 update)</li>
1167 <li>Installanywhere Jalview silently fails to launch</li>
1168 </ul> <em>Applet</em>
1170 <li>Jalview.getFeatureGroups() raises an
1171 ArrayIndexOutOfBoundsException if no feature groups are
1178 <div align="center">
1179 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1185 <li>Alignment prettyprinter doesn't cope with long
1187 <li>clustalx colourscheme colours Ds preferentially when
1188 both D+E are present in over 50% of the column</li>
1189 <li>nucleic acid structures retrieved from PDB do not
1190 import correctly</li>
1191 <li>More columns get selected than were clicked on when a
1192 number of columns are hidden</li>
1193 <li>annotation label popup menu not providing correct
1194 add/hide/show options when rows are hidden or none are
1196 <li>Stockholm format shown in list of readable formats,
1197 and parser copes better with alignments from RFAM.</li>
1198 <li>CSV output of consensus only includes the percentage
1199 of all symbols if sequence logo display is enabled</li>
1201 </ul> <em>Applet</em>
1203 <li>annotation panel disappears when annotation is
1205 </ul> <em>Application</em>
1207 <li>Alignment view not redrawn properly when new
1208 alignment opened where annotation panel is visible but no
1209 annotations are present on alignment</li>
1210 <li>pasted region containing hidden columns is
1211 incorrectly displayed in new alignment window</li>
1212 <li>Jalview slow to complete operations when stdout is
1213 flooded (fix is to close the Jalview console)</li>
1214 <li>typo in AlignmentFrame->View->Hide->all but
1215 selected Rregions menu item.</li>
1216 <li>inconsistent group submenu and Format submenu entry
1217 'Un' or 'Non'conserved</li>
1218 <li>Sequence feature settings are being shared by
1219 multiple distinct alignments</li>
1220 <li>group annotation not recreated when tree partition is
1222 <li>double click on group annotation to select sequences
1223 does not propagate to associated trees</li>
1224 <li>Mac OSX specific issues:
1226 <li>exception raised when mouse clicked on desktop
1227 window background</li>
1228 <li>Desktop menu placed on menu bar and application
1229 name set correctly</li>
1230 <li>sequence feature settings not wide enough for the
1231 save feature colourscheme button</li>
1240 <div align="center">
1241 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1244 <td><em>New Capabilities</em>
1246 <li>URL links generated from description line for
1247 regular-expression based URL links (applet and application)
1249 <li>Non-positional feature URL links are shown in link
1251 <li>Linked viewing of nucleic acid sequences and
1253 <li>Automatic Scrolling option in View menu to display
1254 the currently highlighted region of an alignment.</li>
1255 <li>Order an alignment by sequence length, or using the
1256 average score or total feature count for each sequence.</li>
1257 <li>Shading features by score or associated description</li>
1258 <li>Subdivide alignment and groups based on identity of
1259 selected subsequence (Make Groups from Selection).</li>
1260 <li>New hide/show options including Shift+Control+H to
1261 hide everything but the currently selected region.</li>
1262 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1263 </ul> <em>Application</em>
1265 <li>Fetch DB References capabilities and UI expanded to
1266 support retrieval from DAS sequence sources</li>
1267 <li>Local DAS Sequence sources can be added via the
1268 command line or via the Add local source dialog box.</li>
1269 <li>DAS Dbref and DbxRef feature types are parsed as
1270 database references and protein_name is parsed as
1271 description line (BioSapiens terms).</li>
1272 <li>Enable or disable non-positional feature and database
1273 references in sequence ID tooltip from View menu in
1275 <!-- <li>New hidden columns and rows and representatives capabilities
1276 in annotations file (in progress - not yet fully implemented)</li> -->
1277 <li>Group-associated consensus, sequence logos and
1278 conservation plots</li>
1279 <li>Symbol distributions for each column can be exported
1280 and visualized as sequence logos</li>
1281 <li>Optionally scale multi-character column labels to fit
