3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
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.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
76 <td><div align="left">
80 <!-- JAL-2446 -->Faster and more efficient management and
81 rendering of sequence features
84 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
85 429 rate limit request hander
88 <!-- JAL-2773 -->Structure views don't get updated unless
89 their colours have changed
92 <!-- JAL-2495 -->All linked sequences are highlighted for
93 a structure mousover (Jmol) or selection (Chimera)
96 <!-- JAL-2790 -->'Cancel' button in progress bar for
97 JABAWS AACon, RNAAliFold and Disorder prediction jobs
100 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
101 view from Ensembl locus cross-references
104 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
108 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
109 feature can be disabled
112 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
113 PDB easier retrieval of sequences for lists of IDs
116 <!-- JAL-2758 -->Short names for sequences retrieved from
122 <li>Groovy interpreter updated to 2.4.12</li>
123 <li>Example groovy script for generating a matrix of
124 percent identity scores for current alignment.</li>
126 <em>Testing and Deployment</em>
129 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
133 <td><div align="left">
137 <!-- JAL-2643 -->Pressing tab after updating the colour
138 threshold text field doesn't trigger an update to the
142 <!-- JAL-2682 -->Race condition when parsing sequence ID
146 <!-- JAL-2608 -->Overview windows are also closed when
147 alignment window is closed
150 <!-- JAL-2548 -->Export of features doesn't always respect
154 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
155 takes a long time in Cursor mode
161 <!-- JAL-2777 -->Structures with whitespace chainCode
162 cannot be viewed in Chimera
165 <!-- JAL-2728 -->Protein annotation panel too high in
169 <!-- JAL-2757 -->Can't edit the query after the server
170 error warning icon is shown in Uniprot and PDB Free Text
174 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
177 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
180 <!-- JAL-2739 -->Hidden column marker in last column not
181 rendered when switching back from Wrapped to normal view
184 <!-- JAL-2768 -->Annotation display corrupted when
185 scrolling right in unwapped alignment view
188 <!-- JAL-2542 -->Existing features on subsequence
189 incorrectly relocated when full sequence retrieved from
193 <!-- JAL-2733 -->Last reported memory still shown when
194 Desktop->Show Memory is unticked (OSX only)
197 <!-- JAL-2658 -->Amend Features dialog doesn't allow
198 features of same type and group to be selected for
202 <!-- JAL-2524 -->Jalview becomes sluggish in wide
203 alignments when hidden columns are present
206 <!-- JAL-2392 -->Jalview freezes when loading and
207 displaying several structures
210 <!-- JAL-2732 -->Black outlines left after resizing or
214 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
215 within the Jalview desktop on OSX
218 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
219 when in wrapped alignment mode
222 <!-- JAL-2636 -->Scale mark not shown when close to right
223 hand end of alignment
226 <!-- JAL-2684 -->Pairwise alignment of selected regions of
227 each selected sequence do not have correct start/end
231 <!-- JAL-2793 -->Alignment ruler height set incorrectly
232 after canceling the Alignment Window's Font dialog
235 <!-- JAL-2036 -->Show cross-references not enabled after
236 restoring project until a new view is created
239 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
240 URL links appears when only default EMBL-EBI link is
241 configured (since 2.10.2b2)
244 <!-- JAL-2775 -->Overview redraws whole window when box
248 <!-- JAL-2225 -->Structure viewer doesn't map all chains
249 in a multi-chain structure when viewing alignment
250 involving more than one chain (since 2.10)
253 <!-- JAL-2811 -->Double residue highlights in cursor mode
254 if new selection moves alignment window
257 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
258 arrow key in cursor mode to pass hidden column marker
261 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
262 that produces correctly annotated transcripts and products
265 <!-- JAL-2776 -->Toggling a feature group after first time
266 doesn't update associated structure view
269 <em>Applet</em><br />
272 <!-- JAL-2687 -->Concurrent modification exception when
273 closing alignment panel
276 <em>BioJSON</em><br />
279 <!-- JAL-2546 -->BioJSON export does not preserve
280 non-positional features
283 <em>New Known Issues</em>
286 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
287 sequence features correctly (for many previous versions of
291 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
292 using cursor in wrapped panel other than top
295 <!-- JAL-2791 -->Select columns containing feature ignores
296 graduated colour threshold
299 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
300 always preserve numbering and sequence features
303 <em>Known Java 9 Issues</em>
306 <!-- JAL-2902 -->Groovy Console very slow to open and is
307 not responsive when entering characters (Webstart, Java
314 <td width="60" nowrap>
316 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
317 <em>2/10/2017</em></strong>
320 <td><div align="left">
321 <em>New features in Jalview Desktop</em>
324 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
326 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
330 <td><div align="left">
334 <td width="60" nowrap>
336 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
337 <em>7/9/2017</em></strong>
340 <td><div align="left">
344 <!-- JAL-2588 -->Show gaps in overview window by colouring
345 in grey (sequences used to be coloured grey, and gaps were
349 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
353 <!-- JAL-2587 -->Overview updates immediately on increase
354 in size and progress bar shown as higher resolution
355 overview is recalculated
360 <td><div align="left">
364 <!-- JAL-2664 -->Overview window redraws every hidden
365 column region row by row
368 <!-- JAL-2681 -->duplicate protein sequences shown after
369 retrieving Ensembl crossrefs for sequences from Uniprot
372 <!-- JAL-2603 -->Overview window throws NPE if show boxes
373 format setting is unticked
376 <!-- JAL-2610 -->Groups are coloured wrongly in overview
377 if group has show boxes format setting unticked
380 <!-- JAL-2672,JAL-2665 -->Redraw problems when
381 autoscrolling whilst dragging current selection group to
382 include sequences and columns not currently displayed
385 <!-- JAL-2691 -->Not all chains are mapped when multimeric
386 assemblies are imported via CIF file
389 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
390 displayed when threshold or conservation colouring is also
394 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
398 <!-- JAL-2673 -->Jalview continues to scroll after
399 dragging a selected region off the visible region of the
403 <!-- JAL-2724 -->Cannot apply annotation based
404 colourscheme to all groups in a view
407 <!-- JAL-2511 -->IDs don't line up with sequences
408 initially after font size change using the Font chooser or
415 <td width="60" nowrap>
417 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
420 <td><div align="left">
421 <em>Calculations</em>
425 <!-- JAL-1933 -->Occupancy annotation row shows number of
426 ungapped positions in each column of the alignment.
429 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
430 a calculation dialog box
433 <!-- JAL-2379 -->Revised implementation of PCA for speed
434 and memory efficiency (~30x faster)
437 <!-- JAL-2403 -->Revised implementation of sequence
438 similarity scores as used by Tree, PCA, Shading Consensus
439 and other calculations
442 <!-- JAL-2416 -->Score matrices are stored as resource
443 files within the Jalview codebase
446 <!-- JAL-2500 -->Trees computed on Sequence Feature
447 Similarity may have different topology due to increased
454 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
455 model for alignments and groups
458 <!-- JAL-384 -->Custom shading schemes created via groovy
465 <!-- JAL-2526 -->Efficiency improvements for interacting
466 with alignment and overview windows
469 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
473 <!-- JAL-2388 -->Hidden columns and sequences can be
477 <!-- JAL-2611 -->Click-drag in visible area allows fine
478 adjustment of visible position
482 <em>Data import/export</em>
485 <!-- JAL-2535 -->Posterior probability annotation from
486 Stockholm files imported as sequence associated annotation
489 <!-- JAL-2507 -->More robust per-sequence positional
490 annotation input/output via stockholm flatfile
493 <!-- JAL-2533 -->Sequence names don't include file
494 extension when importing structure files without embedded
495 names or PDB accessions
498 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
499 format sequence substitution matrices
502 <em>User Interface</em>
505 <!-- JAL-2447 --> Experimental Features Checkbox in
506 Desktop's Tools menu to hide or show untested features in
510 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
511 via Overview or sequence motif search operations
514 <!-- JAL-2547 -->Amend sequence features dialog box can be
515 opened by double clicking gaps within sequence feature
519 <!-- JAL-1476 -->Status bar message shown when not enough
520 aligned positions were available to create a 3D structure
524 <em>3D Structure</em>
527 <!-- JAL-2430 -->Hidden regions in alignment views are not
528 coloured in linked structure views
531 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
532 file-based command exchange
535 <!-- JAL-2375 -->Structure chooser automatically shows
536 Cached Structures rather than querying the PDBe if
537 structures are already available for sequences
540 <!-- JAL-2520 -->Structures imported via URL are cached in
541 the Jalview project rather than downloaded again when the
545 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
546 to transfer Chimera's structure attributes as Jalview
547 features, and vice-versa (<strong>Experimental
551 <em>Web Services</em>
554 <!-- JAL-2549 -->Updated JABAWS client to v2.2
557 <!-- JAL-2335 -->Filter non-standard amino acids and
558 nucleotides when submitting to AACon and other MSA
562 <!-- JAL-2316, -->URLs for viewing database
563 cross-references provided by identifiers.org and the
571 <!-- JAL-2344 -->FileFormatI interface for describing and
572 identifying file formats (instead of String constants)
575 <!-- JAL-2228 -->FeatureCounter script refactored for
576 efficiency when counting all displayed features (not
577 backwards compatible with 2.10.1)
580 <em>Example files</em>
583 <!-- JAL-2631 -->Graduated feature colour style example
584 included in the example feature file
587 <em>Documentation</em>
590 <!-- JAL-2339 -->Release notes reformatted for readability
591 with the built-in Java help viewer
594 <!-- JAL-1644 -->Find documentation updated with 'search
595 sequence description' option
601 <!-- JAL-2485, -->External service integration tests for
602 Uniprot REST Free Text Search Client
605 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
608 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
613 <td><div align="left">
614 <em>Calculations</em>
617 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
618 matrix - C->R should be '-3'<br />Old matrix restored
619 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
621 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
622 Jalview's treatment of gaps in PCA and substitution matrix
623 based Tree calculations.<br /> <br />In earlier versions
624 of Jalview, gaps matching gaps were penalised, and gaps
625 matching non-gaps penalised even more. In the PCA
626 calculation, gaps were actually treated as non-gaps - so
627 different costs were applied, which meant Jalview's PCAs
628 were different to those produced by SeqSpace.<br />Jalview
629 now treats gaps in the same way as SeqSpace (ie it scores
630 them as 0). <br /> <br />Enter the following in the
631 Groovy console to restore pre-2.10.2 behaviour:<br />
632 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
633 // for 2.10.1 mode <br />
634 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
635 // to restore 2.10.2 mode <br /> <br /> <em>Note:
636 these settings will affect all subsequent tree and PCA
637 calculations (not recommended)</em></li>
639 <!-- JAL-2424 -->Fixed off-by-one bug that affected
640 scaling of branch lengths for trees computed using
641 Sequence Feature Similarity.
644 <!-- JAL-2377 -->PCA calculation could hang when
645 generating output report when working with highly
649 <!-- JAL-2544 --> Sort by features includes features to
650 right of selected region when gaps present on right-hand
654 <em>User Interface</em>
657 <!-- JAL-2346 -->Reopening Colour by annotation dialog
658 doesn't reselect a specific sequence's associated
659 annotation after it was used for colouring a view
662 <!-- JAL-2419 -->Current selection lost if popup menu
663 opened on a region of alignment without groups
666 <!-- JAL-2374 -->Popup menu not always shown for regions
667 of an alignment with overlapping groups
670 <!-- JAL-2310 -->Finder double counts if both a sequence's
671 name and description match
674 <!-- JAL-2370 -->Hiding column selection containing two
675 hidden regions results in incorrect hidden regions
678 <!-- JAL-2386 -->'Apply to all groups' setting when
679 changing colour does not apply Conservation slider value
683 <!-- JAL-2373 -->Percentage identity and conservation menu
684 items do not show a tick or allow shading to be disabled
687 <!-- JAL-2385 -->Conservation shading or PID threshold
688 lost when base colourscheme changed if slider not visible
691 <!-- JAL-2547 -->Sequence features shown in tooltip for
692 gaps before start of features
695 <!-- JAL-2623 -->Graduated feature colour threshold not
696 restored to UI when feature colour is edited
699 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
700 a time when scrolling vertically in wrapped mode.
