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;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
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.2.10.5">2.10.5</a><br /> <em>4/09/2018</em></strong>
76 <td><div align="left">
81 <td><div align="left">
85 <!-- JAL-247 -->Hidden sequence markers and representative
86 sequence bolding included when exporting alignment as EPS,
87 SVG, PNG or HTML. <em>Display of these can be
88 configured via the Format menu or in batch mode with a
89 jalview properties file.</em>
92 <!-- JAL-3003 -->Alignment is black in exported EPS file
93 when sequences are selected in exported view.</em>
96 <!-- JAL-3059 -->Groups with different coloured borders
97 aren't rendered with correct colour.
100 <!-- JAL-3092 -->Jalview could hang when importing certain types of knotted RNA secondary structure
103 <!-- JAL-3095 -->Sequence highlight in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1
110 <td width="60" nowrap>
112 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
113 <em>7/06/2018</em></strong>
116 <td><div align="left">
120 <!-- JAL-2920 -->Use HGVS nomenclature for variant
121 annotation retrieved from Uniprot
124 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
125 onto the Jalview Desktop
129 <td><div align="left">
133 <!-- JAL-3017 -->Cannot import features with multiple
134 variant elements (blocks import of some Uniprot records)
137 <!-- JAL-2997 -->Clustal files with sequence positions in
138 right-hand column parsed correctly
141 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
142 not alignment area in exported graphic
145 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
146 window has input focus
149 <!-- JAL-2992 -->Annotation panel set too high when
150 annotation added to view (Windows)
153 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
154 network connectivity is poor
157 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
158 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
159 the currently open URL and links from a page viewed in
160 Firefox or Chrome on Windows is now fully supported. If
161 you are using Edge, only links in the page can be
162 dragged, and with Internet Explorer, only the currently
163 open URL in the browser can be dropped onto Jalview.</em>
169 <td width="60" nowrap>
171 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
174 <td><div align="left">
178 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
179 for disabling automatic superposition of multiple
180 structures and open structures in existing views
183 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
184 ID and annotation area margins can be click-dragged to
188 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
192 <!-- JAL-2759 -->Improved performance for large alignments
193 and lots of hidden columns
196 <!-- JAL-2593 -->Improved performance when rendering lots
197 of features (particularly when transparency is disabled)
202 <td><div align="left">
205 <!-- JAL-2899 -->Structure and Overview aren't updated
206 when Colour By Annotation threshold slider is adjusted
209 <!-- JAL-2778 -->Slow redraw when Overview panel shown
210 overlapping alignment panel
213 <!-- JAL-2929 -->Overview doesn't show end of unpadded
217 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
218 improved: CDS not handled correctly if transcript has no
222 <!-- JAL-2321 -->Secondary structure and temperature
223 factor annotation not added to sequence when local PDB
224 file associated with it by drag'n'drop or structure
228 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
229 dialog doesn't import PDB files dropped on an alignment
232 <!-- JAL-2666 -->Linked scrolling via protein horizontal
233 scroll bar doesn't work for some CDS/Protein views
236 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
237 Java 1.8u153 onwards and Java 1.9u4+.
240 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
241 columns in annotation row
244 <!-- JAL-2913 -->Preferences panel's ID Width control is not
245 honored in batch mode
248 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
249 for structures added to existing Jmol view
252 <!-- JAL-2223 -->'View Mappings' includes duplicate
253 entries after importing project with multiple views
256 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
257 protein sequences via SIFTS from associated PDB entries
258 with negative residue numbers or missing residues fails
261 <!-- JAL-2952 -->Exception when shading sequence with negative
262 Temperature Factor values from annotated PDB files (e.g.
263 as generated by CONSURF)
266 <!-- JAL-2920 -->Uniprot 'sequence variant' features
267 tooltip doesn't include a text description of mutation
270 <!-- JAL-2922 -->Invert displayed features very slow when
271 structure and/or overview windows are also shown
274 <!-- JAL-2954 -->Selecting columns from highlighted regions
275 very slow for alignments with large numbers of sequences
278 <!-- JAL-2925 -->Copy Consensus fails for group consensus
279 with 'StringIndexOutOfBounds'
282 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
283 platforms running Java 10
286 <!-- JAL-2960 -->Adding a structure to existing structure
287 view appears to do nothing because the view is hidden behind the alignment view
293 <!-- JAL-2926 -->Copy consensus sequence option in applet
294 should copy the group consensus when popup is opened on it
300 <!-- JAL-2913 -->Fixed ID width preference is not respected
303 <em>New Known Defects</em>
306 <!-- JAL-2973 --> Exceptions occasionally raised when
307 editing a large alignment and overview is displayed
310 <!-- JAL-2974 -->'Overview updating' progress bar is shown
311 repeatedly after a series of edits even when the overview
312 is no longer reflecting updates
315 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
316 structures for protein subsequence (if 'Trim Retrieved
317 Sequences' enabled) or Ensembl isoforms (Workaround in
318 2.10.4 is to fail back to N&W mapping)
325 <td width="60" nowrap>
327 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
330 <td><div align="left">
331 <ul><li>Updated Certum Codesigning Certificate
332 (Valid till 30th November 2018)</li></ul></div></td>
333 <td><div align="left">
336 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
337 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
338 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
339 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
340 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
341 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
342 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
348 <td width="60" nowrap>
350 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
353 <td><div align="left">
357 <!-- JAL-2446 -->Faster and more efficient management and
358 rendering of sequence features
361 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
362 429 rate limit request hander
365 <!-- JAL-2773 -->Structure views don't get updated unless
366 their colours have changed
369 <!-- JAL-2495 -->All linked sequences are highlighted for
370 a structure mousover (Jmol) or selection (Chimera)
373 <!-- JAL-2790 -->'Cancel' button in progress bar for
374 JABAWS AACon, RNAAliFold and Disorder prediction jobs
377 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
378 view from Ensembl locus cross-references
381 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
385 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
386 feature can be disabled
389 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
390 PDB easier retrieval of sequences for lists of IDs
393 <!-- JAL-2758 -->Short names for sequences retrieved from
399 <li>Groovy interpreter updated to 2.4.12</li>
400 <li>Example groovy script for generating a matrix of
401 percent identity scores for current alignment.</li>
403 <em>Testing and Deployment</em>
406 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
410 <td><div align="left">
414 <!-- JAL-2643 -->Pressing tab after updating the colour
415 threshold text field doesn't trigger an update to the
419 <!-- JAL-2682 -->Race condition when parsing sequence ID
423 <!-- JAL-2608 -->Overview windows are also closed when
424 alignment window is closed
427 <!-- JAL-2548 -->Export of features doesn't always respect
431 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
432 takes a long time in Cursor mode
438 <!-- JAL-2777 -->Structures with whitespace chainCode
439 cannot be viewed in Chimera
442 <!-- JAL-2728 -->Protein annotation panel too high in
446 <!-- JAL-2757 -->Can't edit the query after the server
447 error warning icon is shown in Uniprot and PDB Free Text
451 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
454 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
457 <!-- JAL-2739 -->Hidden column marker in last column not
458 rendered when switching back from Wrapped to normal view
461 <!-- JAL-2768 -->Annotation display corrupted when
462 scrolling right in unwapped alignment view
465 <!-- JAL-2542 -->Existing features on subsequence
466 incorrectly relocated when full sequence retrieved from
470 <!-- JAL-2733 -->Last reported memory still shown when
471 Desktop->Show Memory is unticked (OSX only)
474 <!-- JAL-2658 -->Amend Features dialog doesn't allow
475 features of same type and group to be selected for
479 <!-- JAL-2524 -->Jalview becomes sluggish in wide
480 alignments when hidden columns are present
483 <!-- JAL-2392 -->Jalview freezes when loading and
484 displaying several structures
487 <!-- JAL-2732 -->Black outlines left after resizing or
491 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
492 within the Jalview desktop on OSX
495 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
496 when in wrapped alignment mode
499 <!-- JAL-2636 -->Scale mark not shown when close to right
500 hand end of alignment
503 <!-- JAL-2684 -->Pairwise alignment of selected regions of
504 each selected sequence do not have correct start/end
508 <!-- JAL-2793 -->Alignment ruler height set incorrectly
509 after canceling the Alignment Window's Font dialog
512 <!-- JAL-2036 -->Show cross-references not enabled after
513 restoring project until a new view is created
516 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
517 URL links appears when only default EMBL-EBI link is
518 configured (since 2.10.2b2)
521 <!-- JAL-2775 -->Overview redraws whole window when box
525 <!-- JAL-2225 -->Structure viewer doesn't map all chains
526 in a multi-chain structure when viewing alignment
527 involving more than one chain (since 2.10)
530 <!-- JAL-2811 -->Double residue highlights in cursor mode
531 if new selection moves alignment window
534 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
535 arrow key in cursor mode to pass hidden column marker
538 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
539 that produces correctly annotated transcripts and products
542 <!-- JAL-2776 -->Toggling a feature group after first time
543 doesn't update associated structure view
546 <em>Applet</em><br />
549 <!-- JAL-2687 -->Concurrent modification exception when
550 closing alignment panel
553 <em>BioJSON</em><br />
556 <!-- JAL-2546 -->BioJSON export does not preserve
557 non-positional features
560 <em>New Known Issues</em>
563 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
564 sequence features correctly (for many previous versions of
568 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
569 using cursor in wrapped panel other than top
572 <!-- JAL-2791 -->Select columns containing feature ignores
573 graduated colour threshold
576 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
577 always preserve numbering and sequence features
580 <em>Known Java 9 Issues</em>
583 <!-- JAL-2902 -->Groovy Console very slow to open and is
584 not responsive when entering characters (Webstart, Java
591 <td width="60" nowrap>
593 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
594 <em>2/10/2017</em></strong>
597 <td><div align="left">
598 <em>New features in Jalview Desktop</em>
601 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
603 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
607 <td><div align="left">
611 <td width="60" nowrap>
613 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
614 <em>7/9/2017</em></strong>
617 <td><div align="left">
621 <!-- JAL-2588 -->Show gaps in overview window by colouring
622 in grey (sequences used to be coloured grey, and gaps were
626 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
630 <!-- JAL-2587 -->Overview updates immediately on increase
631 in size and progress bar shown as higher resolution
632 overview is recalculated
637 <td><div align="left">
641 <!-- JAL-2664 -->Overview window redraws every hidden
642 column region row by row
645 <!-- JAL-2681 -->duplicate protein sequences shown after
646 retrieving Ensembl crossrefs for sequences from Uniprot
649 <!-- JAL-2603 -->Overview window throws NPE if show boxes
650 format setting is unticked
653 <!-- JAL-2610 -->Groups are coloured wrongly in overview
654 if group has show boxes format setting unticked
657 <!-- JAL-2672,JAL-2665 -->Redraw problems when
658 autoscrolling whilst dragging current selection group to
659 include sequences and columns not currently displayed
662 <!-- JAL-2691 -->Not all chains are mapped when multimeric
663 assemblies are imported via CIF file
666 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
667 displayed when threshold or conservation colouring is also
671 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
675 <!-- JAL-2673 -->Jalview continues to scroll after
676 dragging a selected region off the visible region of the
680 <!-- JAL-2724 -->Cannot apply annotation based
681 colourscheme to all groups in a view
684 <!-- JAL-2511 -->IDs don't line up with sequences
685 initially after font size change using the Font chooser or
692 <td width="60" nowrap>
694 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
697 <td><div align="left">
698 <em>Calculations</em>
702 <!-- JAL-1933 -->Occupancy annotation row shows number of
703 ungapped positions in each column of the alignment.
