3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>6/09/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-3101 -->Default memory for Jalview webstart and
81 InstallAnywhere increased to 1G.
84 <!-- JAL-247 -->Hidden sequence markers and representative
85 sequence bolding included when exporting alignment as EPS,
86 SVG, PNG or HTML. <em>Display is configured via the
87 Format menu, or for command-line use via a jalview
91 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
92 API and sequence data now imported as JSON.
95 <!-- JAL-3065 -->Change in recommended way of starting
96 Jalview via a Java command line: add jars in lib directory
97 to CLASSPATH, rather than via the deprecated java.ext.dirs
104 <!-- JAL-3047 -->Support added to execute test suite
105 instrumented with <a href="http://openclover.org/">Open
110 <td><div align="left">
114 <!-- JAL-2854 -->Annotation obscures sequences if lots of
115 annotation displayed.
118 <!-- JAL-3087 -->Corrupted display when switching to
119 wrapped mode when sequence panel's vertical scrollbar is
123 <!-- JAL-3003 -->Alignment is black in exported EPS file
124 when sequences are selected in exported view.</em>
127 <!-- JAL-3059 -->Groups with different coloured borders
128 aren't rendered with correct colour.
131 <!-- JAL-3092 -->Jalview could hang when importing certain
132 types of knotted RNA secondary structure.
135 <!-- JAL-3095 -->Sequence highlight and selection in
136 trimmed VARNA 2D structure is incorrect for sequences that
140 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
141 annotation when columns are inserted into an alignment,
142 and when exporting as Stockholm flatfile.
145 <!-- JAL-3053 -->Jalview annotation rows containing upper
146 and lower-case 'E' and 'H' do not automatically get
147 treated as RNA secondary structure.
150 <em>Java 10 Issues</em>
153 <!-- JAL-2988 -->OSX - Can't save new files via the File
154 or export menus by typing in a name into the Save dialog
162 <td width="60" nowrap>
164 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
165 <em>7/06/2018</em></strong>
168 <td><div align="left">
172 <!-- JAL-2920 -->Use HGVS nomenclature for variant
173 annotation retrieved from Uniprot
176 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
177 onto the Jalview Desktop
181 <td><div align="left">
185 <!-- JAL-3017 -->Cannot import features with multiple
186 variant elements (blocks import of some Uniprot records)
189 <!-- JAL-2997 -->Clustal files with sequence positions in
190 right-hand column parsed correctly
193 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
194 not alignment area in exported graphic
197 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
198 window has input focus
201 <!-- JAL-2992 -->Annotation panel set too high when
202 annotation added to view (Windows)
205 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
206 network connectivity is poor
209 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
210 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
211 the currently open URL and links from a page viewed in
212 Firefox or Chrome on Windows is now fully supported. If
213 you are using Edge, only links in the page can be
214 dragged, and with Internet Explorer, only the currently
215 open URL in the browser can be dropped onto Jalview.</em>
221 <td width="60" nowrap>
223 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
226 <td><div align="left">
230 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
231 for disabling automatic superposition of multiple
232 structures and open structures in existing views
235 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
236 ID and annotation area margins can be click-dragged to
240 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
244 <!-- JAL-2759 -->Improved performance for large alignments
245 and lots of hidden columns
248 <!-- JAL-2593 -->Improved performance when rendering lots
249 of features (particularly when transparency is disabled)
254 <td><div align="left">
257 <!-- JAL-2899 -->Structure and Overview aren't updated
258 when Colour By Annotation threshold slider is adjusted
261 <!-- JAL-2778 -->Slow redraw when Overview panel shown
262 overlapping alignment panel
265 <!-- JAL-2929 -->Overview doesn't show end of unpadded
269 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
270 improved: CDS not handled correctly if transcript has no
274 <!-- JAL-2321 -->Secondary structure and temperature
275 factor annotation not added to sequence when local PDB
276 file associated with it by drag'n'drop or structure
280 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
281 dialog doesn't import PDB files dropped on an alignment
284 <!-- JAL-2666 -->Linked scrolling via protein horizontal
285 scroll bar doesn't work for some CDS/Protein views
288 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
289 Java 1.8u153 onwards and Java 1.9u4+.
292 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
293 columns in annotation row
296 <!-- JAL-2913 -->Preferences panel's ID Width control is not
297 honored in batch mode
300 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
301 for structures added to existing Jmol view
304 <!-- JAL-2223 -->'View Mappings' includes duplicate
305 entries after importing project with multiple views
308 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
309 protein sequences via SIFTS from associated PDB entries
310 with negative residue numbers or missing residues fails
313 <!-- JAL-2952 -->Exception when shading sequence with negative
314 Temperature Factor values from annotated PDB files (e.g.
315 as generated by CONSURF)
318 <!-- JAL-2920 -->Uniprot 'sequence variant' features
319 tooltip doesn't include a text description of mutation
322 <!-- JAL-2922 -->Invert displayed features very slow when
323 structure and/or overview windows are also shown
326 <!-- JAL-2954 -->Selecting columns from highlighted regions
327 very slow for alignments with large numbers of sequences
330 <!-- JAL-2925 -->Copy Consensus fails for group consensus
331 with 'StringIndexOutOfBounds'
334 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
335 platforms running Java 10
338 <!-- JAL-2960 -->Adding a structure to existing structure
339 view appears to do nothing because the view is hidden behind the alignment view
345 <!-- JAL-2926 -->Copy consensus sequence option in applet
346 should copy the group consensus when popup is opened on it
352 <!-- JAL-2913 -->Fixed ID width preference is not respected
355 <em>New Known Defects</em>
358 <!-- JAL-2973 --> Exceptions occasionally raised when
359 editing a large alignment and overview is displayed
362 <!-- JAL-2974 -->'Overview updating' progress bar is shown
363 repeatedly after a series of edits even when the overview
364 is no longer reflecting updates
367 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
368 structures for protein subsequence (if 'Trim Retrieved
369 Sequences' enabled) or Ensembl isoforms (Workaround in
370 2.10.4 is to fail back to N&W mapping)
377 <td width="60" nowrap>
379 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
382 <td><div align="left">
383 <ul><li>Updated Certum Codesigning Certificate
384 (Valid till 30th November 2018)</li></ul></div></td>
385 <td><div align="left">
388 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
389 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
390 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
391 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
392 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
393 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
394 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
400 <td width="60" nowrap>
402 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
405 <td><div align="left">
409 <!-- JAL-2446 -->Faster and more efficient management and
410 rendering of sequence features
413 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
414 429 rate limit request hander
417 <!-- JAL-2773 -->Structure views don't get updated unless
418 their colours have changed
421 <!-- JAL-2495 -->All linked sequences are highlighted for
422 a structure mousover (Jmol) or selection (Chimera)
425 <!-- JAL-2790 -->'Cancel' button in progress bar for
426 JABAWS AACon, RNAAliFold and Disorder prediction jobs
429 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
430 view from Ensembl locus cross-references
433 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
437 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
438 feature can be disabled
441 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
442 PDB easier retrieval of sequences for lists of IDs
445 <!-- JAL-2758 -->Short names for sequences retrieved from
451 <li>Groovy interpreter updated to 2.4.12</li>
452 <li>Example groovy script for generating a matrix of
453 percent identity scores for current alignment.</li>
455 <em>Testing and Deployment</em>
458 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
462 <td><div align="left">
466 <!-- JAL-2643 -->Pressing tab after updating the colour
467 threshold text field doesn't trigger an update to the
471 <!-- JAL-2682 -->Race condition when parsing sequence ID
475 <!-- JAL-2608 -->Overview windows are also closed when
476 alignment window is closed
479 <!-- JAL-2548 -->Export of features doesn't always respect
483 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
484 takes a long time in Cursor mode
490 <!-- JAL-2777 -->Structures with whitespace chainCode
491 cannot be viewed in Chimera
494 <!-- JAL-2728 -->Protein annotation panel too high in
498 <!-- JAL-2757 -->Can't edit the query after the server
499 error warning icon is shown in Uniprot and PDB Free Text
503 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
506 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
509 <!-- JAL-2739 -->Hidden column marker in last column not
510 rendered when switching back from Wrapped to normal view
513 <!-- JAL-2768 -->Annotation display corrupted when
514 scrolling right in unwapped alignment view
517 <!-- JAL-2542 -->Existing features on subsequence
518 incorrectly relocated when full sequence retrieved from
522 <!-- JAL-2733 -->Last reported memory still shown when
523 Desktop->Show Memory is unticked (OSX only)
526 <!-- JAL-2658 -->Amend Features dialog doesn't allow
527 features of same type and group to be selected for
531 <!-- JAL-2524 -->Jalview becomes sluggish in wide
532 alignments when hidden columns are present
535 <!-- JAL-2392 -->Jalview freezes when loading and
536 displaying several structures
539 <!-- JAL-2732 -->Black outlines left after resizing or
543 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
544 within the Jalview desktop on OSX
547 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
548 when in wrapped alignment mode
551 <!-- JAL-2636 -->Scale mark not shown when close to right
552 hand end of alignment
555 <!-- JAL-2684 -->Pairwise alignment of selected regions of
556 each selected sequence do not have correct start/end
560 <!-- JAL-2793 -->Alignment ruler height set incorrectly
561 after canceling the Alignment Window's Font dialog
564 <!-- JAL-2036 -->Show cross-references not enabled after
565 restoring project until a new view is created
568 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
569 URL links appears when only default EMBL-EBI link is
570 configured (since 2.10.2b2)
573 <!-- JAL-2775 -->Overview redraws whole window when box
577 <!-- JAL-2225 -->Structure viewer doesn't map all chains
578 in a multi-chain structure when viewing alignment
579 involving more than one chain (since 2.10)
582 <!-- JAL-2811 -->Double residue highlights in cursor mode
583 if new selection moves alignment window
586 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
587 arrow key in cursor mode to pass hidden column marker
590 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
591 that produces correctly annotated transcripts and products
594 <!-- JAL-2776 -->Toggling a feature group after first time
595 doesn't update associated structure view
598 <em>Applet</em><br />
601 <!-- JAL-2687 -->Concurrent modification exception when
602 closing alignment panel
605 <em>BioJSON</em><br />
608 <!-- JAL-2546 -->BioJSON export does not preserve
609 non-positional features
612 <em>New Known Issues</em>
615 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
616 sequence features correctly (for many previous versions of
620 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
621 using cursor in wrapped panel other than top
624 <!-- JAL-2791 -->Select columns containing feature ignores
625 graduated colour threshold
628 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
629 always preserve numbering and sequence features
632 <em>Known Java 9 Issues</em>
635 <!-- JAL-2902 -->Groovy Console very slow to open and is
636 not responsive when entering characters (Webstart, Java
643 <td width="60" nowrap>
645 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
646 <em>2/10/2017</em></strong>
649 <td><div align="left">
650 <em>New features in Jalview Desktop</em>
653 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
655 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
659 <td><div align="left">
663 <td width="60" nowrap>
665 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
666 <em>7/9/2017</em></strong>
669 <td><div align="left">
673 <!-- JAL-2588 -->Show gaps in overview window by colouring
674 in grey (sequences used to be coloured grey, and gaps were
678 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
682 <!-- JAL-2587 -->Overview updates immediately on increase
683 in size and progress bar shown as higher resolution
684 overview is recalculated
689 <td><div align="left">
693 <!-- JAL-2664 -->Overview window redraws every hidden
694 column region row by row
697 <!-- JAL-2681 -->duplicate protein sequences shown after
698 retrieving Ensembl crossrefs for sequences from Uniprot
701 <!-- JAL-2603 -->Overview window throws NPE if show boxes
702 format setting is unticked
705 <!-- JAL-2610 -->Groups are coloured wrongly in overview
706 if group has show boxes format setting unticked
709 <!-- JAL-2672,JAL-2665 -->Redraw problems when
710 autoscrolling whilst dragging current selection group to
711 include sequences and columns not currently displayed
714 <!-- JAL-2691 -->Not all chains are mapped when multimeric
715 assemblies are imported via CIF file
718 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
719 displayed when threshold or conservation colouring is also
723 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
727 <!-- JAL-2673 -->Jalview continues to scroll after
728 dragging a selected region off the visible region of the
732 <!-- JAL-2724 -->Cannot apply annotation based
733 colourscheme to all groups in a view
736 <!-- JAL-2511 -->IDs don't line up with sequences
737 initially after font size change using the Font chooser or
744 <td width="60" nowrap>
746 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
749 <td><div align="left">
750 <em>Calculations</em>
754 <!-- JAL-1933 -->Occupancy annotation row shows number of
755 ungapped positions in each column of the alignment.