703 <!-- JAL-2630 -->Structure and alignment overview update
704 as graduate feature colour settings are modified via the
708 <!-- JAL-2034 -->Overview window doesn't always update
709 when a group defined on the alignment is resized
712 <!-- JAL-2605 -->Mouseovers on left/right scale region in
713 wrapped view result in positional status updates
717 <!-- JAL-2563 -->Status bar doesn't show position for
718 ambiguous amino acid and nucleotide symbols
721 <!-- JAL-2602 -->Copy consensus sequence failed if
722 alignment included gapped columns
725 <!-- JAL-2473 -->Minimum size set for Jalview windows so
726 widgets don't permanently disappear
729 <!-- JAL-2503 -->Cannot select or filter quantitative
730 annotation that are shown only as column labels (e.g.
731 T-Coffee column reliability scores)
734 <!-- JAL-2594 -->Exception thrown if trying to create a
735 sequence feature on gaps only
738 <!-- JAL-2504 -->Features created with 'New feature'
739 button from a Find inherit previously defined feature type
740 rather than the Find query string
743 <!-- JAL-2423 -->incorrect title in output window when
744 exporting tree calculated in Jalview
747 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
748 and then revealing them reorders sequences on the
752 <!-- JAL-964 -->Group panel in sequence feature settings
753 doesn't update to reflect available set of groups after
754 interactively adding or modifying features
757 <!-- JAL-2225 -->Sequence Database chooser unusable on
761 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
762 only excluded gaps in current sequence and ignored
769 <!-- JAL-2421 -->Overview window visible region moves
770 erratically when hidden rows or columns are present
773 <!-- JAL-2362 -->Per-residue colourschemes applied via the
774 Structure Viewer's colour menu don't correspond to
778 <!-- JAL-2405 -->Protein specific colours only offered in
779 colour and group colour menu for protein alignments
782 <!-- JAL-2385 -->Colour threshold slider doesn't update to
783 reflect currently selected view or group's shading
787 <!-- JAL-2624 -->Feature colour thresholds not respected
788 when rendered on overview and structures when opacity at
792 <!-- JAL-2589 -->User defined gap colour not shown in
793 overview when features overlaid on alignment
796 <em>Data import/export</em>
799 <!-- JAL-2576 -->Very large alignments take a long time to
803 <!-- JAL-2507 -->Per-sequence RNA secondary structures
804 added after a sequence was imported are not written to
808 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
809 when importing RNA secondary structure via Stockholm
812 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
813 not shown in correct direction for simple pseudoknots
816 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
817 with lightGray or darkGray via features file (but can
821 <!-- JAL-2383 -->Above PID colour threshold not recovered
822 when alignment view imported from project
825 <!-- JAL-2520,JAL-2465 -->No mappings generated between
826 structure and sequences extracted from structure files
827 imported via URL and viewed in Jmol
830 <!-- JAL-2520 -->Structures loaded via URL are saved in
831 Jalview Projects rather than fetched via URL again when
832 the project is loaded and the structure viewed
835 <em>Web Services</em>
838 <!-- JAL-2519 -->EnsemblGenomes example failing after
839 release of Ensembl v.88
842 <!-- JAL-2366 -->Proxy server address and port always
843 appear enabled in Preferences->Connections
846 <!-- JAL-2461 -->DAS registry not found exceptions
847 removed from console output
850 <!-- JAL-2582 -->Cannot retrieve protein products from
851 Ensembl by Peptide ID
854 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
855 created from SIFTs, and spurious 'Couldn't open structure
856 in Chimera' errors raised after April 2017 update (problem
857 due to 'null' string rather than empty string used for
858 residues with no corresponding PDB mapping).
861 <em>Application UI</em>
864 <!-- JAL-2361 -->User Defined Colours not added to Colour
868 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
869 case' residues (button in colourscheme editor debugged and
870 new documentation and tooltips added)
873 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
874 doesn't restore group-specific text colour thresholds
877 <!-- JAL-2243 -->Feature settings panel does not update as
878 new features are added to alignment
881 <!-- JAL-2532 -->Cancel in feature settings reverts
882 changes to feature colours via the Amend features dialog
885 <!-- JAL-2506 -->Null pointer exception when attempting to
886 edit graduated feature colour via amend features dialog
890 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
891 selection menu changes colours of alignment views
894 <!-- JAL-2426 -->Spurious exceptions in console raised
895 from alignment calculation workers after alignment has
899 <!-- JAL-1608 -->Typo in selection popup menu - Create
900 groups now 'Create Group'
903 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
904 Create/Undefine group doesn't always work
907 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
908 shown again after pressing 'Cancel'
911 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
912 adjusts start position in wrap mode
915 <!-- JAL-2563 -->Status bar doesn't show positions for
916 ambiguous amino acids
919 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
920 CDS/Protein view after CDS sequences added for aligned
924 <!-- JAL-2592 -->User defined colourschemes called 'User
925 Defined' don't appear in Colours menu
931 <!-- JAL-2468 -->Switching between Nucleotide and Protein
932 score models doesn't always result in an updated PCA plot
935 <!-- JAL-2442 -->Features not rendered as transparent on
936 overview or linked structure view
939 <!-- JAL-2372 -->Colour group by conservation doesn't
943 <!-- JAL-2517 -->Hitting Cancel after applying
944 user-defined colourscheme doesn't restore original
951 <!-- JAL-2314 -->Unit test failure:
952 jalview.ws.jabaws.RNAStructExportImport setup fails
955 <!-- JAL-2307 -->Unit test failure:
956 jalview.ws.sifts.SiftsClientTest due to compatibility
957 problems with deep array comparison equality asserts in
958 successive versions of TestNG
961 <!-- JAL-2479 -->Relocated StructureChooserTest and
962 ParameterUtilsTest Unit tests to Network suite
965 <em>New Known Issues</em>
968 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
969 phase after a sequence motif find operation
972 <!-- JAL-2550 -->Importing annotation file with rows
973 containing just upper and lower case letters are
974 interpreted as WUSS RNA secondary structure symbols
977 <!-- JAL-2590 -->Cannot load and display Newick trees
978 reliably from eggnog Ortholog database
981 <!-- JAL-2468 -->Status bar shows 'Marked x columns
982 containing features of type Highlight' when 'B' is pressed
983 to mark columns containing highlighted regions.
986 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
987 doesn't always add secondary structure annotation.
992 <td width="60" nowrap>
994 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
997 <td><div align="left">
1001 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1002 for all consensus calculations
1005 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1008 <li>Updated Jalview's Certum code signing certificate
1011 <em>Application</em>
1014 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1015 set of database cross-references, sorted alphabetically
1018 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1019 from database cross references. Users with custom links
1020 will receive a <a href="webServices/urllinks.html#warning">warning
1021 dialog</a> asking them to update their preferences.
1024 <!-- JAL-2287-->Cancel button and escape listener on
1025 dialog warning user about disconnecting Jalview from a
1029 <!-- JAL-2320-->Jalview's Chimera control window closes if
1030 the Chimera it is connected to is shut down
1033 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1034 columns menu item to mark columns containing highlighted
1035 regions (e.g. from structure selections or results of a
1039 <!-- JAL-2284-->Command line option for batch-generation
1040 of HTML pages rendering alignment data with the BioJS
1050 <!-- JAL-2286 -->Columns with more than one modal residue
1051 are not coloured or thresholded according to percent
1052 identity (first observed in Jalview 2.8.2)
1055 <!-- JAL-2301 -->Threonine incorrectly reported as not
1059 <!-- JAL-2318 -->Updates to documentation pages (above PID
1060 threshold, amino acid properties)
1063 <!-- JAL-2292 -->Lower case residues in sequences are not
1064 reported as mapped to residues in a structure file in the
1068 <!--JAL-2324 -->Identical features with non-numeric scores
1069 could be added multiple times to a sequence
1072 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1073 bond features shown as two highlighted residues rather
1074 than a range in linked structure views, and treated
1075 correctly when selecting and computing trees from features
1078 <!-- JAL-2281-->Custom URL links for database
1079 cross-references are matched to database name regardless
1084 <em>Application</em>
1087 <!-- JAL-2282-->Custom URL links for specific database
1088 names without regular expressions also offer links from
1092 <!-- JAL-2315-->Removing a single configured link in the
1093 URL links pane in Connections preferences doesn't actually
1094 update Jalview configuration
1097 <!-- JAL-2272-->CTRL-Click on a selected region to open
1098 the alignment area popup menu doesn't work on El-Capitan
1101 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1102 files with similarly named sequences if dropped onto the
1106 <!-- JAL-2312 -->Additional mappings are shown for PDB
1107 entries where more chains exist in the PDB accession than
1108 are reported in the SIFTS file
1111 <!-- JAL-2317-->Certain structures do not get mapped to
1112 the structure view when displayed with Chimera
1115 <!-- JAL-2317-->No chains shown in the Chimera view
1116 panel's View->Show Chains submenu
1119 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1120 work for wrapped alignment views
1123 <!--JAL-2197 -->Rename UI components for running JPred
1124 predictions from 'JNet' to 'JPred'
1127 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1128 corrupted when annotation panel vertical scroll is not at
1129 first annotation row
1132 <!--JAL-2332 -->Attempting to view structure for Hen
1133 lysozyme results in a PDB Client error dialog box
1136 <!-- JAL-2319 -->Structure View's mapping report switched
1137 ranges for PDB and sequence for SIFTS
1140 SIFTS 'Not_Observed' residues mapped to non-existant
1144 <!-- <em>New Known Issues</em>
1151 <td width="60" nowrap>
1152 <div align="center">
1153 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1154 <em>25/10/2016</em></strong>
1157 <td><em>Application</em>
1159 <li>3D Structure chooser opens with 'Cached structures'
1160 view if structures already loaded</li>
1161 <li>Progress bar reports models as they are loaded to
1162 structure views</li>
1168 <li>Colour by conservation always enabled and no tick
1169 shown in menu when BLOSUM or PID shading applied</li>
1170 <li>FER1_ARATH and FER2_ARATH labels were switched in
1171 example sequences/projects/trees</li>
1173 <em>Application</em>
1175 <li>Jalview projects with views of local PDB structure
1176 files saved on Windows cannot be opened on OSX</li>
1177 <li>Multiple structure views can be opened and superposed
1178 without timeout for structures with multiple models or
1179 multiple sequences in alignment</li>
1180 <li>Cannot import or associated local PDB files without a
1181 PDB ID HEADER line</li>
1182 <li>RMSD is not output in Jmol console when superposition
1184 <li>Drag and drop of URL from Browser fails for Linux and
1185 OSX versions earlier than El Capitan</li>
1186 <li>ENA client ignores invalid content from ENA server</li>
1187 <li>Exceptions are not raised in console when ENA client
1188 attempts to fetch non-existent IDs via Fetch DB Refs UI
1190 <li>Exceptions are not raised in console when a new view
1191 is created on the alignment</li>
1192 <li>OSX right-click fixed for group selections: CMD-click
1193 to insert/remove gaps in groups and CTRL-click to open group
1196 <em>Build and deployment</em>
1198 <li>URL link checker now copes with multi-line anchor
1201 <em>New Known Issues</em>
1203 <li>Drag and drop from URL links in browsers do not work
1210 <td width="60" nowrap>
1211 <div align="center">
1212 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1215 <td><em>General</em>
1218 <!-- JAL-2124 -->Updated Spanish translations.
