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 width="60" nowrap>
48 <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
57 <ul><li>Reinstated the display of default example file on startup</li>
58 <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
64 <td><div align="center">
65 <strong><a name="Jalview.2.8.3">2.8.3</a><br /> <em>13/4/2015</em></strong>
69 </ul> <em>Application</em>
79 <li>Make selection for columns now works on marked columns
80 rather than columns in rubber-band selection region.</li>
82 <!-- issues resolved --> <em>Application</em>
84 </ul> <!-- <em>Applet</em>
86 </ul> <em>General</em>
88 </ul>--> <em>Deployment and Documentation</em>
90 </ul> <em>Application Known issues</em>
92 </ul> <em>Applet Known Issues</em>
98 <td><div align="center">
99 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
103 <li>Updated Java code signing certificate donated by Certum.PL.</li>
104 <li>Features and annotation preserved when performing pairwise
106 <li>RNA pseudoknot annotation can be
107 imported/exported/displayed</li>
108 <li>'colour by annotation' can colour by RNA and
109 protein secondary structure</li>
110 </ul> <em>Application</em>
112 <li>Extract and display secondary structure for sequences with
114 <li>Support for parsing RNAML</li>
115 <li>Annotations menu for layout
117 <li>sort sequence annotation rows by alignment</li>
118 <li>place sequence annotation above/below alignment
121 <li>Output in Stockholm format</li>
122 <li>Internationalisation: improved Spanish (es) translation</li>
123 <li>Structure viewer preferences tab</li>
124 <li>Disorder and Secondary Structure annotation tracks shared
125 between alignments</li>
126 <li>UCSF Chimera launch and linked highlighting from Jalview</li>
127 <li>Show/hide all sequence associated annotation rows for all
128 or current selection</li>
129 <li>disorder and secondary structure predictions available as
130 dataset annotation</li>
131 <li>Per-sequence rna helices colouring</li>
134 <li>Sequence database accessions imported when fetching
135 alignments from Rfam</li>
136 <li>update VARNA version to 3.91</li>
138 <li>New groovy scripts for exporting aligned positions,
139 conservation values, and calculating sum of pairs scores.</li>
140 <li>Command line argument to set default JABAWS server</li>
141 <li>include installation type in build properties and console
143 <li>Updated Jalview project format to preserve dataset annotation</li>
146 <!-- issues resolved --> <em>Application</em>
148 <li>Distinguish alignment and sequence associated RNA
149 structure in structure->view->VARNA</li>
150 <li>Raise dialog box if user deletes all sequences in an
152 <li>Pressing F1 results in documentation opening twice</li>
153 <li>Sequence feature tooltip is wrapped</li>
154 <li>Double click on sequence associated annotation selects
155 only first column</li>
156 <li>Redundancy removal doesn't result in unlinked leaves
158 <li>Undos after several redundancy removals don't undo
160 <li>Hide sequence doesn't hide associated annotation</li>
161 <li>User defined colours dialog box too big to fit on screen
162 and buttons not visible</li>
163 <li>author list isn't updated if already written to jalview
165 <li>Popup menu won't open after retrieving sequence from
167 <li>File open window for associate PDB doesn't open</li>
168 <li>Left-then-right click on a sequence id opens a browser
170 <li>Cannot open sequence feature shading/sort popup menu in
171 feature settings dialog</li>
172 <li>better tooltip placement for some areas of Jalview desktop</li>
173 <li>Allow addition of JABAWS Server which doesn't pass
175 <li>Web services parameters dialog box is too large to fit on
177 <li>Muscle nucleotide alignment preset obscured by tooltip</li>
178 <li>JABAWS preset submenus don't contain newly defined
180 <li>MSA web services warns user if they were launched with
182 <li>Jalview cannot contact DAS Registy when running on Java 8</li>
184 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
185 'Superpose with' submenu not shown when new view created
188 </ul> <!-- <em>Applet</em>
190 </ul> <em>General</em>
192 </ul>--> <em>Deployment and Documentation</em>
194 <li>2G and 1G options in launchApp have no effect on memory
196 <li>launchApp service doesn't automatically open
197 www.jalview.org/examples/exampleFile.jar if no file is given</li>
199 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
200 InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
203 </ul> <em>Application Known issues</em>
206 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
207 corrupted or unreadable alignment display when scrolling alignment
211 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
212 retrieval fails but progress bar continues for DAS retrieval with
216 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
217 flatfile output of visible region has incorrect sequence start/end
220 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
221 rna structure consensus doesn't update when secondary
222 structure tracks are rearranged
225 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
226 invalid rna structure positional highlighting does not highlight
227 position of invalid base pairs
230 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
231 out of memory errors are not raised when saving jalview project
232 from alignment window file menu
235 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
236 Switching to RNA Helices colouring doesn't propagate to
240 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
241 colour by RNA Helices not enabled when user created annotation
245 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
246 Jalview icon not shown on dock in Mountain Lion/Webstart
248 </ul> <em>Applet Known Issues</em>
251 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
252 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
255 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
256 Jalview and Jmol example not compatible with IE9
259 <li>Sort by annotation score doesn't reverse order when
265 <td><div align="center">
266 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
269 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
272 <li>Internationalisation of user interface (usually called
273 i18n support) and translation for Spanish locale</li>
274 <li>Define/Undefine group on current selection with
275 Ctrl-G/Shift Ctrl-G</li>
276 <li>Improved group creation/removal options in
277 alignment/sequence Popup menu</li>
278 <li>Sensible precision for symbol distribution percentages
279 shown in logo tooltip.</li>
280 <li>Annotation panel height set according to amount of
281 annotation when alignment first opened</li>
282 </ul> <em>Application</em>
284 <li>Interactive consensus RNA secondary structure prediction
285 VIENNA RNAAliFold JABA 2.1 service</li>
286 <li>Select columns containing particular features from Feature
288 <li>View all 'representative' PDB structures for selected
290 <li>Update Jalview project format:
292 <li>New file extension for Jalview projects '.jvp'</li>
293 <li>Preserve sequence and annotation dataset (to store
294 secondary structure annotation,etc)</li>
295 <li>Per group and alignment annotation and RNA helix
