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>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li>
82 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and Ensembl services
85 <!-- JAL-2759 -->Improved performance for large alignments and lots of hidden columns
90 <td><div align="left">
93 <!-- JAL-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
96 <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
98 <li><!-- JAL-2930 -->Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.</li>
99 <li><!-- JAL-2924 -->Tooltip shouldn't be displayed for empty columns in annotation row</li>
100 <li><!-- JAL-2913 -->Preferences panel's ID Width control is honored in interactive and batch mode</li>
101 </ul><em>Applet</em><ul>
102 <li><!-- JAL-2926 -->Copy consensus sequence option in applet should copy the group consensus when popup is opened on it</li>
109 <td width="60" nowrap>
111 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
114 <td><div align="left">
115 <ul><li>Updated Certum Codesigning Certificate
116 (Valid till 30th November 2018)</li></ul></div></td>
117 <td><div align="left">
120 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
121 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
122 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
123 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
124 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
125 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
126 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
132 <td width="60" nowrap>
134 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
137 <td><div align="left">
141 <!-- JAL-2446 -->Faster and more efficient management and
142 rendering of sequence features
145 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
146 429 rate limit request hander
149 <!-- JAL-2773 -->Structure views don't get updated unless
150 their colours have changed
153 <!-- JAL-2495 -->All linked sequences are highlighted for
154 a structure mousover (Jmol) or selection (Chimera)
157 <!-- JAL-2790 -->'Cancel' button in progress bar for
158 JABAWS AACon, RNAAliFold and Disorder prediction jobs
161 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
162 view from Ensembl locus cross-references
165 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
169 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
170 feature can be disabled
173 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
174 PDB easier retrieval of sequences for lists of IDs
177 <!-- JAL-2758 -->Short names for sequences retrieved from
183 <li>Groovy interpreter updated to 2.4.12</li>
184 <li>Example groovy script for generating a matrix of
185 percent identity scores for current alignment.</li>
187 <em>Testing and Deployment</em>
190 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
194 <td><div align="left">
198 <!-- JAL-2643 -->Pressing tab after updating the colour
199 threshold text field doesn't trigger an update to the
203 <!-- JAL-2682 -->Race condition when parsing sequence ID
207 <!-- JAL-2608 -->Overview windows are also closed when
208 alignment window is closed
211 <!-- JAL-2548 -->Export of features doesn't always respect
215 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
216 takes a long time in Cursor mode
222 <!-- JAL-2777 -->Structures with whitespace chainCode
223 cannot be viewed in Chimera
226 <!-- JAL-2728 -->Protein annotation panel too high in
230 <!-- JAL-2757 -->Can't edit the query after the server
231 error warning icon is shown in Uniprot and PDB Free Text
235 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
238 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
241 <!-- JAL-2739 -->Hidden column marker in last column not
242 rendered when switching back from Wrapped to normal view
245 <!-- JAL-2768 -->Annotation display corrupted when
246 scrolling right in unwapped alignment view
249 <!-- JAL-2542 -->Existing features on subsequence
250 incorrectly relocated when full sequence retrieved from
254 <!-- JAL-2733 -->Last reported memory still shown when
255 Desktop->Show Memory is unticked (OSX only)
258 <!-- JAL-2658 -->Amend Features dialog doesn't allow
259 features of same type and group to be selected for
263 <!-- JAL-2524 -->Jalview becomes sluggish in wide
264 alignments when hidden columns are present
267 <!-- JAL-2392 -->Jalview freezes when loading and
268 displaying several structures
271 <!-- JAL-2732 -->Black outlines left after resizing or
275 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
276 within the Jalview desktop on OSX
279 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
280 when in wrapped alignment mode
283 <!-- JAL-2636 -->Scale mark not shown when close to right
284 hand end of alignment
287 <!-- JAL-2684 -->Pairwise alignment of selected regions of
288 each selected sequence do not have correct start/end
292 <!-- JAL-2793 -->Alignment ruler height set incorrectly
293 after canceling the Alignment Window's Font dialog
296 <!-- JAL-2036 -->Show cross-references not enabled after
297 restoring project until a new view is created
300 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
301 URL links appears when only default EMBL-EBI link is
302 configured (since 2.10.2b2)
305 <!-- JAL-2775 -->Overview redraws whole window when box
309 <!-- JAL-2225 -->Structure viewer doesn't map all chains
310 in a multi-chain structure when viewing alignment
311 involving more than one chain (since 2.10)
314 <!-- JAL-2811 -->Double residue highlights in cursor mode
315 if new selection moves alignment window
318 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
319 arrow key in cursor mode to pass hidden column marker
322 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
323 that produces correctly annotated transcripts and products
326 <!-- JAL-2776 -->Toggling a feature group after first time
327 doesn't update associated structure view
330 <em>Applet</em><br />
333 <!-- JAL-2687 -->Concurrent modification exception when
334 closing alignment panel
337 <em>BioJSON</em><br />
340 <!-- JAL-2546 -->BioJSON export does not preserve
341 non-positional features
344 <em>New Known Issues</em>
347 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
348 sequence features correctly (for many previous versions of
352 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
353 using cursor in wrapped panel other than top
356 <!-- JAL-2791 -->Select columns containing feature ignores
357 graduated colour threshold
360 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
361 always preserve numbering and sequence features
364 <em>Known Java 9 Issues</em>
367 <!-- JAL-2902 -->Groovy Console very slow to open and is
368 not responsive when entering characters (Webstart, Java
375 <td width="60" nowrap>
377 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
378 <em>2/10/2017</em></strong>
381 <td><div align="left">
382 <em>New features in Jalview Desktop</em>
385 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
387 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
391 <td><div align="left">
395 <td width="60" nowrap>
397 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
398 <em>7/9/2017</em></strong>
401 <td><div align="left">
405 <!-- JAL-2588 -->Show gaps in overview window by colouring
406 in grey (sequences used to be coloured grey, and gaps were
410 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
414 <!-- JAL-2587 -->Overview updates immediately on increase
415 in size and progress bar shown as higher resolution
416 overview is recalculated
421 <td><div align="left">
425 <!-- JAL-2664 -->Overview window redraws every hidden
426 column region row by row
429 <!-- JAL-2681 -->duplicate protein sequences shown after
430 retrieving Ensembl crossrefs for sequences from Uniprot
433 <!-- JAL-2603 -->Overview window throws NPE if show boxes
434 format setting is unticked
437 <!-- JAL-2610 -->Groups are coloured wrongly in overview
438 if group has show boxes format setting unticked
441 <!-- JAL-2672,JAL-2665 -->Redraw problems when
442 autoscrolling whilst dragging current selection group to
443 include sequences and columns not currently displayed
446 <!-- JAL-2691 -->Not all chains are mapped when multimeric
447 assemblies are imported via CIF file
450 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
451 displayed when threshold or conservation colouring is also
455 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
459 <!-- JAL-2673 -->Jalview continues to scroll after
460 dragging a selected region off the visible region of the
464 <!-- JAL-2724 -->Cannot apply annotation based
465 colourscheme to all groups in a view
468 <!-- JAL-2511 -->IDs don't line up with sequences
469 initially after font size change using the Font chooser or
476 <td width="60" nowrap>
478 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
481 <td><div align="left">
482 <em>Calculations</em>
486 <!-- JAL-1933 -->Occupancy annotation row shows number of
487 ungapped positions in each column of the alignment.
490 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
491 a calculation dialog box
494 <!-- JAL-2379 -->Revised implementation of PCA for speed
495 and memory efficiency (~30x faster)
498 <!-- JAL-2403 -->Revised implementation of sequence
499 similarity scores as used by Tree, PCA, Shading Consensus
500 and other calculations
503 <!-- JAL-2416 -->Score matrices are stored as resource
504 files within the Jalview codebase
507 <!-- JAL-2500 -->Trees computed on Sequence Feature
508 Similarity may have different topology due to increased
515 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
516 model for alignments and groups
519 <!-- JAL-384 -->Custom shading schemes created via groovy
526 <!-- JAL-2526 -->Efficiency improvements for interacting
527 with alignment and overview windows
530 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
534 <!-- JAL-2388 -->Hidden columns and sequences can be
538 <!-- JAL-2611 -->Click-drag in visible area allows fine
539 adjustment of visible position
543 <em>Data import/export</em>
546 <!-- JAL-2535 -->Posterior probability annotation from
547 Stockholm files imported as sequence associated annotation
550 <!-- JAL-2507 -->More robust per-sequence positional
551 annotation input/output via stockholm flatfile
554 <!-- JAL-2533 -->Sequence names don't include file
555 extension when importing structure files without embedded
556 names or PDB accessions
559 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
560 format sequence substitution matrices
563 <em>User Interface</em>
566 <!-- JAL-2447 --> Experimental Features Checkbox in
567 Desktop's Tools menu to hide or show untested features in
571 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
572 via Overview or sequence motif search operations
575 <!-- JAL-2547 -->Amend sequence features dialog box can be
576 opened by double clicking gaps within sequence feature
580 <!-- JAL-1476 -->Status bar message shown when not enough
581 aligned positions were available to create a 3D structure
585 <em>3D Structure</em>
588 <!-- JAL-2430 -->Hidden regions in alignment views are not
589 coloured in linked structure views
592 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
593 file-based command exchange
596 <!-- JAL-2375 -->Structure chooser automatically shows
597 Cached Structures rather than querying the PDBe if
598 structures are already available for sequences
601 <!-- JAL-2520 -->Structures imported via URL are cached in
602 the Jalview project rather than downloaded again when the
606 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
607 to transfer Chimera's structure attributes as Jalview
608 features, and vice-versa (<strong>Experimental
612 <em>Web Services</em>
615 <!-- JAL-2549 -->Updated JABAWS client to v2.2
618 <!-- JAL-2335 -->Filter non-standard amino acids and
619 nucleotides when submitting to AACon and other MSA
623 <!-- JAL-2316, -->URLs for viewing database
624 cross-references provided by identifiers.org and the
632 <!-- JAL-2344 -->FileFormatI interface for describing and
633 identifying file formats (instead of String constants)
636 <!-- JAL-2228 -->FeatureCounter script refactored for
637 efficiency when counting all displayed features (not
638 backwards compatible with 2.10.1)
641 <em>Example files</em>
644 <!-- JAL-2631 -->Graduated feature colour style example
645 included in the example feature file
648 <em>Documentation</em>
651 <!-- JAL-2339 -->Release notes reformatted for readability
652 with the built-in Java help viewer
655 <!-- JAL-1644 -->Find documentation updated with 'search
656 sequence description' option
662 <!-- JAL-2485, -->External service integration tests for
663 Uniprot REST Free Text Search Client
666 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
669 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
674 <td><div align="left">
675 <em>Calculations</em>
678 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
679 matrix - C->R should be '-3'<br />Old matrix restored
680 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
682 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
683 Jalview's treatment of gaps in PCA and substitution matrix
684 based Tree calculations.<br /> <br />In earlier versions
685 of Jalview, gaps matching gaps were penalised, and gaps
686 matching non-gaps penalised even more. In the PCA
687 calculation, gaps were actually treated as non-gaps - so
688 different costs were applied, which meant Jalview's PCAs
689 were different to those produced by SeqSpace.<br />Jalview
690 now treats gaps in the same way as SeqSpace (ie it scores
691 them as 0). <br /> <br />Enter the following in the
692 Groovy console to restore pre-2.10.2 behaviour:<br />
693 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
694 // for 2.10.1 mode <br />
695 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
696 // to restore 2.10.2 mode <br /> <br /> <em>Note:
697 these settings will affect all subsequent tree and PCA
698 calculations (not recommended)</em></li>
700 <!-- JAL-2424 -->Fixed off-by-one bug that affected
701 scaling of branch lengths for trees computed using
702 Sequence Feature Similarity.
705 <!-- JAL-2377 -->PCA calculation could hang when
706 generating output report when working with highly
710 <!-- JAL-2544 --> Sort by features includes features to
711 right of selected region when gaps present on right-hand
715 <em>User Interface</em>
718 <!-- JAL-2346 -->Reopening Colour by annotation dialog
719 doesn't reselect a specific sequence's associated
720 annotation after it was used for colouring a view
723 <!-- JAL-2419 -->Current selection lost if popup menu
724 opened on a region of alignment without groups
727 <!-- JAL-2374 -->Popup menu not always shown for regions
728 of an alignment with overlapping groups
731 <!-- JAL-2310 -->Finder double counts if both a sequence's
732 name and description match
735 <!-- JAL-2370 -->Hiding column selection containing two
736 hidden regions results in incorrect hidden regions
739 <!-- JAL-2386 -->'Apply to all groups' setting when
740 changing colour does not apply Conservation slider value
744 <!-- JAL-2373 -->Percentage identity and conservation menu
745 items do not show a tick or allow shading to be disabled
748 <!-- JAL-2385 -->Conservation shading or PID threshold
749 lost when base colourscheme changed if slider not visible
752 <!-- JAL-2547 -->Sequence features shown in tooltip for
753 gaps before start of features
756 <!-- JAL-2623 -->Graduated feature colour threshold not
757 restored to UI when feature colour is edited
760 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
761 a time when scrolling vertically in wrapped mode.
