3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
74 <em>29/01/2019</em></strong>
77 <td><div align="left">
81 <!-- JAL-2865 -->Jalview doesn't hang when closing windows
82 or the overview updates with large alignments.
86 <td><div align="left">
90 <!-- JAL-3035 -->DAS sequence retrieval and annotation
91 capabilities removed from the Jalview Desktop
97 <!-- JAL-2822 -->Start and End should be updated when
98 sequence data at beginning or end of alignment added/removed
102 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
103 sequence features correctly when start of sequence is
104 removed (Known defect since 2.10)
113 <td width="60" nowrap>
115 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
118 <td><div align="left">
122 <!-- JAL-3101 -->Default memory for Jalview webstart and
123 InstallAnywhere increased to 1G.
126 <!-- JAL-247 -->Hidden sequence markers and representative
127 sequence bolding included when exporting alignment as EPS,
128 SVG, PNG or HTML. <em>Display is configured via the
129 Format menu, or for command-line use via a jalview
130 properties file.</em>
133 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
134 API and sequence data now imported as JSON.
137 <!-- JAL-3065 -->Change in recommended way of starting
138 Jalview via a Java command line: add jars in lib directory
139 to CLASSPATH, rather than via the deprecated java.ext.dirs
146 <!-- JAL-3047 -->Support added to execute test suite
147 instrumented with <a href="http://openclover.org/">Open
152 <td><div align="left">
156 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
157 row shown in Feredoxin Structure alignment view of example
161 <!-- JAL-2854 -->Annotation obscures sequences if lots of
162 annotation displayed.
165 <!-- JAL-3107 -->Group conservation/consensus not shown
166 for newly created group when 'Apply to all groups'
170 <!-- JAL-3087 -->Corrupted display when switching to
171 wrapped mode when sequence panel's vertical scrollbar is
175 <!-- JAL-3003 -->Alignment is black in exported EPS file
176 when sequences are selected in exported view.</em>
179 <!-- JAL-3059 -->Groups with different coloured borders
180 aren't rendered with correct colour.
183 <!-- JAL-3092 -->Jalview could hang when importing certain
184 types of knotted RNA secondary structure.
187 <!-- JAL-3095 -->Sequence highlight and selection in
188 trimmed VARNA 2D structure is incorrect for sequences that
192 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
193 annotation when columns are inserted into an alignment,
194 and when exporting as Stockholm flatfile.
197 <!-- JAL-3053 -->Jalview annotation rows containing upper
198 and lower-case 'E' and 'H' do not automatically get
199 treated as RNA secondary structure.
202 <!-- JAL-3106 -->.jvp should be used as default extension
203 (not .jar) when saving a jalview project file.
206 <!-- JAL-3105 -->Mac Users: closing a window correctly
207 transfers focus to previous window on OSX
210 <em>Java 10 Issues Resolved</em>
213 <!-- JAL-2988 -->OSX - Can't save new files via the File
214 or export menus by typing in a name into the Save dialog
218 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
219 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
220 'look and feel' which has improved compatibility with the
221 latest version of OSX.
228 <td width="60" nowrap>
230 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
231 <em>7/06/2018</em></strong>
234 <td><div align="left">
238 <!-- JAL-2920 -->Use HGVS nomenclature for variant
239 annotation retrieved from Uniprot
242 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
243 onto the Jalview Desktop
247 <td><div align="left">
251 <!-- JAL-3017 -->Cannot import features with multiple
252 variant elements (blocks import of some Uniprot records)
255 <!-- JAL-2997 -->Clustal files with sequence positions in
256 right-hand column parsed correctly
259 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
260 not alignment area in exported graphic
263 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
264 window has input focus
267 <!-- JAL-2992 -->Annotation panel set too high when
268 annotation added to view (Windows)
271 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
272 network connectivity is poor
275 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
276 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
277 the currently open URL and links from a page viewed in
278 Firefox or Chrome on Windows is now fully supported. If
279 you are using Edge, only links in the page can be
280 dragged, and with Internet Explorer, only the currently
281 open URL in the browser can be dropped onto Jalview.</em>
287 <td width="60" nowrap>
289 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
292 <td><div align="left">
296 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
297 for disabling automatic superposition of multiple
298 structures and open structures in existing views
301 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
302 ID and annotation area margins can be click-dragged to
306 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
310 <!-- JAL-2759 -->Improved performance for large alignments
311 and lots of hidden columns
314 <!-- JAL-2593 -->Improved performance when rendering lots
315 of features (particularly when transparency is disabled)
320 <td><div align="left">
323 <!-- JAL-2899 -->Structure and Overview aren't updated
324 when Colour By Annotation threshold slider is adjusted
327 <!-- JAL-2778 -->Slow redraw when Overview panel shown
328 overlapping alignment panel
331 <!-- JAL-2929 -->Overview doesn't show end of unpadded
335 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
336 improved: CDS not handled correctly if transcript has no
340 <!-- JAL-2321 -->Secondary structure and temperature
341 factor annotation not added to sequence when local PDB
342 file associated with it by drag'n'drop or structure
346 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
347 dialog doesn't import PDB files dropped on an alignment
350 <!-- JAL-2666 -->Linked scrolling via protein horizontal
351 scroll bar doesn't work for some CDS/Protein views
354 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
355 Java 1.8u153 onwards and Java 1.9u4+.
358 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
359 columns in annotation row
362 <!-- JAL-2913 -->Preferences panel's ID Width control is not
363 honored in batch mode
366 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
367 for structures added to existing Jmol view
370 <!-- JAL-2223 -->'View Mappings' includes duplicate
371 entries after importing project with multiple views
374 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
375 protein sequences via SIFTS from associated PDB entries
376 with negative residue numbers or missing residues fails
379 <!-- JAL-2952 -->Exception when shading sequence with negative
380 Temperature Factor values from annotated PDB files (e.g.
381 as generated by CONSURF)
384 <!-- JAL-2920 -->Uniprot 'sequence variant' features
385 tooltip doesn't include a text description of mutation
388 <!-- JAL-2922 -->Invert displayed features very slow when
389 structure and/or overview windows are also shown
392 <!-- JAL-2954 -->Selecting columns from highlighted regions
393 very slow for alignments with large numbers of sequences
396 <!-- JAL-2925 -->Copy Consensus fails for group consensus
397 with 'StringIndexOutOfBounds'
400 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
401 platforms running Java 10
404 <!-- JAL-2960 -->Adding a structure to existing structure
405 view appears to do nothing because the view is hidden behind the alignment view
411 <!-- JAL-2926 -->Copy consensus sequence option in applet
412 should copy the group consensus when popup is opened on it
418 <!-- JAL-2913 -->Fixed ID width preference is not respected
421 <em>New Known Defects</em>
424 <!-- JAL-2973 --> Exceptions occasionally raised when
425 editing a large alignment and overview is displayed
428 <!-- JAL-2974 -->'Overview updating' progress bar is shown
429 repeatedly after a series of edits even when the overview
430 is no longer reflecting updates
433 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
434 structures for protein subsequence (if 'Trim Retrieved
435 Sequences' enabled) or Ensembl isoforms (Workaround in
436 2.10.4 is to fail back to N&W mapping)
443 <td width="60" nowrap>
445 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
448 <td><div align="left">
449 <ul><li>Updated Certum Codesigning Certificate
450 (Valid till 30th November 2018)</li></ul></div></td>
451 <td><div align="left">
454 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
455 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
456 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
457 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
458 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
459 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
460 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
466 <td width="60" nowrap>
468 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
471 <td><div align="left">
475 <!-- JAL-2446 -->Faster and more efficient management and
476 rendering of sequence features
479 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
480 429 rate limit request hander
483 <!-- JAL-2773 -->Structure views don't get updated unless
484 their colours have changed
487 <!-- JAL-2495 -->All linked sequences are highlighted for
488 a structure mousover (Jmol) or selection (Chimera)
491 <!-- JAL-2790 -->'Cancel' button in progress bar for
492 JABAWS AACon, RNAAliFold and Disorder prediction jobs
495 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
496 view from Ensembl locus cross-references
499 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
503 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
504 feature can be disabled
507 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
508 PDB easier retrieval of sequences for lists of IDs
511 <!-- JAL-2758 -->Short names for sequences retrieved from
517 <li>Groovy interpreter updated to 2.4.12</li>
518 <li>Example groovy script for generating a matrix of
519 percent identity scores for current alignment.</li>
521 <em>Testing and Deployment</em>
524 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
528 <td><div align="left">
532 <!-- JAL-2643 -->Pressing tab after updating the colour
533 threshold text field doesn't trigger an update to the
537 <!-- JAL-2682 -->Race condition when parsing sequence ID
541 <!-- JAL-2608 -->Overview windows are also closed when
542 alignment window is closed
545 <!-- JAL-2548 -->Export of features doesn't always respect
549 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
550 takes a long time in Cursor mode
556 <!-- JAL-2777 -->Structures with whitespace chainCode
557 cannot be viewed in Chimera
560 <!-- JAL-2728 -->Protein annotation panel too high in
564 <!-- JAL-2757 -->Can't edit the query after the server
565 error warning icon is shown in Uniprot and PDB Free Text
569 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
572 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
575 <!-- JAL-2739 -->Hidden column marker in last column not
576 rendered when switching back from Wrapped to normal view
579 <!-- JAL-2768 -->Annotation display corrupted when
580 scrolling right in unwapped alignment view
583 <!-- JAL-2542 -->Existing features on subsequence
584 incorrectly relocated when full sequence retrieved from
588 <!-- JAL-2733 -->Last reported memory still shown when
589 Desktop->Show Memory is unticked (OSX only)
592 <!-- JAL-2658 -->Amend Features dialog doesn't allow
593 features of same type and group to be selected for
597 <!-- JAL-2524 -->Jalview becomes sluggish in wide
598 alignments when hidden columns are present
601 <!-- JAL-2392 -->Jalview freezes when loading and
602 displaying several structures
605 <!-- JAL-2732 -->Black outlines left after resizing or
609 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
610 within the Jalview desktop on OSX
613 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
614 when in wrapped alignment mode
617 <!-- JAL-2636 -->Scale mark not shown when close to right
618 hand end of alignment
621 <!-- JAL-2684 -->Pairwise alignment of selected regions of
622 each selected sequence do not have correct start/end
626 <!-- JAL-2793 -->Alignment ruler height set incorrectly
627 after canceling the Alignment Window's Font dialog
630 <!-- JAL-2036 -->Show cross-references not enabled after
631 restoring project until a new view is created
634 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
635 URL links appears when only default EMBL-EBI link is
636 configured (since 2.10.2b2)
639 <!-- JAL-2775 -->Overview redraws whole window when box
643 <!-- JAL-2225 -->Structure viewer doesn't map all chains
644 in a multi-chain structure when viewing alignment
645 involving more than one chain (since 2.10)
648 <!-- JAL-2811 -->Double residue highlights in cursor mode
649 if new selection moves alignment window
652 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
653 arrow key in cursor mode to pass hidden column marker
656 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
657 that produces correctly annotated transcripts and products
660 <!-- JAL-2776 -->Toggling a feature group after first time
661 doesn't update associated structure view
664 <em>Applet</em><br />
667 <!-- JAL-2687 -->Concurrent modification exception when
668 closing alignment panel
671 <em>BioJSON</em><br />
674 <!-- JAL-2546 -->BioJSON export does not preserve
675 non-positional features
678 <em>New Known Issues</em>
681 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
682 sequence features correctly (for many previous versions of
686 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
687 using cursor in wrapped panel other than top
690 <!-- JAL-2791 -->Select columns containing feature ignores
691 graduated colour threshold
694 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
695 always preserve numbering and sequence features
698 <em>Known Java 9 Issues</em>
701 <!-- JAL-2902 -->Groovy Console very slow to open and is
702 not responsive when entering characters (Webstart, Java
709 <td width="60" nowrap>
711 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
712 <em>2/10/2017</em></strong>
715 <td><div align="left">
716 <em>New features in Jalview Desktop</em>
719 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
721 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
725 <td><div align="left">
729 <td width="60" nowrap>
731 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
732 <em>7/9/2017</em></strong>
735 <td><div align="left">
739 <!-- JAL-2588 -->Show gaps in overview window by colouring
740 in grey (sequences used to be coloured grey, and gaps were
744 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
748 <!-- JAL-2587 -->Overview updates immediately on increase
749 in size and progress bar shown as higher resolution
750 overview is recalculated
755 <td><div align="left">
759 <!-- JAL-2664 -->Overview window redraws every hidden
760 column region row by row
763 <!-- JAL-2681 -->duplicate protein sequences shown after
764 retrieving Ensembl crossrefs for sequences from Uniprot
767 <!-- JAL-2603 -->Overview window throws NPE if show boxes
768 format setting is unticked
771 <!-- JAL-2610 -->Groups are coloured wrongly in overview
772 if group has show boxes format setting unticked
775 <!-- JAL-2672,JAL-2665 -->Redraw problems when
776 autoscrolling whilst dragging current selection group to
777 include sequences and columns not currently displayed
780 <!-- JAL-2691 -->Not all chains are mapped when multimeric
781 assemblies are imported via CIF file
784 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
785 displayed when threshold or conservation colouring is also
789 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
793 <!-- JAL-2673 -->Jalview continues to scroll after
794 dragging a selected region off the visible region of the
798 <!-- JAL-2724 -->Cannot apply annotation based
799 colourscheme to all groups in a view
802 <!-- JAL-2511 -->IDs don't line up with sequences
803 initially after font size change using the Font chooser or
810 <td width="60" nowrap>
812 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
815 <td><div align="left">
816 <em>Calculations</em>
820 <!-- JAL-1933 -->Occupancy annotation row shows number of
821 ungapped positions in each column of the alignment.