1282 within each column of annotation row<!-- todo for applet -->
1284 <li>Optional automatic sort of associated alignment view
1285 when a new tree is opened.</li>
1286 <li>Jalview Java Console</li>
1287 <li>Better placement of desktop window when moving
1288 between different screens.</li>
1289 <li>New preference items for sequence ID tooltip and
1290 consensus annotation</li>
1291 <li>Client to submit sequences and IDs to <a
1292 href="webServices/index.html#envision2">Envision2</a>
1295 <li><em>Vamsas Capabilities</em>
1297 <li>Improved VAMSAS synchronization (Jalview archive
1298 used to preserve views, structures, and tree display
1300 <li>Import of vamsas documents from disk or URL via
1302 <li>Sharing of selected regions between views and
1303 with other VAMSAS applications (Experimental feature!)</li>
1304 <li>Updated API to VAMSAS version 0.2</li>
1306 </ul> <em>Applet</em>
1308 <li>Middle button resizes annotation row height</li>
1311 <li>sortByTree (true/false) - automatically sort the
1312 associated alignment view by the tree when a new tree is
1314 <li>showTreeBootstraps (true/false) - show or hide
1315 branch bootstraps (default is to show them if available)</li>
1316 <li>showTreeDistances (true/false) - show or hide
1317 branch lengths (default is to show them if available)</li>
1318 <li>showUnlinkedTreeNodes (true/false) - indicate if
1319 unassociated nodes should be highlighted in the tree
1321 <li>heightScale and widthScale (1.0 or more) -
1322 increase the height or width of a cell in the alignment
1323 grid relative to the current font size.</li>
1326 <li>Non-positional features displayed in sequence ID
1328 </ul> <em>Other</em>
1330 <li>Features format: graduated colour definitions and
1331 specification of feature scores</li>
1332 <li>Alignment Annotations format: new keywords for group
1333 associated annotation (GROUP_REF) and annotation row display
1334 properties (ROW_PROPERTIES)</li>
1335 <li>XML formats extended to support graduated feature
1336 colourschemes, group associated annotation, and profile
1337 visualization settings.</li></td>
1340 <li>Source field in GFF files parsed as feature source
1341 rather than description</li>
1342 <li>Non-positional features are now included in sequence
1343 feature and gff files (controlled via non-positional feature
1344 visibility in tooltip).</li>
1345 <li>URL links generated for all feature links (bugfix)</li>
1346 <li>Added URL embedding instructions to features file
1348 <li>Codons containing ambiguous nucleotides translated as
1349 'X' in peptide product</li>
1350 <li>Match case switch in find dialog box works for both
1351 sequence ID and sequence string and query strings do not
1352 have to be in upper case to match case-insensitively.</li>
1353 <li>AMSA files only contain first column of
1354 multi-character column annotation labels</li>
1355 <li>Jalview Annotation File generation/parsing consistent
1356 with documentation (e.g. Stockholm annotation can be
1357 exported and re-imported)</li>
1358 <li>PDB files without embedded PDB IDs given a friendly
1360 <li>Find incrementally searches ID string matches as well
1361 as subsequence matches, and correctly reports total number
1365 <li>Better handling of exceptions during sequence
1367 <li>Dasobert generated non-positional feature URL
1368 link text excludes the start_end suffix</li>
1369 <li>DAS feature and source retrieval buttons disabled
1370 when fetch or registry operations in progress.</li>
1371 <li>PDB files retrieved from URLs are cached properly</li>
1372 <li>Sequence description lines properly shared via
1374 <li>Sequence fetcher fetches multiple records for all
1376 <li>Ensured that command line das feature retrieval
1377 completes before alignment figures are generated.</li>
1378 <li>Reduced time taken when opening file browser for
1380 <li>isAligned check prior to calculating tree, PCA or
1381 submitting an MSA to JNet now excludes hidden sequences.</li>
1382 <li>User defined group colours properly recovered
1383 from Jalview projects.</li>
1392 <div align="center">
1393 <strong>2.4.0.b2</strong><br> 28/10/2009
1398 <li>Experimental support for google analytics usage