706 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
707 a calculation dialog box
710 <!-- JAL-2379 -->Revised implementation of PCA for speed
711 and memory efficiency (~30x faster)
714 <!-- JAL-2403 -->Revised implementation of sequence
715 similarity scores as used by Tree, PCA, Shading Consensus
716 and other calculations
719 <!-- JAL-2416 -->Score matrices are stored as resource
720 files within the Jalview codebase
723 <!-- JAL-2500 -->Trees computed on Sequence Feature
724 Similarity may have different topology due to increased
731 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
732 model for alignments and groups
735 <!-- JAL-384 -->Custom shading schemes created via groovy
742 <!-- JAL-2526 -->Efficiency improvements for interacting
743 with alignment and overview windows
746 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
750 <!-- JAL-2388 -->Hidden columns and sequences can be
754 <!-- JAL-2611 -->Click-drag in visible area allows fine
755 adjustment of visible position
759 <em>Data import/export</em>
762 <!-- JAL-2535 -->Posterior probability annotation from
763 Stockholm files imported as sequence associated annotation
766 <!-- JAL-2507 -->More robust per-sequence positional
767 annotation input/output via stockholm flatfile
770 <!-- JAL-2533 -->Sequence names don't include file
771 extension when importing structure files without embedded
772 names or PDB accessions
775 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
776 format sequence substitution matrices
779 <em>User Interface</em>
782 <!-- JAL-2447 --> Experimental Features Checkbox in
783 Desktop's Tools menu to hide or show untested features in
787 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
788 via Overview or sequence motif search operations
791 <!-- JAL-2547 -->Amend sequence features dialog box can be
792 opened by double clicking gaps within sequence feature
796 <!-- JAL-1476 -->Status bar message shown when not enough
797 aligned positions were available to create a 3D structure
801 <em>3D Structure</em>
804 <!-- JAL-2430 -->Hidden regions in alignment views are not
805 coloured in linked structure views
808 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
809 file-based command exchange
812 <!-- JAL-2375 -->Structure chooser automatically shows
813 Cached Structures rather than querying the PDBe if
814 structures are already available for sequences
817 <!-- JAL-2520 -->Structures imported via URL are cached in
818 the Jalview project rather than downloaded again when the
822 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
823 to transfer Chimera's structure attributes as Jalview
824 features, and vice-versa (<strong>Experimental
828 <em>Web Services</em>
831 <!-- JAL-2549 -->Updated JABAWS client to v2.2
834 <!-- JAL-2335 -->Filter non-standard amino acids and
835 nucleotides when submitting to AACon and other MSA
839 <!-- JAL-2316, -->URLs for viewing database
840 cross-references provided by identifiers.org and the
848 <!-- JAL-2344 -->FileFormatI interface for describing and
849 identifying file formats (instead of String constants)
852 <!-- JAL-2228 -->FeatureCounter script refactored for
853 efficiency when counting all displayed features (not
854 backwards compatible with 2.10.1)
857 <em>Example files</em>
860 <!-- JAL-2631 -->Graduated feature colour style example
861 included in the example feature file
864 <em>Documentation</em>
867 <!-- JAL-2339 -->Release notes reformatted for readability
868 with the built-in Java help viewer
871 <!-- JAL-1644 -->Find documentation updated with 'search
872 sequence description' option
878 <!-- JAL-2485, -->External service integration tests for
879 Uniprot REST Free Text Search Client
882 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
885 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
890 <td><div align="left">
891 <em>Calculations</em>
894 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
895 matrix - C->R should be '-3'<br />Old matrix restored
896 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
898 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
899 Jalview's treatment of gaps in PCA and substitution matrix
900 based Tree calculations.<br /> <br />In earlier versions
901 of Jalview, gaps matching gaps were penalised, and gaps
902 matching non-gaps penalised even more. In the PCA
903 calculation, gaps were actually treated as non-gaps - so
904 different costs were applied, which meant Jalview's PCAs
905 were different to those produced by SeqSpace.<br />Jalview
906 now treats gaps in the same way as SeqSpace (ie it scores
907 them as 0). <br /> <br />Enter the following in the
908 Groovy console to restore pre-2.10.2 behaviour:<br />
909 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
910 // for 2.10.1 mode <br />
911 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
912 // to restore 2.10.2 mode <br /> <br /> <em>Note:
913 these settings will affect all subsequent tree and PCA
914 calculations (not recommended)</em></li>
916 <!-- JAL-2424 -->Fixed off-by-one bug that affected
917 scaling of branch lengths for trees computed using
918 Sequence Feature Similarity.
921 <!-- JAL-2377 -->PCA calculation could hang when
922 generating output report when working with highly
926 <!-- JAL-2544 --> Sort by features includes features to
927 right of selected region when gaps present on right-hand
931 <em>User Interface</em>
934 <!-- JAL-2346 -->Reopening Colour by annotation dialog
935 doesn't reselect a specific sequence's associated
936 annotation after it was used for colouring a view
939 <!-- JAL-2419 -->Current selection lost if popup menu
940 opened on a region of alignment without groups
943 <!-- JAL-2374 -->Popup menu not always shown for regions
944 of an alignment with overlapping groups
947 <!-- JAL-2310 -->Finder double counts if both a sequence's
948 name and description match
951 <!-- JAL-2370 -->Hiding column selection containing two
952 hidden regions results in incorrect hidden regions
955 <!-- JAL-2386 -->'Apply to all groups' setting when
956 changing colour does not apply Conservation slider value
960 <!-- JAL-2373 -->Percentage identity and conservation menu
961 items do not show a tick or allow shading to be disabled
964 <!-- JAL-2385 -->Conservation shading or PID threshold
965 lost when base colourscheme changed if slider not visible
968 <!-- JAL-2547 -->Sequence features shown in tooltip for
969 gaps before start of features
972 <!-- JAL-2623 -->Graduated feature colour threshold not
973 restored to UI when feature colour is edited
976 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
977 a time when scrolling vertically in wrapped mode.
980 <!-- JAL-2630 -->Structure and alignment overview update
981 as graduate feature colour settings are modified via the
985 <!-- JAL-2034 -->Overview window doesn't always update
986 when a group defined on the alignment is resized
989 <!-- JAL-2605 -->Mouseovers on left/right scale region in
990 wrapped view result in positional status updates
994 <!-- JAL-2563 -->Status bar doesn't show position for
995 ambiguous amino acid and nucleotide symbols
998 <!-- JAL-2602 -->Copy consensus sequence failed if
999 alignment included gapped columns
1002 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1003 widgets don't permanently disappear
1006 <!-- JAL-2503 -->Cannot select or filter quantitative
1007 annotation that are shown only as column labels (e.g.
1008 T-Coffee column reliability scores)
1011 <!-- JAL-2594 -->Exception thrown if trying to create a
1012 sequence feature on gaps only
1015 <!-- JAL-2504 -->Features created with 'New feature'
1016 button from a Find inherit previously defined feature type
1017 rather than the Find query string
1020 <!-- JAL-2423 -->incorrect title in output window when
1021 exporting tree calculated in Jalview
1024 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1025 and then revealing them reorders sequences on the
1029 <!-- JAL-964 -->Group panel in sequence feature settings
1030 doesn't update to reflect available set of groups after
1031 interactively adding or modifying features
1034 <!-- JAL-2225 -->Sequence Database chooser unusable on
1038 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1039 only excluded gaps in current sequence and ignored
1046 <!-- JAL-2421 -->Overview window visible region moves
1047 erratically when hidden rows or columns are present
1050 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1051 Structure Viewer's colour menu don't correspond to
1055 <!-- JAL-2405 -->Protein specific colours only offered in
1056 colour and group colour menu for protein alignments
1059 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1060 reflect currently selected view or group's shading
1064 <!-- JAL-2624 -->Feature colour thresholds not respected
1065 when rendered on overview and structures when opacity at
1069 <!-- JAL-2589 -->User defined gap colour not shown in
1070 overview when features overlaid on alignment
1073 <em>Data import/export</em>
1076 <!-- JAL-2576 -->Very large alignments take a long time to
1080 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1081 added after a sequence was imported are not written to
1085 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1086 when importing RNA secondary structure via Stockholm
1089 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1090 not shown in correct direction for simple pseudoknots
1093 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1094 with lightGray or darkGray via features file (but can
1098 <!-- JAL-2383 -->Above PID colour threshold not recovered
1099 when alignment view imported from project
1102 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1103 structure and sequences extracted from structure files
1104 imported via URL and viewed in Jmol
1107 <!-- JAL-2520 -->Structures loaded via URL are saved in
1108 Jalview Projects rather than fetched via URL again when
1109 the project is loaded and the structure viewed
1112 <em>Web Services</em>
1115 <!-- JAL-2519 -->EnsemblGenomes example failing after
1116 release of Ensembl v.88
1119 <!-- JAL-2366 -->Proxy server address and port always
1120 appear enabled in Preferences->Connections
1123 <!-- JAL-2461 -->DAS registry not found exceptions
1124 removed from console output
1127 <!-- JAL-2582 -->Cannot retrieve protein products from
1128 Ensembl by Peptide ID
1131 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1132 created from SIFTs, and spurious 'Couldn't open structure
1133 in Chimera' errors raised after April 2017 update (problem
1134 due to 'null' string rather than empty string used for
1135 residues with no corresponding PDB mapping).
1138 <em>Application UI</em>
1141 <!-- JAL-2361 -->User Defined Colours not added to Colour
1145 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1146 case' residues (button in colourscheme editor debugged and
1147 new documentation and tooltips added)
1150 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1151 doesn't restore group-specific text colour thresholds
1154 <!-- JAL-2243 -->Feature settings panel does not update as
1155 new features are added to alignment
1158 <!-- JAL-2532 -->Cancel in feature settings reverts
1159 changes to feature colours via the Amend features dialog
1162 <!-- JAL-2506 -->Null pointer exception when attempting to
1163 edit graduated feature colour via amend features dialog
1167 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1168 selection menu changes colours of alignment views
1171 <!-- JAL-2426 -->Spurious exceptions in console raised
1172 from alignment calculation workers after alignment has
1176 <!-- JAL-1608 -->Typo in selection popup menu - Create
1177 groups now 'Create Group'
1180 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1181 Create/Undefine group doesn't always work
1184 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1185 shown again after pressing 'Cancel'
1188 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1189 adjusts start position in wrap mode
1192 <!-- JAL-2563 -->Status bar doesn't show positions for
1193 ambiguous amino acids
1196 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1197 CDS/Protein view after CDS sequences added for aligned
1201 <!-- JAL-2592 -->User defined colourschemes called 'User
1202 Defined' don't appear in Colours menu
1208 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1209 score models doesn't always result in an updated PCA plot
1212 <!-- JAL-2442 -->Features not rendered as transparent on
1213 overview or linked structure view
1216 <!-- JAL-2372 -->Colour group by conservation doesn't
1220 <!-- JAL-2517 -->Hitting Cancel after applying
1221 user-defined colourscheme doesn't restore original
1228 <!-- JAL-2314 -->Unit test failure:
1229 jalview.ws.jabaws.RNAStructExportImport setup fails
1232 <!-- JAL-2307 -->Unit test failure:
1233 jalview.ws.sifts.SiftsClientTest due to compatibility
1234 problems with deep array comparison equality asserts in
1235 successive versions of TestNG
1238 <!-- JAL-2479 -->Relocated StructureChooserTest and
1239 ParameterUtilsTest Unit tests to Network suite
1242 <em>New Known Issues</em>
1245 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1246 phase after a sequence motif find operation
1249 <!-- JAL-2550 -->Importing annotation file with rows
1250 containing just upper and lower case letters are
1251 interpreted as WUSS RNA secondary structure symbols
1254 <!-- JAL-2590 -->Cannot load and display Newick trees
1255 reliably from eggnog Ortholog database
1258 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1259 containing features of type Highlight' when 'B' is pressed
1260 to mark columns containing highlighted regions.
1263 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1264 doesn't always add secondary structure annotation.
1269 <td width="60" nowrap>
1270 <div align="center">
1271 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1274 <td><div align="left">
1278 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1279 for all consensus calculations
1282 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1285 <li>Updated Jalview's Certum code signing certificate
1288 <em>Application</em>
1291 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1292 set of database cross-references, sorted alphabetically
1295 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1296 from database cross references. Users with custom links
1297 will receive a <a href="webServices/urllinks.html#warning">warning
1298 dialog</a> asking them to update their preferences.