299 <li>New similarity measures for PCA and Tree calculation
301 <li>Experimental support for retrieval and viewing of flanking
302 regions for an alignment</li>
306 <!-- issues resolved --> <em>Application</em>
308 <li>logo keeps spinning and status remains at queued or
309 running after job is cancelled</li>
310 <li>cannot export features from alignments imported from
311 Jalview/VAMSAS projects</li>
312 <li>Buggy slider for web service parameters that take float
314 <li>Newly created RNA secondary structure line doesn't have
315 'display all symbols' flag set</li>
316 <li>T-COFFEE alignment score shading scheme and other
317 annotation shading not saved in jalview project</li>
318 <li>Local file cannot be loaded in freshly downloaded Jalview</li>
319 <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
320 <li>Load file from desktop file browser fails</li>
321 <li>Occasional NPE thrown when calculating large trees</li>
322 <li>Cannot reorder or slide sequences after dragging an
323 alignment onto desktop</li>
324 <li>Colour by annotation dialog throws NPE after using
325 'extract scores' function</li>
326 <li>Loading/cut'n'pasting an empty file leads to a grey
327 alignment window</li>
328 <li>Disorder thresholds rendered incorrectly after performing
329 IUPred disorder prediction</li>
330 <li>Multiple group annotated consensus rows shown when
331 changing 'normalise logo' display setting</li>
332 <li>Find shows blank dialog after 'finished searching' if
333 nothing matches query</li>
334 <li>Null Pointer Exceptions raised when sorting by feature
335 with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
337 <li>Errors in Jmol console when structures in alignment don't
338 overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
340 <li>Not all working JABAWS services are shown in Jalview's
342 <li>JAVAWS version of jalview fails to launch with 'invalid
343 literal/length code'</li>
344 <li>Annotation/RNA Helix colourschemes cannot be applied to
345 alignment with groups (actually fixed in 2.8.0b1)</li>
346 <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
348 </ul> <em>Applet</em>
350 <li>Remove group option is shown even when selection is not a
352 <li>Apply to all groups ticked but colourscheme changes don't
354 <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
355 <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
356 <li>Increased font size for dropdown menus on OSX and embedded windows</li>
359 <li>Consensus sequence for alignments/groups with a single
360 sequence were not calculated</li>
361 <li>annotation files that contain only groups imported as
362 annotation and junk sequences</li>
363 <li>Fasta files with sequences containing '*' incorrectly
364 recognised as PFAM or BLC</li>
365 <li>conservation/PID slider apply all groups option doesn't
366 affect background (2.8.0b1)
368 <li>redundancy highlighting is erratic at 0% and 100%</li>
369 <li>Remove gapped columns fails for sequences with ragged
371 <li>AMSA annotation row with leading spaces is not registered
372 correctly on import</li>
373 <li>Jalview crashes when selecting PCA analysis for certain
375 <li>Opening the colour by annotation dialog for an existing
376 annotation based 'use original colours' colourscheme loses
377 original colours setting</li>
382 <td><div align="center">
383 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
388 <li>Trusted certificates for JalviewLite applet and
389 Jalview Desktop application<br />Certificate was donated by
390 <a href="https://www.certum.eu">Certum</a> to the Jalview
391 open source project).
393 <li>Jalview SRS links replaced by Uniprot and EBI-search
395 <li>Output in Stockholm format</li>
396 <li>Allow import of data from gzipped files</li>
397 <li>Export/import group and sequence associated line
398 graph thresholds</li>
399 <li>Nucleotide substitution matrix that supports RNA and
401 <li>Allow disorder predictions to be made on the current
402 selection (or visible selection) in the same way that JPred
404 <li>Groovy scripting for headless jalview operation</li>
405 </ul> <em>Other improvements</em>
407 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
408 <li>COMBINE statement uses current SEQUENCE_REF and
409 GROUP_REF scope to group annotation rows</li>
410 <li>Support '' style escaping of quotes in Newick
412 <li>Group options for JABAWS service by command line name</li>
413 <li>Empty tooltip shown for JABA service options with a
414 link but no description</li>
415 <li>Select primary source when selecting authority in
416 database fetcher GUI</li>
417 <li>Add .mfa to FASTA file extensions recognised by
419 <li>Annotation label tooltip text wrap</li>
424 <li>Slow scrolling when lots of annotation rows are
426 <li>Lots of NPE (and slowness) after creating RNA
427 secondary structure annotation line</li>
428 <li>Sequence database accessions not imported when
429 fetching alignments from Rfam</li>
430 <li>Incorrect SHMR submission for sequences with
432 <li>View all structures does not always superpose
434 <li>Option widgets in service parameters not updated to
435 reflect user or preset settings</li>
436 <li>Null pointer exceptions for some services without
437 presets or adjustable parameters</li>
438 <li>Discover PDB IDs entry in structure menu doesn't
439 discover PDB xRefs</li>
440 <li>Exception encountered while trying to retrieve
441 features with DAS</li>
442 <li>Lowest value in annotation row isn't coloured
443 when colour by annotation (per sequence) is coloured</li>
444 <li>Keyboard mode P jumps to start of gapped region when
445 residue follows a gap</li>
446 <li>Jalview appears to hang importing an alignment with
447 Wrap as default or after enabling Wrap</li>
448 <li>'Right click to add annotations' message
449 shown in wrap mode when no annotations present</li>
450 <li>Disorder predictions fail with NPE if no automatic
451 annotation already exists on alignment</li>
452 <li>oninit javascript function should be called after
453 initialisation completes</li>
454 <li>Remove redundancy after disorder prediction corrupts
455 alignment window display</li>
456 <li>Example annotation file in documentation is invalid</li>
457 <li>Grouped line graph annotation rows are not exported
458 to annotation file</li>
459 <li>Multi-harmony analysis cannot be run when only two
461 <li>Cannot create multiple groups of line graphs with
462 several 'combine' statements in annotation file</li>
463 <li>Pressing return several times causes Number Format
464 exceptions in keyboard mode</li>
465 <li>Multi-harmony (SHMMR) method doesn't submit
466 correct partitions for input data</li>
467 <li>Translation from DNA to Amino Acids fails</li>
468 <li>Jalview fail to load newick tree with quoted label</li>
469 <li>--headless flag isn't understood</li>
470 <li>ClassCastException when generating EPS in headless
472 <li>Adjusting sequence-associated shading threshold only
473 changes one row's threshold</li>
474 <li>Preferences and Feature settings panel panel
475 doesn't open</li>
476 <li>hide consensus histogram also hides conservation and
477 quality histograms</li>
482 <td><div align="center">
483 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
