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 width="60" nowrap>
50 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
51 <em>6/10/2015</em></strong>
57 <li>Updated Spanish translations of localized text for 2.9</li>
59 <em>Application</em><ul>
60 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
61 <li>Signed OSX InstallAnywhere installer</li></ul>
63 <ul><li>Split frame example added to applet examples page</li>
70 <li>Mapping of cDNA to protein in split frames incorrect when sequence start > 1</li>
71 <li>Fix broken images in filter column by annotation dialog documentation</li>
72 <li>Feature colours not parsed from features file</li>
73 <li>Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description</li>
76 <em>Application</em><ul>
77 <li>Annotations corrupted after BioJS export and reimport</li>
78 <li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
79 <li>Incorrect warning about deleting all data when deleting selected columns</li>
80 <li>Patch to build system for shipping properly signed JNLP templates for webstart launch</li>
81 <li>EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing</li>
82 <li>Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug</li>
85 <li>Reorder sequences mirrored in cDNA/Protein split frame</li>
86 <li>Applet with Jmol examples not loading correctly</li>
92 <td><div align="center">
93 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
97 <li>Linked visualisation and analysis of DNA and Protein
100 <li>Translated cDNA alignments shown as split protein
101 and DNA alignment views</li>
102 <li>Codon consensus annotation for linked protein and
103 cDNA alignment views</li>
104 <li>Link cDNA or Protein product sequences by loading
105 them onto Protein or cDNA alignments</li>
106 <li>Reconstruct linked cDNA alignment from aligned
107 protein sequences</li>
110 <li>Jmol integration updated to Jmol v14.2.14</li>
111 <li>Import and export of Jalview alignment views as <a
112 href="features/bioJsonFormat.html">BioJSON</a></li>
113 <li>New alignment annotation file statements for
114 reference sequences and marking hidden columns</li>
115 <li>Reference sequence based alignment shading to
116 highlight variation</li>
117 <li>Select or hide columns according to alignment
119 <li>Find option for locating sequences by description</li>
120 <li>Conserved physicochemical properties shown in amino
121 acid conservation row</li>
122 <li>Alignments can be sorted by number of RNA helices</li>
123 </ul> <em>Application</em>
125 <li>New cDNA/Protein analysis capabilities
127 <li>Get Cross-References should open a Split Frame
128 view with cDNA/Protein</li>
129 <li>Detect when nucleotide sequences and protein
130 sequences are placed in the same alignment</li>
131 <li>Split cDNA/Protein views are saved in Jalview
136 <li>Use REST API to talk to Chimera</li>
137 <li>Selected regions in Chimera are highlighted in linked
140 <li>VARNA RNA viewer updated to v3.93</li>
141 <li>VARNA views are saved in Jalview Projects</li>
142 <li>Pseudoknots displayed as Jalview RNA annotation can
143 be shown in VARNA</li>
145 <li>Make groups for selection uses marked columns as well
146 as the active selected region</li>
148 <li>Calculate UPGMA and NJ trees using sequence feature
150 <li>New Export options
152 <li>New Export Settings dialog to control hidden
153 region export in flat file generation</li>
155 <li>Export alignment views for display with the <a
156 href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
158 <li>Export scrollable SVG in HTML page</li>
159 <li>Optional embedding of BioJSON data when exporting
160 alignment figures to HTML</li>
162 <li>3D structure retrieval and display
164 <li>Free text and structured queries with the PDBe
166 <li>PDBe Search API based discovery and selection of
167 PDB structures for a sequence set</li>
171 <li>JPred4 employed for protein secondary structure
173 <li>Hide Insertions menu option to hide unaligned columns
174 for one or a group of sequences</li>
175 <li>Automatically hide insertions in alignments imported
176 from the JPred4 web server</li>
177 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
178 system on OSX<br />LGPL libraries courtesy of <a
179 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
181 <li>changed 'View nucleotide structure' submenu to 'View
182 VARNA 2D Structure'</li>
183 <li>change "View protein structure" menu option to "3D
186 </ul> <em>Applet</em>
188 <li>New layout for applet example pages</li>
189 <li>New parameters to enable SplitFrame view
190 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
191 <li>New example demonstrating linked viewing of cDNA and
192 Protein alignments</li>
193 </ul> <em>Development and deployment</em>
195 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
196 <li>Include installation type and git revision in build
197 properties and console log output</li>
198 <li>Jalview Github organisation, and new github site for
199 storing BioJsMSA Templates</li>
200 <li>Jalview's unit tests now managed with TestNG</li>
203 <!-- <em>General</em>
205 </ul> --> <!-- issues resolved --> <em>Application</em>
207 <li>Escape should close any open find dialogs</li>
208 <li>Typo in select-by-features status report</li>
209 <li>Consensus RNA secondary secondary structure
210 predictions are not highlighted in amber</li>
211 <li>Missing gap character in v2.7 example file means
212 alignment appears unaligned when pad-gaps is not enabled</li>
213 <li>First switch to RNA Helices colouring doesn't colour
214 associated structure views</li>
215 <li>ID width preference option is greyed out when auto
216 width checkbox not enabled</li>
217 <li>Stopped a warning dialog from being shown when
218 creating user defined colours</li>
219 <li>'View Mapping' in structure viewer shows sequence
220 mappings for just that viewer's sequences</li>
221 <li>Workaround for superposing PDB files containing
222 multiple models in Chimera</li>
223 <li>Report sequence position in status bar when hovering
224 over Jmol structure</li>
225 <li>Cannot output gaps as '.' symbols with Selection ->
226 output to text box</li>
227 <li>Flat file exports of alignments with hidden columns
228 have incorrect sequence start/end</li>
229 <li>'Aligning' a second chain to a Chimera structure from
231 <li>Colour schemes applied to structure viewers don't
232 work for nucleotide</li>
233 <li>Loading/cut'n'pasting an empty or invalid file leads
234 to a grey/invisible alignment window</li>
235 <li>Exported Jpred annotation from a sequence region
236 imports to different position</li>
237 <li>Space at beginning of sequence feature tooltips shown
238 on some platforms</li>
239 <li>Chimera viewer 'View | Show Chain' menu is not
241 <li>'New View' fails with a Null Pointer Exception in
242 console if Chimera has been opened</li>
243 <li>Mouseover to Chimera not working</li>
244 <li>Miscellaneous ENA XML feature qualifiers not
246 <li>NPE in annotation renderer after 'Extract Scores'</li>
247 <li>If two structures in one Chimera window, mouseover of
248 either sequence shows on first structure</li>
249 <li>'Show annotations' options should not make
250 non-positional annotations visible</li>
251 <li>Subsequence secondary structure annotation not shown
252 in right place after 'view flanking regions'</li>
253 <li>File Save As type unset when current file format is
255 <li>Save as '.jar' option removed for saving Jalview
257 <li>Colour by Sequence colouring in Chimera more
259 <li>Cannot 'add reference annotation' for a sequence in
260 several views on same alignment</li>
261 <li>Cannot show linked products for EMBL / ENA records</li>
262 <li>Jalview's tooltip wraps long texts containing no
264 </ul> <em>Applet</em>
266 <li>Jmol to JalviewLite mouseover/link not working</li>
267 <li>JalviewLite can't import sequences with ID
268 descriptions containing angle brackets</li>
269 </ul> <em>General</em>
271 <li>Cannot export and reimport RNA secondary structure
272 via jalview annotation file</li>
273 <li>Random helix colour palette for colour by annotation
274 with RNA secondary structure</li>
275 <li>Mouseover to cDNA from STOP residue in protein
276 translation doesn't work.</li>
277 <li>hints when using the select by annotation dialog box</li>
278 <li>Jmol alignment incorrect if PDB file has alternate CA
280 <li>FontChooser message dialog appears to hang after
281 choosing 1pt font</li>
282 <li>Peptide secondary structure incorrectly imported from
283 annotation file when annotation display text includes 'e' or
285 <li>Cannot set colour of new feature type whilst creating
287 <li>cDNA translation alignment should not be sequence
289 <li>'Show unconserved' doesn't work for lower case