1221 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1222 for importing structure data to Jalview. Enables mmCIF and
1226 <!-- JAL-192 --->Alignment ruler shows positions relative to
1230 <!-- JAL-2202 -->Position/residue shown in status bar when
1231 mousing over sequence associated annotation
1234 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1238 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1239 '()', canonical '[]' and invalid '{}' base pair populations
1243 <!-- JAL-2092 -->Feature settings popup menu options for
1244 showing or hiding columns containing a feature
1247 <!-- JAL-1557 -->Edit selected group by double clicking on
1248 group and sequence associated annotation labels
1251 <!-- JAL-2236 -->Sequence name added to annotation label in
1252 select/hide columns by annotation and colour by annotation
1256 </ul> <em>Application</em>
1259 <!-- JAL-2050-->Automatically hide introns when opening a
1260 gene/transcript view
1263 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1267 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1268 structure mappings with the EMBL-EBI PDBe SIFTS database
1271 <!-- JAL-2079 -->Updated download sites used for Rfam and
1272 Pfam sources to xfam.org
1275 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1278 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1279 over sequences in Jalview
1282 <!-- JAL-2027-->Support for reverse-complement coding
1283 regions in ENA and EMBL
1286 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1287 for record retrieval via ENA rest API
1290 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1294 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1295 groovy script execution
1298 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1299 alignment window's Calculate menu
1302 <!-- JAL-1812 -->Allow groovy scripts that call
1303 Jalview.getAlignFrames() to run in headless mode
1306 <!-- JAL-2068 -->Support for creating new alignment
1307 calculation workers from groovy scripts
1310 <!-- JAL-1369 --->Store/restore reference sequence in
1314 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1315 associations are now saved/restored from project
1318 <!-- JAL-1993 -->Database selection dialog always shown
1319 before sequence fetcher is opened
1322 <!-- JAL-2183 -->Double click on an entry in Jalview's
1323 database chooser opens a sequence fetcher
1326 <!-- JAL-1563 -->Free-text search client for UniProt using
1327 the UniProt REST API
1330 <!-- JAL-2168 -->-nonews command line parameter to prevent
1331 the news reader opening
1334 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1335 querying stored in preferences
1338 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1342 <!-- JAL-1977-->Tooltips shown on database chooser
1345 <!-- JAL-391 -->Reverse complement function in calculate
1346 menu for nucleotide sequences
1349 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1350 and feature counts preserves alignment ordering (and
1351 debugged for complex feature sets).
1354 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1355 viewing structures with Jalview 2.10
1358 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1359 genome, transcript CCDS and gene ids via the Ensembl and
1360 Ensembl Genomes REST API
1363 <!-- JAL-2049 -->Protein sequence variant annotation
1364 computed for 'sequence_variant' annotation on CDS regions
1368 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1372 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1373 Ref Fetcher fails to match, or otherwise updates sequence
1374 data from external database records.
1377 <!-- JAL-2154 -->Revised Jalview Project format for
1378 efficient recovery of sequence coding and alignment
1379 annotation relationships.
1381 </ul> <!-- <em>Applet</em>
1392 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1396 <!-- JAL-2018-->Export features in Jalview format (again)
1397 includes graduated colourschemes
1400 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1401 working with big alignments and lots of hidden columns
1404 <!-- JAL-2053-->Hidden column markers not always rendered
1405 at right of alignment window
1408 <!-- JAL-2067 -->Tidied up links in help file table of
1412 <!-- JAL-2072 -->Feature based tree calculation not shown
1416 <!-- JAL-2075 -->Hidden columns ignored during feature
1417 based tree calculation
1420 <!-- JAL-2065 -->Alignment view stops updating when show
1421 unconserved enabled for group on alignment
1424 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1428 <!-- JAL-2146 -->Alignment column in status incorrectly
1429 shown as "Sequence position" when mousing over
1433 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1434 hidden columns present
1437 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1438 user created annotation added to alignment
1441 <!-- JAL-1841 -->RNA Structure consensus only computed for
1442 '()' base pair annotation
1445 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1446 in zero scores for all base pairs in RNA Structure
1450 <!-- JAL-2174-->Extend selection with columns containing
1454 <!-- JAL-2275 -->Pfam format writer puts extra space at
1455 beginning of sequence
1458 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1462 <!-- JAL-2238 -->Cannot create groups on an alignment from
1463 from a tree when t-coffee scores are shown
1466 <!-- JAL-1836,1967 -->Cannot import and view PDB
1467 structures with chains containing negative resnums (4q4h)
1470 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1474 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1475 to Clustal, PIR and PileUp output
1478 <!-- JAL-2008 -->Reordering sequence features that are
1479 not visible causes alignment window to repaint
1482 <!-- JAL-2006 -->Threshold sliders don't work in
1483 graduated colour and colour by annotation row for e-value
1484 scores associated with features and annotation rows
1487 <!-- JAL-1797 -->amino acid physicochemical conservation
1488 calculation should be case independent
1491 <!-- JAL-2173 -->Remove annotation also updates hidden
1495 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1496 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1497 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1500 <!-- JAL-2065 -->Null pointer exceptions and redraw
1501 problems when reference sequence defined and 'show
1502 non-conserved' enabled
1505 <!-- JAL-1306 -->Quality and Conservation are now shown on
1506 load even when Consensus calculation is disabled
1509 <!-- JAL-1932 -->Remove right on penultimate column of
1510 alignment does nothing
1513 <em>Application</em>
1516 <!-- JAL-1552-->URLs and links can't be imported by
1517 drag'n'drop on OSX when launched via webstart (note - not
1518 yet fixed for El Capitan)
1521 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1522 output when running on non-gb/us i18n platforms
1525 <!-- JAL-1944 -->Error thrown when exporting a view with
1526 hidden sequences as flat-file alignment
1529 <!-- JAL-2030-->InstallAnywhere distribution fails when
1533 <!-- JAL-2080-->Jalview very slow to launch via webstart
1534 (also hotfix for 2.9.0b2)
1537 <!-- JAL-2085 -->Cannot save project when view has a
1538 reference sequence defined
1541 <!-- JAL-1011 -->Columns are suddenly selected in other
1542 alignments and views when revealing hidden columns
1545 <!-- JAL-1989 -->Hide columns not mirrored in complement
1546 view in a cDNA/Protein splitframe
1549 <!-- JAL-1369 -->Cannot save/restore representative
1550 sequence from project when only one sequence is
1554 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1555 in Structure Chooser
1558 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1559 structure consensus didn't refresh annotation panel
1562 <!-- JAL-1962 -->View mapping in structure view shows
1563 mappings between sequence and all chains in a PDB file
1566 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1567 dialogs format columns correctly, don't display array
1568 data, sort columns according to type
1571 <!-- JAL-1975 -->Export complete shown after destination
1572 file chooser is cancelled during an image export
1575 <!-- JAL-2025 -->Error when querying PDB Service with
1576 sequence name containing special characters
1579 <!-- JAL-2024 -->Manual PDB structure querying should be
1583 <!-- JAL-2104 -->Large tooltips with broken HTML
1584 formatting don't wrap
1587 <!-- JAL-1128 -->Figures exported from wrapped view are
1588 truncated so L looks like I in consensus annotation
1591 <!-- JAL-2003 -->Export features should only export the
1592 currently displayed features for the current selection or
1596 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1597 after fetching cross-references, and restoring from
1601 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1602 followed in the structure viewer
1605 <!-- JAL-2163 -->Titles for individual alignments in
1606 splitframe not restored from project
1609 <!-- JAL-2145 -->missing autocalculated annotation at
1610 trailing end of protein alignment in transcript/product
1611 splitview when pad-gaps not enabled by default
1614 <!-- JAL-1797 -->amino acid physicochemical conservation
1618 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1619 article has been read (reopened issue due to
1620 internationalisation problems)
1623 <!-- JAL-1960 -->Only offer PDB structures in structure
1624 viewer based on sequence name, PDB and UniProt
1629 <!-- JAL-1976 -->No progress bar shown during export of
1633 <!-- JAL-2213 -->Structures not always superimposed after
1634 multiple structures are shown for one or more sequences.
1637 <!-- JAL-1370 -->Reference sequence characters should not
1638 be replaced with '.' when 'Show unconserved' format option
1642 <!-- JAL-1823 -->Cannot specify chain code when entering
1643 specific PDB id for sequence
1646 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1647 'Export hidden sequences' is enabled, but 'export hidden
1648 columns' is disabled.
1651 <!--JAL-2026-->Best Quality option in structure chooser
1652 selects lowest rather than highest resolution structures
1656 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1657 to sequence mapping in 'View Mappings' report
1660 <!-- JAL-2284 -->Unable to read old Jalview projects that
1661 contain non-XML data added after Jalvew wrote project.
1664 <!-- JAL-2118 -->Newly created annotation row reorders
1665 after clicking on it to create new annotation for a
1669 <!-- JAL-1980 -->Null Pointer Exception raised when
1670 pressing Add on an orphaned cut'n'paste window.
1672 <!-- may exclude, this is an external service stability issue JAL-1941
1673 -- > RNA 3D structure not added via DSSR service</li> -->
1678 <!-- JAL-2151 -->Incorrect columns are selected when
1679 hidden columns present before start of sequence
1682 <!-- JAL-1986 -->Missing dependencies on applet pages
1686 <!-- JAL-1947 -->Overview pixel size changes when
1687 sequences are hidden in applet
1690 <!-- JAL-1996 -->Updated instructions for applet
1691 deployment on examples pages.
1698 <td width="60" nowrap>
1699 <div align="center">
1700 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1701 <em>16/10/2015</em></strong>
1704 <td><em>General</em>
1706 <li>Time stamps for signed Jalview application and applet
1711 <em>Application</em>
1713 <li>Duplicate group consensus and conservation rows
1714 shown when tree is partitioned</li>
1715 <li>Erratic behaviour when tree partitions made with
1716 multiple cDNA/Protein split views</li>
1722 <td width="60" nowrap>
1723 <div align="center">
1724 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1725 <em>8/10/2015</em></strong>
1728 <td><em>General</em>
1730 <li>Updated Spanish translations of localized text for
1732 </ul> <em>Application</em>
1734 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1735 <li>Signed OSX InstallAnywhere installer<br></li>
1736 <li>Support for per-sequence based annotations in BioJSON</li>
1737 </ul> <em>Applet</em>
1739 <li>Split frame example added to applet examples page</li>
1740 </ul> <em>Build and Deployment</em>
1743 <!-- JAL-1888 -->New ant target for running Jalview's test
1751 <li>Mapping of cDNA to protein in split frames
1752 incorrect when sequence start > 1</li>
1753 <li>Broken images in filter column by annotation dialog
1755 <li>Feature colours not parsed from features file</li>
1756 <li>Exceptions and incomplete link URLs recovered when
1757 loading a features file containing HTML tags in feature
1761 <em>Application</em>
1763 <li>Annotations corrupted after BioJS export and
1765 <li>Incorrect sequence limits after Fetch DB References
1766 with 'trim retrieved sequences'</li>
1767 <li>Incorrect warning about deleting all data when
1768 deleting selected columns</li>
1769 <li>Patch to build system for shipping properly signed
1770 JNLP templates for webstart launch</li>
1771 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1772 unreleased structures for download or viewing</li>
1773 <li>Tab/space/return keystroke operation of EMBL-PDBe
1774 fetcher/viewer dialogs works correctly</li>
1775 <li>Disabled 'minimise' button on Jalview windows
1776 running on OSX to workaround redraw hang bug</li>
1777 <li>Split cDNA/Protein view position and geometry not
1778 recovered from jalview project</li>