758 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
759 a calculation dialog box
762 <!-- JAL-2379 -->Revised implementation of PCA for speed
763 and memory efficiency (~30x faster)
766 <!-- JAL-2403 -->Revised implementation of sequence
767 similarity scores as used by Tree, PCA, Shading Consensus
768 and other calculations
771 <!-- JAL-2416 -->Score matrices are stored as resource
772 files within the Jalview codebase
775 <!-- JAL-2500 -->Trees computed on Sequence Feature
776 Similarity may have different topology due to increased
783 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
784 model for alignments and groups
787 <!-- JAL-384 -->Custom shading schemes created via groovy
794 <!-- JAL-2526 -->Efficiency improvements for interacting
795 with alignment and overview windows
798 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
802 <!-- JAL-2388 -->Hidden columns and sequences can be
806 <!-- JAL-2611 -->Click-drag in visible area allows fine
807 adjustment of visible position
811 <em>Data import/export</em>
814 <!-- JAL-2535 -->Posterior probability annotation from
815 Stockholm files imported as sequence associated annotation
818 <!-- JAL-2507 -->More robust per-sequence positional
819 annotation input/output via stockholm flatfile
822 <!-- JAL-2533 -->Sequence names don't include file
823 extension when importing structure files without embedded
824 names or PDB accessions
827 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
828 format sequence substitution matrices
831 <em>User Interface</em>
834 <!-- JAL-2447 --> Experimental Features Checkbox in
835 Desktop's Tools menu to hide or show untested features in
839 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
840 via Overview or sequence motif search operations
843 <!-- JAL-2547 -->Amend sequence features dialog box can be
844 opened by double clicking gaps within sequence feature
848 <!-- JAL-1476 -->Status bar message shown when not enough
849 aligned positions were available to create a 3D structure
853 <em>3D Structure</em>
856 <!-- JAL-2430 -->Hidden regions in alignment views are not
857 coloured in linked structure views
860 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
861 file-based command exchange
864 <!-- JAL-2375 -->Structure chooser automatically shows
865 Cached Structures rather than querying the PDBe if
866 structures are already available for sequences
869 <!-- JAL-2520 -->Structures imported via URL are cached in
870 the Jalview project rather than downloaded again when the
874 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
875 to transfer Chimera's structure attributes as Jalview
876 features, and vice-versa (<strong>Experimental
880 <em>Web Services</em>
883 <!-- JAL-2549 -->Updated JABAWS client to v2.2
886 <!-- JAL-2335 -->Filter non-standard amino acids and
887 nucleotides when submitting to AACon and other MSA
891 <!-- JAL-2316, -->URLs for viewing database
892 cross-references provided by identifiers.org and the
900 <!-- JAL-2344 -->FileFormatI interface for describing and
901 identifying file formats (instead of String constants)
904 <!-- JAL-2228 -->FeatureCounter script refactored for
905 efficiency when counting all displayed features (not
906 backwards compatible with 2.10.1)
909 <em>Example files</em>
912 <!-- JAL-2631 -->Graduated feature colour style example
913 included in the example feature file
916 <em>Documentation</em>
919 <!-- JAL-2339 -->Release notes reformatted for readability
920 with the built-in Java help viewer
923 <!-- JAL-1644 -->Find documentation updated with 'search
924 sequence description' option
930 <!-- JAL-2485, -->External service integration tests for
931 Uniprot REST Free Text Search Client
934 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
937 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
942 <td><div align="left">
943 <em>Calculations</em>
946 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
947 matrix - C->R should be '-3'<br />Old matrix restored
948 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
950 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
951 Jalview's treatment of gaps in PCA and substitution matrix
952 based Tree calculations.<br /> <br />In earlier versions
953 of Jalview, gaps matching gaps were penalised, and gaps
954 matching non-gaps penalised even more. In the PCA
955 calculation, gaps were actually treated as non-gaps - so
956 different costs were applied, which meant Jalview's PCAs
957 were different to those produced by SeqSpace.<br />Jalview
958 now treats gaps in the same way as SeqSpace (ie it scores
959 them as 0). <br /> <br />Enter the following in the
960 Groovy console to restore pre-2.10.2 behaviour:<br />
961 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
962 // for 2.10.1 mode <br />
963 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
964 // to restore 2.10.2 mode <br /> <br /> <em>Note:
965 these settings will affect all subsequent tree and PCA
966 calculations (not recommended)</em></li>
968 <!-- JAL-2424 -->Fixed off-by-one bug that affected
969 scaling of branch lengths for trees computed using
970 Sequence Feature Similarity.
973 <!-- JAL-2377 -->PCA calculation could hang when
974 generating output report when working with highly
978 <!-- JAL-2544 --> Sort by features includes features to
979 right of selected region when gaps present on right-hand
983 <em>User Interface</em>
986 <!-- JAL-2346 -->Reopening Colour by annotation dialog
987 doesn't reselect a specific sequence's associated
988 annotation after it was used for colouring a view
991 <!-- JAL-2419 -->Current selection lost if popup menu
992 opened on a region of alignment without groups
995 <!-- JAL-2374 -->Popup menu not always shown for regions
996 of an alignment with overlapping groups
999 <!-- JAL-2310 -->Finder double counts if both a sequence's
1000 name and description match
1003 <!-- JAL-2370 -->Hiding column selection containing two
1004 hidden regions results in incorrect hidden regions
1007 <!-- JAL-2386 -->'Apply to all groups' setting when
1008 changing colour does not apply Conservation slider value
1012 <!-- JAL-2373 -->Percentage identity and conservation menu
1013 items do not show a tick or allow shading to be disabled
1016 <!-- JAL-2385 -->Conservation shading or PID threshold
1017 lost when base colourscheme changed if slider not visible
1020 <!-- JAL-2547 -->Sequence features shown in tooltip for
1021 gaps before start of features
1024 <!-- JAL-2623 -->Graduated feature colour threshold not
1025 restored to UI when feature colour is edited
1028 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1029 a time when scrolling vertically in wrapped mode.
1032 <!-- JAL-2630 -->Structure and alignment overview update
1033 as graduate feature colour settings are modified via the
1037 <!-- JAL-2034 -->Overview window doesn't always update
1038 when a group defined on the alignment is resized
1041 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1042 wrapped view result in positional status updates
1046 <!-- JAL-2563 -->Status bar doesn't show position for
1047 ambiguous amino acid and nucleotide symbols
1050 <!-- JAL-2602 -->Copy consensus sequence failed if
1051 alignment included gapped columns
1054 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1055 widgets don't permanently disappear
1058 <!-- JAL-2503 -->Cannot select or filter quantitative
1059 annotation that are shown only as column labels (e.g.
1060 T-Coffee column reliability scores)
1063 <!-- JAL-2594 -->Exception thrown if trying to create a
1064 sequence feature on gaps only
1067 <!-- JAL-2504 -->Features created with 'New feature'
1068 button from a Find inherit previously defined feature type
1069 rather than the Find query string
1072 <!-- JAL-2423 -->incorrect title in output window when
1073 exporting tree calculated in Jalview
1076 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1077 and then revealing them reorders sequences on the
1081 <!-- JAL-964 -->Group panel in sequence feature settings
1082 doesn't update to reflect available set of groups after
1083 interactively adding or modifying features
1086 <!-- JAL-2225 -->Sequence Database chooser unusable on
1090 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1091 only excluded gaps in current sequence and ignored
1098 <!-- JAL-2421 -->Overview window visible region moves
1099 erratically when hidden rows or columns are present
1102 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1103 Structure Viewer's colour menu don't correspond to
1107 <!-- JAL-2405 -->Protein specific colours only offered in
1108 colour and group colour menu for protein alignments
1111 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1112 reflect currently selected view or group's shading
1116 <!-- JAL-2624 -->Feature colour thresholds not respected
1117 when rendered on overview and structures when opacity at
1121 <!-- JAL-2589 -->User defined gap colour not shown in
1122 overview when features overlaid on alignment
1125 <em>Data import/export</em>
1128 <!-- JAL-2576 -->Very large alignments take a long time to
1132 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1133 added after a sequence was imported are not written to
1137 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1138 when importing RNA secondary structure via Stockholm
1141 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1142 not shown in correct direction for simple pseudoknots
1145 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1146 with lightGray or darkGray via features file (but can
1150 <!-- JAL-2383 -->Above PID colour threshold not recovered
1151 when alignment view imported from project
1154 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1155 structure and sequences extracted from structure files
1156 imported via URL and viewed in Jmol
1159 <!-- JAL-2520 -->Structures loaded via URL are saved in
1160 Jalview Projects rather than fetched via URL again when
1161 the project is loaded and the structure viewed
1164 <em>Web Services</em>
1167 <!-- JAL-2519 -->EnsemblGenomes example failing after
1168 release of Ensembl v.88
1171 <!-- JAL-2366 -->Proxy server address and port always
1172 appear enabled in Preferences->Connections
1175 <!-- JAL-2461 -->DAS registry not found exceptions
1176 removed from console output
1179 <!-- JAL-2582 -->Cannot retrieve protein products from
1180 Ensembl by Peptide ID
1183 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1184 created from SIFTs, and spurious 'Couldn't open structure
1185 in Chimera' errors raised after April 2017 update (problem
1186 due to 'null' string rather than empty string used for
1187 residues with no corresponding PDB mapping).
1190 <em>Application UI</em>
1193 <!-- JAL-2361 -->User Defined Colours not added to Colour
1197 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1198 case' residues (button in colourscheme editor debugged and
1199 new documentation and tooltips added)
1202 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1203 doesn't restore group-specific text colour thresholds
1206 <!-- JAL-2243 -->Feature settings panel does not update as
1207 new features are added to alignment
1210 <!-- JAL-2532 -->Cancel in feature settings reverts
1211 changes to feature colours via the Amend features dialog
1214 <!-- JAL-2506 -->Null pointer exception when attempting to
1215 edit graduated feature colour via amend features dialog
1219 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1220 selection menu changes colours of alignment views
1223 <!-- JAL-2426 -->Spurious exceptions in console raised
1224 from alignment calculation workers after alignment has
1228 <!-- JAL-1608 -->Typo in selection popup menu - Create
1229 groups now 'Create Group'
1232 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1233 Create/Undefine group doesn't always work
1236 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1237 shown again after pressing 'Cancel'
1240 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1241 adjusts start position in wrap mode
1244 <!-- JAL-2563 -->Status bar doesn't show positions for
1245 ambiguous amino acids
1248 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1249 CDS/Protein view after CDS sequences added for aligned
1253 <!-- JAL-2592 -->User defined colourschemes called 'User
1254 Defined' don't appear in Colours menu
1260 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1261 score models doesn't always result in an updated PCA plot
1264 <!-- JAL-2442 -->Features not rendered as transparent on
1265 overview or linked structure view
1268 <!-- JAL-2372 -->Colour group by conservation doesn't
1272 <!-- JAL-2517 -->Hitting Cancel after applying
1273 user-defined colourscheme doesn't restore original
1280 <!-- JAL-2314 -->Unit test failure:
1281 jalview.ws.jabaws.RNAStructExportImport setup fails
1284 <!-- JAL-2307 -->Unit test failure:
1285 jalview.ws.sifts.SiftsClientTest due to compatibility
1286 problems with deep array comparison equality asserts in
1287 successive versions of TestNG
1290 <!-- JAL-2479 -->Relocated StructureChooserTest and
1291 ParameterUtilsTest Unit tests to Network suite
1294 <em>New Known Issues</em>
1297 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1298 phase after a sequence motif find operation
1301 <!-- JAL-2550 -->Importing annotation file with rows
1302 containing just upper and lower case letters are
1303 interpreted as WUSS RNA secondary structure symbols
1306 <!-- JAL-2590 -->Cannot load and display Newick trees
1307 reliably from eggnog Ortholog database
1310 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1311 containing features of type Highlight' when 'B' is pressed
1312 to mark columns containing highlighted regions.
1315 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1316 doesn't always add secondary structure annotation.
1321 <td width="60" nowrap>
1322 <div align="center">
1323 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1326 <td><div align="left">
1330 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1331 for all consensus calculations
1334 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1337 <li>Updated Jalview's Certum code signing certificate
1340 <em>Application</em>
1343 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1344 set of database cross-references, sorted alphabetically
1347 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1348 from database cross references. Users with custom links
1349 will receive a <a href="webServices/urllinks.html#warning">warning
1350 dialog</a> asking them to update their preferences.