824 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
825 a calculation dialog box
828 <!-- JAL-2379 -->Revised implementation of PCA for speed
829 and memory efficiency (~30x faster)
832 <!-- JAL-2403 -->Revised implementation of sequence
833 similarity scores as used by Tree, PCA, Shading Consensus
834 and other calculations
837 <!-- JAL-2416 -->Score matrices are stored as resource
838 files within the Jalview codebase
841 <!-- JAL-2500 -->Trees computed on Sequence Feature
842 Similarity may have different topology due to increased
849 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
850 model for alignments and groups
853 <!-- JAL-384 -->Custom shading schemes created via groovy
860 <!-- JAL-2526 -->Efficiency improvements for interacting
861 with alignment and overview windows
864 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
868 <!-- JAL-2388 -->Hidden columns and sequences can be
872 <!-- JAL-2611 -->Click-drag in visible area allows fine
873 adjustment of visible position
877 <em>Data import/export</em>
880 <!-- JAL-2535 -->Posterior probability annotation from
881 Stockholm files imported as sequence associated annotation
884 <!-- JAL-2507 -->More robust per-sequence positional
885 annotation input/output via stockholm flatfile
888 <!-- JAL-2533 -->Sequence names don't include file
889 extension when importing structure files without embedded
890 names or PDB accessions
893 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
894 format sequence substitution matrices
897 <em>User Interface</em>
900 <!-- JAL-2447 --> Experimental Features Checkbox in
901 Desktop's Tools menu to hide or show untested features in
905 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
906 via Overview or sequence motif search operations
909 <!-- JAL-2547 -->Amend sequence features dialog box can be
910 opened by double clicking gaps within sequence feature
914 <!-- JAL-1476 -->Status bar message shown when not enough
915 aligned positions were available to create a 3D structure
919 <em>3D Structure</em>
922 <!-- JAL-2430 -->Hidden regions in alignment views are not
923 coloured in linked structure views
926 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
927 file-based command exchange
930 <!-- JAL-2375 -->Structure chooser automatically shows
931 Cached Structures rather than querying the PDBe if
932 structures are already available for sequences
935 <!-- JAL-2520 -->Structures imported via URL are cached in
936 the Jalview project rather than downloaded again when the
940 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
941 to transfer Chimera's structure attributes as Jalview
942 features, and vice-versa (<strong>Experimental
946 <em>Web Services</em>
949 <!-- JAL-2549 -->Updated JABAWS client to v2.2
952 <!-- JAL-2335 -->Filter non-standard amino acids and
953 nucleotides when submitting to AACon and other MSA
957 <!-- JAL-2316, -->URLs for viewing database
958 cross-references provided by identifiers.org and the
966 <!-- JAL-2344 -->FileFormatI interface for describing and
967 identifying file formats (instead of String constants)
970 <!-- JAL-2228 -->FeatureCounter script refactored for
971 efficiency when counting all displayed features (not
972 backwards compatible with 2.10.1)
975 <em>Example files</em>
978 <!-- JAL-2631 -->Graduated feature colour style example
979 included in the example feature file
982 <em>Documentation</em>
985 <!-- JAL-2339 -->Release notes reformatted for readability
986 with the built-in Java help viewer
989 <!-- JAL-1644 -->Find documentation updated with 'search
990 sequence description' option
996 <!-- JAL-2485, -->External service integration tests for
997 Uniprot REST Free Text Search Client
1000 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1003 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1008 <td><div align="left">
1009 <em>Calculations</em>
1012 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1013 matrix - C->R should be '-3'<br />Old matrix restored
1014 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1016 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1017 Jalview's treatment of gaps in PCA and substitution matrix
1018 based Tree calculations.<br /> <br />In earlier versions
1019 of Jalview, gaps matching gaps were penalised, and gaps
1020 matching non-gaps penalised even more. In the PCA
1021 calculation, gaps were actually treated as non-gaps - so
1022 different costs were applied, which meant Jalview's PCAs
1023 were different to those produced by SeqSpace.<br />Jalview
1024 now treats gaps in the same way as SeqSpace (ie it scores
1025 them as 0). <br /> <br />Enter the following in the
1026 Groovy console to restore pre-2.10.2 behaviour:<br />
1027 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1028 // for 2.10.1 mode <br />
1029 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1030 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1031 these settings will affect all subsequent tree and PCA
1032 calculations (not recommended)</em></li>
1034 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1035 scaling of branch lengths for trees computed using
1036 Sequence Feature Similarity.
1039 <!-- JAL-2377 -->PCA calculation could hang when
1040 generating output report when working with highly
1041 redundant alignments
1044 <!-- JAL-2544 --> Sort by features includes features to
1045 right of selected region when gaps present on right-hand
1049 <em>User Interface</em>
1052 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1053 doesn't reselect a specific sequence's associated
1054 annotation after it was used for colouring a view
1057 <!-- JAL-2419 -->Current selection lost if popup menu
1058 opened on a region of alignment without groups
1061 <!-- JAL-2374 -->Popup menu not always shown for regions
1062 of an alignment with overlapping groups
1065 <!-- JAL-2310 -->Finder double counts if both a sequence's
1066 name and description match
1069 <!-- JAL-2370 -->Hiding column selection containing two
1070 hidden regions results in incorrect hidden regions
1073 <!-- JAL-2386 -->'Apply to all groups' setting when
1074 changing colour does not apply Conservation slider value
1078 <!-- JAL-2373 -->Percentage identity and conservation menu
1079 items do not show a tick or allow shading to be disabled
1082 <!-- JAL-2385 -->Conservation shading or PID threshold
1083 lost when base colourscheme changed if slider not visible
1086 <!-- JAL-2547 -->Sequence features shown in tooltip for
1087 gaps before start of features
1090 <!-- JAL-2623 -->Graduated feature colour threshold not
1091 restored to UI when feature colour is edited
1094 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1095 a time when scrolling vertically in wrapped mode.
1098 <!-- JAL-2630 -->Structure and alignment overview update
1099 as graduate feature colour settings are modified via the
1103 <!-- JAL-2034 -->Overview window doesn't always update
1104 when a group defined on the alignment is resized
1107 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1108 wrapped view result in positional status updates
1112 <!-- JAL-2563 -->Status bar doesn't show position for
1113 ambiguous amino acid and nucleotide symbols
1116 <!-- JAL-2602 -->Copy consensus sequence failed if
1117 alignment included gapped columns
1120 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1121 widgets don't permanently disappear
1124 <!-- JAL-2503 -->Cannot select or filter quantitative
1125 annotation that are shown only as column labels (e.g.
1126 T-Coffee column reliability scores)
1129 <!-- JAL-2594 -->Exception thrown if trying to create a
1130 sequence feature on gaps only
1133 <!-- JAL-2504 -->Features created with 'New feature'
1134 button from a Find inherit previously defined feature type
1135 rather than the Find query string
1138 <!-- JAL-2423 -->incorrect title in output window when
1139 exporting tree calculated in Jalview
1142 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1143 and then revealing them reorders sequences on the
1147 <!-- JAL-964 -->Group panel in sequence feature settings
1148 doesn't update to reflect available set of groups after
1149 interactively adding or modifying features
1152 <!-- JAL-2225 -->Sequence Database chooser unusable on
1156 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1157 only excluded gaps in current sequence and ignored
1164 <!-- JAL-2421 -->Overview window visible region moves
1165 erratically when hidden rows or columns are present
1168 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1169 Structure Viewer's colour menu don't correspond to
1173 <!-- JAL-2405 -->Protein specific colours only offered in
1174 colour and group colour menu for protein alignments
1177 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1178 reflect currently selected view or group's shading
1182 <!-- JAL-2624 -->Feature colour thresholds not respected
1183 when rendered on overview and structures when opacity at
1187 <!-- JAL-2589 -->User defined gap colour not shown in
1188 overview when features overlaid on alignment
1191 <em>Data import/export</em>
1194 <!-- JAL-2576 -->Very large alignments take a long time to
1198 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1199 added after a sequence was imported are not written to
1203 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1204 when importing RNA secondary structure via Stockholm
1207 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1208 not shown in correct direction for simple pseudoknots
1211 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1212 with lightGray or darkGray via features file (but can
1216 <!-- JAL-2383 -->Above PID colour threshold not recovered
1217 when alignment view imported from project
1220 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1221 structure and sequences extracted from structure files
1222 imported via URL and viewed in Jmol
1225 <!-- JAL-2520 -->Structures loaded via URL are saved in
1226 Jalview Projects rather than fetched via URL again when
1227 the project is loaded and the structure viewed
1230 <em>Web Services</em>
1233 <!-- JAL-2519 -->EnsemblGenomes example failing after
1234 release of Ensembl v.88
1237 <!-- JAL-2366 -->Proxy server address and port always
1238 appear enabled in Preferences->Connections
1241 <!-- JAL-2461 -->DAS registry not found exceptions
1242 removed from console output
1245 <!-- JAL-2582 -->Cannot retrieve protein products from
1246 Ensembl by Peptide ID
1249 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1250 created from SIFTs, and spurious 'Couldn't open structure
1251 in Chimera' errors raised after April 2017 update (problem
1252 due to 'null' string rather than empty string used for
1253 residues with no corresponding PDB mapping).
1256 <em>Application UI</em>
1259 <!-- JAL-2361 -->User Defined Colours not added to Colour
1263 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1264 case' residues (button in colourscheme editor debugged and
1265 new documentation and tooltips added)
1268 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1269 doesn't restore group-specific text colour thresholds
1272 <!-- JAL-2243 -->Feature settings panel does not update as
1273 new features are added to alignment
1276 <!-- JAL-2532 -->Cancel in feature settings reverts
1277 changes to feature colours via the Amend features dialog
1280 <!-- JAL-2506 -->Null pointer exception when attempting to
1281 edit graduated feature colour via amend features dialog
1285 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1286 selection menu changes colours of alignment views
1289 <!-- JAL-2426 -->Spurious exceptions in console raised
1290 from alignment calculation workers after alignment has
1294 <!-- JAL-1608 -->Typo in selection popup menu - Create
1295 groups now 'Create Group'
1298 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1299 Create/Undefine group doesn't always work
1302 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1303 shown again after pressing 'Cancel'
1306 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1307 adjusts start position in wrap mode
1310 <!-- JAL-2563 -->Status bar doesn't show positions for
1311 ambiguous amino acids
1314 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1315 CDS/Protein view after CDS sequences added for aligned
1319 <!-- JAL-2592 -->User defined colourschemes called 'User
1320 Defined' don't appear in Colours menu
1326 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1327 score models doesn't always result in an updated PCA plot
1330 <!-- JAL-2442 -->Features not rendered as transparent on
1331 overview or linked structure view
1334 <!-- JAL-2372 -->Colour group by conservation doesn't
1338 <!-- JAL-2517 -->Hitting Cancel after applying
1339 user-defined colourscheme doesn't restore original
1346 <!-- JAL-2314 -->Unit test failure:
1347 jalview.ws.jabaws.RNAStructExportImport setup fails
1350 <!-- JAL-2307 -->Unit test failure:
1351 jalview.ws.sifts.SiftsClientTest due to compatibility
1352 problems with deep array comparison equality asserts in
1353 successive versions of TestNG
1356 <!-- JAL-2479 -->Relocated StructureChooserTest and
1357 ParameterUtilsTest Unit tests to Network suite
1360 <em>New Known Issues</em>
1363 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1364 phase after a sequence motif find operation
1367 <!-- JAL-2550 -->Importing annotation file with rows
1368 containing just upper and lower case letters are
1369 interpreted as WUSS RNA secondary structure symbols
1372 <!-- JAL-2590 -->Cannot load and display Newick trees
1373 reliably from eggnog Ortholog database
1376 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1377 containing features of type Highlight' when 'B' is pressed
1378 to mark columns containing highlighted regions.
1381 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1382 doesn't always add secondary structure annotation.
1387 <td width="60" nowrap>
1388 <div align="center">
1389 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1392 <td><div align="left">
1396 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1397 for all consensus calculations
1400 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1403 <li>Updated Jalview's Certum code signing certificate
1406 <em>Application</em>
1409 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1410 set of database cross-references, sorted alphabetically
1413 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1414 from database cross references. Users with custom links
1415 will receive a <a href="webServices/urllinks.html#warning">warning
1416 dialog</a> asking them to update their preferences.