1301 <!-- JAL-2287-->Cancel button and escape listener on
1302 dialog warning user about disconnecting Jalview from a
1306 <!-- JAL-2320-->Jalview's Chimera control window closes if
1307 the Chimera it is connected to is shut down
1310 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1311 columns menu item to mark columns containing highlighted
1312 regions (e.g. from structure selections or results of a
1316 <!-- JAL-2284-->Command line option for batch-generation
1317 of HTML pages rendering alignment data with the BioJS
1327 <!-- JAL-2286 -->Columns with more than one modal residue
1328 are not coloured or thresholded according to percent
1329 identity (first observed in Jalview 2.8.2)
1332 <!-- JAL-2301 -->Threonine incorrectly reported as not
1336 <!-- JAL-2318 -->Updates to documentation pages (above PID
1337 threshold, amino acid properties)
1340 <!-- JAL-2292 -->Lower case residues in sequences are not
1341 reported as mapped to residues in a structure file in the
1345 <!--JAL-2324 -->Identical features with non-numeric scores
1346 could be added multiple times to a sequence
1349 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1350 bond features shown as two highlighted residues rather
1351 than a range in linked structure views, and treated
1352 correctly when selecting and computing trees from features
1355 <!-- JAL-2281-->Custom URL links for database
1356 cross-references are matched to database name regardless
1361 <em>Application</em>
1364 <!-- JAL-2282-->Custom URL links for specific database
1365 names without regular expressions also offer links from
1369 <!-- JAL-2315-->Removing a single configured link in the
1370 URL links pane in Connections preferences doesn't actually
1371 update Jalview configuration
1374 <!-- JAL-2272-->CTRL-Click on a selected region to open
1375 the alignment area popup menu doesn't work on El-Capitan
1378 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1379 files with similarly named sequences if dropped onto the
1383 <!-- JAL-2312 -->Additional mappings are shown for PDB
1384 entries where more chains exist in the PDB accession than
1385 are reported in the SIFTS file
1388 <!-- JAL-2317-->Certain structures do not get mapped to
1389 the structure view when displayed with Chimera
1392 <!-- JAL-2317-->No chains shown in the Chimera view
1393 panel's View->Show Chains submenu
1396 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1397 work for wrapped alignment views
1400 <!--JAL-2197 -->Rename UI components for running JPred
1401 predictions from 'JNet' to 'JPred'
1404 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1405 corrupted when annotation panel vertical scroll is not at
1406 first annotation row
1409 <!--JAL-2332 -->Attempting to view structure for Hen
1410 lysozyme results in a PDB Client error dialog box
1413 <!-- JAL-2319 -->Structure View's mapping report switched
1414 ranges for PDB and sequence for SIFTS
1417 SIFTS 'Not_Observed' residues mapped to non-existant
1421 <!-- <em>New Known Issues</em>
1428 <td width="60" nowrap>
1429 <div align="center">
1430 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1431 <em>25/10/2016</em></strong>
1434 <td><em>Application</em>
1436 <li>3D Structure chooser opens with 'Cached structures'
1437 view if structures already loaded</li>
1438 <li>Progress bar reports models as they are loaded to
1439 structure views</li>
1445 <li>Colour by conservation always enabled and no tick
1446 shown in menu when BLOSUM or PID shading applied</li>
1447 <li>FER1_ARATH and FER2_ARATH labels were switched in
1448 example sequences/projects/trees</li>
1450 <em>Application</em>
1452 <li>Jalview projects with views of local PDB structure
1453 files saved on Windows cannot be opened on OSX</li>
1454 <li>Multiple structure views can be opened and superposed
1455 without timeout for structures with multiple models or
1456 multiple sequences in alignment</li>
1457 <li>Cannot import or associated local PDB files without a
1458 PDB ID HEADER line</li>
1459 <li>RMSD is not output in Jmol console when superposition
1461 <li>Drag and drop of URL from Browser fails for Linux and
1462 OSX versions earlier than El Capitan</li>
1463 <li>ENA client ignores invalid content from ENA server</li>
1464 <li>Exceptions are not raised in console when ENA client
1465 attempts to fetch non-existent IDs via Fetch DB Refs UI
1467 <li>Exceptions are not raised in console when a new view
1468 is created on the alignment</li>
1469 <li>OSX right-click fixed for group selections: CMD-click
1470 to insert/remove gaps in groups and CTRL-click to open group
1473 <em>Build and deployment</em>
1475 <li>URL link checker now copes with multi-line anchor
1478 <em>New Known Issues</em>
1480 <li>Drag and drop from URL links in browsers do not work
1487 <td width="60" nowrap>
1488 <div align="center">
1489 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1492 <td><em>General</em>
1495 <!-- JAL-2124 -->Updated Spanish translations.
1498 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1499 for importing structure data to Jalview. Enables mmCIF and
1503 <!-- JAL-192 --->Alignment ruler shows positions relative to
1507 <!-- JAL-2202 -->Position/residue shown in status bar when
1508 mousing over sequence associated annotation
1511 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1515 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1516 '()', canonical '[]' and invalid '{}' base pair populations
1520 <!-- JAL-2092 -->Feature settings popup menu options for
1521 showing or hiding columns containing a feature
1524 <!-- JAL-1557 -->Edit selected group by double clicking on
1525 group and sequence associated annotation labels
1528 <!-- JAL-2236 -->Sequence name added to annotation label in
1529 select/hide columns by annotation and colour by annotation
1533 </ul> <em>Application</em>
1536 <!-- JAL-2050-->Automatically hide introns when opening a
1537 gene/transcript view
1540 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1544 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1545 structure mappings with the EMBL-EBI PDBe SIFTS database
1548 <!-- JAL-2079 -->Updated download sites used for Rfam and
1549 Pfam sources to xfam.org
1552 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1555 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1556 over sequences in Jalview
1559 <!-- JAL-2027-->Support for reverse-complement coding
1560 regions in ENA and EMBL
1563 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1564 for record retrieval via ENA rest API
1567 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1571 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1572 groovy script execution
1575 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1576 alignment window's Calculate menu
1579 <!-- JAL-1812 -->Allow groovy scripts that call
1580 Jalview.getAlignFrames() to run in headless mode
1583 <!-- JAL-2068 -->Support for creating new alignment
1584 calculation workers from groovy scripts
1587 <!-- JAL-1369 --->Store/restore reference sequence in
1591 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1592 associations are now saved/restored from project
1595 <!-- JAL-1993 -->Database selection dialog always shown
1596 before sequence fetcher is opened
1599 <!-- JAL-2183 -->Double click on an entry in Jalview's
1600 database chooser opens a sequence fetcher
1603 <!-- JAL-1563 -->Free-text search client for UniProt using
1604 the UniProt REST API
1607 <!-- JAL-2168 -->-nonews command line parameter to prevent
1608 the news reader opening
1611 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1612 querying stored in preferences
1615 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1619 <!-- JAL-1977-->Tooltips shown on database chooser
1622 <!-- JAL-391 -->Reverse complement function in calculate
1623 menu for nucleotide sequences
1626 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1627 and feature counts preserves alignment ordering (and
1628 debugged for complex feature sets).
1631 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1632 viewing structures with Jalview 2.10
1635 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1636 genome, transcript CCDS and gene ids via the Ensembl and
1637 Ensembl Genomes REST API
1640 <!-- JAL-2049 -->Protein sequence variant annotation
1641 computed for 'sequence_variant' annotation on CDS regions
1645 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1649 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1650 Ref Fetcher fails to match, or otherwise updates sequence
1651 data from external database records.
1654 <!-- JAL-2154 -->Revised Jalview Project format for
1655 efficient recovery of sequence coding and alignment
1656 annotation relationships.
1658 </ul> <!-- <em>Applet</em>
1669 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1673 <!-- JAL-2018-->Export features in Jalview format (again)
1674 includes graduated colourschemes
1677 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1678 working with big alignments and lots of hidden columns
1681 <!-- JAL-2053-->Hidden column markers not always rendered
1682 at right of alignment window
1685 <!-- JAL-2067 -->Tidied up links in help file table of
1689 <!-- JAL-2072 -->Feature based tree calculation not shown
1693 <!-- JAL-2075 -->Hidden columns ignored during feature
1694 based tree calculation
1697 <!-- JAL-2065 -->Alignment view stops updating when show
1698 unconserved enabled for group on alignment
1701 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1705 <!-- JAL-2146 -->Alignment column in status incorrectly
1706 shown as "Sequence position" when mousing over
1710 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1711 hidden columns present
1714 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1715 user created annotation added to alignment
1718 <!-- JAL-1841 -->RNA Structure consensus only computed for
1719 '()' base pair annotation
1722 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1723 in zero scores for all base pairs in RNA Structure
1727 <!-- JAL-2174-->Extend selection with columns containing
1731 <!-- JAL-2275 -->Pfam format writer puts extra space at
1732 beginning of sequence
1735 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1739 <!-- JAL-2238 -->Cannot create groups on an alignment from
1740 from a tree when t-coffee scores are shown
1743 <!-- JAL-1836,1967 -->Cannot import and view PDB
1744 structures with chains containing negative resnums (4q4h)
1747 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1751 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1752 to Clustal, PIR and PileUp output
1755 <!-- JAL-2008 -->Reordering sequence features that are
1756 not visible causes alignment window to repaint
1759 <!-- JAL-2006 -->Threshold sliders don't work in
1760 graduated colour and colour by annotation row for e-value
1761 scores associated with features and annotation rows
1764 <!-- JAL-1797 -->amino acid physicochemical conservation
1765 calculation should be case independent
1768 <!-- JAL-2173 -->Remove annotation also updates hidden
1772 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1773 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1774 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1777 <!-- JAL-2065 -->Null pointer exceptions and redraw
1778 problems when reference sequence defined and 'show
1779 non-conserved' enabled
1782 <!-- JAL-1306 -->Quality and Conservation are now shown on
1783 load even when Consensus calculation is disabled
1786 <!-- JAL-1932 -->Remove right on penultimate column of
1787 alignment does nothing
1790 <em>Application</em>
1793 <!-- JAL-1552-->URLs and links can't be imported by
1794 drag'n'drop on OSX when launched via webstart (note - not
1795 yet fixed for El Capitan)
1798 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1799 output when running on non-gb/us i18n platforms
1802 <!-- JAL-1944 -->Error thrown when exporting a view with
1803 hidden sequences as flat-file alignment
1806 <!-- JAL-2030-->InstallAnywhere distribution fails when
1810 <!-- JAL-2080-->Jalview very slow to launch via webstart
1811 (also hotfix for 2.9.0b2)
1814 <!-- JAL-2085 -->Cannot save project when view has a
1815 reference sequence defined
1818 <!-- JAL-1011 -->Columns are suddenly selected in other
1819 alignments and views when revealing hidden columns
1822 <!-- JAL-1989 -->Hide columns not mirrored in complement
1823 view in a cDNA/Protein splitframe
1826 <!-- JAL-1369 -->Cannot save/restore representative
1827 sequence from project when only one sequence is
1831 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1832 in Structure Chooser
1835 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1836 structure consensus didn't refresh annotation panel
1839 <!-- JAL-1962 -->View mapping in structure view shows
1840 mappings between sequence and all chains in a PDB file
1843 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1844 dialogs format columns correctly, don't display array
1845 data, sort columns according to type
1848 <!-- JAL-1975 -->Export complete shown after destination
1849 file chooser is cancelled during an image export
1852 <!-- JAL-2025 -->Error when querying PDB Service with
1853 sequence name containing special characters
1856 <!-- JAL-2024 -->Manual PDB structure querying should be
1860 <!-- JAL-2104 -->Large tooltips with broken HTML
1861 formatting don't wrap
1864 <!-- JAL-1128 -->Figures exported from wrapped view are
1865 truncated so L looks like I in consensus annotation
1868 <!-- JAL-2003 -->Export features should only export the
1869 currently displayed features for the current selection or
1873 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1874 after fetching cross-references, and restoring from
1878 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1879 followed in the structure viewer
1882 <!-- JAL-2163 -->Titles for individual alignments in
1883 splitframe not restored from project
1886 <!-- JAL-2145 -->missing autocalculated annotation at
1887 trailing end of protein alignment in transcript/product
1888 splitview when pad-gaps not enabled by default
1891 <!-- JAL-1797 -->amino acid physicochemical conservation
1895 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1896 article has been read (reopened issue due to
1897 internationalisation problems)
1900 <!-- JAL-1960 -->Only offer PDB structures in structure
1901 viewer based on sequence name, PDB and UniProt
1906 <!-- JAL-1976 -->No progress bar shown during export of
1910 <!-- JAL-2213 -->Structures not always superimposed after
1911 multiple structures are shown for one or more sequences.
1914 <!-- JAL-1370 -->Reference sequence characters should not
1915 be replaced with '.' when 'Show unconserved' format option
1919 <!-- JAL-1823 -->Cannot specify chain code when entering
1920 specific PDB id for sequence
1923 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1924 'Export hidden sequences' is enabled, but 'export hidden
1925 columns' is disabled.
1928 <!--JAL-2026-->Best Quality option in structure chooser
1929 selects lowest rather than highest resolution structures
1933 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1934 to sequence mapping in 'View Mappings' report
1937 <!-- JAL-2284 -->Unable to read old Jalview projects that
1938 contain non-XML data added after Jalvew wrote project.
1941 <!-- JAL-2118 -->Newly created annotation row reorders
1942 after clicking on it to create new annotation for a
1946 <!-- JAL-1980 -->Null Pointer Exception raised when
1947 pressing Add on an orphaned cut'n'paste window.
1949 <!-- may exclude, this is an external service stability issue JAL-1941
1950 -- > RNA 3D structure not added via DSSR service</li> -->
1955 <!-- JAL-2151 -->Incorrect columns are selected when
1956 hidden columns present before start of sequence
1959 <!-- JAL-1986 -->Missing dependencies on applet pages
1963 <!-- JAL-1947 -->Overview pixel size changes when
1964 sequences are hidden in applet
1967 <!-- JAL-1996 -->Updated instructions for applet
1968 deployment on examples pages.
