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-3104 -->Poorly scaled bar in quality annotation
115 row shown in Feredoxin Structure alignment view of example
119 <!-- JAL-2854 -->Annotation obscures sequences if lots of
120 annotation displayed.
123 <!-- JAL-3107 -->Group conservation/consensus not shown
124 for newly created group when 'Apply to all groups'
128 <!-- JAL-3087 -->Corrupted display when switching to
129 wrapped mode when sequence panel's vertical scrollbar is
133 <!-- JAL-3003 -->Alignment is black in exported EPS file
134 when sequences are selected in exported view.</em>
137 <!-- JAL-3059 -->Groups with different coloured borders
138 aren't rendered with correct colour.
141 <!-- JAL-3092 -->Jalview could hang when importing certain
142 types of knotted RNA secondary structure.
145 <!-- JAL-3095 -->Sequence highlight and selection in
146 trimmed VARNA 2D structure is incorrect for sequences that
150 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
151 annotation when columns are inserted into an alignment,
152 and when exporting as Stockholm flatfile.
155 <!-- JAL-3053 -->Jalview annotation rows containing upper
156 and lower-case 'E' and 'H' do not automatically get
157 treated as RNA secondary structure.
160 <!-- JAL-3106 -->.jvp should be used as default extension
161 (not .jar) when saving a jalview project file.
164 <!-- JAL-3105 -->Mac Users: closing a window correctly
165 transfers focus to previous window on OSX
168 <em>Java 10 Issues</em>
171 <!-- JAL-2988 -->OSX - Can't save new files via the File
172 or export menus by typing in a name into the Save dialog
180 <td width="60" nowrap>
182 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
183 <em>7/06/2018</em></strong>
186 <td><div align="left">
190 <!-- JAL-2920 -->Use HGVS nomenclature for variant
191 annotation retrieved from Uniprot
194 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
195 onto the Jalview Desktop
199 <td><div align="left">
203 <!-- JAL-3017 -->Cannot import features with multiple
204 variant elements (blocks import of some Uniprot records)
207 <!-- JAL-2997 -->Clustal files with sequence positions in
208 right-hand column parsed correctly
211 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
212 not alignment area in exported graphic
215 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
216 window has input focus
219 <!-- JAL-2992 -->Annotation panel set too high when
220 annotation added to view (Windows)
223 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
224 network connectivity is poor
227 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
228 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
229 the currently open URL and links from a page viewed in
230 Firefox or Chrome on Windows is now fully supported. If
231 you are using Edge, only links in the page can be
232 dragged, and with Internet Explorer, only the currently
233 open URL in the browser can be dropped onto Jalview.</em>
239 <td width="60" nowrap>
241 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
244 <td><div align="left">
248 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
249 for disabling automatic superposition of multiple
250 structures and open structures in existing views
253 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
254 ID and annotation area margins can be click-dragged to
258 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
262 <!-- JAL-2759 -->Improved performance for large alignments
263 and lots of hidden columns
266 <!-- JAL-2593 -->Improved performance when rendering lots
267 of features (particularly when transparency is disabled)
272 <td><div align="left">
275 <!-- JAL-2899 -->Structure and Overview aren't updated
276 when Colour By Annotation threshold slider is adjusted
279 <!-- JAL-2778 -->Slow redraw when Overview panel shown
280 overlapping alignment panel
283 <!-- JAL-2929 -->Overview doesn't show end of unpadded
287 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
288 improved: CDS not handled correctly if transcript has no
292 <!-- JAL-2321 -->Secondary structure and temperature
293 factor annotation not added to sequence when local PDB
294 file associated with it by drag'n'drop or structure
298 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
299 dialog doesn't import PDB files dropped on an alignment
302 <!-- JAL-2666 -->Linked scrolling via protein horizontal
303 scroll bar doesn't work for some CDS/Protein views
306 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
307 Java 1.8u153 onwards and Java 1.9u4+.
310 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
311 columns in annotation row
314 <!-- JAL-2913 -->Preferences panel's ID Width control is not
315 honored in batch mode
318 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
319 for structures added to existing Jmol view
322 <!-- JAL-2223 -->'View Mappings' includes duplicate
323 entries after importing project with multiple views
326 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
327 protein sequences via SIFTS from associated PDB entries
328 with negative residue numbers or missing residues fails
331 <!-- JAL-2952 -->Exception when shading sequence with negative
332 Temperature Factor values from annotated PDB files (e.g.
333 as generated by CONSURF)
336 <!-- JAL-2920 -->Uniprot 'sequence variant' features
337 tooltip doesn't include a text description of mutation
340 <!-- JAL-2922 -->Invert displayed features very slow when
341 structure and/or overview windows are also shown
344 <!-- JAL-2954 -->Selecting columns from highlighted regions
345 very slow for alignments with large numbers of sequences
348 <!-- JAL-2925 -->Copy Consensus fails for group consensus
349 with 'StringIndexOutOfBounds'
352 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
353 platforms running Java 10
356 <!-- JAL-2960 -->Adding a structure to existing structure
357 view appears to do nothing because the view is hidden behind the alignment view
363 <!-- JAL-2926 -->Copy consensus sequence option in applet
364 should copy the group consensus when popup is opened on it
370 <!-- JAL-2913 -->Fixed ID width preference is not respected
373 <em>New Known Defects</em>
376 <!-- JAL-2973 --> Exceptions occasionally raised when
377 editing a large alignment and overview is displayed
380 <!-- JAL-2974 -->'Overview updating' progress bar is shown
381 repeatedly after a series of edits even when the overview
382 is no longer reflecting updates
385 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
386 structures for protein subsequence (if 'Trim Retrieved
387 Sequences' enabled) or Ensembl isoforms (Workaround in
388 2.10.4 is to fail back to N&W mapping)
395 <td width="60" nowrap>
397 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
400 <td><div align="left">
401 <ul><li>Updated Certum Codesigning Certificate
402 (Valid till 30th November 2018)</li></ul></div></td>
403 <td><div align="left">
406 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
407 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
408 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
409 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
410 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
411 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
412 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
418 <td width="60" nowrap>
420 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
423 <td><div align="left">
427 <!-- JAL-2446 -->Faster and more efficient management and
428 rendering of sequence features
431 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
432 429 rate limit request hander
435 <!-- JAL-2773 -->Structure views don't get updated unless
436 their colours have changed
439 <!-- JAL-2495 -->All linked sequences are highlighted for
440 a structure mousover (Jmol) or selection (Chimera)
443 <!-- JAL-2790 -->'Cancel' button in progress bar for
444 JABAWS AACon, RNAAliFold and Disorder prediction jobs
447 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
448 view from Ensembl locus cross-references
451 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
455 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
456 feature can be disabled
459 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
460 PDB easier retrieval of sequences for lists of IDs
463 <!-- JAL-2758 -->Short names for sequences retrieved from
469 <li>Groovy interpreter updated to 2.4.12</li>
470 <li>Example groovy script for generating a matrix of
471 percent identity scores for current alignment.</li>
473 <em>Testing and Deployment</em>
476 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
480 <td><div align="left">
484 <!-- JAL-2643 -->Pressing tab after updating the colour
485 threshold text field doesn't trigger an update to the
489 <!-- JAL-2682 -->Race condition when parsing sequence ID
493 <!-- JAL-2608 -->Overview windows are also closed when
494 alignment window is closed
497 <!-- JAL-2548 -->Export of features doesn't always respect
501 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
502 takes a long time in Cursor mode
508 <!-- JAL-2777 -->Structures with whitespace chainCode
509 cannot be viewed in Chimera
512 <!-- JAL-2728 -->Protein annotation panel too high in
516 <!-- JAL-2757 -->Can't edit the query after the server
517 error warning icon is shown in Uniprot and PDB Free Text
521 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
524 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
527 <!-- JAL-2739 -->Hidden column marker in last column not
528 rendered when switching back from Wrapped to normal view
531 <!-- JAL-2768 -->Annotation display corrupted when
532 scrolling right in unwapped alignment view
535 <!-- JAL-2542 -->Existing features on subsequence
536 incorrectly relocated when full sequence retrieved from
540 <!-- JAL-2733 -->Last reported memory still shown when
