3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 <p><strong>Release History</strong></p>
29 <td width="60" nowrap>
31 <em><strong>Release</strong></em>
36 <em><strong>New Features</strong></em>
41 <em><strong>Issues Resolved</strong></em>
46 <td><div align="center">
47 <strong><a name="Jalview.2.9">2.9</a><br /> <em>9/9/2015</em></strong>
51 <li>Linked visualisation and analysis of DNA and Protein
53 <li>Translated cDNA alignments shown as split protein and
54 DNA alignment views</li>
55 <li>Codon consensus annotation for linked protein and
56 cDNA alignment views</li>
57 <li>Add cDNA or Protein product sequences to Protein or
59 <li>Reconstruct linked cDNA alignment from aligned
63 <li>Update Jmol to v14.2n</li>
65 <li>BioJSON data exchange</li>
67 <li>New alignment annotation file statements for
68 reference sequences and marking hidden columns</li>
70 <li>Alignments can be sorted by number of RNA helices</li>
72 <li>Assign a reference sequence to highlight
73 variation and consensus analysis</li>
75 <li>Select or hide columns according to alignment
77 <li>Find option for locating sequences by
80 <li>Conserved physicochemical properties shown in amino
81 acid conservation row</li>
83 </ul> <em>Application</em>
85 <li>Optional embedding of BioJSON data when exporting
86 alignment figures to HTML</li>
87 <li>New Export Settings dialog to control hidden region export in flat file
89 <li>New cDNA/Protein analysis capabilities<ul>
90 <li>Get Cross-References should open a Split Frame view
91 with cDNA/Protein</li>
92 <li>Detect when nucleotide sequences and protein
93 sequences are placed in the same alignment</li>
94 <li>Split cDNA/Protein views are saved in Jalview
96 <li>support '*' in amino acid sequences to indicate stop
100 <li>Use REST API to talk to Chimera</li>
101 <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
103 <li>Calculate UPGMA and NJ trees using sequence feature
106 <li>VARNA RNA viewer updated to v3.93</li>
107 <li>VARNA views are saved in Jalview
109 <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
111 <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
112 <li>change "View protein structure" menu option to "3D
115 <li>Make groups for selection uses marked columns as well
116 as the active selected region</li>
118 <li>allow different similarity matrix calculations for
119 tree building and PCA</li>
121 <li>Export alignment views for display with the <a
122 href="">BioJS MSAViewer</a></li>
123 <li>Scrollable SVG for HTML export</li>
125 <li>Novel data discovery and retrieval mechanism using
127 <li>Smarter technique for selecting PDB structures to
130 <li>JPred4 employed for protein secondary structure
132 <li>Hide Insertions menu option to hide unaligned columns
133 for one or a group of sequences</li>
134 <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
135 </ul> <em>Applet</em>
137 <li>Parameter to enable SplitFrame view</li>? check other
138 parameters in applet ?
139 <li>New example demonstrating linked viewing of cDNA and
140 Protein alignments</li>
141 <li>New layout for applet example pages</li>
143 <em>Development and deployment</em>
144 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
145 <li>Include installation type and git revision in build
146 properties and console log output</li>
147 <li>Github project and web URL for storing BioJsMSA
149 <li>Jalview's unit tests now managed with TestNG</li></td>
152 </ul> <!-- issues resolved --> <em>Application</em>
154 <li>Escape should close any open find dialogs</li>
155 <li>typo in select-by-features status report</li>
156 <li>Consensus RNA secondary secondary structure
157 predictions are not highlighted in amber</li>
158 <li>missing gap character means v2.7 example file appears
159 unaligned REVIEW</li>
160 <li>First switch to RNA Helices colouring doesn't colour
161 associated structure views</li>
162 <li>ID width preference option is greyed out when auto
163 width checkbox not enabled</li>
164 <li>Stopped a warning dialog from being shown when
165 creating user defined colours</li>
166 <li>'View Mapping' in structure viewer shows sequence
167 mappings for just that viewer's sequences</li>
168 <li>Workaround for superposing PDB files containing
169 multiple models in Chimera</li>
170 <li>Report sequence position in status bar when hovering
171 over Jmol structure</li>
172 <li>Cannot output gaps as '.' symbols with Selection ->
173 output to text box</li>
174 <li>Flat file exports of alignments with hidden columns
175 have incorrect sequence start/end</li>
176 <li>'Aligning' a second chain to a Chimera structure from
178 <li>Colour schemes applied to structure viewers don't
179 work for nucleotide</li>
180 <li>Loading/cut'n'pasting an empty or invalid file leads
181 to a grey/invisible alignment window</li>
182 <li>Exported Jpred annotation from a sequence region
183 imports to different position</li>
184 <li>Space at beginning of sequence feature mouseover
185 tooltip on some platforms</li>
186 <li>Chimera viewer 'View | Show Chain' menu is not
188 <li>'New View' fails with a Null Pointer Exception if
189 Chimera has been opened</li>
190 <li>Mouseover to Chimera not working</li>
191 <li>Miscellaneous ENA XML feature qualifiers not
193 <li>NPE in annotation renderer after 'Extract Scores'</li>
194 <li>If two structures in one Chimera window, mouseover of
195 either sequence shows on first structure</li>
196 <li>'Show annotations' options should not make
197 non-positional annotations visible</li>
198 <li>subsequence secondary structure annotation not shown
199 in right place after 'view flanking regions'</li>
200 <li>File Save As type unset when current file format is
202 <li>Native 'Quaqua' dialogs for saving and loading files
204 <li>Save as '.jar' option removed for saving Jalview
206 <li>Colour by Sequence colouring in Chimera more
208 <li>Can disable consensus calculation independently of
209 quality and conservation</li>
210 <li>Cannot 'add reference annotation' for a sequence in
211 several views on same alignment</li>
212 <li>Cannot show linked products for EMBL / ENA records</li>
213 <li>Jalview's tooltip wraps long texts containing no
215 </ul> <em>Applet</em>
216 <li>Jmol to JalviewLite mouseover/link not working</li>
217 <li>JalviewLite can't import sequences with ID descriptions
218 containing angle brackets</li>
220 </ul> <em>General</em>
222 <li>Cannot export and reimport RNA secondary structure
223 via jalview annotation file</li>
224 <li>Random helix colour palette for colour by annotation
225 with RNA secondary structure</li>
226 <li>Mouseover to cDNA from STOP residue in protein
227 translation doesn't work.</li>
228 <li>hints when using the select by annotation dialog box</li>
229 <li>Jmol alignment incorrect if PDB file has alternate CA
231 <li>FontChooser message dialog appears to hang after
232 choosing 1pt font</li>
233 <li>Peptide secondary structure incorrectly imported from
234 annotation file when annotation display text includes 'e' or
236 <li>Cannot set colour of new feature type whilst creating
238 <li>cDNA translation alignment should not be sequence
240 <li>'Show unconserved' doesn't work for lower case
242 <li>Nucleotide ambiguity codes involving R not recognised</li>
243 </ul> <em>Deployment and Documentation</em>
246 </ul> <em>Application Known issues</em>
248 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
249 <li>Misleading message appears after trying to delete
251 <li>Jalview icon not shown in dock after InstallAnywhere
252 version launches</li>
253 <li>Fetching EMBL reference for an RNA sequence results
254 fails with a sequence mismatch</li>
255 <li>Corrupted or unreadable alignment display when
256 scrolling alignment to right</li>
257 <li>ArrayIndexOutOfBoundsException thrown when remove
258 empty columns called on alignment with ragged gapped ends</li>
259 <li>auto calculated alignment annotation rows do not get
260 placed above or below non-autocalculated rows</li>
261 <li>Jalview dekstop becomes sluggish at full screen in
262 ultra-high resolution</li>
263 </ul> <em>Applet Known Issues</em>
265 <li>Core PDB parsing code requires Jmol</li>
266 <li>Sequence canvas panel goes white when alignment
267 window is being resized
272 <td width="60" nowrap>
274 <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
283 <ul><li>Reinstated the display of default example file on startup</li>
284 <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
290 <td><div align="center">
291 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
295 <li>Updated Java code signing certificate donated by Certum.PL.</li>
296 <li>Features and annotation preserved when performing pairwise
298 <li>RNA pseudoknot annotation can be
299 imported/exported/displayed</li>
300 <li>'colour by annotation' can colour by RNA and
301 protein secondary structure</li>
302 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
304 </ul> <em>Application</em>
306 <li>Extract and display secondary structure for sequences with
308 <li>Support for parsing RNAML</li>
309 <li>Annotations menu for layout
311 <li>sort sequence annotation rows by alignment</li>
312 <li>place sequence annotation above/below alignment
315 <li>Output in Stockholm format</li>
316 <li>Internationalisation: improved Spanish (es) translation</li>