1975 <td width="60" nowrap>
1976 <div align="center">
1977 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1978 <em>16/10/2015</em></strong>
1981 <td><em>General</em>
1983 <li>Time stamps for signed Jalview application and applet
1988 <em>Application</em>
1990 <li>Duplicate group consensus and conservation rows
1991 shown when tree is partitioned</li>
1992 <li>Erratic behaviour when tree partitions made with
1993 multiple cDNA/Protein split views</li>
1999 <td width="60" nowrap>
2000 <div align="center">
2001 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2002 <em>8/10/2015</em></strong>
2005 <td><em>General</em>
2007 <li>Updated Spanish translations of localized text for
2009 </ul> <em>Application</em>
2011 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2012 <li>Signed OSX InstallAnywhere installer<br></li>
2013 <li>Support for per-sequence based annotations in BioJSON</li>
2014 </ul> <em>Applet</em>
2016 <li>Split frame example added to applet examples page</li>
2017 </ul> <em>Build and Deployment</em>
2020 <!-- JAL-1888 -->New ant target for running Jalview's test
2028 <li>Mapping of cDNA to protein in split frames
2029 incorrect when sequence start > 1</li>
2030 <li>Broken images in filter column by annotation dialog
2032 <li>Feature colours not parsed from features file</li>
2033 <li>Exceptions and incomplete link URLs recovered when
2034 loading a features file containing HTML tags in feature
2038 <em>Application</em>
2040 <li>Annotations corrupted after BioJS export and
2042 <li>Incorrect sequence limits after Fetch DB References
2043 with 'trim retrieved sequences'</li>
2044 <li>Incorrect warning about deleting all data when
2045 deleting selected columns</li>
2046 <li>Patch to build system for shipping properly signed
2047 JNLP templates for webstart launch</li>
2048 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2049 unreleased structures for download or viewing</li>
2050 <li>Tab/space/return keystroke operation of EMBL-PDBe
2051 fetcher/viewer dialogs works correctly</li>
2052 <li>Disabled 'minimise' button on Jalview windows
2053 running on OSX to workaround redraw hang bug</li>
2054 <li>Split cDNA/Protein view position and geometry not
2055 recovered from jalview project</li>
2056 <li>Initial enabled/disabled state of annotation menu
2057 sorter 'show autocalculated first/last' corresponds to
2059 <li>Restoring of Clustal, RNA Helices and T-Coffee
2060 color schemes from BioJSON</li>
2064 <li>Reorder sequences mirrored in cDNA/Protein split
2066 <li>Applet with Jmol examples not loading correctly</li>
2072 <td><div align="center">
2073 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2075 <td><em>General</em>
2077 <li>Linked visualisation and analysis of DNA and Protein
2080 <li>Translated cDNA alignments shown as split protein
2081 and DNA alignment views</li>
2082 <li>Codon consensus annotation for linked protein and
2083 cDNA alignment views</li>
2084 <li>Link cDNA or Protein product sequences by loading
2085 them onto Protein or cDNA alignments</li>
2086 <li>Reconstruct linked cDNA alignment from aligned
2087 protein sequences</li>
2090 <li>Jmol integration updated to Jmol v14.2.14</li>
2091 <li>Import and export of Jalview alignment views as <a
2092 href="features/bioJsonFormat.html">BioJSON</a></li>
2093 <li>New alignment annotation file statements for
2094 reference sequences and marking hidden columns</li>
2095 <li>Reference sequence based alignment shading to
2096 highlight variation</li>
2097 <li>Select or hide columns according to alignment
2099 <li>Find option for locating sequences by description</li>
2100 <li>Conserved physicochemical properties shown in amino
2101 acid conservation row</li>
2102 <li>Alignments can be sorted by number of RNA helices</li>
2103 </ul> <em>Application</em>
2105 <li>New cDNA/Protein analysis capabilities
2107 <li>Get Cross-References should open a Split Frame
2108 view with cDNA/Protein</li>
2109 <li>Detect when nucleotide sequences and protein
2110 sequences are placed in the same alignment</li>
2111 <li>Split cDNA/Protein views are saved in Jalview
2116 <li>Use REST API to talk to Chimera</li>
2117 <li>Selected regions in Chimera are highlighted in linked
2118 Jalview windows</li>
2120 <li>VARNA RNA viewer updated to v3.93</li>
2121 <li>VARNA views are saved in Jalview Projects</li>
2122 <li>Pseudoknots displayed as Jalview RNA annotation can
2123 be shown in VARNA</li>
2125 <li>Make groups for selection uses marked columns as well
2126 as the active selected region</li>
2128 <li>Calculate UPGMA and NJ trees using sequence feature
2130 <li>New Export options
2132 <li>New Export Settings dialog to control hidden
2133 region export in flat file generation</li>
2135 <li>Export alignment views for display with the <a
2136 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2138 <li>Export scrollable SVG in HTML page</li>
2139 <li>Optional embedding of BioJSON data when exporting
2140 alignment figures to HTML</li>
2142 <li>3D structure retrieval and display
2144 <li>Free text and structured queries with the PDBe
2146 <li>PDBe Search API based discovery and selection of
2147 PDB structures for a sequence set</li>
2151 <li>JPred4 employed for protein secondary structure
2153 <li>Hide Insertions menu option to hide unaligned columns
2154 for one or a group of sequences</li>
2155 <li>Automatically hide insertions in alignments imported
2156 from the JPred4 web server</li>
2157 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2158 system on OSX<br />LGPL libraries courtesy of <a
2159 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2161 <li>changed 'View nucleotide structure' submenu to 'View
2162 VARNA 2D Structure'</li>
2163 <li>change "View protein structure" menu option to "3D
2166 </ul> <em>Applet</em>
2168 <li>New layout for applet example pages</li>
2169 <li>New parameters to enable SplitFrame view
2170 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2171 <li>New example demonstrating linked viewing of cDNA and
2172 Protein alignments</li>
2173 </ul> <em>Development and deployment</em>
2175 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2176 <li>Include installation type and git revision in build
2177 properties and console log output</li>
2178 <li>Jalview Github organisation, and new github site for
2179 storing BioJsMSA Templates</li>
2180 <li>Jalview's unit tests now managed with TestNG</li>
2183 <!-- <em>General</em>
2185 </ul> --> <!-- issues resolved --> <em>Application</em>
2187 <li>Escape should close any open find dialogs</li>
2188 <li>Typo in select-by-features status report</li>
2189 <li>Consensus RNA secondary secondary structure
2190 predictions are not highlighted in amber</li>
2191 <li>Missing gap character in v2.7 example file means
2192 alignment appears unaligned when pad-gaps is not enabled</li>
2193 <li>First switch to RNA Helices colouring doesn't colour
2194 associated structure views</li>
2195 <li>ID width preference option is greyed out when auto
2196 width checkbox not enabled</li>
2197 <li>Stopped a warning dialog from being shown when
2198 creating user defined colours</li>
2199 <li>'View Mapping' in structure viewer shows sequence
2200 mappings for just that viewer's sequences</li>
2201 <li>Workaround for superposing PDB files containing
2202 multiple models in Chimera</li>
2203 <li>Report sequence position in status bar when hovering
2204 over Jmol structure</li>
2205 <li>Cannot output gaps as '.' symbols with Selection ->
2206 output to text box</li>
2207 <li>Flat file exports of alignments with hidden columns
2208 have incorrect sequence start/end</li>
2209 <li>'Aligning' a second chain to a Chimera structure from
2211 <li>Colour schemes applied to structure viewers don't
2212 work for nucleotide</li>
2213 <li>Loading/cut'n'pasting an empty or invalid file leads
2214 to a grey/invisible alignment window</li>
2215 <li>Exported Jpred annotation from a sequence region
2216 imports to different position</li>
2217 <li>Space at beginning of sequence feature tooltips shown
2218 on some platforms</li>
2219 <li>Chimera viewer 'View | Show Chain' menu is not
2221 <li>'New View' fails with a Null Pointer Exception in
2222 console if Chimera has been opened</li>
2223 <li>Mouseover to Chimera not working</li>
2224 <li>Miscellaneous ENA XML feature qualifiers not
2226 <li>NPE in annotation renderer after 'Extract Scores'</li>
2227 <li>If two structures in one Chimera window, mouseover of
2228 either sequence shows on first structure</li>
2229 <li>'Show annotations' options should not make
2230 non-positional annotations visible</li>
2231 <li>Subsequence secondary structure annotation not shown
2232 in right place after 'view flanking regions'</li>
2233 <li>File Save As type unset when current file format is
2235 <li>Save as '.jar' option removed for saving Jalview
2237 <li>Colour by Sequence colouring in Chimera more
2239 <li>Cannot 'add reference annotation' for a sequence in
2240 several views on same alignment</li>
2241 <li>Cannot show linked products for EMBL / ENA records</li>
2242 <li>Jalview's tooltip wraps long texts containing no
2244 </ul> <em>Applet</em>
2246 <li>Jmol to JalviewLite mouseover/link not working</li>
2247 <li>JalviewLite can't import sequences with ID
2248 descriptions containing angle brackets</li>
2249 </ul> <em>General</em>
2251 <li>Cannot export and reimport RNA secondary structure
2252 via jalview annotation file</li>
2253 <li>Random helix colour palette for colour by annotation
2254 with RNA secondary structure</li>
2255 <li>Mouseover to cDNA from STOP residue in protein
2256 translation doesn't work.</li>
2257 <li>hints when using the select by annotation dialog box</li>
2258 <li>Jmol alignment incorrect if PDB file has alternate CA
2260 <li>FontChooser message dialog appears to hang after
2261 choosing 1pt font</li>
2262 <li>Peptide secondary structure incorrectly imported from
2263 annotation file when annotation display text includes 'e' or
2265 <li>Cannot set colour of new feature type whilst creating
2267 <li>cDNA translation alignment should not be sequence
2268 order dependent</li>
2269 <li>'Show unconserved' doesn't work for lower case
2271 <li>Nucleotide ambiguity codes involving R not recognised</li>
2272 </ul> <em>Deployment and Documentation</em>
2274 <li>Applet example pages appear different to the rest of
2275 www.jalview.org</li>
2276 </ul> <em>Application Known issues</em>
2278 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2279 <li>Misleading message appears after trying to delete
2281 <li>Jalview icon not shown in dock after InstallAnywhere
2282 version launches</li>
2283 <li>Fetching EMBL reference for an RNA sequence results
2284 fails with a sequence mismatch</li>
2285 <li>Corrupted or unreadable alignment display when
2286 scrolling alignment to right</li>
2287 <li>ArrayIndexOutOfBoundsException thrown when remove
2288 empty columns called on alignment with ragged gapped ends</li>
2289 <li>auto calculated alignment annotation rows do not get
2290 placed above or below non-autocalculated rows</li>
2291 <li>Jalview dekstop becomes sluggish at full screen in
2292 ultra-high resolution</li>
2293 <li>Cannot disable consensus calculation independently of
2294 quality and conservation</li>
2295 <li>Mouseover highlighting between cDNA and protein can
2296 become sluggish with more than one splitframe shown</li>
2297 </ul> <em>Applet Known Issues</em>
2299 <li>Core PDB parsing code requires Jmol</li>
2300 <li>Sequence canvas panel goes white when alignment
2301 window is being resized</li>
2307 <td><div align="center">
2308 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2310 <td><em>General</em>
2312 <li>Updated Java code signing certificate donated by
2314 <li>Features and annotation preserved when performing
2315 pairwise alignment</li>
2316 <li>RNA pseudoknot annotation can be
2317 imported/exported/displayed</li>
2318 <li>'colour by annotation' can colour by RNA and
2319 protein secondary structure</li>
2320 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2321 post-hoc with 2.9 release</em>)
2324 </ul> <em>Application</em>
2326 <li>Extract and display secondary structure for sequences
2327 with 3D structures</li>
2328 <li>Support for parsing RNAML</li>
2329 <li>Annotations menu for layout
2331 <li>sort sequence annotation rows by alignment</li>
2332 <li>place sequence annotation above/below alignment
2335 <li>Output in Stockholm format</li>
2336 <li>Internationalisation: improved Spanish (es)
2338 <li>Structure viewer preferences tab</li>
2339 <li>Disorder and Secondary Structure annotation tracks
2340 shared between alignments</li>
2341 <li>UCSF Chimera launch and linked highlighting from
2343 <li>Show/hide all sequence associated annotation rows for
2344 all or current selection</li>
2345 <li>disorder and secondary structure predictions
2346 available as dataset annotation</li>
2347 <li>Per-sequence rna helices colouring</li>
2350 <li>Sequence database accessions imported when fetching
2351 alignments from Rfam</li>
2352 <li>update VARNA version to 3.91</li>
2354 <li>New groovy scripts for exporting aligned positions,
2355 conservation values, and calculating sum of pairs scores.</li>
2356 <li>Command line argument to set default JABAWS server</li>
2357 <li>include installation type in build properties and
2358 console log output</li>
2359 <li>Updated Jalview project format to preserve dataset
2363 <!-- issues resolved --> <em>Application</em>
2365 <li>Distinguish alignment and sequence associated RNA
2366 structure in structure->view->VARNA</li>
2367 <li>Raise dialog box if user deletes all sequences in an
2369 <li>Pressing F1 results in documentation opening twice</li>
2370 <li>Sequence feature tooltip is wrapped</li>
2371 <li>Double click on sequence associated annotation