541 Desktop->Show Memory is unticked (OSX only)
544 <!-- JAL-2658 -->Amend Features dialog doesn't allow
545 features of same type and group to be selected for
549 <!-- JAL-2524 -->Jalview becomes sluggish in wide
550 alignments when hidden columns are present
553 <!-- JAL-2392 -->Jalview freezes when loading and
554 displaying several structures
557 <!-- JAL-2732 -->Black outlines left after resizing or
561 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
562 within the Jalview desktop on OSX
565 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
566 when in wrapped alignment mode
569 <!-- JAL-2636 -->Scale mark not shown when close to right
570 hand end of alignment
573 <!-- JAL-2684 -->Pairwise alignment of selected regions of
574 each selected sequence do not have correct start/end
578 <!-- JAL-2793 -->Alignment ruler height set incorrectly
579 after canceling the Alignment Window's Font dialog
582 <!-- JAL-2036 -->Show cross-references not enabled after
583 restoring project until a new view is created
586 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
587 URL links appears when only default EMBL-EBI link is
588 configured (since 2.10.2b2)
591 <!-- JAL-2775 -->Overview redraws whole window when box
595 <!-- JAL-2225 -->Structure viewer doesn't map all chains
596 in a multi-chain structure when viewing alignment
597 involving more than one chain (since 2.10)
600 <!-- JAL-2811 -->Double residue highlights in cursor mode
601 if new selection moves alignment window
604 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
605 arrow key in cursor mode to pass hidden column marker
608 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
609 that produces correctly annotated transcripts and products
612 <!-- JAL-2776 -->Toggling a feature group after first time
613 doesn't update associated structure view
616 <em>Applet</em><br />
619 <!-- JAL-2687 -->Concurrent modification exception when
620 closing alignment panel
623 <em>BioJSON</em><br />
626 <!-- JAL-2546 -->BioJSON export does not preserve
627 non-positional features
630 <em>New Known Issues</em>
633 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
634 sequence features correctly (for many previous versions of
638 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
639 using cursor in wrapped panel other than top
642 <!-- JAL-2791 -->Select columns containing feature ignores
643 graduated colour threshold
646 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
647 always preserve numbering and sequence features
650 <em>Known Java 9 Issues</em>
653 <!-- JAL-2902 -->Groovy Console very slow to open and is
654 not responsive when entering characters (Webstart, Java
661 <td width="60" nowrap>
663 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
664 <em>2/10/2017</em></strong>
667 <td><div align="left">
668 <em>New features in Jalview Desktop</em>
671 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
673 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
677 <td><div align="left">
681 <td width="60" nowrap>
683 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
684 <em>7/9/2017</em></strong>
687 <td><div align="left">
691 <!-- JAL-2588 -->Show gaps in overview window by colouring
692 in grey (sequences used to be coloured grey, and gaps were
696 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
700 <!-- JAL-2587 -->Overview updates immediately on increase
701 in size and progress bar shown as higher resolution
702 overview is recalculated
707 <td><div align="left">
711 <!-- JAL-2664 -->Overview window redraws every hidden
712 column region row by row
715 <!-- JAL-2681 -->duplicate protein sequences shown after
716 retrieving Ensembl crossrefs for sequences from Uniprot
719 <!-- JAL-2603 -->Overview window throws NPE if show boxes
720 format setting is unticked
723 <!-- JAL-2610 -->Groups are coloured wrongly in overview
724 if group has show boxes format setting unticked
727 <!-- JAL-2672,JAL-2665 -->Redraw problems when
728 autoscrolling whilst dragging current selection group to
729 include sequences and columns not currently displayed
732 <!-- JAL-2691 -->Not all chains are mapped when multimeric
733 assemblies are imported via CIF file
736 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
737 displayed when threshold or conservation colouring is also
741 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
745 <!-- JAL-2673 -->Jalview continues to scroll after
746 dragging a selected region off the visible region of the
750 <!-- JAL-2724 -->Cannot apply annotation based
751 colourscheme to all groups in a view
754 <!-- JAL-2511 -->IDs don't line up with sequences
755 initially after font size change using the Font chooser or
762 <td width="60" nowrap>
764 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
767 <td><div align="left">
768 <em>Calculations</em>
772 <!-- JAL-1933 -->Occupancy annotation row shows number of
773 ungapped positions in each column of the alignment.
776 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
777 a calculation dialog box
780 <!-- JAL-2379 -->Revised implementation of PCA for speed
781 and memory efficiency (~30x faster)
784 <!-- JAL-2403 -->Revised implementation of sequence
785 similarity scores as used by Tree, PCA, Shading Consensus
786 and other calculations
789 <!-- JAL-2416 -->Score matrices are stored as resource
790 files within the Jalview codebase
793 <!-- JAL-2500 -->Trees computed on Sequence Feature
794 Similarity may have different topology due to increased
801 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
802 model for alignments and groups
805 <!-- JAL-384 -->Custom shading schemes created via groovy
812 <!-- JAL-2526 -->Efficiency improvements for interacting
813 with alignment and overview windows
816 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
820 <!-- JAL-2388 -->Hidden columns and sequences can be
824 <!-- JAL-2611 -->Click-drag in visible area allows fine
825 adjustment of visible position
829 <em>Data import/export</em>
832 <!-- JAL-2535 -->Posterior probability annotation from
833 Stockholm files imported as sequence associated annotation
836 <!-- JAL-2507 -->More robust per-sequence positional
837 annotation input/output via stockholm flatfile
840 <!-- JAL-2533 -->Sequence names don't include file
841 extension when importing structure files without embedded
842 names or PDB accessions
845 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
846 format sequence substitution matrices
849 <em>User Interface</em>
852 <!-- JAL-2447 --> Experimental Features Checkbox in
853 Desktop's Tools menu to hide or show untested features in
857 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
858 via Overview or sequence motif search operations
861 <!-- JAL-2547 -->Amend sequence features dialog box can be
862 opened by double clicking gaps within sequence feature
866 <!-- JAL-1476 -->Status bar message shown when not enough
867 aligned positions were available to create a 3D structure
871 <em>3D Structure</em>
874 <!-- JAL-2430 -->Hidden regions in alignment views are not
875 coloured in linked structure views
878 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
879 file-based command exchange
882 <!-- JAL-2375 -->Structure chooser automatically shows
883 Cached Structures rather than querying the PDBe if
884 structures are already available for sequences
887 <!-- JAL-2520 -->Structures imported via URL are cached in
888 the Jalview project rather than downloaded again when the
892 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
893 to transfer Chimera's structure attributes as Jalview
894 features, and vice-versa (<strong>Experimental
898 <em>Web Services</em>
901 <!-- JAL-2549 -->Updated JABAWS client to v2.2
904 <!-- JAL-2335 -->Filter non-standard amino acids and
905 nucleotides when submitting to AACon and other MSA
909 <!-- JAL-2316, -->URLs for viewing database
910 cross-references provided by identifiers.org and the
918 <!-- JAL-2344 -->FileFormatI interface for describing and
919 identifying file formats (instead of String constants)
922 <!-- JAL-2228 -->FeatureCounter script refactored for
923 efficiency when counting all displayed features (not
924 backwards compatible with 2.10.1)
927 <em>Example files</em>
930 <!-- JAL-2631 -->Graduated feature colour style example
931 included in the example feature file
934 <em>Documentation</em>
937 <!-- JAL-2339 -->Release notes reformatted for readability
938 with the built-in Java help viewer
941 <!-- JAL-1644 -->Find documentation updated with 'search
942 sequence description' option
948 <!-- JAL-2485, -->External service integration tests for
949 Uniprot REST Free Text Search Client
952 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
955 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
960 <td><div align="left">
961 <em>Calculations</em>
964 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
965 matrix - C->R should be '-3'<br />Old matrix restored
966 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
968 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
969 Jalview's treatment of gaps in PCA and substitution matrix
970 based Tree calculations.<br /> <br />In earlier versions
971 of Jalview, gaps matching gaps were penalised, and gaps
972 matching non-gaps penalised even more. In the PCA
973 calculation, gaps were actually treated as non-gaps - so
974 different costs were applied, which meant Jalview's PCAs
975 were different to those produced by SeqSpace.<br />Jalview
976 now treats gaps in the same way as SeqSpace (ie it scores
977 them as 0). <br /> <br />Enter the following in the
978 Groovy console to restore pre-2.10.2 behaviour:<br />
979 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
980 // for 2.10.1 mode <br />
981 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
982 // to restore 2.10.2 mode <br /> <br /> <em>Note:
983 these settings will affect all subsequent tree and PCA
984 calculations (not recommended)</em></li>
986 <!-- JAL-2424 -->Fixed off-by-one bug that affected
987 scaling of branch lengths for trees computed using
988 Sequence Feature Similarity.
991 <!-- JAL-2377 -->PCA calculation could hang when
992 generating output report when working with highly
996 <!-- JAL-2544 --> Sort by features includes features to
997 right of selected region when gaps present on right-hand
1001 <em>User Interface</em>
1004 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1005 doesn't reselect a specific sequence's associated
1006 annotation after it was used for colouring a view
1009 <!-- JAL-2419 -->Current selection lost if popup menu
1010 opened on a region of alignment without groups
1013 <!-- JAL-2374 -->Popup menu not always shown for regions
1014 of an alignment with overlapping groups
1017 <!-- JAL-2310 -->Finder double counts if both a sequence's
1018 name and description match
1021 <!-- JAL-2370 -->Hiding column selection containing two
1022 hidden regions results in incorrect hidden regions
1025 <!-- JAL-2386 -->'Apply to all groups' setting when
1026 changing colour does not apply Conservation slider value
1030 <!-- JAL-2373 -->Percentage identity and conservation menu
1031 items do not show a tick or allow shading to be disabled
1034 <!-- JAL-2385 -->Conservation shading or PID threshold
1035 lost when base colourscheme changed if slider not visible
1038 <!-- JAL-2547 -->Sequence features shown in tooltip for
1039 gaps before start of features
1042 <!-- JAL-2623 -->Graduated feature colour threshold not
1043 restored to UI when feature colour is edited
1046 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1047 a time when scrolling vertically in wrapped mode.
1050 <!-- JAL-2630 -->Structure and alignment overview update
1051 as graduate feature colour settings are modified via the
1055 <!-- JAL-2034 -->Overview window doesn't always update
1056 when a group defined on the alignment is resized
1059 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1060 wrapped view result in positional status updates
1064 <!-- JAL-2563 -->Status bar doesn't show position for
1065 ambiguous amino acid and nucleotide symbols
1068 <!-- JAL-2602 -->Copy consensus sequence failed if
1069 alignment included gapped columns
1072 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1073 widgets don't permanently disappear
1076 <!-- JAL-2503 -->Cannot select or filter quantitative
1077 annotation that are shown only as column labels (e.g.
1078 T-Coffee column reliability scores)
1081 <!-- JAL-2594 -->Exception thrown if trying to create a
1082 sequence feature on gaps only
1085 <!-- JAL-2504 -->Features created with 'New feature'
1086 button from a Find inherit previously defined feature type
1087 rather than the Find query string
1090 <!-- JAL-2423 -->incorrect title in output window when
1091 exporting tree calculated in Jalview
1094 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1095 and then revealing them reorders sequences on the
1099 <!-- JAL-964 -->Group panel in sequence feature settings
1100 doesn't update to reflect available set of groups after
1101 interactively adding or modifying features
1104 <!-- JAL-2225 -->Sequence Database chooser unusable on
1108 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1109 only excluded gaps in current sequence and ignored
1116 <!-- JAL-2421 -->Overview window visible region moves
1117 erratically when hidden rows or columns are present
1120 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1121 Structure Viewer's colour menu don't correspond to
1125 <!-- JAL-2405 -->Protein specific colours only offered in
1126 colour and group colour menu for protein alignments
1129 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1130 reflect currently selected view or group's shading
1134 <!-- JAL-2624 -->Feature colour thresholds not respected
1135 when rendered on overview and structures when opacity at
1139 <!-- JAL-2589 -->User defined gap colour not shown in
1140 overview when features overlaid on alignment
1143 <em>Data import/export</em>
1146 <!-- JAL-2576 -->Very large alignments take a long time to
1150 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1151 added after a sequence was imported are not written to
1155 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1156 when importing RNA secondary structure via Stockholm
1159 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1160 not shown in correct direction for simple pseudoknots
1163 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1164 with lightGray or darkGray via features file (but can
1168 <!-- JAL-2383 -->Above PID colour threshold not recovered
1169 when alignment view imported from project
1172 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1173 structure and sequences extracted from structure files
1174 imported via URL and viewed in Jmol
1177 <!-- JAL-2520 -->Structures loaded via URL are saved in
1178 Jalview Projects rather than fetched via URL again when
1179 the project is loaded and the structure viewed
1182 <em>Web Services</em>
1185 <!-- JAL-2519 -->EnsemblGenomes example failing after
1186 release of Ensembl v.88
1189 <!-- JAL-2366 -->Proxy server address and port always
1190 appear enabled in Preferences->Connections
1193 <!-- JAL-2461 -->DAS registry not found exceptions
1194 removed from console output
1197 <!-- JAL-2582 -->Cannot retrieve protein products from
1198 Ensembl by Peptide ID
1201 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1202 created from SIFTs, and spurious 'Couldn't open structure
1203 in Chimera' errors raised after April 2017 update (problem
1204 due to 'null' string rather than empty string used for
1205 residues with no corresponding PDB mapping).
1208 <em>Application UI</em>
1211 <!-- JAL-2361 -->User Defined Colours not added to Colour
1215 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1216 case' residues (button in colourscheme editor debugged and
1217 new documentation and tooltips added)
1220 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1221 doesn't restore group-specific text colour thresholds
1224 <!-- JAL-2243 -->Feature settings panel does not update as
1225 new features are added to alignment
1228 <!-- JAL-2532 -->Cancel in feature settings reverts
1229 changes to feature colours via the Amend features dialog
1232 <!-- JAL-2506 -->Null pointer exception when attempting to
1233 edit graduated feature colour via amend features dialog
1237 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1238 selection menu changes colours of alignment views
1241 <!-- JAL-2426 -->Spurious exceptions in console raised
1242 from alignment calculation workers after alignment has
1246 <!-- JAL-1608 -->Typo in selection popup menu - Create
1247 groups now 'Create Group'
1250 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1251 Create/Undefine group doesn't always work
1254 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1255 shown again after pressing 'Cancel'
1258 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1259 adjusts start position in wrap mode
1262 <!-- JAL-2563 -->Status bar doesn't show positions for
1263 ambiguous amino acids
1266 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1267 CDS/Protein view after CDS sequences added for aligned
1271 <!-- JAL-2592 -->User defined colourschemes called 'User
1272 Defined' don't appear in Colours menu
1278 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1279 score models doesn't always result in an updated PCA plot
1282 <!-- JAL-2442 -->Features not rendered as transparent on
1283 overview or linked structure view
1286 <!-- JAL-2372 -->Colour group by conservation doesn't
1290 <!-- JAL-2517 -->Hitting Cancel after applying
1291 user-defined colourscheme doesn't restore original
1298 <!-- JAL-2314 -->Unit test failure:
1299 jalview.ws.jabaws.RNAStructExportImport setup fails
1302 <!-- JAL-2307 -->Unit test failure:
1303 jalview.ws.sifts.SiftsClientTest due to compatibility
1304 problems with deep array comparison equality asserts in
1305 successive versions of TestNG
1308 <!-- JAL-2479 -->Relocated StructureChooserTest and
1309 ParameterUtilsTest Unit tests to Network suite
1312 <em>New Known Issues</em>
1315 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1316 phase after a sequence motif find operation
1319 <!-- JAL-2550 -->Importing annotation file with rows
1320 containing just upper and lower case letters are
1321 interpreted as WUSS RNA secondary structure symbols
1324 <!-- JAL-2590 -->Cannot load and display Newick trees
1325 reliably from eggnog Ortholog database
1328 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1329 containing features of type Highlight' when 'B' is pressed
1330 to mark columns containing highlighted regions.
1333 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1334 doesn't always add secondary structure annotation.