291 <li>Nucleotide ambiguity codes involving R not recognised</li>
292 </ul> <em>Deployment and Documentation</em>
294 <li>Applet example pages appear different to the rest of
296 </ul> <em>Application Known issues</em>
298 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
299 <li>Misleading message appears after trying to delete
301 <li>Jalview icon not shown in dock after InstallAnywhere
302 version launches</li>
303 <li>Fetching EMBL reference for an RNA sequence results
304 fails with a sequence mismatch</li>
305 <li>Corrupted or unreadable alignment display when
306 scrolling alignment to right</li>
307 <li>ArrayIndexOutOfBoundsException thrown when remove
308 empty columns called on alignment with ragged gapped ends</li>
309 <li>auto calculated alignment annotation rows do not get
310 placed above or below non-autocalculated rows</li>
311 <li>Jalview dekstop becomes sluggish at full screen in
312 ultra-high resolution</li>
313 <li>Cannot disable consensus calculation independently of
314 quality and conservation</li>
315 <li>Mouseover highlighting between cDNA and protein can
316 become sluggish with more than one splitframe shown</li>
317 </ul> <em>Applet Known Issues</em>
319 <li>Core PDB parsing code requires Jmol</li>
320 <li>Sequence canvas panel goes white when alignment
321 window is being resized</li>
327 <td><div align="center">
328 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
332 <li>Updated Java code signing certificate donated by
334 <li>Features and annotation preserved when performing
335 pairwise alignment</li>
336 <li>RNA pseudoknot annotation can be
337 imported/exported/displayed</li>
338 <li>'colour by annotation' can colour by RNA and
339 protein secondary structure</li>
340 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
341 post-hoc with 2.9 release</em>)
344 </ul> <em>Application</em>
346 <li>Extract and display secondary structure for sequences
347 with 3D structures</li>
348 <li>Support for parsing RNAML</li>
349 <li>Annotations menu for layout
351 <li>sort sequence annotation rows by alignment</li>
352 <li>place sequence annotation above/below alignment
355 <li>Output in Stockholm format</li>
356 <li>Internationalisation: improved Spanish (es)
358 <li>Structure viewer preferences tab</li>
359 <li>Disorder and Secondary Structure annotation tracks
360 shared between alignments</li>
361 <li>UCSF Chimera launch and linked highlighting from
363 <li>Show/hide all sequence associated annotation rows for
364 all or current selection</li>
365 <li>disorder and secondary structure predictions
366 available as dataset annotation</li>
367 <li>Per-sequence rna helices colouring</li>
370 <li>Sequence database accessions imported when fetching
371 alignments from Rfam</li>
372 <li>update VARNA version to 3.91</li>
374 <li>New groovy scripts for exporting aligned positions,
375 conservation values, and calculating sum of pairs scores.</li>
376 <li>Command line argument to set default JABAWS server</li>
377 <li>include installation type in build properties and
378 console log output</li>
379 <li>Updated Jalview project format to preserve dataset
383 <!-- issues resolved --> <em>Application</em>
385 <li>Distinguish alignment and sequence associated RNA
386 structure in structure->view->VARNA</li>
387 <li>Raise dialog box if user deletes all sequences in an
389 <li>Pressing F1 results in documentation opening twice</li>
390 <li>Sequence feature tooltip is wrapped</li>
391 <li>Double click on sequence associated annotation
392 selects only first column</li>
393 <li>Redundancy removal doesn't result in unlinked
394 leaves shown in tree</li>
395 <li>Undos after several redundancy removals don't undo
397 <li>Hide sequence doesn't hide associated annotation</li>
398 <li>User defined colours dialog box too big to fit on
399 screen and buttons not visible</li>
400 <li>author list isn't updated if already written to
401 Jalview properties</li>
402 <li>Popup menu won't open after retrieving sequence
404 <li>File open window for associate PDB doesn't open</li>
405 <li>Left-then-right click on a sequence id opens a
406 browser search window</li>
407 <li>Cannot open sequence feature shading/sort popup menu
408 in feature settings dialog</li>
409 <li>better tooltip placement for some areas of Jalview
411 <li>Allow addition of JABAWS Server which doesn't
413 <li>Web services parameters dialog box is too large to
415 <li>Muscle nucleotide alignment preset obscured by
417 <li>JABAWS preset submenus don't contain newly
418 defined user preset</li>
419 <li>MSA web services warns user if they were launched
420 with invalid input</li>
421 <li>Jalview cannot contact DAS Registy when running on
424 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
425 'Superpose with' submenu not shown when new view
429 </ul> <!-- <em>Applet</em>
431 </ul> <em>General</em>
433 </ul>--> <em>Deployment and Documentation</em>
435 <li>2G and 1G options in launchApp have no effect on
436 memory allocation</li>
437 <li>launchApp service doesn't automatically open
438 www.jalview.org/examples/exampleFile.jar if no file is given</li>
440 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
441 InstallAnywhere reports cannot find valid JVM when Java
444 </ul> <em>Application Known issues</em>
447 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
448 corrupted or unreadable alignment display when scrolling
452 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
453 retrieval fails but progress bar continues for DAS retrieval
454 with large number of ID
457 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
458 flatfile output of visible region has incorrect sequence
462 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
463 rna structure consensus doesn't update when secondary
464 structure tracks are rearranged
467 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
468 invalid rna structure positional highlighting does not
469 highlight position of invalid base pairs
472 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
473 out of memory errors are not raised when saving Jalview
474 project from alignment window file menu
477 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
478 Switching to RNA Helices colouring doesn't propagate to
482 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
483 colour by RNA Helices not enabled when user created
484 annotation added to alignment
487 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
488 Jalview icon not shown on dock in Mountain Lion/Webstart
490 </ul> <em>Applet Known Issues</em>
493 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
494 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
497 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
498 Jalview and Jmol example not compatible with IE9
501 <li>Sort by annotation score doesn't reverse order
507 <td><div align="center">
508 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
511 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
514 <li>Internationalisation of user interface (usually
515 called i18n support) and translation for Spanish locale</li>
516 <li>Define/Undefine group on current selection with
517 Ctrl-G/Shift Ctrl-G</li>
518 <li>Improved group creation/removal options in
519 alignment/sequence Popup menu</li>
520 <li>Sensible precision for symbol distribution
521 percentages shown in logo tooltip.</li>
522 <li>Annotation panel height set according to amount of
523 annotation when alignment first opened</li>
524 </ul> <em>Application</em>
526 <li>Interactive consensus RNA secondary structure
527 prediction VIENNA RNAAliFold JABA 2.1 service</li>
528 <li>Select columns containing particular features from
529 Feature Settings dialog</li>
530 <li>View all 'representative' PDB structures for selected
532 <li>Update Jalview project format:
534 <li>New file extension for Jalview projects '.jvp'</li>
535 <li>Preserve sequence and annotation dataset (to
536 store secondary structure annotation,etc)</li>
537 <li>Per group and alignment annotation and RNA helix
541 <li>New similarity measures for PCA and Tree calculation
543 <li>Experimental support for retrieval and viewing of
544 flanking regions for an alignment</li>
548 <!-- issues resolved --> <em>Application</em>
550 <li>logo keeps spinning and status remains at queued or
551 running after job is cancelled</li>
552 <li>cannot export features from alignments imported from
553 Jalview/VAMSAS projects</li>
554 <li>Buggy slider for web service parameters that take
556 <li>Newly created RNA secondary structure line doesn't
557 have 'display all symbols' flag set</li>
558 <li>T-COFFEE alignment score shading scheme and other
559 annotation shading not saved in Jalview project</li>