2372 selects only first column</li>
2373 <li>Redundancy removal doesn't result in unlinked
2374 leaves shown in tree</li>
2375 <li>Undos after several redundancy removals don't undo
2377 <li>Hide sequence doesn't hide associated annotation</li>
2378 <li>User defined colours dialog box too big to fit on
2379 screen and buttons not visible</li>
2380 <li>author list isn't updated if already written to
2381 Jalview properties</li>
2382 <li>Popup menu won't open after retrieving sequence
2384 <li>File open window for associate PDB doesn't open</li>
2385 <li>Left-then-right click on a sequence id opens a
2386 browser search window</li>
2387 <li>Cannot open sequence feature shading/sort popup menu
2388 in feature settings dialog</li>
2389 <li>better tooltip placement for some areas of Jalview
2391 <li>Allow addition of JABAWS Server which doesn't
2392 pass validation</li>
2393 <li>Web services parameters dialog box is too large to
2395 <li>Muscle nucleotide alignment preset obscured by
2397 <li>JABAWS preset submenus don't contain newly
2398 defined user preset</li>
2399 <li>MSA web services warns user if they were launched
2400 with invalid input</li>
2401 <li>Jalview cannot contact DAS Registy when running on
2404 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2405 'Superpose with' submenu not shown when new view
2409 </ul> <!-- <em>Applet</em>
2411 </ul> <em>General</em>
2413 </ul>--> <em>Deployment and Documentation</em>
2415 <li>2G and 1G options in launchApp have no effect on
2416 memory allocation</li>
2417 <li>launchApp service doesn't automatically open
2418 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2420 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2421 InstallAnywhere reports cannot find valid JVM when Java
2422 1.7_055 is available
2424 </ul> <em>Application Known issues</em>
2427 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2428 corrupted or unreadable alignment display when scrolling
2432 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2433 retrieval fails but progress bar continues for DAS retrieval
2434 with large number of ID
2437 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2438 flatfile output of visible region has incorrect sequence
2442 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2443 rna structure consensus doesn't update when secondary
2444 structure tracks are rearranged
2447 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2448 invalid rna structure positional highlighting does not
2449 highlight position of invalid base pairs
2452 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2453 out of memory errors are not raised when saving Jalview
2454 project from alignment window file menu
2457 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2458 Switching to RNA Helices colouring doesn't propagate to
2462 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2463 colour by RNA Helices not enabled when user created
2464 annotation added to alignment
2467 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2468 Jalview icon not shown on dock in Mountain Lion/Webstart
2470 </ul> <em>Applet Known Issues</em>
2473 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2474 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2477 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2478 Jalview and Jmol example not compatible with IE9
2481 <li>Sort by annotation score doesn't reverse order
2487 <td><div align="center">
2488 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2491 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2494 <li>Internationalisation of user interface (usually
2495 called i18n support) and translation for Spanish locale</li>
2496 <li>Define/Undefine group on current selection with
2497 Ctrl-G/Shift Ctrl-G</li>
2498 <li>Improved group creation/removal options in
2499 alignment/sequence Popup menu</li>
2500 <li>Sensible precision for symbol distribution
2501 percentages shown in logo tooltip.</li>
2502 <li>Annotation panel height set according to amount of
2503 annotation when alignment first opened</li>
2504 </ul> <em>Application</em>
2506 <li>Interactive consensus RNA secondary structure
2507 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2508 <li>Select columns containing particular features from
2509 Feature Settings dialog</li>
2510 <li>View all 'representative' PDB structures for selected
2512 <li>Update Jalview project format:
2514 <li>New file extension for Jalview projects '.jvp'</li>
2515 <li>Preserve sequence and annotation dataset (to
2516 store secondary structure annotation,etc)</li>
2517 <li>Per group and alignment annotation and RNA helix
2521 <li>New similarity measures for PCA and Tree calculation
2523 <li>Experimental support for retrieval and viewing of
2524 flanking regions for an alignment</li>
2528 <!-- issues resolved --> <em>Application</em>
2530 <li>logo keeps spinning and status remains at queued or
2531 running after job is cancelled</li>
2532 <li>cannot export features from alignments imported from
2533 Jalview/VAMSAS projects</li>
2534 <li>Buggy slider for web service parameters that take
2536 <li>Newly created RNA secondary structure line doesn't
2537 have 'display all symbols' flag set</li>
2538 <li>T-COFFEE alignment score shading scheme and other
2539 annotation shading not saved in Jalview project</li>
2540 <li>Local file cannot be loaded in freshly downloaded
2542 <li>Jalview icon not shown on dock in Mountain
2544 <li>Load file from desktop file browser fails</li>
2545 <li>Occasional NPE thrown when calculating large trees</li>
2546 <li>Cannot reorder or slide sequences after dragging an
2547 alignment onto desktop</li>
2548 <li>Colour by annotation dialog throws NPE after using
2549 'extract scores' function</li>
2550 <li>Loading/cut'n'pasting an empty file leads to a grey
2551 alignment window</li>
2552 <li>Disorder thresholds rendered incorrectly after
2553 performing IUPred disorder prediction</li>
2554 <li>Multiple group annotated consensus rows shown when
2555 changing 'normalise logo' display setting</li>
2556 <li>Find shows blank dialog after 'finished searching' if
2557 nothing matches query</li>
2558 <li>Null Pointer Exceptions raised when sorting by
2559 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2561 <li>Errors in Jmol console when structures in alignment
2562 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2564 <li>Not all working JABAWS services are shown in
2566 <li>JAVAWS version of Jalview fails to launch with
2567 'invalid literal/length code'</li>
2568 <li>Annotation/RNA Helix colourschemes cannot be applied
2569 to alignment with groups (actually fixed in 2.8.0b1)</li>
2570 <li>RNA Helices and T-Coffee Scores available as default
2573 </ul> <em>Applet</em>
2575 <li>Remove group option is shown even when selection is
2577 <li>Apply to all groups ticked but colourscheme changes
2578 don't affect groups</li>
2579 <li>Documented RNA Helices and T-Coffee Scores as valid
2580 colourscheme name</li>
2581 <li>Annotation labels drawn on sequence IDs when
2582 Annotation panel is not displayed</li>
2583 <li>Increased font size for dropdown menus on OSX and
2584 embedded windows</li>
2585 </ul> <em>Other</em>
2587 <li>Consensus sequence for alignments/groups with a
2588 single sequence were not calculated</li>
2589 <li>annotation files that contain only groups imported as
2590 annotation and junk sequences</li>
2591 <li>Fasta files with sequences containing '*' incorrectly
2592 recognised as PFAM or BLC</li>
2593 <li>conservation/PID slider apply all groups option
2594 doesn't affect background (2.8.0b1)
2596 <li>redundancy highlighting is erratic at 0% and 100%</li>
2597 <li>Remove gapped columns fails for sequences with ragged
2599 <li>AMSA annotation row with leading spaces is not
2600 registered correctly on import</li>
2601 <li>Jalview crashes when selecting PCA analysis for
2602 certain alignments</li>
2603 <li>Opening the colour by annotation dialog for an
2604 existing annotation based 'use original colours'
2605 colourscheme loses original colours setting</li>
2610 <td><div align="center">
2611 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2612 <em>30/1/2014</em></strong>
2616 <li>Trusted certificates for JalviewLite applet and
2617 Jalview Desktop application<br />Certificate was donated by
2618 <a href="https://www.certum.eu">Certum</a> to the Jalview
2619 open source project).
2621 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2622 <li>Output in Stockholm format</li>
2623 <li>Allow import of data from gzipped files</li>
2624 <li>Export/import group and sequence associated line
2625 graph thresholds</li>
2626 <li>Nucleotide substitution matrix that supports RNA and
2627 ambiguity codes</li>
2628 <li>Allow disorder predictions to be made on the current
2629 selection (or visible selection) in the same way that JPred
2631 <li>Groovy scripting for headless Jalview operation</li>
2632 </ul> <em>Other improvements</em>
2634 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2635 <li>COMBINE statement uses current SEQUENCE_REF and
2636 GROUP_REF scope to group annotation rows</li>
2637 <li>Support '' style escaping of quotes in Newick
2639 <li>Group options for JABAWS service by command line name</li>
2640 <li>Empty tooltip shown for JABA service options with a
2641 link but no description</li>
2642 <li>Select primary source when selecting authority in
2643 database fetcher GUI</li>
2644 <li>Add .mfa to FASTA file extensions recognised by
2646 <li>Annotation label tooltip text wrap</li>
2651 <li>Slow scrolling when lots of annotation rows are
2653 <li>Lots of NPE (and slowness) after creating RNA
2654 secondary structure annotation line</li>
2655 <li>Sequence database accessions not imported when
2656 fetching alignments from Rfam</li>
2657 <li>Incorrect SHMR submission for sequences with
2659 <li>View all structures does not always superpose
2661 <li>Option widgets in service parameters not updated to
2662 reflect user or preset settings</li>
2663 <li>Null pointer exceptions for some services without
2664 presets or adjustable parameters</li>
2665 <li>Discover PDB IDs entry in structure menu doesn't
2666 discover PDB xRefs</li>
2667 <li>Exception encountered while trying to retrieve
2668 features with DAS</li>
2669 <li>Lowest value in annotation row isn't coloured
2670 when colour by annotation (per sequence) is coloured</li>
2671 <li>Keyboard mode P jumps to start of gapped region when
2672 residue follows a gap</li>
2673 <li>Jalview appears to hang importing an alignment with
2674 Wrap as default or after enabling Wrap</li>
2675 <li>'Right click to add annotations' message
2676 shown in wrap mode when no annotations present</li>
2677 <li>Disorder predictions fail with NPE if no automatic
2678 annotation already exists on alignment</li>
2679 <li>oninit javascript function should be called after
2680 initialisation completes</li>
2681 <li>Remove redundancy after disorder prediction corrupts
2682 alignment window display</li>
2683 <li>Example annotation file in documentation is invalid</li>
2684 <li>Grouped line graph annotation rows are not exported
2685 to annotation file</li>
2686 <li>Multi-harmony analysis cannot be run when only two
2688 <li>Cannot create multiple groups of line graphs with
2689 several 'combine' statements in annotation file</li>
2690 <li>Pressing return several times causes Number Format
2691 exceptions in keyboard mode</li>
2692 <li>Multi-harmony (SHMMR) method doesn't submit
2693 correct partitions for input data</li>
2694 <li>Translation from DNA to Amino Acids fails</li>
2695 <li>Jalview fail to load newick tree with quoted label</li>
2696 <li>--headless flag isn't understood</li>
2697 <li>ClassCastException when generating EPS in headless
2699 <li>Adjusting sequence-associated shading threshold only
2700 changes one row's threshold</li>
2701 <li>Preferences and Feature settings panel panel
2702 doesn't open</li>
2703 <li>hide consensus histogram also hides conservation and
2704 quality histograms</li>
2709 <td><div align="center">
2710 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2712 <td><em>Application</em>
2714 <li>Support for JABAWS 2.0 Services (AACon alignment
2715 conservation, protein disorder and Clustal Omega)</li>
2716 <li>JABAWS server status indicator in Web Services
2718 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2719 in Jalview alignment window</li>
2720 <li>Updated Jalview build and deploy framework for OSX
2721 mountain lion, windows 7, and 8</li>
2722 <li>Nucleotide substitution matrix for PCA that supports
2723 RNA and ambiguity codes</li>
2725 <li>Improved sequence database retrieval GUI</li>
2726 <li>Support fetching and database reference look up
2727 against multiple DAS sources (Fetch all from in 'fetch db
2729 <li>Jalview project improvements
2731 <li>Store and retrieve the 'belowAlignment'
2732 flag for annotation</li>
2733 <li>calcId attribute to group annotation rows on the
2735 <li>Store AACon calculation settings for a view in
2736 Jalview project</li>
2740 <li>horizontal scrolling gesture support</li>
2741 <li>Visual progress indicator when PCA calculation is
2743 <li>Simpler JABA web services menus</li>
2744 <li>visual indication that web service results are still
2745 being retrieved from server</li>
2746 <li>Serialise the dialogs that are shown when Jalview
2747 starts up for first time</li>
2748 <li>Jalview user agent string for interacting with HTTP
2750 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2752 <li>Examples directory and Groovy library included in
2753 InstallAnywhere distribution</li>
2754 </ul> <em>Applet</em>
2756 <li>RNA alignment and secondary structure annotation
2757 visualization applet example</li>
2758 </ul> <em>General</em>