485 <td><em>Application</em>
486 <ul><li>Support for JABAWS 2.0 Services (AACon alignment
487 conservation, protein disorder and Clustal Omega)</li>
488 <li>JABAWS server status indicator in Web Services preferences
490 <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
491 Jalview alignment window</li>
492 <li>Updated Jalview build and deploy framework for OSX mountain
493 lion, windows 7, and 8</li>
494 <li>Nucleotide substitution matrix for PCA that supports RNA
495 and ambiguity codes</li>
497 <li>Improved sequence database retrieval GUI</li>
498 <li>Support fetching and database reference look up against
499 multiple DAS sources (Fetch all from in 'fetch db refs')</li>
500 <li>Jalview project improvements
502 <li>Store and retrieve the 'belowAlignment' flag for
504 <li>calcId attribute to group annotation rows on the
506 <li>Store AACon calculation settings for a view in Jalview
511 <li>horizontal scrolling gesture support</li>
512 <li>Visual progress indicator when PCA calculation is running</li>
513 <li>Simpler JABA web services menus</li>
514 <li>visual indication that web service results are still being
515 retrieved from server</li>
516 <li>Serialise the dialogs that are shown when Jalview starts up
518 <li>Jalview user agent string for interacting with HTTP
520 <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
522 <li>Examples directory and Groovy library included in
523 InstallAnywhere distribution</li>
524 </ul> <em>Applet</em>
526 <li>RNA alignment and secondary structure annotation
527 visualization applet example</li>
528 </ul> <em>General</em>
530 <li>Normalise option for consensus sequence logo</li>
531 <li>Reset button in PCA window to return dimensions to
533 <li>Allow seqspace or Jalview variant of alignment PCA
535 <li>PCA with either nucleic acid and protein substitution
537 <li>Allow windows containing HTML reports to be exported in
539 <li>Interactive display and editing of RNA secondary structure
541 <li>RNA Helix Alignment Colouring</li>
542 <li>RNA base pair logo consensus</li>
543 <li>Parse sequence associated secondary structure information
544 in Stockholm files</li>
545 <li>HTML Export database accessions and annotation information
546 presented in tooltip for sequences</li>
547 <li>Import secondary structure from LOCARNA clustalw style RNA
549 <li>import and visualise T-COFFEE quality scores for an
551 <li>'colour by annotation' per sequence option to
552 shade each sequence according to its associated alignment
554 <li>New Jalview Logo</li>
555 </ul> <em>Documentation and Development</em>
557 <li>documentation for score matrices used in Jalview</li>
558 <li>New Website!</li>
560 <td><em>Application</em>
562 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
563 wsdbfetch REST service</li>
564 <li>Stop windows being moved outside desktop on OSX</li>
565 <li>Filetype associations not installed for webstart launch</li>
566 <li>Jalview does not always retrieve progress of a JABAWS job
567 execution in full once it is complete</li>
568 <li>revise SHMR RSBS definition to ensure alignment is
569 uploaded via ali_file parameter</li>
570 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
571 <li>View all structures superposed fails with exception</li>
572 <li>Jnet job queues forever if a very short sequence is
573 submitted for prediction</li>
574 <li>Cut and paste menu not opened when mouse clicked on
576 <li>Putting fractional value into integer text box in
577 alignment parameter dialog causes Jalview to hang</li>
578 <li>Structure view highlighting doesn't work on windows 7
580 <li>View all structures fails with exception shown in
582 <li>Characters in filename associated with PDBEntry not
583 escaped in a platform independent way</li>
584 <li>Jalview desktop fails to launch with exception when using
586 <li>Tree calculation reports 'you must have 2 or more
587 sequences selected' when selection is empty</li>
588 <li>Jalview desktop fails to launch with jar signature failure
589 when java web start temporary file caching is disabled</li>
590 <li>DAS Sequence retrieval with range qualification results in
591 sequence xref which includes range qualification</li>
592 <li>Errors during processing of command line arguments cause
593 progress bar (JAL-898) to be removed</li>
594 <li>Replace comma for semi-colon option not disabled for DAS
595 sources in sequence fetcher</li>
596 <li>Cannot close news reader when JABAWS server warning dialog
598 <li>Option widgets not updated to reflect user settings</li>
599 <li>Edited sequence not submitted to web service</li>
600 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
601 <li>InstallAnywhere installer doesn't unpack and run on
602 OSX Mountain Lion</li>
603 <li>Annotation panel not given a scroll bar when sequences
604 with alignment annotation are pasted into the alignment</li>
605 <li>Sequence associated annotation rows not associated when
606 loaded from Jalview project</li>
607 <li>Browser launch fails with NPE on java 1.7</li>
608 <li>JABAWS alignment marked as finished when job was cancelled
609 or job failed due to invalid input</li>
610 <li>NPE with v2.7 example when clicking on Tree associated
612 <li>Exceptions when copy/paste sequences with grouped
613 annotation rows to new window</li>
614 </ul> <em>Applet</em>
616 <li>Sequence features are momentarily displayed before they
617 are hidden using hidefeaturegroups applet parameter</li>
618 <li>loading features via javascript API automatically enables
620 <li>scrollToColumnIn javascript API method doesn't work</li>
621 </ul> <em>General</em>
623 <li>Redundancy removal fails for rna alignment</li>
624 <li>PCA calculation fails when sequence has been selected and
626 <li>PCA window shows grey box when first opened on OSX</li>
627 <li>Letters coloured pink in sequence logo when alignment
628 coloured with clustalx</li>
629 <li>Choosing fonts without letter symbols defined causes
630 exceptions and redraw errors</li>
631 <li>Initial PCA plot view is not same as manually reconfigured
633 <li>Grouped annotation graph label has incorrect line colour</li>
634 <li>Grouped annotation graph label display is corrupted for
641 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
644 <td><em>Application</em>
646 <li>Jalview Desktop News Reader</li>
647 <li>Tweaked default layout of web services menu</li>
648 <li>View/alignment association menu to enable user to easily
649 specify which alignment a multi-structure view takes its
650 colours/correspondences from</li>
651 <li>Allow properties file location to be specified as URL</li>
652 <li>Extend Jalview project to preserve associations between
653 many alignment views and a single Jmol display</li>
654 <li>Store annotation row height in Jalview project file</li>
655 <li>Annotation row column label formatting attributes stored
657 <li>Annotation row order for auto-calculated annotation rows
658 preserved in Jalview project file</li>
659 <li>Visual progress indication when Jalview state is saved
660 using Desktop window menu</li>
661 <li>Visual indication that command line arguments are still
663 <li>Groovy script execution from URL</li>
664 <li>Colour by annotation default min and max colours in