1353 <!-- JAL-2287-->Cancel button and escape listener on
1354 dialog warning user about disconnecting Jalview from a
1358 <!-- JAL-2320-->Jalview's Chimera control window closes if
1359 the Chimera it is connected to is shut down
1362 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1363 columns menu item to mark columns containing highlighted
1364 regions (e.g. from structure selections or results of a
1368 <!-- JAL-2284-->Command line option for batch-generation
1369 of HTML pages rendering alignment data with the BioJS
1379 <!-- JAL-2286 -->Columns with more than one modal residue
1380 are not coloured or thresholded according to percent
1381 identity (first observed in Jalview 2.8.2)
1384 <!-- JAL-2301 -->Threonine incorrectly reported as not
1388 <!-- JAL-2318 -->Updates to documentation pages (above PID
1389 threshold, amino acid properties)
1392 <!-- JAL-2292 -->Lower case residues in sequences are not
1393 reported as mapped to residues in a structure file in the
1397 <!--JAL-2324 -->Identical features with non-numeric scores
1398 could be added multiple times to a sequence
1401 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1402 bond features shown as two highlighted residues rather
1403 than a range in linked structure views, and treated
1404 correctly when selecting and computing trees from features
1407 <!-- JAL-2281-->Custom URL links for database
1408 cross-references are matched to database name regardless
1413 <em>Application</em>
1416 <!-- JAL-2282-->Custom URL links for specific database
1417 names without regular expressions also offer links from
1421 <!-- JAL-2315-->Removing a single configured link in the
1422 URL links pane in Connections preferences doesn't actually
1423 update Jalview configuration
1426 <!-- JAL-2272-->CTRL-Click on a selected region to open
1427 the alignment area popup menu doesn't work on El-Capitan
1430 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1431 files with similarly named sequences if dropped onto the
1435 <!-- JAL-2312 -->Additional mappings are shown for PDB
1436 entries where more chains exist in the PDB accession than
1437 are reported in the SIFTS file
1440 <!-- JAL-2317-->Certain structures do not get mapped to
1441 the structure view when displayed with Chimera
1444 <!-- JAL-2317-->No chains shown in the Chimera view
1445 panel's View->Show Chains submenu
1448 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1449 work for wrapped alignment views
1452 <!--JAL-2197 -->Rename UI components for running JPred
1453 predictions from 'JNet' to 'JPred'
1456 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1457 corrupted when annotation panel vertical scroll is not at
1458 first annotation row
1461 <!--JAL-2332 -->Attempting to view structure for Hen
1462 lysozyme results in a PDB Client error dialog box
1465 <!-- JAL-2319 -->Structure View's mapping report switched
1466 ranges for PDB and sequence for SIFTS
1469 SIFTS 'Not_Observed' residues mapped to non-existant
1473 <!-- <em>New Known Issues</em>
1480 <td width="60" nowrap>
1481 <div align="center">
1482 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1483 <em>25/10/2016</em></strong>
1486 <td><em>Application</em>
1488 <li>3D Structure chooser opens with 'Cached structures'
1489 view if structures already loaded</li>
1490 <li>Progress bar reports models as they are loaded to
1491 structure views</li>
1497 <li>Colour by conservation always enabled and no tick
1498 shown in menu when BLOSUM or PID shading applied</li>
1499 <li>FER1_ARATH and FER2_ARATH labels were switched in
1500 example sequences/projects/trees</li>
1502 <em>Application</em>
1504 <li>Jalview projects with views of local PDB structure
1505 files saved on Windows cannot be opened on OSX</li>
1506 <li>Multiple structure views can be opened and superposed
1507 without timeout for structures with multiple models or
1508 multiple sequences in alignment</li>
1509 <li>Cannot import or associated local PDB files without a
1510 PDB ID HEADER line</li>
1511 <li>RMSD is not output in Jmol console when superposition
1513 <li>Drag and drop of URL from Browser fails for Linux and
1514 OSX versions earlier than El Capitan</li>
1515 <li>ENA client ignores invalid content from ENA server</li>
1516 <li>Exceptions are not raised in console when ENA client
1517 attempts to fetch non-existent IDs via Fetch DB Refs UI
1519 <li>Exceptions are not raised in console when a new view
1520 is created on the alignment</li>
1521 <li>OSX right-click fixed for group selections: CMD-click
1522 to insert/remove gaps in groups and CTRL-click to open group
1525 <em>Build and deployment</em>
1527 <li>URL link checker now copes with multi-line anchor
1530 <em>New Known Issues</em>
1532 <li>Drag and drop from URL links in browsers do not work
1539 <td width="60" nowrap>
1540 <div align="center">
1541 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1544 <td><em>General</em>
1547 <!-- JAL-2124 -->Updated Spanish translations.
1550 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1551 for importing structure data to Jalview. Enables mmCIF and
1555 <!-- JAL-192 --->Alignment ruler shows positions relative to
1559 <!-- JAL-2202 -->Position/residue shown in status bar when
1560 mousing over sequence associated annotation
1563 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1567 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1568 '()', canonical '[]' and invalid '{}' base pair populations
1572 <!-- JAL-2092 -->Feature settings popup menu options for
1573 showing or hiding columns containing a feature
1576 <!-- JAL-1557 -->Edit selected group by double clicking on
1577 group and sequence associated annotation labels
1580 <!-- JAL-2236 -->Sequence name added to annotation label in
1581 select/hide columns by annotation and colour by annotation
1585 </ul> <em>Application</em>
1588 <!-- JAL-2050-->Automatically hide introns when opening a
1589 gene/transcript view
1592 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1596 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1597 structure mappings with the EMBL-EBI PDBe SIFTS database
1600 <!-- JAL-2079 -->Updated download sites used for Rfam and
1601 Pfam sources to xfam.org
1604 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1607 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1608 over sequences in Jalview
1611 <!-- JAL-2027-->Support for reverse-complement coding
1612 regions in ENA and EMBL
1615 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1616 for record retrieval via ENA rest API
1619 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1623 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1624 groovy script execution
1627 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1628 alignment window's Calculate menu
1631 <!-- JAL-1812 -->Allow groovy scripts that call
1632 Jalview.getAlignFrames() to run in headless mode
1635 <!-- JAL-2068 -->Support for creating new alignment
1636 calculation workers from groovy scripts
1639 <!-- JAL-1369 --->Store/restore reference sequence in
1643 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1644 associations are now saved/restored from project
1647 <!-- JAL-1993 -->Database selection dialog always shown
1648 before sequence fetcher is opened
1651 <!-- JAL-2183 -->Double click on an entry in Jalview's
1652 database chooser opens a sequence fetcher
1655 <!-- JAL-1563 -->Free-text search client for UniProt using
1656 the UniProt REST API
1659 <!-- JAL-2168 -->-nonews command line parameter to prevent
1660 the news reader opening
1663 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1664 querying stored in preferences
1667 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1671 <!-- JAL-1977-->Tooltips shown on database chooser
1674 <!-- JAL-391 -->Reverse complement function in calculate
1675 menu for nucleotide sequences
1678 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1679 and feature counts preserves alignment ordering (and
1680 debugged for complex feature sets).
1683 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1684 viewing structures with Jalview 2.10
1687 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1688 genome, transcript CCDS and gene ids via the Ensembl and
1689 Ensembl Genomes REST API
1692 <!-- JAL-2049 -->Protein sequence variant annotation
1693 computed for 'sequence_variant' annotation on CDS regions
1697 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1701 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1702 Ref Fetcher fails to match, or otherwise updates sequence
1703 data from external database records.
1706 <!-- JAL-2154 -->Revised Jalview Project format for
1707 efficient recovery of sequence coding and alignment
1708 annotation relationships.
1710 </ul> <!-- <em>Applet</em>
1721 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1725 <!-- JAL-2018-->Export features in Jalview format (again)
1726 includes graduated colourschemes
1729 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1730 working with big alignments and lots of hidden columns
1733 <!-- JAL-2053-->Hidden column markers not always rendered
1734 at right of alignment window
1737 <!-- JAL-2067 -->Tidied up links in help file table of
1741 <!-- JAL-2072 -->Feature based tree calculation not shown
1745 <!-- JAL-2075 -->Hidden columns ignored during feature
1746 based tree calculation
1749 <!-- JAL-2065 -->Alignment view stops updating when show
1750 unconserved enabled for group on alignment
1753 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1757 <!-- JAL-2146 -->Alignment column in status incorrectly
1758 shown as "Sequence position" when mousing over
1762 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1763 hidden columns present
1766 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1767 user created annotation added to alignment
1770 <!-- JAL-1841 -->RNA Structure consensus only computed for
1771 '()' base pair annotation
1774 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1775 in zero scores for all base pairs in RNA Structure
1779 <!-- JAL-2174-->Extend selection with columns containing
1783 <!-- JAL-2275 -->Pfam format writer puts extra space at
1784 beginning of sequence
1787 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1791 <!-- JAL-2238 -->Cannot create groups on an alignment from
1792 from a tree when t-coffee scores are shown
1795 <!-- JAL-1836,1967 -->Cannot import and view PDB
1796 structures with chains containing negative resnums (4q4h)
1799 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1803 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1804 to Clustal, PIR and PileUp output
1807 <!-- JAL-2008 -->Reordering sequence features that are
1808 not visible causes alignment window to repaint
1811 <!-- JAL-2006 -->Threshold sliders don't work in
1812 graduated colour and colour by annotation row for e-value
1813 scores associated with features and annotation rows
1816 <!-- JAL-1797 -->amino acid physicochemical conservation
1817 calculation should be case independent
1820 <!-- JAL-2173 -->Remove annotation also updates hidden
1824 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1825 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1826 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1829 <!-- JAL-2065 -->Null pointer exceptions and redraw
1830 problems when reference sequence defined and 'show
1831 non-conserved' enabled
1834 <!-- JAL-1306 -->Quality and Conservation are now shown on
1835 load even when Consensus calculation is disabled
1838 <!-- JAL-1932 -->Remove right on penultimate column of
1839 alignment does nothing
1842 <em>Application</em>
1845 <!-- JAL-1552-->URLs and links can't be imported by
1846 drag'n'drop on OSX when launched via webstart (note - not
1847 yet fixed for El Capitan)
1850 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1851 output when running on non-gb/us i18n platforms
1854 <!-- JAL-1944 -->Error thrown when exporting a view with
1855 hidden sequences as flat-file alignment
1858 <!-- JAL-2030-->InstallAnywhere distribution fails when
1862 <!-- JAL-2080-->Jalview very slow to launch via webstart
1863 (also hotfix for 2.9.0b2)
1866 <!-- JAL-2085 -->Cannot save project when view has a
1867 reference sequence defined
1870 <!-- JAL-1011 -->Columns are suddenly selected in other
1871 alignments and views when revealing hidden columns
1874 <!-- JAL-1989 -->Hide columns not mirrored in complement
1875 view in a cDNA/Protein splitframe
1878 <!-- JAL-1369 -->Cannot save/restore representative
1879 sequence from project when only one sequence is
1883 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1884 in Structure Chooser
1887 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1888 structure consensus didn't refresh annotation panel
1891 <!-- JAL-1962 -->View mapping in structure view shows
1892 mappings between sequence and all chains in a PDB file
1895 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1896 dialogs format columns correctly, don't display array
1897 data, sort columns according to type
1900 <!-- JAL-1975 -->Export complete shown after destination
1901 file chooser is cancelled during an image export
1904 <!-- JAL-2025 -->Error when querying PDB Service with
1905 sequence name containing special characters
1908 <!-- JAL-2024 -->Manual PDB structure querying should be
1912 <!-- JAL-2104 -->Large tooltips with broken HTML
1913 formatting don't wrap
1916 <!-- JAL-1128 -->Figures exported from wrapped view are
1917 truncated so L looks like I in consensus annotation
1920 <!-- JAL-2003 -->Export features should only export the
1921 currently displayed features for the current selection or
1925 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1926 after fetching cross-references, and restoring from
1930 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1931 followed in the structure viewer
1934 <!-- JAL-2163 -->Titles for individual alignments in
1935 splitframe not restored from project
1938 <!-- JAL-2145 -->missing autocalculated annotation at
1939 trailing end of protein alignment in transcript/product
1940 splitview when pad-gaps not enabled by default
1943 <!-- JAL-1797 -->amino acid physicochemical conservation
1947 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1948 article has been read (reopened issue due to
1949 internationalisation problems)
1952 <!-- JAL-1960 -->Only offer PDB structures in structure
1953 viewer based on sequence name, PDB and UniProt
1958 <!-- JAL-1976 -->No progress bar shown during export of
1962 <!-- JAL-2213 -->Structures not always superimposed after
1963 multiple structures are shown for one or more sequences.
1966 <!-- JAL-1370 -->Reference sequence characters should not
1967 be replaced with '.' when 'Show unconserved' format option
1971 <!-- JAL-1823 -->Cannot specify chain code when entering
1972 specific PDB id for sequence
1975 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1976 'Export hidden sequences' is enabled, but 'export hidden
1977 columns' is disabled.
1980 <!--JAL-2026-->Best Quality option in structure chooser
1981 selects lowest rather than highest resolution structures
1985 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1986 to sequence mapping in 'View Mappings' report
1989 <!-- JAL-2284 -->Unable to read old Jalview projects that
1990 contain non-XML data added after Jalvew wrote project.
1993 <!-- JAL-2118 -->Newly created annotation row reorders
1994 after clicking on it to create new annotation for a
1998 <!-- JAL-1980 -->Null Pointer Exception raised when
1999 pressing Add on an orphaned cut'n'paste window.
2001 <!-- may exclude, this is an external service stability issue JAL-1941
2002 -- > RNA 3D structure not added via DSSR service</li> -->
2007 <!-- JAL-2151 -->Incorrect columns are selected when
2008 hidden columns present before start of sequence
2011 <!-- JAL-1986 -->Missing dependencies on applet pages
2015 <!-- JAL-1947 -->Overview pixel size changes when
2016 sequences are hidden in applet
2019 <!-- JAL-1996 -->Updated instructions for applet
2020 deployment on examples pages.