317 <li>Structure viewer preferences tab</li>
318 <li>Disorder and Secondary Structure annotation tracks shared
319 between alignments</li>
320 <li>UCSF Chimera launch and linked highlighting from Jalview</li>
321 <li>Show/hide all sequence associated annotation rows for all
322 or current selection</li>
323 <li>disorder and secondary structure predictions available as
324 dataset annotation</li>
325 <li>Per-sequence rna helices colouring</li>
328 <li>Sequence database accessions imported when fetching
329 alignments from Rfam</li>
330 <li>update VARNA version to 3.91</li>
332 <li>New groovy scripts for exporting aligned positions,
333 conservation values, and calculating sum of pairs scores.</li>
334 <li>Command line argument to set default JABAWS server</li>
335 <li>include installation type in build properties and console
337 <li>Updated Jalview project format to preserve dataset annotation</li>
340 <!-- issues resolved --> <em>Application</em>
342 <li>Distinguish alignment and sequence associated RNA
343 structure in structure->view->VARNA</li>
344 <li>Raise dialog box if user deletes all sequences in an
346 <li>Pressing F1 results in documentation opening twice</li>
347 <li>Sequence feature tooltip is wrapped</li>
348 <li>Double click on sequence associated annotation selects
349 only first column</li>
350 <li>Redundancy removal doesn't result in unlinked leaves
352 <li>Undos after several redundancy removals don't undo
354 <li>Hide sequence doesn't hide associated annotation</li>
355 <li>User defined colours dialog box too big to fit on screen
356 and buttons not visible</li>
357 <li>author list isn't updated if already written to Jalview
359 <li>Popup menu won't open after retrieving sequence from
361 <li>File open window for associate PDB doesn't open</li>
362 <li>Left-then-right click on a sequence id opens a browser
364 <li>Cannot open sequence feature shading/sort popup menu in
365 feature settings dialog</li>
366 <li>better tooltip placement for some areas of Jalview desktop</li>
367 <li>Allow addition of JABAWS Server which doesn't pass
369 <li>Web services parameters dialog box is too large to fit on
371 <li>Muscle nucleotide alignment preset obscured by tooltip</li>
372 <li>JABAWS preset submenus don't contain newly defined
374 <li>MSA web services warns user if they were launched with
376 <li>Jalview cannot contact DAS Registy when running on Java 8</li>
378 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
379 'Superpose with' submenu not shown when new view created
382 </ul> <!-- <em>Applet</em>
384 </ul> <em>General</em>
386 </ul>--> <em>Deployment and Documentation</em>
388 <li>2G and 1G options in launchApp have no effect on memory
390 <li>launchApp service doesn't automatically open
391 www.jalview.org/examples/exampleFile.jar if no file is given</li>
393 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
394 InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
397 </ul> <em>Application Known issues</em>
400 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
401 corrupted or unreadable alignment display when scrolling alignment
405 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
406 retrieval fails but progress bar continues for DAS retrieval with
410 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
411 flatfile output of visible region has incorrect sequence start/end
414 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
415 rna structure consensus doesn't update when secondary
416 structure tracks are rearranged
419 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
420 invalid rna structure positional highlighting does not highlight
421 position of invalid base pairs
424 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
425 out of memory errors are not raised when saving Jalview project
426 from alignment window file menu
429 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
430 Switching to RNA Helices colouring doesn't propagate to
434 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
435 colour by RNA Helices not enabled when user created annotation
439 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
440 Jalview icon not shown on dock in Mountain Lion/Webstart
442 </ul> <em>Applet Known Issues</em>
445 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
446 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
449 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
450 Jalview and Jmol example not compatible with IE9
453 <li>Sort by annotation score doesn't reverse order when
459 <td><div align="center">
460 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
463 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
466 <li>Internationalisation of user interface (usually called
467 i18n support) and translation for Spanish locale</li>
468 <li>Define/Undefine group on current selection with
469 Ctrl-G/Shift Ctrl-G</li>
470 <li>Improved group creation/removal options in
471 alignment/sequence Popup menu</li>
472 <li>Sensible precision for symbol distribution percentages
473 shown in logo tooltip.</li>
474 <li>Annotation panel height set according to amount of
475 annotation when alignment first opened</li>
476 </ul> <em>Application</em>
478 <li>Interactive consensus RNA secondary structure prediction
479 VIENNA RNAAliFold JABA 2.1 service</li>
480 <li>Select columns containing particular features from Feature
482 <li>View all 'representative' PDB structures for selected
484 <li>Update Jalview project format:
486 <li>New file extension for Jalview projects '.jvp'</li>
487 <li>Preserve sequence and annotation dataset (to store
488 secondary structure annotation,etc)</li>
489 <li>Per group and alignment annotation and RNA helix
493 <li>New similarity measures for PCA and Tree calculation
495 <li>Experimental support for retrieval and viewing of flanking
496 regions for an alignment</li>
500 <!-- issues resolved --> <em>Application</em>
502 <li>logo keeps spinning and status remains at queued or
503 running after job is cancelled</li>
504 <li>cannot export features from alignments imported from
505 Jalview/VAMSAS projects</li>
506 <li>Buggy slider for web service parameters that take float
508 <li>Newly created RNA secondary structure line doesn't have
509 'display all symbols' flag set</li>
510 <li>T-COFFEE alignment score shading scheme and other
511 annotation shading not saved in Jalview project</li>
512 <li>Local file cannot be loaded in freshly downloaded Jalview</li>
513 <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
514 <li>Load file from desktop file browser fails</li>
515 <li>Occasional NPE thrown when calculating large trees</li>
516 <li>Cannot reorder or slide sequences after dragging an
517 alignment onto desktop</li>
518 <li>Colour by annotation dialog throws NPE after using
519 'extract scores' function</li>
520 <li>Loading/cut'n'pasting an empty file leads to a grey
521 alignment window</li>
522 <li>Disorder thresholds rendered incorrectly after performing
523 IUPred disorder prediction</li>
524 <li>Multiple group annotated consensus rows shown when
525 changing 'normalise logo' display setting</li>
526 <li>Find shows blank dialog after 'finished searching' if
527 nothing matches query</li>
528 <li>Null Pointer Exceptions raised when sorting by feature
529 with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
531 <li>Errors in Jmol console when structures in alignment don't
532 overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
534 <li>Not all working JABAWS services are shown in Jalview's
536 <li>JAVAWS version of Jalview fails to launch with 'invalid
537 literal/length code'</li>
538 <li>Annotation/RNA Helix colourschemes cannot be applied to
539 alignment with groups (actually fixed in 2.8.0b1)</li>
540 <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
542 </ul> <em>Applet</em>
544 <li>Remove group option is shown even when selection is not a
546 <li>Apply to all groups ticked but colourscheme changes don't
548 <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
549 <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
550 <li>Increased font size for dropdown menus on OSX and embedded windows</li>
553 <li>Consensus sequence for alignments/groups with a single
554 sequence were not calculated</li>
555 <li>annotation files that contain only groups imported as
556 annotation and junk sequences</li>
557 <li>Fasta files with sequences containing '*' incorrectly
558 recognised as PFAM or BLC</li>
559 <li>conservation/PID slider apply all groups option doesn't
560 affect background (2.8.0b1)
562 <li>redundancy highlighting is erratic at 0% and 100%</li>
563 <li>Remove gapped columns fails for sequences with ragged
565 <li>AMSA annotation row with leading spaces is not registered
566 correctly on import</li>
567 <li>Jalview crashes when selecting PCA analysis for certain
569 <li>Opening the colour by annotation dialog for an existing
570 annotation based 'use original colours' colourscheme loses
571 original colours setting</li>
576 <td><div align="center">
577 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
582 <li>Trusted certificates for JalviewLite applet and
583 Jalview Desktop application<br />Certificate was donated by
584 <a href="https://www.certum.eu">Certum</a> to the Jalview
585 open source project).