666 <li>Automatically associate PDB files dragged onto an
667 alignment with sequences that have high similarity and matching
669 <li>Update JGoogleAnalytics to latest release (0.3)</li>
670 <li>'view structures' option to open many structures
672 <li>Sort associated views menu option for tree panel</li>
673 <li>Group all JABA and non-JABA services for a particular
674 analysis function in its own submenu</li>
675 </ul> <em>Applet</em>
677 <li>Userdefined and autogenerated annotation rows for groups</li>
678 <li>Adjustment of alignment annotation pane height</li>
679 <li>Annotation scrollbar for annotation panel</li>
680 <li>Drag to reorder annotation rows in annotation panel</li>
681 <li>'automaticScrolling' parameter</li>
682 <li>Allow sequences with partial ID string matches to be
683 annotated from GFF/Jalview features files</li>
684 <li>Sequence logo annotation row in applet</li>
685 <li>Absolute paths relative to host server in applet
686 parameters are treated as such</li>
687 <li>New in the JalviewLite javascript API:
689 <li>JalviewLite.js javascript library</li>
690 <li>Javascript callbacks for
692 <li>Applet initialisation</li>
693 <li>Sequence/alignment mouse-overs and selections</li>
696 <li>scrollTo row and column alignment scrolling functions</li>
697 <li>Select sequence/alignment regions from javascript</li>
698 <li>javascript structure viewer harness to pass messages
699 between Jmol and Jalview when running as distinct applets</li>
700 <li>sortBy method</li>
701 <li>Set of applet and application examples shipped with
703 <li>New example to demonstrate JalviewLite and Jmol
704 javascript message exchange</li>
706 </ul> <em>General</em>
708 <li>Enable Jmol displays to be associated with multiple
709 multiple alignments</li>
710 <li>Option to automatically sort alignment with new tree</li>
711 <li>User configurable link to enable redirects to a
712 www.Jalview.org mirror</li>
713 <li>Jmol colours option for Jmol displays</li>
714 <li>Configurable newline string when writing alignment and
715 other flat files</li>
716 <li>Allow alignment annotation description lines to contain
718 </ul> <em>Documentation and Development</em>
720 <li>Add groovy test harness for bulk load testing to examples
722 <li>Groovy script to load and align a set of sequences using a
723 web service before displaying the result in the Jalview desktop</li>
724 <li>Restructured javascript and applet api documentation</li>
725 <li>Ant target to publish example html files with applet
727 <li>Netbeans project for building Jalview from source</li>
728 <li>ant task to create online javadoc for Jalview source</li>
730 <td><em>Application</em>
732 <li>User defined colourscheme throws exception when current
733 built in colourscheme is saved as new scheme</li>
734 <li>AlignFrame->Save in application pops up save dialog for
735 valid filename/format</li>
736 <li>Cannot view associated structure for Uniprot sequence</li>
737 <li>PDB file association breaks for Uniprot sequence P37173</li>
738 <li>Associate PDB from file dialog does not tell you which
739 sequence is to be associated with the file</li>
740 <li>Find All raises null pointer exception when query only
741 matches sequence IDs</li>
742 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
743 <li>Jalview project with Jmol views created with Jalview 2.4
744 cannot be loaded</li>
745 <li>Filetype associations not installed for webstart launch</li>
746 <li>Two or more chains in a single PDB file associated with
747 sequences in different alignments do not get coloured by their
748 associated sequence</li>
749 <li>Visibility status of autocalculated annotation row not
750 preserved when project is loaded</li>
751 <li>Annotation row height and visibility attributes not stored
752 in Jalview project</li>
753 <li>Tree bootstraps are not preserved when saved as a Jalview
755 <li>Envision2 workflow tooltips are corrupted</li>
756 <li>Enabling show group conservation also enables colour by
758 <li>Duplicate group associated conservation or consensus
759 created on new view</li>
760 <li>Annotation scrollbar not displayed after 'show all
761 hidden annotation rows' option selected</li>
762 <li>Alignment quality not updated after alignment annotation
763 row is hidden then shown</li>
764 <li>Preserve colouring of structures coloured by sequences in
765 pre Jalview 2.7 projects</li>
766 <li>Web service job parameter dialog is not laid out properly
768 <li>Web services menu not refreshed after 'reset
769 services' button is pressed in preferences</li>
770 <li>Annotation off by one in Jalview v2_3 example project</li>
771 <li>Structures imported from file and saved in project get
772 name like jalview_pdb1234.txt when reloaded</li>
773 <li>Jalview does not always retrieve progress of a JABAWS job
774 execution in full once it is complete</li>
775 </ul> <em>Applet</em>
777 <li>Alignment height set incorrectly when lots of annotation
778 rows are displayed</li>
779 <li>Relative URLs in feature HTML text not resolved to
781 <li>View follows highlighting does not work for positions in
783 <li><= shown as = in tooltip</li>
784 <li>Export features raises exception when no features exist</li>
785 <li>Separator string used for serialising lists of IDs for
786 javascript api is modified when separator string provided as
788 <li>Null pointer exception when selecting tree leaves for
789 alignment with no existing selection</li>
790 <li>Relative URLs for datasources assumed to be relative to
791 applet's codebase</li>
792 <li>Status bar not updated after finished searching and search
793 wraps around to first result</li>
794 <li>StructureSelectionManager instance shared between several
795 Jalview applets causes race conditions and memory leaks</li>
796 <li>Hover tooltip and mouseover of position on structure not
797 sent from Jmol in applet</li>
798 <li>Certain sequences of javascript method calls to applet API
799 fatally hang browser</li>
800 </ul> <em>General</em>
802 <li>View follows structure mouseover scrolls beyond position
803 with wrapped view and hidden regions</li>
804 <li>Find sequence position moves to wrong residue with/without
806 <li>Sequence length given in alignment properties window is
808 <li>InvalidNumberFormat exceptions thrown when trying to
809 import PDB like structure files</li>
810 <li>Positional search results are only highlighted between
811 user-supplied sequence start/end bounds</li>
812 <li>End attribute of sequence is not validated</li>
813 <li>Find dialog only finds first sequence containing a given
814 sequence position</li>
815 <li>Sequence numbering not preserved in MSF alignment output</li>
816 <li>Jalview PDB file reader does not extract sequence from
817 nucleotide chains correctly</li>
818 <li>Structure colours not updated when tree partition changed
820 <li>Sequence associated secondary structure not correctly
821 parsed in interleaved stockholm</li>
822 <li>Colour by annotation dialog does not restore current state
824 <li>Hiding (nearly) all sequences doesn't work properly</li>
825 <li>Sequences containing lowercase letters are not properly
826 associated with their pdb files</li>
827 </ul> <em>Documentation and Development</em>
829 <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