764 <!-- JAL-2630 -->Structure and alignment overview update
765 as graduate feature colour settings are modified via the
769 <!-- JAL-2034 -->Overview window doesn't always update
770 when a group defined on the alignment is resized
773 <!-- JAL-2605 -->Mouseovers on left/right scale region in
774 wrapped view result in positional status updates
778 <!-- JAL-2563 -->Status bar doesn't show position for
779 ambiguous amino acid and nucleotide symbols
782 <!-- JAL-2602 -->Copy consensus sequence failed if
783 alignment included gapped columns
786 <!-- JAL-2473 -->Minimum size set for Jalview windows so
787 widgets don't permanently disappear
790 <!-- JAL-2503 -->Cannot select or filter quantitative
791 annotation that are shown only as column labels (e.g.
792 T-Coffee column reliability scores)
795 <!-- JAL-2594 -->Exception thrown if trying to create a
796 sequence feature on gaps only
799 <!-- JAL-2504 -->Features created with 'New feature'
800 button from a Find inherit previously defined feature type
801 rather than the Find query string
804 <!-- JAL-2423 -->incorrect title in output window when
805 exporting tree calculated in Jalview
808 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
809 and then revealing them reorders sequences on the
813 <!-- JAL-964 -->Group panel in sequence feature settings
814 doesn't update to reflect available set of groups after
815 interactively adding or modifying features
818 <!-- JAL-2225 -->Sequence Database chooser unusable on
822 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
823 only excluded gaps in current sequence and ignored
830 <!-- JAL-2421 -->Overview window visible region moves
831 erratically when hidden rows or columns are present
834 <!-- JAL-2362 -->Per-residue colourschemes applied via the
835 Structure Viewer's colour menu don't correspond to
839 <!-- JAL-2405 -->Protein specific colours only offered in
840 colour and group colour menu for protein alignments
843 <!-- JAL-2385 -->Colour threshold slider doesn't update to
844 reflect currently selected view or group's shading
848 <!-- JAL-2624 -->Feature colour thresholds not respected
849 when rendered on overview and structures when opacity at
853 <!-- JAL-2589 -->User defined gap colour not shown in
854 overview when features overlaid on alignment
857 <em>Data import/export</em>
860 <!-- JAL-2576 -->Very large alignments take a long time to
864 <!-- JAL-2507 -->Per-sequence RNA secondary structures
865 added after a sequence was imported are not written to
869 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
870 when importing RNA secondary structure via Stockholm
873 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
874 not shown in correct direction for simple pseudoknots
877 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
878 with lightGray or darkGray via features file (but can
882 <!-- JAL-2383 -->Above PID colour threshold not recovered
883 when alignment view imported from project
886 <!-- JAL-2520,JAL-2465 -->No mappings generated between
887 structure and sequences extracted from structure files
888 imported via URL and viewed in Jmol
891 <!-- JAL-2520 -->Structures loaded via URL are saved in
892 Jalview Projects rather than fetched via URL again when
893 the project is loaded and the structure viewed
896 <em>Web Services</em>
899 <!-- JAL-2519 -->EnsemblGenomes example failing after
900 release of Ensembl v.88
903 <!-- JAL-2366 -->Proxy server address and port always
904 appear enabled in Preferences->Connections
907 <!-- JAL-2461 -->DAS registry not found exceptions
908 removed from console output
911 <!-- JAL-2582 -->Cannot retrieve protein products from
912 Ensembl by Peptide ID
915 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
916 created from SIFTs, and spurious 'Couldn't open structure
917 in Chimera' errors raised after April 2017 update (problem
918 due to 'null' string rather than empty string used for
919 residues with no corresponding PDB mapping).
922 <em>Application UI</em>
925 <!-- JAL-2361 -->User Defined Colours not added to Colour
929 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
930 case' residues (button in colourscheme editor debugged and
931 new documentation and tooltips added)
934 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
935 doesn't restore group-specific text colour thresholds
938 <!-- JAL-2243 -->Feature settings panel does not update as
939 new features are added to alignment
942 <!-- JAL-2532 -->Cancel in feature settings reverts
943 changes to feature colours via the Amend features dialog
946 <!-- JAL-2506 -->Null pointer exception when attempting to
947 edit graduated feature colour via amend features dialog
951 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
952 selection menu changes colours of alignment views
955 <!-- JAL-2426 -->Spurious exceptions in console raised
956 from alignment calculation workers after alignment has
960 <!-- JAL-1608 -->Typo in selection popup menu - Create
961 groups now 'Create Group'
964 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
965 Create/Undefine group doesn't always work
968 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
969 shown again after pressing 'Cancel'
972 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
973 adjusts start position in wrap mode
976 <!-- JAL-2563 -->Status bar doesn't show positions for
977 ambiguous amino acids
980 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
981 CDS/Protein view after CDS sequences added for aligned
985 <!-- JAL-2592 -->User defined colourschemes called 'User
986 Defined' don't appear in Colours menu
992 <!-- JAL-2468 -->Switching between Nucleotide and Protein
993 score models doesn't always result in an updated PCA plot
996 <!-- JAL-2442 -->Features not rendered as transparent on
997 overview or linked structure view
1000 <!-- JAL-2372 -->Colour group by conservation doesn't
1004 <!-- JAL-2517 -->Hitting Cancel after applying
1005 user-defined colourscheme doesn't restore original
1012 <!-- JAL-2314 -->Unit test failure:
1013 jalview.ws.jabaws.RNAStructExportImport setup fails
1016 <!-- JAL-2307 -->Unit test failure:
1017 jalview.ws.sifts.SiftsClientTest due to compatibility
1018 problems with deep array comparison equality asserts in
1019 successive versions of TestNG
1022 <!-- JAL-2479 -->Relocated StructureChooserTest and
1023 ParameterUtilsTest Unit tests to Network suite
1026 <em>New Known Issues</em>
1029 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1030 phase after a sequence motif find operation
1033 <!-- JAL-2550 -->Importing annotation file with rows
1034 containing just upper and lower case letters are
1035 interpreted as WUSS RNA secondary structure symbols
1038 <!-- JAL-2590 -->Cannot load and display Newick trees
1039 reliably from eggnog Ortholog database
1042 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1043 containing features of type Highlight' when 'B' is pressed
1044 to mark columns containing highlighted regions.
1047 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1048 doesn't always add secondary structure annotation.
1053 <td width="60" nowrap>
1054 <div align="center">
1055 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1058 <td><div align="left">
1062 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1063 for all consensus calculations
1066 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1069 <li>Updated Jalview's Certum code signing certificate
1072 <em>Application</em>
1075 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1076 set of database cross-references, sorted alphabetically
1079 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1080 from database cross references. Users with custom links
1081 will receive a <a href="webServices/urllinks.html#warning">warning
1082 dialog</a> asking them to update their preferences.
1085 <!-- JAL-2287-->Cancel button and escape listener on
1086 dialog warning user about disconnecting Jalview from a
1090 <!-- JAL-2320-->Jalview's Chimera control window closes if
1091 the Chimera it is connected to is shut down
1094 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1095 columns menu item to mark columns containing highlighted
1096 regions (e.g. from structure selections or results of a
1100 <!-- JAL-2284-->Command line option for batch-generation
1101 of HTML pages rendering alignment data with the BioJS
1111 <!-- JAL-2286 -->Columns with more than one modal residue
1112 are not coloured or thresholded according to percent
1113 identity (first observed in Jalview 2.8.2)
1116 <!-- JAL-2301 -->Threonine incorrectly reported as not
1120 <!-- JAL-2318 -->Updates to documentation pages (above PID
1121 threshold, amino acid properties)
1124 <!-- JAL-2292 -->Lower case residues in sequences are not
1125 reported as mapped to residues in a structure file in the
1129 <!--JAL-2324 -->Identical features with non-numeric scores
1130 could be added multiple times to a sequence
1133 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1134 bond features shown as two highlighted residues rather
1135 than a range in linked structure views, and treated
1136 correctly when selecting and computing trees from features
1139 <!-- JAL-2281-->Custom URL links for database
1140 cross-references are matched to database name regardless
1145 <em>Application</em>
1148 <!-- JAL-2282-->Custom URL links for specific database
1149 names without regular expressions also offer links from
1153 <!-- JAL-2315-->Removing a single configured link in the
1154 URL links pane in Connections preferences doesn't actually
1155 update Jalview configuration
1158 <!-- JAL-2272-->CTRL-Click on a selected region to open
1159 the alignment area popup menu doesn't work on El-Capitan
1162 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1163 files with similarly named sequences if dropped onto the
1167 <!-- JAL-2312 -->Additional mappings are shown for PDB
1168 entries where more chains exist in the PDB accession than
1169 are reported in the SIFTS file
1172 <!-- JAL-2317-->Certain structures do not get mapped to
1173 the structure view when displayed with Chimera
1176 <!-- JAL-2317-->No chains shown in the Chimera view
1177 panel's View->Show Chains submenu
1180 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1181 work for wrapped alignment views
1184 <!--JAL-2197 -->Rename UI components for running JPred
1185 predictions from 'JNet' to 'JPred'
1188 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1189 corrupted when annotation panel vertical scroll is not at
1190 first annotation row
1193 <!--JAL-2332 -->Attempting to view structure for Hen
1194 lysozyme results in a PDB Client error dialog box
1197 <!-- JAL-2319 -->Structure View's mapping report switched
1198 ranges for PDB and sequence for SIFTS
1201 SIFTS 'Not_Observed' residues mapped to non-existant
1205 <!-- <em>New Known Issues</em>
1212 <td width="60" nowrap>
1213 <div align="center">
1214 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1215 <em>25/10/2016</em></strong>
1218 <td><em>Application</em>
1220 <li>3D Structure chooser opens with 'Cached structures'
1221 view if structures already loaded</li>
1222 <li>Progress bar reports models as they are loaded to
1223 structure views</li>
1229 <li>Colour by conservation always enabled and no tick
1230 shown in menu when BLOSUM or PID shading applied</li>
1231 <li>FER1_ARATH and FER2_ARATH labels were switched in
1232 example sequences/projects/trees</li>
1234 <em>Application</em>
1236 <li>Jalview projects with views of local PDB structure
1237 files saved on Windows cannot be opened on OSX</li>
1238 <li>Multiple structure views can be opened and superposed
1239 without timeout for structures with multiple models or
1240 multiple sequences in alignment</li>
1241 <li>Cannot import or associated local PDB files without a
1242 PDB ID HEADER line</li>
1243 <li>RMSD is not output in Jmol console when superposition
1245 <li>Drag and drop of URL from Browser fails for Linux and
1246 OSX versions earlier than El Capitan</li>
1247 <li>ENA client ignores invalid content from ENA server</li>
1248 <li>Exceptions are not raised in console when ENA client
1249 attempts to fetch non-existent IDs via Fetch DB Refs UI
1251 <li>Exceptions are not raised in console when a new view
1252 is created on the alignment</li>
1253 <li>OSX right-click fixed for group selections: CMD-click
1254 to insert/remove gaps in groups and CTRL-click to open group
1257 <em>Build and deployment</em>
1259 <li>URL link checker now copes with multi-line anchor
1262 <em>New Known Issues</em>
1264 <li>Drag and drop from URL links in browsers do not work
1271 <td width="60" nowrap>
1272 <div align="center">
1273 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1276 <td><em>General</em>
1279 <!-- JAL-2124 -->Updated Spanish translations.