560 <li>Local file cannot be loaded in freshly downloaded
562 <li>Jalview icon not shown on dock in Mountain
564 <li>Load file from desktop file browser fails</li>
565 <li>Occasional NPE thrown when calculating large trees</li>
566 <li>Cannot reorder or slide sequences after dragging an
567 alignment onto desktop</li>
568 <li>Colour by annotation dialog throws NPE after using
569 'extract scores' function</li>
570 <li>Loading/cut'n'pasting an empty file leads to a grey
571 alignment window</li>
572 <li>Disorder thresholds rendered incorrectly after
573 performing IUPred disorder prediction</li>
574 <li>Multiple group annotated consensus rows shown when
575 changing 'normalise logo' display setting</li>
576 <li>Find shows blank dialog after 'finished searching' if
577 nothing matches query</li>
578 <li>Null Pointer Exceptions raised when sorting by
579 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
581 <li>Errors in Jmol console when structures in alignment
582 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
584 <li>Not all working JABAWS services are shown in
586 <li>JAVAWS version of Jalview fails to launch with
587 'invalid literal/length code'</li>
588 <li>Annotation/RNA Helix colourschemes cannot be applied
589 to alignment with groups (actually fixed in 2.8.0b1)</li>
590 <li>RNA Helices and T-Coffee Scores available as default
593 </ul> <em>Applet</em>
595 <li>Remove group option is shown even when selection is
597 <li>Apply to all groups ticked but colourscheme changes
598 don't affect groups</li>
599 <li>Documented RNA Helices and T-Coffee Scores as valid
600 colourscheme name</li>
601 <li>Annotation labels drawn on sequence IDs when
602 Annotation panel is not displayed</li>
603 <li>Increased font size for dropdown menus on OSX and
604 embedded windows</li>
607 <li>Consensus sequence for alignments/groups with a
608 single sequence were not calculated</li>
609 <li>annotation files that contain only groups imported as
610 annotation and junk sequences</li>
611 <li>Fasta files with sequences containing '*' incorrectly
612 recognised as PFAM or BLC</li>
613 <li>conservation/PID slider apply all groups option
614 doesn't affect background (2.8.0b1)
616 <li>redundancy highlighting is erratic at 0% and 100%</li>
617 <li>Remove gapped columns fails for sequences with ragged
619 <li>AMSA annotation row with leading spaces is not
620 registered correctly on import</li>
621 <li>Jalview crashes when selecting PCA analysis for
622 certain alignments</li>
623 <li>Opening the colour by annotation dialog for an
624 existing annotation based 'use original colours'
625 colourscheme loses original colours setting</li>
630 <td><div align="center">
631 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
632 <em>30/1/2014</em></strong>
636 <li>Trusted certificates for JalviewLite applet and
637 Jalview Desktop application<br />Certificate was donated by
638 <a href="https://www.certum.eu">Certum</a> to the Jalview
639 open source project).
641 <li>Jalview SRS links replaced by Uniprot and EBI-search
643 <li>Output in Stockholm format</li>
644 <li>Allow import of data from gzipped files</li>
645 <li>Export/import group and sequence associated line
646 graph thresholds</li>
647 <li>Nucleotide substitution matrix that supports RNA and
649 <li>Allow disorder predictions to be made on the current
650 selection (or visible selection) in the same way that JPred
652 <li>Groovy scripting for headless Jalview operation</li>
653 </ul> <em>Other improvements</em>
655 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
656 <li>COMBINE statement uses current SEQUENCE_REF and
657 GROUP_REF scope to group annotation rows</li>
658 <li>Support '' style escaping of quotes in Newick
660 <li>Group options for JABAWS service by command line name</li>
661 <li>Empty tooltip shown for JABA service options with a
662 link but no description</li>
663 <li>Select primary source when selecting authority in
664 database fetcher GUI</li>
665 <li>Add .mfa to FASTA file extensions recognised by
667 <li>Annotation label tooltip text wrap</li>
672 <li>Slow scrolling when lots of annotation rows are
674 <li>Lots of NPE (and slowness) after creating RNA
675 secondary structure annotation line</li>
676 <li>Sequence database accessions not imported when
677 fetching alignments from Rfam</li>
678 <li>Incorrect SHMR submission for sequences with
680 <li>View all structures does not always superpose
682 <li>Option widgets in service parameters not updated to
683 reflect user or preset settings</li>
684 <li>Null pointer exceptions for some services without
685 presets or adjustable parameters</li>
686 <li>Discover PDB IDs entry in structure menu doesn't
687 discover PDB xRefs</li>
688 <li>Exception encountered while trying to retrieve
689 features with DAS</li>
690 <li>Lowest value in annotation row isn't coloured
691 when colour by annotation (per sequence) is coloured</li>
692 <li>Keyboard mode P jumps to start of gapped region when
693 residue follows a gap</li>
694 <li>Jalview appears to hang importing an alignment with
695 Wrap as default or after enabling Wrap</li>
696 <li>'Right click to add annotations' message
697 shown in wrap mode when no annotations present</li>
698 <li>Disorder predictions fail with NPE if no automatic
699 annotation already exists on alignment</li>
700 <li>oninit javascript function should be called after
701 initialisation completes</li>
702 <li>Remove redundancy after disorder prediction corrupts
703 alignment window display</li>
704 <li>Example annotation file in documentation is invalid</li>
705 <li>Grouped line graph annotation rows are not exported
706 to annotation file</li>
707 <li>Multi-harmony analysis cannot be run when only two
709 <li>Cannot create multiple groups of line graphs with
710 several 'combine' statements in annotation file</li>
711 <li>Pressing return several times causes Number Format
712 exceptions in keyboard mode</li>
713 <li>Multi-harmony (SHMMR) method doesn't submit
714 correct partitions for input data</li>
715 <li>Translation from DNA to Amino Acids fails</li>
716 <li>Jalview fail to load newick tree with quoted label</li>
717 <li>--headless flag isn't understood</li>
718 <li>ClassCastException when generating EPS in headless
720 <li>Adjusting sequence-associated shading threshold only
721 changes one row's threshold</li>
722 <li>Preferences and Feature settings panel panel
723 doesn't open</li>
724 <li>hide consensus histogram also hides conservation and
725 quality histograms</li>
730 <td><div align="center">
731 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
733 <td><em>Application</em>
735 <li>Support for JABAWS 2.0 Services (AACon alignment
736 conservation, protein disorder and Clustal Omega)</li>
737 <li>JABAWS server status indicator in Web Services
739 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
740 in Jalview alignment window</li>
741 <li>Updated Jalview build and deploy framework for OSX
742 mountain lion, windows 7, and 8</li>
743 <li>Nucleotide substitution matrix for PCA that supports
744 RNA and ambiguity codes</li>
746 <li>Improved sequence database retrieval GUI</li>
747 <li>Support fetching and database reference look up
748 against multiple DAS sources (Fetch all from in 'fetch db
750 <li>Jalview project improvements
752 <li>Store and retrieve the 'belowAlignment'
753 flag for annotation</li>
754 <li>calcId attribute to group annotation rows on the
756 <li>Store AACon calculation settings for a view in
761 <li>horizontal scrolling gesture support</li>
762 <li>Visual progress indicator when PCA calculation is
764 <li>Simpler JABA web services menus</li>
765 <li>visual indication that web service results are still
766 being retrieved from server</li>
767 <li>Serialise the dialogs that are shown when Jalview
768 starts up for first time</li>
769 <li>Jalview user agent string for interacting with HTTP
771 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
773 <li>Examples directory and Groovy library included in
774 InstallAnywhere distribution</li>
775 </ul> <em>Applet</em>
777 <li>RNA alignment and secondary structure annotation
778 visualization applet example</li>
779 </ul> <em>General</em>
781 <li>Normalise option for consensus sequence logo</li>
782 <li>Reset button in PCA window to return dimensions to
784 <li>Allow seqspace or Jalview variant of alignment PCA
786 <li>PCA with either nucleic acid and protein substitution
788 <li>Allow windows containing HTML reports to be exported
790 <li>Interactive display and editing of RNA secondary
791 structure contacts</li>
792 <li>RNA Helix Alignment Colouring</li>
793 <li>RNA base pair logo consensus</li>
794 <li>Parse sequence associated secondary structure