836 <strong><a name="Jalview2.6.1">2.6.1</a>
837 </strong><br> <em>15/11/2010</em>
839 <td><em>Application</em>
841 <li>New warning dialog when the Jalview Desktop cannot contact
843 <li>JABA service parameters for a preset are shown in service
845 <li>JABA Service menu entries reworded</li>
849 <li>Modeller PIR IO broken - cannot correctly import a pir
850 file emitted by Jalview</li>
851 <li>Existing feature settings transferred to new alignment
852 view created from cut'n'paste</li>
853 <li>Improved test for mixed amino/nucleotide chains when
854 parsing PDB files</li>
855 <li>Consensus and conservation annotation rows occasionally
856 become blank for all new windows</li>
857 <li>Exception raised when right clicking above sequences in
858 wrapped view mode</li>
859 </ul> <em>Application</em>
861 <li>multiple multiply aligned structure views cause cpu usage
862 to hit 100% and computer to hang</li>
863 <li>Web Service parameter layout breaks for long user
865 <li>Jaba service discovery hangs desktop if Jaba server is
871 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
872 <em>26/9/2010</em></div>
874 <td><em>Application</em>
876 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
877 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
878 <li>Web Services preference tab</li>
879 <li>Analysis parameters dialog box and user defined preferences</li>
880 <li>Improved speed and layout of Envision2 service menu</li>
881 <li>Superpose structures using associated sequence alignment</li>
882 <li>Export coordinates and projection as CSV from PCA viewer</li>
886 <li>enable javascript: execution by the applet via the link out
891 <li>Updated the Jmol Jalview interface to work with Jmol series
893 <li>The Jalview Desktop and JalviewLite applet now require Java
895 <li>Allow Jalview feature colour specification for GFF sequence
896 annotation files</li>
897 <li>New 'colour by label' keword in Jalview feature file type
898 colour specification</li>
899 <li>New Jalview Desktop Groovy API method that allows a script
900 to check if it being run in an interactive session or in a batch
901 operation from the Jalview command line</li>
906 <li>clustalx colourscheme colours Ds preferentially when both
907 D+E are present in over 50% of the column</li>
912 <li>typo in AlignmentFrame->View->Hide->all but
913 selected Regions menu item</li>
914 <li>sequence fetcher replaces ',' for ';' when the ',' is part
915 of a valid accession ID</li>
916 <li>fatal OOM if object retrieved by sequence fetcher runs out
918 <li>unhandled Out of Memory Error when viewing pca analysis
920 <li>InstallAnywhere builds fail to launch on OS X java 10.5
921 update 4 (due to apple Java 1.6 update)</li>
922 <li>Installanywhere Jalview silently fails to launch</li>
926 <li>Jalview.getFeatureGroups() raises an
927 ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
933 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
934 <em>14/6/2010</em></div>
939 <li>Alignment prettyprinter doesn't cope with long sequence IDs
941 <li>clustalx colourscheme colours Ds preferentially when both
942 D+E are present in over 50% of the column</li>
943 <li>nucleic acid structures retrieved from PDB do not import
945 <li>More columns get selected than were clicked on when a number
946 of columns are hidden</li>
947 <li>annotation label popup menu not providing correct
948 add/hide/show options when rows are hidden or none are present</li>
949 <li>Stockholm format shown in list of readable formats, and
950 parser copes better with alignments from RFAM.</li>
951 <li>CSV output of consensus only includes the percentage of all
952 symbols if sequence logo display is enabled</li>
957 <li>annotation panel disappears when annotation is
962 <li>Alignment view not redrawn properly when new alignment
963 opened where annotation panel is visible but no annotations are
964 present on alignment</li>
965 <li>pasted region containing hidden columns is incorrectly
966 displayed in new alignment window</li>
967 <li>Jalview slow to complete operations when stdout is flooded
968 (fix is to close the Jalview console)</li>
969 <li>typo in AlignmentFrame->View->Hide->all but
970 selected Rregions menu item.</li>
971 <li>inconsistent group submenu and Format submenu entry 'Un' or
973 <li>Sequence feature settings are being shared by multiple
974 distinct alignments</li>
975 <li>group annotation not recreated when tree partition is
977 <li>double click on group annotation to select sequences does
978 not propagate to associated trees</li>
979 <li>Mac OSX specific issues:
981 <li>exception raised when mouse clicked on desktop window
983 <li>Desktop menu placed on menu bar and application name set
985 <li>sequence feature settings not wide enough for the save
986 feature colourscheme button</li>
995 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
996 <em>30/4/2010</em></div>
998 <td><em>New Capabilities</em>
1000 <li>URL links generated from description line for
1001 regular-expression based URL links (applet and application)
1002 <li>Non-positional feature URL links are shown in link menu</li>
1003 <li>Linked viewing of nucleic acid sequences and structures</li>
1004 <li>Automatic Scrolling option in View menu to display the
1005 currently highlighted region of an alignment.</li>
1006 <li>Order an alignment by sequence length, or using the average
1007 score or total feature count for each sequence.</li>
1008 <li>Shading features by score or associated description</li>
1009 <li>Subdivide alignment and groups based on identity of selected
1010 subsequence (Make Groups from Selection).</li>
1011 <li>New hide/show options including Shift+Control+H to hide
1012 everything but the currently selected region.</li>
1013 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1015 <em>Application</em>
1017 <li>Fetch DB References capabilities and UI expanded to support
1018 retrieval from DAS sequence sources</li>
1019 <li>Local DAS Sequence sources can be added via the command line
1020 or via the Add local source dialog box.</li>
1021 <li>DAS Dbref and DbxRef feature types are parsed as database
1022 references and protein_name is parsed as description line (BioSapiens
1024 <li>Enable or disable non-positional feature and database
1025 references in sequence ID tooltip from View menu in application.</li>
1026 <!-- <li>New hidden columns and rows and representatives capabilities
1027 in annotations file (in progress - not yet fully implemented)</li> -->
1028 <li>Group-associated consensus, sequence logos and conservation
1030 <li>Symbol distributions for each column can be exported and
1031 visualized as sequence logos</li>
1032 <li>Optionally scale multi-character column labels to fit within
1033 each column of annotation row<!-- todo for applet --></li>
1034 <li>Optional automatic sort of associated alignment view when a
1035 new tree is opened.</li>
1036 <li>Jalview Java Console</li>
1037 <li>Better placement of desktop window when moving between
1038 different screens.</li>
1039 <li>New preference items for sequence ID tooltip and consensus
1041 <li>Client to submit sequences and IDs to <a
1042 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
1043 <li><em>Vamsas Capabilities</em>