1419 <!-- JAL-2287-->Cancel button and escape listener on
1420 dialog warning user about disconnecting Jalview from a
1424 <!-- JAL-2320-->Jalview's Chimera control window closes if
1425 the Chimera it is connected to is shut down
1428 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1429 columns menu item to mark columns containing highlighted
1430 regions (e.g. from structure selections or results of a
1434 <!-- JAL-2284-->Command line option for batch-generation
1435 of HTML pages rendering alignment data with the BioJS
1445 <!-- JAL-2286 -->Columns with more than one modal residue
1446 are not coloured or thresholded according to percent
1447 identity (first observed in Jalview 2.8.2)
1450 <!-- JAL-2301 -->Threonine incorrectly reported as not
1454 <!-- JAL-2318 -->Updates to documentation pages (above PID
1455 threshold, amino acid properties)
1458 <!-- JAL-2292 -->Lower case residues in sequences are not
1459 reported as mapped to residues in a structure file in the
1463 <!--JAL-2324 -->Identical features with non-numeric scores
1464 could be added multiple times to a sequence
1467 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1468 bond features shown as two highlighted residues rather
1469 than a range in linked structure views, and treated
1470 correctly when selecting and computing trees from features
1473 <!-- JAL-2281-->Custom URL links for database
1474 cross-references are matched to database name regardless
1479 <em>Application</em>
1482 <!-- JAL-2282-->Custom URL links for specific database
1483 names without regular expressions also offer links from
1487 <!-- JAL-2315-->Removing a single configured link in the
1488 URL links pane in Connections preferences doesn't actually
1489 update Jalview configuration
1492 <!-- JAL-2272-->CTRL-Click on a selected region to open
1493 the alignment area popup menu doesn't work on El-Capitan
1496 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1497 files with similarly named sequences if dropped onto the
1501 <!-- JAL-2312 -->Additional mappings are shown for PDB
1502 entries where more chains exist in the PDB accession than
1503 are reported in the SIFTS file
1506 <!-- JAL-2317-->Certain structures do not get mapped to
1507 the structure view when displayed with Chimera
1510 <!-- JAL-2317-->No chains shown in the Chimera view
1511 panel's View->Show Chains submenu
1514 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1515 work for wrapped alignment views
1518 <!--JAL-2197 -->Rename UI components for running JPred
1519 predictions from 'JNet' to 'JPred'
1522 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1523 corrupted when annotation panel vertical scroll is not at
1524 first annotation row
1527 <!--JAL-2332 -->Attempting to view structure for Hen
1528 lysozyme results in a PDB Client error dialog box
1531 <!-- JAL-2319 -->Structure View's mapping report switched
1532 ranges for PDB and sequence for SIFTS
1535 SIFTS 'Not_Observed' residues mapped to non-existant
1539 <!-- <em>New Known Issues</em>
1546 <td width="60" nowrap>
1547 <div align="center">
1548 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1549 <em>25/10/2016</em></strong>
1552 <td><em>Application</em>
1554 <li>3D Structure chooser opens with 'Cached structures'
1555 view if structures already loaded</li>
1556 <li>Progress bar reports models as they are loaded to
1557 structure views</li>
1563 <li>Colour by conservation always enabled and no tick
1564 shown in menu when BLOSUM or PID shading applied</li>
1565 <li>FER1_ARATH and FER2_ARATH labels were switched in
1566 example sequences/projects/trees</li>
1568 <em>Application</em>
1570 <li>Jalview projects with views of local PDB structure
1571 files saved on Windows cannot be opened on OSX</li>
1572 <li>Multiple structure views can be opened and superposed
1573 without timeout for structures with multiple models or
1574 multiple sequences in alignment</li>
1575 <li>Cannot import or associated local PDB files without a
1576 PDB ID HEADER line</li>
1577 <li>RMSD is not output in Jmol console when superposition
1579 <li>Drag and drop of URL from Browser fails for Linux and
1580 OSX versions earlier than El Capitan</li>
1581 <li>ENA client ignores invalid content from ENA server</li>
1582 <li>Exceptions are not raised in console when ENA client
1583 attempts to fetch non-existent IDs via Fetch DB Refs UI
1585 <li>Exceptions are not raised in console when a new view
1586 is created on the alignment</li>
1587 <li>OSX right-click fixed for group selections: CMD-click
1588 to insert/remove gaps in groups and CTRL-click to open group
1591 <em>Build and deployment</em>
1593 <li>URL link checker now copes with multi-line anchor
1596 <em>New Known Issues</em>
1598 <li>Drag and drop from URL links in browsers do not work
1605 <td width="60" nowrap>
1606 <div align="center">
1607 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1610 <td><em>General</em>
1613 <!-- JAL-2124 -->Updated Spanish translations.
1616 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1617 for importing structure data to Jalview. Enables mmCIF and
1621 <!-- JAL-192 --->Alignment ruler shows positions relative to
1625 <!-- JAL-2202 -->Position/residue shown in status bar when
1626 mousing over sequence associated annotation
1629 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1633 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1634 '()', canonical '[]' and invalid '{}' base pair populations
1638 <!-- JAL-2092 -->Feature settings popup menu options for
1639 showing or hiding columns containing a feature
1642 <!-- JAL-1557 -->Edit selected group by double clicking on
1643 group and sequence associated annotation labels
1646 <!-- JAL-2236 -->Sequence name added to annotation label in
1647 select/hide columns by annotation and colour by annotation
1651 </ul> <em>Application</em>
1654 <!-- JAL-2050-->Automatically hide introns when opening a
1655 gene/transcript view
1658 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1662 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1663 structure mappings with the EMBL-EBI PDBe SIFTS database
1666 <!-- JAL-2079 -->Updated download sites used for Rfam and
1667 Pfam sources to xfam.org
1670 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1673 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1674 over sequences in Jalview
1677 <!-- JAL-2027-->Support for reverse-complement coding
1678 regions in ENA and EMBL
1681 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1682 for record retrieval via ENA rest API
1685 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1689 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1690 groovy script execution
1693 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1694 alignment window's Calculate menu
1697 <!-- JAL-1812 -->Allow groovy scripts that call
1698 Jalview.getAlignFrames() to run in headless mode
1701 <!-- JAL-2068 -->Support for creating new alignment
1702 calculation workers from groovy scripts
1705 <!-- JAL-1369 --->Store/restore reference sequence in
1709 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1710 associations are now saved/restored from project
1713 <!-- JAL-1993 -->Database selection dialog always shown
1714 before sequence fetcher is opened
1717 <!-- JAL-2183 -->Double click on an entry in Jalview's
1718 database chooser opens a sequence fetcher
1721 <!-- JAL-1563 -->Free-text search client for UniProt using
1722 the UniProt REST API
1725 <!-- JAL-2168 -->-nonews command line parameter to prevent
1726 the news reader opening
1729 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1730 querying stored in preferences
1733 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1737 <!-- JAL-1977-->Tooltips shown on database chooser
1740 <!-- JAL-391 -->Reverse complement function in calculate
1741 menu for nucleotide sequences
1744 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1745 and feature counts preserves alignment ordering (and
1746 debugged for complex feature sets).
1749 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1750 viewing structures with Jalview 2.10
1753 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1754 genome, transcript CCDS and gene ids via the Ensembl and
1755 Ensembl Genomes REST API
1758 <!-- JAL-2049 -->Protein sequence variant annotation
1759 computed for 'sequence_variant' annotation on CDS regions
1763 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1767 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1768 Ref Fetcher fails to match, or otherwise updates sequence
1769 data from external database records.
1772 <!-- JAL-2154 -->Revised Jalview Project format for
1773 efficient recovery of sequence coding and alignment
1774 annotation relationships.
1776 </ul> <!-- <em>Applet</em>
1787 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1791 <!-- JAL-2018-->Export features in Jalview format (again)
1792 includes graduated colourschemes
1795 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1796 working with big alignments and lots of hidden columns
1799 <!-- JAL-2053-->Hidden column markers not always rendered
1800 at right of alignment window
1803 <!-- JAL-2067 -->Tidied up links in help file table of
1807 <!-- JAL-2072 -->Feature based tree calculation not shown
1811 <!-- JAL-2075 -->Hidden columns ignored during feature
1812 based tree calculation
1815 <!-- JAL-2065 -->Alignment view stops updating when show
1816 unconserved enabled for group on alignment
1819 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1823 <!-- JAL-2146 -->Alignment column in status incorrectly
1824 shown as "Sequence position" when mousing over
1828 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1829 hidden columns present
1832 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1833 user created annotation added to alignment
1836 <!-- JAL-1841 -->RNA Structure consensus only computed for
1837 '()' base pair annotation
1840 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1841 in zero scores for all base pairs in RNA Structure
1845 <!-- JAL-2174-->Extend selection with columns containing
1849 <!-- JAL-2275 -->Pfam format writer puts extra space at
1850 beginning of sequence
1853 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1857 <!-- JAL-2238 -->Cannot create groups on an alignment from
1858 from a tree when t-coffee scores are shown
1861 <!-- JAL-1836,1967 -->Cannot import and view PDB
1862 structures with chains containing negative resnums (4q4h)
1865 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1869 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1870 to Clustal, PIR and PileUp output
1873 <!-- JAL-2008 -->Reordering sequence features that are
1874 not visible causes alignment window to repaint
1877 <!-- JAL-2006 -->Threshold sliders don't work in
1878 graduated colour and colour by annotation row for e-value
1879 scores associated with features and annotation rows
1882 <!-- JAL-1797 -->amino acid physicochemical conservation
1883 calculation should be case independent
1886 <!-- JAL-2173 -->Remove annotation also updates hidden
1890 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1891 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1892 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1895 <!-- JAL-2065 -->Null pointer exceptions and redraw
1896 problems when reference sequence defined and 'show
1897 non-conserved' enabled
1900 <!-- JAL-1306 -->Quality and Conservation are now shown on
1901 load even when Consensus calculation is disabled
1904 <!-- JAL-1932 -->Remove right on penultimate column of
1905 alignment does nothing
1908 <em>Application</em>
1911 <!-- JAL-1552-->URLs and links can't be imported by
1912 drag'n'drop on OSX when launched via webstart (note - not
1913 yet fixed for El Capitan)
1916 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1917 output when running on non-gb/us i18n platforms
1920 <!-- JAL-1944 -->Error thrown when exporting a view with
1921 hidden sequences as flat-file alignment
1924 <!-- JAL-2030-->InstallAnywhere distribution fails when
1928 <!-- JAL-2080-->Jalview very slow to launch via webstart
1929 (also hotfix for 2.9.0b2)
1932 <!-- JAL-2085 -->Cannot save project when view has a
1933 reference sequence defined
1936 <!-- JAL-1011 -->Columns are suddenly selected in other
1937 alignments and views when revealing hidden columns
1940 <!-- JAL-1989 -->Hide columns not mirrored in complement
1941 view in a cDNA/Protein splitframe
1944 <!-- JAL-1369 -->Cannot save/restore representative
1945 sequence from project when only one sequence is
1949 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1950 in Structure Chooser
1953 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1954 structure consensus didn't refresh annotation panel
1957 <!-- JAL-1962 -->View mapping in structure view shows
1958 mappings between sequence and all chains in a PDB file
1961 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1962 dialogs format columns correctly, don't display array
1963 data, sort columns according to type
1966 <!-- JAL-1975 -->Export complete shown after destination
1967 file chooser is cancelled during an image export
1970 <!-- JAL-2025 -->Error when querying PDB Service with
1971 sequence name containing special characters
1974 <!-- JAL-2024 -->Manual PDB structure querying should be
1978 <!-- JAL-2104 -->Large tooltips with broken HTML
1979 formatting don't wrap
1982 <!-- JAL-1128 -->Figures exported from wrapped view are
1983 truncated so L looks like I in consensus annotation
1986 <!-- JAL-2003 -->Export features should only export the
1987 currently displayed features for the current selection or
1991 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1992 after fetching cross-references, and restoring from
1996 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1997 followed in the structure viewer
2000 <!-- JAL-2163 -->Titles for individual alignments in
2001 splitframe not restored from project
2004 <!-- JAL-2145 -->missing autocalculated annotation at
2005 trailing end of protein alignment in transcript/product
2006 splitview when pad-gaps not enabled by default
2009 <!-- JAL-1797 -->amino acid physicochemical conservation
2013 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2014 article has been read (reopened issue due to
2015 internationalisation problems)
2018 <!-- JAL-1960 -->Only offer PDB structures in structure
2019 viewer based on sequence name, PDB and UniProt
2024 <!-- JAL-1976 -->No progress bar shown during export of
2028 <!-- JAL-2213 -->Structures not always superimposed after
2029 multiple structures are shown for one or more sequences.
2032 <!-- JAL-1370 -->Reference sequence characters should not
2033 be replaced with '.' when 'Show unconserved' format option
2037 <!-- JAL-1823 -->Cannot specify chain code when entering
2038 specific PDB id for sequence
2041 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2042 'Export hidden sequences' is enabled, but 'export hidden
2043 columns' is disabled.
2046 <!--JAL-2026-->Best Quality option in structure chooser
2047 selects lowest rather than highest resolution structures
2051 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2052 to sequence mapping in 'View Mappings' report
2055 <!-- JAL-2284 -->Unable to read old Jalview projects that
2056 contain non-XML data added after Jalvew wrote project.
2059 <!-- JAL-2118 -->Newly created annotation row reorders
2060 after clicking on it to create new annotation for a
2064 <!-- JAL-1980 -->Null Pointer Exception raised when
2065 pressing Add on an orphaned cut'n'paste window.