1282 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1283 for importing structure data to Jalview. Enables mmCIF and
1287 <!-- JAL-192 --->Alignment ruler shows positions relative to
1291 <!-- JAL-2202 -->Position/residue shown in status bar when
1292 mousing over sequence associated annotation
1295 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1299 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1300 '()', canonical '[]' and invalid '{}' base pair populations
1304 <!-- JAL-2092 -->Feature settings popup menu options for
1305 showing or hiding columns containing a feature
1308 <!-- JAL-1557 -->Edit selected group by double clicking on
1309 group and sequence associated annotation labels
1312 <!-- JAL-2236 -->Sequence name added to annotation label in
1313 select/hide columns by annotation and colour by annotation
1317 </ul> <em>Application</em>
1320 <!-- JAL-2050-->Automatically hide introns when opening a
1321 gene/transcript view
1324 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1328 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1329 structure mappings with the EMBL-EBI PDBe SIFTS database
1332 <!-- JAL-2079 -->Updated download sites used for Rfam and
1333 Pfam sources to xfam.org
1336 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1339 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1340 over sequences in Jalview
1343 <!-- JAL-2027-->Support for reverse-complement coding
1344 regions in ENA and EMBL
1347 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1348 for record retrieval via ENA rest API
1351 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1355 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1356 groovy script execution
1359 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1360 alignment window's Calculate menu
1363 <!-- JAL-1812 -->Allow groovy scripts that call
1364 Jalview.getAlignFrames() to run in headless mode
1367 <!-- JAL-2068 -->Support for creating new alignment
1368 calculation workers from groovy scripts
1371 <!-- JAL-1369 --->Store/restore reference sequence in
1375 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1376 associations are now saved/restored from project
1379 <!-- JAL-1993 -->Database selection dialog always shown
1380 before sequence fetcher is opened
1383 <!-- JAL-2183 -->Double click on an entry in Jalview's
1384 database chooser opens a sequence fetcher
1387 <!-- JAL-1563 -->Free-text search client for UniProt using
1388 the UniProt REST API
1391 <!-- JAL-2168 -->-nonews command line parameter to prevent
1392 the news reader opening
1395 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1396 querying stored in preferences
1399 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1403 <!-- JAL-1977-->Tooltips shown on database chooser
1406 <!-- JAL-391 -->Reverse complement function in calculate
1407 menu for nucleotide sequences
1410 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1411 and feature counts preserves alignment ordering (and
1412 debugged for complex feature sets).
1415 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1416 viewing structures with Jalview 2.10
1419 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1420 genome, transcript CCDS and gene ids via the Ensembl and
1421 Ensembl Genomes REST API
1424 <!-- JAL-2049 -->Protein sequence variant annotation
1425 computed for 'sequence_variant' annotation on CDS regions
1429 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1433 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1434 Ref Fetcher fails to match, or otherwise updates sequence
1435 data from external database records.
1438 <!-- JAL-2154 -->Revised Jalview Project format for
1439 efficient recovery of sequence coding and alignment
1440 annotation relationships.
1442 </ul> <!-- <em>Applet</em>
1453 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1457 <!-- JAL-2018-->Export features in Jalview format (again)
1458 includes graduated colourschemes
1461 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1462 working with big alignments and lots of hidden columns
1465 <!-- JAL-2053-->Hidden column markers not always rendered
1466 at right of alignment window
1469 <!-- JAL-2067 -->Tidied up links in help file table of
1473 <!-- JAL-2072 -->Feature based tree calculation not shown
1477 <!-- JAL-2075 -->Hidden columns ignored during feature
1478 based tree calculation
1481 <!-- JAL-2065 -->Alignment view stops updating when show
1482 unconserved enabled for group on alignment
1485 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1489 <!-- JAL-2146 -->Alignment column in status incorrectly
1490 shown as "Sequence position" when mousing over
1494 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1495 hidden columns present
1498 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1499 user created annotation added to alignment
1502 <!-- JAL-1841 -->RNA Structure consensus only computed for
1503 '()' base pair annotation
1506 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1507 in zero scores for all base pairs in RNA Structure
1511 <!-- JAL-2174-->Extend selection with columns containing
1515 <!-- JAL-2275 -->Pfam format writer puts extra space at
1516 beginning of sequence
1519 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1523 <!-- JAL-2238 -->Cannot create groups on an alignment from
1524 from a tree when t-coffee scores are shown
1527 <!-- JAL-1836,1967 -->Cannot import and view PDB
1528 structures with chains containing negative resnums (4q4h)
1531 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1535 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1536 to Clustal, PIR and PileUp output
1539 <!-- JAL-2008 -->Reordering sequence features that are
1540 not visible causes alignment window to repaint
1543 <!-- JAL-2006 -->Threshold sliders don't work in
1544 graduated colour and colour by annotation row for e-value
1545 scores associated with features and annotation rows
1548 <!-- JAL-1797 -->amino acid physicochemical conservation
1549 calculation should be case independent
1552 <!-- JAL-2173 -->Remove annotation also updates hidden
1556 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1557 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1558 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1561 <!-- JAL-2065 -->Null pointer exceptions and redraw
1562 problems when reference sequence defined and 'show
1563 non-conserved' enabled
1566 <!-- JAL-1306 -->Quality and Conservation are now shown on
1567 load even when Consensus calculation is disabled
1570 <!-- JAL-1932 -->Remove right on penultimate column of
1571 alignment does nothing
1574 <em>Application</em>
1577 <!-- JAL-1552-->URLs and links can't be imported by
1578 drag'n'drop on OSX when launched via webstart (note - not
1579 yet fixed for El Capitan)
1582 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1583 output when running on non-gb/us i18n platforms
1586 <!-- JAL-1944 -->Error thrown when exporting a view with
1587 hidden sequences as flat-file alignment
1590 <!-- JAL-2030-->InstallAnywhere distribution fails when
1594 <!-- JAL-2080-->Jalview very slow to launch via webstart
1595 (also hotfix for 2.9.0b2)
1598 <!-- JAL-2085 -->Cannot save project when view has a
1599 reference sequence defined
1602 <!-- JAL-1011 -->Columns are suddenly selected in other
1603 alignments and views when revealing hidden columns
1606 <!-- JAL-1989 -->Hide columns not mirrored in complement
1607 view in a cDNA/Protein splitframe
1610 <!-- JAL-1369 -->Cannot save/restore representative
1611 sequence from project when only one sequence is
1615 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1616 in Structure Chooser
1619 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1620 structure consensus didn't refresh annotation panel
1623 <!-- JAL-1962 -->View mapping in structure view shows
1624 mappings between sequence and all chains in a PDB file
1627 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1628 dialogs format columns correctly, don't display array
1629 data, sort columns according to type
1632 <!-- JAL-1975 -->Export complete shown after destination
1633 file chooser is cancelled during an image export
1636 <!-- JAL-2025 -->Error when querying PDB Service with
1637 sequence name containing special characters
1640 <!-- JAL-2024 -->Manual PDB structure querying should be
1644 <!-- JAL-2104 -->Large tooltips with broken HTML
1645 formatting don't wrap
1648 <!-- JAL-1128 -->Figures exported from wrapped view are
1649 truncated so L looks like I in consensus annotation
1652 <!-- JAL-2003 -->Export features should only export the
1653 currently displayed features for the current selection or
1657 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1658 after fetching cross-references, and restoring from
1662 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1663 followed in the structure viewer
1666 <!-- JAL-2163 -->Titles for individual alignments in
1667 splitframe not restored from project
1670 <!-- JAL-2145 -->missing autocalculated annotation at
1671 trailing end of protein alignment in transcript/product
1672 splitview when pad-gaps not enabled by default
1675 <!-- JAL-1797 -->amino acid physicochemical conservation
1679 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1680 article has been read (reopened issue due to
1681 internationalisation problems)
1684 <!-- JAL-1960 -->Only offer PDB structures in structure
1685 viewer based on sequence name, PDB and UniProt
1690 <!-- JAL-1976 -->No progress bar shown during export of
1694 <!-- JAL-2213 -->Structures not always superimposed after
1695 multiple structures are shown for one or more sequences.
1698 <!-- JAL-1370 -->Reference sequence characters should not
1699 be replaced with '.' when 'Show unconserved' format option
1703 <!-- JAL-1823 -->Cannot specify chain code when entering
1704 specific PDB id for sequence
1707 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1708 'Export hidden sequences' is enabled, but 'export hidden
1709 columns' is disabled.
1712 <!--JAL-2026-->Best Quality option in structure chooser
1713 selects lowest rather than highest resolution structures
1717 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1718 to sequence mapping in 'View Mappings' report
1721 <!-- JAL-2284 -->Unable to read old Jalview projects that
1722 contain non-XML data added after Jalvew wrote project.
1725 <!-- JAL-2118 -->Newly created annotation row reorders
1726 after clicking on it to create new annotation for a
1730 <!-- JAL-1980 -->Null Pointer Exception raised when
1731 pressing Add on an orphaned cut'n'paste window.
1733 <!-- may exclude, this is an external service stability issue JAL-1941
1734 -- > RNA 3D structure not added via DSSR service</li> -->
1739 <!-- JAL-2151 -->Incorrect columns are selected when
1740 hidden columns present before start of sequence
1743 <!-- JAL-1986 -->Missing dependencies on applet pages
1747 <!-- JAL-1947 -->Overview pixel size changes when
1748 sequences are hidden in applet
1751 <!-- JAL-1996 -->Updated instructions for applet
1752 deployment on examples pages.