1045 <li>Improved VAMSAS synchronization (Jalview archive used to
1046 preserve views, structures, and tree display settings)</li>
1047 <li>Import of vamsas documents from disk or URL via command
1049 <li>Sharing of selected regions between views and with other
1050 VAMSAS applications (Experimental feature!)</li>
1051 <li>Updated API to VAMSAS version 0.2</li>
1057 <li>Middle button resizes annotation row height</li>
1060 <li>sortByTree (true/false) - automatically sort the associated
1061 alignment view by the tree when a new tree is opened.</li>
1062 <li>showTreeBootstraps (true/false) - show or hide branch
1063 bootstraps (default is to show them if available)</li>
1064 <li>showTreeDistances (true/false) - show or hide branch
1065 lengths (default is to show them if available)</li>
1066 <li>showUnlinkedTreeNodes (true/false) - indicate if
1067 unassociated nodes should be highlighted in the tree view</li>
1068 <li>heightScale and widthScale (1.0 or more) - increase the
1069 height or width of a cell in the alignment grid relative to the
1070 current font size.</li>
1073 <li>Non-positional features displayed in sequence ID tooltip</li>
1077 <li>Features format: graduated colour definitions and
1078 specification of feature scores</li>
1079 <li>Alignment Annotations format: new keywords for group
1080 associated annotation (GROUP_REF) and annotation row display
1081 properties (ROW_PROPERTIES)</li>
1082 <li>XML formats extended to support graduated feature
1083 colourschemes, group associated annotation, and profile visualization
1088 <li>Source field in GFF files parsed as feature source rather
1089 than description</li>
1090 <li>Non-positional features are now included in sequence feature
1091 and gff files (controlled via non-positional feature visibility in
1093 <li>URL links generated for all feature links (bugfix)</li>
1094 <li>Added URL embedding instructions to features file
1096 <li>Codons containing ambiguous nucleotides translated as 'X' in
1097 peptide product</li>
1098 <li>Match case switch in find dialog box works for both sequence
1099 ID and sequence string and query strings do not have to be in upper
1100 case to match case-insensitively.</li>
1101 <li>AMSA files only contain first column of multi-character
1102 column annotation labels</li>
1103 <li>Jalview Annotation File generation/parsing consistent with
1104 documentation (e.g. Stockholm annotation can be exported and
1106 <li>PDB files without embedded PDB IDs given a friendly name</li>
1107 <li>Find incrementally searches ID string matches as well as
1108 subsequence matches, and correctly reports total number of both.</li>
1111 <li>Better handling of exceptions during sequence retrieval</li>
1112 <li>Dasobert generated non-positional feature URL link text
1113 excludes the start_end suffix</li>
1114 <li>DAS feature and source retrieval buttons disabled when
1115 fetch or registry operations in progress.</li>
1116 <li>PDB files retrieved from URLs are cached properly</li>
1117 <li>Sequence description lines properly shared via VAMSAS</li>
1118 <li>Sequence fetcher fetches multiple records for all data
1120 <li>Ensured that command line das feature retrieval completes
1121 before alignment figures are generated.</li>
1122 <li>Reduced time taken when opening file browser for first
1124 <li>isAligned check prior to calculating tree, PCA or
1125 submitting an MSA to JNet now excludes hidden sequences.</li>
1126 <li>User defined group colours properly recovered from Jalview
1136 <div align="center"><strong>2.4.0.b2</strong><br>
1141 <li>Experimental support for google analytics usage tracking.</li>
1142 <li>Jalview privacy settings (user preferences and docs).</li>
1147 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
1148 <li>Exception when feature created from selection beyond length
1150 <li>Allow synthetic PDB files to be imported gracefully</li>
1151 <li>Sequence associated annotation rows associate with all
1152 sequences with a given id</li>
1153 <li>Find function matches case-insensitively for sequence ID
1154 string searches</li>
1155 <li>Non-standard characters do not cause pairwise alignment to
1156 fail with exception</li>
1158 <em>Application Issues</em>
1160 <li>Sequences are now validated against EMBL database</li>
1161 <li>Sequence fetcher fetches multiple records for all data
1164 <em>InstallAnywhere Issues</em>
1166 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
1167 installAnywhere mechanism)</li>
1168 <li>Command line launching of JARs from InstallAnywhere version
1169 (java class versioning error fixed)</li>
1176 <div align="center"><strong>2.4</strong><br>
1179 <td><em>User Interface</em>
1181 <li>Linked highlighting of codon and amino acid from translation
1182 and protein products</li>
1183 <li>Linked highlighting of structure associated with residue
1184 mapping to codon position</li>
1185 <li>Sequence Fetcher provides example accession numbers and
1187 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
1188 <li>Extract score function to parse whitespace separated numeric
1189 data in description line</li>
1190 <li>Column labels in alignment annotation can be centred.</li>
1191 <li>Tooltip for sequence associated annotation give name of
1194 <em>Web Services and URL fetching</em>
1196 <li>JPred3 web service</li>
1197 <li>Prototype sequence search client (no public services
1199 <li>Fetch either seed alignment or full alignment from PFAM</li>
1200 <li>URL Links created for matching database cross references as
1201 well as sequence ID</li>
1202 <li>URL Links can be created using regular-expressions</li>
1204 <em>Sequence Database Connectivity</em>
1206 <li>Retrieval of cross-referenced sequences from other databases
1208 <li>Generalised database reference retrieval and validation to
1209 all fetchable databases</li>
1210 <li>Fetch sequences from DAS sources supporting the sequence
1213 <em>Import and Export</em>
1214 <li>export annotation rows as CSV for spreadsheet import</li>
1215 <li>Jalview projects record alignment dataset associations, EMBL
1216 products, and cDNA sequence mappings</li>
1217 <li>Sequence Group colour can be specified in Annotation File</li>
1218 <li>Ad-hoc colouring of group in Annotation File using RGB
1219 triplet as name of colourscheme</li>
1221 <em>VAMSAS Client capabilities (Experimental)</em>
1223 <li>treenode binding for VAMSAS tree exchange</li>
1224 <li>local editing and update of sequences in VAMSAS alignments
1226 <li>Create new or select existing session to join</li>
1227 <li>load and save of vamsas documents</li>
1229 <em>Application command line</em>
1231 <li>-tree parameter to open trees (introduced for passing from
1233 <li>-fetchfrom command line argument to specify nicknames of DAS
1234 servers to query for alignment features</li>
1235 <li>-dasserver command line argument to add new servers that are
1236 also automatically queried for features</li>
1237 <li>-groovy command line argument executes a given groovy script
1238 after all input data has been loaded and parsed</li>
1240 <em>Applet-Application data exchange</em>
1242 <li>Trees passed as applet parameters can be passed to
1243 application (when using "View in full application")</li>