587 <li>Jalview SRS links replaced by Uniprot and EBI-search
589 <li>Output in Stockholm format</li>
590 <li>Allow import of data from gzipped files</li>
591 <li>Export/import group and sequence associated line
592 graph thresholds</li>
593 <li>Nucleotide substitution matrix that supports RNA and
595 <li>Allow disorder predictions to be made on the current
596 selection (or visible selection) in the same way that JPred
598 <li>Groovy scripting for headless Jalview operation</li>
599 </ul> <em>Other improvements</em>
601 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
602 <li>COMBINE statement uses current SEQUENCE_REF and
603 GROUP_REF scope to group annotation rows</li>
604 <li>Support '' style escaping of quotes in Newick
606 <li>Group options for JABAWS service by command line name</li>
607 <li>Empty tooltip shown for JABA service options with a
608 link but no description</li>
609 <li>Select primary source when selecting authority in
610 database fetcher GUI</li>
611 <li>Add .mfa to FASTA file extensions recognised by
613 <li>Annotation label tooltip text wrap</li>
618 <li>Slow scrolling when lots of annotation rows are
620 <li>Lots of NPE (and slowness) after creating RNA
621 secondary structure annotation line</li>
622 <li>Sequence database accessions not imported when
623 fetching alignments from Rfam</li>
624 <li>Incorrect SHMR submission for sequences with
626 <li>View all structures does not always superpose
628 <li>Option widgets in service parameters not updated to
629 reflect user or preset settings</li>
630 <li>Null pointer exceptions for some services without
631 presets or adjustable parameters</li>
632 <li>Discover PDB IDs entry in structure menu doesn't
633 discover PDB xRefs</li>
634 <li>Exception encountered while trying to retrieve
635 features with DAS</li>
636 <li>Lowest value in annotation row isn't coloured
637 when colour by annotation (per sequence) is coloured</li>
638 <li>Keyboard mode P jumps to start of gapped region when
639 residue follows a gap</li>
640 <li>Jalview appears to hang importing an alignment with
641 Wrap as default or after enabling Wrap</li>
642 <li>'Right click to add annotations' message
643 shown in wrap mode when no annotations present</li>
644 <li>Disorder predictions fail with NPE if no automatic
645 annotation already exists on alignment</li>
646 <li>oninit javascript function should be called after
647 initialisation completes</li>
648 <li>Remove redundancy after disorder prediction corrupts
649 alignment window display</li>
650 <li>Example annotation file in documentation is invalid</li>
651 <li>Grouped line graph annotation rows are not exported
652 to annotation file</li>
653 <li>Multi-harmony analysis cannot be run when only two
655 <li>Cannot create multiple groups of line graphs with
656 several 'combine' statements in annotation file</li>
657 <li>Pressing return several times causes Number Format
658 exceptions in keyboard mode</li>
659 <li>Multi-harmony (SHMMR) method doesn't submit
660 correct partitions for input data</li>
661 <li>Translation from DNA to Amino Acids fails</li>
662 <li>Jalview fail to load newick tree with quoted label</li>
663 <li>--headless flag isn't understood</li>
664 <li>ClassCastException when generating EPS in headless
666 <li>Adjusting sequence-associated shading threshold only
667 changes one row's threshold</li>
668 <li>Preferences and Feature settings panel panel
669 doesn't open</li>
670 <li>hide consensus histogram also hides conservation and
671 quality histograms</li>
676 <td><div align="center">
677 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
679 <td><em>Application</em>
680 <ul><li>Support for JABAWS 2.0 Services (AACon alignment
681 conservation, protein disorder and Clustal Omega)</li>
682 <li>JABAWS server status indicator in Web Services preferences
684 <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
685 Jalview alignment window</li>
686 <li>Updated Jalview build and deploy framework for OSX mountain
687 lion, windows 7, and 8</li>
688 <li>Nucleotide substitution matrix for PCA that supports RNA
689 and ambiguity codes</li>
691 <li>Improved sequence database retrieval GUI</li>
692 <li>Support fetching and database reference look up against
693 multiple DAS sources (Fetch all from in 'fetch db refs')</li>
694 <li>Jalview project improvements
696 <li>Store and retrieve the 'belowAlignment' flag for
698 <li>calcId attribute to group annotation rows on the
700 <li>Store AACon calculation settings for a view in Jalview
705 <li>horizontal scrolling gesture support</li>
706 <li>Visual progress indicator when PCA calculation is running</li>
707 <li>Simpler JABA web services menus</li>
708 <li>visual indication that web service results are still being
709 retrieved from server</li>
710 <li>Serialise the dialogs that are shown when Jalview starts up
712 <li>Jalview user agent string for interacting with HTTP
714 <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
716 <li>Examples directory and Groovy library included in
717 InstallAnywhere distribution</li>
718 </ul> <em>Applet</em>
720 <li>RNA alignment and secondary structure annotation
721 visualization applet example</li>
722 </ul> <em>General</em>
724 <li>Normalise option for consensus sequence logo</li>
725 <li>Reset button in PCA window to return dimensions to
727 <li>Allow seqspace or Jalview variant of alignment PCA
729 <li>PCA with either nucleic acid and protein substitution
731 <li>Allow windows containing HTML reports to be exported in
733 <li>Interactive display and editing of RNA secondary structure
735 <li>RNA Helix Alignment Colouring</li>
736 <li>RNA base pair logo consensus</li>
737 <li>Parse sequence associated secondary structure information
738 in Stockholm files</li>
739 <li>HTML Export database accessions and annotation information
740 presented in tooltip for sequences</li>
741 <li>Import secondary structure from LOCARNA clustalw style RNA
743 <li>import and visualise T-COFFEE quality scores for an
745 <li>'colour by annotation' per sequence option to
746 shade each sequence according to its associated alignment
748 <li>New Jalview Logo</li>
749 </ul> <em>Documentation and Development</em>
751 <li>documentation for score matrices used in Jalview</li>
752 <li>New Website!</li>
754 <td><em>Application</em>
756 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
757 wsdbfetch REST service</li>
758 <li>Stop windows being moved outside desktop on OSX</li>
759 <li>Filetype associations not installed for webstart launch</li>
760 <li>Jalview does not always retrieve progress of a JABAWS job
761 execution in full once it is complete</li>
762 <li>revise SHMR RSBS definition to ensure alignment is
763 uploaded via ali_file parameter</li>
764 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
765 <li>View all structures superposed fails with exception</li>
766 <li>Jnet job queues forever if a very short sequence is
767 submitted for prediction</li>
768 <li>Cut and paste menu not opened when mouse clicked on
770 <li>Putting fractional value into integer text box in
771 alignment parameter dialog causes Jalview to hang</li>
772 <li>Structure view highlighting doesn't work on windows 7
774 <li>View all structures fails with exception shown in
776 <li>Characters in filename associated with PDBEntry not
777 escaped in a platform independent way</li>
778 <li>Jalview desktop fails to launch with exception when using
780 <li>Tree calculation reports 'you must have 2 or more
781 sequences selected' when selection is empty</li>
782 <li>Jalview desktop fails to launch with jar signature failure
783 when java web start temporary file caching is disabled</li>
784 <li>DAS Sequence retrieval with range qualification results in
785 sequence xref which includes range qualification</li>
786 <li>Errors during processing of command line arguments cause
787 progress bar (JAL-898) to be removed</li>
788 <li>Replace comma for semi-colon option not disabled for DAS
789 sources in sequence fetcher</li>