2067 <!-- may exclude, this is an external service stability issue JAL-1941
2068 -- > RNA 3D structure not added via DSSR service</li> -->
2073 <!-- JAL-2151 -->Incorrect columns are selected when
2074 hidden columns present before start of sequence
2077 <!-- JAL-1986 -->Missing dependencies on applet pages
2081 <!-- JAL-1947 -->Overview pixel size changes when
2082 sequences are hidden in applet
2085 <!-- JAL-1996 -->Updated instructions for applet
2086 deployment on examples pages.
2093 <td width="60" nowrap>
2094 <div align="center">
2095 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2096 <em>16/10/2015</em></strong>
2099 <td><em>General</em>
2101 <li>Time stamps for signed Jalview application and applet
2106 <em>Application</em>
2108 <li>Duplicate group consensus and conservation rows
2109 shown when tree is partitioned</li>
2110 <li>Erratic behaviour when tree partitions made with
2111 multiple cDNA/Protein split views</li>
2117 <td width="60" nowrap>
2118 <div align="center">
2119 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2120 <em>8/10/2015</em></strong>
2123 <td><em>General</em>
2125 <li>Updated Spanish translations of localized text for
2127 </ul> <em>Application</em>
2129 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2130 <li>Signed OSX InstallAnywhere installer<br></li>
2131 <li>Support for per-sequence based annotations in BioJSON</li>
2132 </ul> <em>Applet</em>
2134 <li>Split frame example added to applet examples page</li>
2135 </ul> <em>Build and Deployment</em>
2138 <!-- JAL-1888 -->New ant target for running Jalview's test
2146 <li>Mapping of cDNA to protein in split frames
2147 incorrect when sequence start > 1</li>
2148 <li>Broken images in filter column by annotation dialog
2150 <li>Feature colours not parsed from features file</li>
2151 <li>Exceptions and incomplete link URLs recovered when
2152 loading a features file containing HTML tags in feature
2156 <em>Application</em>
2158 <li>Annotations corrupted after BioJS export and
2160 <li>Incorrect sequence limits after Fetch DB References
2161 with 'trim retrieved sequences'</li>
2162 <li>Incorrect warning about deleting all data when
2163 deleting selected columns</li>
2164 <li>Patch to build system for shipping properly signed
2165 JNLP templates for webstart launch</li>
2166 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2167 unreleased structures for download or viewing</li>
2168 <li>Tab/space/return keystroke operation of EMBL-PDBe
2169 fetcher/viewer dialogs works correctly</li>
2170 <li>Disabled 'minimise' button on Jalview windows
2171 running on OSX to workaround redraw hang bug</li>
2172 <li>Split cDNA/Protein view position and geometry not
2173 recovered from jalview project</li>
2174 <li>Initial enabled/disabled state of annotation menu
2175 sorter 'show autocalculated first/last' corresponds to
2177 <li>Restoring of Clustal, RNA Helices and T-Coffee
2178 color schemes from BioJSON</li>
2182 <li>Reorder sequences mirrored in cDNA/Protein split
2184 <li>Applet with Jmol examples not loading correctly</li>
2190 <td><div align="center">
2191 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2193 <td><em>General</em>
2195 <li>Linked visualisation and analysis of DNA and Protein
2198 <li>Translated cDNA alignments shown as split protein
2199 and DNA alignment views</li>
2200 <li>Codon consensus annotation for linked protein and
2201 cDNA alignment views</li>
2202 <li>Link cDNA or Protein product sequences by loading
2203 them onto Protein or cDNA alignments</li>
2204 <li>Reconstruct linked cDNA alignment from aligned
2205 protein sequences</li>
2208 <li>Jmol integration updated to Jmol v14.2.14</li>
2209 <li>Import and export of Jalview alignment views as <a
2210 href="features/bioJsonFormat.html">BioJSON</a></li>
2211 <li>New alignment annotation file statements for
2212 reference sequences and marking hidden columns</li>
2213 <li>Reference sequence based alignment shading to
2214 highlight variation</li>
2215 <li>Select or hide columns according to alignment
2217 <li>Find option for locating sequences by description</li>
2218 <li>Conserved physicochemical properties shown in amino
2219 acid conservation row</li>
2220 <li>Alignments can be sorted by number of RNA helices</li>
2221 </ul> <em>Application</em>
2223 <li>New cDNA/Protein analysis capabilities
2225 <li>Get Cross-References should open a Split Frame
2226 view with cDNA/Protein</li>
2227 <li>Detect when nucleotide sequences and protein
2228 sequences are placed in the same alignment</li>
2229 <li>Split cDNA/Protein views are saved in Jalview
2234 <li>Use REST API to talk to Chimera</li>
2235 <li>Selected regions in Chimera are highlighted in linked
2236 Jalview windows</li>
2238 <li>VARNA RNA viewer updated to v3.93</li>
2239 <li>VARNA views are saved in Jalview Projects</li>
2240 <li>Pseudoknots displayed as Jalview RNA annotation can
2241 be shown in VARNA</li>
2243 <li>Make groups for selection uses marked columns as well
2244 as the active selected region</li>
2246 <li>Calculate UPGMA and NJ trees using sequence feature
2248 <li>New Export options
2250 <li>New Export Settings dialog to control hidden
2251 region export in flat file generation</li>
2253 <li>Export alignment views for display with the <a
2254 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2256 <li>Export scrollable SVG in HTML page</li>
2257 <li>Optional embedding of BioJSON data when exporting
2258 alignment figures to HTML</li>
2260 <li>3D structure retrieval and display
2262 <li>Free text and structured queries with the PDBe
2264 <li>PDBe Search API based discovery and selection of
2265 PDB structures for a sequence set</li>
2269 <li>JPred4 employed for protein secondary structure
2271 <li>Hide Insertions menu option to hide unaligned columns
2272 for one or a group of sequences</li>
2273 <li>Automatically hide insertions in alignments imported
2274 from the JPred4 web server</li>
2275 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2276 system on OSX<br />LGPL libraries courtesy of <a
2277 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2279 <li>changed 'View nucleotide structure' submenu to 'View
2280 VARNA 2D Structure'</li>
2281 <li>change "View protein structure" menu option to "3D
2284 </ul> <em>Applet</em>
2286 <li>New layout for applet example pages</li>
2287 <li>New parameters to enable SplitFrame view
2288 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2289 <li>New example demonstrating linked viewing of cDNA and
2290 Protein alignments</li>
2291 </ul> <em>Development and deployment</em>
2293 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2294 <li>Include installation type and git revision in build
2295 properties and console log output</li>
2296 <li>Jalview Github organisation, and new github site for
2297 storing BioJsMSA Templates</li>
2298 <li>Jalview's unit tests now managed with TestNG</li>
2301 <!-- <em>General</em>
2303 </ul> --> <!-- issues resolved --> <em>Application</em>
2305 <li>Escape should close any open find dialogs</li>
2306 <li>Typo in select-by-features status report</li>
2307 <li>Consensus RNA secondary secondary structure
2308 predictions are not highlighted in amber</li>
2309 <li>Missing gap character in v2.7 example file means
2310 alignment appears unaligned when pad-gaps is not enabled</li>
2311 <li>First switch to RNA Helices colouring doesn't colour
2312 associated structure views</li>
2313 <li>ID width preference option is greyed out when auto
2314 width checkbox not enabled</li>
2315 <li>Stopped a warning dialog from being shown when
2316 creating user defined colours</li>
2317 <li>'View Mapping' in structure viewer shows sequence
2318 mappings for just that viewer's sequences</li>
2319 <li>Workaround for superposing PDB files containing
2320 multiple models in Chimera</li>
2321 <li>Report sequence position in status bar when hovering
2322 over Jmol structure</li>
2323 <li>Cannot output gaps as '.' symbols with Selection ->
2324 output to text box</li>
2325 <li>Flat file exports of alignments with hidden columns
2326 have incorrect sequence start/end</li>
2327 <li>'Aligning' a second chain to a Chimera structure from
2329 <li>Colour schemes applied to structure viewers don't
2330 work for nucleotide</li>
2331 <li>Loading/cut'n'pasting an empty or invalid file leads
2332 to a grey/invisible alignment window</li>
2333 <li>Exported Jpred annotation from a sequence region
2334 imports to different position</li>
2335 <li>Space at beginning of sequence feature tooltips shown
2336 on some platforms</li>
2337 <li>Chimera viewer 'View | Show Chain' menu is not
2339 <li>'New View' fails with a Null Pointer Exception in
2340 console if Chimera has been opened</li>
2341 <li>Mouseover to Chimera not working</li>
2342 <li>Miscellaneous ENA XML feature qualifiers not
2344 <li>NPE in annotation renderer after 'Extract Scores'</li>
2345 <li>If two structures in one Chimera window, mouseover of
2346 either sequence shows on first structure</li>
2347 <li>'Show annotations' options should not make
2348 non-positional annotations visible</li>
2349 <li>Subsequence secondary structure annotation not shown
2350 in right place after 'view flanking regions'</li>
2351 <li>File Save As type unset when current file format is
2353 <li>Save as '.jar' option removed for saving Jalview
2355 <li>Colour by Sequence colouring in Chimera more
2357 <li>Cannot 'add reference annotation' for a sequence in
2358 several views on same alignment</li>
2359 <li>Cannot show linked products for EMBL / ENA records</li>
2360 <li>Jalview's tooltip wraps long texts containing no
2362 </ul> <em>Applet</em>
2364 <li>Jmol to JalviewLite mouseover/link not working</li>
2365 <li>JalviewLite can't import sequences with ID
2366 descriptions containing angle brackets</li>
2367 </ul> <em>General</em>
2369 <li>Cannot export and reimport RNA secondary structure
2370 via jalview annotation file</li>
2371 <li>Random helix colour palette for colour by annotation
2372 with RNA secondary structure</li>
2373 <li>Mouseover to cDNA from STOP residue in protein
2374 translation doesn't work.</li>
2375 <li>hints when using the select by annotation dialog box</li>
2376 <li>Jmol alignment incorrect if PDB file has alternate CA
2378 <li>FontChooser message dialog appears to hang after
2379 choosing 1pt font</li>
2380 <li>Peptide secondary structure incorrectly imported from
2381 annotation file when annotation display text includes 'e' or
2383 <li>Cannot set colour of new feature type whilst creating
2385 <li>cDNA translation alignment should not be sequence
2386 order dependent</li>
2387 <li>'Show unconserved' doesn't work for lower case
2389 <li>Nucleotide ambiguity codes involving R not recognised</li>
2390 </ul> <em>Deployment and Documentation</em>
2392 <li>Applet example pages appear different to the rest of
2393 www.jalview.org</li>
2394 </ul> <em>Application Known issues</em>
2396 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2397 <li>Misleading message appears after trying to delete
2399 <li>Jalview icon not shown in dock after InstallAnywhere
2400 version launches</li>
2401 <li>Fetching EMBL reference for an RNA sequence results
2402 fails with a sequence mismatch</li>
2403 <li>Corrupted or unreadable alignment display when
2404 scrolling alignment to right</li>
2405 <li>ArrayIndexOutOfBoundsException thrown when remove
2406 empty columns called on alignment with ragged gapped ends</li>
2407 <li>auto calculated alignment annotation rows do not get
2408 placed above or below non-autocalculated rows</li>
2409 <li>Jalview dekstop becomes sluggish at full screen in
2410 ultra-high resolution</li>
2411 <li>Cannot disable consensus calculation independently of
2412 quality and conservation</li>
2413 <li>Mouseover highlighting between cDNA and protein can
2414 become sluggish with more than one splitframe shown</li>
2415 </ul> <em>Applet Known Issues</em>
2417 <li>Core PDB parsing code requires Jmol</li>
2418 <li>Sequence canvas panel goes white when alignment
2419 window is being resized</li>
2425 <td><div align="center">
2426 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2428 <td><em>General</em>
2430 <li>Updated Java code signing certificate donated by
2432 <li>Features and annotation preserved when performing
2433 pairwise alignment</li>
2434 <li>RNA pseudoknot annotation can be
2435 imported/exported/displayed</li>
2436 <li>'colour by annotation' can colour by RNA and
2437 protein secondary structure</li>
2438 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2439 post-hoc with 2.9 release</em>)
2442 </ul> <em>Application</em>
2444 <li>Extract and display secondary structure for sequences
2445 with 3D structures</li>
2446 <li>Support for parsing RNAML</li>
2447 <li>Annotations menu for layout
2449 <li>sort sequence annotation rows by alignment</li>
2450 <li>place sequence annotation above/below alignment
2453 <li>Output in Stockholm format</li>
2454 <li>Internationalisation: improved Spanish (es)
2456 <li>Structure viewer preferences tab</li>
2457 <li>Disorder and Secondary Structure annotation tracks
2458 shared between alignments</li>
2459 <li>UCSF Chimera launch and linked highlighting from
2461 <li>Show/hide all sequence associated annotation rows for
2462 all or current selection</li>
2463 <li>disorder and secondary structure predictions
2464 available as dataset annotation</li>
2465 <li>Per-sequence rna helices colouring</li>
2468 <li>Sequence database accessions imported when fetching
2469 alignments from Rfam</li>
2470 <li>update VARNA version to 3.91</li>
2472 <li>New groovy scripts for exporting aligned positions,
2473 conservation values, and calculating sum of pairs scores.</li>
2474 <li>Command line argument to set default JABAWS server</li>
2475 <li>include installation type in build properties and
2476 console log output</li>
2477 <li>Updated Jalview project format to preserve dataset