2027 <td width="60" nowrap>
2028 <div align="center">
2029 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2030 <em>16/10/2015</em></strong>
2033 <td><em>General</em>
2035 <li>Time stamps for signed Jalview application and applet
2040 <em>Application</em>
2042 <li>Duplicate group consensus and conservation rows
2043 shown when tree is partitioned</li>
2044 <li>Erratic behaviour when tree partitions made with
2045 multiple cDNA/Protein split views</li>
2051 <td width="60" nowrap>
2052 <div align="center">
2053 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2054 <em>8/10/2015</em></strong>
2057 <td><em>General</em>
2059 <li>Updated Spanish translations of localized text for
2061 </ul> <em>Application</em>
2063 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2064 <li>Signed OSX InstallAnywhere installer<br></li>
2065 <li>Support for per-sequence based annotations in BioJSON</li>
2066 </ul> <em>Applet</em>
2068 <li>Split frame example added to applet examples page</li>
2069 </ul> <em>Build and Deployment</em>
2072 <!-- JAL-1888 -->New ant target for running Jalview's test
2080 <li>Mapping of cDNA to protein in split frames
2081 incorrect when sequence start > 1</li>
2082 <li>Broken images in filter column by annotation dialog
2084 <li>Feature colours not parsed from features file</li>
2085 <li>Exceptions and incomplete link URLs recovered when
2086 loading a features file containing HTML tags in feature
2090 <em>Application</em>
2092 <li>Annotations corrupted after BioJS export and
2094 <li>Incorrect sequence limits after Fetch DB References
2095 with 'trim retrieved sequences'</li>
2096 <li>Incorrect warning about deleting all data when
2097 deleting selected columns</li>
2098 <li>Patch to build system for shipping properly signed
2099 JNLP templates for webstart launch</li>
2100 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2101 unreleased structures for download or viewing</li>
2102 <li>Tab/space/return keystroke operation of EMBL-PDBe
2103 fetcher/viewer dialogs works correctly</li>
2104 <li>Disabled 'minimise' button on Jalview windows
2105 running on OSX to workaround redraw hang bug</li>
2106 <li>Split cDNA/Protein view position and geometry not
2107 recovered from jalview project</li>
2108 <li>Initial enabled/disabled state of annotation menu
2109 sorter 'show autocalculated first/last' corresponds to
2111 <li>Restoring of Clustal, RNA Helices and T-Coffee
2112 color schemes from BioJSON</li>
2116 <li>Reorder sequences mirrored in cDNA/Protein split
2118 <li>Applet with Jmol examples not loading correctly</li>
2124 <td><div align="center">
2125 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2127 <td><em>General</em>
2129 <li>Linked visualisation and analysis of DNA and Protein
2132 <li>Translated cDNA alignments shown as split protein
2133 and DNA alignment views</li>
2134 <li>Codon consensus annotation for linked protein and
2135 cDNA alignment views</li>
2136 <li>Link cDNA or Protein product sequences by loading
2137 them onto Protein or cDNA alignments</li>
2138 <li>Reconstruct linked cDNA alignment from aligned
2139 protein sequences</li>
2142 <li>Jmol integration updated to Jmol v14.2.14</li>
2143 <li>Import and export of Jalview alignment views as <a
2144 href="features/bioJsonFormat.html">BioJSON</a></li>
2145 <li>New alignment annotation file statements for
2146 reference sequences and marking hidden columns</li>
2147 <li>Reference sequence based alignment shading to
2148 highlight variation</li>
2149 <li>Select or hide columns according to alignment
2151 <li>Find option for locating sequences by description</li>
2152 <li>Conserved physicochemical properties shown in amino
2153 acid conservation row</li>
2154 <li>Alignments can be sorted by number of RNA helices</li>
2155 </ul> <em>Application</em>
2157 <li>New cDNA/Protein analysis capabilities
2159 <li>Get Cross-References should open a Split Frame
2160 view with cDNA/Protein</li>
2161 <li>Detect when nucleotide sequences and protein
2162 sequences are placed in the same alignment</li>
2163 <li>Split cDNA/Protein views are saved in Jalview
2168 <li>Use REST API to talk to Chimera</li>
2169 <li>Selected regions in Chimera are highlighted in linked
2170 Jalview windows</li>
2172 <li>VARNA RNA viewer updated to v3.93</li>
2173 <li>VARNA views are saved in Jalview Projects</li>
2174 <li>Pseudoknots displayed as Jalview RNA annotation can
2175 be shown in VARNA</li>
2177 <li>Make groups for selection uses marked columns as well
2178 as the active selected region</li>
2180 <li>Calculate UPGMA and NJ trees using sequence feature
2182 <li>New Export options
2184 <li>New Export Settings dialog to control hidden
2185 region export in flat file generation</li>
2187 <li>Export alignment views for display with the <a
2188 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2190 <li>Export scrollable SVG in HTML page</li>
2191 <li>Optional embedding of BioJSON data when exporting
2192 alignment figures to HTML</li>
2194 <li>3D structure retrieval and display
2196 <li>Free text and structured queries with the PDBe
2198 <li>PDBe Search API based discovery and selection of
2199 PDB structures for a sequence set</li>
2203 <li>JPred4 employed for protein secondary structure
2205 <li>Hide Insertions menu option to hide unaligned columns
2206 for one or a group of sequences</li>
2207 <li>Automatically hide insertions in alignments imported
2208 from the JPred4 web server</li>
2209 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2210 system on OSX<br />LGPL libraries courtesy of <a
2211 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2213 <li>changed 'View nucleotide structure' submenu to 'View
2214 VARNA 2D Structure'</li>
2215 <li>change "View protein structure" menu option to "3D
2218 </ul> <em>Applet</em>
2220 <li>New layout for applet example pages</li>
2221 <li>New parameters to enable SplitFrame view
2222 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2223 <li>New example demonstrating linked viewing of cDNA and
2224 Protein alignments</li>
2225 </ul> <em>Development and deployment</em>
2227 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2228 <li>Include installation type and git revision in build
2229 properties and console log output</li>
2230 <li>Jalview Github organisation, and new github site for
2231 storing BioJsMSA Templates</li>
2232 <li>Jalview's unit tests now managed with TestNG</li>
2235 <!-- <em>General</em>
2237 </ul> --> <!-- issues resolved --> <em>Application</em>
2239 <li>Escape should close any open find dialogs</li>
2240 <li>Typo in select-by-features status report</li>
2241 <li>Consensus RNA secondary secondary structure
2242 predictions are not highlighted in amber</li>
2243 <li>Missing gap character in v2.7 example file means
2244 alignment appears unaligned when pad-gaps is not enabled</li>
2245 <li>First switch to RNA Helices colouring doesn't colour
2246 associated structure views</li>
2247 <li>ID width preference option is greyed out when auto
2248 width checkbox not enabled</li>
2249 <li>Stopped a warning dialog from being shown when
2250 creating user defined colours</li>
2251 <li>'View Mapping' in structure viewer shows sequence
2252 mappings for just that viewer's sequences</li>
2253 <li>Workaround for superposing PDB files containing
2254 multiple models in Chimera</li>
2255 <li>Report sequence position in status bar when hovering
2256 over Jmol structure</li>
2257 <li>Cannot output gaps as '.' symbols with Selection ->
2258 output to text box</li>
2259 <li>Flat file exports of alignments with hidden columns
2260 have incorrect sequence start/end</li>
2261 <li>'Aligning' a second chain to a Chimera structure from
2263 <li>Colour schemes applied to structure viewers don't
2264 work for nucleotide</li>
2265 <li>Loading/cut'n'pasting an empty or invalid file leads
2266 to a grey/invisible alignment window</li>
2267 <li>Exported Jpred annotation from a sequence region
2268 imports to different position</li>
2269 <li>Space at beginning of sequence feature tooltips shown
2270 on some platforms</li>
2271 <li>Chimera viewer 'View | Show Chain' menu is not
2273 <li>'New View' fails with a Null Pointer Exception in
2274 console if Chimera has been opened</li>
2275 <li>Mouseover to Chimera not working</li>
2276 <li>Miscellaneous ENA XML feature qualifiers not
2278 <li>NPE in annotation renderer after 'Extract Scores'</li>
2279 <li>If two structures in one Chimera window, mouseover of
2280 either sequence shows on first structure</li>
2281 <li>'Show annotations' options should not make
2282 non-positional annotations visible</li>
2283 <li>Subsequence secondary structure annotation not shown
2284 in right place after 'view flanking regions'</li>
2285 <li>File Save As type unset when current file format is
2287 <li>Save as '.jar' option removed for saving Jalview
2289 <li>Colour by Sequence colouring in Chimera more
2291 <li>Cannot 'add reference annotation' for a sequence in
2292 several views on same alignment</li>
2293 <li>Cannot show linked products for EMBL / ENA records</li>
2294 <li>Jalview's tooltip wraps long texts containing no
2296 </ul> <em>Applet</em>
2298 <li>Jmol to JalviewLite mouseover/link not working</li>
2299 <li>JalviewLite can't import sequences with ID
2300 descriptions containing angle brackets</li>
2301 </ul> <em>General</em>
2303 <li>Cannot export and reimport RNA secondary structure
2304 via jalview annotation file</li>
2305 <li>Random helix colour palette for colour by annotation
2306 with RNA secondary structure</li>
2307 <li>Mouseover to cDNA from STOP residue in protein
2308 translation doesn't work.</li>
2309 <li>hints when using the select by annotation dialog box</li>
2310 <li>Jmol alignment incorrect if PDB file has alternate CA
2312 <li>FontChooser message dialog appears to hang after
2313 choosing 1pt font</li>
2314 <li>Peptide secondary structure incorrectly imported from
2315 annotation file when annotation display text includes 'e' or
2317 <li>Cannot set colour of new feature type whilst creating
2319 <li>cDNA translation alignment should not be sequence
2320 order dependent</li>
2321 <li>'Show unconserved' doesn't work for lower case
2323 <li>Nucleotide ambiguity codes involving R not recognised</li>
2324 </ul> <em>Deployment and Documentation</em>
2326 <li>Applet example pages appear different to the rest of
2327 www.jalview.org</li>
2328 </ul> <em>Application Known issues</em>
2330 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2331 <li>Misleading message appears after trying to delete
2333 <li>Jalview icon not shown in dock after InstallAnywhere
2334 version launches</li>
2335 <li>Fetching EMBL reference for an RNA sequence results
2336 fails with a sequence mismatch</li>
2337 <li>Corrupted or unreadable alignment display when
2338 scrolling alignment to right</li>
2339 <li>ArrayIndexOutOfBoundsException thrown when remove
2340 empty columns called on alignment with ragged gapped ends</li>
2341 <li>auto calculated alignment annotation rows do not get
2342 placed above or below non-autocalculated rows</li>
2343 <li>Jalview dekstop becomes sluggish at full screen in
2344 ultra-high resolution</li>
2345 <li>Cannot disable consensus calculation independently of
2346 quality and conservation</li>
2347 <li>Mouseover highlighting between cDNA and protein can
2348 become sluggish with more than one splitframe shown</li>
2349 </ul> <em>Applet Known Issues</em>
2351 <li>Core PDB parsing code requires Jmol</li>
2352 <li>Sequence canvas panel goes white when alignment
2353 window is being resized</li>
2359 <td><div align="center">
2360 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2362 <td><em>General</em>
2364 <li>Updated Java code signing certificate donated by
2366 <li>Features and annotation preserved when performing
2367 pairwise alignment</li>
2368 <li>RNA pseudoknot annotation can be
2369 imported/exported/displayed</li>
2370 <li>'colour by annotation' can colour by RNA and
2371 protein secondary structure</li>
2372 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2373 post-hoc with 2.9 release</em>)
2376 </ul> <em>Application</em>
2378 <li>Extract and display secondary structure for sequences
2379 with 3D structures</li>
2380 <li>Support for parsing RNAML</li>
2381 <li>Annotations menu for layout
2383 <li>sort sequence annotation rows by alignment</li>
2384 <li>place sequence annotation above/below alignment
2387 <li>Output in Stockholm format</li>
2388 <li>Internationalisation: improved Spanish (es)
2390 <li>Structure viewer preferences tab</li>
2391 <li>Disorder and Secondary Structure annotation tracks
2392 shared between alignments</li>
2393 <li>UCSF Chimera launch and linked highlighting from
2395 <li>Show/hide all sequence associated annotation rows for
2396 all or current selection</li>
2397 <li>disorder and secondary structure predictions
2398 available as dataset annotation</li>
2399 <li>Per-sequence rna helices colouring</li>
2402 <li>Sequence database accessions imported when fetching
2403 alignments from Rfam</li>
2404 <li>update VARNA version to 3.91</li>
2406 <li>New groovy scripts for exporting aligned positions,
2407 conservation values, and calculating sum of pairs scores.</li>
2408 <li>Command line argument to set default JABAWS server</li>
2409 <li>include installation type in build properties and
2410 console log output</li>
2411 <li>Updated Jalview project format to preserve dataset
2415 <!-- issues resolved --> <em>Application</em>
2417 <li>Distinguish alignment and sequence associated RNA
2418 structure in structure->view->VARNA</li>
2419 <li>Raise dialog box if user deletes all sequences in an
2421 <li>Pressing F1 results in documentation opening twice</li>
2422 <li>Sequence feature tooltip is wrapped</li>
2423 <li>Double click on sequence associated annotation