790 <li>Cannot close news reader when JABAWS server warning dialog
792 <li>Option widgets not updated to reflect user settings</li>
793 <li>Edited sequence not submitted to web service</li>
794 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
795 <li>InstallAnywhere installer doesn't unpack and run on
796 OSX Mountain Lion</li>
797 <li>Annotation panel not given a scroll bar when sequences
798 with alignment annotation are pasted into the alignment</li>
799 <li>Sequence associated annotation rows not associated when
800 loaded from Jalview project</li>
801 <li>Browser launch fails with NPE on java 1.7</li>
802 <li>JABAWS alignment marked as finished when job was cancelled
803 or job failed due to invalid input</li>
804 <li>NPE with v2.7 example when clicking on Tree associated
806 <li>Exceptions when copy/paste sequences with grouped
807 annotation rows to new window</li>
808 </ul> <em>Applet</em>
810 <li>Sequence features are momentarily displayed before they
811 are hidden using hidefeaturegroups applet parameter</li>
812 <li>loading features via javascript API automatically enables
814 <li>scrollToColumnIn javascript API method doesn't work</li>
815 </ul> <em>General</em>
817 <li>Redundancy removal fails for rna alignment</li>
818 <li>PCA calculation fails when sequence has been selected and
820 <li>PCA window shows grey box when first opened on OSX</li>
821 <li>Letters coloured pink in sequence logo when alignment
822 coloured with clustalx</li>
823 <li>Choosing fonts without letter symbols defined causes
824 exceptions and redraw errors</li>
825 <li>Initial PCA plot view is not same as manually reconfigured
827 <li>Grouped annotation graph label has incorrect line colour</li>
828 <li>Grouped annotation graph label display is corrupted for
835 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
838 <td><em>Application</em>
840 <li>Jalview Desktop News Reader</li>
841 <li>Tweaked default layout of web services menu</li>
842 <li>View/alignment association menu to enable user to easily
843 specify which alignment a multi-structure view takes its
844 colours/correspondences from</li>
845 <li>Allow properties file location to be specified as URL</li>
846 <li>Extend Jalview project to preserve associations between
847 many alignment views and a single Jmol display</li>
848 <li>Store annotation row height in Jalview project file</li>
849 <li>Annotation row column label formatting attributes stored
851 <li>Annotation row order for auto-calculated annotation rows
852 preserved in Jalview project file</li>
853 <li>Visual progress indication when Jalview state is saved
854 using Desktop window menu</li>
855 <li>Visual indication that command line arguments are still
857 <li>Groovy script execution from URL</li>
858 <li>Colour by annotation default min and max colours in
860 <li>Automatically associate PDB files dragged onto an
861 alignment with sequences that have high similarity and matching
863 <li>Update JGoogleAnalytics to latest release (0.3)</li>
864 <li>'view structures' option to open many structures
866 <li>Sort associated views menu option for tree panel</li>
867 <li>Group all JABA and non-JABA services for a particular
868 analysis function in its own submenu</li>
869 </ul> <em>Applet</em>
871 <li>Userdefined and autogenerated annotation rows for groups</li>
872 <li>Adjustment of alignment annotation pane height</li>
873 <li>Annotation scrollbar for annotation panel</li>
874 <li>Drag to reorder annotation rows in annotation panel</li>
875 <li>'automaticScrolling' parameter</li>
876 <li>Allow sequences with partial ID string matches to be
877 annotated from GFF/Jalview features files</li>
878 <li>Sequence logo annotation row in applet</li>
879 <li>Absolute paths relative to host server in applet
880 parameters are treated as such</li>
881 <li>New in the JalviewLite javascript API:
883 <li>JalviewLite.js javascript library</li>
884 <li>Javascript callbacks for
886 <li>Applet initialisation</li>
887 <li>Sequence/alignment mouse-overs and selections</li>
890 <li>scrollTo row and column alignment scrolling functions</li>
891 <li>Select sequence/alignment regions from javascript</li>
892 <li>javascript structure viewer harness to pass messages
893 between Jmol and Jalview when running as distinct applets</li>
894 <li>sortBy method</li>
895 <li>Set of applet and application examples shipped with
897 <li>New example to demonstrate JalviewLite and Jmol
898 javascript message exchange</li>
900 </ul> <em>General</em>
902 <li>Enable Jmol displays to be associated with multiple
903 multiple alignments</li>
904 <li>Option to automatically sort alignment with new tree</li>
905 <li>User configurable link to enable redirects to a
906 www.Jalview.org mirror</li>
907 <li>Jmol colours option for Jmol displays</li>
908 <li>Configurable newline string when writing alignment and
909 other flat files</li>
910 <li>Allow alignment annotation description lines to contain
912 </ul> <em>Documentation and Development</em>
914 <li>Add groovy test harness for bulk load testing to examples
916 <li>Groovy script to load and align a set of sequences using a
917 web service before displaying the result in the Jalview desktop</li>
918 <li>Restructured javascript and applet api documentation</li>
919 <li>Ant target to publish example html files with applet
921 <li>Netbeans project for building Jalview from source</li>
922 <li>ant task to create online javadoc for Jalview source</li>
924 <td><em>Application</em>
926 <li>User defined colourscheme throws exception when current
927 built in colourscheme is saved as new scheme</li>
928 <li>AlignFrame->Save in application pops up save dialog for
929 valid filename/format</li>
930 <li>Cannot view associated structure for Uniprot sequence</li>
931 <li>PDB file association breaks for Uniprot sequence P37173</li>
932 <li>Associate PDB from file dialog does not tell you which
933 sequence is to be associated with the file</li>
934 <li>Find All raises null pointer exception when query only
935 matches sequence IDs</li>
936 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
937 <li>Jalview project with Jmol views created with Jalview 2.4
938 cannot be loaded</li>
939 <li>Filetype associations not installed for webstart launch</li>
940 <li>Two or more chains in a single PDB file associated with
941 sequences in different alignments do not get coloured by their
942 associated sequence</li>
943 <li>Visibility status of autocalculated annotation row not
944 preserved when project is loaded</li>
945 <li>Annotation row height and visibility attributes not stored
946 in Jalview project</li>
947 <li>Tree bootstraps are not preserved when saved as a Jalview
949 <li>Envision2 workflow tooltips are corrupted</li>
950 <li>Enabling show group conservation also enables colour by
952 <li>Duplicate group associated conservation or consensus
953 created on new view</li>
954 <li>Annotation scrollbar not displayed after 'show all
955 hidden annotation rows' option selected</li>
956 <li>Alignment quality not updated after alignment annotation
957 row is hidden then shown</li>
958 <li>Preserve colouring of structures coloured by sequences in
959 pre Jalview 2.7 projects</li>
960 <li>Web service job parameter dialog is not laid out properly
962 <li>Web services menu not refreshed after 'reset
963 services' button is pressed in preferences</li>
964 <li>Annotation off by one in Jalview v2_3 example project</li>
965 <li>Structures imported from file and saved in project get
966 name like jalview_pdb1234.txt when reloaded</li>
967 <li>Jalview does not always retrieve progress of a JABAWS job
968 execution in full once it is complete</li>
969 </ul> <em>Applet</em>
971 <li>Alignment height set incorrectly when lots of annotation
972 rows are displayed</li>
973 <li>Relative URLs in feature HTML text not resolved to
975 <li>View follows highlighting does not work for positions in
977 <li><= shown as = in tooltip</li>
978 <li>Export features raises exception when no features exist</li>