1400 <li>Jalview privacy settings (user preferences and docs).</li>
1405 <li>Race condition in applet preventing startup in
1407 <li>Exception when feature created from selection beyond
1408 length of sequence.</li>
1409 <li>Allow synthetic PDB files to be imported gracefully</li>
1410 <li>Sequence associated annotation rows associate with
1411 all sequences with a given id</li>
1412 <li>Find function matches case-insensitively for sequence
1413 ID string searches</li>
1414 <li>Non-standard characters do not cause pairwise
1415 alignment to fail with exception</li>
1416 </ul> <em>Application Issues</em>
1418 <li>Sequences are now validated against EMBL database</li>
1419 <li>Sequence fetcher fetches multiple records for all
1421 </ul> <em>InstallAnywhere Issues</em>
1423 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1424 issue with installAnywhere mechanism)</li>
1425 <li>Command line launching of JARs from InstallAnywhere
1426 version (java class versioning error fixed)</li>
1433 <div align="center">
1434 <strong>2.4</strong><br> 27/8/2008
1437 <td><em>User Interface</em>
1439 <li>Linked highlighting of codon and amino acid from
1440 translation and protein products</li>
1441 <li>Linked highlighting of structure associated with
1442 residue mapping to codon position</li>
1443 <li>Sequence Fetcher provides example accession numbers
1444 and 'clear' button</li>
1445 <li>MemoryMonitor added as an option under Desktop's
1447 <li>Extract score function to parse whitespace separated
1448 numeric data in description line</li>
1449 <li>Column labels in alignment annotation can be centred.</li>
1450 <li>Tooltip for sequence associated annotation give name
1452 </ul> <em>Web Services and URL fetching</em>
1454 <li>JPred3 web service</li>
1455 <li>Prototype sequence search client (no public services
1457 <li>Fetch either seed alignment or full alignment from
1459 <li>URL Links created for matching database cross
1460 references as well as sequence ID</li>
1461 <li>URL Links can be created using regular-expressions</li>
1462 </ul> <em>Sequence Database Connectivity</em>
1464 <li>Retrieval of cross-referenced sequences from other
1466 <li>Generalised database reference retrieval and
1467 validation to all fetchable databases</li>
1468 <li>Fetch sequences from DAS sources supporting the
1469 sequence command</li>
1470 </ul> <em>Import and Export</em>
1471 <li>export annotation rows as CSV for spreadsheet import</li>
1472 <li>Jalview projects record alignment dataset associations,
1473 EMBL products, and cDNA sequence mappings</li>
1474 <li>Sequence Group colour can be specified in Annotation
1476 <li>Ad-hoc colouring of group in Annotation File using RGB
1477 triplet as name of colourscheme</li>
1478 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
1480 <li>treenode binding for VAMSAS tree exchange</li>
1481 <li>local editing and update of sequences in VAMSAS
1482 alignments (experimental)</li>
1483 <li>Create new or select existing session to join</li>
1484 <li>load and save of vamsas documents</li>
1485 </ul> <em>Application command line</em>
1487 <li>-tree parameter to open trees (introduced for passing
1489 <li>-fetchfrom command line argument to specify nicknames
1490 of DAS servers to query for alignment features</li>
1491 <li>-dasserver command line argument to add new servers
1492 that are also automatically queried for features</li>
1493 <li>-groovy command line argument executes a given groovy
1494 script after all input data has been loaded and parsed</li>
1495 </ul> <em>Applet-Application data exchange</em>
1497 <li>Trees passed as applet parameters can be passed to
1498 application (when using "View in full
1499 application")</li>
1500 </ul> <em>Applet Parameters</em>
1502 <li>feature group display control parameter</li>
1503 <li>debug parameter</li>
1504 <li>showbutton parameter</li>
1505 </ul> <em>Applet API methods</em>
1507 <li>newView public method</li>
1508 <li>Window (current view) specific get/set public methods</li>
1509 <li>Feature display control methods</li>
1510 <li>get list of currently selected sequences</li>
1511 </ul> <em>New Jalview distribution features</em>