1245 <em>Applet Parameters</em>
1247 <li>feature group display control parameter</li>
1248 <li>debug parameter</li>
1249 <li>showbutton parameter</li>
1251 <em>Applet API methods</em>
1253 <li>newView public method</li>
1254 <li>Window (current view) specific get/set public methods</li>
1255 <li>Feature display control methods</li>
1256 <li>get list of currently selected sequences</li>
1258 <em>New Jalview distribution features</em>
1260 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1261 <li>RELEASE file gives build properties for the latest Jalview
1263 <li>Java 1.1 Applet build made easier and donotobfuscate
1264 property controls execution of obfuscator</li>
1265 <li>Build target for generating source distribution</li>
1266 <li>Debug flag for javacc</li>
1267 <li>.jalview_properties file is documented (slightly) in
1268 jalview.bin.Cache</li>
1269 <li>Continuous Build Integration for stable and development
1270 version of Application, Applet and source distribution</li>
1276 <li>selected region output includes visible annotations (for
1277 certain formats)</li>
1278 <li>edit label/displaychar contains existing label/char for
1280 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1281 <li>shorter peptide product names from EMBL records</li>
1282 <li>Newick string generator makes compact representations</li>
1283 <li>bootstrap values parsed correctly for tree files with
1285 <li>pathological filechooser bug avoided by not allowing
1286 filenames containing a ':'</li>
1287 <li>Fixed exception when parsing GFF files containing global
1288 sequence features</li>
1289 <li>Alignment datasets are finalized only when number of
1290 references from alignment sequences goes to zero</li>
1291 <li>Close of tree branch colour box without colour selection
1292 causes cascading exceptions</li>
1293 <li>occasional negative imgwidth exceptions</li>
1294 <li>better reporting of non-fatal warnings to user when file
1296 <li>Save works when Jalview project is default format</li>
1297 <li>Save as dialog opened if current alignment format is not a
1298 valid output format</li>
1299 <li>Uniprot canonical names introduced for both das and vamsas</li>
1300 <li>Histidine should be midblue (not pink!) in Zappo</li>
1301 <li>error messages passed up and output when data read fails</li>
1302 <li>edit undo recovers previous dataset sequence when sequence
1304 <li>allow PDB files without pdb ID HEADER lines (like those
1305 generated by MODELLER) to be read in properly</li>
1306 <li>allow reading of JPred concise files as a normal filetype</li>
1307 <li>Stockholm annotation parsing and alignment properties import
1308 fixed for PFAM records</li>
1309 <li>Structure view windows have correct name in Desktop window
1311 <li>annotation consisting of sequence associated scores can be
1312 read and written correctly to annotation file</li>
1313 <li>Aligned cDNA translation to aligned peptide works correctly</li>
1314 <li>Fixed display of hidden sequence markers and non-italic font
1315 for representatives in Applet</li>
1316 <li>Applet Menus are always embedded in applet window on Macs.</li>
1317 <li>Newly shown features appear at top of stack (in Applet)</li>
1318 <li>Annotations added via parameter not drawn properly due to
1319 null pointer exceptions</li>
1320 <li>Secondary structure lines are drawn starting from first
1321 column of alignment</li>
1322 <li>Uniprot XML import updated for new schema release in July
1324 <li>Sequence feature to sequence ID match for Features file is
1325 case-insensitive</li>
1326 <li>Sequence features read from Features file appended to all
1327 sequences with matching IDs</li>
1328 <li>PDB structure coloured correctly for associated views
1329 containing a sub-sequence</li>
1330 <li>PDB files can be retrieved by applet from Jar files</li>
1331 <li>feature and annotation file applet parameters referring to
1332 different directories are retrieved correctly</li>
1333 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1334 <li>Fixed application hang whilst waiting for splash-screen
1335 version check to complete</li>
1336 <li>Applet properly URLencodes input parameter values when
1337 passing them to the launchApp service</li>
1338 <li>display name and local features preserved in results
1339 retrieved from web service</li>
1340 <li>Visual delay indication for sequence retrieval and sequence
1341 fetcher initialisation</li>
1342 <li>updated Application to use DAS 1.53e version of dasobert DAS
1344 <li>Re-instated Full AMSA support and .amsa file association</li>
1345 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1352 <div align="center"><strong>2.3</strong><br>
1357 <li>Jmol 11.0.2 integration</li>
1358 <li>PDB views stored in Jalview XML files</li>
1359 <li>Slide sequences</li>
1360 <li>Edit sequence in place</li>
1361 <li>EMBL CDS features</li>
1362 <li>DAS Feature mapping</li>
1363 <li>Feature ordering</li>
1364 <li>Alignment Properties</li>
1365 <li>Annotation Scores</li>
1366 <li>Sort by scores</li>
1367 <li>Feature/annotation editing in applet</li>
1372 <li>Headless state operation in 2.2.1</li>
1373 <li>Incorrect and unstable DNA pairwise alignment</li>
1374 <li>Cut and paste of sequences with annotation</li>
1375 <li>Feature group display state in XML</li>
1376 <li>Feature ordering in XML</li>
1377 <li>blc file iteration selection using filename # suffix</li>
1378 <li>Stockholm alignment properties</li>
1379 <li>Stockhom alignment secondary structure annotation</li>
1380 <li>2.2.1 applet had no feature transparency</li>
1381 <li>Number pad keys can be used in cursor mode</li>
1382 <li>Structure Viewer mirror image resolved</li>
1389 <div align="center"><strong>2.2.1</strong><br>
1394 <li>Non standard characters can be read and displayed
1395 <li>Annotations/Features can be imported/exported to the applet
1397 <li>Applet allows editing of sequence/annotation/group name
1399 <li>Preference setting to display sequence name in italics
1400 <li>Annotation file format extended to allow Sequence_groups to
1402 <li>Default opening of alignment overview panel can be specified
1404 <li>PDB residue numbering annotation added to associated
1410 <li>Applet crash under certain Linux OS with Java 1.6 installed
1411 <li>Annotation file export / import bugs fixed
1412 <li>PNG / EPS image output bugs fixed
1418 <div align="center"><strong>2.2</strong><br>
1423 <li>Multiple views on alignment
1424 <li>Sequence feature editing
1425 <li>"Reload" alignment
1426 <li>"Save" to current filename
1427 <li>Background dependent text colour
1428 <li>Right align sequence ids
1429 <li>User-defined lower case residue colours
1432 <li>Menu item accelerator keys
1433 <li>Control-V pastes to current alignment
1434 <li>Cancel button for DAS Feature Fetching
1435 <li>PCA and PDB Viewers zoom via mouse roller
1436 <li>User-defined sub-tree colours and sub-tree selection
1437 <li>'New Window' button on the 'Output to Text box'
1442 <li>New memory efficient Undo/Redo System
1443 <li>Optimised symbol lookups and conservation/consensus
1445 <li>Region Conservation/Consensus recalculated after edits
1446 <li>Fixed Remove Empty Columns Bug (empty columns at end of
1448 <li>Slowed DAS Feature Fetching for increased robustness.