1339 <td width="60" nowrap>
1340 <div align="center">
1341 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1344 <td><div align="left">
1348 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1349 for all consensus calculations
1352 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1355 <li>Updated Jalview's Certum code signing certificate
1358 <em>Application</em>
1361 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1362 set of database cross-references, sorted alphabetically
1365 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1366 from database cross references. Users with custom links
1367 will receive a <a href="webServices/urllinks.html#warning">warning
1368 dialog</a> asking them to update their preferences.
1371 <!-- JAL-2287-->Cancel button and escape listener on
1372 dialog warning user about disconnecting Jalview from a
1376 <!-- JAL-2320-->Jalview's Chimera control window closes if
1377 the Chimera it is connected to is shut down
1380 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1381 columns menu item to mark columns containing highlighted
1382 regions (e.g. from structure selections or results of a
1386 <!-- JAL-2284-->Command line option for batch-generation
1387 of HTML pages rendering alignment data with the BioJS
1397 <!-- JAL-2286 -->Columns with more than one modal residue
1398 are not coloured or thresholded according to percent
1399 identity (first observed in Jalview 2.8.2)
1402 <!-- JAL-2301 -->Threonine incorrectly reported as not
1406 <!-- JAL-2318 -->Updates to documentation pages (above PID
1407 threshold, amino acid properties)
1410 <!-- JAL-2292 -->Lower case residues in sequences are not
1411 reported as mapped to residues in a structure file in the
1415 <!--JAL-2324 -->Identical features with non-numeric scores
1416 could be added multiple times to a sequence
1419 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1420 bond features shown as two highlighted residues rather
1421 than a range in linked structure views, and treated
1422 correctly when selecting and computing trees from features
1425 <!-- JAL-2281-->Custom URL links for database
1426 cross-references are matched to database name regardless
1431 <em>Application</em>
1434 <!-- JAL-2282-->Custom URL links for specific database
1435 names without regular expressions also offer links from
1439 <!-- JAL-2315-->Removing a single configured link in the
1440 URL links pane in Connections preferences doesn't actually
1441 update Jalview configuration
1444 <!-- JAL-2272-->CTRL-Click on a selected region to open
1445 the alignment area popup menu doesn't work on El-Capitan
1448 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1449 files with similarly named sequences if dropped onto the
1453 <!-- JAL-2312 -->Additional mappings are shown for PDB
1454 entries where more chains exist in the PDB accession than
1455 are reported in the SIFTS file
1458 <!-- JAL-2317-->Certain structures do not get mapped to
1459 the structure view when displayed with Chimera
1462 <!-- JAL-2317-->No chains shown in the Chimera view
1463 panel's View->Show Chains submenu
1466 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1467 work for wrapped alignment views
1470 <!--JAL-2197 -->Rename UI components for running JPred
1471 predictions from 'JNet' to 'JPred'
1474 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1475 corrupted when annotation panel vertical scroll is not at
1476 first annotation row
1479 <!--JAL-2332 -->Attempting to view structure for Hen
1480 lysozyme results in a PDB Client error dialog box
1483 <!-- JAL-2319 -->Structure View's mapping report switched
1484 ranges for PDB and sequence for SIFTS
1487 SIFTS 'Not_Observed' residues mapped to non-existant
1491 <!-- <em>New Known Issues</em>
1498 <td width="60" nowrap>
1499 <div align="center">
1500 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1501 <em>25/10/2016</em></strong>
1504 <td><em>Application</em>
1506 <li>3D Structure chooser opens with 'Cached structures'
1507 view if structures already loaded</li>
1508 <li>Progress bar reports models as they are loaded to
1509 structure views</li>
1515 <li>Colour by conservation always enabled and no tick
1516 shown in menu when BLOSUM or PID shading applied</li>
1517 <li>FER1_ARATH and FER2_ARATH labels were switched in
1518 example sequences/projects/trees</li>
1520 <em>Application</em>
1522 <li>Jalview projects with views of local PDB structure
1523 files saved on Windows cannot be opened on OSX</li>
1524 <li>Multiple structure views can be opened and superposed
1525 without timeout for structures with multiple models or
1526 multiple sequences in alignment</li>
1527 <li>Cannot import or associated local PDB files without a
1528 PDB ID HEADER line</li>
1529 <li>RMSD is not output in Jmol console when superposition
1531 <li>Drag and drop of URL from Browser fails for Linux and
1532 OSX versions earlier than El Capitan</li>
1533 <li>ENA client ignores invalid content from ENA server</li>
1534 <li>Exceptions are not raised in console when ENA client
1535 attempts to fetch non-existent IDs via Fetch DB Refs UI
1537 <li>Exceptions are not raised in console when a new view
1538 is created on the alignment</li>
1539 <li>OSX right-click fixed for group selections: CMD-click
1540 to insert/remove gaps in groups and CTRL-click to open group
1543 <em>Build and deployment</em>
1545 <li>URL link checker now copes with multi-line anchor
1548 <em>New Known Issues</em>
1550 <li>Drag and drop from URL links in browsers do not work
1557 <td width="60" nowrap>
1558 <div align="center">
1559 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1562 <td><em>General</em>
1565 <!-- JAL-2124 -->Updated Spanish translations.
1568 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1569 for importing structure data to Jalview. Enables mmCIF and
1573 <!-- JAL-192 --->Alignment ruler shows positions relative to
1577 <!-- JAL-2202 -->Position/residue shown in status bar when
1578 mousing over sequence associated annotation
1581 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1585 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1586 '()', canonical '[]' and invalid '{}' base pair populations
1590 <!-- JAL-2092 -->Feature settings popup menu options for
1591 showing or hiding columns containing a feature
1594 <!-- JAL-1557 -->Edit selected group by double clicking on
1595 group and sequence associated annotation labels
1598 <!-- JAL-2236 -->Sequence name added to annotation label in
1599 select/hide columns by annotation and colour by annotation
1603 </ul> <em>Application</em>
1606 <!-- JAL-2050-->Automatically hide introns when opening a
1607 gene/transcript view
1610 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1614 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1615 structure mappings with the EMBL-EBI PDBe SIFTS database
1618 <!-- JAL-2079 -->Updated download sites used for Rfam and
1619 Pfam sources to xfam.org
1622 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1625 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1626 over sequences in Jalview
1629 <!-- JAL-2027-->Support for reverse-complement coding
1630 regions in ENA and EMBL
1633 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1634 for record retrieval via ENA rest API
1637 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1641 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1642 groovy script execution
1645 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1646 alignment window's Calculate menu
1649 <!-- JAL-1812 -->Allow groovy scripts that call
1650 Jalview.getAlignFrames() to run in headless mode
1653 <!-- JAL-2068 -->Support for creating new alignment
1654 calculation workers from groovy scripts
1657 <!-- JAL-1369 --->Store/restore reference sequence in
1661 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1662 associations are now saved/restored from project
1665 <!-- JAL-1993 -->Database selection dialog always shown
1666 before sequence fetcher is opened
1669 <!-- JAL-2183 -->Double click on an entry in Jalview's
1670 database chooser opens a sequence fetcher
1673 <!-- JAL-1563 -->Free-text search client for UniProt using
1674 the UniProt REST API
1677 <!-- JAL-2168 -->-nonews command line parameter to prevent
1678 the news reader opening
1681 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1682 querying stored in preferences
1685 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1689 <!-- JAL-1977-->Tooltips shown on database chooser
1692 <!-- JAL-391 -->Reverse complement function in calculate
1693 menu for nucleotide sequences
1696 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1697 and feature counts preserves alignment ordering (and
1698 debugged for complex feature sets).
1701 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1702 viewing structures with Jalview 2.10
1705 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1706 genome, transcript CCDS and gene ids via the Ensembl and
1707 Ensembl Genomes REST API
1710 <!-- JAL-2049 -->Protein sequence variant annotation
1711 computed for 'sequence_variant' annotation on CDS regions
1715 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1719 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1720 Ref Fetcher fails to match, or otherwise updates sequence
1721 data from external database records.
1724 <!-- JAL-2154 -->Revised Jalview Project format for
1725 efficient recovery of sequence coding and alignment
1726 annotation relationships.