795 information in Stockholm files</li>
796 <li>HTML Export database accessions and annotation
797 information presented in tooltip for sequences</li>
798 <li>Import secondary structure from LOCARNA clustalw
799 style RNA alignment files</li>
800 <li>import and visualise T-COFFEE quality scores for an
802 <li>'colour by annotation' per sequence option to
803 shade each sequence according to its associated alignment
805 <li>New Jalview Logo</li>
806 </ul> <em>Documentation and Development</em>
808 <li>documentation for score matrices used in Jalview</li>
809 <li>New Website!</li>
811 <td><em>Application</em>
813 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
814 wsdbfetch REST service</li>
815 <li>Stop windows being moved outside desktop on OSX</li>
816 <li>Filetype associations not installed for webstart
818 <li>Jalview does not always retrieve progress of a JABAWS
819 job execution in full once it is complete</li>
820 <li>revise SHMR RSBS definition to ensure alignment is
821 uploaded via ali_file parameter</li>
822 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
823 <li>View all structures superposed fails with exception</li>
824 <li>Jnet job queues forever if a very short sequence is
825 submitted for prediction</li>
826 <li>Cut and paste menu not opened when mouse clicked on
828 <li>Putting fractional value into integer text box in
829 alignment parameter dialog causes Jalview to hang</li>
830 <li>Structure view highlighting doesn't work on
832 <li>View all structures fails with exception shown in
834 <li>Characters in filename associated with PDBEntry not
835 escaped in a platform independent way</li>
836 <li>Jalview desktop fails to launch with exception when
838 <li>Tree calculation reports 'you must have 2 or more
839 sequences selected' when selection is empty</li>
840 <li>Jalview desktop fails to launch with jar signature
841 failure when java web start temporary file caching is
843 <li>DAS Sequence retrieval with range qualification
844 results in sequence xref which includes range qualification</li>
845 <li>Errors during processing of command line arguments
846 cause progress bar (JAL-898) to be removed</li>
847 <li>Replace comma for semi-colon option not disabled for
848 DAS sources in sequence fetcher</li>
849 <li>Cannot close news reader when JABAWS server warning
851 <li>Option widgets not updated to reflect user settings</li>
852 <li>Edited sequence not submitted to web service</li>
853 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
854 <li>InstallAnywhere installer doesn't unpack and run
855 on OSX Mountain Lion</li>
856 <li>Annotation panel not given a scroll bar when
857 sequences with alignment annotation are pasted into the
859 <li>Sequence associated annotation rows not associated
860 when loaded from Jalview project</li>
861 <li>Browser launch fails with NPE on java 1.7</li>
862 <li>JABAWS alignment marked as finished when job was
863 cancelled or job failed due to invalid input</li>
864 <li>NPE with v2.7 example when clicking on Tree
865 associated with all views</li>
866 <li>Exceptions when copy/paste sequences with grouped
867 annotation rows to new window</li>
868 </ul> <em>Applet</em>
870 <li>Sequence features are momentarily displayed before
871 they are hidden using hidefeaturegroups applet parameter</li>
872 <li>loading features via javascript API automatically
873 enables feature display</li>
874 <li>scrollToColumnIn javascript API method doesn't
876 </ul> <em>General</em>
878 <li>Redundancy removal fails for rna alignment</li>
879 <li>PCA calculation fails when sequence has been selected
880 and then deselected</li>
881 <li>PCA window shows grey box when first opened on OSX</li>
882 <li>Letters coloured pink in sequence logo when alignment
883 coloured with clustalx</li>
884 <li>Choosing fonts without letter symbols defined causes
885 exceptions and redraw errors</li>
886 <li>Initial PCA plot view is not same as manually
887 reconfigured view</li>
888 <li>Grouped annotation graph label has incorrect line
890 <li>Grouped annotation graph label display is corrupted
891 for lots of labels</li>
897 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
900 <td><em>Application</em>
902 <li>Jalview Desktop News Reader</li>
903 <li>Tweaked default layout of web services menu</li>
904 <li>View/alignment association menu to enable user to
905 easily specify which alignment a multi-structure view takes
906 its colours/correspondences from</li>
907 <li>Allow properties file location to be specified as URL</li>
908 <li>Extend Jalview project to preserve associations
909 between many alignment views and a single Jmol display</li>
910 <li>Store annotation row height in Jalview project file</li>
911 <li>Annotation row column label formatting attributes
912 stored in project file</li>
913 <li>Annotation row order for auto-calculated annotation
914 rows preserved in Jalview project file</li>
915 <li>Visual progress indication when Jalview state is
916 saved using Desktop window menu</li>
917 <li>Visual indication that command line arguments are
918 still being processed</li>
919 <li>Groovy script execution from URL</li>
920 <li>Colour by annotation default min and max colours in
922 <li>Automatically associate PDB files dragged onto an
923 alignment with sequences that have high similarity and
925 <li>Update JGoogleAnalytics to latest release (0.3)</li>
926 <li>'view structures' option to open many
927 structures in same window</li>
928 <li>Sort associated views menu option for tree panel</li>
929 <li>Group all JABA and non-JABA services for a particular
930 analysis function in its own submenu</li>
931 </ul> <em>Applet</em>
933 <li>Userdefined and autogenerated annotation rows for
935 <li>Adjustment of alignment annotation pane height</li>
936 <li>Annotation scrollbar for annotation panel</li>
937 <li>Drag to reorder annotation rows in annotation panel</li>
938 <li>'automaticScrolling' parameter</li>
939 <li>Allow sequences with partial ID string matches to be
940 annotated from GFF/Jalview features files</li>
941 <li>Sequence logo annotation row in applet</li>
942 <li>Absolute paths relative to host server in applet
943 parameters are treated as such</li>
944 <li>New in the JalviewLite javascript API:
946 <li>JalviewLite.js javascript library</li>
947 <li>Javascript callbacks for
949 <li>Applet initialisation</li>
950 <li>Sequence/alignment mouse-overs and selections</li>
953 <li>scrollTo row and column alignment scrolling
955 <li>Select sequence/alignment regions from javascript</li>
956 <li>javascript structure viewer harness to pass
957 messages between Jmol and Jalview when running as
958 distinct applets</li>
959 <li>sortBy method</li>
960 <li>Set of applet and application examples shipped
961 with documentation</li>
962 <li>New example to demonstrate JalviewLite and Jmol
963 javascript message exchange</li>
965 </ul> <em>General</em>
967 <li>Enable Jmol displays to be associated with multiple
968 multiple alignments</li>
969 <li>Option to automatically sort alignment with new tree</li>
970 <li>User configurable link to enable redirects to a
971 www.Jalview.org mirror</li>
972 <li>Jmol colours option for Jmol displays</li>
973 <li>Configurable newline string when writing alignment
974 and other flat files</li>
975 <li>Allow alignment annotation description lines to
976 contain html tags</li>
977 </ul> <em>Documentation and Development</em>
979 <li>Add groovy test harness for bulk load testing to
981 <li>Groovy script to load and align a set of sequences
982 using a web service before displaying the result in the
984 <li>Restructured javascript and applet api documentation</li>
985 <li>Ant target to publish example html files with applet
987 <li>Netbeans project for building Jalview from source</li>
988 <li>ant task to create online javadoc for Jalview source</li>
990 <td><em>Application</em>
992 <li>User defined colourscheme throws exception when
993 current built in colourscheme is saved as new scheme</li>
994 <li>AlignFrame->Save in application pops up save
995 dialog for valid filename/format</li>
996 <li>Cannot view associated structure for Uniprot sequence</li>
997 <li>PDB file association breaks for Uniprot sequence
999 <li>Associate PDB from file dialog does not tell you
1000 which sequence is to be associated with the file</li>
1001 <li>Find All raises null pointer exception when query
1002 only matches sequence IDs</li>
1003 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1004 <li>Jalview project with Jmol views created with Jalview
1005 2.4 cannot be loaded</li>
1006 <li>Filetype associations not installed for webstart
1008 <li>Two or more chains in a single PDB file associated