2424 selects only first column</li>
2425 <li>Redundancy removal doesn't result in unlinked
2426 leaves shown in tree</li>
2427 <li>Undos after several redundancy removals don't undo
2429 <li>Hide sequence doesn't hide associated annotation</li>
2430 <li>User defined colours dialog box too big to fit on
2431 screen and buttons not visible</li>
2432 <li>author list isn't updated if already written to
2433 Jalview properties</li>
2434 <li>Popup menu won't open after retrieving sequence
2436 <li>File open window for associate PDB doesn't open</li>
2437 <li>Left-then-right click on a sequence id opens a
2438 browser search window</li>
2439 <li>Cannot open sequence feature shading/sort popup menu
2440 in feature settings dialog</li>
2441 <li>better tooltip placement for some areas of Jalview
2443 <li>Allow addition of JABAWS Server which doesn't
2444 pass validation</li>
2445 <li>Web services parameters dialog box is too large to
2447 <li>Muscle nucleotide alignment preset obscured by
2449 <li>JABAWS preset submenus don't contain newly
2450 defined user preset</li>
2451 <li>MSA web services warns user if they were launched
2452 with invalid input</li>
2453 <li>Jalview cannot contact DAS Registy when running on
2456 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2457 'Superpose with' submenu not shown when new view
2461 </ul> <!-- <em>Applet</em>
2463 </ul> <em>General</em>
2465 </ul>--> <em>Deployment and Documentation</em>
2467 <li>2G and 1G options in launchApp have no effect on
2468 memory allocation</li>
2469 <li>launchApp service doesn't automatically open
2470 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2472 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2473 InstallAnywhere reports cannot find valid JVM when Java
2474 1.7_055 is available
2476 </ul> <em>Application Known issues</em>
2479 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2480 corrupted or unreadable alignment display when scrolling
2484 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2485 retrieval fails but progress bar continues for DAS retrieval
2486 with large number of ID
2489 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2490 flatfile output of visible region has incorrect sequence
2494 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2495 rna structure consensus doesn't update when secondary
2496 structure tracks are rearranged
2499 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2500 invalid rna structure positional highlighting does not
2501 highlight position of invalid base pairs
2504 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2505 out of memory errors are not raised when saving Jalview
2506 project from alignment window file menu
2509 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2510 Switching to RNA Helices colouring doesn't propagate to
2514 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2515 colour by RNA Helices not enabled when user created
2516 annotation added to alignment
2519 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2520 Jalview icon not shown on dock in Mountain Lion/Webstart
2522 </ul> <em>Applet Known Issues</em>
2525 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2526 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2529 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2530 Jalview and Jmol example not compatible with IE9
2533 <li>Sort by annotation score doesn't reverse order
2539 <td><div align="center">
2540 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2543 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2546 <li>Internationalisation of user interface (usually
2547 called i18n support) and translation for Spanish locale</li>
2548 <li>Define/Undefine group on current selection with
2549 Ctrl-G/Shift Ctrl-G</li>
2550 <li>Improved group creation/removal options in
2551 alignment/sequence Popup menu</li>
2552 <li>Sensible precision for symbol distribution
2553 percentages shown in logo tooltip.</li>
2554 <li>Annotation panel height set according to amount of
2555 annotation when alignment first opened</li>
2556 </ul> <em>Application</em>
2558 <li>Interactive consensus RNA secondary structure
2559 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2560 <li>Select columns containing particular features from
2561 Feature Settings dialog</li>
2562 <li>View all 'representative' PDB structures for selected
2564 <li>Update Jalview project format:
2566 <li>New file extension for Jalview projects '.jvp'</li>
2567 <li>Preserve sequence and annotation dataset (to
2568 store secondary structure annotation,etc)</li>
2569 <li>Per group and alignment annotation and RNA helix
2573 <li>New similarity measures for PCA and Tree calculation
2575 <li>Experimental support for retrieval and viewing of
2576 flanking regions for an alignment</li>
2580 <!-- issues resolved --> <em>Application</em>
2582 <li>logo keeps spinning and status remains at queued or
2583 running after job is cancelled</li>
2584 <li>cannot export features from alignments imported from
2585 Jalview/VAMSAS projects</li>
2586 <li>Buggy slider for web service parameters that take
2588 <li>Newly created RNA secondary structure line doesn't
2589 have 'display all symbols' flag set</li>
2590 <li>T-COFFEE alignment score shading scheme and other
2591 annotation shading not saved in Jalview project</li>
2592 <li>Local file cannot be loaded in freshly downloaded
2594 <li>Jalview icon not shown on dock in Mountain
2596 <li>Load file from desktop file browser fails</li>
2597 <li>Occasional NPE thrown when calculating large trees</li>
2598 <li>Cannot reorder or slide sequences after dragging an
2599 alignment onto desktop</li>
2600 <li>Colour by annotation dialog throws NPE after using
2601 'extract scores' function</li>
2602 <li>Loading/cut'n'pasting an empty file leads to a grey
2603 alignment window</li>
2604 <li>Disorder thresholds rendered incorrectly after
2605 performing IUPred disorder prediction</li>
2606 <li>Multiple group annotated consensus rows shown when
2607 changing 'normalise logo' display setting</li>
2608 <li>Find shows blank dialog after 'finished searching' if
2609 nothing matches query</li>
2610 <li>Null Pointer Exceptions raised when sorting by
2611 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2613 <li>Errors in Jmol console when structures in alignment
2614 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2616 <li>Not all working JABAWS services are shown in
2618 <li>JAVAWS version of Jalview fails to launch with
2619 'invalid literal/length code'</li>
2620 <li>Annotation/RNA Helix colourschemes cannot be applied
2621 to alignment with groups (actually fixed in 2.8.0b1)</li>
2622 <li>RNA Helices and T-Coffee Scores available as default
2625 </ul> <em>Applet</em>
2627 <li>Remove group option is shown even when selection is
2629 <li>Apply to all groups ticked but colourscheme changes
2630 don't affect groups</li>
2631 <li>Documented RNA Helices and T-Coffee Scores as valid
2632 colourscheme name</li>
2633 <li>Annotation labels drawn on sequence IDs when
2634 Annotation panel is not displayed</li>
2635 <li>Increased font size for dropdown menus on OSX and
2636 embedded windows</li>
2637 </ul> <em>Other</em>
2639 <li>Consensus sequence for alignments/groups with a
2640 single sequence were not calculated</li>
2641 <li>annotation files that contain only groups imported as
2642 annotation and junk sequences</li>
2643 <li>Fasta files with sequences containing '*' incorrectly
2644 recognised as PFAM or BLC</li>
2645 <li>conservation/PID slider apply all groups option
2646 doesn't affect background (2.8.0b1)
2648 <li>redundancy highlighting is erratic at 0% and 100%</li>
2649 <li>Remove gapped columns fails for sequences with ragged
2651 <li>AMSA annotation row with leading spaces is not
2652 registered correctly on import</li>
2653 <li>Jalview crashes when selecting PCA analysis for
2654 certain alignments</li>
2655 <li>Opening the colour by annotation dialog for an
2656 existing annotation based 'use original colours'
2657 colourscheme loses original colours setting</li>
2662 <td><div align="center">
2663 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2664 <em>30/1/2014</em></strong>
2668 <li>Trusted certificates for JalviewLite applet and
2669 Jalview Desktop application<br />Certificate was donated by
2670 <a href="https://www.certum.eu">Certum</a> to the Jalview
2671 open source project).
2673 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2674 <li>Output in Stockholm format</li>
2675 <li>Allow import of data from gzipped files</li>
2676 <li>Export/import group and sequence associated line
2677 graph thresholds</li>
2678 <li>Nucleotide substitution matrix that supports RNA and
2679 ambiguity codes</li>
2680 <li>Allow disorder predictions to be made on the current
2681 selection (or visible selection) in the same way that JPred
2683 <li>Groovy scripting for headless Jalview operation</li>
2684 </ul> <em>Other improvements</em>
2686 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2687 <li>COMBINE statement uses current SEQUENCE_REF and
2688 GROUP_REF scope to group annotation rows</li>
2689 <li>Support '' style escaping of quotes in Newick
2691 <li>Group options for JABAWS service by command line name</li>
2692 <li>Empty tooltip shown for JABA service options with a
2693 link but no description</li>
2694 <li>Select primary source when selecting authority in
2695 database fetcher GUI</li>
2696 <li>Add .mfa to FASTA file extensions recognised by
2698 <li>Annotation label tooltip text wrap</li>
2703 <li>Slow scrolling when lots of annotation rows are
2705 <li>Lots of NPE (and slowness) after creating RNA
2706 secondary structure annotation line</li>
2707 <li>Sequence database accessions not imported when
2708 fetching alignments from Rfam</li>
2709 <li>Incorrect SHMR submission for sequences with
2711 <li>View all structures does not always superpose
2713 <li>Option widgets in service parameters not updated to
2714 reflect user or preset settings</li>
2715 <li>Null pointer exceptions for some services without
2716 presets or adjustable parameters</li>
2717 <li>Discover PDB IDs entry in structure menu doesn't
2718 discover PDB xRefs</li>
2719 <li>Exception encountered while trying to retrieve
2720 features with DAS</li>
2721 <li>Lowest value in annotation row isn't coloured
2722 when colour by annotation (per sequence) is coloured</li>
2723 <li>Keyboard mode P jumps to start of gapped region when
2724 residue follows a gap</li>
2725 <li>Jalview appears to hang importing an alignment with
2726 Wrap as default or after enabling Wrap</li>
2727 <li>'Right click to add annotations' message
2728 shown in wrap mode when no annotations present</li>
2729 <li>Disorder predictions fail with NPE if no automatic
2730 annotation already exists on alignment</li>
2731 <li>oninit javascript function should be called after
2732 initialisation completes</li>
2733 <li>Remove redundancy after disorder prediction corrupts
2734 alignment window display</li>
2735 <li>Example annotation file in documentation is invalid</li>
2736 <li>Grouped line graph annotation rows are not exported
2737 to annotation file</li>
2738 <li>Multi-harmony analysis cannot be run when only two
2740 <li>Cannot create multiple groups of line graphs with
2741 several 'combine' statements in annotation file</li>
2742 <li>Pressing return several times causes Number Format
2743 exceptions in keyboard mode</li>
2744 <li>Multi-harmony (SHMMR) method doesn't submit
2745 correct partitions for input data</li>
2746 <li>Translation from DNA to Amino Acids fails</li>
2747 <li>Jalview fail to load newick tree with quoted label</li>
2748 <li>--headless flag isn't understood</li>
2749 <li>ClassCastException when generating EPS in headless
2751 <li>Adjusting sequence-associated shading threshold only
2752 changes one row's threshold</li>
2753 <li>Preferences and Feature settings panel panel
2754 doesn't open</li>
2755 <li>hide consensus histogram also hides conservation and
2756 quality histograms</li>
2761 <td><div align="center">
2762 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2764 <td><em>Application</em>
2766 <li>Support for JABAWS 2.0 Services (AACon alignment
2767 conservation, protein disorder and Clustal Omega)</li>
2768 <li>JABAWS server status indicator in Web Services
2770 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2771 in Jalview alignment window</li>
2772 <li>Updated Jalview build and deploy framework for OSX
2773 mountain lion, windows 7, and 8</li>
2774 <li>Nucleotide substitution matrix for PCA that supports
2775 RNA and ambiguity codes</li>
2777 <li>Improved sequence database retrieval GUI</li>
2778 <li>Support fetching and database reference look up
2779 against multiple DAS sources (Fetch all from in 'fetch db
2781 <li>Jalview project improvements
2783 <li>Store and retrieve the 'belowAlignment'
2784 flag for annotation</li>
2785 <li>calcId attribute to group annotation rows on the
2787 <li>Store AACon calculation settings for a view in
2788 Jalview project</li>
2792 <li>horizontal scrolling gesture support</li>
2793 <li>Visual progress indicator when PCA calculation is
2795 <li>Simpler JABA web services menus</li>
2796 <li>visual indication that web service results are still
2797 being retrieved from server</li>
2798 <li>Serialise the dialogs that are shown when Jalview
2799 starts up for first time</li>
2800 <li>Jalview user agent string for interacting with HTTP
2802 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2804 <li>Examples directory and Groovy library included in
2805 InstallAnywhere distribution</li>
2806 </ul> <em>Applet</em>
2808 <li>RNA alignment and secondary structure annotation
2809 visualization applet example</li>
2810 </ul> <em>General</em>