2481 <!-- issues resolved --> <em>Application</em>
2483 <li>Distinguish alignment and sequence associated RNA
2484 structure in structure->view->VARNA</li>
2485 <li>Raise dialog box if user deletes all sequences in an
2487 <li>Pressing F1 results in documentation opening twice</li>
2488 <li>Sequence feature tooltip is wrapped</li>
2489 <li>Double click on sequence associated annotation
2490 selects only first column</li>
2491 <li>Redundancy removal doesn't result in unlinked
2492 leaves shown in tree</li>
2493 <li>Undos after several redundancy removals don't undo
2495 <li>Hide sequence doesn't hide associated annotation</li>
2496 <li>User defined colours dialog box too big to fit on
2497 screen and buttons not visible</li>
2498 <li>author list isn't updated if already written to
2499 Jalview properties</li>
2500 <li>Popup menu won't open after retrieving sequence
2502 <li>File open window for associate PDB doesn't open</li>
2503 <li>Left-then-right click on a sequence id opens a
2504 browser search window</li>
2505 <li>Cannot open sequence feature shading/sort popup menu
2506 in feature settings dialog</li>
2507 <li>better tooltip placement for some areas of Jalview
2509 <li>Allow addition of JABAWS Server which doesn't
2510 pass validation</li>
2511 <li>Web services parameters dialog box is too large to
2513 <li>Muscle nucleotide alignment preset obscured by
2515 <li>JABAWS preset submenus don't contain newly
2516 defined user preset</li>
2517 <li>MSA web services warns user if they were launched
2518 with invalid input</li>
2519 <li>Jalview cannot contact DAS Registy when running on
2522 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2523 'Superpose with' submenu not shown when new view
2527 </ul> <!-- <em>Applet</em>
2529 </ul> <em>General</em>
2531 </ul>--> <em>Deployment and Documentation</em>
2533 <li>2G and 1G options in launchApp have no effect on
2534 memory allocation</li>
2535 <li>launchApp service doesn't automatically open
2536 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2538 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2539 InstallAnywhere reports cannot find valid JVM when Java
2540 1.7_055 is available
2542 </ul> <em>Application Known issues</em>
2545 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2546 corrupted or unreadable alignment display when scrolling
2550 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2551 retrieval fails but progress bar continues for DAS retrieval
2552 with large number of ID
2555 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2556 flatfile output of visible region has incorrect sequence
2560 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2561 rna structure consensus doesn't update when secondary
2562 structure tracks are rearranged
2565 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2566 invalid rna structure positional highlighting does not
2567 highlight position of invalid base pairs
2570 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2571 out of memory errors are not raised when saving Jalview
2572 project from alignment window file menu
2575 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2576 Switching to RNA Helices colouring doesn't propagate to
2580 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2581 colour by RNA Helices not enabled when user created
2582 annotation added to alignment
2585 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2586 Jalview icon not shown on dock in Mountain Lion/Webstart
2588 </ul> <em>Applet Known Issues</em>
2591 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2592 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2595 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2596 Jalview and Jmol example not compatible with IE9
2599 <li>Sort by annotation score doesn't reverse order
2605 <td><div align="center">
2606 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2609 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2612 <li>Internationalisation of user interface (usually
2613 called i18n support) and translation for Spanish locale</li>
2614 <li>Define/Undefine group on current selection with
2615 Ctrl-G/Shift Ctrl-G</li>
2616 <li>Improved group creation/removal options in
2617 alignment/sequence Popup menu</li>
2618 <li>Sensible precision for symbol distribution
2619 percentages shown in logo tooltip.</li>
2620 <li>Annotation panel height set according to amount of
2621 annotation when alignment first opened</li>
2622 </ul> <em>Application</em>
2624 <li>Interactive consensus RNA secondary structure
2625 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2626 <li>Select columns containing particular features from
2627 Feature Settings dialog</li>
2628 <li>View all 'representative' PDB structures for selected
2630 <li>Update Jalview project format:
2632 <li>New file extension for Jalview projects '.jvp'</li>
2633 <li>Preserve sequence and annotation dataset (to
2634 store secondary structure annotation,etc)</li>
2635 <li>Per group and alignment annotation and RNA helix
2639 <li>New similarity measures for PCA and Tree calculation
2641 <li>Experimental support for retrieval and viewing of
2642 flanking regions for an alignment</li>
2646 <!-- issues resolved --> <em>Application</em>
2648 <li>logo keeps spinning and status remains at queued or
2649 running after job is cancelled</li>
2650 <li>cannot export features from alignments imported from
2651 Jalview/VAMSAS projects</li>
2652 <li>Buggy slider for web service parameters that take
2654 <li>Newly created RNA secondary structure line doesn't
2655 have 'display all symbols' flag set</li>
2656 <li>T-COFFEE alignment score shading scheme and other
2657 annotation shading not saved in Jalview project</li>
2658 <li>Local file cannot be loaded in freshly downloaded
2660 <li>Jalview icon not shown on dock in Mountain
2662 <li>Load file from desktop file browser fails</li>
2663 <li>Occasional NPE thrown when calculating large trees</li>
2664 <li>Cannot reorder or slide sequences after dragging an
2665 alignment onto desktop</li>
2666 <li>Colour by annotation dialog throws NPE after using
2667 'extract scores' function</li>
2668 <li>Loading/cut'n'pasting an empty file leads to a grey
2669 alignment window</li>
2670 <li>Disorder thresholds rendered incorrectly after
2671 performing IUPred disorder prediction</li>
2672 <li>Multiple group annotated consensus rows shown when
2673 changing 'normalise logo' display setting</li>
2674 <li>Find shows blank dialog after 'finished searching' if
2675 nothing matches query</li>
2676 <li>Null Pointer Exceptions raised when sorting by
2677 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2679 <li>Errors in Jmol console when structures in alignment
2680 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2682 <li>Not all working JABAWS services are shown in
2684 <li>JAVAWS version of Jalview fails to launch with
2685 'invalid literal/length code'</li>
2686 <li>Annotation/RNA Helix colourschemes cannot be applied
2687 to alignment with groups (actually fixed in 2.8.0b1)</li>
2688 <li>RNA Helices and T-Coffee Scores available as default
2691 </ul> <em>Applet</em>
2693 <li>Remove group option is shown even when selection is
2695 <li>Apply to all groups ticked but colourscheme changes
2696 don't affect groups</li>
2697 <li>Documented RNA Helices and T-Coffee Scores as valid
2698 colourscheme name</li>
2699 <li>Annotation labels drawn on sequence IDs when
2700 Annotation panel is not displayed</li>
2701 <li>Increased font size for dropdown menus on OSX and
2702 embedded windows</li>
2703 </ul> <em>Other</em>
2705 <li>Consensus sequence for alignments/groups with a
2706 single sequence were not calculated</li>
2707 <li>annotation files that contain only groups imported as
2708 annotation and junk sequences</li>
2709 <li>Fasta files with sequences containing '*' incorrectly
2710 recognised as PFAM or BLC</li>
2711 <li>conservation/PID slider apply all groups option
2712 doesn't affect background (2.8.0b1)
2714 <li>redundancy highlighting is erratic at 0% and 100%</li>
2715 <li>Remove gapped columns fails for sequences with ragged
2717 <li>AMSA annotation row with leading spaces is not
2718 registered correctly on import</li>
2719 <li>Jalview crashes when selecting PCA analysis for
2720 certain alignments</li>
2721 <li>Opening the colour by annotation dialog for an
2722 existing annotation based 'use original colours'
2723 colourscheme loses original colours setting</li>
2728 <td><div align="center">
2729 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2730 <em>30/1/2014</em></strong>
2734 <li>Trusted certificates for JalviewLite applet and
2735 Jalview Desktop application<br />Certificate was donated by
2736 <a href="https://www.certum.eu">Certum</a> to the Jalview
2737 open source project).
2739 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2740 <li>Output in Stockholm format</li>
2741 <li>Allow import of data from gzipped files</li>
2742 <li>Export/import group and sequence associated line
2743 graph thresholds</li>
2744 <li>Nucleotide substitution matrix that supports RNA and
2745 ambiguity codes</li>
2746 <li>Allow disorder predictions to be made on the current
2747 selection (or visible selection) in the same way that JPred
2749 <li>Groovy scripting for headless Jalview operation</li>
2750 </ul> <em>Other improvements</em>
2752 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2753 <li>COMBINE statement uses current SEQUENCE_REF and
2754 GROUP_REF scope to group annotation rows</li>
2755 <li>Support '' style escaping of quotes in Newick
2757 <li>Group options for JABAWS service by command line name</li>
2758 <li>Empty tooltip shown for JABA service options with a
2759 link but no description</li>
2760 <li>Select primary source when selecting authority in
2761 database fetcher GUI</li>
2762 <li>Add .mfa to FASTA file extensions recognised by
2764 <li>Annotation label tooltip text wrap</li>
2769 <li>Slow scrolling when lots of annotation rows are
2771 <li>Lots of NPE (and slowness) after creating RNA
2772 secondary structure annotation line</li>
2773 <li>Sequence database accessions not imported when
2774 fetching alignments from Rfam</li>
2775 <li>Incorrect SHMR submission for sequences with
2777 <li>View all structures does not always superpose
2779 <li>Option widgets in service parameters not updated to
2780 reflect user or preset settings</li>
2781 <li>Null pointer exceptions for some services without
2782 presets or adjustable parameters</li>
2783 <li>Discover PDB IDs entry in structure menu doesn't
2784 discover PDB xRefs</li>
2785 <li>Exception encountered while trying to retrieve
2786 features with DAS</li>
2787 <li>Lowest value in annotation row isn't coloured
2788 when colour by annotation (per sequence) is coloured</li>
2789 <li>Keyboard mode P jumps to start of gapped region when
2790 residue follows a gap</li>
2791 <li>Jalview appears to hang importing an alignment with
2792 Wrap as default or after enabling Wrap</li>
2793 <li>'Right click to add annotations' message
2794 shown in wrap mode when no annotations present</li>
2795 <li>Disorder predictions fail with NPE if no automatic
2796 annotation already exists on alignment</li>
2797 <li>oninit javascript function should be called after
2798 initialisation completes</li>
2799 <li>Remove redundancy after disorder prediction corrupts
2800 alignment window display</li>
2801 <li>Example annotation file in documentation is invalid</li>
2802 <li>Grouped line graph annotation rows are not exported
2803 to annotation file</li>
2804 <li>Multi-harmony analysis cannot be run when only two
2806 <li>Cannot create multiple groups of line graphs with
2807 several 'combine' statements in annotation file</li>
2808 <li>Pressing return several times causes Number Format
2809 exceptions in keyboard mode</li>
2810 <li>Multi-harmony (SHMMR) method doesn't submit
2811 correct partitions for input data</li>
2812 <li>Translation from DNA to Amino Acids fails</li>
2813 <li>Jalview fail to load newick tree with quoted label</li>
2814 <li>--headless flag isn't understood</li>
2815 <li>ClassCastException when generating EPS in headless
2817 <li>Adjusting sequence-associated shading threshold only
2818 changes one row's threshold</li>
2819 <li>Preferences and Feature settings panel panel
2820 doesn't open</li>
2821 <li>hide consensus histogram also hides conservation and
2822 quality histograms</li>
2827 <td><div align="center">
2828 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2830 <td><em>Application</em>
2832 <li>Support for JABAWS 2.0 Services (AACon alignment
2833 conservation, protein disorder and Clustal Omega)</li>
2834 <li>JABAWS server status indicator in Web Services
2836 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2837 in Jalview alignment window</li>
2838 <li>Updated Jalview build and deploy framework for OSX
2839 mountain lion, windows 7, and 8</li>
2840 <li>Nucleotide substitution matrix for PCA that supports
2841 RNA and ambiguity codes</li>
2843 <li>Improved sequence database retrieval GUI</li>
2844 <li>Support fetching and database reference look up
2845 against multiple DAS sources (Fetch all from in 'fetch db
2847 <li>Jalview project improvements
2849 <li>Store and retrieve the 'belowAlignment'
2850 flag for annotation</li>
2851 <li>calcId attribute to group annotation rows on the
2853 <li>Store AACon calculation settings for a view in
2854 Jalview project</li>
2858 <li>horizontal scrolling gesture support</li>
2859 <li>Visual progress indicator when PCA calculation is
2861 <li>Simpler JABA web services menus</li>
2862 <li>visual indication that web service results are still
2863 being retrieved from server</li>
2864 <li>Serialise the dialogs that are shown when Jalview
2865 starts up for first time</li>
2866 <li>Jalview user agent string for interacting with HTTP