1779 <li>Initial enabled/disabled state of annotation menu
1780 sorter 'show autocalculated first/last' corresponds to
1782 <li>Restoring of Clustal, RNA Helices and T-Coffee
1783 color schemes from BioJSON</li>
1787 <li>Reorder sequences mirrored in cDNA/Protein split
1789 <li>Applet with Jmol examples not loading correctly</li>
1795 <td><div align="center">
1796 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1798 <td><em>General</em>
1800 <li>Linked visualisation and analysis of DNA and Protein
1803 <li>Translated cDNA alignments shown as split protein
1804 and DNA alignment views</li>
1805 <li>Codon consensus annotation for linked protein and
1806 cDNA alignment views</li>
1807 <li>Link cDNA or Protein product sequences by loading
1808 them onto Protein or cDNA alignments</li>
1809 <li>Reconstruct linked cDNA alignment from aligned
1810 protein sequences</li>
1813 <li>Jmol integration updated to Jmol v14.2.14</li>
1814 <li>Import and export of Jalview alignment views as <a
1815 href="features/bioJsonFormat.html">BioJSON</a></li>
1816 <li>New alignment annotation file statements for
1817 reference sequences and marking hidden columns</li>
1818 <li>Reference sequence based alignment shading to
1819 highlight variation</li>
1820 <li>Select or hide columns according to alignment
1822 <li>Find option for locating sequences by description</li>
1823 <li>Conserved physicochemical properties shown in amino
1824 acid conservation row</li>
1825 <li>Alignments can be sorted by number of RNA helices</li>
1826 </ul> <em>Application</em>
1828 <li>New cDNA/Protein analysis capabilities
1830 <li>Get Cross-References should open a Split Frame
1831 view with cDNA/Protein</li>
1832 <li>Detect when nucleotide sequences and protein
1833 sequences are placed in the same alignment</li>
1834 <li>Split cDNA/Protein views are saved in Jalview
1839 <li>Use REST API to talk to Chimera</li>
1840 <li>Selected regions in Chimera are highlighted in linked
1841 Jalview windows</li>
1843 <li>VARNA RNA viewer updated to v3.93</li>
1844 <li>VARNA views are saved in Jalview Projects</li>
1845 <li>Pseudoknots displayed as Jalview RNA annotation can
1846 be shown in VARNA</li>
1848 <li>Make groups for selection uses marked columns as well
1849 as the active selected region</li>
1851 <li>Calculate UPGMA and NJ trees using sequence feature
1853 <li>New Export options
1855 <li>New Export Settings dialog to control hidden
1856 region export in flat file generation</li>
1858 <li>Export alignment views for display with the <a
1859 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1861 <li>Export scrollable SVG in HTML page</li>
1862 <li>Optional embedding of BioJSON data when exporting
1863 alignment figures to HTML</li>
1865 <li>3D structure retrieval and display
1867 <li>Free text and structured queries with the PDBe
1869 <li>PDBe Search API based discovery and selection of
1870 PDB structures for a sequence set</li>
1874 <li>JPred4 employed for protein secondary structure
1876 <li>Hide Insertions menu option to hide unaligned columns
1877 for one or a group of sequences</li>
1878 <li>Automatically hide insertions in alignments imported
1879 from the JPred4 web server</li>
1880 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1881 system on OSX<br />LGPL libraries courtesy of <a
1882 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1884 <li>changed 'View nucleotide structure' submenu to 'View
1885 VARNA 2D Structure'</li>
1886 <li>change "View protein structure" menu option to "3D
1889 </ul> <em>Applet</em>
1891 <li>New layout for applet example pages</li>
1892 <li>New parameters to enable SplitFrame view
1893 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1894 <li>New example demonstrating linked viewing of cDNA and
1895 Protein alignments</li>
1896 </ul> <em>Development and deployment</em>
1898 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1899 <li>Include installation type and git revision in build
1900 properties and console log output</li>
1901 <li>Jalview Github organisation, and new github site for
1902 storing BioJsMSA Templates</li>
1903 <li>Jalview's unit tests now managed with TestNG</li>
1906 <!-- <em>General</em>
1908 </ul> --> <!-- issues resolved --> <em>Application</em>
1910 <li>Escape should close any open find dialogs</li>
1911 <li>Typo in select-by-features status report</li>
1912 <li>Consensus RNA secondary secondary structure
1913 predictions are not highlighted in amber</li>
1914 <li>Missing gap character in v2.7 example file means
1915 alignment appears unaligned when pad-gaps is not enabled</li>
1916 <li>First switch to RNA Helices colouring doesn't colour
1917 associated structure views</li>
1918 <li>ID width preference option is greyed out when auto
1919 width checkbox not enabled</li>
1920 <li>Stopped a warning dialog from being shown when
1921 creating user defined colours</li>
1922 <li>'View Mapping' in structure viewer shows sequence
1923 mappings for just that viewer's sequences</li>
1924 <li>Workaround for superposing PDB files containing
1925 multiple models in Chimera</li>
1926 <li>Report sequence position in status bar when hovering
1927 over Jmol structure</li>
1928 <li>Cannot output gaps as '.' symbols with Selection ->
1929 output to text box</li>
1930 <li>Flat file exports of alignments with hidden columns
1931 have incorrect sequence start/end</li>
1932 <li>'Aligning' a second chain to a Chimera structure from
1934 <li>Colour schemes applied to structure viewers don't
1935 work for nucleotide</li>
1936 <li>Loading/cut'n'pasting an empty or invalid file leads
1937 to a grey/invisible alignment window</li>
1938 <li>Exported Jpred annotation from a sequence region
1939 imports to different position</li>
1940 <li>Space at beginning of sequence feature tooltips shown
1941 on some platforms</li>
1942 <li>Chimera viewer 'View | Show Chain' menu is not
1944 <li>'New View' fails with a Null Pointer Exception in
1945 console if Chimera has been opened</li>
1946 <li>Mouseover to Chimera not working</li>
1947 <li>Miscellaneous ENA XML feature qualifiers not
1949 <li>NPE in annotation renderer after 'Extract Scores'</li>
1950 <li>If two structures in one Chimera window, mouseover of
1951 either sequence shows on first structure</li>
1952 <li>'Show annotations' options should not make
1953 non-positional annotations visible</li>
1954 <li>Subsequence secondary structure annotation not shown
1955 in right place after 'view flanking regions'</li>
1956 <li>File Save As type unset when current file format is
1958 <li>Save as '.jar' option removed for saving Jalview
1960 <li>Colour by Sequence colouring in Chimera more
1962 <li>Cannot 'add reference annotation' for a sequence in
1963 several views on same alignment</li>
1964 <li>Cannot show linked products for EMBL / ENA records</li>
1965 <li>Jalview's tooltip wraps long texts containing no
1967 </ul> <em>Applet</em>
1969 <li>Jmol to JalviewLite mouseover/link not working</li>
1970 <li>JalviewLite can't import sequences with ID
1971 descriptions containing angle brackets</li>
1972 </ul> <em>General</em>
1974 <li>Cannot export and reimport RNA secondary structure
1975 via jalview annotation file</li>
1976 <li>Random helix colour palette for colour by annotation
1977 with RNA secondary structure</li>
1978 <li>Mouseover to cDNA from STOP residue in protein
1979 translation doesn't work.</li>
1980 <li>hints when using the select by annotation dialog box</li>
1981 <li>Jmol alignment incorrect if PDB file has alternate CA
1983 <li>FontChooser message dialog appears to hang after
1984 choosing 1pt font</li>
1985 <li>Peptide secondary structure incorrectly imported from
1986 annotation file when annotation display text includes 'e' or
1988 <li>Cannot set colour of new feature type whilst creating
1990 <li>cDNA translation alignment should not be sequence
1991 order dependent</li>
1992 <li>'Show unconserved' doesn't work for lower case
1994 <li>Nucleotide ambiguity codes involving R not recognised</li>
1995 </ul> <em>Deployment and Documentation</em>
1997 <li>Applet example pages appear different to the rest of
1998 www.jalview.org</li>
1999 </ul> <em>Application Known issues</em>
2001 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2002 <li>Misleading message appears after trying to delete
2004 <li>Jalview icon not shown in dock after InstallAnywhere
2005 version launches</li>
2006 <li>Fetching EMBL reference for an RNA sequence results
2007 fails with a sequence mismatch</li>
2008 <li>Corrupted or unreadable alignment display when
2009 scrolling alignment to right</li>
2010 <li>ArrayIndexOutOfBoundsException thrown when remove
2011 empty columns called on alignment with ragged gapped ends</li>
2012 <li>auto calculated alignment annotation rows do not get
2013 placed above or below non-autocalculated rows</li>
2014 <li>Jalview dekstop becomes sluggish at full screen in
2015 ultra-high resolution</li>
2016 <li>Cannot disable consensus calculation independently of
2017 quality and conservation</li>
2018 <li>Mouseover highlighting between cDNA and protein can
2019 become sluggish with more than one splitframe shown</li>
2020 </ul> <em>Applet Known Issues</em>
2022 <li>Core PDB parsing code requires Jmol</li>
2023 <li>Sequence canvas panel goes white when alignment
2024 window is being resized</li>
2030 <td><div align="center">
2031 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2033 <td><em>General</em>
2035 <li>Updated Java code signing certificate donated by
2037 <li>Features and annotation preserved when performing
2038 pairwise alignment</li>
2039 <li>RNA pseudoknot annotation can be
2040 imported/exported/displayed</li>
2041 <li>'colour by annotation' can colour by RNA and
2042 protein secondary structure</li>
2043 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2044 post-hoc with 2.9 release</em>)
2047 </ul> <em>Application</em>
2049 <li>Extract and display secondary structure for sequences
2050 with 3D structures</li>
2051 <li>Support for parsing RNAML</li>
2052 <li>Annotations menu for layout
2054 <li>sort sequence annotation rows by alignment</li>
2055 <li>place sequence annotation above/below alignment
2058 <li>Output in Stockholm format</li>
2059 <li>Internationalisation: improved Spanish (es)
2061 <li>Structure viewer preferences tab</li>
2062 <li>Disorder and Secondary Structure annotation tracks
2063 shared between alignments</li>
2064 <li>UCSF Chimera launch and linked highlighting from
2066 <li>Show/hide all sequence associated annotation rows for
2067 all or current selection</li>
2068 <li>disorder and secondary structure predictions
2069 available as dataset annotation</li>
2070 <li>Per-sequence rna helices colouring</li>
2073 <li>Sequence database accessions imported when fetching
2074 alignments from Rfam</li>
2075 <li>update VARNA version to 3.91</li>
2077 <li>New groovy scripts for exporting aligned positions,
2078 conservation values, and calculating sum of pairs scores.</li>
2079 <li>Command line argument to set default JABAWS server</li>
2080 <li>include installation type in build properties and
2081 console log output</li>
2082 <li>Updated Jalview project format to preserve dataset
2086 <!-- issues resolved --> <em>Application</em>
2088 <li>Distinguish alignment and sequence associated RNA
2089 structure in structure->view->VARNA</li>
2090 <li>Raise dialog box if user deletes all sequences in an
2092 <li>Pressing F1 results in documentation opening twice</li>
2093 <li>Sequence feature tooltip is wrapped</li>
2094 <li>Double click on sequence associated annotation
2095 selects only first column</li>
2096 <li>Redundancy removal doesn't result in unlinked
2097 leaves shown in tree</li>
2098 <li>Undos after several redundancy removals don't undo
2100 <li>Hide sequence doesn't hide associated annotation</li>
2101 <li>User defined colours dialog box too big to fit on
2102 screen and buttons not visible</li>
2103 <li>author list isn't updated if already written to
2104 Jalview properties</li>
2105 <li>Popup menu won't open after retrieving sequence
2107 <li>File open window for associate PDB doesn't open</li>
2108 <li>Left-then-right click on a sequence id opens a
2109 browser search window</li>
2110 <li>Cannot open sequence feature shading/sort popup menu
2111 in feature settings dialog</li>
2112 <li>better tooltip placement for some areas of Jalview
2114 <li>Allow addition of JABAWS Server which doesn't
2115 pass validation</li>
2116 <li>Web services parameters dialog box is too large to
2118 <li>Muscle nucleotide alignment preset obscured by
2120 <li>JABAWS preset submenus don't contain newly
2121 defined user preset</li>
2122 <li>MSA web services warns user if they were launched
2123 with invalid input</li>
2124 <li>Jalview cannot contact DAS Registy when running on
2127 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2128 'Superpose with' submenu not shown when new view
2132 </ul> <!-- <em>Applet</em>
2134 </ul> <em>General</em>
2136 </ul>--> <em>Deployment and Documentation</em>
2138 <li>2G and 1G options in launchApp have no effect on
2139 memory allocation</li>
2140 <li>launchApp service doesn't automatically open
2141 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2143 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2144 InstallAnywhere reports cannot find valid JVM when Java