1449 <li>Made angle brackets in ASCII feature descriptions display
1451 <li>Re-instated Zoom function for PCA
1452 <li>Sequence descriptions conserved in web service analysis
1454 <li>Uniprot ID discoverer uses any word separated by ∣
1455 <li>WsDbFetch query/result association resolved
1456 <li>Tree leaf to sequence mapping improved
1457 <li>Smooth fonts switch moved to FontChooser dialog box.
1463 <div align="center"><strong>2.1.1</strong><br>
1468 <li>Copy consensus sequence to clipboard</li>
1473 <li>Image output - rightmost residues are rendered if sequence
1474 id panel has been resized</li>
1475 <li>Image output - all offscreen group boundaries are rendered</li>
1476 <li>Annotation files with sequence references - all elements in
1477 file are relative to sequence position</li>
1478 <li>Mac Applet users can use Alt key for group editing</li>
1484 <div align="center"><strong>2.1</strong><br>
1489 <li>MAFFT Multiple Alignment in default Web Service list</li>
1490 <li>DAS Feature fetching</li>
1491 <li>Hide sequences and columns</li>
1492 <li>Export Annotations and Features</li>
1493 <li>GFF file reading / writing</li>
1494 <li>Associate structures with sequences from local PDB files</li>
1495 <li>Add sequences to exisiting alignment</li>
1496 <li>Recently opened files / URL lists</li>
1497 <li>Applet can launch the full application</li>
1498 <li>Applet has transparency for features (Java 1.2 required)</li>
1499 <li>Applet has user defined colours parameter</li>
1500 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
1505 <li>Redundancy Panel reinstalled in the Applet</li>
1506 <li>Monospaced font - EPS / rescaling bug fixed</li>
1507 <li>Annotation files with sequence references bug fixed</li>
1513 <div align="center"><strong>2.08.1</strong><br>
1518 <li>Change case of selected region from Popup menu</li>
1519 <li>Choose to match case when searching</li>
1520 <li>Middle mouse button and mouse movement can compress / expand
1521 the visible width and height of the alignment</li>
1526 <li>Annotation Panel displays complete JNet results</li>
1532 <div align="center"><strong>2.08b</strong><br>
1538 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1539 <li>Righthand label on wrapped alignments shows correct value</li>
1545 <div align="center"><strong>2.08</strong><br>
1550 <li>Editing can be locked to the selection area</li>
1551 <li>Keyboard editing</li>
1552 <li>Create sequence features from searches</li>
1553 <li>Precalculated annotations can be loaded onto alignments</li>
1554 <li>Features file allows grouping of features</li>
1555 <li>Annotation Colouring scheme added</li>
1556 <li>Smooth fonts off by default - Faster rendering</li>
1557 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1562 <li>Drag & Drop fixed on Linux</li>
1563 <li>Jalview Archive file faster to load/save, sequence
1564 descriptions saved.</li>
1570 <div align="center"><strong>2.07</strong><br>
1575 <li>PDB Structure Viewer enhanced</li>
1576 <li>Sequence Feature retrieval and display enhanced</li>
1577 <li>Choose to output sequence start-end after sequence name for
1579 <li>Sequence Fetcher WSDBFetch@EBI</li>
1580 <li>Applet can read feature files, PDB files and can be used for
1581 HTML form input</li>
1586 <li>HTML output writes groups and features</li>
1587 <li>Group editing is Control and mouse click</li>
1588 <li>File IO bugs</li>
1594 <div align="center"><strong>2.06</strong><br>
1599 <li>View annotations in wrapped mode</li>
1600 <li>More options for PCA viewer</li>
1605 <li>GUI bugs resolved</li>
1606 <li>Runs with -nodisplay from command line</li>
1612 <div align="center"><strong>2.05b</strong><br>
1617 <li>Choose EPS export as lineart or text</li>
1618 <li>Jar files are executable</li>
1619 <li>Can read in Uracil - maps to unknown residue</li>
1624 <li>Known OutOfMemory errors give warning message</li>
1625 <li>Overview window calculated more efficiently</li>
1626 <li>Several GUI bugs resolved</li>
1632 <div align="center"><strong>2.05</strong><br>
1637 <li>Edit and annotate in "Wrapped" view</li>
1642 <li>Several GUI bugs resolved</li>
1648 <div align="center"><strong>2.04</strong><br>
1653 <li>Hold down mouse wheel & scroll to change font size</li>
1658 <li>Improved JPred client reliability</li>
1659 <li>Improved loading of Jalview files</li>
1665 <div align="center"><strong>2.03</strong><br>
1670 <li>Set Proxy server name and port in preferences</li>
1671 <li>Multiple URL links from sequence ids</li>
1672 <li>User Defined Colours can have a scheme name and added to
1674 <li>Choose to ignore gaps in consensus calculation</li>
1675 <li>Unix users can set default web browser</li>
1676 <li>Runs without GUI for batch processing</li>
1677 <li>Dynamically generated Web Service Menus</li>
1682 <li>InstallAnywhere download for Sparc Solaris</li>
1688 <div align="center"><strong>2.02</strong><br>
1694 <li>Copy & Paste order of sequences maintains alignment
1701 <div align="center"><strong>2.01</strong><br>
1706 <li>Use delete key for deleting selection.</li>
1707 <li>Use Mouse wheel to scroll sequences.</li>
1708 <li>Help file updated to describe how to add alignment
1710 <li>Version and build date written to build properties file.</li>
1711 <li>InstallAnywhere installation will check for updates at
1712 launch of Jalview.</li>
1717 <li>Delete gaps bug fixed.</li>
1718 <li>FileChooser sorts columns.</li>
1719 <li>Can remove groups one by one.</li>
1720 <li>Filechooser icons installed.</li>
1721 <li>Finder ignores return character when searching. Return key
1722 will initiate a search.<br>
1729 <div align="center"><strong>2.0</strong><br>
1734 <li>New codebase</li>