2812 <li>Normalise option for consensus sequence logo</li>
2813 <li>Reset button in PCA window to return dimensions to
2815 <li>Allow seqspace or Jalview variant of alignment PCA
2817 <li>PCA with either nucleic acid and protein substitution
2819 <li>Allow windows containing HTML reports to be exported
2821 <li>Interactive display and editing of RNA secondary
2822 structure contacts</li>
2823 <li>RNA Helix Alignment Colouring</li>
2824 <li>RNA base pair logo consensus</li>
2825 <li>Parse sequence associated secondary structure
2826 information in Stockholm files</li>
2827 <li>HTML Export database accessions and annotation
2828 information presented in tooltip for sequences</li>
2829 <li>Import secondary structure from LOCARNA clustalw
2830 style RNA alignment files</li>
2831 <li>import and visualise T-COFFEE quality scores for an
2833 <li>'colour by annotation' per sequence option to
2834 shade each sequence according to its associated alignment
2836 <li>New Jalview Logo</li>
2837 </ul> <em>Documentation and Development</em>
2839 <li>documentation for score matrices used in Jalview</li>
2840 <li>New Website!</li>
2842 <td><em>Application</em>
2844 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2845 wsdbfetch REST service</li>
2846 <li>Stop windows being moved outside desktop on OSX</li>
2847 <li>Filetype associations not installed for webstart
2849 <li>Jalview does not always retrieve progress of a JABAWS
2850 job execution in full once it is complete</li>
2851 <li>revise SHMR RSBS definition to ensure alignment is
2852 uploaded via ali_file parameter</li>
2853 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2854 <li>View all structures superposed fails with exception</li>
2855 <li>Jnet job queues forever if a very short sequence is
2856 submitted for prediction</li>
2857 <li>Cut and paste menu not opened when mouse clicked on
2859 <li>Putting fractional value into integer text box in
2860 alignment parameter dialog causes Jalview to hang</li>
2861 <li>Structure view highlighting doesn't work on
2863 <li>View all structures fails with exception shown in
2865 <li>Characters in filename associated with PDBEntry not
2866 escaped in a platform independent way</li>
2867 <li>Jalview desktop fails to launch with exception when
2869 <li>Tree calculation reports 'you must have 2 or more
2870 sequences selected' when selection is empty</li>
2871 <li>Jalview desktop fails to launch with jar signature
2872 failure when java web start temporary file caching is
2874 <li>DAS Sequence retrieval with range qualification
2875 results in sequence xref which includes range qualification</li>
2876 <li>Errors during processing of command line arguments
2877 cause progress bar (JAL-898) to be removed</li>
2878 <li>Replace comma for semi-colon option not disabled for
2879 DAS sources in sequence fetcher</li>
2880 <li>Cannot close news reader when JABAWS server warning
2881 dialog is shown</li>
2882 <li>Option widgets not updated to reflect user settings</li>
2883 <li>Edited sequence not submitted to web service</li>
2884 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2885 <li>InstallAnywhere installer doesn't unpack and run
2886 on OSX Mountain Lion</li>
2887 <li>Annotation panel not given a scroll bar when
2888 sequences with alignment annotation are pasted into the
2890 <li>Sequence associated annotation rows not associated
2891 when loaded from Jalview project</li>
2892 <li>Browser launch fails with NPE on java 1.7</li>
2893 <li>JABAWS alignment marked as finished when job was
2894 cancelled or job failed due to invalid input</li>
2895 <li>NPE with v2.7 example when clicking on Tree
2896 associated with all views</li>
2897 <li>Exceptions when copy/paste sequences with grouped
2898 annotation rows to new window</li>
2899 </ul> <em>Applet</em>
2901 <li>Sequence features are momentarily displayed before
2902 they are hidden using hidefeaturegroups applet parameter</li>
2903 <li>loading features via javascript API automatically
2904 enables feature display</li>
2905 <li>scrollToColumnIn javascript API method doesn't
2907 </ul> <em>General</em>
2909 <li>Redundancy removal fails for rna alignment</li>
2910 <li>PCA calculation fails when sequence has been selected
2911 and then deselected</li>
2912 <li>PCA window shows grey box when first opened on OSX</li>
2913 <li>Letters coloured pink in sequence logo when alignment
2914 coloured with clustalx</li>
2915 <li>Choosing fonts without letter symbols defined causes
2916 exceptions and redraw errors</li>
2917 <li>Initial PCA plot view is not same as manually
2918 reconfigured view</li>
2919 <li>Grouped annotation graph label has incorrect line
2921 <li>Grouped annotation graph label display is corrupted
2922 for lots of labels</li>
2927 <div align="center">
2928 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2931 <td><em>Application</em>
2933 <li>Jalview Desktop News Reader</li>
2934 <li>Tweaked default layout of web services menu</li>
2935 <li>View/alignment association menu to enable user to
2936 easily specify which alignment a multi-structure view takes
2937 its colours/correspondences from</li>
2938 <li>Allow properties file location to be specified as URL</li>
2939 <li>Extend Jalview project to preserve associations
2940 between many alignment views and a single Jmol display</li>
2941 <li>Store annotation row height in Jalview project file</li>
2942 <li>Annotation row column label formatting attributes
2943 stored in project file</li>
2944 <li>Annotation row order for auto-calculated annotation
2945 rows preserved in Jalview project file</li>
2946 <li>Visual progress indication when Jalview state is
2947 saved using Desktop window menu</li>
2948 <li>Visual indication that command line arguments are
2949 still being processed</li>
2950 <li>Groovy script execution from URL</li>
2951 <li>Colour by annotation default min and max colours in
2953 <li>Automatically associate PDB files dragged onto an
2954 alignment with sequences that have high similarity and
2956 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2957 <li>'view structures' option to open many
2958 structures in same window</li>
2959 <li>Sort associated views menu option for tree panel</li>
2960 <li>Group all JABA and non-JABA services for a particular
2961 analysis function in its own submenu</li>
2962 </ul> <em>Applet</em>
2964 <li>Userdefined and autogenerated annotation rows for
2966 <li>Adjustment of alignment annotation pane height</li>
2967 <li>Annotation scrollbar for annotation panel</li>
2968 <li>Drag to reorder annotation rows in annotation panel</li>
2969 <li>'automaticScrolling' parameter</li>
2970 <li>Allow sequences with partial ID string matches to be
2971 annotated from GFF/Jalview features files</li>
2972 <li>Sequence logo annotation row in applet</li>
2973 <li>Absolute paths relative to host server in applet
2974 parameters are treated as such</li>
2975 <li>New in the JalviewLite javascript API:
2977 <li>JalviewLite.js javascript library</li>
2978 <li>Javascript callbacks for
2980 <li>Applet initialisation</li>
2981 <li>Sequence/alignment mouse-overs and selections</li>
2984 <li>scrollTo row and column alignment scrolling
2986 <li>Select sequence/alignment regions from javascript</li>
2987 <li>javascript structure viewer harness to pass
2988 messages between Jmol and Jalview when running as
2989 distinct applets</li>
2990 <li>sortBy method</li>
2991 <li>Set of applet and application examples shipped
2992 with documentation</li>
2993 <li>New example to demonstrate JalviewLite and Jmol
2994 javascript message exchange</li>
2996 </ul> <em>General</em>
2998 <li>Enable Jmol displays to be associated with multiple
2999 multiple alignments</li>
3000 <li>Option to automatically sort alignment with new tree</li>
3001 <li>User configurable link to enable redirects to a
3002 www.Jalview.org mirror</li>
3003 <li>Jmol colours option for Jmol displays</li>
3004 <li>Configurable newline string when writing alignment
3005 and other flat files</li>
3006 <li>Allow alignment annotation description lines to
3007 contain html tags</li>
3008 </ul> <em>Documentation and Development</em>
3010 <li>Add groovy test harness for bulk load testing to
3012 <li>Groovy script to load and align a set of sequences
3013 using a web service before displaying the result in the
3014 Jalview desktop</li>
3015 <li>Restructured javascript and applet api documentation</li>
3016 <li>Ant target to publish example html files with applet
3018 <li>Netbeans project for building Jalview from source</li>
3019 <li>ant task to create online javadoc for Jalview source</li>
3021 <td><em>Application</em>
3023 <li>User defined colourscheme throws exception when
3024 current built in colourscheme is saved as new scheme</li>
3025 <li>AlignFrame->Save in application pops up save
3026 dialog for valid filename/format</li>
3027 <li>Cannot view associated structure for UniProt sequence</li>
3028 <li>PDB file association breaks for UniProt sequence
3030 <li>Associate PDB from file dialog does not tell you
3031 which sequence is to be associated with the file</li>
3032 <li>Find All raises null pointer exception when query
3033 only matches sequence IDs</li>
3034 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3035 <li>Jalview project with Jmol views created with Jalview
3036 2.4 cannot be loaded</li>
3037 <li>Filetype associations not installed for webstart
3039 <li>Two or more chains in a single PDB file associated
3040 with sequences in different alignments do not get coloured
3041 by their associated sequence</li>
3042 <li>Visibility status of autocalculated annotation row
3043 not preserved when project is loaded</li>
3044 <li>Annotation row height and visibility attributes not
3045 stored in Jalview project</li>
3046 <li>Tree bootstraps are not preserved when saved as a
3047 Jalview project</li>
3048 <li>Envision2 workflow tooltips are corrupted</li>
3049 <li>Enabling show group conservation also enables colour
3050 by conservation</li>
3051 <li>Duplicate group associated conservation or consensus
3052 created on new view</li>
3053 <li>Annotation scrollbar not displayed after 'show
3054 all hidden annotation rows' option selected</li>
3055 <li>Alignment quality not updated after alignment
3056 annotation row is hidden then shown</li>
3057 <li>Preserve colouring of structures coloured by
3058 sequences in pre Jalview 2.7 projects</li>
3059 <li>Web service job parameter dialog is not laid out
3061 <li>Web services menu not refreshed after 'reset
3062 services' button is pressed in preferences</li>
3063 <li>Annotation off by one in Jalview v2_3 example project</li>
3064 <li>Structures imported from file and saved in project
3065 get name like jalview_pdb1234.txt when reloaded</li>
3066 <li>Jalview does not always retrieve progress of a JABAWS
3067 job execution in full once it is complete</li>
3068 </ul> <em>Applet</em>
3070 <li>Alignment height set incorrectly when lots of
3071 annotation rows are displayed</li>
3072 <li>Relative URLs in feature HTML text not resolved to
3074 <li>View follows highlighting does not work for positions
3076 <li><= shown as = in tooltip</li>
3077 <li>Export features raises exception when no features
3079 <li>Separator string used for serialising lists of IDs
3080 for javascript api is modified when separator string
3081 provided as parameter</li>
3082 <li>Null pointer exception when selecting tree leaves for
3083 alignment with no existing selection</li>
3084 <li>Relative URLs for datasources assumed to be relative
3085 to applet's codebase</li>
3086 <li>Status bar not updated after finished searching and
3087 search wraps around to first result</li>
3088 <li>StructureSelectionManager instance shared between
3089 several Jalview applets causes race conditions and memory
3091 <li>Hover tooltip and mouseover of position on structure
3092 not sent from Jmol in applet</li>
3093 <li>Certain sequences of javascript method calls to
3094 applet API fatally hang browser</li>
3095 </ul> <em>General</em>
3097 <li>View follows structure mouseover scrolls beyond
3098 position with wrapped view and hidden regions</li>
3099 <li>Find sequence position moves to wrong residue
3100 with/without hidden columns</li>
3101 <li>Sequence length given in alignment properties window
3103 <li>InvalidNumberFormat exceptions thrown when trying to
3104 import PDB like structure files</li>
3105 <li>Positional search results are only highlighted
3106 between user-supplied sequence start/end bounds</li>
3107 <li>End attribute of sequence is not validated</li>
3108 <li>Find dialog only finds first sequence containing a
3109 given sequence position</li>
3110 <li>Sequence numbering not preserved in MSF alignment
3112 <li>Jalview PDB file reader does not extract sequence
3113 from nucleotide chains correctly</li>
3114 <li>Structure colours not updated when tree partition
3115 changed in alignment</li>
3116 <li>Sequence associated secondary structure not correctly
3117 parsed in interleaved stockholm</li>
3118 <li>Colour by annotation dialog does not restore current
3120 <li>Hiding (nearly) all sequences doesn't work
3122 <li>Sequences containing lowercase letters are not
3123 properly associated with their pdb files</li>
3124 </ul> <em>Documentation and Development</em>
3126 <li>schemas/JalviewWsParamSet.xsd corrupted by
3127 ApplyCopyright tool</li>
3132 <div align="center">
3133 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3136 <td><em>Application</em>
3138 <li>New warning dialog when the Jalview Desktop cannot
3139 contact web services</li>
3140 <li>JABA service parameters for a preset are shown in
3141 service job window</li>
3142 <li>JABA Service menu entries reworded</li>
3146 <li>Modeller PIR IO broken - cannot correctly import a
3147 pir file emitted by Jalview</li>