2868 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2870 <li>Examples directory and Groovy library included in
2871 InstallAnywhere distribution</li>
2872 </ul> <em>Applet</em>
2874 <li>RNA alignment and secondary structure annotation
2875 visualization applet example</li>
2876 </ul> <em>General</em>
2878 <li>Normalise option for consensus sequence logo</li>
2879 <li>Reset button in PCA window to return dimensions to
2881 <li>Allow seqspace or Jalview variant of alignment PCA
2883 <li>PCA with either nucleic acid and protein substitution
2885 <li>Allow windows containing HTML reports to be exported
2887 <li>Interactive display and editing of RNA secondary
2888 structure contacts</li>
2889 <li>RNA Helix Alignment Colouring</li>
2890 <li>RNA base pair logo consensus</li>
2891 <li>Parse sequence associated secondary structure
2892 information in Stockholm files</li>
2893 <li>HTML Export database accessions and annotation
2894 information presented in tooltip for sequences</li>
2895 <li>Import secondary structure from LOCARNA clustalw
2896 style RNA alignment files</li>
2897 <li>import and visualise T-COFFEE quality scores for an
2899 <li>'colour by annotation' per sequence option to
2900 shade each sequence according to its associated alignment
2902 <li>New Jalview Logo</li>
2903 </ul> <em>Documentation and Development</em>
2905 <li>documentation for score matrices used in Jalview</li>
2906 <li>New Website!</li>
2908 <td><em>Application</em>
2910 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2911 wsdbfetch REST service</li>
2912 <li>Stop windows being moved outside desktop on OSX</li>
2913 <li>Filetype associations not installed for webstart
2915 <li>Jalview does not always retrieve progress of a JABAWS
2916 job execution in full once it is complete</li>
2917 <li>revise SHMR RSBS definition to ensure alignment is
2918 uploaded via ali_file parameter</li>
2919 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2920 <li>View all structures superposed fails with exception</li>
2921 <li>Jnet job queues forever if a very short sequence is
2922 submitted for prediction</li>
2923 <li>Cut and paste menu not opened when mouse clicked on
2925 <li>Putting fractional value into integer text box in
2926 alignment parameter dialog causes Jalview to hang</li>
2927 <li>Structure view highlighting doesn't work on
2929 <li>View all structures fails with exception shown in
2931 <li>Characters in filename associated with PDBEntry not
2932 escaped in a platform independent way</li>
2933 <li>Jalview desktop fails to launch with exception when
2935 <li>Tree calculation reports 'you must have 2 or more
2936 sequences selected' when selection is empty</li>
2937 <li>Jalview desktop fails to launch with jar signature
2938 failure when java web start temporary file caching is
2940 <li>DAS Sequence retrieval with range qualification
2941 results in sequence xref which includes range qualification</li>
2942 <li>Errors during processing of command line arguments
2943 cause progress bar (JAL-898) to be removed</li>
2944 <li>Replace comma for semi-colon option not disabled for
2945 DAS sources in sequence fetcher</li>
2946 <li>Cannot close news reader when JABAWS server warning
2947 dialog is shown</li>
2948 <li>Option widgets not updated to reflect user settings</li>
2949 <li>Edited sequence not submitted to web service</li>
2950 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2951 <li>InstallAnywhere installer doesn't unpack and run
2952 on OSX Mountain Lion</li>
2953 <li>Annotation panel not given a scroll bar when
2954 sequences with alignment annotation are pasted into the
2956 <li>Sequence associated annotation rows not associated
2957 when loaded from Jalview project</li>
2958 <li>Browser launch fails with NPE on java 1.7</li>
2959 <li>JABAWS alignment marked as finished when job was
2960 cancelled or job failed due to invalid input</li>
2961 <li>NPE with v2.7 example when clicking on Tree
2962 associated with all views</li>
2963 <li>Exceptions when copy/paste sequences with grouped
2964 annotation rows to new window</li>
2965 </ul> <em>Applet</em>
2967 <li>Sequence features are momentarily displayed before
2968 they are hidden using hidefeaturegroups applet parameter</li>
2969 <li>loading features via javascript API automatically
2970 enables feature display</li>
2971 <li>scrollToColumnIn javascript API method doesn't
2973 </ul> <em>General</em>
2975 <li>Redundancy removal fails for rna alignment</li>
2976 <li>PCA calculation fails when sequence has been selected
2977 and then deselected</li>
2978 <li>PCA window shows grey box when first opened on OSX</li>
2979 <li>Letters coloured pink in sequence logo when alignment
2980 coloured with clustalx</li>
2981 <li>Choosing fonts without letter symbols defined causes
2982 exceptions and redraw errors</li>
2983 <li>Initial PCA plot view is not same as manually
2984 reconfigured view</li>
2985 <li>Grouped annotation graph label has incorrect line
2987 <li>Grouped annotation graph label display is corrupted
2988 for lots of labels</li>
2993 <div align="center">
2994 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2997 <td><em>Application</em>
2999 <li>Jalview Desktop News Reader</li>
3000 <li>Tweaked default layout of web services menu</li>
3001 <li>View/alignment association menu to enable user to
3002 easily specify which alignment a multi-structure view takes
3003 its colours/correspondences from</li>
3004 <li>Allow properties file location to be specified as URL</li>
3005 <li>Extend Jalview project to preserve associations
3006 between many alignment views and a single Jmol display</li>
3007 <li>Store annotation row height in Jalview project file</li>
3008 <li>Annotation row column label formatting attributes
3009 stored in project file</li>
3010 <li>Annotation row order for auto-calculated annotation
3011 rows preserved in Jalview project file</li>
3012 <li>Visual progress indication when Jalview state is
3013 saved using Desktop window menu</li>
3014 <li>Visual indication that command line arguments are
3015 still being processed</li>
3016 <li>Groovy script execution from URL</li>
3017 <li>Colour by annotation default min and max colours in
3019 <li>Automatically associate PDB files dragged onto an
3020 alignment with sequences that have high similarity and
3022 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3023 <li>'view structures' option to open many
3024 structures in same window</li>
3025 <li>Sort associated views menu option for tree panel</li>
3026 <li>Group all JABA and non-JABA services for a particular
3027 analysis function in its own submenu</li>
3028 </ul> <em>Applet</em>
3030 <li>Userdefined and autogenerated annotation rows for
3032 <li>Adjustment of alignment annotation pane height</li>
3033 <li>Annotation scrollbar for annotation panel</li>
3034 <li>Drag to reorder annotation rows in annotation panel</li>
3035 <li>'automaticScrolling' parameter</li>
3036 <li>Allow sequences with partial ID string matches to be
3037 annotated from GFF/Jalview features files</li>
3038 <li>Sequence logo annotation row in applet</li>
3039 <li>Absolute paths relative to host server in applet
3040 parameters are treated as such</li>
3041 <li>New in the JalviewLite javascript API:
3043 <li>JalviewLite.js javascript library</li>
3044 <li>Javascript callbacks for
3046 <li>Applet initialisation</li>
3047 <li>Sequence/alignment mouse-overs and selections</li>
3050 <li>scrollTo row and column alignment scrolling
3052 <li>Select sequence/alignment regions from javascript</li>
3053 <li>javascript structure viewer harness to pass
3054 messages between Jmol and Jalview when running as
3055 distinct applets</li>
3056 <li>sortBy method</li>
3057 <li>Set of applet and application examples shipped
3058 with documentation</li>
3059 <li>New example to demonstrate JalviewLite and Jmol
3060 javascript message exchange</li>
3062 </ul> <em>General</em>
3064 <li>Enable Jmol displays to be associated with multiple
3065 multiple alignments</li>
3066 <li>Option to automatically sort alignment with new tree</li>
3067 <li>User configurable link to enable redirects to a
3068 www.Jalview.org mirror</li>
3069 <li>Jmol colours option for Jmol displays</li>
3070 <li>Configurable newline string when writing alignment
3071 and other flat files</li>
3072 <li>Allow alignment annotation description lines to
3073 contain html tags</li>
3074 </ul> <em>Documentation and Development</em>
3076 <li>Add groovy test harness for bulk load testing to
3078 <li>Groovy script to load and align a set of sequences
3079 using a web service before displaying the result in the
3080 Jalview desktop</li>
3081 <li>Restructured javascript and applet api documentation</li>
3082 <li>Ant target to publish example html files with applet
3084 <li>Netbeans project for building Jalview from source</li>
3085 <li>ant task to create online javadoc for Jalview source</li>
3087 <td><em>Application</em>
3089 <li>User defined colourscheme throws exception when
3090 current built in colourscheme is saved as new scheme</li>
3091 <li>AlignFrame->Save in application pops up save
3092 dialog for valid filename/format</li>
3093 <li>Cannot view associated structure for UniProt sequence</li>
3094 <li>PDB file association breaks for UniProt sequence
3096 <li>Associate PDB from file dialog does not tell you
3097 which sequence is to be associated with the file</li>
3098 <li>Find All raises null pointer exception when query
3099 only matches sequence IDs</li>
3100 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3101 <li>Jalview project with Jmol views created with Jalview
3102 2.4 cannot be loaded</li>
3103 <li>Filetype associations not installed for webstart
3105 <li>Two or more chains in a single PDB file associated
3106 with sequences in different alignments do not get coloured
3107 by their associated sequence</li>
3108 <li>Visibility status of autocalculated annotation row
3109 not preserved when project is loaded</li>
3110 <li>Annotation row height and visibility attributes not
3111 stored in Jalview project</li>
3112 <li>Tree bootstraps are not preserved when saved as a
3113 Jalview project</li>
3114 <li>Envision2 workflow tooltips are corrupted</li>
3115 <li>Enabling show group conservation also enables colour
3116 by conservation</li>
3117 <li>Duplicate group associated conservation or consensus
3118 created on new view</li>
3119 <li>Annotation scrollbar not displayed after 'show
3120 all hidden annotation rows' option selected</li>
3121 <li>Alignment quality not updated after alignment
3122 annotation row is hidden then shown</li>
3123 <li>Preserve colouring of structures coloured by
3124 sequences in pre Jalview 2.7 projects</li>
3125 <li>Web service job parameter dialog is not laid out
3127 <li>Web services menu not refreshed after 'reset
3128 services' button is pressed in preferences</li>
3129 <li>Annotation off by one in Jalview v2_3 example project</li>
3130 <li>Structures imported from file and saved in project
3131 get name like jalview_pdb1234.txt when reloaded</li>
3132 <li>Jalview does not always retrieve progress of a JABAWS
3133 job execution in full once it is complete</li>
3134 </ul> <em>Applet</em>
3136 <li>Alignment height set incorrectly when lots of
3137 annotation rows are displayed</li>
3138 <li>Relative URLs in feature HTML text not resolved to
3140 <li>View follows highlighting does not work for positions
3142 <li><= shown as = in tooltip</li>
3143 <li>Export features raises exception when no features
3145 <li>Separator string used for serialising lists of IDs
3146 for javascript api is modified when separator string
3147 provided as parameter</li>
3148 <li>Null pointer exception when selecting tree leaves for
3149 alignment with no existing selection</li>
3150 <li>Relative URLs for datasources assumed to be relative
3151 to applet's codebase</li>
3152 <li>Status bar not updated after finished searching and
3153 search wraps around to first result</li>
3154 <li>StructureSelectionManager instance shared between
3155 several Jalview applets causes race conditions and memory
3157 <li>Hover tooltip and mouseover of position on structure
3158 not sent from Jmol in applet</li>
3159 <li>Certain sequences of javascript method calls to
3160 applet API fatally hang browser</li>
3161 </ul> <em>General</em>
3163 <li>View follows structure mouseover scrolls beyond
3164 position with wrapped view and hidden regions</li>
3165 <li>Find sequence position moves to wrong residue
3166 with/without hidden columns</li>
3167 <li>Sequence length given in alignment properties window
3169 <li>InvalidNumberFormat exceptions thrown when trying to
3170 import PDB like structure files</li>
3171 <li>Positional search results are only highlighted
3172 between user-supplied sequence start/end bounds</li>
3173 <li>End attribute of sequence is not validated</li>
3174 <li>Find dialog only finds first sequence containing a
3175 given sequence position</li>
3176 <li>Sequence numbering not preserved in MSF alignment
3178 <li>Jalview PDB file reader does not extract sequence
3179 from nucleotide chains correctly</li>
3180 <li>Structure colours not updated when tree partition
3181 changed in alignment</li>
3182 <li>Sequence associated secondary structure not correctly
3183 parsed in interleaved stockholm</li>
3184 <li>Colour by annotation dialog does not restore current
3186 <li>Hiding (nearly) all sequences doesn't work
3188 <li>Sequences containing lowercase letters are not
3189 properly associated with their pdb files</li>
3190 </ul> <em>Documentation and Development</em>
3192 <li>schemas/JalviewWsParamSet.xsd corrupted by
3193 ApplyCopyright tool</li>
3198 <div align="center">
3199 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3202 <td><em>Application</em>
3204 <li>New warning dialog when the Jalview Desktop cannot
3205 contact web services</li>
3206 <li>JABA service parameters for a preset are shown in