1728 </ul> <!-- <em>Applet</em>
1739 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1743 <!-- JAL-2018-->Export features in Jalview format (again)
1744 includes graduated colourschemes
1747 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1748 working with big alignments and lots of hidden columns
1751 <!-- JAL-2053-->Hidden column markers not always rendered
1752 at right of alignment window
1755 <!-- JAL-2067 -->Tidied up links in help file table of
1759 <!-- JAL-2072 -->Feature based tree calculation not shown
1763 <!-- JAL-2075 -->Hidden columns ignored during feature
1764 based tree calculation
1767 <!-- JAL-2065 -->Alignment view stops updating when show
1768 unconserved enabled for group on alignment
1771 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1775 <!-- JAL-2146 -->Alignment column in status incorrectly
1776 shown as "Sequence position" when mousing over
1780 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1781 hidden columns present
1784 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1785 user created annotation added to alignment
1788 <!-- JAL-1841 -->RNA Structure consensus only computed for
1789 '()' base pair annotation
1792 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1793 in zero scores for all base pairs in RNA Structure
1797 <!-- JAL-2174-->Extend selection with columns containing
1801 <!-- JAL-2275 -->Pfam format writer puts extra space at
1802 beginning of sequence
1805 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1809 <!-- JAL-2238 -->Cannot create groups on an alignment from
1810 from a tree when t-coffee scores are shown
1813 <!-- JAL-1836,1967 -->Cannot import and view PDB
1814 structures with chains containing negative resnums (4q4h)
1817 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1821 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1822 to Clustal, PIR and PileUp output
1825 <!-- JAL-2008 -->Reordering sequence features that are
1826 not visible causes alignment window to repaint
1829 <!-- JAL-2006 -->Threshold sliders don't work in
1830 graduated colour and colour by annotation row for e-value
1831 scores associated with features and annotation rows
1834 <!-- JAL-1797 -->amino acid physicochemical conservation
1835 calculation should be case independent
1838 <!-- JAL-2173 -->Remove annotation also updates hidden
1842 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1843 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1844 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1847 <!-- JAL-2065 -->Null pointer exceptions and redraw
1848 problems when reference sequence defined and 'show
1849 non-conserved' enabled
1852 <!-- JAL-1306 -->Quality and Conservation are now shown on
1853 load even when Consensus calculation is disabled
1856 <!-- JAL-1932 -->Remove right on penultimate column of
1857 alignment does nothing
1860 <em>Application</em>
1863 <!-- JAL-1552-->URLs and links can't be imported by
1864 drag'n'drop on OSX when launched via webstart (note - not
1865 yet fixed for El Capitan)
1868 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1869 output when running on non-gb/us i18n platforms
1872 <!-- JAL-1944 -->Error thrown when exporting a view with
1873 hidden sequences as flat-file alignment
1876 <!-- JAL-2030-->InstallAnywhere distribution fails when
1880 <!-- JAL-2080-->Jalview very slow to launch via webstart
1881 (also hotfix for 2.9.0b2)
1884 <!-- JAL-2085 -->Cannot save project when view has a
1885 reference sequence defined
1888 <!-- JAL-1011 -->Columns are suddenly selected in other
1889 alignments and views when revealing hidden columns
1892 <!-- JAL-1989 -->Hide columns not mirrored in complement
1893 view in a cDNA/Protein splitframe
1896 <!-- JAL-1369 -->Cannot save/restore representative
1897 sequence from project when only one sequence is
1901 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1902 in Structure Chooser
1905 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1906 structure consensus didn't refresh annotation panel
1909 <!-- JAL-1962 -->View mapping in structure view shows
1910 mappings between sequence and all chains in a PDB file
1913 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1914 dialogs format columns correctly, don't display array
1915 data, sort columns according to type
1918 <!-- JAL-1975 -->Export complete shown after destination
1919 file chooser is cancelled during an image export
1922 <!-- JAL-2025 -->Error when querying PDB Service with
1923 sequence name containing special characters
1926 <!-- JAL-2024 -->Manual PDB structure querying should be
1930 <!-- JAL-2104 -->Large tooltips with broken HTML
1931 formatting don't wrap
1934 <!-- JAL-1128 -->Figures exported from wrapped view are
1935 truncated so L looks like I in consensus annotation
1938 <!-- JAL-2003 -->Export features should only export the
1939 currently displayed features for the current selection or
1943 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1944 after fetching cross-references, and restoring from
1948 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1949 followed in the structure viewer
1952 <!-- JAL-2163 -->Titles for individual alignments in
1953 splitframe not restored from project
1956 <!-- JAL-2145 -->missing autocalculated annotation at
1957 trailing end of protein alignment in transcript/product
1958 splitview when pad-gaps not enabled by default
1961 <!-- JAL-1797 -->amino acid physicochemical conservation
1965 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1966 article has been read (reopened issue due to
1967 internationalisation problems)
1970 <!-- JAL-1960 -->Only offer PDB structures in structure
1971 viewer based on sequence name, PDB and UniProt
1976 <!-- JAL-1976 -->No progress bar shown during export of
1980 <!-- JAL-2213 -->Structures not always superimposed after
1981 multiple structures are shown for one or more sequences.
1984 <!-- JAL-1370 -->Reference sequence characters should not
1985 be replaced with '.' when 'Show unconserved' format option
1989 <!-- JAL-1823 -->Cannot specify chain code when entering
1990 specific PDB id for sequence
1993 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1994 'Export hidden sequences' is enabled, but 'export hidden
1995 columns' is disabled.
1998 <!--JAL-2026-->Best Quality option in structure chooser
1999 selects lowest rather than highest resolution structures
2003 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2004 to sequence mapping in 'View Mappings' report
2007 <!-- JAL-2284 -->Unable to read old Jalview projects that
2008 contain non-XML data added after Jalvew wrote project.
2011 <!-- JAL-2118 -->Newly created annotation row reorders
2012 after clicking on it to create new annotation for a
2016 <!-- JAL-1980 -->Null Pointer Exception raised when
2017 pressing Add on an orphaned cut'n'paste window.
2019 <!-- may exclude, this is an external service stability issue JAL-1941
2020 -- > RNA 3D structure not added via DSSR service</li> -->
2025 <!-- JAL-2151 -->Incorrect columns are selected when
2026 hidden columns present before start of sequence
2029 <!-- JAL-1986 -->Missing dependencies on applet pages
2033 <!-- JAL-1947 -->Overview pixel size changes when
2034 sequences are hidden in applet
2037 <!-- JAL-1996 -->Updated instructions for applet
2038 deployment on examples pages.