2145 1.7_055 is available
2147 </ul> <em>Application Known issues</em>
2150 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2151 corrupted or unreadable alignment display when scrolling
2155 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2156 retrieval fails but progress bar continues for DAS retrieval
2157 with large number of ID
2160 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2161 flatfile output of visible region has incorrect sequence
2165 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2166 rna structure consensus doesn't update when secondary
2167 structure tracks are rearranged
2170 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2171 invalid rna structure positional highlighting does not
2172 highlight position of invalid base pairs
2175 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2176 out of memory errors are not raised when saving Jalview
2177 project from alignment window file menu
2180 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2181 Switching to RNA Helices colouring doesn't propagate to
2185 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2186 colour by RNA Helices not enabled when user created
2187 annotation added to alignment
2190 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2191 Jalview icon not shown on dock in Mountain Lion/Webstart
2193 </ul> <em>Applet Known Issues</em>
2196 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2197 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2200 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2201 Jalview and Jmol example not compatible with IE9
2204 <li>Sort by annotation score doesn't reverse order
2210 <td><div align="center">
2211 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2214 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2217 <li>Internationalisation of user interface (usually
2218 called i18n support) and translation for Spanish locale</li>
2219 <li>Define/Undefine group on current selection with
2220 Ctrl-G/Shift Ctrl-G</li>
2221 <li>Improved group creation/removal options in
2222 alignment/sequence Popup menu</li>
2223 <li>Sensible precision for symbol distribution
2224 percentages shown in logo tooltip.</li>
2225 <li>Annotation panel height set according to amount of
2226 annotation when alignment first opened</li>
2227 </ul> <em>Application</em>
2229 <li>Interactive consensus RNA secondary structure
2230 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2231 <li>Select columns containing particular features from
2232 Feature Settings dialog</li>
2233 <li>View all 'representative' PDB structures for selected
2235 <li>Update Jalview project format:
2237 <li>New file extension for Jalview projects '.jvp'</li>
2238 <li>Preserve sequence and annotation dataset (to
2239 store secondary structure annotation,etc)</li>
2240 <li>Per group and alignment annotation and RNA helix
2244 <li>New similarity measures for PCA and Tree calculation
2246 <li>Experimental support for retrieval and viewing of
2247 flanking regions for an alignment</li>
2251 <!-- issues resolved --> <em>Application</em>
2253 <li>logo keeps spinning and status remains at queued or
2254 running after job is cancelled</li>
2255 <li>cannot export features from alignments imported from
2256 Jalview/VAMSAS projects</li>
2257 <li>Buggy slider for web service parameters that take
2259 <li>Newly created RNA secondary structure line doesn't
2260 have 'display all symbols' flag set</li>
2261 <li>T-COFFEE alignment score shading scheme and other
2262 annotation shading not saved in Jalview project</li>
2263 <li>Local file cannot be loaded in freshly downloaded
2265 <li>Jalview icon not shown on dock in Mountain
2267 <li>Load file from desktop file browser fails</li>
2268 <li>Occasional NPE thrown when calculating large trees</li>
2269 <li>Cannot reorder or slide sequences after dragging an
2270 alignment onto desktop</li>
2271 <li>Colour by annotation dialog throws NPE after using
2272 'extract scores' function</li>
2273 <li>Loading/cut'n'pasting an empty file leads to a grey
2274 alignment window</li>
2275 <li>Disorder thresholds rendered incorrectly after
2276 performing IUPred disorder prediction</li>
2277 <li>Multiple group annotated consensus rows shown when
2278 changing 'normalise logo' display setting</li>
2279 <li>Find shows blank dialog after 'finished searching' if
2280 nothing matches query</li>
2281 <li>Null Pointer Exceptions raised when sorting by
2282 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2284 <li>Errors in Jmol console when structures in alignment
2285 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2287 <li>Not all working JABAWS services are shown in
2289 <li>JAVAWS version of Jalview fails to launch with
2290 'invalid literal/length code'</li>
2291 <li>Annotation/RNA Helix colourschemes cannot be applied
2292 to alignment with groups (actually fixed in 2.8.0b1)</li>
2293 <li>RNA Helices and T-Coffee Scores available as default
2296 </ul> <em>Applet</em>
2298 <li>Remove group option is shown even when selection is
2300 <li>Apply to all groups ticked but colourscheme changes
2301 don't affect groups</li>
2302 <li>Documented RNA Helices and T-Coffee Scores as valid
2303 colourscheme name</li>
2304 <li>Annotation labels drawn on sequence IDs when
2305 Annotation panel is not displayed</li>
2306 <li>Increased font size for dropdown menus on OSX and
2307 embedded windows</li>
2308 </ul> <em>Other</em>
2310 <li>Consensus sequence for alignments/groups with a
2311 single sequence were not calculated</li>
2312 <li>annotation files that contain only groups imported as
2313 annotation and junk sequences</li>
2314 <li>Fasta files with sequences containing '*' incorrectly
2315 recognised as PFAM or BLC</li>
2316 <li>conservation/PID slider apply all groups option
2317 doesn't affect background (2.8.0b1)
2319 <li>redundancy highlighting is erratic at 0% and 100%</li>
2320 <li>Remove gapped columns fails for sequences with ragged
2322 <li>AMSA annotation row with leading spaces is not
2323 registered correctly on import</li>
2324 <li>Jalview crashes when selecting PCA analysis for
2325 certain alignments</li>
2326 <li>Opening the colour by annotation dialog for an
2327 existing annotation based 'use original colours'
2328 colourscheme loses original colours setting</li>
2333 <td><div align="center">
2334 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2335 <em>30/1/2014</em></strong>
2339 <li>Trusted certificates for JalviewLite applet and
2340 Jalview Desktop application<br />Certificate was donated by
2341 <a href="https://www.certum.eu">Certum</a> to the Jalview
2342 open source project).
2344 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2345 <li>Output in Stockholm format</li>
2346 <li>Allow import of data from gzipped files</li>
2347 <li>Export/import group and sequence associated line
2348 graph thresholds</li>
2349 <li>Nucleotide substitution matrix that supports RNA and
2350 ambiguity codes</li>
2351 <li>Allow disorder predictions to be made on the current
2352 selection (or visible selection) in the same way that JPred
2354 <li>Groovy scripting for headless Jalview operation</li>
2355 </ul> <em>Other improvements</em>
2357 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2358 <li>COMBINE statement uses current SEQUENCE_REF and
2359 GROUP_REF scope to group annotation rows</li>
2360 <li>Support '' style escaping of quotes in Newick
2362 <li>Group options for JABAWS service by command line name</li>
2363 <li>Empty tooltip shown for JABA service options with a
2364 link but no description</li>
2365 <li>Select primary source when selecting authority in
2366 database fetcher GUI</li>
2367 <li>Add .mfa to FASTA file extensions recognised by
2369 <li>Annotation label tooltip text wrap</li>
2374 <li>Slow scrolling when lots of annotation rows are
2376 <li>Lots of NPE (and slowness) after creating RNA
2377 secondary structure annotation line</li>
2378 <li>Sequence database accessions not imported when
2379 fetching alignments from Rfam</li>
2380 <li>Incorrect SHMR submission for sequences with
2382 <li>View all structures does not always superpose
2384 <li>Option widgets in service parameters not updated to
2385 reflect user or preset settings</li>
2386 <li>Null pointer exceptions for some services without
2387 presets or adjustable parameters</li>
2388 <li>Discover PDB IDs entry in structure menu doesn't
2389 discover PDB xRefs</li>
2390 <li>Exception encountered while trying to retrieve
2391 features with DAS</li>
2392 <li>Lowest value in annotation row isn't coloured
2393 when colour by annotation (per sequence) is coloured</li>
2394 <li>Keyboard mode P jumps to start of gapped region when
2395 residue follows a gap</li>
2396 <li>Jalview appears to hang importing an alignment with
2397 Wrap as default or after enabling Wrap</li>
2398 <li>'Right click to add annotations' message
2399 shown in wrap mode when no annotations present</li>
2400 <li>Disorder predictions fail with NPE if no automatic
2401 annotation already exists on alignment</li>
2402 <li>oninit javascript function should be called after
2403 initialisation completes</li>
2404 <li>Remove redundancy after disorder prediction corrupts
2405 alignment window display</li>
2406 <li>Example annotation file in documentation is invalid</li>
2407 <li>Grouped line graph annotation rows are not exported
2408 to annotation file</li>
2409 <li>Multi-harmony analysis cannot be run when only two
2411 <li>Cannot create multiple groups of line graphs with
2412 several 'combine' statements in annotation file</li>
2413 <li>Pressing return several times causes Number Format
2414 exceptions in keyboard mode</li>
2415 <li>Multi-harmony (SHMMR) method doesn't submit
2416 correct partitions for input data</li>
2417 <li>Translation from DNA to Amino Acids fails</li>
2418 <li>Jalview fail to load newick tree with quoted label</li>
2419 <li>--headless flag isn't understood</li>
2420 <li>ClassCastException when generating EPS in headless
2422 <li>Adjusting sequence-associated shading threshold only
2423 changes one row's threshold</li>
2424 <li>Preferences and Feature settings panel panel
2425 doesn't open</li>
2426 <li>hide consensus histogram also hides conservation and
2427 quality histograms</li>
2432 <td><div align="center">
2433 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2435 <td><em>Application</em>
2437 <li>Support for JABAWS 2.0 Services (AACon alignment
2438 conservation, protein disorder and Clustal Omega)</li>
2439 <li>JABAWS server status indicator in Web Services
2441 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2442 in Jalview alignment window</li>
2443 <li>Updated Jalview build and deploy framework for OSX
2444 mountain lion, windows 7, and 8</li>
2445 <li>Nucleotide substitution matrix for PCA that supports
2446 RNA and ambiguity codes</li>
2448 <li>Improved sequence database retrieval GUI</li>
2449 <li>Support fetching and database reference look up
2450 against multiple DAS sources (Fetch all from in 'fetch db
2452 <li>Jalview project improvements
2454 <li>Store and retrieve the 'belowAlignment'
2455 flag for annotation</li>
2456 <li>calcId attribute to group annotation rows on the
2458 <li>Store AACon calculation settings for a view in
2459 Jalview project</li>
2463 <li>horizontal scrolling gesture support</li>
2464 <li>Visual progress indicator when PCA calculation is
2466 <li>Simpler JABA web services menus</li>
2467 <li>visual indication that web service results are still
2468 being retrieved from server</li>
2469 <li>Serialise the dialogs that are shown when Jalview
2470 starts up for first time</li>
2471 <li>Jalview user agent string for interacting with HTTP
2473 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2475 <li>Examples directory and Groovy library included in
2476 InstallAnywhere distribution</li>
2477 </ul> <em>Applet</em>
2479 <li>RNA alignment and secondary structure annotation
2480 visualization applet example</li>
2481 </ul> <em>General</em>
2483 <li>Normalise option for consensus sequence logo</li>
2484 <li>Reset button in PCA window to return dimensions to
2486 <li>Allow seqspace or Jalview variant of alignment PCA
2488 <li>PCA with either nucleic acid and protein substitution
2490 <li>Allow windows containing HTML reports to be exported
2492 <li>Interactive display and editing of RNA secondary
2493 structure contacts</li>
2494 <li>RNA Helix Alignment Colouring</li>
2495 <li>RNA base pair logo consensus</li>
2496 <li>Parse sequence associated secondary structure
2497 information in Stockholm files</li>
2498 <li>HTML Export database accessions and annotation
2499 information presented in tooltip for sequences</li>
2500 <li>Import secondary structure from LOCARNA clustalw
2501 style RNA alignment files</li>
2502 <li>import and visualise T-COFFEE quality scores for an
2504 <li>'colour by annotation' per sequence option to
2505 shade each sequence according to its associated alignment
2507 <li>New Jalview Logo</li>
2508 </ul> <em>Documentation and Development</em>
2510 <li>documentation for score matrices used in Jalview</li>
2511 <li>New Website!</li>
2513 <td><em>Application</em>
2515 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2516 wsdbfetch REST service</li>
2517 <li>Stop windows being moved outside desktop on OSX</li>