3207 service job window</li>
3208 <li>JABA Service menu entries reworded</li>
3212 <li>Modeller PIR IO broken - cannot correctly import a
3213 pir file emitted by Jalview</li>
3214 <li>Existing feature settings transferred to new
3215 alignment view created from cut'n'paste</li>
3216 <li>Improved test for mixed amino/nucleotide chains when
3217 parsing PDB files</li>
3218 <li>Consensus and conservation annotation rows
3219 occasionally become blank for all new windows</li>
3220 <li>Exception raised when right clicking above sequences
3221 in wrapped view mode</li>
3222 </ul> <em>Application</em>
3224 <li>multiple multiply aligned structure views cause cpu
3225 usage to hit 100% and computer to hang</li>
3226 <li>Web Service parameter layout breaks for long user
3227 parameter names</li>
3228 <li>Jaba service discovery hangs desktop if Jaba server
3235 <div align="center">
3236 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3239 <td><em>Application</em>
3241 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3242 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3245 <li>Web Services preference tab</li>
3246 <li>Analysis parameters dialog box and user defined
3248 <li>Improved speed and layout of Envision2 service menu</li>
3249 <li>Superpose structures using associated sequence
3251 <li>Export coordinates and projection as CSV from PCA
3253 </ul> <em>Applet</em>
3255 <li>enable javascript: execution by the applet via the
3256 link out mechanism</li>
3257 </ul> <em>Other</em>
3259 <li>Updated the Jmol Jalview interface to work with Jmol
3261 <li>The Jalview Desktop and JalviewLite applet now
3262 require Java 1.5</li>
3263 <li>Allow Jalview feature colour specification for GFF
3264 sequence annotation files</li>
3265 <li>New 'colour by label' keword in Jalview feature file
3266 type colour specification</li>
3267 <li>New Jalview Desktop Groovy API method that allows a
3268 script to check if it being run in an interactive session or
3269 in a batch operation from the Jalview command line</li>
3273 <li>clustalx colourscheme colours Ds preferentially when
3274 both D+E are present in over 50% of the column</li>
3275 </ul> <em>Application</em>
3277 <li>typo in AlignmentFrame->View->Hide->all but
3278 selected Regions menu item</li>
3279 <li>sequence fetcher replaces ',' for ';' when the ',' is
3280 part of a valid accession ID</li>
3281 <li>fatal OOM if object retrieved by sequence fetcher
3282 runs out of memory</li>
3283 <li>unhandled Out of Memory Error when viewing pca
3284 analysis results</li>
3285 <li>InstallAnywhere builds fail to launch on OS X java
3286 10.5 update 4 (due to apple Java 1.6 update)</li>
3287 <li>Installanywhere Jalview silently fails to launch</li>
3288 </ul> <em>Applet</em>
3290 <li>Jalview.getFeatureGroups() raises an
3291 ArrayIndexOutOfBoundsException if no feature groups are
3298 <div align="center">
3299 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3305 <li>Alignment prettyprinter doesn't cope with long
3307 <li>clustalx colourscheme colours Ds preferentially when
3308 both D+E are present in over 50% of the column</li>
3309 <li>nucleic acid structures retrieved from PDB do not
3310 import correctly</li>
3311 <li>More columns get selected than were clicked on when a
3312 number of columns are hidden</li>
3313 <li>annotation label popup menu not providing correct
3314 add/hide/show options when rows are hidden or none are
3316 <li>Stockholm format shown in list of readable formats,
3317 and parser copes better with alignments from RFAM.</li>
3318 <li>CSV output of consensus only includes the percentage
3319 of all symbols if sequence logo display is enabled</li>
3321 </ul> <em>Applet</em>
3323 <li>annotation panel disappears when annotation is
3325 </ul> <em>Application</em>
3327 <li>Alignment view not redrawn properly when new
3328 alignment opened where annotation panel is visible but no
3329 annotations are present on alignment</li>
3330 <li>pasted region containing hidden columns is
3331 incorrectly displayed in new alignment window</li>
3332 <li>Jalview slow to complete operations when stdout is
3333 flooded (fix is to close the Jalview console)</li>
3334 <li>typo in AlignmentFrame->View->Hide->all but
3335 selected Rregions menu item.</li>
3336 <li>inconsistent group submenu and Format submenu entry
3337 'Un' or 'Non'conserved</li>
3338 <li>Sequence feature settings are being shared by
3339 multiple distinct alignments</li>
3340 <li>group annotation not recreated when tree partition is
3342 <li>double click on group annotation to select sequences
3343 does not propagate to associated trees</li>
3344 <li>Mac OSX specific issues:
3346 <li>exception raised when mouse clicked on desktop
3347 window background</li>
3348 <li>Desktop menu placed on menu bar and application
3349 name set correctly</li>
3350 <li>sequence feature settings not wide enough for the
3351 save feature colourscheme button</li>
3360 <div align="center">
3361 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3364 <td><em>New Capabilities</em>
3366 <li>URL links generated from description line for
3367 regular-expression based URL links (applet and application)
3369 <li>Non-positional feature URL links are shown in link
3371 <li>Linked viewing of nucleic acid sequences and
3373 <li>Automatic Scrolling option in View menu to display
3374 the currently highlighted region of an alignment.</li>
3375 <li>Order an alignment by sequence length, or using the
3376 average score or total feature count for each sequence.</li>
3377 <li>Shading features by score or associated description</li>
3378 <li>Subdivide alignment and groups based on identity of
3379 selected subsequence (Make Groups from Selection).</li>
3380 <li>New hide/show options including Shift+Control+H to
3381 hide everything but the currently selected region.</li>
3382 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3383 </ul> <em>Application</em>
3385 <li>Fetch DB References capabilities and UI expanded to
3386 support retrieval from DAS sequence sources</li>
3387 <li>Local DAS Sequence sources can be added via the
3388 command line or via the Add local source dialog box.</li>
3389 <li>DAS Dbref and DbxRef feature types are parsed as
3390 database references and protein_name is parsed as
3391 description line (BioSapiens terms).</li>
3392 <li>Enable or disable non-positional feature and database
3393 references in sequence ID tooltip from View menu in
3395 <!-- <li>New hidden columns and rows and representatives capabilities
3396 in annotations file (in progress - not yet fully implemented)</li> -->
3397 <li>Group-associated consensus, sequence logos and
3398 conservation plots</li>
3399 <li>Symbol distributions for each column can be exported
3400 and visualized as sequence logos</li>
3401 <li>Optionally scale multi-character column labels to fit
3402 within each column of annotation row<!-- todo for applet -->
3404 <li>Optional automatic sort of associated alignment view
3405 when a new tree is opened.</li>
3406 <li>Jalview Java Console</li>
3407 <li>Better placement of desktop window when moving
3408 between different screens.</li>
3409 <li>New preference items for sequence ID tooltip and
3410 consensus annotation</li>
3411 <li>Client to submit sequences and IDs to Envision2
3413 <li><em>Vamsas Capabilities</em>
3415 <li>Improved VAMSAS synchronization (Jalview archive
3416 used to preserve views, structures, and tree display
3418 <li>Import of vamsas documents from disk or URL via
3420 <li>Sharing of selected regions between views and
3421 with other VAMSAS applications (Experimental feature!)</li>
3422 <li>Updated API to VAMSAS version 0.2</li>
3424 </ul> <em>Applet</em>
3426 <li>Middle button resizes annotation row height</li>
3429 <li>sortByTree (true/false) - automatically sort the
3430 associated alignment view by the tree when a new tree is
3432 <li>showTreeBootstraps (true/false) - show or hide
3433 branch bootstraps (default is to show them if available)</li>
3434 <li>showTreeDistances (true/false) - show or hide
3435 branch lengths (default is to show them if available)</li>
3436 <li>showUnlinkedTreeNodes (true/false) - indicate if
3437 unassociated nodes should be highlighted in the tree
3439 <li>heightScale and widthScale (1.0 or more) -
3440 increase the height or width of a cell in the alignment
3441 grid relative to the current font size.</li>
3444 <li>Non-positional features displayed in sequence ID
3446 </ul> <em>Other</em>
3448 <li>Features format: graduated colour definitions and
3449 specification of feature scores</li>
3450 <li>Alignment Annotations format: new keywords for group
3451 associated annotation (GROUP_REF) and annotation row display
3452 properties (ROW_PROPERTIES)</li>
3453 <li>XML formats extended to support graduated feature
3454 colourschemes, group associated annotation, and profile
3455 visualization settings.</li></td>
3458 <li>Source field in GFF files parsed as feature source
3459 rather than description</li>
3460 <li>Non-positional features are now included in sequence
3461 feature and gff files (controlled via non-positional feature
3462 visibility in tooltip).</li>
3463 <li>URL links generated for all feature links (bugfix)</li>
3464 <li>Added URL embedding instructions to features file
3466 <li>Codons containing ambiguous nucleotides translated as
3467 'X' in peptide product</li>
3468 <li>Match case switch in find dialog box works for both
3469 sequence ID and sequence string and query strings do not
3470 have to be in upper case to match case-insensitively.</li>
3471 <li>AMSA files only contain first column of
3472 multi-character column annotation labels</li>
3473 <li>Jalview Annotation File generation/parsing consistent
3474 with documentation (e.g. Stockholm annotation can be
3475 exported and re-imported)</li>
3476 <li>PDB files without embedded PDB IDs given a friendly
3478 <li>Find incrementally searches ID string matches as well
3479 as subsequence matches, and correctly reports total number
3483 <li>Better handling of exceptions during sequence
3485 <li>Dasobert generated non-positional feature URL
3486 link text excludes the start_end suffix</li>
3487 <li>DAS feature and source retrieval buttons disabled
3488 when fetch or registry operations in progress.</li>
3489 <li>PDB files retrieved from URLs are cached properly</li>
3490 <li>Sequence description lines properly shared via
3492 <li>Sequence fetcher fetches multiple records for all
3494 <li>Ensured that command line das feature retrieval
3495 completes before alignment figures are generated.</li>
3496 <li>Reduced time taken when opening file browser for
3498 <li>isAligned check prior to calculating tree, PCA or
3499 submitting an MSA to JNet now excludes hidden sequences.</li>
3500 <li>User defined group colours properly recovered
3501 from Jalview projects.</li>
3510 <div align="center">
3511 <strong>2.4.0.b2</strong><br> 28/10/2009
3516 <li>Experimental support for google analytics usage
3518 <li>Jalview privacy settings (user preferences and docs).</li>
3523 <li>Race condition in applet preventing startup in
3525 <li>Exception when feature created from selection beyond
3526 length of sequence.</li>
3527 <li>Allow synthetic PDB files to be imported gracefully</li>
3528 <li>Sequence associated annotation rows associate with
3529 all sequences with a given id</li>
3530 <li>Find function matches case-insensitively for sequence
3531 ID string searches</li>
3532 <li>Non-standard characters do not cause pairwise
3533 alignment to fail with exception</li>
3534 </ul> <em>Application Issues</em>
3536 <li>Sequences are now validated against EMBL database</li>
3537 <li>Sequence fetcher fetches multiple records for all
3539 </ul> <em>InstallAnywhere Issues</em>
3541 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3542 issue with installAnywhere mechanism)</li>
3543 <li>Command line launching of JARs from InstallAnywhere
3544 version (java class versioning error fixed)</li>
3551 <div align="center">
3552 <strong>2.4</strong><br> 27/8/2008
3555 <td><em>User Interface</em>
3557 <li>Linked highlighting of codon and amino acid from
3558 translation and protein products</li>
3559 <li>Linked highlighting of structure associated with
3560 residue mapping to codon position</li>
3561 <li>Sequence Fetcher provides example accession numbers
3562 and 'clear' button</li>
3563 <li>MemoryMonitor added as an option under Desktop's
3565 <li>Extract score function to parse whitespace separated
3566 numeric data in description line</li>
3567 <li>Column labels in alignment annotation can be centred.</li>
3568 <li>Tooltip for sequence associated annotation give name
3570 </ul> <em>Web Services and URL fetching</em>
3572 <li>JPred3 web service</li>
3573 <li>Prototype sequence search client (no public services
3575 <li>Fetch either seed alignment or full alignment from
3577 <li>URL Links created for matching database cross
3578 references as well as sequence ID</li>
3579 <li>URL Links can be created using regular-expressions</li>
3580 </ul> <em>Sequence Database Connectivity</em>
3582 <li>Retrieval of cross-referenced sequences from other
3584 <li>Generalised database reference retrieval and
3585 validation to all fetchable databases</li>
3586 <li>Fetch sequences from DAS sources supporting the
3587 sequence command</li>
3588 </ul> <em>Import and Export</em>
3589 <li>export annotation rows as CSV for spreadsheet import</li>
3590 <li>Jalview projects record alignment dataset associations,
3591 EMBL products, and cDNA sequence mappings</li>
3592 <li>Sequence Group colour can be specified in Annotation
3594 <li>Ad-hoc colouring of group in Annotation File using RGB
3595 triplet as name of colourscheme</li>
3596 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3598 <li>treenode binding for VAMSAS tree exchange</li>
3599 <li>local editing and update of sequences in VAMSAS