2045 <td width="60" nowrap>
2046 <div align="center">
2047 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2048 <em>16/10/2015</em></strong>
2051 <td><em>General</em>
2053 <li>Time stamps for signed Jalview application and applet
2058 <em>Application</em>
2060 <li>Duplicate group consensus and conservation rows
2061 shown when tree is partitioned</li>
2062 <li>Erratic behaviour when tree partitions made with
2063 multiple cDNA/Protein split views</li>
2069 <td width="60" nowrap>
2070 <div align="center">
2071 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2072 <em>8/10/2015</em></strong>
2075 <td><em>General</em>
2077 <li>Updated Spanish translations of localized text for
2079 </ul> <em>Application</em>
2081 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2082 <li>Signed OSX InstallAnywhere installer<br></li>
2083 <li>Support for per-sequence based annotations in BioJSON</li>
2084 </ul> <em>Applet</em>
2086 <li>Split frame example added to applet examples page</li>
2087 </ul> <em>Build and Deployment</em>
2090 <!-- JAL-1888 -->New ant target for running Jalview's test
2098 <li>Mapping of cDNA to protein in split frames
2099 incorrect when sequence start > 1</li>
2100 <li>Broken images in filter column by annotation dialog
2102 <li>Feature colours not parsed from features file</li>
2103 <li>Exceptions and incomplete link URLs recovered when
2104 loading a features file containing HTML tags in feature
2108 <em>Application</em>
2110 <li>Annotations corrupted after BioJS export and
2112 <li>Incorrect sequence limits after Fetch DB References
2113 with 'trim retrieved sequences'</li>
2114 <li>Incorrect warning about deleting all data when
2115 deleting selected columns</li>
2116 <li>Patch to build system for shipping properly signed
2117 JNLP templates for webstart launch</li>
2118 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2119 unreleased structures for download or viewing</li>
2120 <li>Tab/space/return keystroke operation of EMBL-PDBe
2121 fetcher/viewer dialogs works correctly</li>
2122 <li>Disabled 'minimise' button on Jalview windows
2123 running on OSX to workaround redraw hang bug</li>
2124 <li>Split cDNA/Protein view position and geometry not
2125 recovered from jalview project</li>
2126 <li>Initial enabled/disabled state of annotation menu
2127 sorter 'show autocalculated first/last' corresponds to
2129 <li>Restoring of Clustal, RNA Helices and T-Coffee
2130 color schemes from BioJSON</li>
2134 <li>Reorder sequences mirrored in cDNA/Protein split
2136 <li>Applet with Jmol examples not loading correctly</li>
2142 <td><div align="center">
2143 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2145 <td><em>General</em>
2147 <li>Linked visualisation and analysis of DNA and Protein
2150 <li>Translated cDNA alignments shown as split protein
2151 and DNA alignment views</li>
2152 <li>Codon consensus annotation for linked protein and
2153 cDNA alignment views</li>
2154 <li>Link cDNA or Protein product sequences by loading
2155 them onto Protein or cDNA alignments</li>
2156 <li>Reconstruct linked cDNA alignment from aligned
2157 protein sequences</li>
2160 <li>Jmol integration updated to Jmol v14.2.14</li>
2161 <li>Import and export of Jalview alignment views as <a
2162 href="features/bioJsonFormat.html">BioJSON</a></li>
2163 <li>New alignment annotation file statements for
2164 reference sequences and marking hidden columns</li>
2165 <li>Reference sequence based alignment shading to
2166 highlight variation</li>
2167 <li>Select or hide columns according to alignment
2169 <li>Find option for locating sequences by description</li>
2170 <li>Conserved physicochemical properties shown in amino
2171 acid conservation row</li>
2172 <li>Alignments can be sorted by number of RNA helices</li>
2173 </ul> <em>Application</em>
2175 <li>New cDNA/Protein analysis capabilities
2177 <li>Get Cross-References should open a Split Frame
2178 view with cDNA/Protein</li>
2179 <li>Detect when nucleotide sequences and protein
2180 sequences are placed in the same alignment</li>
2181 <li>Split cDNA/Protein views are saved in Jalview
2186 <li>Use REST API to talk to Chimera</li>
2187 <li>Selected regions in Chimera are highlighted in linked
2188 Jalview windows</li>
2190 <li>VARNA RNA viewer updated to v3.93</li>
2191 <li>VARNA views are saved in Jalview Projects</li>
2192 <li>Pseudoknots displayed as Jalview RNA annotation can
2193 be shown in VARNA</li>
2195 <li>Make groups for selection uses marked columns as well
2196 as the active selected region</li>
2198 <li>Calculate UPGMA and NJ trees using sequence feature
2200 <li>New Export options
2202 <li>New Export Settings dialog to control hidden
2203 region export in flat file generation</li>
2205 <li>Export alignment views for display with the <a
2206 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2208 <li>Export scrollable SVG in HTML page</li>
2209 <li>Optional embedding of BioJSON data when exporting
2210 alignment figures to HTML</li>
2212 <li>3D structure retrieval and display
2214 <li>Free text and structured queries with the PDBe
2216 <li>PDBe Search API based discovery and selection of
2217 PDB structures for a sequence set</li>
2221 <li>JPred4 employed for protein secondary structure
2223 <li>Hide Insertions menu option to hide unaligned columns
2224 for one or a group of sequences</li>
2225 <li>Automatically hide insertions in alignments imported
2226 from the JPred4 web server</li>
2227 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2228 system on OSX<br />LGPL libraries courtesy of <a
2229 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2231 <li>changed 'View nucleotide structure' submenu to 'View
2232 VARNA 2D Structure'</li>
2233 <li>change "View protein structure" menu option to "3D
2236 </ul> <em>Applet</em>
2238 <li>New layout for applet example pages</li>
2239 <li>New parameters to enable SplitFrame view
2240 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2241 <li>New example demonstrating linked viewing of cDNA and
2242 Protein alignments</li>
2243 </ul> <em>Development and deployment</em>
2245 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2246 <li>Include installation type and git revision in build
2247 properties and console log output</li>
2248 <li>Jalview Github organisation, and new github site for
2249 storing BioJsMSA Templates</li>
2250 <li>Jalview's unit tests now managed with TestNG</li>
2253 <!-- <em>General</em>
2255 </ul> --> <!-- issues resolved --> <em>Application</em>
2257 <li>Escape should close any open find dialogs</li>
2258 <li>Typo in select-by-features status report</li>
2259 <li>Consensus RNA secondary secondary structure
2260 predictions are not highlighted in amber</li>
2261 <li>Missing gap character in v2.7 example file means
2262 alignment appears unaligned when pad-gaps is not enabled</li>
2263 <li>First switch to RNA Helices colouring doesn't colour
2264 associated structure views</li>
2265 <li>ID width preference option is greyed out when auto
2266 width checkbox not enabled</li>
2267 <li>Stopped a warning dialog from being shown when
2268 creating user defined colours</li>
2269 <li>'View Mapping' in structure viewer shows sequence
2270 mappings for just that viewer's sequences</li>
2271 <li>Workaround for superposing PDB files containing
2272 multiple models in Chimera</li>
2273 <li>Report sequence position in status bar when hovering
2274 over Jmol structure</li>
2275 <li>Cannot output gaps as '.' symbols with Selection ->
2276 output to text box</li>
2277 <li>Flat file exports of alignments with hidden columns
2278 have incorrect sequence start/end</li>
2279 <li>'Aligning' a second chain to a Chimera structure from
2281 <li>Colour schemes applied to structure viewers don't
2282 work for nucleotide</li>
2283 <li>Loading/cut'n'pasting an empty or invalid file leads
2284 to a grey/invisible alignment window</li>
2285 <li>Exported Jpred annotation from a sequence region
2286 imports to different position</li>
2287 <li>Space at beginning of sequence feature tooltips shown
2288 on some platforms</li>
2289 <li>Chimera viewer 'View | Show Chain' menu is not
2291 <li>'New View' fails with a Null Pointer Exception in
2292 console if Chimera has been opened</li>
2293 <li>Mouseover to Chimera not working</li>
2294 <li>Miscellaneous ENA XML feature qualifiers not
2296 <li>NPE in annotation renderer after 'Extract Scores'</li>
2297 <li>If two structures in one Chimera window, mouseover of
2298 either sequence shows on first structure</li>
2299 <li>'Show annotations' options should not make
2300 non-positional annotations visible</li>
2301 <li>Subsequence secondary structure annotation not shown
2302 in right place after 'view flanking regions'</li>
2303 <li>File Save As type unset when current file format is
2305 <li>Save as '.jar' option removed for saving Jalview
2307 <li>Colour by Sequence colouring in Chimera more
2309 <li>Cannot 'add reference annotation' for a sequence in
2310 several views on same alignment</li>
2311 <li>Cannot show linked products for EMBL / ENA records</li>
2312 <li>Jalview's tooltip wraps long texts containing no
2314 </ul> <em>Applet</em>
2316 <li>Jmol to JalviewLite mouseover/link not working</li>