1513 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1514 <li>RELEASE file gives build properties for the latest
1515 Jalview release.</li>
1516 <li>Java 1.1 Applet build made easier and donotobfuscate
1517 property controls execution of obfuscator</li>
1518 <li>Build target for generating source distribution</li>
1519 <li>Debug flag for javacc</li>
1520 <li>.jalview_properties file is documented (slightly) in
1521 jalview.bin.Cache</li>
1522 <li>Continuous Build Integration for stable and
1523 development version of Application, Applet and source
1528 <li>selected region output includes visible annotations
1529 (for certain formats)</li>
1530 <li>edit label/displaychar contains existing label/char
1532 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1533 <li>shorter peptide product names from EMBL records</li>
1534 <li>Newick string generator makes compact representations</li>
1535 <li>bootstrap values parsed correctly for tree files with
1537 <li>pathological filechooser bug avoided by not allowing
1538 filenames containing a ':'</li>
1539 <li>Fixed exception when parsing GFF files containing
1540 global sequence features</li>
1541 <li>Alignment datasets are finalized only when number of
1542 references from alignment sequences goes to zero</li>
1543 <li>Close of tree branch colour box without colour
1544 selection causes cascading exceptions</li>
1545 <li>occasional negative imgwidth exceptions</li>
1546 <li>better reporting of non-fatal warnings to user when
1547 file parsing fails.</li>
1548 <li>Save works when Jalview project is default format</li>
1549 <li>Save as dialog opened if current alignment format is
1550 not a valid output format</li>
1551 <li>Uniprot canonical names introduced for both das and
1553 <li>Histidine should be midblue (not pink!) in Zappo</li>
1554 <li>error messages passed up and output when data read
1556 <li>edit undo recovers previous dataset sequence when
1557 sequence is edited</li>
1558 <li>allow PDB files without pdb ID HEADER lines (like
1559 those generated by MODELLER) to be read in properly</li>
1560 <li>allow reading of JPred concise files as a normal
1562 <li>Stockholm annotation parsing and alignment properties
1563 import fixed for PFAM records</li>
1564 <li>Structure view windows have correct name in Desktop
1566 <li>annotation consisting of sequence associated scores
1567 can be read and written correctly to annotation file</li>
1568 <li>Aligned cDNA translation to aligned peptide works
1570 <li>Fixed display of hidden sequence markers and
1571 non-italic font for representatives in Applet</li>
1572 <li>Applet Menus are always embedded in applet window on
1574 <li>Newly shown features appear at top of stack (in
1576 <li>Annotations added via parameter not drawn properly
1577 due to null pointer exceptions</li>
1578 <li>Secondary structure lines are drawn starting from
1579 first column of alignment</li>
1580 <li>Uniprot XML import updated for new schema release in
1582 <li>Sequence feature to sequence ID match for Features
1583 file is case-insensitive</li>
1584 <li>Sequence features read from Features file appended to
1585 all sequences with matching IDs</li>
1586 <li>PDB structure coloured correctly for associated views
1587 containing a sub-sequence</li>
1588 <li>PDB files can be retrieved by applet from Jar files</li>
1589 <li>feature and annotation file applet parameters
1590 referring to different directories are retrieved correctly</li>
1591 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1592 <li>Fixed application hang whilst waiting for
1593 splash-screen version check to complete</li>
1594 <li>Applet properly URLencodes input parameter values
1595 when passing them to the launchApp service</li>
1596 <li>display name and local features preserved in results
1597 retrieved from web service</li>
1598 <li>Visual delay indication for sequence retrieval and
1599 sequence fetcher initialisation</li>
1600 <li>updated Application to use DAS 1.53e version of
1601 dasobert DAS client</li>
1602 <li>Re-instated Full AMSA support and .amsa file
1604 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1612 <div align="center">
1613 <strong>2.3</strong><br> 9/5/07
1618 <li>Jmol 11.0.2 integration</li>