979 <li>Separator string used for serialising lists of IDs for
980 javascript api is modified when separator string provided as
982 <li>Null pointer exception when selecting tree leaves for
983 alignment with no existing selection</li>
984 <li>Relative URLs for datasources assumed to be relative to
985 applet's codebase</li>
986 <li>Status bar not updated after finished searching and search
987 wraps around to first result</li>
988 <li>StructureSelectionManager instance shared between several
989 Jalview applets causes race conditions and memory leaks</li>
990 <li>Hover tooltip and mouseover of position on structure not
991 sent from Jmol in applet</li>
992 <li>Certain sequences of javascript method calls to applet API
993 fatally hang browser</li>
994 </ul> <em>General</em>
996 <li>View follows structure mouseover scrolls beyond position
997 with wrapped view and hidden regions</li>
998 <li>Find sequence position moves to wrong residue with/without
1000 <li>Sequence length given in alignment properties window is
1002 <li>InvalidNumberFormat exceptions thrown when trying to
1003 import PDB like structure files</li>
1004 <li>Positional search results are only highlighted between
1005 user-supplied sequence start/end bounds</li>
1006 <li>End attribute of sequence is not validated</li>
1007 <li>Find dialog only finds first sequence containing a given
1008 sequence position</li>
1009 <li>Sequence numbering not preserved in MSF alignment output</li>
1010 <li>Jalview PDB file reader does not extract sequence from
1011 nucleotide chains correctly</li>
1012 <li>Structure colours not updated when tree partition changed
1014 <li>Sequence associated secondary structure not correctly
1015 parsed in interleaved stockholm</li>
1016 <li>Colour by annotation dialog does not restore current state
1018 <li>Hiding (nearly) all sequences doesn't work properly</li>
1019 <li>Sequences containing lowercase letters are not properly
1020 associated with their pdb files</li>
1021 </ul> <em>Documentation and Development</em>
1023 <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
1029 <div align="center">
1030 <strong><a name="Jalview2.6.1">2.6.1</a>
1031 </strong><br> <em>15/11/2010</em>
1033 <td><em>Application</em>
1035 <li>New warning dialog when the Jalview Desktop cannot contact
1037 <li>JABA service parameters for a preset are shown in service
1039 <li>JABA Service menu entries reworded</li>
1043 <li>Modeller PIR IO broken - cannot correctly import a pir
1044 file emitted by Jalview</li>
1045 <li>Existing feature settings transferred to new alignment
1046 view created from cut'n'paste</li>
1047 <li>Improved test for mixed amino/nucleotide chains when
1048 parsing PDB files</li>
1049 <li>Consensus and conservation annotation rows occasionally
1050 become blank for all new windows</li>
1051 <li>Exception raised when right clicking above sequences in
1052 wrapped view mode</li>
1053 </ul> <em>Application</em>
1055 <li>multiple multiply aligned structure views cause cpu usage
1056 to hit 100% and computer to hang</li>
1057 <li>Web Service parameter layout breaks for long user
1058 parameter names</li>
1059 <li>Jaba service discovery hangs desktop if Jaba server is
1065 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
1066 <em>26/9/2010</em></div>
1068 <td><em>Application</em>
1070 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1071 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
1072 <li>Web Services preference tab</li>
1073 <li>Analysis parameters dialog box and user defined preferences</li>
1074 <li>Improved speed and layout of Envision2 service menu</li>
1075 <li>Superpose structures using associated sequence alignment</li>
1076 <li>Export coordinates and projection as CSV from PCA viewer</li>
1080 <li>enable javascript: execution by the applet via the link out
1085 <li>Updated the Jmol Jalview interface to work with Jmol series
1087 <li>The Jalview Desktop and JalviewLite applet now require Java
1089 <li>Allow Jalview feature colour specification for GFF sequence
1090 annotation files</li>
1091 <li>New 'colour by label' keword in Jalview feature file type
1092 colour specification</li>
1093 <li>New Jalview Desktop Groovy API method that allows a script
1094 to check if it being run in an interactive session or in a batch
1095 operation from the Jalview command line</li>
1100 <li>clustalx colourscheme colours Ds preferentially when both
1101 D+E are present in over 50% of the column</li>
1104 <em>Application</em>
1106 <li>typo in AlignmentFrame->View->Hide->all but
1107 selected Regions menu item</li>
1108 <li>sequence fetcher replaces ',' for ';' when the ',' is part
1109 of a valid accession ID</li>
1110 <li>fatal OOM if object retrieved by sequence fetcher runs out
1112 <li>unhandled Out of Memory Error when viewing pca analysis
1114 <li>InstallAnywhere builds fail to launch on OS X java 10.5
1115 update 4 (due to apple Java 1.6 update)</li>
1116 <li>Installanywhere Jalview silently fails to launch</li>
1120 <li>Jalview.getFeatureGroups() raises an
1121 ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
1127 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
1128 <em>14/6/2010</em></div>
1133 <li>Alignment prettyprinter doesn't cope with long sequence IDs
1135 <li>clustalx colourscheme colours Ds preferentially when both
1136 D+E are present in over 50% of the column</li>
1137 <li>nucleic acid structures retrieved from PDB do not import
1139 <li>More columns get selected than were clicked on when a number
1140 of columns are hidden</li>
1141 <li>annotation label popup menu not providing correct
1142 add/hide/show options when rows are hidden or none are present</li>
1143 <li>Stockholm format shown in list of readable formats, and
1144 parser copes better with alignments from RFAM.</li>
1145 <li>CSV output of consensus only includes the percentage of all
1146 symbols if sequence logo display is enabled</li>
1151 <li>annotation panel disappears when annotation is
1154 <em>Application</em>
1156 <li>Alignment view not redrawn properly when new alignment
1157 opened where annotation panel is visible but no annotations are
1158 present on alignment</li>
1159 <li>pasted region containing hidden columns is incorrectly
1160 displayed in new alignment window</li>
1161 <li>Jalview slow to complete operations when stdout is flooded
1162 (fix is to close the Jalview console)</li>
1163 <li>typo in AlignmentFrame->View->Hide->all but
1164 selected Rregions menu item.</li>
1165 <li>inconsistent group submenu and Format submenu entry 'Un' or
1167 <li>Sequence feature settings are being shared by multiple
1168 distinct alignments</li>
1169 <li>group annotation not recreated when tree partition is
1171 <li>double click on group annotation to select sequences does
1172 not propagate to associated trees</li>
1173 <li>Mac OSX specific issues:
1175 <li>exception raised when mouse clicked on desktop window
1177 <li>Desktop menu placed on menu bar and application name set
1179 <li>sequence feature settings not wide enough for the save
1180 feature colourscheme button</li>
1189 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
1190 <em>30/4/2010</em></div>
1192 <td><em>New Capabilities</em>
1194 <li>URL links generated from description line for
1195 regular-expression based URL links (applet and application)
1196 <li>Non-positional feature URL links are shown in link menu</li>
1197 <li>Linked viewing of nucleic acid sequences and structures</li>
1198 <li>Automatic Scrolling option in View menu to display the
1199 currently highlighted region of an alignment.</li>
1200 <li>Order an alignment by sequence length, or using the average
1201 score or total feature count for each sequence.</li>
1202 <li>Shading features by score or associated description</li>
1203 <li>Subdivide alignment and groups based on identity of selected
1204 subsequence (Make Groups from Selection).</li>
1205 <li>New hide/show options including Shift+Control+H to hide