2317 <li>JalviewLite can't import sequences with ID
2318 descriptions containing angle brackets</li>
2319 </ul> <em>General</em>
2321 <li>Cannot export and reimport RNA secondary structure
2322 via jalview annotation file</li>
2323 <li>Random helix colour palette for colour by annotation
2324 with RNA secondary structure</li>
2325 <li>Mouseover to cDNA from STOP residue in protein
2326 translation doesn't work.</li>
2327 <li>hints when using the select by annotation dialog box</li>
2328 <li>Jmol alignment incorrect if PDB file has alternate CA
2330 <li>FontChooser message dialog appears to hang after
2331 choosing 1pt font</li>
2332 <li>Peptide secondary structure incorrectly imported from
2333 annotation file when annotation display text includes 'e' or
2335 <li>Cannot set colour of new feature type whilst creating
2337 <li>cDNA translation alignment should not be sequence
2338 order dependent</li>
2339 <li>'Show unconserved' doesn't work for lower case
2341 <li>Nucleotide ambiguity codes involving R not recognised</li>
2342 </ul> <em>Deployment and Documentation</em>
2344 <li>Applet example pages appear different to the rest of
2345 www.jalview.org</li>
2346 </ul> <em>Application Known issues</em>
2348 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2349 <li>Misleading message appears after trying to delete
2351 <li>Jalview icon not shown in dock after InstallAnywhere
2352 version launches</li>
2353 <li>Fetching EMBL reference for an RNA sequence results
2354 fails with a sequence mismatch</li>
2355 <li>Corrupted or unreadable alignment display when
2356 scrolling alignment to right</li>
2357 <li>ArrayIndexOutOfBoundsException thrown when remove
2358 empty columns called on alignment with ragged gapped ends</li>
2359 <li>auto calculated alignment annotation rows do not get
2360 placed above or below non-autocalculated rows</li>
2361 <li>Jalview dekstop becomes sluggish at full screen in
2362 ultra-high resolution</li>
2363 <li>Cannot disable consensus calculation independently of
2364 quality and conservation</li>
2365 <li>Mouseover highlighting between cDNA and protein can
2366 become sluggish with more than one splitframe shown</li>
2367 </ul> <em>Applet Known Issues</em>
2369 <li>Core PDB parsing code requires Jmol</li>
2370 <li>Sequence canvas panel goes white when alignment
2371 window is being resized</li>
2377 <td><div align="center">
2378 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2380 <td><em>General</em>
2382 <li>Updated Java code signing certificate donated by
2384 <li>Features and annotation preserved when performing
2385 pairwise alignment</li>
2386 <li>RNA pseudoknot annotation can be
2387 imported/exported/displayed</li>
2388 <li>'colour by annotation' can colour by RNA and
2389 protein secondary structure</li>
2390 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2391 post-hoc with 2.9 release</em>)
2394 </ul> <em>Application</em>
2396 <li>Extract and display secondary structure for sequences
2397 with 3D structures</li>
2398 <li>Support for parsing RNAML</li>
2399 <li>Annotations menu for layout
2401 <li>sort sequence annotation rows by alignment</li>
2402 <li>place sequence annotation above/below alignment
2405 <li>Output in Stockholm format</li>
2406 <li>Internationalisation: improved Spanish (es)
2408 <li>Structure viewer preferences tab</li>
2409 <li>Disorder and Secondary Structure annotation tracks
2410 shared between alignments</li>
2411 <li>UCSF Chimera launch and linked highlighting from
2413 <li>Show/hide all sequence associated annotation rows for
2414 all or current selection</li>
2415 <li>disorder and secondary structure predictions
2416 available as dataset annotation</li>
2417 <li>Per-sequence rna helices colouring</li>
2420 <li>Sequence database accessions imported when fetching
2421 alignments from Rfam</li>
2422 <li>update VARNA version to 3.91</li>
2424 <li>New groovy scripts for exporting aligned positions,
2425 conservation values, and calculating sum of pairs scores.</li>
2426 <li>Command line argument to set default JABAWS server</li>
2427 <li>include installation type in build properties and
2428 console log output</li>
2429 <li>Updated Jalview project format to preserve dataset
2433 <!-- issues resolved --> <em>Application</em>
2435 <li>Distinguish alignment and sequence associated RNA
2436 structure in structure->view->VARNA</li>
2437 <li>Raise dialog box if user deletes all sequences in an
2439 <li>Pressing F1 results in documentation opening twice</li>
2440 <li>Sequence feature tooltip is wrapped</li>
2441 <li>Double click on sequence associated annotation
2442 selects only first column</li>
2443 <li>Redundancy removal doesn't result in unlinked
2444 leaves shown in tree</li>
2445 <li>Undos after several redundancy removals don't undo
2447 <li>Hide sequence doesn't hide associated annotation</li>
2448 <li>User defined colours dialog box too big to fit on
2449 screen and buttons not visible</li>
2450 <li>author list isn't updated if already written to
2451 Jalview properties</li>
2452 <li>Popup menu won't open after retrieving sequence
2454 <li>File open window for associate PDB doesn't open</li>
2455 <li>Left-then-right click on a sequence id opens a
2456 browser search window</li>
2457 <li>Cannot open sequence feature shading/sort popup menu
2458 in feature settings dialog</li>
2459 <li>better tooltip placement for some areas of Jalview
2461 <li>Allow addition of JABAWS Server which doesn't
2462 pass validation</li>
2463 <li>Web services parameters dialog box is too large to
2465 <li>Muscle nucleotide alignment preset obscured by
2467 <li>JABAWS preset submenus don't contain newly
2468 defined user preset</li>
2469 <li>MSA web services warns user if they were launched
2470 with invalid input</li>
2471 <li>Jalview cannot contact DAS Registy when running on
2474 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2475 'Superpose with' submenu not shown when new view
2479 </ul> <!-- <em>Applet</em>
2481 </ul> <em>General</em>
2483 </ul>--> <em>Deployment and Documentation</em>
2485 <li>2G and 1G options in launchApp have no effect on
2486 memory allocation</li>
2487 <li>launchApp service doesn't automatically open
2488 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2490 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2491 InstallAnywhere reports cannot find valid JVM when Java
2492 1.7_055 is available
2494 </ul> <em>Application Known issues</em>
2497 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2498 corrupted or unreadable alignment display when scrolling
2502 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2503 retrieval fails but progress bar continues for DAS retrieval
2504 with large number of ID
2507 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2508 flatfile output of visible region has incorrect sequence
2512 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2513 rna structure consensus doesn't update when secondary
2514 structure tracks are rearranged
2517 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2518 invalid rna structure positional highlighting does not
2519 highlight position of invalid base pairs
2522 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2523 out of memory errors are not raised when saving Jalview
2524 project from alignment window file menu
2527 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2528 Switching to RNA Helices colouring doesn't propagate to
2532 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2533 colour by RNA Helices not enabled when user created
2534 annotation added to alignment
2537 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2538 Jalview icon not shown on dock in Mountain Lion/Webstart
2540 </ul> <em>Applet Known Issues</em>
2543 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2544 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2547 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2548 Jalview and Jmol example not compatible with IE9
2551 <li>Sort by annotation score doesn't reverse order
2557 <td><div align="center">
2558 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2561 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2564 <li>Internationalisation of user interface (usually
2565 called i18n support) and translation for Spanish locale</li>
2566 <li>Define/Undefine group on current selection with
2567 Ctrl-G/Shift Ctrl-G</li>
2568 <li>Improved group creation/removal options in
2569 alignment/sequence Popup menu</li>
2570 <li>Sensible precision for symbol distribution
2571 percentages shown in logo tooltip.</li>
2572 <li>Annotation panel height set according to amount of
2573 annotation when alignment first opened</li>
2574 </ul> <em>Application</em>
2576 <li>Interactive consensus RNA secondary structure
2577 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2578 <li>Select columns containing particular features from
2579 Feature Settings dialog</li>
2580 <li>View all 'representative' PDB structures for selected
2582 <li>Update Jalview project format:
2584 <li>New file extension for Jalview projects '.jvp'</li>
2585 <li>Preserve sequence and annotation dataset (to
2586 store secondary structure annotation,etc)</li>
2587 <li>Per group and alignment annotation and RNA helix