1619 <li>PDB views stored in Jalview XML files</li>
1620 <li>Slide sequences</li>
1621 <li>Edit sequence in place</li>
1622 <li>EMBL CDS features</li>
1623 <li>DAS Feature mapping</li>
1624 <li>Feature ordering</li>
1625 <li>Alignment Properties</li>
1626 <li>Annotation Scores</li>
1627 <li>Sort by scores</li>
1628 <li>Feature/annotation editing in applet</li>
1633 <li>Headless state operation in 2.2.1</li>
1634 <li>Incorrect and unstable DNA pairwise alignment</li>
1635 <li>Cut and paste of sequences with annotation</li>
1636 <li>Feature group display state in XML</li>
1637 <li>Feature ordering in XML</li>
1638 <li>blc file iteration selection using filename # suffix</li>
1639 <li>Stockholm alignment properties</li>
1640 <li>Stockhom alignment secondary structure annotation</li>
1641 <li>2.2.1 applet had no feature transparency</li>
1642 <li>Number pad keys can be used in cursor mode</li>
1643 <li>Structure Viewer mirror image resolved</li>
1650 <div align="center">
1651 <strong>2.2.1</strong><br> 12/2/07
1656 <li>Non standard characters can be read and displayed
1657 <li>Annotations/Features can be imported/exported to the
1659 <li>Applet allows editing of sequence/annotation/group
1660 name & description
1661 <li>Preference setting to display sequence name in
1663 <li>Annotation file format extended to allow
1664 Sequence_groups to be defined
1665 <li>Default opening of alignment overview panel can be
1666 specified in preferences
1667 <li>PDB residue numbering annotation added to associated
1673 <li>Applet crash under certain Linux OS with Java 1.6
1675 <li>Annotation file export / import bugs fixed
1676 <li>PNG / EPS image output bugs fixed
1682 <div align="center">
1683 <strong>2.2</strong><br> 27/11/06
1688 <li>Multiple views on alignment
1689 <li>Sequence feature editing
1690 <li>"Reload" alignment
1691 <li>"Save" to current filename
1692 <li>Background dependent text colour
1693 <li>Right align sequence ids
1694 <li>User-defined lower case residue colours
1697 <li>Menu item accelerator keys
1698 <li>Control-V pastes to current alignment
1699 <li>Cancel button for DAS Feature Fetching
1700 <li>PCA and PDB Viewers zoom via mouse roller
1701 <li>User-defined sub-tree colours and sub-tree selection
1703 <li>'New Window' button on the 'Output to Text box'
1708 <li>New memory efficient Undo/Redo System
1709 <li>Optimised symbol lookups and conservation/consensus
1711 <li>Region Conservation/Consensus recalculated after
1713 <li>Fixed Remove Empty Columns Bug (empty columns at end
1715 <li>Slowed DAS Feature Fetching for increased robustness.
1717 <li>Made angle brackets in ASCII feature descriptions
1719 <li>Re-instated Zoom function for PCA
1720 <li>Sequence descriptions conserved in web service
1722 <li>Uniprot ID discoverer uses any word separated by
1724 <li>WsDbFetch query/result association resolved
1725 <li>Tree leaf to sequence mapping improved
1726 <li>Smooth fonts switch moved to FontChooser dialog box.
1733 <div align="center">
1734 <strong>2.1.1</strong><br> 12/9/06
1739 <li>Copy consensus sequence to clipboard</li>
1744 <li>Image output - rightmost residues are rendered if
1745 sequence id panel has been resized</li>
1746 <li>Image output - all offscreen group boundaries are
1748 <li>Annotation files with sequence references - all
1749 elements in file are relative to sequence position</li>
1750 <li>Mac Applet users can use Alt key for group editing</li>
1756 <div align="center">
1757 <strong>2.1</strong><br> 22/8/06
1762 <li>MAFFT Multiple Alignment in default Web Service list</li>
1763 <li>DAS Feature fetching</li>
1764 <li>Hide sequences and columns</li>
1765 <li>Export Annotations and Features</li>
1766 <li>GFF file reading / writing</li>
1767 <li>Associate structures with sequences from local PDB
1769 <li>Add sequences to exisiting alignment</li>
1770 <li>Recently opened files / URL lists</li>
1771 <li>Applet can launch the full application</li>
1772 <li>Applet has transparency for features (Java 1.2
1774 <li>Applet has user defined colours parameter</li>
1775 <li>Applet can load sequences from parameter
1776 "sequence<em>x</em>"
1782 <li>Redundancy Panel reinstalled in the Applet</li>