1759 <td width="60" nowrap>
1760 <div align="center">
1761 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1762 <em>16/10/2015</em></strong>
1765 <td><em>General</em>
1767 <li>Time stamps for signed Jalview application and applet
1772 <em>Application</em>
1774 <li>Duplicate group consensus and conservation rows
1775 shown when tree is partitioned</li>
1776 <li>Erratic behaviour when tree partitions made with
1777 multiple cDNA/Protein split views</li>
1783 <td width="60" nowrap>
1784 <div align="center">
1785 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1786 <em>8/10/2015</em></strong>
1789 <td><em>General</em>
1791 <li>Updated Spanish translations of localized text for
1793 </ul> <em>Application</em>
1795 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1796 <li>Signed OSX InstallAnywhere installer<br></li>
1797 <li>Support for per-sequence based annotations in BioJSON</li>
1798 </ul> <em>Applet</em>
1800 <li>Split frame example added to applet examples page</li>
1801 </ul> <em>Build and Deployment</em>
1804 <!-- JAL-1888 -->New ant target for running Jalview's test
1812 <li>Mapping of cDNA to protein in split frames
1813 incorrect when sequence start > 1</li>
1814 <li>Broken images in filter column by annotation dialog
1816 <li>Feature colours not parsed from features file</li>
1817 <li>Exceptions and incomplete link URLs recovered when
1818 loading a features file containing HTML tags in feature
1822 <em>Application</em>
1824 <li>Annotations corrupted after BioJS export and
1826 <li>Incorrect sequence limits after Fetch DB References
1827 with 'trim retrieved sequences'</li>
1828 <li>Incorrect warning about deleting all data when
1829 deleting selected columns</li>
1830 <li>Patch to build system for shipping properly signed
1831 JNLP templates for webstart launch</li>
1832 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1833 unreleased structures for download or viewing</li>
1834 <li>Tab/space/return keystroke operation of EMBL-PDBe
1835 fetcher/viewer dialogs works correctly</li>
1836 <li>Disabled 'minimise' button on Jalview windows
1837 running on OSX to workaround redraw hang bug</li>
1838 <li>Split cDNA/Protein view position and geometry not
1839 recovered from jalview project</li>
1840 <li>Initial enabled/disabled state of annotation menu
1841 sorter 'show autocalculated first/last' corresponds to
1843 <li>Restoring of Clustal, RNA Helices and T-Coffee
1844 color schemes from BioJSON</li>
1848 <li>Reorder sequences mirrored in cDNA/Protein split
1850 <li>Applet with Jmol examples not loading correctly</li>
1856 <td><div align="center">
1857 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1859 <td><em>General</em>
1861 <li>Linked visualisation and analysis of DNA and Protein
1864 <li>Translated cDNA alignments shown as split protein
1865 and DNA alignment views</li>
1866 <li>Codon consensus annotation for linked protein and
1867 cDNA alignment views</li>
1868 <li>Link cDNA or Protein product sequences by loading
1869 them onto Protein or cDNA alignments</li>
1870 <li>Reconstruct linked cDNA alignment from aligned
1871 protein sequences</li>
1874 <li>Jmol integration updated to Jmol v14.2.14</li>
1875 <li>Import and export of Jalview alignment views as <a
1876 href="features/bioJsonFormat.html">BioJSON</a></li>
1877 <li>New alignment annotation file statements for
1878 reference sequences and marking hidden columns</li>
1879 <li>Reference sequence based alignment shading to
1880 highlight variation</li>
1881 <li>Select or hide columns according to alignment
1883 <li>Find option for locating sequences by description</li>
1884 <li>Conserved physicochemical properties shown in amino
1885 acid conservation row</li>
1886 <li>Alignments can be sorted by number of RNA helices</li>
1887 </ul> <em>Application</em>
1889 <li>New cDNA/Protein analysis capabilities
1891 <li>Get Cross-References should open a Split Frame
1892 view with cDNA/Protein</li>
1893 <li>Detect when nucleotide sequences and protein
1894 sequences are placed in the same alignment</li>
1895 <li>Split cDNA/Protein views are saved in Jalview
1900 <li>Use REST API to talk to Chimera</li>
1901 <li>Selected regions in Chimera are highlighted in linked
1902 Jalview windows</li>
1904 <li>VARNA RNA viewer updated to v3.93</li>
1905 <li>VARNA views are saved in Jalview Projects</li>
1906 <li>Pseudoknots displayed as Jalview RNA annotation can
1907 be shown in VARNA</li>
1909 <li>Make groups for selection uses marked columns as well
1910 as the active selected region</li>
1912 <li>Calculate UPGMA and NJ trees using sequence feature
1914 <li>New Export options
1916 <li>New Export Settings dialog to control hidden
1917 region export in flat file generation</li>
1919 <li>Export alignment views for display with the <a
1920 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1922 <li>Export scrollable SVG in HTML page</li>
1923 <li>Optional embedding of BioJSON data when exporting
1924 alignment figures to HTML</li>
1926 <li>3D structure retrieval and display
1928 <li>Free text and structured queries with the PDBe
1930 <li>PDBe Search API based discovery and selection of
1931 PDB structures for a sequence set</li>
1935 <li>JPred4 employed for protein secondary structure
1937 <li>Hide Insertions menu option to hide unaligned columns
1938 for one or a group of sequences</li>
1939 <li>Automatically hide insertions in alignments imported
1940 from the JPred4 web server</li>
1941 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1942 system on OSX<br />LGPL libraries courtesy of <a
1943 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1945 <li>changed 'View nucleotide structure' submenu to 'View
1946 VARNA 2D Structure'</li>
1947 <li>change "View protein structure" menu option to "3D
1950 </ul> <em>Applet</em>
1952 <li>New layout for applet example pages</li>
1953 <li>New parameters to enable SplitFrame view
1954 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1955 <li>New example demonstrating linked viewing of cDNA and
1956 Protein alignments</li>
1957 </ul> <em>Development and deployment</em>
1959 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1960 <li>Include installation type and git revision in build
1961 properties and console log output</li>
1962 <li>Jalview Github organisation, and new github site for
1963 storing BioJsMSA Templates</li>
1964 <li>Jalview's unit tests now managed with TestNG</li>
1967 <!-- <em>General</em>
1969 </ul> --> <!-- issues resolved --> <em>Application</em>
1971 <li>Escape should close any open find dialogs</li>
1972 <li>Typo in select-by-features status report</li>
1973 <li>Consensus RNA secondary secondary structure
1974 predictions are not highlighted in amber</li>
1975 <li>Missing gap character in v2.7 example file means
1976 alignment appears unaligned when pad-gaps is not enabled</li>
1977 <li>First switch to RNA Helices colouring doesn't colour
1978 associated structure views</li>
1979 <li>ID width preference option is greyed out when auto
1980 width checkbox not enabled</li>
1981 <li>Stopped a warning dialog from being shown when
1982 creating user defined colours</li>
1983 <li>'View Mapping' in structure viewer shows sequence
1984 mappings for just that viewer's sequences</li>
1985 <li>Workaround for superposing PDB files containing
1986 multiple models in Chimera</li>
1987 <li>Report sequence position in status bar when hovering
1988 over Jmol structure</li>
1989 <li>Cannot output gaps as '.' symbols with Selection ->
1990 output to text box</li>
1991 <li>Flat file exports of alignments with hidden columns
1992 have incorrect sequence start/end</li>
1993 <li>'Aligning' a second chain to a Chimera structure from
1995 <li>Colour schemes applied to structure viewers don't
1996 work for nucleotide</li>
1997 <li>Loading/cut'n'pasting an empty or invalid file leads
1998 to a grey/invisible alignment window</li>
1999 <li>Exported Jpred annotation from a sequence region
2000 imports to different position</li>
2001 <li>Space at beginning of sequence feature tooltips shown
2002 on some platforms</li>
2003 <li>Chimera viewer 'View | Show Chain' menu is not
2005 <li>'New View' fails with a Null Pointer Exception in
2006 console if Chimera has been opened</li>
2007 <li>Mouseover to Chimera not working</li>
2008 <li>Miscellaneous ENA XML feature qualifiers not
2010 <li>NPE in annotation renderer after 'Extract Scores'</li>
2011 <li>If two structures in one Chimera window, mouseover of
2012 either sequence shows on first structure</li>
2013 <li>'Show annotations' options should not make
2014 non-positional annotations visible</li>
2015 <li>Subsequence secondary structure annotation not shown
2016 in right place after 'view flanking regions'</li>
2017 <li>File Save As type unset when current file format is
2019 <li>Save as '.jar' option removed for saving Jalview
2021 <li>Colour by Sequence colouring in Chimera more
2023 <li>Cannot 'add reference annotation' for a sequence in
2024 several views on same alignment</li>
2025 <li>Cannot show linked products for EMBL / ENA records</li>
2026 <li>Jalview's tooltip wraps long texts containing no
2028 </ul> <em>Applet</em>
2030 <li>Jmol to JalviewLite mouseover/link not working</li>
2031 <li>JalviewLite can't import sequences with ID
2032 descriptions containing angle brackets</li>
2033 </ul> <em>General</em>
2035 <li>Cannot export and reimport RNA secondary structure
2036 via jalview annotation file</li>
2037 <li>Random helix colour palette for colour by annotation
2038 with RNA secondary structure</li>
2039 <li>Mouseover to cDNA from STOP residue in protein
2040 translation doesn't work.</li>
2041 <li>hints when using the select by annotation dialog box</li>
2042 <li>Jmol alignment incorrect if PDB file has alternate CA
2044 <li>FontChooser message dialog appears to hang after
2045 choosing 1pt font</li>
2046 <li>Peptide secondary structure incorrectly imported from
2047 annotation file when annotation display text includes 'e' or
2049 <li>Cannot set colour of new feature type whilst creating
2051 <li>cDNA translation alignment should not be sequence
2052 order dependent</li>
2053 <li>'Show unconserved' doesn't work for lower case
2055 <li>Nucleotide ambiguity codes involving R not recognised</li>
2056 </ul> <em>Deployment and Documentation</em>
2058 <li>Applet example pages appear different to the rest of
2059 www.jalview.org</li>
2060 </ul> <em>Application Known issues</em>
2062 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2063 <li>Misleading message appears after trying to delete
2065 <li>Jalview icon not shown in dock after InstallAnywhere
2066 version launches</li>
2067 <li>Fetching EMBL reference for an RNA sequence results
2068 fails with a sequence mismatch</li>
2069 <li>Corrupted or unreadable alignment display when
2070 scrolling alignment to right</li>
2071 <li>ArrayIndexOutOfBoundsException thrown when remove
2072 empty columns called on alignment with ragged gapped ends</li>
2073 <li>auto calculated alignment annotation rows do not get
2074 placed above or below non-autocalculated rows</li>
2075 <li>Jalview dekstop becomes sluggish at full screen in
2076 ultra-high resolution</li>
2077 <li>Cannot disable consensus calculation independently of
2078 quality and conservation</li>
2079 <li>Mouseover highlighting between cDNA and protein can
2080 become sluggish with more than one splitframe shown</li>
2081 </ul> <em>Applet Known Issues</em>
2083 <li>Core PDB parsing code requires Jmol</li>
2084 <li>Sequence canvas panel goes white when alignment
2085 window is being resized</li>
2091 <td><div align="center">
2092 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2094 <td><em>General</em>
2096 <li>Updated Java code signing certificate donated by
2098 <li>Features and annotation preserved when performing
2099 pairwise alignment</li>
2100 <li>RNA pseudoknot annotation can be
2101 imported/exported/displayed</li>
2102 <li>'colour by annotation' can colour by RNA and
2103 protein secondary structure</li>
2104 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2105 post-hoc with 2.9 release</em>)
2108 </ul> <em>Application</em>
2110 <li>Extract and display secondary structure for sequences
2111 with 3D structures</li>
2112 <li>Support for parsing RNAML</li>
2113 <li>Annotations menu for layout
2115 <li>sort sequence annotation rows by alignment</li>
2116 <li>place sequence annotation above/below alignment
2119 <li>Output in Stockholm format</li>
2120 <li>Internationalisation: improved Spanish (es)
2122 <li>Structure viewer preferences tab</li>
2123 <li>Disorder and Secondary Structure annotation tracks
2124 shared between alignments</li>
2125 <li>UCSF Chimera launch and linked highlighting from
2127 <li>Show/hide all sequence associated annotation rows for
2128 all or current selection</li>
2129 <li>disorder and secondary structure predictions
2130 available as dataset annotation</li>
2131 <li>Per-sequence rna helices colouring</li>
2134 <li>Sequence database accessions imported when fetching
2135 alignments from Rfam</li>
2136 <li>update VARNA version to 3.91</li>
2138 <li>New groovy scripts for exporting aligned positions,
2139 conservation values, and calculating sum of pairs scores.</li>
2140 <li>Command line argument to set default JABAWS server</li>
2141 <li>include installation type in build properties and
2142 console log output</li>
2143 <li>Updated Jalview project format to preserve dataset
2147 <!-- issues resolved --> <em>Application</em>
2149 <li>Distinguish alignment and sequence associated RNA
2150 structure in structure->view->VARNA</li>
2151 <li>Raise dialog box if user deletes all sequences in an
2153 <li>Pressing F1 results in documentation opening twice</li>
2154 <li>Sequence feature tooltip is wrapped</li>
2155 <li>Double click on sequence associated annotation