1009 with sequences in different alignments do not get coloured
1010 by their associated sequence</li>
1011 <li>Visibility status of autocalculated annotation row
1012 not preserved when project is loaded</li>
1013 <li>Annotation row height and visibility attributes not
1014 stored in Jalview project</li>
1015 <li>Tree bootstraps are not preserved when saved as a
1016 Jalview project</li>
1017 <li>Envision2 workflow tooltips are corrupted</li>
1018 <li>Enabling show group conservation also enables colour
1019 by conservation</li>
1020 <li>Duplicate group associated conservation or consensus
1021 created on new view</li>
1022 <li>Annotation scrollbar not displayed after 'show
1023 all hidden annotation rows' option selected</li>
1024 <li>Alignment quality not updated after alignment
1025 annotation row is hidden then shown</li>
1026 <li>Preserve colouring of structures coloured by
1027 sequences in pre Jalview 2.7 projects</li>
1028 <li>Web service job parameter dialog is not laid out
1030 <li>Web services menu not refreshed after 'reset
1031 services' button is pressed in preferences</li>
1032 <li>Annotation off by one in Jalview v2_3 example project</li>
1033 <li>Structures imported from file and saved in project
1034 get name like jalview_pdb1234.txt when reloaded</li>
1035 <li>Jalview does not always retrieve progress of a JABAWS
1036 job execution in full once it is complete</li>
1037 </ul> <em>Applet</em>
1039 <li>Alignment height set incorrectly when lots of
1040 annotation rows are displayed</li>
1041 <li>Relative URLs in feature HTML text not resolved to
1043 <li>View follows highlighting does not work for positions
1045 <li><= shown as = in tooltip</li>
1046 <li>Export features raises exception when no features
1048 <li>Separator string used for serialising lists of IDs
1049 for javascript api is modified when separator string
1050 provided as parameter</li>
1051 <li>Null pointer exception when selecting tree leaves for
1052 alignment with no existing selection</li>
1053 <li>Relative URLs for datasources assumed to be relative
1054 to applet's codebase</li>
1055 <li>Status bar not updated after finished searching and
1056 search wraps around to first result</li>
1057 <li>StructureSelectionManager instance shared between
1058 several Jalview applets causes race conditions and memory
1060 <li>Hover tooltip and mouseover of position on structure
1061 not sent from Jmol in applet</li>
1062 <li>Certain sequences of javascript method calls to
1063 applet API fatally hang browser</li>
1064 </ul> <em>General</em>
1066 <li>View follows structure mouseover scrolls beyond
1067 position with wrapped view and hidden regions</li>
1068 <li>Find sequence position moves to wrong residue
1069 with/without hidden columns</li>
1070 <li>Sequence length given in alignment properties window
1072 <li>InvalidNumberFormat exceptions thrown when trying to
1073 import PDB like structure files</li>
1074 <li>Positional search results are only highlighted
1075 between user-supplied sequence start/end bounds</li>
1076 <li>End attribute of sequence is not validated</li>
1077 <li>Find dialog only finds first sequence containing a
1078 given sequence position</li>
1079 <li>Sequence numbering not preserved in MSF alignment
1081 <li>Jalview PDB file reader does not extract sequence
1082 from nucleotide chains correctly</li>
1083 <li>Structure colours not updated when tree partition
1084 changed in alignment</li>
1085 <li>Sequence associated secondary structure not correctly
1086 parsed in interleaved stockholm</li>
1087 <li>Colour by annotation dialog does not restore current
1089 <li>Hiding (nearly) all sequences doesn't work
1091 <li>Sequences containing lowercase letters are not
1092 properly associated with their pdb files</li>
1093 </ul> <em>Documentation and Development</em>
1095 <li>schemas/JalviewWsParamSet.xsd corrupted by
1096 ApplyCopyright tool</li>
1101 <div align="center">
1102 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1105 <td><em>Application</em>
1107 <li>New warning dialog when the Jalview Desktop cannot
1108 contact web services</li>
1109 <li>JABA service parameters for a preset are shown in
1110 service job window</li>
1111 <li>JABA Service menu entries reworded</li>
1115 <li>Modeller PIR IO broken - cannot correctly import a
1116 pir file emitted by Jalview</li>
1117 <li>Existing feature settings transferred to new
1118 alignment view created from cut'n'paste</li>
1119 <li>Improved test for mixed amino/nucleotide chains when
1120 parsing PDB files</li>
1121 <li>Consensus and conservation annotation rows
1122 occasionally become blank for all new windows</li>
1123 <li>Exception raised when right clicking above sequences
1124 in wrapped view mode</li>
1125 </ul> <em>Application</em>
1127 <li>multiple multiply aligned structure views cause cpu
1128 usage to hit 100% and computer to hang</li>
1129 <li>Web Service parameter layout breaks for long user
1130 parameter names</li>
1131 <li>Jaba service discovery hangs desktop if Jaba server
1138 <div align="center">
1139 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1142 <td><em>Application</em>
1144 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1145 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1148 <li>Web Services preference tab</li>
1149 <li>Analysis parameters dialog box and user defined
1151 <li>Improved speed and layout of Envision2 service menu</li>
1152 <li>Superpose structures using associated sequence
1154 <li>Export coordinates and projection as CSV from PCA
1156 </ul> <em>Applet</em>
1158 <li>enable javascript: execution by the applet via the
1159 link out mechanism</li>
1160 </ul> <em>Other</em>
1162 <li>Updated the Jmol Jalview interface to work with Jmol
1164 <li>The Jalview Desktop and JalviewLite applet now
1165 require Java 1.5</li>
1166 <li>Allow Jalview feature colour specification for GFF
1167 sequence annotation files</li>
1168 <li>New 'colour by label' keword in Jalview feature file
1169 type colour specification</li>
1170 <li>New Jalview Desktop Groovy API method that allows a
1171 script to check if it being run in an interactive session or
1172 in a batch operation from the Jalview command line</li>
1176 <li>clustalx colourscheme colours Ds preferentially when
1177 both D+E are present in over 50% of the column</li>
1178 </ul> <em>Application</em>
1180 <li>typo in AlignmentFrame->View->Hide->all but
1181 selected Regions menu item</li>
1182 <li>sequence fetcher replaces ',' for ';' when the ',' is
1183 part of a valid accession ID</li>
1184 <li>fatal OOM if object retrieved by sequence fetcher
1185 runs out of memory</li>
1186 <li>unhandled Out of Memory Error when viewing pca
1187 analysis results</li>
1188 <li>InstallAnywhere builds fail to launch on OS X java
1189 10.5 update 4 (due to apple Java 1.6 update)</li>
1190 <li>Installanywhere Jalview silently fails to launch</li>
1191 </ul> <em>Applet</em>
1193 <li>Jalview.getFeatureGroups() raises an
1194 ArrayIndexOutOfBoundsException if no feature groups are
1201 <div align="center">
1202 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1208 <li>Alignment prettyprinter doesn't cope with long
1210 <li>clustalx colourscheme colours Ds preferentially when
1211 both D+E are present in over 50% of the column</li>
1212 <li>nucleic acid structures retrieved from PDB do not
1213 import correctly</li>
1214 <li>More columns get selected than were clicked on when a
1215 number of columns are hidden</li>
1216 <li>annotation label popup menu not providing correct
1217 add/hide/show options when rows are hidden or none are
1219 <li>Stockholm format shown in list of readable formats,
1220 and parser copes better with alignments from RFAM.</li>
1221 <li>CSV output of consensus only includes the percentage
1222 of all symbols if sequence logo display is enabled</li>
1224 </ul> <em>Applet</em>
1226 <li>annotation panel disappears when annotation is
1228 </ul> <em>Application</em>
1230 <li>Alignment view not redrawn properly when new
1231 alignment opened where annotation panel is visible but no
1232 annotations are present on alignment</li>
1233 <li>pasted region containing hidden columns is
1234 incorrectly displayed in new alignment window</li>
1235 <li>Jalview slow to complete operations when stdout is
1236 flooded (fix is to close the Jalview console)</li>
1237 <li>typo in AlignmentFrame->View->Hide->all but
1238 selected Rregions menu item.</li>
1239 <li>inconsistent group submenu and Format submenu entry
1240 'Un' or 'Non'conserved</li>
1241 <li>Sequence feature settings are being shared by
1242 multiple distinct alignments</li>
1243 <li>group annotation not recreated when tree partition is
1245 <li>double click on group annotation to select sequences