2760 <li>Normalise option for consensus sequence logo</li>
2761 <li>Reset button in PCA window to return dimensions to
2763 <li>Allow seqspace or Jalview variant of alignment PCA
2765 <li>PCA with either nucleic acid and protein substitution
2767 <li>Allow windows containing HTML reports to be exported
2769 <li>Interactive display and editing of RNA secondary
2770 structure contacts</li>
2771 <li>RNA Helix Alignment Colouring</li>
2772 <li>RNA base pair logo consensus</li>
2773 <li>Parse sequence associated secondary structure
2774 information in Stockholm files</li>
2775 <li>HTML Export database accessions and annotation
2776 information presented in tooltip for sequences</li>
2777 <li>Import secondary structure from LOCARNA clustalw
2778 style RNA alignment files</li>
2779 <li>import and visualise T-COFFEE quality scores for an
2781 <li>'colour by annotation' per sequence option to
2782 shade each sequence according to its associated alignment
2784 <li>New Jalview Logo</li>
2785 </ul> <em>Documentation and Development</em>
2787 <li>documentation for score matrices used in Jalview</li>
2788 <li>New Website!</li>
2790 <td><em>Application</em>
2792 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2793 wsdbfetch REST service</li>
2794 <li>Stop windows being moved outside desktop on OSX</li>
2795 <li>Filetype associations not installed for webstart
2797 <li>Jalview does not always retrieve progress of a JABAWS
2798 job execution in full once it is complete</li>
2799 <li>revise SHMR RSBS definition to ensure alignment is
2800 uploaded via ali_file parameter</li>
2801 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2802 <li>View all structures superposed fails with exception</li>
2803 <li>Jnet job queues forever if a very short sequence is
2804 submitted for prediction</li>
2805 <li>Cut and paste menu not opened when mouse clicked on
2807 <li>Putting fractional value into integer text box in
2808 alignment parameter dialog causes Jalview to hang</li>
2809 <li>Structure view highlighting doesn't work on
2811 <li>View all structures fails with exception shown in
2813 <li>Characters in filename associated with PDBEntry not
2814 escaped in a platform independent way</li>
2815 <li>Jalview desktop fails to launch with exception when
2817 <li>Tree calculation reports 'you must have 2 or more
2818 sequences selected' when selection is empty</li>
2819 <li>Jalview desktop fails to launch with jar signature
2820 failure when java web start temporary file caching is
2822 <li>DAS Sequence retrieval with range qualification
2823 results in sequence xref which includes range qualification</li>
2824 <li>Errors during processing of command line arguments
2825 cause progress bar (JAL-898) to be removed</li>
2826 <li>Replace comma for semi-colon option not disabled for
2827 DAS sources in sequence fetcher</li>
2828 <li>Cannot close news reader when JABAWS server warning
2829 dialog is shown</li>
2830 <li>Option widgets not updated to reflect user settings</li>
2831 <li>Edited sequence not submitted to web service</li>
2832 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2833 <li>InstallAnywhere installer doesn't unpack and run
2834 on OSX Mountain Lion</li>
2835 <li>Annotation panel not given a scroll bar when
2836 sequences with alignment annotation are pasted into the
2838 <li>Sequence associated annotation rows not associated
2839 when loaded from Jalview project</li>
2840 <li>Browser launch fails with NPE on java 1.7</li>
2841 <li>JABAWS alignment marked as finished when job was
2842 cancelled or job failed due to invalid input</li>
2843 <li>NPE with v2.7 example when clicking on Tree
2844 associated with all views</li>
2845 <li>Exceptions when copy/paste sequences with grouped
2846 annotation rows to new window</li>
2847 </ul> <em>Applet</em>
2849 <li>Sequence features are momentarily displayed before
2850 they are hidden using hidefeaturegroups applet parameter</li>
2851 <li>loading features via javascript API automatically
2852 enables feature display</li>
2853 <li>scrollToColumnIn javascript API method doesn't
2855 </ul> <em>General</em>
2857 <li>Redundancy removal fails for rna alignment</li>
2858 <li>PCA calculation fails when sequence has been selected
2859 and then deselected</li>
2860 <li>PCA window shows grey box when first opened on OSX</li>
2861 <li>Letters coloured pink in sequence logo when alignment
2862 coloured with clustalx</li>
2863 <li>Choosing fonts without letter symbols defined causes
2864 exceptions and redraw errors</li>
2865 <li>Initial PCA plot view is not same as manually
2866 reconfigured view</li>
2867 <li>Grouped annotation graph label has incorrect line
2869 <li>Grouped annotation graph label display is corrupted
2870 for lots of labels</li>
2875 <div align="center">
2876 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2879 <td><em>Application</em>
2881 <li>Jalview Desktop News Reader</li>
2882 <li>Tweaked default layout of web services menu</li>
2883 <li>View/alignment association menu to enable user to
2884 easily specify which alignment a multi-structure view takes
2885 its colours/correspondences from</li>
2886 <li>Allow properties file location to be specified as URL</li>
2887 <li>Extend Jalview project to preserve associations
2888 between many alignment views and a single Jmol display</li>
2889 <li>Store annotation row height in Jalview project file</li>
2890 <li>Annotation row column label formatting attributes
2891 stored in project file</li>
2892 <li>Annotation row order for auto-calculated annotation
2893 rows preserved in Jalview project file</li>
2894 <li>Visual progress indication when Jalview state is
2895 saved using Desktop window menu</li>
2896 <li>Visual indication that command line arguments are
2897 still being processed</li>
2898 <li>Groovy script execution from URL</li>
2899 <li>Colour by annotation default min and max colours in
2901 <li>Automatically associate PDB files dragged onto an
2902 alignment with sequences that have high similarity and
2904 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2905 <li>'view structures' option to open many
2906 structures in same window</li>
2907 <li>Sort associated views menu option for tree panel</li>
2908 <li>Group all JABA and non-JABA services for a particular
2909 analysis function in its own submenu</li>
2910 </ul> <em>Applet</em>
2912 <li>Userdefined and autogenerated annotation rows for
2914 <li>Adjustment of alignment annotation pane height</li>
2915 <li>Annotation scrollbar for annotation panel</li>
2916 <li>Drag to reorder annotation rows in annotation panel</li>
2917 <li>'automaticScrolling' parameter</li>
2918 <li>Allow sequences with partial ID string matches to be
2919 annotated from GFF/Jalview features files</li>
2920 <li>Sequence logo annotation row in applet</li>
2921 <li>Absolute paths relative to host server in applet
2922 parameters are treated as such</li>
2923 <li>New in the JalviewLite javascript API:
2925 <li>JalviewLite.js javascript library</li>
2926 <li>Javascript callbacks for
2928 <li>Applet initialisation</li>
2929 <li>Sequence/alignment mouse-overs and selections</li>
2932 <li>scrollTo row and column alignment scrolling
2934 <li>Select sequence/alignment regions from javascript</li>
2935 <li>javascript structure viewer harness to pass
2936 messages between Jmol and Jalview when running as
2937 distinct applets</li>
2938 <li>sortBy method</li>
2939 <li>Set of applet and application examples shipped
2940 with documentation</li>
2941 <li>New example to demonstrate JalviewLite and Jmol
2942 javascript message exchange</li>
2944 </ul> <em>General</em>
2946 <li>Enable Jmol displays to be associated with multiple
2947 multiple alignments</li>
2948 <li>Option to automatically sort alignment with new tree</li>
2949 <li>User configurable link to enable redirects to a
2950 www.Jalview.org mirror</li>
2951 <li>Jmol colours option for Jmol displays</li>
2952 <li>Configurable newline string when writing alignment
2953 and other flat files</li>
2954 <li>Allow alignment annotation description lines to
2955 contain html tags</li>
2956 </ul> <em>Documentation and Development</em>
2958 <li>Add groovy test harness for bulk load testing to
2960 <li>Groovy script to load and align a set of sequences
2961 using a web service before displaying the result in the
2962 Jalview desktop</li>
2963 <li>Restructured javascript and applet api documentation</li>
2964 <li>Ant target to publish example html files with applet
2966 <li>Netbeans project for building Jalview from source</li>
2967 <li>ant task to create online javadoc for Jalview source</li>
2969 <td><em>Application</em>
2971 <li>User defined colourscheme throws exception when
2972 current built in colourscheme is saved as new scheme</li>
2973 <li>AlignFrame->Save in application pops up save
2974 dialog for valid filename/format</li>
2975 <li>Cannot view associated structure for UniProt sequence</li>
2976 <li>PDB file association breaks for UniProt sequence
2978 <li>Associate PDB from file dialog does not tell you
2979 which sequence is to be associated with the file</li>
2980 <li>Find All raises null pointer exception when query
2981 only matches sequence IDs</li>
2982 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2983 <li>Jalview project with Jmol views created with Jalview
2984 2.4 cannot be loaded</li>
2985 <li>Filetype associations not installed for webstart
2987 <li>Two or more chains in a single PDB file associated
2988 with sequences in different alignments do not get coloured
2989 by their associated sequence</li>
2990 <li>Visibility status of autocalculated annotation row
2991 not preserved when project is loaded</li>
2992 <li>Annotation row height and visibility attributes not
2993 stored in Jalview project</li>
2994 <li>Tree bootstraps are not preserved when saved as a
2995 Jalview project</li>
2996 <li>Envision2 workflow tooltips are corrupted</li>
2997 <li>Enabling show group conservation also enables colour
2998 by conservation</li>
2999 <li>Duplicate group associated conservation or consensus
3000 created on new view</li>
3001 <li>Annotation scrollbar not displayed after 'show
3002 all hidden annotation rows' option selected</li>
3003 <li>Alignment quality not updated after alignment
3004 annotation row is hidden then shown</li>
3005 <li>Preserve colouring of structures coloured by
3006 sequences in pre Jalview 2.7 projects</li>
3007 <li>Web service job parameter dialog is not laid out
3009 <li>Web services menu not refreshed after 'reset
3010 services' button is pressed in preferences</li>
3011 <li>Annotation off by one in Jalview v2_3 example project</li>
3012 <li>Structures imported from file and saved in project
3013 get name like jalview_pdb1234.txt when reloaded</li>
3014 <li>Jalview does not always retrieve progress of a JABAWS
3015 job execution in full once it is complete</li>
3016 </ul> <em>Applet</em>
3018 <li>Alignment height set incorrectly when lots of
3019 annotation rows are displayed</li>
3020 <li>Relative URLs in feature HTML text not resolved to
3022 <li>View follows highlighting does not work for positions
3024 <li><= shown as = in tooltip</li>
3025 <li>Export features raises exception when no features
3027 <li>Separator string used for serialising lists of IDs
3028 for javascript api is modified when separator string
3029 provided as parameter</li>
3030 <li>Null pointer exception when selecting tree leaves for
3031 alignment with no existing selection</li>
3032 <li>Relative URLs for datasources assumed to be relative
3033 to applet's codebase</li>
3034 <li>Status bar not updated after finished searching and
3035 search wraps around to first result</li>
3036 <li>StructureSelectionManager instance shared between
3037 several Jalview applets causes race conditions and memory
3039 <li>Hover tooltip and mouseover of position on structure
3040 not sent from Jmol in applet</li>
3041 <li>Certain sequences of javascript method calls to
3042 applet API fatally hang browser</li>
3043 </ul> <em>General</em>
3045 <li>View follows structure mouseover scrolls beyond
3046 position with wrapped view and hidden regions</li>
3047 <li>Find sequence position moves to wrong residue
3048 with/without hidden columns</li>
3049 <li>Sequence length given in alignment properties window
3051 <li>InvalidNumberFormat exceptions thrown when trying to
3052 import PDB like structure files</li>
3053 <li>Positional search results are only highlighted
3054 between user-supplied sequence start/end bounds</li>
3055 <li>End attribute of sequence is not validated</li>
3056 <li>Find dialog only finds first sequence containing a
3057 given sequence position</li>
3058 <li>Sequence numbering not preserved in MSF alignment
3060 <li>Jalview PDB file reader does not extract sequence
3061 from nucleotide chains correctly</li>
3062 <li>Structure colours not updated when tree partition
3063 changed in alignment</li>
3064 <li>Sequence associated secondary structure not correctly
3065 parsed in interleaved stockholm</li>
3066 <li>Colour by annotation dialog does not restore current
3068 <li>Hiding (nearly) all sequences doesn't work
3070 <li>Sequences containing lowercase letters are not
3071 properly associated with their pdb files</li>
3072 </ul> <em>Documentation and Development</em>
3074 <li>schemas/JalviewWsParamSet.xsd corrupted by
3075 ApplyCopyright tool</li>
3080 <div align="center">
3081 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3084 <td><em>Application</em>
3086 <li>New warning dialog when the Jalview Desktop cannot
3087 contact web services</li>
3088 <li>JABA service parameters for a preset are shown in
3089 service job window</li>
3090 <li>JABA Service menu entries reworded</li>
3094 <li>Modeller PIR IO broken - cannot correctly import a
3095 pir file emitted by Jalview</li>