1206 everything but the currently selected region.</li>
1207 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1209 <em>Application</em>
1211 <li>Fetch DB References capabilities and UI expanded to support
1212 retrieval from DAS sequence sources</li>
1213 <li>Local DAS Sequence sources can be added via the command line
1214 or via the Add local source dialog box.</li>
1215 <li>DAS Dbref and DbxRef feature types are parsed as database
1216 references and protein_name is parsed as description line (BioSapiens
1218 <li>Enable or disable non-positional feature and database
1219 references in sequence ID tooltip from View menu in application.</li>
1220 <!-- <li>New hidden columns and rows and representatives capabilities
1221 in annotations file (in progress - not yet fully implemented)</li> -->
1222 <li>Group-associated consensus, sequence logos and conservation
1224 <li>Symbol distributions for each column can be exported and
1225 visualized as sequence logos</li>
1226 <li>Optionally scale multi-character column labels to fit within
1227 each column of annotation row<!-- todo for applet --></li>
1228 <li>Optional automatic sort of associated alignment view when a
1229 new tree is opened.</li>
1230 <li>Jalview Java Console</li>
1231 <li>Better placement of desktop window when moving between
1232 different screens.</li>
1233 <li>New preference items for sequence ID tooltip and consensus
1235 <li>Client to submit sequences and IDs to <a
1236 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
1237 <li><em>Vamsas Capabilities</em>
1239 <li>Improved VAMSAS synchronization (Jalview archive used to
1240 preserve views, structures, and tree display settings)</li>
1241 <li>Import of vamsas documents from disk or URL via command
1243 <li>Sharing of selected regions between views and with other
1244 VAMSAS applications (Experimental feature!)</li>
1245 <li>Updated API to VAMSAS version 0.2</li>
1251 <li>Middle button resizes annotation row height</li>
1254 <li>sortByTree (true/false) - automatically sort the associated
1255 alignment view by the tree when a new tree is opened.</li>
1256 <li>showTreeBootstraps (true/false) - show or hide branch
1257 bootstraps (default is to show them if available)</li>
1258 <li>showTreeDistances (true/false) - show or hide branch
1259 lengths (default is to show them if available)</li>
1260 <li>showUnlinkedTreeNodes (true/false) - indicate if
1261 unassociated nodes should be highlighted in the tree view</li>
1262 <li>heightScale and widthScale (1.0 or more) - increase the
1263 height or width of a cell in the alignment grid relative to the
1264 current font size.</li>
1267 <li>Non-positional features displayed in sequence ID tooltip</li>
1271 <li>Features format: graduated colour definitions and
1272 specification of feature scores</li>
1273 <li>Alignment Annotations format: new keywords for group
1274 associated annotation (GROUP_REF) and annotation row display
1275 properties (ROW_PROPERTIES)</li>
1276 <li>XML formats extended to support graduated feature
1277 colourschemes, group associated annotation, and profile visualization
1282 <li>Source field in GFF files parsed as feature source rather
1283 than description</li>
1284 <li>Non-positional features are now included in sequence feature
1285 and gff files (controlled via non-positional feature visibility in
1287 <li>URL links generated for all feature links (bugfix)</li>
1288 <li>Added URL embedding instructions to features file
1290 <li>Codons containing ambiguous nucleotides translated as 'X' in
1291 peptide product</li>
1292 <li>Match case switch in find dialog box works for both sequence
1293 ID and sequence string and query strings do not have to be in upper
1294 case to match case-insensitively.</li>
1295 <li>AMSA files only contain first column of multi-character
1296 column annotation labels</li>
1297 <li>Jalview Annotation File generation/parsing consistent with
1298 documentation (e.g. Stockholm annotation can be exported and
1300 <li>PDB files without embedded PDB IDs given a friendly name</li>
1301 <li>Find incrementally searches ID string matches as well as
1302 subsequence matches, and correctly reports total number of both.</li>
1305 <li>Better handling of exceptions during sequence retrieval</li>
1306 <li>Dasobert generated non-positional feature URL link text
1307 excludes the start_end suffix</li>
1308 <li>DAS feature and source retrieval buttons disabled when
1309 fetch or registry operations in progress.</li>
1310 <li>PDB files retrieved from URLs are cached properly</li>
1311 <li>Sequence description lines properly shared via VAMSAS</li>
1312 <li>Sequence fetcher fetches multiple records for all data
1314 <li>Ensured that command line das feature retrieval completes
1315 before alignment figures are generated.</li>
1316 <li>Reduced time taken when opening file browser for first
1318 <li>isAligned check prior to calculating tree, PCA or
1319 submitting an MSA to JNet now excludes hidden sequences.</li>
1320 <li>User defined group colours properly recovered from Jalview
1330 <div align="center"><strong>2.4.0.b2</strong><br>
1335 <li>Experimental support for google analytics usage tracking.</li>
1336 <li>Jalview privacy settings (user preferences and docs).</li>
1341 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
1342 <li>Exception when feature created from selection beyond length
1344 <li>Allow synthetic PDB files to be imported gracefully</li>
1345 <li>Sequence associated annotation rows associate with all
1346 sequences with a given id</li>
1347 <li>Find function matches case-insensitively for sequence ID
1348 string searches</li>
1349 <li>Non-standard characters do not cause pairwise alignment to
1350 fail with exception</li>
1352 <em>Application Issues</em>
1354 <li>Sequences are now validated against EMBL database</li>
1355 <li>Sequence fetcher fetches multiple records for all data
1358 <em>InstallAnywhere Issues</em>
1360 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
1361 installAnywhere mechanism)</li>
1362 <li>Command line launching of JARs from InstallAnywhere version
1363 (java class versioning error fixed)</li>
1370 <div align="center"><strong>2.4</strong><br>
1373 <td><em>User Interface</em>
1375 <li>Linked highlighting of codon and amino acid from translation
1376 and protein products</li>
1377 <li>Linked highlighting of structure associated with residue
1378 mapping to codon position</li>
1379 <li>Sequence Fetcher provides example accession numbers and
1381 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
1382 <li>Extract score function to parse whitespace separated numeric
1383 data in description line</li>
1384 <li>Column labels in alignment annotation can be centred.</li>
1385 <li>Tooltip for sequence associated annotation give name of
1388 <em>Web Services and URL fetching</em>
1390 <li>JPred3 web service</li>
1391 <li>Prototype sequence search client (no public services
1393 <li>Fetch either seed alignment or full alignment from PFAM</li>
1394 <li>URL Links created for matching database cross references as
1395 well as sequence ID</li>
1396 <li>URL Links can be created using regular-expressions</li>
1398 <em>Sequence Database Connectivity</em>
1400 <li>Retrieval of cross-referenced sequences from other databases
1402 <li>Generalised database reference retrieval and validation to
1403 all fetchable databases</li>
1404 <li>Fetch sequences from DAS sources supporting the sequence
1407 <em>Import and Export</em>
1408 <li>export annotation rows as CSV for spreadsheet import</li>
1409 <li>Jalview projects record alignment dataset associations, EMBL
1410 products, and cDNA sequence mappings</li>
1411 <li>Sequence Group colour can be specified in Annotation File</li>
1412 <li>Ad-hoc colouring of group in Annotation File using RGB
1413 triplet as name of colourscheme</li>
1415 <em>VAMSAS Client capabilities (Experimental)</em>
1417 <li>treenode binding for VAMSAS tree exchange</li>
1418 <li>local editing and update of sequences in VAMSAS alignments