3148 <li>Existing feature settings transferred to new
3149 alignment view created from cut'n'paste</li>
3150 <li>Improved test for mixed amino/nucleotide chains when
3151 parsing PDB files</li>
3152 <li>Consensus and conservation annotation rows
3153 occasionally become blank for all new windows</li>
3154 <li>Exception raised when right clicking above sequences
3155 in wrapped view mode</li>
3156 </ul> <em>Application</em>
3158 <li>multiple multiply aligned structure views cause cpu
3159 usage to hit 100% and computer to hang</li>
3160 <li>Web Service parameter layout breaks for long user
3161 parameter names</li>
3162 <li>Jaba service discovery hangs desktop if Jaba server
3169 <div align="center">
3170 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3173 <td><em>Application</em>
3175 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3176 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3179 <li>Web Services preference tab</li>
3180 <li>Analysis parameters dialog box and user defined
3182 <li>Improved speed and layout of Envision2 service menu</li>
3183 <li>Superpose structures using associated sequence
3185 <li>Export coordinates and projection as CSV from PCA
3187 </ul> <em>Applet</em>
3189 <li>enable javascript: execution by the applet via the
3190 link out mechanism</li>
3191 </ul> <em>Other</em>
3193 <li>Updated the Jmol Jalview interface to work with Jmol
3195 <li>The Jalview Desktop and JalviewLite applet now
3196 require Java 1.5</li>
3197 <li>Allow Jalview feature colour specification for GFF
3198 sequence annotation files</li>
3199 <li>New 'colour by label' keword in Jalview feature file
3200 type colour specification</li>
3201 <li>New Jalview Desktop Groovy API method that allows a
3202 script to check if it being run in an interactive session or
3203 in a batch operation from the Jalview command line</li>
3207 <li>clustalx colourscheme colours Ds preferentially when
3208 both D+E are present in over 50% of the column</li>
3209 </ul> <em>Application</em>
3211 <li>typo in AlignmentFrame->View->Hide->all but
3212 selected Regions menu item</li>
3213 <li>sequence fetcher replaces ',' for ';' when the ',' is
3214 part of a valid accession ID</li>
3215 <li>fatal OOM if object retrieved by sequence fetcher
3216 runs out of memory</li>
3217 <li>unhandled Out of Memory Error when viewing pca
3218 analysis results</li>
3219 <li>InstallAnywhere builds fail to launch on OS X java
3220 10.5 update 4 (due to apple Java 1.6 update)</li>
3221 <li>Installanywhere Jalview silently fails to launch</li>
3222 </ul> <em>Applet</em>
3224 <li>Jalview.getFeatureGroups() raises an
3225 ArrayIndexOutOfBoundsException if no feature groups are
3232 <div align="center">
3233 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3239 <li>Alignment prettyprinter doesn't cope with long
3241 <li>clustalx colourscheme colours Ds preferentially when
3242 both D+E are present in over 50% of the column</li>
3243 <li>nucleic acid structures retrieved from PDB do not
3244 import correctly</li>
3245 <li>More columns get selected than were clicked on when a
3246 number of columns are hidden</li>
3247 <li>annotation label popup menu not providing correct
3248 add/hide/show options when rows are hidden or none are
3250 <li>Stockholm format shown in list of readable formats,
3251 and parser copes better with alignments from RFAM.</li>
3252 <li>CSV output of consensus only includes the percentage
3253 of all symbols if sequence logo display is enabled</li>
3255 </ul> <em>Applet</em>
3257 <li>annotation panel disappears when annotation is
3259 </ul> <em>Application</em>
3261 <li>Alignment view not redrawn properly when new
3262 alignment opened where annotation panel is visible but no
3263 annotations are present on alignment</li>
3264 <li>pasted region containing hidden columns is
3265 incorrectly displayed in new alignment window</li>
3266 <li>Jalview slow to complete operations when stdout is
3267 flooded (fix is to close the Jalview console)</li>
3268 <li>typo in AlignmentFrame->View->Hide->all but
3269 selected Rregions menu item.</li>
3270 <li>inconsistent group submenu and Format submenu entry
3271 'Un' or 'Non'conserved</li>
3272 <li>Sequence feature settings are being shared by
3273 multiple distinct alignments</li>
3274 <li>group annotation not recreated when tree partition is
3276 <li>double click on group annotation to select sequences
3277 does not propagate to associated trees</li>
3278 <li>Mac OSX specific issues:
3280 <li>exception raised when mouse clicked on desktop
3281 window background</li>
3282 <li>Desktop menu placed on menu bar and application
3283 name set correctly</li>
3284 <li>sequence feature settings not wide enough for the
3285 save feature colourscheme button</li>
3294 <div align="center">
3295 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3298 <td><em>New Capabilities</em>
3300 <li>URL links generated from description line for
3301 regular-expression based URL links (applet and application)
3303 <li>Non-positional feature URL links are shown in link
3305 <li>Linked viewing of nucleic acid sequences and
3307 <li>Automatic Scrolling option in View menu to display
3308 the currently highlighted region of an alignment.</li>
3309 <li>Order an alignment by sequence length, or using the
3310 average score or total feature count for each sequence.</li>
3311 <li>Shading features by score or associated description</li>
3312 <li>Subdivide alignment and groups based on identity of
3313 selected subsequence (Make Groups from Selection).</li>
3314 <li>New hide/show options including Shift+Control+H to
3315 hide everything but the currently selected region.</li>
3316 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3317 </ul> <em>Application</em>
3319 <li>Fetch DB References capabilities and UI expanded to
3320 support retrieval from DAS sequence sources</li>
3321 <li>Local DAS Sequence sources can be added via the
3322 command line or via the Add local source dialog box.</li>
3323 <li>DAS Dbref and DbxRef feature types are parsed as
3324 database references and protein_name is parsed as
3325 description line (BioSapiens terms).</li>
3326 <li>Enable or disable non-positional feature and database
3327 references in sequence ID tooltip from View menu in
3329 <!-- <li>New hidden columns and rows and representatives capabilities
3330 in annotations file (in progress - not yet fully implemented)</li> -->
3331 <li>Group-associated consensus, sequence logos and
3332 conservation plots</li>
3333 <li>Symbol distributions for each column can be exported
3334 and visualized as sequence logos</li>
3335 <li>Optionally scale multi-character column labels to fit
3336 within each column of annotation row<!-- todo for applet -->
3338 <li>Optional automatic sort of associated alignment view
3339 when a new tree is opened.</li>
3340 <li>Jalview Java Console</li>
3341 <li>Better placement of desktop window when moving
3342 between different screens.</li>
3343 <li>New preference items for sequence ID tooltip and
3344 consensus annotation</li>
3345 <li>Client to submit sequences and IDs to Envision2
3347 <li><em>Vamsas Capabilities</em>
3349 <li>Improved VAMSAS synchronization (Jalview archive
3350 used to preserve views, structures, and tree display
3352 <li>Import of vamsas documents from disk or URL via
3354 <li>Sharing of selected regions between views and
3355 with other VAMSAS applications (Experimental feature!)</li>
3356 <li>Updated API to VAMSAS version 0.2</li>
3358 </ul> <em>Applet</em>
3360 <li>Middle button resizes annotation row height</li>
3363 <li>sortByTree (true/false) - automatically sort the
3364 associated alignment view by the tree when a new tree is
3366 <li>showTreeBootstraps (true/false) - show or hide
3367 branch bootstraps (default is to show them if available)</li>
3368 <li>showTreeDistances (true/false) - show or hide
3369 branch lengths (default is to show them if available)</li>
3370 <li>showUnlinkedTreeNodes (true/false) - indicate if
3371 unassociated nodes should be highlighted in the tree
3373 <li>heightScale and widthScale (1.0 or more) -
3374 increase the height or width of a cell in the alignment
3375 grid relative to the current font size.</li>
3378 <li>Non-positional features displayed in sequence ID
3380 </ul> <em>Other</em>
3382 <li>Features format: graduated colour definitions and
3383 specification of feature scores</li>
3384 <li>Alignment Annotations format: new keywords for group
3385 associated annotation (GROUP_REF) and annotation row display
3386 properties (ROW_PROPERTIES)</li>
3387 <li>XML formats extended to support graduated feature
3388 colourschemes, group associated annotation, and profile
3389 visualization settings.</li></td>
3392 <li>Source field in GFF files parsed as feature source
3393 rather than description</li>
3394 <li>Non-positional features are now included in sequence
3395 feature and gff files (controlled via non-positional feature
3396 visibility in tooltip).</li>
3397 <li>URL links generated for all feature links (bugfix)</li>
3398 <li>Added URL embedding instructions to features file
3400 <li>Codons containing ambiguous nucleotides translated as
3401 'X' in peptide product</li>
3402 <li>Match case switch in find dialog box works for both
3403 sequence ID and sequence string and query strings do not
3404 have to be in upper case to match case-insensitively.</li>
3405 <li>AMSA files only contain first column of
3406 multi-character column annotation labels</li>
3407 <li>Jalview Annotation File generation/parsing consistent
3408 with documentation (e.g. Stockholm annotation can be
3409 exported and re-imported)</li>
3410 <li>PDB files without embedded PDB IDs given a friendly
3412 <li>Find incrementally searches ID string matches as well
3413 as subsequence matches, and correctly reports total number
3417 <li>Better handling of exceptions during sequence
3419 <li>Dasobert generated non-positional feature URL
3420 link text excludes the start_end suffix</li>
3421 <li>DAS feature and source retrieval buttons disabled
3422 when fetch or registry operations in progress.</li>
3423 <li>PDB files retrieved from URLs are cached properly</li>
3424 <li>Sequence description lines properly shared via
3426 <li>Sequence fetcher fetches multiple records for all
3428 <li>Ensured that command line das feature retrieval
3429 completes before alignment figures are generated.</li>
3430 <li>Reduced time taken when opening file browser for
3432 <li>isAligned check prior to calculating tree, PCA or
3433 submitting an MSA to JNet now excludes hidden sequences.</li>
3434 <li>User defined group colours properly recovered
3435 from Jalview projects.</li>
3444 <div align="center">
3445 <strong>2.4.0.b2</strong><br> 28/10/2009
3450 <li>Experimental support for google analytics usage
3452 <li>Jalview privacy settings (user preferences and docs).</li>
3457 <li>Race condition in applet preventing startup in
3459 <li>Exception when feature created from selection beyond
3460 length of sequence.</li>
3461 <li>Allow synthetic PDB files to be imported gracefully</li>
3462 <li>Sequence associated annotation rows associate with
3463 all sequences with a given id</li>
3464 <li>Find function matches case-insensitively for sequence
3465 ID string searches</li>
3466 <li>Non-standard characters do not cause pairwise
3467 alignment to fail with exception</li>
3468 </ul> <em>Application Issues</em>
3470 <li>Sequences are now validated against EMBL database</li>
3471 <li>Sequence fetcher fetches multiple records for all
3473 </ul> <em>InstallAnywhere Issues</em>
3475 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3476 issue with installAnywhere mechanism)</li>
3477 <li>Command line launching of JARs from InstallAnywhere
3478 version (java class versioning error fixed)</li>
3485 <div align="center">
3486 <strong>2.4</strong><br> 27/8/2008
3489 <td><em>User Interface</em>
3491 <li>Linked highlighting of codon and amino acid from
3492 translation and protein products</li>
3493 <li>Linked highlighting of structure associated with
3494 residue mapping to codon position</li>
3495 <li>Sequence Fetcher provides example accession numbers
3496 and 'clear' button</li>
3497 <li>MemoryMonitor added as an option under Desktop's
3499 <li>Extract score function to parse whitespace separated
3500 numeric data in description line</li>
3501 <li>Column labels in alignment annotation can be centred.</li>
3502 <li>Tooltip for sequence associated annotation give name
3504 </ul> <em>Web Services and URL fetching</em>
3506 <li>JPred3 web service</li>
3507 <li>Prototype sequence search client (no public services
3509 <li>Fetch either seed alignment or full alignment from
3511 <li>URL Links created for matching database cross
3512 references as well as sequence ID</li>
3513 <li>URL Links can be created using regular-expressions</li>
3514 </ul> <em>Sequence Database Connectivity</em>
3516 <li>Retrieval of cross-referenced sequences from other
3518 <li>Generalised database reference retrieval and
3519 validation to all fetchable databases</li>
3520 <li>Fetch sequences from DAS sources supporting the
3521 sequence command</li>
3522 </ul> <em>Import and Export</em>
3523 <li>export annotation rows as CSV for spreadsheet import</li>
3524 <li>Jalview projects record alignment dataset associations,
3525 EMBL products, and cDNA sequence mappings</li>
3526 <li>Sequence Group colour can be specified in Annotation
3528 <li>Ad-hoc colouring of group in Annotation File using RGB
3529 triplet as name of colourscheme</li>
3530 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3532 <li>treenode binding for VAMSAS tree exchange</li>
3533 <li>local editing and update of sequences in VAMSAS
3534 alignments (experimental)</li>
3535 <li>Create new or select existing session to join</li>