2156 selects only first column</li>
2157 <li>Redundancy removal doesn't result in unlinked
2158 leaves shown in tree</li>
2159 <li>Undos after several redundancy removals don't undo
2161 <li>Hide sequence doesn't hide associated annotation</li>
2162 <li>User defined colours dialog box too big to fit on
2163 screen and buttons not visible</li>
2164 <li>author list isn't updated if already written to
2165 Jalview properties</li>
2166 <li>Popup menu won't open after retrieving sequence
2168 <li>File open window for associate PDB doesn't open</li>
2169 <li>Left-then-right click on a sequence id opens a
2170 browser search window</li>
2171 <li>Cannot open sequence feature shading/sort popup menu
2172 in feature settings dialog</li>
2173 <li>better tooltip placement for some areas of Jalview
2175 <li>Allow addition of JABAWS Server which doesn't
2176 pass validation</li>
2177 <li>Web services parameters dialog box is too large to
2179 <li>Muscle nucleotide alignment preset obscured by
2181 <li>JABAWS preset submenus don't contain newly
2182 defined user preset</li>
2183 <li>MSA web services warns user if they were launched
2184 with invalid input</li>
2185 <li>Jalview cannot contact DAS Registy when running on
2188 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2189 'Superpose with' submenu not shown when new view
2193 </ul> <!-- <em>Applet</em>
2195 </ul> <em>General</em>
2197 </ul>--> <em>Deployment and Documentation</em>
2199 <li>2G and 1G options in launchApp have no effect on
2200 memory allocation</li>
2201 <li>launchApp service doesn't automatically open
2202 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2204 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2205 InstallAnywhere reports cannot find valid JVM when Java
2206 1.7_055 is available
2208 </ul> <em>Application Known issues</em>
2211 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2212 corrupted or unreadable alignment display when scrolling
2216 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2217 retrieval fails but progress bar continues for DAS retrieval
2218 with large number of ID
2221 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2222 flatfile output of visible region has incorrect sequence
2226 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2227 rna structure consensus doesn't update when secondary
2228 structure tracks are rearranged
2231 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2232 invalid rna structure positional highlighting does not
2233 highlight position of invalid base pairs
2236 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2237 out of memory errors are not raised when saving Jalview
2238 project from alignment window file menu
2241 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2242 Switching to RNA Helices colouring doesn't propagate to
2246 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2247 colour by RNA Helices not enabled when user created
2248 annotation added to alignment
2251 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2252 Jalview icon not shown on dock in Mountain Lion/Webstart
2254 </ul> <em>Applet Known Issues</em>
2257 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2258 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2261 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2262 Jalview and Jmol example not compatible with IE9
2265 <li>Sort by annotation score doesn't reverse order
2271 <td><div align="center">
2272 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2275 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2278 <li>Internationalisation of user interface (usually
2279 called i18n support) and translation for Spanish locale</li>
2280 <li>Define/Undefine group on current selection with
2281 Ctrl-G/Shift Ctrl-G</li>
2282 <li>Improved group creation/removal options in
2283 alignment/sequence Popup menu</li>
2284 <li>Sensible precision for symbol distribution
2285 percentages shown in logo tooltip.</li>
2286 <li>Annotation panel height set according to amount of
2287 annotation when alignment first opened</li>
2288 </ul> <em>Application</em>
2290 <li>Interactive consensus RNA secondary structure
2291 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2292 <li>Select columns containing particular features from
2293 Feature Settings dialog</li>
2294 <li>View all 'representative' PDB structures for selected
2296 <li>Update Jalview project format:
2298 <li>New file extension for Jalview projects '.jvp'</li>
2299 <li>Preserve sequence and annotation dataset (to
2300 store secondary structure annotation,etc)</li>
2301 <li>Per group and alignment annotation and RNA helix
2305 <li>New similarity measures for PCA and Tree calculation
2307 <li>Experimental support for retrieval and viewing of
2308 flanking regions for an alignment</li>
2312 <!-- issues resolved --> <em>Application</em>
2314 <li>logo keeps spinning and status remains at queued or
2315 running after job is cancelled</li>
2316 <li>cannot export features from alignments imported from
2317 Jalview/VAMSAS projects</li>
2318 <li>Buggy slider for web service parameters that take
2320 <li>Newly created RNA secondary structure line doesn't
2321 have 'display all symbols' flag set</li>
2322 <li>T-COFFEE alignment score shading scheme and other
2323 annotation shading not saved in Jalview project</li>
2324 <li>Local file cannot be loaded in freshly downloaded
2326 <li>Jalview icon not shown on dock in Mountain
2328 <li>Load file from desktop file browser fails</li>
2329 <li>Occasional NPE thrown when calculating large trees</li>
2330 <li>Cannot reorder or slide sequences after dragging an
2331 alignment onto desktop</li>
2332 <li>Colour by annotation dialog throws NPE after using
2333 'extract scores' function</li>
2334 <li>Loading/cut'n'pasting an empty file leads to a grey
2335 alignment window</li>
2336 <li>Disorder thresholds rendered incorrectly after
2337 performing IUPred disorder prediction</li>
2338 <li>Multiple group annotated consensus rows shown when
2339 changing 'normalise logo' display setting</li>
2340 <li>Find shows blank dialog after 'finished searching' if
2341 nothing matches query</li>
2342 <li>Null Pointer Exceptions raised when sorting by
2343 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2345 <li>Errors in Jmol console when structures in alignment
2346 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2348 <li>Not all working JABAWS services are shown in
2350 <li>JAVAWS version of Jalview fails to launch with
2351 'invalid literal/length code'</li>
2352 <li>Annotation/RNA Helix colourschemes cannot be applied
2353 to alignment with groups (actually fixed in 2.8.0b1)</li>
2354 <li>RNA Helices and T-Coffee Scores available as default
2357 </ul> <em>Applet</em>
2359 <li>Remove group option is shown even when selection is
2361 <li>Apply to all groups ticked but colourscheme changes
2362 don't affect groups</li>
2363 <li>Documented RNA Helices and T-Coffee Scores as valid
2364 colourscheme name</li>
2365 <li>Annotation labels drawn on sequence IDs when
2366 Annotation panel is not displayed</li>
2367 <li>Increased font size for dropdown menus on OSX and
2368 embedded windows</li>
2369 </ul> <em>Other</em>
2371 <li>Consensus sequence for alignments/groups with a
2372 single sequence were not calculated</li>
2373 <li>annotation files that contain only groups imported as
2374 annotation and junk sequences</li>
2375 <li>Fasta files with sequences containing '*' incorrectly
2376 recognised as PFAM or BLC</li>
2377 <li>conservation/PID slider apply all groups option
2378 doesn't affect background (2.8.0b1)
2380 <li>redundancy highlighting is erratic at 0% and 100%</li>
2381 <li>Remove gapped columns fails for sequences with ragged
2383 <li>AMSA annotation row with leading spaces is not
2384 registered correctly on import</li>
2385 <li>Jalview crashes when selecting PCA analysis for
2386 certain alignments</li>
2387 <li>Opening the colour by annotation dialog for an
2388 existing annotation based 'use original colours'
2389 colourscheme loses original colours setting</li>
2394 <td><div align="center">
2395 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2396 <em>30/1/2014</em></strong>
2400 <li>Trusted certificates for JalviewLite applet and
2401 Jalview Desktop application<br />Certificate was donated by
2402 <a href="https://www.certum.eu">Certum</a> to the Jalview
2403 open source project).
2405 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2406 <li>Output in Stockholm format</li>
2407 <li>Allow import of data from gzipped files</li>
2408 <li>Export/import group and sequence associated line
2409 graph thresholds</li>
2410 <li>Nucleotide substitution matrix that supports RNA and
2411 ambiguity codes</li>
2412 <li>Allow disorder predictions to be made on the current
2413 selection (or visible selection) in the same way that JPred
2415 <li>Groovy scripting for headless Jalview operation</li>
2416 </ul> <em>Other improvements</em>
2418 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2419 <li>COMBINE statement uses current SEQUENCE_REF and
2420 GROUP_REF scope to group annotation rows</li>
2421 <li>Support '' style escaping of quotes in Newick
2423 <li>Group options for JABAWS service by command line name</li>
2424 <li>Empty tooltip shown for JABA service options with a
2425 link but no description</li>
2426 <li>Select primary source when selecting authority in
2427 database fetcher GUI</li>
2428 <li>Add .mfa to FASTA file extensions recognised by
2430 <li>Annotation label tooltip text wrap</li>
2435 <li>Slow scrolling when lots of annotation rows are
2437 <li>Lots of NPE (and slowness) after creating RNA
2438 secondary structure annotation line</li>
2439 <li>Sequence database accessions not imported when
2440 fetching alignments from Rfam</li>
2441 <li>Incorrect SHMR submission for sequences with
2443 <li>View all structures does not always superpose
2445 <li>Option widgets in service parameters not updated to
2446 reflect user or preset settings</li>
2447 <li>Null pointer exceptions for some services without
2448 presets or adjustable parameters</li>
2449 <li>Discover PDB IDs entry in structure menu doesn't
2450 discover PDB xRefs</li>
2451 <li>Exception encountered while trying to retrieve
2452 features with DAS</li>
2453 <li>Lowest value in annotation row isn't coloured
2454 when colour by annotation (per sequence) is coloured</li>
2455 <li>Keyboard mode P jumps to start of gapped region when
2456 residue follows a gap</li>
2457 <li>Jalview appears to hang importing an alignment with
2458 Wrap as default or after enabling Wrap</li>
2459 <li>'Right click to add annotations' message
2460 shown in wrap mode when no annotations present</li>
2461 <li>Disorder predictions fail with NPE if no automatic
2462 annotation already exists on alignment</li>
2463 <li>oninit javascript function should be called after
2464 initialisation completes</li>
2465 <li>Remove redundancy after disorder prediction corrupts
2466 alignment window display</li>
2467 <li>Example annotation file in documentation is invalid</li>
2468 <li>Grouped line graph annotation rows are not exported
2469 to annotation file</li>
2470 <li>Multi-harmony analysis cannot be run when only two
2472 <li>Cannot create multiple groups of line graphs with
2473 several 'combine' statements in annotation file</li>
2474 <li>Pressing return several times causes Number Format
2475 exceptions in keyboard mode</li>
2476 <li>Multi-harmony (SHMMR) method doesn't submit
2477 correct partitions for input data</li>
2478 <li>Translation from DNA to Amino Acids fails</li>
2479 <li>Jalview fail to load newick tree with quoted label</li>
2480 <li>--headless flag isn't understood</li>
2481 <li>ClassCastException when generating EPS in headless
2483 <li>Adjusting sequence-associated shading threshold only
2484 changes one row's threshold</li>
2485 <li>Preferences and Feature settings panel panel
2486 doesn't open</li>
2487 <li>hide consensus histogram also hides conservation and
2488 quality histograms</li>
2493 <td><div align="center">
2494 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2496 <td><em>Application</em>
2498 <li>Support for JABAWS 2.0 Services (AACon alignment
2499 conservation, protein disorder and Clustal Omega)</li>
2500 <li>JABAWS server status indicator in Web Services
2502 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2503 in Jalview alignment window</li>
2504 <li>Updated Jalview build and deploy framework for OSX
2505 mountain lion, windows 7, and 8</li>
2506 <li>Nucleotide substitution matrix for PCA that supports
2507 RNA and ambiguity codes</li>
2509 <li>Improved sequence database retrieval GUI</li>
2510 <li>Support fetching and database reference look up
2511 against multiple DAS sources (Fetch all from in 'fetch db
2513 <li>Jalview project improvements
2515 <li>Store and retrieve the 'belowAlignment'
2516 flag for annotation</li>
2517 <li>calcId attribute to group annotation rows on the
2519 <li>Store AACon calculation settings for a view in
2520 Jalview project</li>
2524 <li>horizontal scrolling gesture support</li>
2525 <li>Visual progress indicator when PCA calculation is
2527 <li>Simpler JABA web services menus</li>
2528 <li>visual indication that web service results are still
2529 being retrieved from server</li>
2530 <li>Serialise the dialogs that are shown when Jalview
2531 starts up for first time</li>
2532 <li>Jalview user agent string for interacting with HTTP
2534 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2536 <li>Examples directory and Groovy library included in
2537 InstallAnywhere distribution</li>
2538 </ul> <em>Applet</em>
2540 <li>RNA alignment and secondary structure annotation
2541 visualization applet example</li>
2542 </ul> <em>General</em>