3600 alignments (experimental)</li>
3601 <li>Create new or select existing session to join</li>
3602 <li>load and save of vamsas documents</li>
3603 </ul> <em>Application command line</em>
3605 <li>-tree parameter to open trees (introduced for passing
3607 <li>-fetchfrom command line argument to specify nicknames
3608 of DAS servers to query for alignment features</li>
3609 <li>-dasserver command line argument to add new servers
3610 that are also automatically queried for features</li>
3611 <li>-groovy command line argument executes a given groovy
3612 script after all input data has been loaded and parsed</li>
3613 </ul> <em>Applet-Application data exchange</em>
3615 <li>Trees passed as applet parameters can be passed to
3616 application (when using "View in full
3617 application")</li>
3618 </ul> <em>Applet Parameters</em>
3620 <li>feature group display control parameter</li>
3621 <li>debug parameter</li>
3622 <li>showbutton parameter</li>
3623 </ul> <em>Applet API methods</em>
3625 <li>newView public method</li>
3626 <li>Window (current view) specific get/set public methods</li>
3627 <li>Feature display control methods</li>
3628 <li>get list of currently selected sequences</li>
3629 </ul> <em>New Jalview distribution features</em>
3631 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3632 <li>RELEASE file gives build properties for the latest
3633 Jalview release.</li>
3634 <li>Java 1.1 Applet build made easier and donotobfuscate
3635 property controls execution of obfuscator</li>
3636 <li>Build target for generating source distribution</li>
3637 <li>Debug flag for javacc</li>
3638 <li>.jalview_properties file is documented (slightly) in
3639 jalview.bin.Cache</li>
3640 <li>Continuous Build Integration for stable and
3641 development version of Application, Applet and source
3646 <li>selected region output includes visible annotations
3647 (for certain formats)</li>
3648 <li>edit label/displaychar contains existing label/char
3650 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3651 <li>shorter peptide product names from EMBL records</li>
3652 <li>Newick string generator makes compact representations</li>
3653 <li>bootstrap values parsed correctly for tree files with
3655 <li>pathological filechooser bug avoided by not allowing
3656 filenames containing a ':'</li>
3657 <li>Fixed exception when parsing GFF files containing
3658 global sequence features</li>
3659 <li>Alignment datasets are finalized only when number of
3660 references from alignment sequences goes to zero</li>
3661 <li>Close of tree branch colour box without colour
3662 selection causes cascading exceptions</li>
3663 <li>occasional negative imgwidth exceptions</li>
3664 <li>better reporting of non-fatal warnings to user when
3665 file parsing fails.</li>
3666 <li>Save works when Jalview project is default format</li>
3667 <li>Save as dialog opened if current alignment format is
3668 not a valid output format</li>
3669 <li>UniProt canonical names introduced for both das and
3671 <li>Histidine should be midblue (not pink!) in Zappo</li>
3672 <li>error messages passed up and output when data read
3674 <li>edit undo recovers previous dataset sequence when
3675 sequence is edited</li>
3676 <li>allow PDB files without pdb ID HEADER lines (like
3677 those generated by MODELLER) to be read in properly</li>
3678 <li>allow reading of JPred concise files as a normal
3680 <li>Stockholm annotation parsing and alignment properties
3681 import fixed for PFAM records</li>
3682 <li>Structure view windows have correct name in Desktop
3684 <li>annotation consisting of sequence associated scores
3685 can be read and written correctly to annotation file</li>
3686 <li>Aligned cDNA translation to aligned peptide works
3688 <li>Fixed display of hidden sequence markers and
3689 non-italic font for representatives in Applet</li>
3690 <li>Applet Menus are always embedded in applet window on
3692 <li>Newly shown features appear at top of stack (in
3694 <li>Annotations added via parameter not drawn properly
3695 due to null pointer exceptions</li>
3696 <li>Secondary structure lines are drawn starting from
3697 first column of alignment</li>
3698 <li>UniProt XML import updated for new schema release in
3700 <li>Sequence feature to sequence ID match for Features
3701 file is case-insensitive</li>
3702 <li>Sequence features read from Features file appended to
3703 all sequences with matching IDs</li>
3704 <li>PDB structure coloured correctly for associated views
3705 containing a sub-sequence</li>
3706 <li>PDB files can be retrieved by applet from Jar files</li>
3707 <li>feature and annotation file applet parameters
3708 referring to different directories are retrieved correctly</li>
3709 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3710 <li>Fixed application hang whilst waiting for
3711 splash-screen version check to complete</li>
3712 <li>Applet properly URLencodes input parameter values
3713 when passing them to the launchApp service</li>
3714 <li>display name and local features preserved in results
3715 retrieved from web service</li>
3716 <li>Visual delay indication for sequence retrieval and
3717 sequence fetcher initialisation</li>
3718 <li>updated Application to use DAS 1.53e version of
3719 dasobert DAS client</li>
3720 <li>Re-instated Full AMSA support and .amsa file
3722 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3730 <div align="center">
3731 <strong>2.3</strong><br> 9/5/07
3736 <li>Jmol 11.0.2 integration</li>
3737 <li>PDB views stored in Jalview XML files</li>
3738 <li>Slide sequences</li>
3739 <li>Edit sequence in place</li>
3740 <li>EMBL CDS features</li>
3741 <li>DAS Feature mapping</li>
3742 <li>Feature ordering</li>
3743 <li>Alignment Properties</li>
3744 <li>Annotation Scores</li>
3745 <li>Sort by scores</li>
3746 <li>Feature/annotation editing in applet</li>
3751 <li>Headless state operation in 2.2.1</li>
3752 <li>Incorrect and unstable DNA pairwise alignment</li>
3753 <li>Cut and paste of sequences with annotation</li>
3754 <li>Feature group display state in XML</li>
3755 <li>Feature ordering in XML</li>
3756 <li>blc file iteration selection using filename # suffix</li>
3757 <li>Stockholm alignment properties</li>
3758 <li>Stockhom alignment secondary structure annotation</li>
3759 <li>2.2.1 applet had no feature transparency</li>
3760 <li>Number pad keys can be used in cursor mode</li>
3761 <li>Structure Viewer mirror image resolved</li>
3768 <div align="center">
3769 <strong>2.2.1</strong><br> 12/2/07
3774 <li>Non standard characters can be read and displayed
3775 <li>Annotations/Features can be imported/exported to the
3777 <li>Applet allows editing of sequence/annotation/group
3778 name & description
3779 <li>Preference setting to display sequence name in
3781 <li>Annotation file format extended to allow
3782 Sequence_groups to be defined
3783 <li>Default opening of alignment overview panel can be
3784 specified in preferences
3785 <li>PDB residue numbering annotation added to associated
3791 <li>Applet crash under certain Linux OS with Java 1.6
3793 <li>Annotation file export / import bugs fixed
3794 <li>PNG / EPS image output bugs fixed
3800 <div align="center">
3801 <strong>2.2</strong><br> 27/11/06
3806 <li>Multiple views on alignment
3807 <li>Sequence feature editing
3808 <li>"Reload" alignment
3809 <li>"Save" to current filename
3810 <li>Background dependent text colour
3811 <li>Right align sequence ids
3812 <li>User-defined lower case residue colours
3815 <li>Menu item accelerator keys
3816 <li>Control-V pastes to current alignment
3817 <li>Cancel button for DAS Feature Fetching
3818 <li>PCA and PDB Viewers zoom via mouse roller
3819 <li>User-defined sub-tree colours and sub-tree selection
3821 <li>'New Window' button on the 'Output to Text box'
3826 <li>New memory efficient Undo/Redo System
3827 <li>Optimised symbol lookups and conservation/consensus
3829 <li>Region Conservation/Consensus recalculated after
3831 <li>Fixed Remove Empty Columns Bug (empty columns at end
3833 <li>Slowed DAS Feature Fetching for increased robustness.
3835 <li>Made angle brackets in ASCII feature descriptions
3837 <li>Re-instated Zoom function for PCA
3838 <li>Sequence descriptions conserved in web service
3840 <li>UniProt ID discoverer uses any word separated by
3842 <li>WsDbFetch query/result association resolved
3843 <li>Tree leaf to sequence mapping improved
3844 <li>Smooth fonts switch moved to FontChooser dialog box.
3851 <div align="center">
3852 <strong>2.1.1</strong><br> 12/9/06
3857 <li>Copy consensus sequence to clipboard</li>
3862 <li>Image output - rightmost residues are rendered if
3863 sequence id panel has been resized</li>
3864 <li>Image output - all offscreen group boundaries are
3866 <li>Annotation files with sequence references - all
3867 elements in file are relative to sequence position</li>
3868 <li>Mac Applet users can use Alt key for group editing</li>
3874 <div align="center">
3875 <strong>2.1</strong><br> 22/8/06
3880 <li>MAFFT Multiple Alignment in default Web Service list</li>
3881 <li>DAS Feature fetching</li>
3882 <li>Hide sequences and columns</li>
3883 <li>Export Annotations and Features</li>
3884 <li>GFF file reading / writing</li>
3885 <li>Associate structures with sequences from local PDB
3887 <li>Add sequences to exisiting alignment</li>
3888 <li>Recently opened files / URL lists</li>
3889 <li>Applet can launch the full application</li>
3890 <li>Applet has transparency for features (Java 1.2
3892 <li>Applet has user defined colours parameter</li>
3893 <li>Applet can load sequences from parameter
3894 "sequence<em>x</em>"
3900 <li>Redundancy Panel reinstalled in the Applet</li>
3901 <li>Monospaced font - EPS / rescaling bug fixed</li>
3902 <li>Annotation files with sequence references bug fixed</li>
3908 <div align="center">
3909 <strong>2.08.1</strong><br> 2/5/06
3914 <li>Change case of selected region from Popup menu</li>
3915 <li>Choose to match case when searching</li>
3916 <li>Middle mouse button and mouse movement can compress /
3917 expand the visible width and height of the alignment</li>
3922 <li>Annotation Panel displays complete JNet results</li>
3928 <div align="center">
3929 <strong>2.08b</strong><br> 18/4/06
3935 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3936 <li>Righthand label on wrapped alignments shows correct
3943 <div align="center">
3944 <strong>2.08</strong><br> 10/4/06
3949 <li>Editing can be locked to the selection area</li>
3950 <li>Keyboard editing</li>
3951 <li>Create sequence features from searches</li>
3952 <li>Precalculated annotations can be loaded onto
3954 <li>Features file allows grouping of features</li>
3955 <li>Annotation Colouring scheme added</li>
3956 <li>Smooth fonts off by default - Faster rendering</li>
3957 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3962 <li>Drag & Drop fixed on Linux</li>
3963 <li>Jalview Archive file faster to load/save, sequence
3964 descriptions saved.</li>
3970 <div align="center">
3971 <strong>2.07</strong><br> 12/12/05
3976 <li>PDB Structure Viewer enhanced</li>
3977 <li>Sequence Feature retrieval and display enhanced</li>
3978 <li>Choose to output sequence start-end after sequence
3979 name for file output</li>
3980 <li>Sequence Fetcher WSDBFetch@EBI</li>
3981 <li>Applet can read feature files, PDB files and can be
3982 used for HTML form input</li>
3987 <li>HTML output writes groups and features</li>
3988 <li>Group editing is Control and mouse click</li>
3989 <li>File IO bugs</li>
3995 <div align="center">
3996 <strong>2.06</strong><br> 28/9/05
4001 <li>View annotations in wrapped mode</li>
4002 <li>More options for PCA viewer</li>
4007 <li>GUI bugs resolved</li>
4008 <li>Runs with -nodisplay from command line</li>
4014 <div align="center">
4015 <strong>2.05b</strong><br> 15/9/05
4020 <li>Choose EPS export as lineart or text</li>
4021 <li>Jar files are executable</li>
4022 <li>Can read in Uracil - maps to unknown residue</li>
4027 <li>Known OutOfMemory errors give warning message</li>
4028 <li>Overview window calculated more efficiently</li>
4029 <li>Several GUI bugs resolved</li>
4035 <div align="center">
4036 <strong>2.05</strong><br> 30/8/05
4041 <li>Edit and annotate in "Wrapped" view</li>
4046 <li>Several GUI bugs resolved</li>
4052 <div align="center">
4053 <strong>2.04</strong><br> 24/8/05
4058 <li>Hold down mouse wheel & scroll to change font
4064 <li>Improved JPred client reliability</li>
4065 <li>Improved loading of Jalview files</li>
4071 <div align="center">
4072 <strong>2.03</strong><br> 18/8/05
4077 <li>Set Proxy server name and port in preferences</li>
4078 <li>Multiple URL links from sequence ids</li>
4079 <li>User Defined Colours can have a scheme name and added
4081 <li>Choose to ignore gaps in consensus calculation</li>
4082 <li>Unix users can set default web browser</li>
4083 <li>Runs without GUI for batch processing</li>
4084 <li>Dynamically generated Web Service Menus</li>
4089 <li>InstallAnywhere download for Sparc Solaris</li>
4095 <div align="center">
4096 <strong>2.02</strong><br> 18/7/05
4102 <li>Copy & Paste order of sequences maintains
4103 alignment order.</li>
4109 <div align="center">
4110 <strong>2.01</strong><br> 12/7/05
4115 <li>Use delete key for deleting selection.</li>
4116 <li>Use Mouse wheel to scroll sequences.</li>
4117 <li>Help file updated to describe how to add alignment
4119 <li>Version and build date written to build properties
4121 <li>InstallAnywhere installation will check for updates
4122 at launch of Jalview.</li>
4127 <li>Delete gaps bug fixed.</li>
4128 <li>FileChooser sorts columns.</li>
4129 <li>Can remove groups one by one.</li>
4130 <li>Filechooser icons installed.</li>
4131 <li>Finder ignores return character when searching.
4132 Return key will initiate a search.<br>
4139 <div align="center">
4140 <strong>2.0</strong><br> 20/6/05
4145 <li>New codebase</li>