3096 <li>Existing feature settings transferred to new
3097 alignment view created from cut'n'paste</li>
3098 <li>Improved test for mixed amino/nucleotide chains when
3099 parsing PDB files</li>
3100 <li>Consensus and conservation annotation rows
3101 occasionally become blank for all new windows</li>
3102 <li>Exception raised when right clicking above sequences
3103 in wrapped view mode</li>
3104 </ul> <em>Application</em>
3106 <li>multiple multiply aligned structure views cause cpu
3107 usage to hit 100% and computer to hang</li>
3108 <li>Web Service parameter layout breaks for long user
3109 parameter names</li>
3110 <li>Jaba service discovery hangs desktop if Jaba server
3117 <div align="center">
3118 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3121 <td><em>Application</em>
3123 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3124 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3127 <li>Web Services preference tab</li>
3128 <li>Analysis parameters dialog box and user defined
3130 <li>Improved speed and layout of Envision2 service menu</li>
3131 <li>Superpose structures using associated sequence
3133 <li>Export coordinates and projection as CSV from PCA
3135 </ul> <em>Applet</em>
3137 <li>enable javascript: execution by the applet via the
3138 link out mechanism</li>
3139 </ul> <em>Other</em>
3141 <li>Updated the Jmol Jalview interface to work with Jmol
3143 <li>The Jalview Desktop and JalviewLite applet now
3144 require Java 1.5</li>
3145 <li>Allow Jalview feature colour specification for GFF
3146 sequence annotation files</li>
3147 <li>New 'colour by label' keword in Jalview feature file
3148 type colour specification</li>
3149 <li>New Jalview Desktop Groovy API method that allows a
3150 script to check if it being run in an interactive session or
3151 in a batch operation from the Jalview command line</li>
3155 <li>clustalx colourscheme colours Ds preferentially when
3156 both D+E are present in over 50% of the column</li>
3157 </ul> <em>Application</em>
3159 <li>typo in AlignmentFrame->View->Hide->all but
3160 selected Regions menu item</li>
3161 <li>sequence fetcher replaces ',' for ';' when the ',' is
3162 part of a valid accession ID</li>
3163 <li>fatal OOM if object retrieved by sequence fetcher
3164 runs out of memory</li>
3165 <li>unhandled Out of Memory Error when viewing pca
3166 analysis results</li>
3167 <li>InstallAnywhere builds fail to launch on OS X java
3168 10.5 update 4 (due to apple Java 1.6 update)</li>
3169 <li>Installanywhere Jalview silently fails to launch</li>
3170 </ul> <em>Applet</em>
3172 <li>Jalview.getFeatureGroups() raises an
3173 ArrayIndexOutOfBoundsException if no feature groups are
3180 <div align="center">
3181 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3187 <li>Alignment prettyprinter doesn't cope with long
3189 <li>clustalx colourscheme colours Ds preferentially when
3190 both D+E are present in over 50% of the column</li>
3191 <li>nucleic acid structures retrieved from PDB do not
3192 import correctly</li>
3193 <li>More columns get selected than were clicked on when a
3194 number of columns are hidden</li>
3195 <li>annotation label popup menu not providing correct
3196 add/hide/show options when rows are hidden or none are
3198 <li>Stockholm format shown in list of readable formats,
3199 and parser copes better with alignments from RFAM.</li>
3200 <li>CSV output of consensus only includes the percentage
3201 of all symbols if sequence logo display is enabled</li>
3203 </ul> <em>Applet</em>
3205 <li>annotation panel disappears when annotation is
3207 </ul> <em>Application</em>
3209 <li>Alignment view not redrawn properly when new
3210 alignment opened where annotation panel is visible but no
3211 annotations are present on alignment</li>
3212 <li>pasted region containing hidden columns is
3213 incorrectly displayed in new alignment window</li>
3214 <li>Jalview slow to complete operations when stdout is
3215 flooded (fix is to close the Jalview console)</li>
3216 <li>typo in AlignmentFrame->View->Hide->all but
3217 selected Rregions menu item.</li>
3218 <li>inconsistent group submenu and Format submenu entry
3219 'Un' or 'Non'conserved</li>
3220 <li>Sequence feature settings are being shared by
3221 multiple distinct alignments</li>
3222 <li>group annotation not recreated when tree partition is
3224 <li>double click on group annotation to select sequences
3225 does not propagate to associated trees</li>
3226 <li>Mac OSX specific issues:
3228 <li>exception raised when mouse clicked on desktop
3229 window background</li>
3230 <li>Desktop menu placed on menu bar and application
3231 name set correctly</li>
3232 <li>sequence feature settings not wide enough for the
3233 save feature colourscheme button</li>
3242 <div align="center">
3243 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3246 <td><em>New Capabilities</em>
3248 <li>URL links generated from description line for
3249 regular-expression based URL links (applet and application)
3251 <li>Non-positional feature URL links are shown in link
3253 <li>Linked viewing of nucleic acid sequences and
3255 <li>Automatic Scrolling option in View menu to display
3256 the currently highlighted region of an alignment.</li>
3257 <li>Order an alignment by sequence length, or using the
3258 average score or total feature count for each sequence.</li>
3259 <li>Shading features by score or associated description</li>
3260 <li>Subdivide alignment and groups based on identity of
3261 selected subsequence (Make Groups from Selection).</li>
3262 <li>New hide/show options including Shift+Control+H to
3263 hide everything but the currently selected region.</li>
3264 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3265 </ul> <em>Application</em>
3267 <li>Fetch DB References capabilities and UI expanded to
3268 support retrieval from DAS sequence sources</li>
3269 <li>Local DAS Sequence sources can be added via the
3270 command line or via the Add local source dialog box.</li>
3271 <li>DAS Dbref and DbxRef feature types are parsed as
3272 database references and protein_name is parsed as
3273 description line (BioSapiens terms).</li>
3274 <li>Enable or disable non-positional feature and database
3275 references in sequence ID tooltip from View menu in
3277 <!-- <li>New hidden columns and rows and representatives capabilities
3278 in annotations file (in progress - not yet fully implemented)</li> -->
3279 <li>Group-associated consensus, sequence logos and
3280 conservation plots</li>
3281 <li>Symbol distributions for each column can be exported
3282 and visualized as sequence logos</li>
3283 <li>Optionally scale multi-character column labels to fit
3284 within each column of annotation row<!-- todo for applet -->
3286 <li>Optional automatic sort of associated alignment view
3287 when a new tree is opened.</li>
3288 <li>Jalview Java Console</li>
3289 <li>Better placement of desktop window when moving
3290 between different screens.</li>
3291 <li>New preference items for sequence ID tooltip and
3292 consensus annotation</li>
3293 <li>Client to submit sequences and IDs to Envision2
3295 <li><em>Vamsas Capabilities</em>
3297 <li>Improved VAMSAS synchronization (Jalview archive
3298 used to preserve views, structures, and tree display
3300 <li>Import of vamsas documents from disk or URL via
3302 <li>Sharing of selected regions between views and
3303 with other VAMSAS applications (Experimental feature!)</li>
3304 <li>Updated API to VAMSAS version 0.2</li>
3306 </ul> <em>Applet</em>
3308 <li>Middle button resizes annotation row height</li>
3311 <li>sortByTree (true/false) - automatically sort the
3312 associated alignment view by the tree when a new tree is
3314 <li>showTreeBootstraps (true/false) - show or hide
3315 branch bootstraps (default is to show them if available)</li>
3316 <li>showTreeDistances (true/false) - show or hide
3317 branch lengths (default is to show them if available)</li>
3318 <li>showUnlinkedTreeNodes (true/false) - indicate if
3319 unassociated nodes should be highlighted in the tree
3321 <li>heightScale and widthScale (1.0 or more) -
3322 increase the height or width of a cell in the alignment
3323 grid relative to the current font size.</li>
3326 <li>Non-positional features displayed in sequence ID
3328 </ul> <em>Other</em>
3330 <li>Features format: graduated colour definitions and
3331 specification of feature scores</li>
3332 <li>Alignment Annotations format: new keywords for group
3333 associated annotation (GROUP_REF) and annotation row display
3334 properties (ROW_PROPERTIES)</li>
3335 <li>XML formats extended to support graduated feature
3336 colourschemes, group associated annotation, and profile
3337 visualization settings.</li></td>
3340 <li>Source field in GFF files parsed as feature source
3341 rather than description</li>
3342 <li>Non-positional features are now included in sequence
3343 feature and gff files (controlled via non-positional feature
3344 visibility in tooltip).</li>
3345 <li>URL links generated for all feature links (bugfix)</li>
3346 <li>Added URL embedding instructions to features file
3348 <li>Codons containing ambiguous nucleotides translated as
3349 'X' in peptide product</li>
3350 <li>Match case switch in find dialog box works for both
3351 sequence ID and sequence string and query strings do not
3352 have to be in upper case to match case-insensitively.</li>
3353 <li>AMSA files only contain first column of
3354 multi-character column annotation labels</li>
3355 <li>Jalview Annotation File generation/parsing consistent
3356 with documentation (e.g. Stockholm annotation can be
3357 exported and re-imported)</li>
3358 <li>PDB files without embedded PDB IDs given a friendly
3360 <li>Find incrementally searches ID string matches as well
3361 as subsequence matches, and correctly reports total number
3365 <li>Better handling of exceptions during sequence
3367 <li>Dasobert generated non-positional feature URL
3368 link text excludes the start_end suffix</li>
3369 <li>DAS feature and source retrieval buttons disabled
3370 when fetch or registry operations in progress.</li>
3371 <li>PDB files retrieved from URLs are cached properly</li>
3372 <li>Sequence description lines properly shared via
3374 <li>Sequence fetcher fetches multiple records for all
3376 <li>Ensured that command line das feature retrieval
3377 completes before alignment figures are generated.</li>
3378 <li>Reduced time taken when opening file browser for
3380 <li>isAligned check prior to calculating tree, PCA or
3381 submitting an MSA to JNet now excludes hidden sequences.</li>
3382 <li>User defined group colours properly recovered
3383 from Jalview projects.</li>
3392 <div align="center">
3393 <strong>2.4.0.b2</strong><br> 28/10/2009
3398 <li>Experimental support for google analytics usage
3400 <li>Jalview privacy settings (user preferences and docs).</li>
3405 <li>Race condition in applet preventing startup in
3407 <li>Exception when feature created from selection beyond
3408 length of sequence.</li>
3409 <li>Allow synthetic PDB files to be imported gracefully</li>
3410 <li>Sequence associated annotation rows associate with
3411 all sequences with a given id</li>
3412 <li>Find function matches case-insensitively for sequence
3413 ID string searches</li>
3414 <li>Non-standard characters do not cause pairwise
3415 alignment to fail with exception</li>
3416 </ul> <em>Application Issues</em>
3418 <li>Sequences are now validated against EMBL database</li>
3419 <li>Sequence fetcher fetches multiple records for all
3421 </ul> <em>InstallAnywhere Issues</em>
3423 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3424 issue with installAnywhere mechanism)</li>
3425 <li>Command line launching of JARs from InstallAnywhere
3426 version (java class versioning error fixed)</li>
3433 <div align="center">
3434 <strong>2.4</strong><br> 27/8/2008
3437 <td><em>User Interface</em>
3439 <li>Linked highlighting of codon and amino acid from
3440 translation and protein products</li>
3441 <li>Linked highlighting of structure associated with
3442 residue mapping to codon position</li>
3443 <li>Sequence Fetcher provides example accession numbers
3444 and 'clear' button</li>
3445 <li>MemoryMonitor added as an option under Desktop's
3447 <li>Extract score function to parse whitespace separated
3448 numeric data in description line</li>
3449 <li>Column labels in alignment annotation can be centred.</li>
3450 <li>Tooltip for sequence associated annotation give name
3452 </ul> <em>Web Services and URL fetching</em>
3454 <li>JPred3 web service</li>
3455 <li>Prototype sequence search client (no public services
3457 <li>Fetch either seed alignment or full alignment from
3459 <li>URL Links created for matching database cross
3460 references as well as sequence ID</li>
3461 <li>URL Links can be created using regular-expressions</li>
3462 </ul> <em>Sequence Database Connectivity</em>
3464 <li>Retrieval of cross-referenced sequences from other
3466 <li>Generalised database reference retrieval and
3467 validation to all fetchable databases</li>
3468 <li>Fetch sequences from DAS sources supporting the
3469 sequence command</li>
3470 </ul> <em>Import and Export</em>
3471 <li>export annotation rows as CSV for spreadsheet import</li>
3472 <li>Jalview projects record alignment dataset associations,
3473 EMBL products, and cDNA sequence mappings</li>
3474 <li>Sequence Group colour can be specified in Annotation
3476 <li>Ad-hoc colouring of group in Annotation File using RGB
3477 triplet as name of colourscheme</li>
3478 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3480 <li>treenode binding for VAMSAS tree exchange</li>
3481 <li>local editing and update of sequences in VAMSAS
3482 alignments (experimental)</li>
3483 <li>Create new or select existing session to join</li>