2544 <li>Normalise option for consensus sequence logo</li>
2545 <li>Reset button in PCA window to return dimensions to
2547 <li>Allow seqspace or Jalview variant of alignment PCA
2549 <li>PCA with either nucleic acid and protein substitution
2551 <li>Allow windows containing HTML reports to be exported
2553 <li>Interactive display and editing of RNA secondary
2554 structure contacts</li>
2555 <li>RNA Helix Alignment Colouring</li>
2556 <li>RNA base pair logo consensus</li>
2557 <li>Parse sequence associated secondary structure
2558 information in Stockholm files</li>
2559 <li>HTML Export database accessions and annotation
2560 information presented in tooltip for sequences</li>
2561 <li>Import secondary structure from LOCARNA clustalw
2562 style RNA alignment files</li>
2563 <li>import and visualise T-COFFEE quality scores for an
2565 <li>'colour by annotation' per sequence option to
2566 shade each sequence according to its associated alignment
2568 <li>New Jalview Logo</li>
2569 </ul> <em>Documentation and Development</em>
2571 <li>documentation for score matrices used in Jalview</li>
2572 <li>New Website!</li>
2574 <td><em>Application</em>
2576 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2577 wsdbfetch REST service</li>
2578 <li>Stop windows being moved outside desktop on OSX</li>
2579 <li>Filetype associations not installed for webstart
2581 <li>Jalview does not always retrieve progress of a JABAWS
2582 job execution in full once it is complete</li>
2583 <li>revise SHMR RSBS definition to ensure alignment is
2584 uploaded via ali_file parameter</li>
2585 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2586 <li>View all structures superposed fails with exception</li>
2587 <li>Jnet job queues forever if a very short sequence is
2588 submitted for prediction</li>
2589 <li>Cut and paste menu not opened when mouse clicked on
2591 <li>Putting fractional value into integer text box in
2592 alignment parameter dialog causes Jalview to hang</li>
2593 <li>Structure view highlighting doesn't work on
2595 <li>View all structures fails with exception shown in
2597 <li>Characters in filename associated with PDBEntry not
2598 escaped in a platform independent way</li>
2599 <li>Jalview desktop fails to launch with exception when
2601 <li>Tree calculation reports 'you must have 2 or more
2602 sequences selected' when selection is empty</li>
2603 <li>Jalview desktop fails to launch with jar signature
2604 failure when java web start temporary file caching is
2606 <li>DAS Sequence retrieval with range qualification
2607 results in sequence xref which includes range qualification</li>
2608 <li>Errors during processing of command line arguments
2609 cause progress bar (JAL-898) to be removed</li>
2610 <li>Replace comma for semi-colon option not disabled for
2611 DAS sources in sequence fetcher</li>
2612 <li>Cannot close news reader when JABAWS server warning
2613 dialog is shown</li>
2614 <li>Option widgets not updated to reflect user settings</li>
2615 <li>Edited sequence not submitted to web service</li>
2616 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2617 <li>InstallAnywhere installer doesn't unpack and run
2618 on OSX Mountain Lion</li>
2619 <li>Annotation panel not given a scroll bar when
2620 sequences with alignment annotation are pasted into the
2622 <li>Sequence associated annotation rows not associated
2623 when loaded from Jalview project</li>
2624 <li>Browser launch fails with NPE on java 1.7</li>
2625 <li>JABAWS alignment marked as finished when job was
2626 cancelled or job failed due to invalid input</li>
2627 <li>NPE with v2.7 example when clicking on Tree
2628 associated with all views</li>
2629 <li>Exceptions when copy/paste sequences with grouped
2630 annotation rows to new window</li>
2631 </ul> <em>Applet</em>
2633 <li>Sequence features are momentarily displayed before
2634 they are hidden using hidefeaturegroups applet parameter</li>
2635 <li>loading features via javascript API automatically
2636 enables feature display</li>
2637 <li>scrollToColumnIn javascript API method doesn't
2639 </ul> <em>General</em>
2641 <li>Redundancy removal fails for rna alignment</li>
2642 <li>PCA calculation fails when sequence has been selected
2643 and then deselected</li>
2644 <li>PCA window shows grey box when first opened on OSX</li>
2645 <li>Letters coloured pink in sequence logo when alignment
2646 coloured with clustalx</li>
2647 <li>Choosing fonts without letter symbols defined causes
2648 exceptions and redraw errors</li>
2649 <li>Initial PCA plot view is not same as manually
2650 reconfigured view</li>
2651 <li>Grouped annotation graph label has incorrect line
2653 <li>Grouped annotation graph label display is corrupted
2654 for lots of labels</li>
2659 <div align="center">
2660 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2663 <td><em>Application</em>
2665 <li>Jalview Desktop News Reader</li>
2666 <li>Tweaked default layout of web services menu</li>
2667 <li>View/alignment association menu to enable user to
2668 easily specify which alignment a multi-structure view takes
2669 its colours/correspondences from</li>
2670 <li>Allow properties file location to be specified as URL</li>
2671 <li>Extend Jalview project to preserve associations
2672 between many alignment views and a single Jmol display</li>
2673 <li>Store annotation row height in Jalview project file</li>
2674 <li>Annotation row column label formatting attributes
2675 stored in project file</li>
2676 <li>Annotation row order for auto-calculated annotation
2677 rows preserved in Jalview project file</li>
2678 <li>Visual progress indication when Jalview state is
2679 saved using Desktop window menu</li>
2680 <li>Visual indication that command line arguments are
2681 still being processed</li>
2682 <li>Groovy script execution from URL</li>
2683 <li>Colour by annotation default min and max colours in
2685 <li>Automatically associate PDB files dragged onto an
2686 alignment with sequences that have high similarity and
2688 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2689 <li>'view structures' option to open many
2690 structures in same window</li>
2691 <li>Sort associated views menu option for tree panel</li>
2692 <li>Group all JABA and non-JABA services for a particular
2693 analysis function in its own submenu</li>
2694 </ul> <em>Applet</em>
2696 <li>Userdefined and autogenerated annotation rows for
2698 <li>Adjustment of alignment annotation pane height</li>
2699 <li>Annotation scrollbar for annotation panel</li>
2700 <li>Drag to reorder annotation rows in annotation panel</li>
2701 <li>'automaticScrolling' parameter</li>
2702 <li>Allow sequences with partial ID string matches to be
2703 annotated from GFF/Jalview features files</li>
2704 <li>Sequence logo annotation row in applet</li>
2705 <li>Absolute paths relative to host server in applet
2706 parameters are treated as such</li>
2707 <li>New in the JalviewLite javascript API:
2709 <li>JalviewLite.js javascript library</li>
2710 <li>Javascript callbacks for
2712 <li>Applet initialisation</li>
2713 <li>Sequence/alignment mouse-overs and selections</li>
2716 <li>scrollTo row and column alignment scrolling
2718 <li>Select sequence/alignment regions from javascript</li>
2719 <li>javascript structure viewer harness to pass
2720 messages between Jmol and Jalview when running as
2721 distinct applets</li>
2722 <li>sortBy method</li>
2723 <li>Set of applet and application examples shipped
2724 with documentation</li>
2725 <li>New example to demonstrate JalviewLite and Jmol
2726 javascript message exchange</li>
2728 </ul> <em>General</em>
2730 <li>Enable Jmol displays to be associated with multiple
2731 multiple alignments</li>
2732 <li>Option to automatically sort alignment with new tree</li>
2733 <li>User configurable link to enable redirects to a
2734 www.Jalview.org mirror</li>
2735 <li>Jmol colours option for Jmol displays</li>
2736 <li>Configurable newline string when writing alignment
2737 and other flat files</li>
2738 <li>Allow alignment annotation description lines to
2739 contain html tags</li>
2740 </ul> <em>Documentation and Development</em>
2742 <li>Add groovy test harness for bulk load testing to
2744 <li>Groovy script to load and align a set of sequences
2745 using a web service before displaying the result in the
2746 Jalview desktop</li>
2747 <li>Restructured javascript and applet api documentation</li>
2748 <li>Ant target to publish example html files with applet
2750 <li>Netbeans project for building Jalview from source</li>
2751 <li>ant task to create online javadoc for Jalview source</li>
2753 <td><em>Application</em>
2755 <li>User defined colourscheme throws exception when
2756 current built in colourscheme is saved as new scheme</li>
2757 <li>AlignFrame->Save in application pops up save
2758 dialog for valid filename/format</li>
2759 <li>Cannot view associated structure for UniProt sequence</li>
2760 <li>PDB file association breaks for UniProt sequence
2762 <li>Associate PDB from file dialog does not tell you
2763 which sequence is to be associated with the file</li>
2764 <li>Find All raises null pointer exception when query
2765 only matches sequence IDs</li>
2766 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2767 <li>Jalview project with Jmol views created with Jalview
2768 2.4 cannot be loaded</li>
2769 <li>Filetype associations not installed for webstart
2771 <li>Two or more chains in a single PDB file associated
2772 with sequences in different alignments do not get coloured
2773 by their associated sequence</li>
2774 <li>Visibility status of autocalculated annotation row
2775 not preserved when project is loaded</li>
2776 <li>Annotation row height and visibility attributes not
2777 stored in Jalview project</li>
2778 <li>Tree bootstraps are not preserved when saved as a
2779 Jalview project</li>
2780 <li>Envision2 workflow tooltips are corrupted</li>
2781 <li>Enabling show group conservation also enables colour
2782 by conservation</li>
2783 <li>Duplicate group associated conservation or consensus
2784 created on new view</li>
2785 <li>Annotation scrollbar not displayed after 'show
2786 all hidden annotation rows' option selected</li>
2787 <li>Alignment quality not updated after alignment
2788 annotation row is hidden then shown</li>
2789 <li>Preserve colouring of structures coloured by
2790 sequences in pre Jalview 2.7 projects</li>
2791 <li>Web service job parameter dialog is not laid out
2793 <li>Web services menu not refreshed after 'reset
2794 services' button is pressed in preferences</li>
2795 <li>Annotation off by one in Jalview v2_3 example project</li>
2796 <li>Structures imported from file and saved in project
2797 get name like jalview_pdb1234.txt when reloaded</li>
2798 <li>Jalview does not always retrieve progress of a JABAWS
2799 job execution in full once it is complete</li>
2800 </ul> <em>Applet</em>
2802 <li>Alignment height set incorrectly when lots of
2803 annotation rows are displayed</li>
2804 <li>Relative URLs in feature HTML text not resolved to
2806 <li>View follows highlighting does not work for positions
2808 <li><= shown as = in tooltip</li>
2809 <li>Export features raises exception when no features
2811 <li>Separator string used for serialising lists of IDs
2812 for javascript api is modified when separator string
2813 provided as parameter</li>
2814 <li>Null pointer exception when selecting tree leaves for
2815 alignment with no existing selection</li>
2816 <li>Relative URLs for datasources assumed to be relative
2817 to applet's codebase</li>
2818 <li>Status bar not updated after finished searching and
2819 search wraps around to first result</li>
2820 <li>StructureSelectionManager instance shared between
2821 several Jalview applets causes race conditions and memory
2823 <li>Hover tooltip and mouseover of position on structure
2824 not sent from Jmol in applet</li>
2825 <li>Certain sequences of javascript method calls to
2826 applet API fatally hang browser</li>
2827 </ul> <em>General</em>
2829 <li>View follows structure mouseover scrolls beyond
2830 position with wrapped view and hidden regions</li>
2831 <li>Find sequence position moves to wrong residue
2832 with/without hidden columns</li>
2833 <li>Sequence length given in alignment properties window
2835 <li>InvalidNumberFormat exceptions thrown when trying to
2836 import PDB like structure files</li>
2837 <li>Positional search results are only highlighted
2838 between user-supplied sequence start/end bounds</li>
2839 <li>End attribute of sequence is not validated</li>
2840 <li>Find dialog only finds first sequence containing a
2841 given sequence position</li>
2842 <li>Sequence numbering not preserved in MSF alignment
2844 <li>Jalview PDB file reader does not extract sequence
2845 from nucleotide chains correctly</li>
2846 <li>Structure colours not updated when tree partition
2847 changed in alignment</li>
2848 <li>Sequence associated secondary structure not correctly
2849 parsed in interleaved stockholm</li>
2850 <li>Colour by annotation dialog does not restore current
2852 <li>Hiding (nearly) all sequences doesn't work
2854 <li>Sequences containing lowercase letters are not
2855 properly associated with their pdb files</li>
2856 </ul> <em>Documentation and Development</em>
2858 <li>schemas/JalviewWsParamSet.xsd corrupted by
2859 ApplyCopyright tool</li>
2864 <div align="center">
2865 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2868 <td><em>Application</em>
2870 <li>New warning dialog when the Jalview Desktop cannot
2871 contact web services</li>
2872 <li>JABA service parameters for a preset are shown in
2873 service job window</li>
2874 <li>JABA Service menu entries reworded</li>
2878 <li>Modeller PIR IO broken - cannot correctly import a
2879 pir file emitted by Jalview</li>