2518 <li>Filetype associations not installed for webstart
2520 <li>Jalview does not always retrieve progress of a JABAWS
2521 job execution in full once it is complete</li>
2522 <li>revise SHMR RSBS definition to ensure alignment is
2523 uploaded via ali_file parameter</li>
2524 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2525 <li>View all structures superposed fails with exception</li>
2526 <li>Jnet job queues forever if a very short sequence is
2527 submitted for prediction</li>
2528 <li>Cut and paste menu not opened when mouse clicked on
2530 <li>Putting fractional value into integer text box in
2531 alignment parameter dialog causes Jalview to hang</li>
2532 <li>Structure view highlighting doesn't work on
2534 <li>View all structures fails with exception shown in
2536 <li>Characters in filename associated with PDBEntry not
2537 escaped in a platform independent way</li>
2538 <li>Jalview desktop fails to launch with exception when
2540 <li>Tree calculation reports 'you must have 2 or more
2541 sequences selected' when selection is empty</li>
2542 <li>Jalview desktop fails to launch with jar signature
2543 failure when java web start temporary file caching is
2545 <li>DAS Sequence retrieval with range qualification
2546 results in sequence xref which includes range qualification</li>
2547 <li>Errors during processing of command line arguments
2548 cause progress bar (JAL-898) to be removed</li>
2549 <li>Replace comma for semi-colon option not disabled for
2550 DAS sources in sequence fetcher</li>
2551 <li>Cannot close news reader when JABAWS server warning
2552 dialog is shown</li>
2553 <li>Option widgets not updated to reflect user settings</li>
2554 <li>Edited sequence not submitted to web service</li>
2555 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2556 <li>InstallAnywhere installer doesn't unpack and run
2557 on OSX Mountain Lion</li>
2558 <li>Annotation panel not given a scroll bar when
2559 sequences with alignment annotation are pasted into the
2561 <li>Sequence associated annotation rows not associated
2562 when loaded from Jalview project</li>
2563 <li>Browser launch fails with NPE on java 1.7</li>
2564 <li>JABAWS alignment marked as finished when job was
2565 cancelled or job failed due to invalid input</li>
2566 <li>NPE with v2.7 example when clicking on Tree
2567 associated with all views</li>
2568 <li>Exceptions when copy/paste sequences with grouped
2569 annotation rows to new window</li>
2570 </ul> <em>Applet</em>
2572 <li>Sequence features are momentarily displayed before
2573 they are hidden using hidefeaturegroups applet parameter</li>
2574 <li>loading features via javascript API automatically
2575 enables feature display</li>
2576 <li>scrollToColumnIn javascript API method doesn't
2578 </ul> <em>General</em>
2580 <li>Redundancy removal fails for rna alignment</li>
2581 <li>PCA calculation fails when sequence has been selected
2582 and then deselected</li>
2583 <li>PCA window shows grey box when first opened on OSX</li>
2584 <li>Letters coloured pink in sequence logo when alignment
2585 coloured with clustalx</li>
2586 <li>Choosing fonts without letter symbols defined causes
2587 exceptions and redraw errors</li>
2588 <li>Initial PCA plot view is not same as manually
2589 reconfigured view</li>
2590 <li>Grouped annotation graph label has incorrect line
2592 <li>Grouped annotation graph label display is corrupted
2593 for lots of labels</li>
2598 <div align="center">
2599 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2602 <td><em>Application</em>
2604 <li>Jalview Desktop News Reader</li>
2605 <li>Tweaked default layout of web services menu</li>
2606 <li>View/alignment association menu to enable user to
2607 easily specify which alignment a multi-structure view takes
2608 its colours/correspondences from</li>
2609 <li>Allow properties file location to be specified as URL</li>
2610 <li>Extend Jalview project to preserve associations
2611 between many alignment views and a single Jmol display</li>
2612 <li>Store annotation row height in Jalview project file</li>
2613 <li>Annotation row column label formatting attributes
2614 stored in project file</li>
2615 <li>Annotation row order for auto-calculated annotation
2616 rows preserved in Jalview project file</li>
2617 <li>Visual progress indication when Jalview state is
2618 saved using Desktop window menu</li>
2619 <li>Visual indication that command line arguments are
2620 still being processed</li>
2621 <li>Groovy script execution from URL</li>
2622 <li>Colour by annotation default min and max colours in
2624 <li>Automatically associate PDB files dragged onto an
2625 alignment with sequences that have high similarity and
2627 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2628 <li>'view structures' option to open many
2629 structures in same window</li>
2630 <li>Sort associated views menu option for tree panel</li>
2631 <li>Group all JABA and non-JABA services for a particular
2632 analysis function in its own submenu</li>
2633 </ul> <em>Applet</em>
2635 <li>Userdefined and autogenerated annotation rows for
2637 <li>Adjustment of alignment annotation pane height</li>
2638 <li>Annotation scrollbar for annotation panel</li>
2639 <li>Drag to reorder annotation rows in annotation panel</li>
2640 <li>'automaticScrolling' parameter</li>
2641 <li>Allow sequences with partial ID string matches to be
2642 annotated from GFF/Jalview features files</li>
2643 <li>Sequence logo annotation row in applet</li>
2644 <li>Absolute paths relative to host server in applet
2645 parameters are treated as such</li>
2646 <li>New in the JalviewLite javascript API:
2648 <li>JalviewLite.js javascript library</li>
2649 <li>Javascript callbacks for
2651 <li>Applet initialisation</li>
2652 <li>Sequence/alignment mouse-overs and selections</li>
2655 <li>scrollTo row and column alignment scrolling
2657 <li>Select sequence/alignment regions from javascript</li>
2658 <li>javascript structure viewer harness to pass
2659 messages between Jmol and Jalview when running as
2660 distinct applets</li>
2661 <li>sortBy method</li>
2662 <li>Set of applet and application examples shipped
2663 with documentation</li>
2664 <li>New example to demonstrate JalviewLite and Jmol
2665 javascript message exchange</li>
2667 </ul> <em>General</em>
2669 <li>Enable Jmol displays to be associated with multiple
2670 multiple alignments</li>
2671 <li>Option to automatically sort alignment with new tree</li>
2672 <li>User configurable link to enable redirects to a
2673 www.Jalview.org mirror</li>
2674 <li>Jmol colours option for Jmol displays</li>
2675 <li>Configurable newline string when writing alignment
2676 and other flat files</li>
2677 <li>Allow alignment annotation description lines to
2678 contain html tags</li>
2679 </ul> <em>Documentation and Development</em>
2681 <li>Add groovy test harness for bulk load testing to
2683 <li>Groovy script to load and align a set of sequences
2684 using a web service before displaying the result in the
2685 Jalview desktop</li>
2686 <li>Restructured javascript and applet api documentation</li>
2687 <li>Ant target to publish example html files with applet
2689 <li>Netbeans project for building Jalview from source</li>
2690 <li>ant task to create online javadoc for Jalview source</li>
2692 <td><em>Application</em>
2694 <li>User defined colourscheme throws exception when
2695 current built in colourscheme is saved as new scheme</li>
2696 <li>AlignFrame->Save in application pops up save
2697 dialog for valid filename/format</li>
2698 <li>Cannot view associated structure for UniProt sequence</li>
2699 <li>PDB file association breaks for UniProt sequence
2701 <li>Associate PDB from file dialog does not tell you
2702 which sequence is to be associated with the file</li>
2703 <li>Find All raises null pointer exception when query
2704 only matches sequence IDs</li>
2705 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2706 <li>Jalview project with Jmol views created with Jalview
2707 2.4 cannot be loaded</li>
2708 <li>Filetype associations not installed for webstart
2710 <li>Two or more chains in a single PDB file associated
2711 with sequences in different alignments do not get coloured
2712 by their associated sequence</li>
2713 <li>Visibility status of autocalculated annotation row
2714 not preserved when project is loaded</li>
2715 <li>Annotation row height and visibility attributes not
2716 stored in Jalview project</li>
2717 <li>Tree bootstraps are not preserved when saved as a
2718 Jalview project</li>
2719 <li>Envision2 workflow tooltips are corrupted</li>
2720 <li>Enabling show group conservation also enables colour
2721 by conservation</li>
2722 <li>Duplicate group associated conservation or consensus
2723 created on new view</li>
2724 <li>Annotation scrollbar not displayed after 'show
2725 all hidden annotation rows' option selected</li>
2726 <li>Alignment quality not updated after alignment
2727 annotation row is hidden then shown</li>
2728 <li>Preserve colouring of structures coloured by
2729 sequences in pre Jalview 2.7 projects</li>
2730 <li>Web service job parameter dialog is not laid out
2732 <li>Web services menu not refreshed after 'reset
2733 services' button is pressed in preferences</li>
2734 <li>Annotation off by one in Jalview v2_3 example project</li>
2735 <li>Structures imported from file and saved in project
2736 get name like jalview_pdb1234.txt when reloaded</li>
2737 <li>Jalview does not always retrieve progress of a JABAWS
2738 job execution in full once it is complete</li>
2739 </ul> <em>Applet</em>
2741 <li>Alignment height set incorrectly when lots of
2742 annotation rows are displayed</li>
2743 <li>Relative URLs in feature HTML text not resolved to
2745 <li>View follows highlighting does not work for positions
2747 <li><= shown as = in tooltip</li>
2748 <li>Export features raises exception when no features
2750 <li>Separator string used for serialising lists of IDs
2751 for javascript api is modified when separator string
2752 provided as parameter</li>
2753 <li>Null pointer exception when selecting tree leaves for
2754 alignment with no existing selection</li>
2755 <li>Relative URLs for datasources assumed to be relative
2756 to applet's codebase</li>
2757 <li>Status bar not updated after finished searching and
2758 search wraps around to first result</li>
2759 <li>StructureSelectionManager instance shared between
2760 several Jalview applets causes race conditions and memory
2762 <li>Hover tooltip and mouseover of position on structure
2763 not sent from Jmol in applet</li>
2764 <li>Certain sequences of javascript method calls to
2765 applet API fatally hang browser</li>
2766 </ul> <em>General</em>
2768 <li>View follows structure mouseover scrolls beyond
2769 position with wrapped view and hidden regions</li>
2770 <li>Find sequence position moves to wrong residue
2771 with/without hidden columns</li>
2772 <li>Sequence length given in alignment properties window
2774 <li>InvalidNumberFormat exceptions thrown when trying to
2775 import PDB like structure files</li>
2776 <li>Positional search results are only highlighted
2777 between user-supplied sequence start/end bounds</li>
2778 <li>End attribute of sequence is not validated</li>
2779 <li>Find dialog only finds first sequence containing a
2780 given sequence position</li>
2781 <li>Sequence numbering not preserved in MSF alignment
2783 <li>Jalview PDB file reader does not extract sequence
2784 from nucleotide chains correctly</li>
2785 <li>Structure colours not updated when tree partition
2786 changed in alignment</li>
2787 <li>Sequence associated secondary structure not correctly
2788 parsed in interleaved stockholm</li>
2789 <li>Colour by annotation dialog does not restore current
2791 <li>Hiding (nearly) all sequences doesn't work
2793 <li>Sequences containing lowercase letters are not
2794 properly associated with their pdb files</li>
2795 </ul> <em>Documentation and Development</em>
2797 <li>schemas/JalviewWsParamSet.xsd corrupted by
2798 ApplyCopyright tool</li>
2803 <div align="center">
2804 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2807 <td><em>Application</em>
2809 <li>New warning dialog when the Jalview Desktop cannot
2810 contact web services</li>
2811 <li>JABA service parameters for a preset are shown in
2812 service job window</li>
2813 <li>JABA Service menu entries reworded</li>
2817 <li>Modeller PIR IO broken - cannot correctly import a
2818 pir file emitted by Jalview</li>
2819 <li>Existing feature settings transferred to new
2820 alignment view created from cut'n'paste</li>
2821 <li>Improved test for mixed amino/nucleotide chains when
2822 parsing PDB files</li>
2823 <li>Consensus and conservation annotation rows
2824 occasionally become blank for all new windows</li>
2825 <li>Exception raised when right clicking above sequences
2826 in wrapped view mode</li>
2827 </ul> <em>Application</em>
2829 <li>multiple multiply aligned structure views cause cpu
2830 usage to hit 100% and computer to hang</li>
2831 <li>Web Service parameter layout breaks for long user
2832 parameter names</li>
2833 <li>Jaba service discovery hangs desktop if Jaba server
2840 <div align="center">
2841 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2844 <td><em>Application</em>
2846 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2847 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2850 <li>Web Services preference tab</li>