3536 <li>load and save of vamsas documents</li>
3537 </ul> <em>Application command line</em>
3539 <li>-tree parameter to open trees (introduced for passing
3541 <li>-fetchfrom command line argument to specify nicknames
3542 of DAS servers to query for alignment features</li>
3543 <li>-dasserver command line argument to add new servers
3544 that are also automatically queried for features</li>
3545 <li>-groovy command line argument executes a given groovy
3546 script after all input data has been loaded and parsed</li>
3547 </ul> <em>Applet-Application data exchange</em>
3549 <li>Trees passed as applet parameters can be passed to
3550 application (when using "View in full
3551 application")</li>
3552 </ul> <em>Applet Parameters</em>
3554 <li>feature group display control parameter</li>
3555 <li>debug parameter</li>
3556 <li>showbutton parameter</li>
3557 </ul> <em>Applet API methods</em>
3559 <li>newView public method</li>
3560 <li>Window (current view) specific get/set public methods</li>
3561 <li>Feature display control methods</li>
3562 <li>get list of currently selected sequences</li>
3563 </ul> <em>New Jalview distribution features</em>
3565 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3566 <li>RELEASE file gives build properties for the latest
3567 Jalview release.</li>
3568 <li>Java 1.1 Applet build made easier and donotobfuscate
3569 property controls execution of obfuscator</li>
3570 <li>Build target for generating source distribution</li>
3571 <li>Debug flag for javacc</li>
3572 <li>.jalview_properties file is documented (slightly) in
3573 jalview.bin.Cache</li>
3574 <li>Continuous Build Integration for stable and
3575 development version of Application, Applet and source
3580 <li>selected region output includes visible annotations
3581 (for certain formats)</li>
3582 <li>edit label/displaychar contains existing label/char
3584 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3585 <li>shorter peptide product names from EMBL records</li>
3586 <li>Newick string generator makes compact representations</li>
3587 <li>bootstrap values parsed correctly for tree files with
3589 <li>pathological filechooser bug avoided by not allowing
3590 filenames containing a ':'</li>
3591 <li>Fixed exception when parsing GFF files containing
3592 global sequence features</li>
3593 <li>Alignment datasets are finalized only when number of
3594 references from alignment sequences goes to zero</li>
3595 <li>Close of tree branch colour box without colour
3596 selection causes cascading exceptions</li>
3597 <li>occasional negative imgwidth exceptions</li>
3598 <li>better reporting of non-fatal warnings to user when
3599 file parsing fails.</li>
3600 <li>Save works when Jalview project is default format</li>
3601 <li>Save as dialog opened if current alignment format is
3602 not a valid output format</li>
3603 <li>UniProt canonical names introduced for both das and
3605 <li>Histidine should be midblue (not pink!) in Zappo</li>
3606 <li>error messages passed up and output when data read
3608 <li>edit undo recovers previous dataset sequence when
3609 sequence is edited</li>
3610 <li>allow PDB files without pdb ID HEADER lines (like
3611 those generated by MODELLER) to be read in properly</li>
3612 <li>allow reading of JPred concise files as a normal
3614 <li>Stockholm annotation parsing and alignment properties
3615 import fixed for PFAM records</li>
3616 <li>Structure view windows have correct name in Desktop
3618 <li>annotation consisting of sequence associated scores
3619 can be read and written correctly to annotation file</li>
3620 <li>Aligned cDNA translation to aligned peptide works
3622 <li>Fixed display of hidden sequence markers and
3623 non-italic font for representatives in Applet</li>
3624 <li>Applet Menus are always embedded in applet window on
3626 <li>Newly shown features appear at top of stack (in
3628 <li>Annotations added via parameter not drawn properly
3629 due to null pointer exceptions</li>
3630 <li>Secondary structure lines are drawn starting from
3631 first column of alignment</li>
3632 <li>UniProt XML import updated for new schema release in
3634 <li>Sequence feature to sequence ID match for Features
3635 file is case-insensitive</li>
3636 <li>Sequence features read from Features file appended to
3637 all sequences with matching IDs</li>
3638 <li>PDB structure coloured correctly for associated views
3639 containing a sub-sequence</li>
3640 <li>PDB files can be retrieved by applet from Jar files</li>
3641 <li>feature and annotation file applet parameters
3642 referring to different directories are retrieved correctly</li>
3643 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3644 <li>Fixed application hang whilst waiting for
3645 splash-screen version check to complete</li>
3646 <li>Applet properly URLencodes input parameter values
3647 when passing them to the launchApp service</li>
3648 <li>display name and local features preserved in results
3649 retrieved from web service</li>
3650 <li>Visual delay indication for sequence retrieval and
3651 sequence fetcher initialisation</li>
3652 <li>updated Application to use DAS 1.53e version of
3653 dasobert DAS client</li>
3654 <li>Re-instated Full AMSA support and .amsa file
3656 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3664 <div align="center">
3665 <strong>2.3</strong><br> 9/5/07
3670 <li>Jmol 11.0.2 integration</li>
3671 <li>PDB views stored in Jalview XML files</li>
3672 <li>Slide sequences</li>
3673 <li>Edit sequence in place</li>
3674 <li>EMBL CDS features</li>
3675 <li>DAS Feature mapping</li>
3676 <li>Feature ordering</li>
3677 <li>Alignment Properties</li>
3678 <li>Annotation Scores</li>
3679 <li>Sort by scores</li>
3680 <li>Feature/annotation editing in applet</li>
3685 <li>Headless state operation in 2.2.1</li>
3686 <li>Incorrect and unstable DNA pairwise alignment</li>
3687 <li>Cut and paste of sequences with annotation</li>
3688 <li>Feature group display state in XML</li>
3689 <li>Feature ordering in XML</li>
3690 <li>blc file iteration selection using filename # suffix</li>
3691 <li>Stockholm alignment properties</li>
3692 <li>Stockhom alignment secondary structure annotation</li>
3693 <li>2.2.1 applet had no feature transparency</li>
3694 <li>Number pad keys can be used in cursor mode</li>
3695 <li>Structure Viewer mirror image resolved</li>
3702 <div align="center">
3703 <strong>2.2.1</strong><br> 12/2/07
3708 <li>Non standard characters can be read and displayed
3709 <li>Annotations/Features can be imported/exported to the
3711 <li>Applet allows editing of sequence/annotation/group
3712 name & description
3713 <li>Preference setting to display sequence name in
3715 <li>Annotation file format extended to allow
3716 Sequence_groups to be defined
3717 <li>Default opening of alignment overview panel can be
3718 specified in preferences
3719 <li>PDB residue numbering annotation added to associated
3725 <li>Applet crash under certain Linux OS with Java 1.6
3727 <li>Annotation file export / import bugs fixed
3728 <li>PNG / EPS image output bugs fixed
3734 <div align="center">
3735 <strong>2.2</strong><br> 27/11/06
3740 <li>Multiple views on alignment
3741 <li>Sequence feature editing
3742 <li>"Reload" alignment
3743 <li>"Save" to current filename
3744 <li>Background dependent text colour
3745 <li>Right align sequence ids
3746 <li>User-defined lower case residue colours
3749 <li>Menu item accelerator keys
3750 <li>Control-V pastes to current alignment
3751 <li>Cancel button for DAS Feature Fetching
3752 <li>PCA and PDB Viewers zoom via mouse roller
3753 <li>User-defined sub-tree colours and sub-tree selection
3755 <li>'New Window' button on the 'Output to Text box'
3760 <li>New memory efficient Undo/Redo System
3761 <li>Optimised symbol lookups and conservation/consensus
3763 <li>Region Conservation/Consensus recalculated after
3765 <li>Fixed Remove Empty Columns Bug (empty columns at end
3767 <li>Slowed DAS Feature Fetching for increased robustness.
3769 <li>Made angle brackets in ASCII feature descriptions
3771 <li>Re-instated Zoom function for PCA
3772 <li>Sequence descriptions conserved in web service
3774 <li>UniProt ID discoverer uses any word separated by
3776 <li>WsDbFetch query/result association resolved
3777 <li>Tree leaf to sequence mapping improved
3778 <li>Smooth fonts switch moved to FontChooser dialog box.
3785 <div align="center">
3786 <strong>2.1.1</strong><br> 12/9/06
3791 <li>Copy consensus sequence to clipboard</li>
3796 <li>Image output - rightmost residues are rendered if
3797 sequence id panel has been resized</li>
3798 <li>Image output - all offscreen group boundaries are
3800 <li>Annotation files with sequence references - all
3801 elements in file are relative to sequence position</li>
3802 <li>Mac Applet users can use Alt key for group editing</li>
3808 <div align="center">
3809 <strong>2.1</strong><br> 22/8/06
3814 <li>MAFFT Multiple Alignment in default Web Service list</li>
3815 <li>DAS Feature fetching</li>
3816 <li>Hide sequences and columns</li>
3817 <li>Export Annotations and Features</li>
3818 <li>GFF file reading / writing</li>
3819 <li>Associate structures with sequences from local PDB
3821 <li>Add sequences to exisiting alignment</li>
3822 <li>Recently opened files / URL lists</li>
3823 <li>Applet can launch the full application</li>
3824 <li>Applet has transparency for features (Java 1.2
3826 <li>Applet has user defined colours parameter</li>
3827 <li>Applet can load sequences from parameter
3828 "sequence<em>x</em>"
3834 <li>Redundancy Panel reinstalled in the Applet</li>
3835 <li>Monospaced font - EPS / rescaling bug fixed</li>
3836 <li>Annotation files with sequence references bug fixed</li>
3842 <div align="center">
3843 <strong>2.08.1</strong><br> 2/5/06
3848 <li>Change case of selected region from Popup menu</li>
3849 <li>Choose to match case when searching</li>
3850 <li>Middle mouse button and mouse movement can compress /
3851 expand the visible width and height of the alignment</li>
3856 <li>Annotation Panel displays complete JNet results</li>
3862 <div align="center">
3863 <strong>2.08b</strong><br> 18/4/06
3869 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3870 <li>Righthand label on wrapped alignments shows correct
3877 <div align="center">
3878 <strong>2.08</strong><br> 10/4/06
3883 <li>Editing can be locked to the selection area</li>
3884 <li>Keyboard editing</li>
3885 <li>Create sequence features from searches</li>
3886 <li>Precalculated annotations can be loaded onto
3888 <li>Features file allows grouping of features</li>
3889 <li>Annotation Colouring scheme added</li>
3890 <li>Smooth fonts off by default - Faster rendering</li>
3891 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3896 <li>Drag & Drop fixed on Linux</li>
3897 <li>Jalview Archive file faster to load/save, sequence
3898 descriptions saved.</li>
3904 <div align="center">
3905 <strong>2.07</strong><br> 12/12/05
3910 <li>PDB Structure Viewer enhanced</li>
3911 <li>Sequence Feature retrieval and display enhanced</li>
3912 <li>Choose to output sequence start-end after sequence
3913 name for file output</li>
3914 <li>Sequence Fetcher WSDBFetch@EBI</li>
3915 <li>Applet can read feature files, PDB files and can be
3916 used for HTML form input</li>
3921 <li>HTML output writes groups and features</li>
3922 <li>Group editing is Control and mouse click</li>
3923 <li>File IO bugs</li>
3929 <div align="center">
3930 <strong>2.06</strong><br> 28/9/05
3935 <li>View annotations in wrapped mode</li>
3936 <li>More options for PCA viewer</li>
3941 <li>GUI bugs resolved</li>
3942 <li>Runs with -nodisplay from command line</li>
3948 <div align="center">
3949 <strong>2.05b</strong><br> 15/9/05
3954 <li>Choose EPS export as lineart or text</li>
3955 <li>Jar files are executable</li>
3956 <li>Can read in Uracil - maps to unknown residue</li>
3961 <li>Known OutOfMemory errors give warning message</li>
3962 <li>Overview window calculated more efficiently</li>
3963 <li>Several GUI bugs resolved</li>
3969 <div align="center">
3970 <strong>2.05</strong><br> 30/8/05
3975 <li>Edit and annotate in "Wrapped" view</li>
3980 <li>Several GUI bugs resolved</li>
3986 <div align="center">
3987 <strong>2.04</strong><br> 24/8/05
3992 <li>Hold down mouse wheel & scroll to change font
3998 <li>Improved JPred client reliability</li>
3999 <li>Improved loading of Jalview files</li>
4005 <div align="center">
4006 <strong>2.03</strong><br> 18/8/05
4011 <li>Set Proxy server name and port in preferences</li>
4012 <li>Multiple URL links from sequence ids</li>
4013 <li>User Defined Colours can have a scheme name and added
4015 <li>Choose to ignore gaps in consensus calculation</li>
4016 <li>Unix users can set default web browser</li>
4017 <li>Runs without GUI for batch processing</li>
4018 <li>Dynamically generated Web Service Menus</li>
4023 <li>InstallAnywhere download for Sparc Solaris</li>
4029 <div align="center">
4030 <strong>2.02</strong><br> 18/7/05
4036 <li>Copy & Paste order of sequences maintains
4037 alignment order.</li>
4043 <div align="center">
4044 <strong>2.01</strong><br> 12/7/05
4049 <li>Use delete key for deleting selection.</li>
4050 <li>Use Mouse wheel to scroll sequences.</li>
4051 <li>Help file updated to describe how to add alignment
4053 <li>Version and build date written to build properties
4055 <li>InstallAnywhere installation will check for updates
4056 at launch of Jalview.</li>
4061 <li>Delete gaps bug fixed.</li>
4062 <li>FileChooser sorts columns.</li>
4063 <li>Can remove groups one by one.</li>
4064 <li>Filechooser icons installed.</li>
4065 <li>Finder ignores return character when searching.
4066 Return key will initiate a search.<br>
4073 <div align="center">
4074 <strong>2.0</strong><br> 20/6/05
4079 <li>New codebase</li>