2880 <li>Existing feature settings transferred to new
2881 alignment view created from cut'n'paste</li>
2882 <li>Improved test for mixed amino/nucleotide chains when
2883 parsing PDB files</li>
2884 <li>Consensus and conservation annotation rows
2885 occasionally become blank for all new windows</li>
2886 <li>Exception raised when right clicking above sequences
2887 in wrapped view mode</li>
2888 </ul> <em>Application</em>
2890 <li>multiple multiply aligned structure views cause cpu
2891 usage to hit 100% and computer to hang</li>
2892 <li>Web Service parameter layout breaks for long user
2893 parameter names</li>
2894 <li>Jaba service discovery hangs desktop if Jaba server
2901 <div align="center">
2902 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2905 <td><em>Application</em>
2907 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2908 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2911 <li>Web Services preference tab</li>
2912 <li>Analysis parameters dialog box and user defined
2914 <li>Improved speed and layout of Envision2 service menu</li>
2915 <li>Superpose structures using associated sequence
2917 <li>Export coordinates and projection as CSV from PCA
2919 </ul> <em>Applet</em>
2921 <li>enable javascript: execution by the applet via the
2922 link out mechanism</li>
2923 </ul> <em>Other</em>
2925 <li>Updated the Jmol Jalview interface to work with Jmol
2927 <li>The Jalview Desktop and JalviewLite applet now
2928 require Java 1.5</li>
2929 <li>Allow Jalview feature colour specification for GFF
2930 sequence annotation files</li>
2931 <li>New 'colour by label' keword in Jalview feature file
2932 type colour specification</li>
2933 <li>New Jalview Desktop Groovy API method that allows a
2934 script to check if it being run in an interactive session or
2935 in a batch operation from the Jalview command line</li>
2939 <li>clustalx colourscheme colours Ds preferentially when
2940 both D+E are present in over 50% of the column</li>
2941 </ul> <em>Application</em>
2943 <li>typo in AlignmentFrame->View->Hide->all but
2944 selected Regions menu item</li>
2945 <li>sequence fetcher replaces ',' for ';' when the ',' is
2946 part of a valid accession ID</li>
2947 <li>fatal OOM if object retrieved by sequence fetcher
2948 runs out of memory</li>
2949 <li>unhandled Out of Memory Error when viewing pca
2950 analysis results</li>
2951 <li>InstallAnywhere builds fail to launch on OS X java
2952 10.5 update 4 (due to apple Java 1.6 update)</li>
2953 <li>Installanywhere Jalview silently fails to launch</li>
2954 </ul> <em>Applet</em>
2956 <li>Jalview.getFeatureGroups() raises an
2957 ArrayIndexOutOfBoundsException if no feature groups are
2964 <div align="center">
2965 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2971 <li>Alignment prettyprinter doesn't cope with long
2973 <li>clustalx colourscheme colours Ds preferentially when
2974 both D+E are present in over 50% of the column</li>
2975 <li>nucleic acid structures retrieved from PDB do not
2976 import correctly</li>
2977 <li>More columns get selected than were clicked on when a
2978 number of columns are hidden</li>
2979 <li>annotation label popup menu not providing correct
2980 add/hide/show options when rows are hidden or none are
2982 <li>Stockholm format shown in list of readable formats,
2983 and parser copes better with alignments from RFAM.</li>
2984 <li>CSV output of consensus only includes the percentage
2985 of all symbols if sequence logo display is enabled</li>
2987 </ul> <em>Applet</em>
2989 <li>annotation panel disappears when annotation is
2991 </ul> <em>Application</em>
2993 <li>Alignment view not redrawn properly when new
2994 alignment opened where annotation panel is visible but no
2995 annotations are present on alignment</li>
2996 <li>pasted region containing hidden columns is
2997 incorrectly displayed in new alignment window</li>
2998 <li>Jalview slow to complete operations when stdout is
2999 flooded (fix is to close the Jalview console)</li>
3000 <li>typo in AlignmentFrame->View->Hide->all but
3001 selected Rregions menu item.</li>
3002 <li>inconsistent group submenu and Format submenu entry
3003 'Un' or 'Non'conserved</li>
3004 <li>Sequence feature settings are being shared by
3005 multiple distinct alignments</li>
3006 <li>group annotation not recreated when tree partition is
3008 <li>double click on group annotation to select sequences
3009 does not propagate to associated trees</li>
3010 <li>Mac OSX specific issues:
3012 <li>exception raised when mouse clicked on desktop
3013 window background</li>
3014 <li>Desktop menu placed on menu bar and application
3015 name set correctly</li>
3016 <li>sequence feature settings not wide enough for the
3017 save feature colourscheme button</li>
3026 <div align="center">
3027 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3030 <td><em>New Capabilities</em>
3032 <li>URL links generated from description line for
3033 regular-expression based URL links (applet and application)
3035 <li>Non-positional feature URL links are shown in link
3037 <li>Linked viewing of nucleic acid sequences and
3039 <li>Automatic Scrolling option in View menu to display
3040 the currently highlighted region of an alignment.</li>
3041 <li>Order an alignment by sequence length, or using the
3042 average score or total feature count for each sequence.</li>
3043 <li>Shading features by score or associated description</li>
3044 <li>Subdivide alignment and groups based on identity of
3045 selected subsequence (Make Groups from Selection).</li>
3046 <li>New hide/show options including Shift+Control+H to
3047 hide everything but the currently selected region.</li>
3048 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3049 </ul> <em>Application</em>
3051 <li>Fetch DB References capabilities and UI expanded to
3052 support retrieval from DAS sequence sources</li>
3053 <li>Local DAS Sequence sources can be added via the
3054 command line or via the Add local source dialog box.</li>
3055 <li>DAS Dbref and DbxRef feature types are parsed as
3056 database references and protein_name is parsed as
3057 description line (BioSapiens terms).</li>
3058 <li>Enable or disable non-positional feature and database
3059 references in sequence ID tooltip from View menu in
3061 <!-- <li>New hidden columns and rows and representatives capabilities
3062 in annotations file (in progress - not yet fully implemented)</li> -->
3063 <li>Group-associated consensus, sequence logos and
3064 conservation plots</li>
3065 <li>Symbol distributions for each column can be exported
3066 and visualized as sequence logos</li>
3067 <li>Optionally scale multi-character column labels to fit
3068 within each column of annotation row<!-- todo for applet -->
3070 <li>Optional automatic sort of associated alignment view
3071 when a new tree is opened.</li>
3072 <li>Jalview Java Console</li>
3073 <li>Better placement of desktop window when moving
3074 between different screens.</li>
3075 <li>New preference items for sequence ID tooltip and
3076 consensus annotation</li>
3077 <li>Client to submit sequences and IDs to Envision2
3079 <li><em>Vamsas Capabilities</em>
3081 <li>Improved VAMSAS synchronization (Jalview archive
3082 used to preserve views, structures, and tree display
3084 <li>Import of vamsas documents from disk or URL via
3086 <li>Sharing of selected regions between views and
3087 with other VAMSAS applications (Experimental feature!)</li>
3088 <li>Updated API to VAMSAS version 0.2</li>
3090 </ul> <em>Applet</em>
3092 <li>Middle button resizes annotation row height</li>
3095 <li>sortByTree (true/false) - automatically sort the
3096 associated alignment view by the tree when a new tree is
3098 <li>showTreeBootstraps (true/false) - show or hide
3099 branch bootstraps (default is to show them if available)</li>
3100 <li>showTreeDistances (true/false) - show or hide
3101 branch lengths (default is to show them if available)</li>
3102 <li>showUnlinkedTreeNodes (true/false) - indicate if
3103 unassociated nodes should be highlighted in the tree
3105 <li>heightScale and widthScale (1.0 or more) -
3106 increase the height or width of a cell in the alignment
3107 grid relative to the current font size.</li>
3110 <li>Non-positional features displayed in sequence ID
3112 </ul> <em>Other</em>
3114 <li>Features format: graduated colour definitions and
3115 specification of feature scores</li>
3116 <li>Alignment Annotations format: new keywords for group
3117 associated annotation (GROUP_REF) and annotation row display
3118 properties (ROW_PROPERTIES)</li>
3119 <li>XML formats extended to support graduated feature
3120 colourschemes, group associated annotation, and profile
3121 visualization settings.</li></td>
3124 <li>Source field in GFF files parsed as feature source
3125 rather than description</li>
3126 <li>Non-positional features are now included in sequence
3127 feature and gff files (controlled via non-positional feature
3128 visibility in tooltip).</li>
3129 <li>URL links generated for all feature links (bugfix)</li>
3130 <li>Added URL embedding instructions to features file
3132 <li>Codons containing ambiguous nucleotides translated as
3133 'X' in peptide product</li>
3134 <li>Match case switch in find dialog box works for both
3135 sequence ID and sequence string and query strings do not
3136 have to be in upper case to match case-insensitively.</li>
3137 <li>AMSA files only contain first column of
3138 multi-character column annotation labels</li>
3139 <li>Jalview Annotation File generation/parsing consistent
3140 with documentation (e.g. Stockholm annotation can be
3141 exported and re-imported)</li>
3142 <li>PDB files without embedded PDB IDs given a friendly
3144 <li>Find incrementally searches ID string matches as well
3145 as subsequence matches, and correctly reports total number
3149 <li>Better handling of exceptions during sequence
3151 <li>Dasobert generated non-positional feature URL
3152 link text excludes the start_end suffix</li>
3153 <li>DAS feature and source retrieval buttons disabled
3154 when fetch or registry operations in progress.</li>
3155 <li>PDB files retrieved from URLs are cached properly</li>
3156 <li>Sequence description lines properly shared via
3158 <li>Sequence fetcher fetches multiple records for all
3160 <li>Ensured that command line das feature retrieval
3161 completes before alignment figures are generated.</li>
3162 <li>Reduced time taken when opening file browser for
3164 <li>isAligned check prior to calculating tree, PCA or
3165 submitting an MSA to JNet now excludes hidden sequences.</li>
3166 <li>User defined group colours properly recovered
3167 from Jalview projects.</li>
3176 <div align="center">
3177 <strong>2.4.0.b2</strong><br> 28/10/2009
3182 <li>Experimental support for google analytics usage
3184 <li>Jalview privacy settings (user preferences and docs).</li>
3189 <li>Race condition in applet preventing startup in
3191 <li>Exception when feature created from selection beyond
3192 length of sequence.</li>
3193 <li>Allow synthetic PDB files to be imported gracefully</li>
3194 <li>Sequence associated annotation rows associate with
3195 all sequences with a given id</li>
3196 <li>Find function matches case-insensitively for sequence
3197 ID string searches</li>
3198 <li>Non-standard characters do not cause pairwise
3199 alignment to fail with exception</li>
3200 </ul> <em>Application Issues</em>
3202 <li>Sequences are now validated against EMBL database</li>
3203 <li>Sequence fetcher fetches multiple records for all
3205 </ul> <em>InstallAnywhere Issues</em>
3207 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3208 issue with installAnywhere mechanism)</li>
3209 <li>Command line launching of JARs from InstallAnywhere
3210 version (java class versioning error fixed)</li>
3217 <div align="center">
3218 <strong>2.4</strong><br> 27/8/2008
3221 <td><em>User Interface</em>
3223 <li>Linked highlighting of codon and amino acid from
3224 translation and protein products</li>
3225 <li>Linked highlighting of structure associated with
3226 residue mapping to codon position</li>
3227 <li>Sequence Fetcher provides example accession numbers
3228 and 'clear' button</li>
3229 <li>MemoryMonitor added as an option under Desktop's
3231 <li>Extract score function to parse whitespace separated
3232 numeric data in description line</li>
3233 <li>Column labels in alignment annotation can be centred.</li>
3234 <li>Tooltip for sequence associated annotation give name
3236 </ul> <em>Web Services and URL fetching</em>
3238 <li>JPred3 web service</li>
3239 <li>Prototype sequence search client (no public services
3241 <li>Fetch either seed alignment or full alignment from
3243 <li>URL Links created for matching database cross
3244 references as well as sequence ID</li>
3245 <li>URL Links can be created using regular-expressions</li>
3246 </ul> <em>Sequence Database Connectivity</em>
3248 <li>Retrieval of cross-referenced sequences from other
3250 <li>Generalised database reference retrieval and
3251 validation to all fetchable databases</li>
3252 <li>Fetch sequences from DAS sources supporting the
3253 sequence command</li>
3254 </ul> <em>Import and Export</em>
3255 <li>export annotation rows as CSV for spreadsheet import</li>
3256 <li>Jalview projects record alignment dataset associations,
3257 EMBL products, and cDNA sequence mappings</li>
3258 <li>Sequence Group colour can be specified in Annotation
3260 <li>Ad-hoc colouring of group in Annotation File using RGB
3261 triplet as name of colourscheme</li>
3262 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3264 <li>treenode binding for VAMSAS tree exchange</li>
3265 <li>local editing and update of sequences in VAMSAS
3266 alignments (experimental)</li>
3267 <li>Create new or select existing session to join</li>