1783 <li>Monospaced font - EPS / rescaling bug fixed</li>
1784 <li>Annotation files with sequence references bug fixed</li>
1790 <div align="center">
1791 <strong>2.08.1</strong><br> 2/5/06
1796 <li>Change case of selected region from Popup menu</li>
1797 <li>Choose to match case when searching</li>
1798 <li>Middle mouse button and mouse movement can compress /
1799 expand the visible width and height of the alignment</li>
1804 <li>Annotation Panel displays complete JNet results</li>
1810 <div align="center">
1811 <strong>2.08b</strong><br> 18/4/06
1817 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1818 <li>Righthand label on wrapped alignments shows correct
1825 <div align="center">
1826 <strong>2.08</strong><br> 10/4/06
1831 <li>Editing can be locked to the selection area</li>
1832 <li>Keyboard editing</li>
1833 <li>Create sequence features from searches</li>
1834 <li>Precalculated annotations can be loaded onto
1836 <li>Features file allows grouping of features</li>
1837 <li>Annotation Colouring scheme added</li>
1838 <li>Smooth fonts off by default - Faster rendering</li>
1839 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1844 <li>Drag & Drop fixed on Linux</li>
1845 <li>Jalview Archive file faster to load/save, sequence
1846 descriptions saved.</li>
1852 <div align="center">
1853 <strong>2.07</strong><br> 12/12/05
1858 <li>PDB Structure Viewer enhanced</li>
1859 <li>Sequence Feature retrieval and display enhanced</li>
1860 <li>Choose to output sequence start-end after sequence
1861 name for file output</li>
1862 <li>Sequence Fetcher WSDBFetch@EBI</li>
1863 <li>Applet can read feature files, PDB files and can be
1864 used for HTML form input</li>
1869 <li>HTML output writes groups and features</li>
1870 <li>Group editing is Control and mouse click</li>
1871 <li>File IO bugs</li>
1877 <div align="center">
1878 <strong>2.06</strong><br> 28/9/05
1883 <li>View annotations in wrapped mode</li>
1884 <li>More options for PCA viewer</li>
1889 <li>GUI bugs resolved</li>
1890 <li>Runs with -nodisplay from command line</li>
1896 <div align="center">
1897 <strong>2.05b</strong><br> 15/9/05
1902 <li>Choose EPS export as lineart or text</li>
1903 <li>Jar files are executable</li>
1904 <li>Can read in Uracil - maps to unknown residue</li>
1909 <li>Known OutOfMemory errors give warning message</li>
1910 <li>Overview window calculated more efficiently</li>
1911 <li>Several GUI bugs resolved</li>
1917 <div align="center">
1918 <strong>2.05</strong><br> 30/8/05
1923 <li>Edit and annotate in "Wrapped" view</li>
1928 <li>Several GUI bugs resolved</li>
1934 <div align="center">
1935 <strong>2.04</strong><br> 24/8/05
1940 <li>Hold down mouse wheel & scroll to change font
1946 <li>Improved JPred client reliability</li>
1947 <li>Improved loading of Jalview files</li>
1953 <div align="center">
1954 <strong>2.03</strong><br> 18/8/05
1959 <li>Set Proxy server name and port in preferences</li>
1960 <li>Multiple URL links from sequence ids</li>
1961 <li>User Defined Colours can have a scheme name and added
1963 <li>Choose to ignore gaps in consensus calculation</li>
1964 <li>Unix users can set default web browser</li>
1965 <li>Runs without GUI for batch processing</li>
1966 <li>Dynamically generated Web Service Menus</li>
1971 <li>InstallAnywhere download for Sparc Solaris</li>
1977 <div align="center">
1978 <strong>2.02</strong><br> 18/7/05
1984 <li>Copy & Paste order of sequences maintains
1985 alignment order.</li>
1991 <div align="center">
1992 <strong>2.01</strong><br> 12/7/05
1997 <li>Use delete key for deleting selection.</li>
1998 <li>Use Mouse wheel to scroll sequences.</li>
1999 <li>Help file updated to describe how to add alignment
2001 <li>Version and build date written to build properties
2003 <li>InstallAnywhere installation will check for updates
2004 at launch of Jalview.</li>
2009 <li>Delete gaps bug fixed.</li>
2010 <li>FileChooser sorts columns.</li>
2011 <li>Can remove groups one by one.</li>
2012 <li>Filechooser icons installed.</li>
2013 <li>Finder ignores return character when searching.
2014 Return key will initiate a search.<br>
2021 <div align="center">
2022 <strong>2.0</strong><br> 20/6/05
2027 <li>New codebase</li>