2851 <li>Analysis parameters dialog box and user defined
2853 <li>Improved speed and layout of Envision2 service menu</li>
2854 <li>Superpose structures using associated sequence
2856 <li>Export coordinates and projection as CSV from PCA
2858 </ul> <em>Applet</em>
2860 <li>enable javascript: execution by the applet via the
2861 link out mechanism</li>
2862 </ul> <em>Other</em>
2864 <li>Updated the Jmol Jalview interface to work with Jmol
2866 <li>The Jalview Desktop and JalviewLite applet now
2867 require Java 1.5</li>
2868 <li>Allow Jalview feature colour specification for GFF
2869 sequence annotation files</li>
2870 <li>New 'colour by label' keword in Jalview feature file
2871 type colour specification</li>
2872 <li>New Jalview Desktop Groovy API method that allows a
2873 script to check if it being run in an interactive session or
2874 in a batch operation from the Jalview command line</li>
2878 <li>clustalx colourscheme colours Ds preferentially when
2879 both D+E are present in over 50% of the column</li>
2880 </ul> <em>Application</em>
2882 <li>typo in AlignmentFrame->View->Hide->all but
2883 selected Regions menu item</li>
2884 <li>sequence fetcher replaces ',' for ';' when the ',' is
2885 part of a valid accession ID</li>
2886 <li>fatal OOM if object retrieved by sequence fetcher
2887 runs out of memory</li>
2888 <li>unhandled Out of Memory Error when viewing pca
2889 analysis results</li>
2890 <li>InstallAnywhere builds fail to launch on OS X java
2891 10.5 update 4 (due to apple Java 1.6 update)</li>
2892 <li>Installanywhere Jalview silently fails to launch</li>
2893 </ul> <em>Applet</em>
2895 <li>Jalview.getFeatureGroups() raises an
2896 ArrayIndexOutOfBoundsException if no feature groups are
2903 <div align="center">
2904 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2910 <li>Alignment prettyprinter doesn't cope with long
2912 <li>clustalx colourscheme colours Ds preferentially when
2913 both D+E are present in over 50% of the column</li>
2914 <li>nucleic acid structures retrieved from PDB do not
2915 import correctly</li>
2916 <li>More columns get selected than were clicked on when a
2917 number of columns are hidden</li>
2918 <li>annotation label popup menu not providing correct
2919 add/hide/show options when rows are hidden or none are
2921 <li>Stockholm format shown in list of readable formats,
2922 and parser copes better with alignments from RFAM.</li>
2923 <li>CSV output of consensus only includes the percentage
2924 of all symbols if sequence logo display is enabled</li>
2926 </ul> <em>Applet</em>
2928 <li>annotation panel disappears when annotation is
2930 </ul> <em>Application</em>
2932 <li>Alignment view not redrawn properly when new
2933 alignment opened where annotation panel is visible but no
2934 annotations are present on alignment</li>
2935 <li>pasted region containing hidden columns is
2936 incorrectly displayed in new alignment window</li>
2937 <li>Jalview slow to complete operations when stdout is
2938 flooded (fix is to close the Jalview console)</li>
2939 <li>typo in AlignmentFrame->View->Hide->all but
2940 selected Rregions menu item.</li>
2941 <li>inconsistent group submenu and Format submenu entry
2942 'Un' or 'Non'conserved</li>
2943 <li>Sequence feature settings are being shared by
2944 multiple distinct alignments</li>
2945 <li>group annotation not recreated when tree partition is
2947 <li>double click on group annotation to select sequences
2948 does not propagate to associated trees</li>
2949 <li>Mac OSX specific issues:
2951 <li>exception raised when mouse clicked on desktop
2952 window background</li>
2953 <li>Desktop menu placed on menu bar and application
2954 name set correctly</li>
2955 <li>sequence feature settings not wide enough for the
2956 save feature colourscheme button</li>
2965 <div align="center">
2966 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2969 <td><em>New Capabilities</em>
2971 <li>URL links generated from description line for
2972 regular-expression based URL links (applet and application)
2974 <li>Non-positional feature URL links are shown in link
2976 <li>Linked viewing of nucleic acid sequences and
2978 <li>Automatic Scrolling option in View menu to display
2979 the currently highlighted region of an alignment.</li>
2980 <li>Order an alignment by sequence length, or using the
2981 average score or total feature count for each sequence.</li>
2982 <li>Shading features by score or associated description</li>
2983 <li>Subdivide alignment and groups based on identity of
2984 selected subsequence (Make Groups from Selection).</li>
2985 <li>New hide/show options including Shift+Control+H to
2986 hide everything but the currently selected region.</li>
2987 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2988 </ul> <em>Application</em>
2990 <li>Fetch DB References capabilities and UI expanded to
2991 support retrieval from DAS sequence sources</li>
2992 <li>Local DAS Sequence sources can be added via the
2993 command line or via the Add local source dialog box.</li>
2994 <li>DAS Dbref and DbxRef feature types are parsed as
2995 database references and protein_name is parsed as
2996 description line (BioSapiens terms).</li>
2997 <li>Enable or disable non-positional feature and database
2998 references in sequence ID tooltip from View menu in
3000 <!-- <li>New hidden columns and rows and representatives capabilities
3001 in annotations file (in progress - not yet fully implemented)</li> -->
3002 <li>Group-associated consensus, sequence logos and
3003 conservation plots</li>
3004 <li>Symbol distributions for each column can be exported
3005 and visualized as sequence logos</li>
3006 <li>Optionally scale multi-character column labels to fit
3007 within each column of annotation row<!-- todo for applet -->
3009 <li>Optional automatic sort of associated alignment view
3010 when a new tree is opened.</li>
3011 <li>Jalview Java Console</li>
3012 <li>Better placement of desktop window when moving
3013 between different screens.</li>
3014 <li>New preference items for sequence ID tooltip and
3015 consensus annotation</li>
3016 <li>Client to submit sequences and IDs to Envision2
3018 <li><em>Vamsas Capabilities</em>
3020 <li>Improved VAMSAS synchronization (Jalview archive
3021 used to preserve views, structures, and tree display
3023 <li>Import of vamsas documents from disk or URL via
3025 <li>Sharing of selected regions between views and
3026 with other VAMSAS applications (Experimental feature!)</li>
3027 <li>Updated API to VAMSAS version 0.2</li>
3029 </ul> <em>Applet</em>
3031 <li>Middle button resizes annotation row height</li>
3034 <li>sortByTree (true/false) - automatically sort the
3035 associated alignment view by the tree when a new tree is
3037 <li>showTreeBootstraps (true/false) - show or hide
3038 branch bootstraps (default is to show them if available)</li>
3039 <li>showTreeDistances (true/false) - show or hide
3040 branch lengths (default is to show them if available)</li>
3041 <li>showUnlinkedTreeNodes (true/false) - indicate if
3042 unassociated nodes should be highlighted in the tree
3044 <li>heightScale and widthScale (1.0 or more) -
3045 increase the height or width of a cell in the alignment
3046 grid relative to the current font size.</li>
3049 <li>Non-positional features displayed in sequence ID
3051 </ul> <em>Other</em>
3053 <li>Features format: graduated colour definitions and
3054 specification of feature scores</li>
3055 <li>Alignment Annotations format: new keywords for group
3056 associated annotation (GROUP_REF) and annotation row display
3057 properties (ROW_PROPERTIES)</li>
3058 <li>XML formats extended to support graduated feature
3059 colourschemes, group associated annotation, and profile
3060 visualization settings.</li></td>
3063 <li>Source field in GFF files parsed as feature source
3064 rather than description</li>
3065 <li>Non-positional features are now included in sequence
3066 feature and gff files (controlled via non-positional feature
3067 visibility in tooltip).</li>
3068 <li>URL links generated for all feature links (bugfix)</li>
3069 <li>Added URL embedding instructions to features file
3071 <li>Codons containing ambiguous nucleotides translated as
3072 'X' in peptide product</li>
3073 <li>Match case switch in find dialog box works for both
3074 sequence ID and sequence string and query strings do not
3075 have to be in upper case to match case-insensitively.</li>
3076 <li>AMSA files only contain first column of
3077 multi-character column annotation labels</li>
3078 <li>Jalview Annotation File generation/parsing consistent
3079 with documentation (e.g. Stockholm annotation can be
3080 exported and re-imported)</li>
3081 <li>PDB files without embedded PDB IDs given a friendly
3083 <li>Find incrementally searches ID string matches as well
3084 as subsequence matches, and correctly reports total number
3088 <li>Better handling of exceptions during sequence
3090 <li>Dasobert generated non-positional feature URL
3091 link text excludes the start_end suffix</li>
3092 <li>DAS feature and source retrieval buttons disabled
3093 when fetch or registry operations in progress.</li>
3094 <li>PDB files retrieved from URLs are cached properly</li>
3095 <li>Sequence description lines properly shared via
3097 <li>Sequence fetcher fetches multiple records for all
3099 <li>Ensured that command line das feature retrieval
3100 completes before alignment figures are generated.</li>
3101 <li>Reduced time taken when opening file browser for
3103 <li>isAligned check prior to calculating tree, PCA or
3104 submitting an MSA to JNet now excludes hidden sequences.</li>
3105 <li>User defined group colours properly recovered
3106 from Jalview projects.</li>
3115 <div align="center">
3116 <strong>2.4.0.b2</strong><br> 28/10/2009
3121 <li>Experimental support for google analytics usage
3123 <li>Jalview privacy settings (user preferences and docs).</li>
3128 <li>Race condition in applet preventing startup in
3130 <li>Exception when feature created from selection beyond
3131 length of sequence.</li>
3132 <li>Allow synthetic PDB files to be imported gracefully</li>
3133 <li>Sequence associated annotation rows associate with
3134 all sequences with a given id</li>
3135 <li>Find function matches case-insensitively for sequence
3136 ID string searches</li>
3137 <li>Non-standard characters do not cause pairwise
3138 alignment to fail with exception</li>
3139 </ul> <em>Application Issues</em>
3141 <li>Sequences are now validated against EMBL database</li>
3142 <li>Sequence fetcher fetches multiple records for all
3144 </ul> <em>InstallAnywhere Issues</em>
3146 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3147 issue with installAnywhere mechanism)</li>
3148 <li>Command line launching of JARs from InstallAnywhere
3149 version (java class versioning error fixed)</li>
3156 <div align="center">
3157 <strong>2.4</strong><br> 27/8/2008
3160 <td><em>User Interface</em>
3162 <li>Linked highlighting of codon and amino acid from
3163 translation and protein products</li>
3164 <li>Linked highlighting of structure associated with
3165 residue mapping to codon position</li>
3166 <li>Sequence Fetcher provides example accession numbers
3167 and 'clear' button</li>
3168 <li>MemoryMonitor added as an option under Desktop's
3170 <li>Extract score function to parse whitespace separated
3171 numeric data in description line</li>
3172 <li>Column labels in alignment annotation can be centred.</li>
3173 <li>Tooltip for sequence associated annotation give name
3175 </ul> <em>Web Services and URL fetching</em>
3177 <li>JPred3 web service</li>
3178 <li>Prototype sequence search client (no public services
3180 <li>Fetch either seed alignment or full alignment from
3182 <li>URL Links created for matching database cross
3183 references as well as sequence ID</li>
3184 <li>URL Links can be created using regular-expressions</li>
3185 </ul> <em>Sequence Database Connectivity</em>
3187 <li>Retrieval of cross-referenced sequences from other
3189 <li>Generalised database reference retrieval and
3190 validation to all fetchable databases</li>
3191 <li>Fetch sequences from DAS sources supporting the
3192 sequence command</li>
3193 </ul> <em>Import and Export</em>
3194 <li>export annotation rows as CSV for spreadsheet import</li>
3195 <li>Jalview projects record alignment dataset associations,
3196 EMBL products, and cDNA sequence mappings</li>
3197 <li>Sequence Group colour can be specified in Annotation
3199 <li>Ad-hoc colouring of group in Annotation File using RGB
3200 triplet as name of colourscheme</li>
3201 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3203 <li>treenode binding for VAMSAS tree exchange</li>
3204 <li>local editing and update of sequences in VAMSAS
3205 alignments (experimental)</li>
3206 <li>Create new or select existing session to join</li>
3207 <li>load and save of vamsas documents</li>
3208 </ul> <em>Application command line</em>
3210 <li>-tree parameter to open trees (introduced for passing
3212 <li>-fetchfrom command line argument to specify nicknames
3213 of DAS servers to query for alignment features</li>
3214 <li>-dasserver command line argument to add new servers
3215 that are also automatically queried for features</li>