3268 <li>load and save of vamsas documents</li>
3269 </ul> <em>Application command line</em>
3271 <li>-tree parameter to open trees (introduced for passing
3273 <li>-fetchfrom command line argument to specify nicknames
3274 of DAS servers to query for alignment features</li>
3275 <li>-dasserver command line argument to add new servers
3276 that are also automatically queried for features</li>
3277 <li>-groovy command line argument executes a given groovy
3278 script after all input data has been loaded and parsed</li>
3279 </ul> <em>Applet-Application data exchange</em>
3281 <li>Trees passed as applet parameters can be passed to
3282 application (when using "View in full
3283 application")</li>
3284 </ul> <em>Applet Parameters</em>
3286 <li>feature group display control parameter</li>
3287 <li>debug parameter</li>
3288 <li>showbutton parameter</li>
3289 </ul> <em>Applet API methods</em>
3291 <li>newView public method</li>
3292 <li>Window (current view) specific get/set public methods</li>
3293 <li>Feature display control methods</li>
3294 <li>get list of currently selected sequences</li>
3295 </ul> <em>New Jalview distribution features</em>
3297 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3298 <li>RELEASE file gives build properties for the latest
3299 Jalview release.</li>
3300 <li>Java 1.1 Applet build made easier and donotobfuscate
3301 property controls execution of obfuscator</li>
3302 <li>Build target for generating source distribution</li>
3303 <li>Debug flag for javacc</li>
3304 <li>.jalview_properties file is documented (slightly) in
3305 jalview.bin.Cache</li>
3306 <li>Continuous Build Integration for stable and
3307 development version of Application, Applet and source
3312 <li>selected region output includes visible annotations
3313 (for certain formats)</li>
3314 <li>edit label/displaychar contains existing label/char
3316 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3317 <li>shorter peptide product names from EMBL records</li>
3318 <li>Newick string generator makes compact representations</li>
3319 <li>bootstrap values parsed correctly for tree files with
3321 <li>pathological filechooser bug avoided by not allowing
3322 filenames containing a ':'</li>
3323 <li>Fixed exception when parsing GFF files containing
3324 global sequence features</li>
3325 <li>Alignment datasets are finalized only when number of
3326 references from alignment sequences goes to zero</li>
3327 <li>Close of tree branch colour box without colour
3328 selection causes cascading exceptions</li>
3329 <li>occasional negative imgwidth exceptions</li>
3330 <li>better reporting of non-fatal warnings to user when
3331 file parsing fails.</li>
3332 <li>Save works when Jalview project is default format</li>
3333 <li>Save as dialog opened if current alignment format is
3334 not a valid output format</li>
3335 <li>UniProt canonical names introduced for both das and
3337 <li>Histidine should be midblue (not pink!) in Zappo</li>
3338 <li>error messages passed up and output when data read
3340 <li>edit undo recovers previous dataset sequence when
3341 sequence is edited</li>
3342 <li>allow PDB files without pdb ID HEADER lines (like
3343 those generated by MODELLER) to be read in properly</li>
3344 <li>allow reading of JPred concise files as a normal
3346 <li>Stockholm annotation parsing and alignment properties
3347 import fixed for PFAM records</li>
3348 <li>Structure view windows have correct name in Desktop
3350 <li>annotation consisting of sequence associated scores
3351 can be read and written correctly to annotation file</li>
3352 <li>Aligned cDNA translation to aligned peptide works
3354 <li>Fixed display of hidden sequence markers and
3355 non-italic font for representatives in Applet</li>
3356 <li>Applet Menus are always embedded in applet window on
3358 <li>Newly shown features appear at top of stack (in
3360 <li>Annotations added via parameter not drawn properly
3361 due to null pointer exceptions</li>
3362 <li>Secondary structure lines are drawn starting from
3363 first column of alignment</li>
3364 <li>UniProt XML import updated for new schema release in
3366 <li>Sequence feature to sequence ID match for Features
3367 file is case-insensitive</li>
3368 <li>Sequence features read from Features file appended to
3369 all sequences with matching IDs</li>
3370 <li>PDB structure coloured correctly for associated views
3371 containing a sub-sequence</li>
3372 <li>PDB files can be retrieved by applet from Jar files</li>
3373 <li>feature and annotation file applet parameters
3374 referring to different directories are retrieved correctly</li>
3375 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3376 <li>Fixed application hang whilst waiting for
3377 splash-screen version check to complete</li>
3378 <li>Applet properly URLencodes input parameter values
3379 when passing them to the launchApp service</li>
3380 <li>display name and local features preserved in results
3381 retrieved from web service</li>
3382 <li>Visual delay indication for sequence retrieval and
3383 sequence fetcher initialisation</li>
3384 <li>updated Application to use DAS 1.53e version of
3385 dasobert DAS client</li>
3386 <li>Re-instated Full AMSA support and .amsa file
3388 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3396 <div align="center">
3397 <strong>2.3</strong><br> 9/5/07
3402 <li>Jmol 11.0.2 integration</li>
3403 <li>PDB views stored in Jalview XML files</li>
3404 <li>Slide sequences</li>
3405 <li>Edit sequence in place</li>
3406 <li>EMBL CDS features</li>
3407 <li>DAS Feature mapping</li>
3408 <li>Feature ordering</li>
3409 <li>Alignment Properties</li>
3410 <li>Annotation Scores</li>
3411 <li>Sort by scores</li>
3412 <li>Feature/annotation editing in applet</li>
3417 <li>Headless state operation in 2.2.1</li>
3418 <li>Incorrect and unstable DNA pairwise alignment</li>
3419 <li>Cut and paste of sequences with annotation</li>
3420 <li>Feature group display state in XML</li>
3421 <li>Feature ordering in XML</li>
3422 <li>blc file iteration selection using filename # suffix</li>
3423 <li>Stockholm alignment properties</li>
3424 <li>Stockhom alignment secondary structure annotation</li>
3425 <li>2.2.1 applet had no feature transparency</li>
3426 <li>Number pad keys can be used in cursor mode</li>
3427 <li>Structure Viewer mirror image resolved</li>
3434 <div align="center">
3435 <strong>2.2.1</strong><br> 12/2/07
3440 <li>Non standard characters can be read and displayed
3441 <li>Annotations/Features can be imported/exported to the
3443 <li>Applet allows editing of sequence/annotation/group
3444 name & description
3445 <li>Preference setting to display sequence name in
3447 <li>Annotation file format extended to allow
3448 Sequence_groups to be defined
3449 <li>Default opening of alignment overview panel can be
3450 specified in preferences
3451 <li>PDB residue numbering annotation added to associated
3457 <li>Applet crash under certain Linux OS with Java 1.6
3459 <li>Annotation file export / import bugs fixed
3460 <li>PNG / EPS image output bugs fixed
3466 <div align="center">
3467 <strong>2.2</strong><br> 27/11/06
3472 <li>Multiple views on alignment
3473 <li>Sequence feature editing
3474 <li>"Reload" alignment
3475 <li>"Save" to current filename
3476 <li>Background dependent text colour
3477 <li>Right align sequence ids
3478 <li>User-defined lower case residue colours
3481 <li>Menu item accelerator keys
3482 <li>Control-V pastes to current alignment
3483 <li>Cancel button for DAS Feature Fetching
3484 <li>PCA and PDB Viewers zoom via mouse roller
3485 <li>User-defined sub-tree colours and sub-tree selection
3487 <li>'New Window' button on the 'Output to Text box'
3492 <li>New memory efficient Undo/Redo System
3493 <li>Optimised symbol lookups and conservation/consensus
3495 <li>Region Conservation/Consensus recalculated after
3497 <li>Fixed Remove Empty Columns Bug (empty columns at end
3499 <li>Slowed DAS Feature Fetching for increased robustness.
3501 <li>Made angle brackets in ASCII feature descriptions
3503 <li>Re-instated Zoom function for PCA
3504 <li>Sequence descriptions conserved in web service
3506 <li>UniProt ID discoverer uses any word separated by
3508 <li>WsDbFetch query/result association resolved
3509 <li>Tree leaf to sequence mapping improved
3510 <li>Smooth fonts switch moved to FontChooser dialog box.
3517 <div align="center">
3518 <strong>2.1.1</strong><br> 12/9/06
3523 <li>Copy consensus sequence to clipboard</li>
3528 <li>Image output - rightmost residues are rendered if
3529 sequence id panel has been resized</li>
3530 <li>Image output - all offscreen group boundaries are
3532 <li>Annotation files with sequence references - all
3533 elements in file are relative to sequence position</li>
3534 <li>Mac Applet users can use Alt key for group editing</li>
3540 <div align="center">
3541 <strong>2.1</strong><br> 22/8/06
3546 <li>MAFFT Multiple Alignment in default Web Service list</li>
3547 <li>DAS Feature fetching</li>
3548 <li>Hide sequences and columns</li>
3549 <li>Export Annotations and Features</li>
3550 <li>GFF file reading / writing</li>
3551 <li>Associate structures with sequences from local PDB
3553 <li>Add sequences to exisiting alignment</li>
3554 <li>Recently opened files / URL lists</li>
3555 <li>Applet can launch the full application</li>
3556 <li>Applet has transparency for features (Java 1.2
3558 <li>Applet has user defined colours parameter</li>
3559 <li>Applet can load sequences from parameter
3560 "sequence<em>x</em>"
3566 <li>Redundancy Panel reinstalled in the Applet</li>
3567 <li>Monospaced font - EPS / rescaling bug fixed</li>
3568 <li>Annotation files with sequence references bug fixed</li>
3574 <div align="center">
3575 <strong>2.08.1</strong><br> 2/5/06
3580 <li>Change case of selected region from Popup menu</li>
3581 <li>Choose to match case when searching</li>
3582 <li>Middle mouse button and mouse movement can compress /
3583 expand the visible width and height of the alignment</li>
3588 <li>Annotation Panel displays complete JNet results</li>
3594 <div align="center">
3595 <strong>2.08b</strong><br> 18/4/06
3601 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3602 <li>Righthand label on wrapped alignments shows correct
3609 <div align="center">
3610 <strong>2.08</strong><br> 10/4/06
3615 <li>Editing can be locked to the selection area</li>
3616 <li>Keyboard editing</li>
3617 <li>Create sequence features from searches</li>
3618 <li>Precalculated annotations can be loaded onto
3620 <li>Features file allows grouping of features</li>
3621 <li>Annotation Colouring scheme added</li>
3622 <li>Smooth fonts off by default - Faster rendering</li>
3623 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3628 <li>Drag & Drop fixed on Linux</li>
3629 <li>Jalview Archive file faster to load/save, sequence
3630 descriptions saved.</li>
3636 <div align="center">
3637 <strong>2.07</strong><br> 12/12/05
3642 <li>PDB Structure Viewer enhanced</li>
3643 <li>Sequence Feature retrieval and display enhanced</li>
3644 <li>Choose to output sequence start-end after sequence
3645 name for file output</li>
3646 <li>Sequence Fetcher WSDBFetch@EBI</li>
3647 <li>Applet can read feature files, PDB files and can be
3648 used for HTML form input</li>
3653 <li>HTML output writes groups and features</li>
3654 <li>Group editing is Control and mouse click</li>
3655 <li>File IO bugs</li>
3661 <div align="center">
3662 <strong>2.06</strong><br> 28/9/05
3667 <li>View annotations in wrapped mode</li>
3668 <li>More options for PCA viewer</li>
3673 <li>GUI bugs resolved</li>
3674 <li>Runs with -nodisplay from command line</li>
3680 <div align="center">
3681 <strong>2.05b</strong><br> 15/9/05
3686 <li>Choose EPS export as lineart or text</li>
3687 <li>Jar files are executable</li>
3688 <li>Can read in Uracil - maps to unknown residue</li>
3693 <li>Known OutOfMemory errors give warning message</li>
3694 <li>Overview window calculated more efficiently</li>
3695 <li>Several GUI bugs resolved</li>
3701 <div align="center">
3702 <strong>2.05</strong><br> 30/8/05
3707 <li>Edit and annotate in "Wrapped" view</li>
3712 <li>Several GUI bugs resolved</li>
3718 <div align="center">
3719 <strong>2.04</strong><br> 24/8/05
3724 <li>Hold down mouse wheel & scroll to change font
3730 <li>Improved JPred client reliability</li>
3731 <li>Improved loading of Jalview files</li>
3737 <div align="center">
3738 <strong>2.03</strong><br> 18/8/05
3743 <li>Set Proxy server name and port in preferences</li>
3744 <li>Multiple URL links from sequence ids</li>
3745 <li>User Defined Colours can have a scheme name and added
3747 <li>Choose to ignore gaps in consensus calculation</li>
3748 <li>Unix users can set default web browser</li>
3749 <li>Runs without GUI for batch processing</li>
3750 <li>Dynamically generated Web Service Menus</li>
3755 <li>InstallAnywhere download for Sparc Solaris</li>
3761 <div align="center">
3762 <strong>2.02</strong><br> 18/7/05
3768 <li>Copy & Paste order of sequences maintains
3769 alignment order.</li>
3775 <div align="center">
3776 <strong>2.01</strong><br> 12/7/05
3781 <li>Use delete key for deleting selection.</li>
3782 <li>Use Mouse wheel to scroll sequences.</li>
3783 <li>Help file updated to describe how to add alignment
3785 <li>Version and build date written to build properties
3787 <li>InstallAnywhere installation will check for updates
3788 at launch of Jalview.</li>
3793 <li>Delete gaps bug fixed.</li>
3794 <li>FileChooser sorts columns.</li>
3795 <li>Can remove groups one by one.</li>
3796 <li>Filechooser icons installed.</li>
3797 <li>Finder ignores return character when searching.
3798 Return key will initiate a search.<br>
3805 <div align="center">
3806 <strong>2.0</strong><br> 20/6/05
3811 <li>New codebase</li>