1420 <li>Create new or select existing session to join</li>
1421 <li>load and save of vamsas documents</li>
1423 <em>Application command line</em>
1425 <li>-tree parameter to open trees (introduced for passing from
1427 <li>-fetchfrom command line argument to specify nicknames of DAS
1428 servers to query for alignment features</li>
1429 <li>-dasserver command line argument to add new servers that are
1430 also automatically queried for features</li>
1431 <li>-groovy command line argument executes a given groovy script
1432 after all input data has been loaded and parsed</li>
1434 <em>Applet-Application data exchange</em>
1436 <li>Trees passed as applet parameters can be passed to
1437 application (when using "View in full application")</li>
1439 <em>Applet Parameters</em>
1441 <li>feature group display control parameter</li>
1442 <li>debug parameter</li>
1443 <li>showbutton parameter</li>
1445 <em>Applet API methods</em>
1447 <li>newView public method</li>
1448 <li>Window (current view) specific get/set public methods</li>
1449 <li>Feature display control methods</li>
1450 <li>get list of currently selected sequences</li>
1452 <em>New Jalview distribution features</em>
1454 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1455 <li>RELEASE file gives build properties for the latest Jalview
1457 <li>Java 1.1 Applet build made easier and donotobfuscate
1458 property controls execution of obfuscator</li>
1459 <li>Build target for generating source distribution</li>
1460 <li>Debug flag for javacc</li>
1461 <li>.jalview_properties file is documented (slightly) in
1462 jalview.bin.Cache</li>
1463 <li>Continuous Build Integration for stable and development
1464 version of Application, Applet and source distribution</li>
1470 <li>selected region output includes visible annotations (for
1471 certain formats)</li>
1472 <li>edit label/displaychar contains existing label/char for
1474 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1475 <li>shorter peptide product names from EMBL records</li>
1476 <li>Newick string generator makes compact representations</li>
1477 <li>bootstrap values parsed correctly for tree files with
1479 <li>pathological filechooser bug avoided by not allowing
1480 filenames containing a ':'</li>
1481 <li>Fixed exception when parsing GFF files containing global
1482 sequence features</li>
1483 <li>Alignment datasets are finalized only when number of
1484 references from alignment sequences goes to zero</li>
1485 <li>Close of tree branch colour box without colour selection
1486 causes cascading exceptions</li>
1487 <li>occasional negative imgwidth exceptions</li>
1488 <li>better reporting of non-fatal warnings to user when file
1490 <li>Save works when Jalview project is default format</li>
1491 <li>Save as dialog opened if current alignment format is not a
1492 valid output format</li>
1493 <li>Uniprot canonical names introduced for both das and vamsas</li>
1494 <li>Histidine should be midblue (not pink!) in Zappo</li>
1495 <li>error messages passed up and output when data read fails</li>
1496 <li>edit undo recovers previous dataset sequence when sequence
1498 <li>allow PDB files without pdb ID HEADER lines (like those
1499 generated by MODELLER) to be read in properly</li>
1500 <li>allow reading of JPred concise files as a normal filetype</li>
1501 <li>Stockholm annotation parsing and alignment properties import
1502 fixed for PFAM records</li>
1503 <li>Structure view windows have correct name in Desktop window
1505 <li>annotation consisting of sequence associated scores can be
1506 read and written correctly to annotation file</li>
1507 <li>Aligned cDNA translation to aligned peptide works correctly</li>
1508 <li>Fixed display of hidden sequence markers and non-italic font
1509 for representatives in Applet</li>
1510 <li>Applet Menus are always embedded in applet window on Macs.</li>
1511 <li>Newly shown features appear at top of stack (in Applet)</li>
1512 <li>Annotations added via parameter not drawn properly due to
1513 null pointer exceptions</li>
1514 <li>Secondary structure lines are drawn starting from first
1515 column of alignment</li>
1516 <li>Uniprot XML import updated for new schema release in July
1518 <li>Sequence feature to sequence ID match for Features file is
1519 case-insensitive</li>
1520 <li>Sequence features read from Features file appended to all
1521 sequences with matching IDs</li>
1522 <li>PDB structure coloured correctly for associated views
1523 containing a sub-sequence</li>
1524 <li>PDB files can be retrieved by applet from Jar files</li>
1525 <li>feature and annotation file applet parameters referring to
1526 different directories are retrieved correctly</li>
1527 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1528 <li>Fixed application hang whilst waiting for splash-screen
1529 version check to complete</li>
1530 <li>Applet properly URLencodes input parameter values when
1531 passing them to the launchApp service</li>
1532 <li>display name and local features preserved in results
1533 retrieved from web service</li>
1534 <li>Visual delay indication for sequence retrieval and sequence
1535 fetcher initialisation</li>
1536 <li>updated Application to use DAS 1.53e version of dasobert DAS
1538 <li>Re-instated Full AMSA support and .amsa file association</li>
1539 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1546 <div align="center"><strong>2.3</strong><br>
1551 <li>Jmol 11.0.2 integration</li>
1552 <li>PDB views stored in Jalview XML files</li>
1553 <li>Slide sequences</li>
1554 <li>Edit sequence in place</li>
1555 <li>EMBL CDS features</li>
1556 <li>DAS Feature mapping</li>
1557 <li>Feature ordering</li>
1558 <li>Alignment Properties</li>
1559 <li>Annotation Scores</li>
1560 <li>Sort by scores</li>
1561 <li>Feature/annotation editing in applet</li>
1566 <li>Headless state operation in 2.2.1</li>
1567 <li>Incorrect and unstable DNA pairwise alignment</li>
1568 <li>Cut and paste of sequences with annotation</li>
1569 <li>Feature group display state in XML</li>
1570 <li>Feature ordering in XML</li>
1571 <li>blc file iteration selection using filename # suffix</li>
1572 <li>Stockholm alignment properties</li>
1573 <li>Stockhom alignment secondary structure annotation</li>
1574 <li>2.2.1 applet had no feature transparency</li>
1575 <li>Number pad keys can be used in cursor mode</li>
1576 <li>Structure Viewer mirror image resolved</li>
1583 <div align="center"><strong>2.2.1</strong><br>
1588 <li>Non standard characters can be read and displayed
1589 <li>Annotations/Features can be imported/exported to the applet
1591 <li>Applet allows editing of sequence/annotation/group name
1593 <li>Preference setting to display sequence name in italics
1594 <li>Annotation file format extended to allow Sequence_groups to
1596 <li>Default opening of alignment overview panel can be specified
1598 <li>PDB residue numbering annotation added to associated
1604 <li>Applet crash under certain Linux OS with Java 1.6 installed
1605 <li>Annotation file export / import bugs fixed
1606 <li>PNG / EPS image output bugs fixed
1612 <div align="center"><strong>2.2</strong><br>
1617 <li>Multiple views on alignment
1618 <li>Sequence feature editing
1619 <li>"Reload" alignment
1620 <li>"Save" to current filename
1621 <li>Background dependent text colour
1622 <li>Right align sequence ids
1623 <li>User-defined lower case residue colours
1626 <li>Menu item accelerator keys
1627 <li>Control-V pastes to current alignment
1628 <li>Cancel button for DAS Feature Fetching
1629 <li>PCA and PDB Viewers zoom via mouse roller
1630 <li>User-defined sub-tree colours and sub-tree selection
1631 <li>'New Window' button on the 'Output to Text box'
1636 <li>New memory efficient Undo/Redo System
1637 <li>Optimised symbol lookups and conservation/consensus
1639 <li>Region Conservation/Consensus recalculated after edits
1640 <li>Fixed Remove Empty Columns Bug (empty columns at end of
1642 <li>Slowed DAS Feature Fetching for increased robustness.