1246 does not propagate to associated trees</li>
1247 <li>Mac OSX specific issues:
1249 <li>exception raised when mouse clicked on desktop
1250 window background</li>
1251 <li>Desktop menu placed on menu bar and application
1252 name set correctly</li>
1253 <li>sequence feature settings not wide enough for the
1254 save feature colourscheme button</li>
1263 <div align="center">
1264 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1267 <td><em>New Capabilities</em>
1269 <li>URL links generated from description line for
1270 regular-expression based URL links (applet and application)
1272 <li>Non-positional feature URL links are shown in link
1274 <li>Linked viewing of nucleic acid sequences and
1276 <li>Automatic Scrolling option in View menu to display
1277 the currently highlighted region of an alignment.</li>
1278 <li>Order an alignment by sequence length, or using the
1279 average score or total feature count for each sequence.</li>
1280 <li>Shading features by score or associated description</li>
1281 <li>Subdivide alignment and groups based on identity of
1282 selected subsequence (Make Groups from Selection).</li>
1283 <li>New hide/show options including Shift+Control+H to
1284 hide everything but the currently selected region.</li>
1285 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1286 </ul> <em>Application</em>
1288 <li>Fetch DB References capabilities and UI expanded to
1289 support retrieval from DAS sequence sources</li>
1290 <li>Local DAS Sequence sources can be added via the
1291 command line or via the Add local source dialog box.</li>
1292 <li>DAS Dbref and DbxRef feature types are parsed as
1293 database references and protein_name is parsed as
1294 description line (BioSapiens terms).</li>
1295 <li>Enable or disable non-positional feature and database
1296 references in sequence ID tooltip from View menu in
1298 <!-- <li>New hidden columns and rows and representatives capabilities
1299 in annotations file (in progress - not yet fully implemented)</li> -->
1300 <li>Group-associated consensus, sequence logos and
1301 conservation plots</li>
1302 <li>Symbol distributions for each column can be exported
1303 and visualized as sequence logos</li>
1304 <li>Optionally scale multi-character column labels to fit
1305 within each column of annotation row<!-- todo for applet -->
1307 <li>Optional automatic sort of associated alignment view
1308 when a new tree is opened.</li>
1309 <li>Jalview Java Console</li>
1310 <li>Better placement of desktop window when moving
1311 between different screens.</li>
1312 <li>New preference items for sequence ID tooltip and
1313 consensus annotation</li>
1314 <li>Client to submit sequences and IDs to <a
1315 href="webServices/index.html#envision2">Envision2</a>
1318 <li><em>Vamsas Capabilities</em>
1320 <li>Improved VAMSAS synchronization (Jalview archive
1321 used to preserve views, structures, and tree display
1323 <li>Import of vamsas documents from disk or URL via
1325 <li>Sharing of selected regions between views and
1326 with other VAMSAS applications (Experimental feature!)</li>
1327 <li>Updated API to VAMSAS version 0.2</li>
1329 </ul> <em>Applet</em>
1331 <li>Middle button resizes annotation row height</li>
1334 <li>sortByTree (true/false) - automatically sort the
1335 associated alignment view by the tree when a new tree is
1337 <li>showTreeBootstraps (true/false) - show or hide
1338 branch bootstraps (default is to show them if available)</li>
1339 <li>showTreeDistances (true/false) - show or hide
1340 branch lengths (default is to show them if available)</li>
1341 <li>showUnlinkedTreeNodes (true/false) - indicate if
1342 unassociated nodes should be highlighted in the tree
1344 <li>heightScale and widthScale (1.0 or more) -
1345 increase the height or width of a cell in the alignment
1346 grid relative to the current font size.</li>
1349 <li>Non-positional features displayed in sequence ID
1351 </ul> <em>Other</em>
1353 <li>Features format: graduated colour definitions and
1354 specification of feature scores</li>
1355 <li>Alignment Annotations format: new keywords for group
1356 associated annotation (GROUP_REF) and annotation row display
1357 properties (ROW_PROPERTIES)</li>
1358 <li>XML formats extended to support graduated feature
1359 colourschemes, group associated annotation, and profile
1360 visualization settings.</li></td>
1363 <li>Source field in GFF files parsed as feature source
1364 rather than description</li>
1365 <li>Non-positional features are now included in sequence
1366 feature and gff files (controlled via non-positional feature
1367 visibility in tooltip).</li>
1368 <li>URL links generated for all feature links (bugfix)</li>
1369 <li>Added URL embedding instructions to features file
1371 <li>Codons containing ambiguous nucleotides translated as
1372 'X' in peptide product</li>
1373 <li>Match case switch in find dialog box works for both
1374 sequence ID and sequence string and query strings do not
1375 have to be in upper case to match case-insensitively.</li>
1376 <li>AMSA files only contain first column of
1377 multi-character column annotation labels</li>
1378 <li>Jalview Annotation File generation/parsing consistent
1379 with documentation (e.g. Stockholm annotation can be
1380 exported and re-imported)</li>
1381 <li>PDB files without embedded PDB IDs given a friendly
1383 <li>Find incrementally searches ID string matches as well
1384 as subsequence matches, and correctly reports total number
1388 <li>Better handling of exceptions during sequence
1390 <li>Dasobert generated non-positional feature URL
1391 link text excludes the start_end suffix</li>
1392 <li>DAS feature and source retrieval buttons disabled
1393 when fetch or registry operations in progress.</li>
1394 <li>PDB files retrieved from URLs are cached properly</li>
1395 <li>Sequence description lines properly shared via
1397 <li>Sequence fetcher fetches multiple records for all
1399 <li>Ensured that command line das feature retrieval
1400 completes before alignment figures are generated.</li>
1401 <li>Reduced time taken when opening file browser for
1403 <li>isAligned check prior to calculating tree, PCA or
1404 submitting an MSA to JNet now excludes hidden sequences.</li>
1405 <li>User defined group colours properly recovered
1406 from Jalview projects.</li>
1415 <div align="center">
1416 <strong>2.4.0.b2</strong><br> 28/10/2009
1421 <li>Experimental support for google analytics usage
1423 <li>Jalview privacy settings (user preferences and docs).</li>
1428 <li>Race condition in applet preventing startup in
1430 <li>Exception when feature created from selection beyond
1431 length of sequence.</li>
1432 <li>Allow synthetic PDB files to be imported gracefully</li>
1433 <li>Sequence associated annotation rows associate with
1434 all sequences with a given id</li>
1435 <li>Find function matches case-insensitively for sequence
1436 ID string searches</li>
1437 <li>Non-standard characters do not cause pairwise
1438 alignment to fail with exception</li>
1439 </ul> <em>Application Issues</em>
1441 <li>Sequences are now validated against EMBL database</li>
1442 <li>Sequence fetcher fetches multiple records for all
1444 </ul> <em>InstallAnywhere Issues</em>
1446 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1447 issue with installAnywhere mechanism)</li>
1448 <li>Command line launching of JARs from InstallAnywhere
1449 version (java class versioning error fixed)</li>
1456 <div align="center">
1457 <strong>2.4</strong><br> 27/8/2008
1460 <td><em>User Interface</em>
1462 <li>Linked highlighting of codon and amino acid from
1463 translation and protein products</li>
1464 <li>Linked highlighting of structure associated with
1465 residue mapping to codon position</li>
1466 <li>Sequence Fetcher provides example accession numbers
1467 and 'clear' button</li>
1468 <li>MemoryMonitor added as an option under Desktop's
1470 <li>Extract score function to parse whitespace separated
1471 numeric data in description line</li>
1472 <li>Column labels in alignment annotation can be centred.</li>
1473 <li>Tooltip for sequence associated annotation give name
1475 </ul> <em>Web Services and URL fetching</em>
1477 <li>JPred3 web service</li>
1478 <li>Prototype sequence search client (no public services
1480 <li>Fetch either seed alignment or full alignment from
1482 <li>URL Links created for matching database cross
1483 references as well as sequence ID</li>
1484 <li>URL Links can be created using regular-expressions</li>
1485 </ul> <em>Sequence Database Connectivity</em>
1487 <li>Retrieval of cross-referenced sequences from other
1489 <li>Generalised database reference retrieval and
1490 validation to all fetchable databases</li>