3216 <li>-groovy command line argument executes a given groovy
3217 script after all input data has been loaded and parsed</li>
3218 </ul> <em>Applet-Application data exchange</em>
3220 <li>Trees passed as applet parameters can be passed to
3221 application (when using "View in full
3222 application")</li>
3223 </ul> <em>Applet Parameters</em>
3225 <li>feature group display control parameter</li>
3226 <li>debug parameter</li>
3227 <li>showbutton parameter</li>
3228 </ul> <em>Applet API methods</em>
3230 <li>newView public method</li>
3231 <li>Window (current view) specific get/set public methods</li>
3232 <li>Feature display control methods</li>
3233 <li>get list of currently selected sequences</li>
3234 </ul> <em>New Jalview distribution features</em>
3236 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3237 <li>RELEASE file gives build properties for the latest
3238 Jalview release.</li>
3239 <li>Java 1.1 Applet build made easier and donotobfuscate
3240 property controls execution of obfuscator</li>
3241 <li>Build target for generating source distribution</li>
3242 <li>Debug flag for javacc</li>
3243 <li>.jalview_properties file is documented (slightly) in
3244 jalview.bin.Cache</li>
3245 <li>Continuous Build Integration for stable and
3246 development version of Application, Applet and source
3251 <li>selected region output includes visible annotations
3252 (for certain formats)</li>
3253 <li>edit label/displaychar contains existing label/char
3255 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3256 <li>shorter peptide product names from EMBL records</li>
3257 <li>Newick string generator makes compact representations</li>
3258 <li>bootstrap values parsed correctly for tree files with
3260 <li>pathological filechooser bug avoided by not allowing
3261 filenames containing a ':'</li>
3262 <li>Fixed exception when parsing GFF files containing
3263 global sequence features</li>
3264 <li>Alignment datasets are finalized only when number of
3265 references from alignment sequences goes to zero</li>
3266 <li>Close of tree branch colour box without colour
3267 selection causes cascading exceptions</li>
3268 <li>occasional negative imgwidth exceptions</li>
3269 <li>better reporting of non-fatal warnings to user when
3270 file parsing fails.</li>
3271 <li>Save works when Jalview project is default format</li>
3272 <li>Save as dialog opened if current alignment format is
3273 not a valid output format</li>
3274 <li>UniProt canonical names introduced for both das and
3276 <li>Histidine should be midblue (not pink!) in Zappo</li>
3277 <li>error messages passed up and output when data read
3279 <li>edit undo recovers previous dataset sequence when
3280 sequence is edited</li>
3281 <li>allow PDB files without pdb ID HEADER lines (like
3282 those generated by MODELLER) to be read in properly</li>
3283 <li>allow reading of JPred concise files as a normal
3285 <li>Stockholm annotation parsing and alignment properties
3286 import fixed for PFAM records</li>
3287 <li>Structure view windows have correct name in Desktop
3289 <li>annotation consisting of sequence associated scores
3290 can be read and written correctly to annotation file</li>
3291 <li>Aligned cDNA translation to aligned peptide works
3293 <li>Fixed display of hidden sequence markers and
3294 non-italic font for representatives in Applet</li>
3295 <li>Applet Menus are always embedded in applet window on
3297 <li>Newly shown features appear at top of stack (in
3299 <li>Annotations added via parameter not drawn properly
3300 due to null pointer exceptions</li>
3301 <li>Secondary structure lines are drawn starting from
3302 first column of alignment</li>
3303 <li>UniProt XML import updated for new schema release in
3305 <li>Sequence feature to sequence ID match for Features
3306 file is case-insensitive</li>
3307 <li>Sequence features read from Features file appended to
3308 all sequences with matching IDs</li>
3309 <li>PDB structure coloured correctly for associated views
3310 containing a sub-sequence</li>
3311 <li>PDB files can be retrieved by applet from Jar files</li>
3312 <li>feature and annotation file applet parameters
3313 referring to different directories are retrieved correctly</li>
3314 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3315 <li>Fixed application hang whilst waiting for
3316 splash-screen version check to complete</li>
3317 <li>Applet properly URLencodes input parameter values
3318 when passing them to the launchApp service</li>
3319 <li>display name and local features preserved in results
3320 retrieved from web service</li>
3321 <li>Visual delay indication for sequence retrieval and
3322 sequence fetcher initialisation</li>
3323 <li>updated Application to use DAS 1.53e version of
3324 dasobert DAS client</li>
3325 <li>Re-instated Full AMSA support and .amsa file
3327 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3335 <div align="center">
3336 <strong>2.3</strong><br> 9/5/07
3341 <li>Jmol 11.0.2 integration</li>
3342 <li>PDB views stored in Jalview XML files</li>
3343 <li>Slide sequences</li>
3344 <li>Edit sequence in place</li>
3345 <li>EMBL CDS features</li>
3346 <li>DAS Feature mapping</li>
3347 <li>Feature ordering</li>
3348 <li>Alignment Properties</li>
3349 <li>Annotation Scores</li>
3350 <li>Sort by scores</li>
3351 <li>Feature/annotation editing in applet</li>
3356 <li>Headless state operation in 2.2.1</li>
3357 <li>Incorrect and unstable DNA pairwise alignment</li>
3358 <li>Cut and paste of sequences with annotation</li>
3359 <li>Feature group display state in XML</li>
3360 <li>Feature ordering in XML</li>
3361 <li>blc file iteration selection using filename # suffix</li>
3362 <li>Stockholm alignment properties</li>
3363 <li>Stockhom alignment secondary structure annotation</li>
3364 <li>2.2.1 applet had no feature transparency</li>
3365 <li>Number pad keys can be used in cursor mode</li>
3366 <li>Structure Viewer mirror image resolved</li>
3373 <div align="center">
3374 <strong>2.2.1</strong><br> 12/2/07
3379 <li>Non standard characters can be read and displayed
3380 <li>Annotations/Features can be imported/exported to the
3382 <li>Applet allows editing of sequence/annotation/group
3383 name & description
3384 <li>Preference setting to display sequence name in
3386 <li>Annotation file format extended to allow
3387 Sequence_groups to be defined
3388 <li>Default opening of alignment overview panel can be
3389 specified in preferences
3390 <li>PDB residue numbering annotation added to associated
3396 <li>Applet crash under certain Linux OS with Java 1.6
3398 <li>Annotation file export / import bugs fixed
3399 <li>PNG / EPS image output bugs fixed
3405 <div align="center">
3406 <strong>2.2</strong><br> 27/11/06
3411 <li>Multiple views on alignment
3412 <li>Sequence feature editing
3413 <li>"Reload" alignment
3414 <li>"Save" to current filename
3415 <li>Background dependent text colour
3416 <li>Right align sequence ids
3417 <li>User-defined lower case residue colours
3420 <li>Menu item accelerator keys
3421 <li>Control-V pastes to current alignment
3422 <li>Cancel button for DAS Feature Fetching
3423 <li>PCA and PDB Viewers zoom via mouse roller
3424 <li>User-defined sub-tree colours and sub-tree selection
3426 <li>'New Window' button on the 'Output to Text box'
3431 <li>New memory efficient Undo/Redo System
3432 <li>Optimised symbol lookups and conservation/consensus
3434 <li>Region Conservation/Consensus recalculated after
3436 <li>Fixed Remove Empty Columns Bug (empty columns at end
3438 <li>Slowed DAS Feature Fetching for increased robustness.
3440 <li>Made angle brackets in ASCII feature descriptions
3442 <li>Re-instated Zoom function for PCA
3443 <li>Sequence descriptions conserved in web service
3445 <li>UniProt ID discoverer uses any word separated by
3447 <li>WsDbFetch query/result association resolved
3448 <li>Tree leaf to sequence mapping improved
3449 <li>Smooth fonts switch moved to FontChooser dialog box.
3456 <div align="center">
3457 <strong>2.1.1</strong><br> 12/9/06
3462 <li>Copy consensus sequence to clipboard</li>
3467 <li>Image output - rightmost residues are rendered if
3468 sequence id panel has been resized</li>
3469 <li>Image output - all offscreen group boundaries are
3471 <li>Annotation files with sequence references - all
3472 elements in file are relative to sequence position</li>
3473 <li>Mac Applet users can use Alt key for group editing</li>
3479 <div align="center">
3480 <strong>2.1</strong><br> 22/8/06
3485 <li>MAFFT Multiple Alignment in default Web Service list</li>
3486 <li>DAS Feature fetching</li>
3487 <li>Hide sequences and columns</li>
3488 <li>Export Annotations and Features</li>
3489 <li>GFF file reading / writing</li>
3490 <li>Associate structures with sequences from local PDB
3492 <li>Add sequences to exisiting alignment</li>
3493 <li>Recently opened files / URL lists</li>
3494 <li>Applet can launch the full application</li>
3495 <li>Applet has transparency for features (Java 1.2
3497 <li>Applet has user defined colours parameter</li>
3498 <li>Applet can load sequences from parameter
3499 "sequence<em>x</em>"
3505 <li>Redundancy Panel reinstalled in the Applet</li>
3506 <li>Monospaced font - EPS / rescaling bug fixed</li>
3507 <li>Annotation files with sequence references bug fixed</li>
3513 <div align="center">
3514 <strong>2.08.1</strong><br> 2/5/06
3519 <li>Change case of selected region from Popup menu</li>
3520 <li>Choose to match case when searching</li>
3521 <li>Middle mouse button and mouse movement can compress /
3522 expand the visible width and height of the alignment</li>
3527 <li>Annotation Panel displays complete JNet results</li>
3533 <div align="center">
3534 <strong>2.08b</strong><br> 18/4/06
3540 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3541 <li>Righthand label on wrapped alignments shows correct
3548 <div align="center">
3549 <strong>2.08</strong><br> 10/4/06
3554 <li>Editing can be locked to the selection area</li>
3555 <li>Keyboard editing</li>
3556 <li>Create sequence features from searches</li>
3557 <li>Precalculated annotations can be loaded onto
3559 <li>Features file allows grouping of features</li>
3560 <li>Annotation Colouring scheme added</li>
3561 <li>Smooth fonts off by default - Faster rendering</li>
3562 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3567 <li>Drag & Drop fixed on Linux</li>
3568 <li>Jalview Archive file faster to load/save, sequence
3569 descriptions saved.</li>
3575 <div align="center">
3576 <strong>2.07</strong><br> 12/12/05
3581 <li>PDB Structure Viewer enhanced</li>
3582 <li>Sequence Feature retrieval and display enhanced</li>
3583 <li>Choose to output sequence start-end after sequence
3584 name for file output</li>
3585 <li>Sequence Fetcher WSDBFetch@EBI</li>
3586 <li>Applet can read feature files, PDB files and can be
3587 used for HTML form input</li>
3592 <li>HTML output writes groups and features</li>
3593 <li>Group editing is Control and mouse click</li>
3594 <li>File IO bugs</li>
3600 <div align="center">
3601 <strong>2.06</strong><br> 28/9/05
3606 <li>View annotations in wrapped mode</li>
3607 <li>More options for PCA viewer</li>
3612 <li>GUI bugs resolved</li>
3613 <li>Runs with -nodisplay from command line</li>
3619 <div align="center">
3620 <strong>2.05b</strong><br> 15/9/05
3625 <li>Choose EPS export as lineart or text</li>
3626 <li>Jar files are executable</li>
3627 <li>Can read in Uracil - maps to unknown residue</li>
3632 <li>Known OutOfMemory errors give warning message</li>
3633 <li>Overview window calculated more efficiently</li>
3634 <li>Several GUI bugs resolved</li>
3640 <div align="center">
3641 <strong>2.05</strong><br> 30/8/05
3646 <li>Edit and annotate in "Wrapped" view</li>
3651 <li>Several GUI bugs resolved</li>
3657 <div align="center">
3658 <strong>2.04</strong><br> 24/8/05
3663 <li>Hold down mouse wheel & scroll to change font
3669 <li>Improved JPred client reliability</li>
3670 <li>Improved loading of Jalview files</li>
3676 <div align="center">
3677 <strong>2.03</strong><br> 18/8/05
3682 <li>Set Proxy server name and port in preferences</li>
3683 <li>Multiple URL links from sequence ids</li>
3684 <li>User Defined Colours can have a scheme name and added
3686 <li>Choose to ignore gaps in consensus calculation</li>
3687 <li>Unix users can set default web browser</li>
3688 <li>Runs without GUI for batch processing</li>
3689 <li>Dynamically generated Web Service Menus</li>
3694 <li>InstallAnywhere download for Sparc Solaris</li>
3700 <div align="center">
3701 <strong>2.02</strong><br> 18/7/05
3707 <li>Copy & Paste order of sequences maintains
3708 alignment order.</li>
3714 <div align="center">
3715 <strong>2.01</strong><br> 12/7/05
3720 <li>Use delete key for deleting selection.</li>
3721 <li>Use Mouse wheel to scroll sequences.</li>
3722 <li>Help file updated to describe how to add alignment
3724 <li>Version and build date written to build properties
3726 <li>InstallAnywhere installation will check for updates
3727 at launch of Jalview.</li>
3732 <li>Delete gaps bug fixed.</li>
3733 <li>FileChooser sorts columns.</li>
3734 <li>Can remove groups one by one.</li>
3735 <li>Filechooser icons installed.</li>
3736 <li>Finder ignores return character when searching.
3737 Return key will initiate a search.<br>
3744 <div align="center">
3745 <strong>2.0</strong><br> 20/6/05
3750 <li>New codebase</li>