1643 <li>Made angle brackets in ASCII feature descriptions display
1645 <li>Re-instated Zoom function for PCA
1646 <li>Sequence descriptions conserved in web service analysis
1648 <li>Uniprot ID discoverer uses any word separated by ∣
1649 <li>WsDbFetch query/result association resolved
1650 <li>Tree leaf to sequence mapping improved
1651 <li>Smooth fonts switch moved to FontChooser dialog box.
1657 <div align="center"><strong>2.1.1</strong><br>
1662 <li>Copy consensus sequence to clipboard</li>
1667 <li>Image output - rightmost residues are rendered if sequence
1668 id panel has been resized</li>
1669 <li>Image output - all offscreen group boundaries are rendered</li>
1670 <li>Annotation files with sequence references - all elements in
1671 file are relative to sequence position</li>
1672 <li>Mac Applet users can use Alt key for group editing</li>
1678 <div align="center"><strong>2.1</strong><br>
1683 <li>MAFFT Multiple Alignment in default Web Service list</li>
1684 <li>DAS Feature fetching</li>
1685 <li>Hide sequences and columns</li>
1686 <li>Export Annotations and Features</li>
1687 <li>GFF file reading / writing</li>
1688 <li>Associate structures with sequences from local PDB files</li>
1689 <li>Add sequences to exisiting alignment</li>
1690 <li>Recently opened files / URL lists</li>
1691 <li>Applet can launch the full application</li>
1692 <li>Applet has transparency for features (Java 1.2 required)</li>
1693 <li>Applet has user defined colours parameter</li>
1694 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
1699 <li>Redundancy Panel reinstalled in the Applet</li>
1700 <li>Monospaced font - EPS / rescaling bug fixed</li>
1701 <li>Annotation files with sequence references bug fixed</li>
1707 <div align="center"><strong>2.08.1</strong><br>
1712 <li>Change case of selected region from Popup menu</li>
1713 <li>Choose to match case when searching</li>
1714 <li>Middle mouse button and mouse movement can compress / expand
1715 the visible width and height of the alignment</li>
1720 <li>Annotation Panel displays complete JNet results</li>
1726 <div align="center"><strong>2.08b</strong><br>
1732 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1733 <li>Righthand label on wrapped alignments shows correct value</li>
1739 <div align="center"><strong>2.08</strong><br>
1744 <li>Editing can be locked to the selection area</li>
1745 <li>Keyboard editing</li>
1746 <li>Create sequence features from searches</li>
1747 <li>Precalculated annotations can be loaded onto alignments</li>
1748 <li>Features file allows grouping of features</li>
1749 <li>Annotation Colouring scheme added</li>
1750 <li>Smooth fonts off by default - Faster rendering</li>
1751 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1756 <li>Drag & Drop fixed on Linux</li>
1757 <li>Jalview Archive file faster to load/save, sequence
1758 descriptions saved.</li>
1764 <div align="center"><strong>2.07</strong><br>
1769 <li>PDB Structure Viewer enhanced</li>
1770 <li>Sequence Feature retrieval and display enhanced</li>
1771 <li>Choose to output sequence start-end after sequence name for
1773 <li>Sequence Fetcher WSDBFetch@EBI</li>
1774 <li>Applet can read feature files, PDB files and can be used for
1775 HTML form input</li>
1780 <li>HTML output writes groups and features</li>
1781 <li>Group editing is Control and mouse click</li>
1782 <li>File IO bugs</li>
1788 <div align="center"><strong>2.06</strong><br>
1793 <li>View annotations in wrapped mode</li>
1794 <li>More options for PCA viewer</li>
1799 <li>GUI bugs resolved</li>
1800 <li>Runs with -nodisplay from command line</li>
1806 <div align="center"><strong>2.05b</strong><br>
1811 <li>Choose EPS export as lineart or text</li>
1812 <li>Jar files are executable</li>
1813 <li>Can read in Uracil - maps to unknown residue</li>
1818 <li>Known OutOfMemory errors give warning message</li>
1819 <li>Overview window calculated more efficiently</li>
1820 <li>Several GUI bugs resolved</li>
1826 <div align="center"><strong>2.05</strong><br>
1831 <li>Edit and annotate in "Wrapped" view</li>
1836 <li>Several GUI bugs resolved</li>
1842 <div align="center"><strong>2.04</strong><br>
1847 <li>Hold down mouse wheel & scroll to change font size</li>
1852 <li>Improved JPred client reliability</li>
1853 <li>Improved loading of Jalview files</li>
1859 <div align="center"><strong>2.03</strong><br>
1864 <li>Set Proxy server name and port in preferences</li>
1865 <li>Multiple URL links from sequence ids</li>
1866 <li>User Defined Colours can have a scheme name and added to
1868 <li>Choose to ignore gaps in consensus calculation</li>
1869 <li>Unix users can set default web browser</li>
1870 <li>Runs without GUI for batch processing</li>
1871 <li>Dynamically generated Web Service Menus</li>
1876 <li>InstallAnywhere download for Sparc Solaris</li>
1882 <div align="center"><strong>2.02</strong><br>
1888 <li>Copy & Paste order of sequences maintains alignment
1895 <div align="center"><strong>2.01</strong><br>
1900 <li>Use delete key for deleting selection.</li>
1901 <li>Use Mouse wheel to scroll sequences.</li>
1902 <li>Help file updated to describe how to add alignment
1904 <li>Version and build date written to build properties file.</li>
1905 <li>InstallAnywhere installation will check for updates at
1906 launch of Jalview.</li>
1911 <li>Delete gaps bug fixed.</li>
1912 <li>FileChooser sorts columns.</li>
1913 <li>Can remove groups one by one.</li>
1914 <li>Filechooser icons installed.</li>
1915 <li>Finder ignores return character when searching. Return key
1916 will initiate a search.<br>
1923 <div align="center"><strong>2.0</strong><br>
1928 <li>New codebase</li>