1491 <li>Fetch sequences from DAS sources supporting the
1492 sequence command</li>
1493 </ul> <em>Import and Export</em>
1494 <li>export annotation rows as CSV for spreadsheet import</li>
1495 <li>Jalview projects record alignment dataset associations,
1496 EMBL products, and cDNA sequence mappings</li>
1497 <li>Sequence Group colour can be specified in Annotation
1499 <li>Ad-hoc colouring of group in Annotation File using RGB
1500 triplet as name of colourscheme</li>
1501 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
1503 <li>treenode binding for VAMSAS tree exchange</li>
1504 <li>local editing and update of sequences in VAMSAS
1505 alignments (experimental)</li>
1506 <li>Create new or select existing session to join</li>
1507 <li>load and save of vamsas documents</li>
1508 </ul> <em>Application command line</em>
1510 <li>-tree parameter to open trees (introduced for passing
1512 <li>-fetchfrom command line argument to specify nicknames
1513 of DAS servers to query for alignment features</li>
1514 <li>-dasserver command line argument to add new servers
1515 that are also automatically queried for features</li>
1516 <li>-groovy command line argument executes a given groovy
1517 script after all input data has been loaded and parsed</li>
1518 </ul> <em>Applet-Application data exchange</em>
1520 <li>Trees passed as applet parameters can be passed to
1521 application (when using "View in full
1522 application")</li>
1523 </ul> <em>Applet Parameters</em>
1525 <li>feature group display control parameter</li>
1526 <li>debug parameter</li>
1527 <li>showbutton parameter</li>
1528 </ul> <em>Applet API methods</em>
1530 <li>newView public method</li>
1531 <li>Window (current view) specific get/set public methods</li>
1532 <li>Feature display control methods</li>
1533 <li>get list of currently selected sequences</li>
1534 </ul> <em>New Jalview distribution features</em>
1536 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1537 <li>RELEASE file gives build properties for the latest
1538 Jalview release.</li>
1539 <li>Java 1.1 Applet build made easier and donotobfuscate
1540 property controls execution of obfuscator</li>
1541 <li>Build target for generating source distribution</li>
1542 <li>Debug flag for javacc</li>
1543 <li>.jalview_properties file is documented (slightly) in
1544 jalview.bin.Cache</li>
1545 <li>Continuous Build Integration for stable and
1546 development version of Application, Applet and source
1551 <li>selected region output includes visible annotations
1552 (for certain formats)</li>
1553 <li>edit label/displaychar contains existing label/char
1555 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1556 <li>shorter peptide product names from EMBL records</li>
1557 <li>Newick string generator makes compact representations</li>
1558 <li>bootstrap values parsed correctly for tree files with
1560 <li>pathological filechooser bug avoided by not allowing
1561 filenames containing a ':'</li>
1562 <li>Fixed exception when parsing GFF files containing
1563 global sequence features</li>
1564 <li>Alignment datasets are finalized only when number of
1565 references from alignment sequences goes to zero</li>
1566 <li>Close of tree branch colour box without colour
1567 selection causes cascading exceptions</li>
1568 <li>occasional negative imgwidth exceptions</li>
1569 <li>better reporting of non-fatal warnings to user when
1570 file parsing fails.</li>
1571 <li>Save works when Jalview project is default format</li>
1572 <li>Save as dialog opened if current alignment format is
1573 not a valid output format</li>
1574 <li>Uniprot canonical names introduced for both das and
1576 <li>Histidine should be midblue (not pink!) in Zappo</li>
1577 <li>error messages passed up and output when data read
1579 <li>edit undo recovers previous dataset sequence when
1580 sequence is edited</li>
1581 <li>allow PDB files without pdb ID HEADER lines (like
1582 those generated by MODELLER) to be read in properly</li>
1583 <li>allow reading of JPred concise files as a normal
1585 <li>Stockholm annotation parsing and alignment properties
1586 import fixed for PFAM records</li>
1587 <li>Structure view windows have correct name in Desktop
1589 <li>annotation consisting of sequence associated scores
1590 can be read and written correctly to annotation file</li>
1591 <li>Aligned cDNA translation to aligned peptide works
1593 <li>Fixed display of hidden sequence markers and
1594 non-italic font for representatives in Applet</li>
1595 <li>Applet Menus are always embedded in applet window on
1597 <li>Newly shown features appear at top of stack (in
1599 <li>Annotations added via parameter not drawn properly
1600 due to null pointer exceptions</li>
1601 <li>Secondary structure lines are drawn starting from
1602 first column of alignment</li>
1603 <li>Uniprot XML import updated for new schema release in
1605 <li>Sequence feature to sequence ID match for Features
1606 file is case-insensitive</li>
1607 <li>Sequence features read from Features file appended to
1608 all sequences with matching IDs</li>
1609 <li>PDB structure coloured correctly for associated views
1610 containing a sub-sequence</li>
1611 <li>PDB files can be retrieved by applet from Jar files</li>
1612 <li>feature and annotation file applet parameters
1613 referring to different directories are retrieved correctly</li>
1614 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1615 <li>Fixed application hang whilst waiting for
1616 splash-screen version check to complete</li>
1617 <li>Applet properly URLencodes input parameter values
1618 when passing them to the launchApp service</li>
1619 <li>display name and local features preserved in results
1620 retrieved from web service</li>
1621 <li>Visual delay indication for sequence retrieval and
1622 sequence fetcher initialisation</li>
1623 <li>updated Application to use DAS 1.53e version of
1624 dasobert DAS client</li>
1625 <li>Re-instated Full AMSA support and .amsa file
1627 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1635 <div align="center">
1636 <strong>2.3</strong><br> 9/5/07
1641 <li>Jmol 11.0.2 integration</li>
1642 <li>PDB views stored in Jalview XML files</li>
1643 <li>Slide sequences</li>
1644 <li>Edit sequence in place</li>
1645 <li>EMBL CDS features</li>
1646 <li>DAS Feature mapping</li>
1647 <li>Feature ordering</li>
1648 <li>Alignment Properties</li>
1649 <li>Annotation Scores</li>
1650 <li>Sort by scores</li>
1651 <li>Feature/annotation editing in applet</li>
1656 <li>Headless state operation in 2.2.1</li>
1657 <li>Incorrect and unstable DNA pairwise alignment</li>
1658 <li>Cut and paste of sequences with annotation</li>
1659 <li>Feature group display state in XML</li>
1660 <li>Feature ordering in XML</li>
1661 <li>blc file iteration selection using filename # suffix</li>
1662 <li>Stockholm alignment properties</li>
1663 <li>Stockhom alignment secondary structure annotation</li>
1664 <li>2.2.1 applet had no feature transparency</li>
1665 <li>Number pad keys can be used in cursor mode</li>
1666 <li>Structure Viewer mirror image resolved</li>
1673 <div align="center">
1674 <strong>2.2.1</strong><br> 12/2/07
1679 <li>Non standard characters can be read and displayed
1680 <li>Annotations/Features can be imported/exported to the
1682 <li>Applet allows editing of sequence/annotation/group
1683 name & description
1684 <li>Preference setting to display sequence name in
1686 <li>Annotation file format extended to allow
1687 Sequence_groups to be defined
1688 <li>Default opening of alignment overview panel can be
1689 specified in preferences
1690 <li>PDB residue numbering annotation added to associated
1696 <li>Applet crash under certain Linux OS with Java 1.6
1698 <li>Annotation file export / import bugs fixed
1699 <li>PNG / EPS image output bugs fixed
1705 <div align="center">
1706 <strong>2.2</strong><br> 27/11/06
1711 <li>Multiple views on alignment
1712 <li>Sequence feature editing
1713 <li>"Reload" alignment
1714 <li>"Save" to current filename
1715 <li>Background dependent text colour
1716 <li>Right align sequence ids
1717 <li>User-defined lower case residue colours
1720 <li>Menu item accelerator keys
1721 <li>Control-V pastes to current alignment
1722 <li>Cancel button for DAS Feature Fetching
1723 <li>PCA and PDB Viewers zoom via mouse roller
1724 <li>User-defined sub-tree colours and sub-tree selection
1726 <li>'New Window' button on the 'Output to Text box'
1731 <li>New memory efficient Undo/Redo System
1732 <li>Optimised symbol lookups and conservation/consensus
1734 <li>Region Conservation/Consensus recalculated after
1736 <li>Fixed Remove Empty Columns Bug (empty columns at end
1738 <li>Slowed DAS Feature Fetching for increased robustness.