3484 <li>load and save of vamsas documents</li>
3485 </ul> <em>Application command line</em>
3487 <li>-tree parameter to open trees (introduced for passing
3489 <li>-fetchfrom command line argument to specify nicknames
3490 of DAS servers to query for alignment features</li>
3491 <li>-dasserver command line argument to add new servers
3492 that are also automatically queried for features</li>
3493 <li>-groovy command line argument executes a given groovy
3494 script after all input data has been loaded and parsed</li>
3495 </ul> <em>Applet-Application data exchange</em>
3497 <li>Trees passed as applet parameters can be passed to
3498 application (when using "View in full
3499 application")</li>
3500 </ul> <em>Applet Parameters</em>
3502 <li>feature group display control parameter</li>
3503 <li>debug parameter</li>
3504 <li>showbutton parameter</li>
3505 </ul> <em>Applet API methods</em>
3507 <li>newView public method</li>
3508 <li>Window (current view) specific get/set public methods</li>
3509 <li>Feature display control methods</li>
3510 <li>get list of currently selected sequences</li>
3511 </ul> <em>New Jalview distribution features</em>
3513 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3514 <li>RELEASE file gives build properties for the latest
3515 Jalview release.</li>
3516 <li>Java 1.1 Applet build made easier and donotobfuscate
3517 property controls execution of obfuscator</li>
3518 <li>Build target for generating source distribution</li>
3519 <li>Debug flag for javacc</li>
3520 <li>.jalview_properties file is documented (slightly) in
3521 jalview.bin.Cache</li>
3522 <li>Continuous Build Integration for stable and
3523 development version of Application, Applet and source
3528 <li>selected region output includes visible annotations
3529 (for certain formats)</li>
3530 <li>edit label/displaychar contains existing label/char
3532 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3533 <li>shorter peptide product names from EMBL records</li>
3534 <li>Newick string generator makes compact representations</li>
3535 <li>bootstrap values parsed correctly for tree files with
3537 <li>pathological filechooser bug avoided by not allowing
3538 filenames containing a ':'</li>
3539 <li>Fixed exception when parsing GFF files containing
3540 global sequence features</li>
3541 <li>Alignment datasets are finalized only when number of
3542 references from alignment sequences goes to zero</li>
3543 <li>Close of tree branch colour box without colour
3544 selection causes cascading exceptions</li>
3545 <li>occasional negative imgwidth exceptions</li>
3546 <li>better reporting of non-fatal warnings to user when
3547 file parsing fails.</li>
3548 <li>Save works when Jalview project is default format</li>
3549 <li>Save as dialog opened if current alignment format is
3550 not a valid output format</li>
3551 <li>UniProt canonical names introduced for both das and
3553 <li>Histidine should be midblue (not pink!) in Zappo</li>
3554 <li>error messages passed up and output when data read
3556 <li>edit undo recovers previous dataset sequence when
3557 sequence is edited</li>
3558 <li>allow PDB files without pdb ID HEADER lines (like
3559 those generated by MODELLER) to be read in properly</li>
3560 <li>allow reading of JPred concise files as a normal
3562 <li>Stockholm annotation parsing and alignment properties
3563 import fixed for PFAM records</li>
3564 <li>Structure view windows have correct name in Desktop
3566 <li>annotation consisting of sequence associated scores
3567 can be read and written correctly to annotation file</li>
3568 <li>Aligned cDNA translation to aligned peptide works
3570 <li>Fixed display of hidden sequence markers and
3571 non-italic font for representatives in Applet</li>
3572 <li>Applet Menus are always embedded in applet window on
3574 <li>Newly shown features appear at top of stack (in
3576 <li>Annotations added via parameter not drawn properly
3577 due to null pointer exceptions</li>
3578 <li>Secondary structure lines are drawn starting from
3579 first column of alignment</li>
3580 <li>UniProt XML import updated for new schema release in
3582 <li>Sequence feature to sequence ID match for Features
3583 file is case-insensitive</li>
3584 <li>Sequence features read from Features file appended to
3585 all sequences with matching IDs</li>
3586 <li>PDB structure coloured correctly for associated views
3587 containing a sub-sequence</li>
3588 <li>PDB files can be retrieved by applet from Jar files</li>
3589 <li>feature and annotation file applet parameters
3590 referring to different directories are retrieved correctly</li>
3591 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3592 <li>Fixed application hang whilst waiting for
3593 splash-screen version check to complete</li>
3594 <li>Applet properly URLencodes input parameter values
3595 when passing them to the launchApp service</li>
3596 <li>display name and local features preserved in results
3597 retrieved from web service</li>
3598 <li>Visual delay indication for sequence retrieval and
3599 sequence fetcher initialisation</li>
3600 <li>updated Application to use DAS 1.53e version of
3601 dasobert DAS client</li>
3602 <li>Re-instated Full AMSA support and .amsa file
3604 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3612 <div align="center">
3613 <strong>2.3</strong><br> 9/5/07
3618 <li>Jmol 11.0.2 integration</li>
3619 <li>PDB views stored in Jalview XML files</li>
3620 <li>Slide sequences</li>
3621 <li>Edit sequence in place</li>
3622 <li>EMBL CDS features</li>
3623 <li>DAS Feature mapping</li>
3624 <li>Feature ordering</li>
3625 <li>Alignment Properties</li>
3626 <li>Annotation Scores</li>
3627 <li>Sort by scores</li>
3628 <li>Feature/annotation editing in applet</li>
3633 <li>Headless state operation in 2.2.1</li>
3634 <li>Incorrect and unstable DNA pairwise alignment</li>
3635 <li>Cut and paste of sequences with annotation</li>
3636 <li>Feature group display state in XML</li>
3637 <li>Feature ordering in XML</li>
3638 <li>blc file iteration selection using filename # suffix</li>
3639 <li>Stockholm alignment properties</li>
3640 <li>Stockhom alignment secondary structure annotation</li>
3641 <li>2.2.1 applet had no feature transparency</li>
3642 <li>Number pad keys can be used in cursor mode</li>
3643 <li>Structure Viewer mirror image resolved</li>
3650 <div align="center">
3651 <strong>2.2.1</strong><br> 12/2/07
3656 <li>Non standard characters can be read and displayed
3657 <li>Annotations/Features can be imported/exported to the
3659 <li>Applet allows editing of sequence/annotation/group
3660 name & description
3661 <li>Preference setting to display sequence name in
3663 <li>Annotation file format extended to allow
3664 Sequence_groups to be defined
3665 <li>Default opening of alignment overview panel can be
3666 specified in preferences
3667 <li>PDB residue numbering annotation added to associated
3673 <li>Applet crash under certain Linux OS with Java 1.6
3675 <li>Annotation file export / import bugs fixed
3676 <li>PNG / EPS image output bugs fixed
3682 <div align="center">
3683 <strong>2.2</strong><br> 27/11/06
3688 <li>Multiple views on alignment
3689 <li>Sequence feature editing
3690 <li>"Reload" alignment
3691 <li>"Save" to current filename
3692 <li>Background dependent text colour
3693 <li>Right align sequence ids
3694 <li>User-defined lower case residue colours
3697 <li>Menu item accelerator keys
3698 <li>Control-V pastes to current alignment
3699 <li>Cancel button for DAS Feature Fetching
3700 <li>PCA and PDB Viewers zoom via mouse roller
3701 <li>User-defined sub-tree colours and sub-tree selection
3703 <li>'New Window' button on the 'Output to Text box'
3708 <li>New memory efficient Undo/Redo System
3709 <li>Optimised symbol lookups and conservation/consensus
3711 <li>Region Conservation/Consensus recalculated after
3713 <li>Fixed Remove Empty Columns Bug (empty columns at end
3715 <li>Slowed DAS Feature Fetching for increased robustness.
3717 <li>Made angle brackets in ASCII feature descriptions
3719 <li>Re-instated Zoom function for PCA
3720 <li>Sequence descriptions conserved in web service
3722 <li>UniProt ID discoverer uses any word separated by
3724 <li>WsDbFetch query/result association resolved
3725 <li>Tree leaf to sequence mapping improved
3726 <li>Smooth fonts switch moved to FontChooser dialog box.
3733 <div align="center">
3734 <strong>2.1.1</strong><br> 12/9/06
3739 <li>Copy consensus sequence to clipboard</li>
3744 <li>Image output - rightmost residues are rendered if
3745 sequence id panel has been resized</li>
3746 <li>Image output - all offscreen group boundaries are
3748 <li>Annotation files with sequence references - all
3749 elements in file are relative to sequence position</li>
3750 <li>Mac Applet users can use Alt key for group editing</li>
3756 <div align="center">
3757 <strong>2.1</strong><br> 22/8/06
3762 <li>MAFFT Multiple Alignment in default Web Service list</li>
3763 <li>DAS Feature fetching</li>
3764 <li>Hide sequences and columns</li>
3765 <li>Export Annotations and Features</li>
3766 <li>GFF file reading / writing</li>
3767 <li>Associate structures with sequences from local PDB
3769 <li>Add sequences to exisiting alignment</li>
3770 <li>Recently opened files / URL lists</li>
3771 <li>Applet can launch the full application</li>
3772 <li>Applet has transparency for features (Java 1.2
3774 <li>Applet has user defined colours parameter</li>
3775 <li>Applet can load sequences from parameter
3776 "sequence<em>x</em>"
3782 <li>Redundancy Panel reinstalled in the Applet</li>
3783 <li>Monospaced font - EPS / rescaling bug fixed</li>
3784 <li>Annotation files with sequence references bug fixed</li>
3790 <div align="center">
3791 <strong>2.08.1</strong><br> 2/5/06
3796 <li>Change case of selected region from Popup menu</li>
3797 <li>Choose to match case when searching</li>
3798 <li>Middle mouse button and mouse movement can compress /
3799 expand the visible width and height of the alignment</li>
3804 <li>Annotation Panel displays complete JNet results</li>
3810 <div align="center">
3811 <strong>2.08b</strong><br> 18/4/06
3817 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3818 <li>Righthand label on wrapped alignments shows correct
3825 <div align="center">
3826 <strong>2.08</strong><br> 10/4/06
3831 <li>Editing can be locked to the selection area</li>
3832 <li>Keyboard editing</li>
3833 <li>Create sequence features from searches</li>
3834 <li>Precalculated annotations can be loaded onto
3836 <li>Features file allows grouping of features</li>
3837 <li>Annotation Colouring scheme added</li>
3838 <li>Smooth fonts off by default - Faster rendering</li>
3839 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3844 <li>Drag & Drop fixed on Linux</li>
3845 <li>Jalview Archive file faster to load/save, sequence
3846 descriptions saved.</li>
3852 <div align="center">
3853 <strong>2.07</strong><br> 12/12/05
3858 <li>PDB Structure Viewer enhanced</li>
3859 <li>Sequence Feature retrieval and display enhanced</li>
3860 <li>Choose to output sequence start-end after sequence
3861 name for file output</li>
3862 <li>Sequence Fetcher WSDBFetch@EBI</li>
3863 <li>Applet can read feature files, PDB files and can be
3864 used for HTML form input</li>
3869 <li>HTML output writes groups and features</li>
3870 <li>Group editing is Control and mouse click</li>
3871 <li>File IO bugs</li>
3877 <div align="center">
3878 <strong>2.06</strong><br> 28/9/05
3883 <li>View annotations in wrapped mode</li>
3884 <li>More options for PCA viewer</li>
3889 <li>GUI bugs resolved</li>
3890 <li>Runs with -nodisplay from command line</li>
3896 <div align="center">
3897 <strong>2.05b</strong><br> 15/9/05
3902 <li>Choose EPS export as lineart or text</li>
3903 <li>Jar files are executable</li>
3904 <li>Can read in Uracil - maps to unknown residue</li>
3909 <li>Known OutOfMemory errors give warning message</li>
3910 <li>Overview window calculated more efficiently</li>
3911 <li>Several GUI bugs resolved</li>
3917 <div align="center">
3918 <strong>2.05</strong><br> 30/8/05
3923 <li>Edit and annotate in "Wrapped" view</li>
3928 <li>Several GUI bugs resolved</li>
3934 <div align="center">
3935 <strong>2.04</strong><br> 24/8/05
3940 <li>Hold down mouse wheel & scroll to change font
3946 <li>Improved JPred client reliability</li>
3947 <li>Improved loading of Jalview files</li>
3953 <div align="center">
3954 <strong>2.03</strong><br> 18/8/05
3959 <li>Set Proxy server name and port in preferences</li>
3960 <li>Multiple URL links from sequence ids</li>
3961 <li>User Defined Colours can have a scheme name and added
3963 <li>Choose to ignore gaps in consensus calculation</li>
3964 <li>Unix users can set default web browser</li>
3965 <li>Runs without GUI for batch processing</li>
3966 <li>Dynamically generated Web Service Menus</li>
3971 <li>InstallAnywhere download for Sparc Solaris</li>
3977 <div align="center">
3978 <strong>2.02</strong><br> 18/7/05
3984 <li>Copy & Paste order of sequences maintains
3985 alignment order.</li>
3991 <div align="center">
3992 <strong>2.01</strong><br> 12/7/05
3997 <li>Use delete key for deleting selection.</li>
3998 <li>Use Mouse wheel to scroll sequences.</li>
3999 <li>Help file updated to describe how to add alignment
4001 <li>Version and build date written to build properties
4003 <li>InstallAnywhere installation will check for updates
4004 at launch of Jalview.</li>
4009 <li>Delete gaps bug fixed.</li>
4010 <li>FileChooser sorts columns.</li>
4011 <li>Can remove groups one by one.</li>
4012 <li>Filechooser icons installed.</li>
4013 <li>Finder ignores return character when searching.
4014 Return key will initiate a search.<br>
4021 <div align="center">
4022 <strong>2.0</strong><br> 20/6/05
4027 <li>New codebase</li>