1740 <li>Made angle brackets in ASCII feature descriptions
1742 <li>Re-instated Zoom function for PCA
1743 <li>Sequence descriptions conserved in web service
1745 <li>Uniprot ID discoverer uses any word separated by
1747 <li>WsDbFetch query/result association resolved
1748 <li>Tree leaf to sequence mapping improved
1749 <li>Smooth fonts switch moved to FontChooser dialog box.
1756 <div align="center">
1757 <strong>2.1.1</strong><br> 12/9/06
1762 <li>Copy consensus sequence to clipboard</li>
1767 <li>Image output - rightmost residues are rendered if
1768 sequence id panel has been resized</li>
1769 <li>Image output - all offscreen group boundaries are
1771 <li>Annotation files with sequence references - all
1772 elements in file are relative to sequence position</li>
1773 <li>Mac Applet users can use Alt key for group editing</li>
1779 <div align="center">
1780 <strong>2.1</strong><br> 22/8/06
1785 <li>MAFFT Multiple Alignment in default Web Service list</li>
1786 <li>DAS Feature fetching</li>
1787 <li>Hide sequences and columns</li>
1788 <li>Export Annotations and Features</li>
1789 <li>GFF file reading / writing</li>
1790 <li>Associate structures with sequences from local PDB
1792 <li>Add sequences to exisiting alignment</li>
1793 <li>Recently opened files / URL lists</li>
1794 <li>Applet can launch the full application</li>
1795 <li>Applet has transparency for features (Java 1.2
1797 <li>Applet has user defined colours parameter</li>
1798 <li>Applet can load sequences from parameter
1799 "sequence<em>x</em>"
1805 <li>Redundancy Panel reinstalled in the Applet</li>
1806 <li>Monospaced font - EPS / rescaling bug fixed</li>
1807 <li>Annotation files with sequence references bug fixed</li>
1813 <div align="center">
1814 <strong>2.08.1</strong><br> 2/5/06
1819 <li>Change case of selected region from Popup menu</li>
1820 <li>Choose to match case when searching</li>
1821 <li>Middle mouse button and mouse movement can compress /
1822 expand the visible width and height of the alignment</li>
1827 <li>Annotation Panel displays complete JNet results</li>
1833 <div align="center">
1834 <strong>2.08b</strong><br> 18/4/06
1840 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1841 <li>Righthand label on wrapped alignments shows correct
1848 <div align="center">
1849 <strong>2.08</strong><br> 10/4/06
1854 <li>Editing can be locked to the selection area</li>
1855 <li>Keyboard editing</li>
1856 <li>Create sequence features from searches</li>
1857 <li>Precalculated annotations can be loaded onto
1859 <li>Features file allows grouping of features</li>
1860 <li>Annotation Colouring scheme added</li>
1861 <li>Smooth fonts off by default - Faster rendering</li>
1862 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1867 <li>Drag & Drop fixed on Linux</li>
1868 <li>Jalview Archive file faster to load/save, sequence
1869 descriptions saved.</li>
1875 <div align="center">
1876 <strong>2.07</strong><br> 12/12/05
1881 <li>PDB Structure Viewer enhanced</li>
1882 <li>Sequence Feature retrieval and display enhanced</li>
1883 <li>Choose to output sequence start-end after sequence
1884 name for file output</li>
1885 <li>Sequence Fetcher WSDBFetch@EBI</li>
1886 <li>Applet can read feature files, PDB files and can be
1887 used for HTML form input</li>
1892 <li>HTML output writes groups and features</li>
1893 <li>Group editing is Control and mouse click</li>
1894 <li>File IO bugs</li>
1900 <div align="center">
1901 <strong>2.06</strong><br> 28/9/05
1906 <li>View annotations in wrapped mode</li>
1907 <li>More options for PCA viewer</li>
1912 <li>GUI bugs resolved</li>
1913 <li>Runs with -nodisplay from command line</li>
1919 <div align="center">
1920 <strong>2.05b</strong><br> 15/9/05
1925 <li>Choose EPS export as lineart or text</li>
1926 <li>Jar files are executable</li>
1927 <li>Can read in Uracil - maps to unknown residue</li>
1932 <li>Known OutOfMemory errors give warning message</li>
1933 <li>Overview window calculated more efficiently</li>
1934 <li>Several GUI bugs resolved</li>
1940 <div align="center">
1941 <strong>2.05</strong><br> 30/8/05
1946 <li>Edit and annotate in "Wrapped" view</li>
1951 <li>Several GUI bugs resolved</li>
1957 <div align="center">
1958 <strong>2.04</strong><br> 24/8/05
1963 <li>Hold down mouse wheel & scroll to change font
1969 <li>Improved JPred client reliability</li>
1970 <li>Improved loading of Jalview files</li>
1976 <div align="center">
1977 <strong>2.03</strong><br> 18/8/05
1982 <li>Set Proxy server name and port in preferences</li>
1983 <li>Multiple URL links from sequence ids</li>
1984 <li>User Defined Colours can have a scheme name and added
1986 <li>Choose to ignore gaps in consensus calculation</li>
1987 <li>Unix users can set default web browser</li>
1988 <li>Runs without GUI for batch processing</li>
1989 <li>Dynamically generated Web Service Menus</li>
1994 <li>InstallAnywhere download for Sparc Solaris</li>
2000 <div align="center">
2001 <strong>2.02</strong><br> 18/7/05
2007 <li>Copy & Paste order of sequences maintains
2008 alignment order.</li>
2014 <div align="center">
2015 <strong>2.01</strong><br> 12/7/05
2020 <li>Use delete key for deleting selection.</li>
2021 <li>Use Mouse wheel to scroll sequences.</li>
2022 <li>Help file updated to describe how to add alignment
2024 <li>Version and build date written to build properties
2026 <li>InstallAnywhere installation will check for updates
2027 at launch of Jalview.</li>
2032 <li>Delete gaps bug fixed.</li>
2033 <li>FileChooser sorts columns.</li>
2034 <li>Can remove groups one by one.</li>
2035 <li>Filechooser icons installed.</li>
2036 <li>Finder ignores return character when searching.
2037 Return key will initiate a search.<br>
2044 <div align="center">
2045 <strong>2.0</strong><br> 20/6/05
2050 <li>New codebase</li>