2591 <li>New similarity measures for PCA and Tree calculation
2593 <li>Experimental support for retrieval and viewing of
2594 flanking regions for an alignment</li>
2598 <!-- issues resolved --> <em>Application</em>
2600 <li>logo keeps spinning and status remains at queued or
2601 running after job is cancelled</li>
2602 <li>cannot export features from alignments imported from
2603 Jalview/VAMSAS projects</li>
2604 <li>Buggy slider for web service parameters that take
2606 <li>Newly created RNA secondary structure line doesn't
2607 have 'display all symbols' flag set</li>
2608 <li>T-COFFEE alignment score shading scheme and other
2609 annotation shading not saved in Jalview project</li>
2610 <li>Local file cannot be loaded in freshly downloaded
2612 <li>Jalview icon not shown on dock in Mountain
2614 <li>Load file from desktop file browser fails</li>
2615 <li>Occasional NPE thrown when calculating large trees</li>
2616 <li>Cannot reorder or slide sequences after dragging an
2617 alignment onto desktop</li>
2618 <li>Colour by annotation dialog throws NPE after using
2619 'extract scores' function</li>
2620 <li>Loading/cut'n'pasting an empty file leads to a grey
2621 alignment window</li>
2622 <li>Disorder thresholds rendered incorrectly after
2623 performing IUPred disorder prediction</li>
2624 <li>Multiple group annotated consensus rows shown when
2625 changing 'normalise logo' display setting</li>
2626 <li>Find shows blank dialog after 'finished searching' if
2627 nothing matches query</li>
2628 <li>Null Pointer Exceptions raised when sorting by
2629 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2631 <li>Errors in Jmol console when structures in alignment
2632 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2634 <li>Not all working JABAWS services are shown in
2636 <li>JAVAWS version of Jalview fails to launch with
2637 'invalid literal/length code'</li>
2638 <li>Annotation/RNA Helix colourschemes cannot be applied
2639 to alignment with groups (actually fixed in 2.8.0b1)</li>
2640 <li>RNA Helices and T-Coffee Scores available as default
2643 </ul> <em>Applet</em>
2645 <li>Remove group option is shown even when selection is
2647 <li>Apply to all groups ticked but colourscheme changes
2648 don't affect groups</li>
2649 <li>Documented RNA Helices and T-Coffee Scores as valid
2650 colourscheme name</li>
2651 <li>Annotation labels drawn on sequence IDs when
2652 Annotation panel is not displayed</li>
2653 <li>Increased font size for dropdown menus on OSX and
2654 embedded windows</li>
2655 </ul> <em>Other</em>
2657 <li>Consensus sequence for alignments/groups with a
2658 single sequence were not calculated</li>
2659 <li>annotation files that contain only groups imported as
2660 annotation and junk sequences</li>
2661 <li>Fasta files with sequences containing '*' incorrectly
2662 recognised as PFAM or BLC</li>
2663 <li>conservation/PID slider apply all groups option
2664 doesn't affect background (2.8.0b1)
2666 <li>redundancy highlighting is erratic at 0% and 100%</li>
2667 <li>Remove gapped columns fails for sequences with ragged
2669 <li>AMSA annotation row with leading spaces is not
2670 registered correctly on import</li>
2671 <li>Jalview crashes when selecting PCA analysis for
2672 certain alignments</li>
2673 <li>Opening the colour by annotation dialog for an
2674 existing annotation based 'use original colours'
2675 colourscheme loses original colours setting</li>
2680 <td><div align="center">
2681 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2682 <em>30/1/2014</em></strong>
2686 <li>Trusted certificates for JalviewLite applet and
2687 Jalview Desktop application<br />Certificate was donated by
2688 <a href="https://www.certum.eu">Certum</a> to the Jalview
2689 open source project).
2691 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2692 <li>Output in Stockholm format</li>
2693 <li>Allow import of data from gzipped files</li>
2694 <li>Export/import group and sequence associated line
2695 graph thresholds</li>
2696 <li>Nucleotide substitution matrix that supports RNA and
2697 ambiguity codes</li>
2698 <li>Allow disorder predictions to be made on the current
2699 selection (or visible selection) in the same way that JPred
2701 <li>Groovy scripting for headless Jalview operation</li>
2702 </ul> <em>Other improvements</em>
2704 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2705 <li>COMBINE statement uses current SEQUENCE_REF and
2706 GROUP_REF scope to group annotation rows</li>
2707 <li>Support '' style escaping of quotes in Newick
2709 <li>Group options for JABAWS service by command line name</li>
2710 <li>Empty tooltip shown for JABA service options with a
2711 link but no description</li>
2712 <li>Select primary source when selecting authority in
2713 database fetcher GUI</li>
2714 <li>Add .mfa to FASTA file extensions recognised by
2716 <li>Annotation label tooltip text wrap</li>
2721 <li>Slow scrolling when lots of annotation rows are
2723 <li>Lots of NPE (and slowness) after creating RNA
2724 secondary structure annotation line</li>
2725 <li>Sequence database accessions not imported when
2726 fetching alignments from Rfam</li>
2727 <li>Incorrect SHMR submission for sequences with
2729 <li>View all structures does not always superpose
2731 <li>Option widgets in service parameters not updated to
2732 reflect user or preset settings</li>
2733 <li>Null pointer exceptions for some services without
2734 presets or adjustable parameters</li>
2735 <li>Discover PDB IDs entry in structure menu doesn't
2736 discover PDB xRefs</li>
2737 <li>Exception encountered while trying to retrieve
2738 features with DAS</li>
2739 <li>Lowest value in annotation row isn't coloured
2740 when colour by annotation (per sequence) is coloured</li>
2741 <li>Keyboard mode P jumps to start of gapped region when
2742 residue follows a gap</li>
2743 <li>Jalview appears to hang importing an alignment with
2744 Wrap as default or after enabling Wrap</li>
2745 <li>'Right click to add annotations' message
2746 shown in wrap mode when no annotations present</li>
2747 <li>Disorder predictions fail with NPE if no automatic
2748 annotation already exists on alignment</li>
2749 <li>oninit javascript function should be called after
2750 initialisation completes</li>
2751 <li>Remove redundancy after disorder prediction corrupts
2752 alignment window display</li>
2753 <li>Example annotation file in documentation is invalid</li>
2754 <li>Grouped line graph annotation rows are not exported
2755 to annotation file</li>
2756 <li>Multi-harmony analysis cannot be run when only two
2758 <li>Cannot create multiple groups of line graphs with
2759 several 'combine' statements in annotation file</li>
2760 <li>Pressing return several times causes Number Format
2761 exceptions in keyboard mode</li>
2762 <li>Multi-harmony (SHMMR) method doesn't submit
2763 correct partitions for input data</li>
2764 <li>Translation from DNA to Amino Acids fails</li>
2765 <li>Jalview fail to load newick tree with quoted label</li>
2766 <li>--headless flag isn't understood</li>
2767 <li>ClassCastException when generating EPS in headless
2769 <li>Adjusting sequence-associated shading threshold only
2770 changes one row's threshold</li>
2771 <li>Preferences and Feature settings panel panel
2772 doesn't open</li>
2773 <li>hide consensus histogram also hides conservation and
2774 quality histograms</li>
2779 <td><div align="center">
2780 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2782 <td><em>Application</em>
2784 <li>Support for JABAWS 2.0 Services (AACon alignment
2785 conservation, protein disorder and Clustal Omega)</li>
2786 <li>JABAWS server status indicator in Web Services
2788 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2789 in Jalview alignment window</li>
2790 <li>Updated Jalview build and deploy framework for OSX
2791 mountain lion, windows 7, and 8</li>
2792 <li>Nucleotide substitution matrix for PCA that supports
2793 RNA and ambiguity codes</li>
2795 <li>Improved sequence database retrieval GUI</li>
2796 <li>Support fetching and database reference look up
2797 against multiple DAS sources (Fetch all from in 'fetch db
2799 <li>Jalview project improvements
2801 <li>Store and retrieve the 'belowAlignment'
2802 flag for annotation</li>
2803 <li>calcId attribute to group annotation rows on the
2805 <li>Store AACon calculation settings for a view in
2806 Jalview project</li>
2810 <li>horizontal scrolling gesture support</li>
2811 <li>Visual progress indicator when PCA calculation is
2813 <li>Simpler JABA web services menus</li>
2814 <li>visual indication that web service results are still
2815 being retrieved from server</li>
2816 <li>Serialise the dialogs that are shown when Jalview
2817 starts up for first time</li>
2818 <li>Jalview user agent string for interacting with HTTP
2820 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2822 <li>Examples directory and Groovy library included in
2823 InstallAnywhere distribution</li>
2824 </ul> <em>Applet</em>
2826 <li>RNA alignment and secondary structure annotation
2827 visualization applet example</li>
2828 </ul> <em>General</em>
2830 <li>Normalise option for consensus sequence logo</li>
2831 <li>Reset button in PCA window to return dimensions to
2833 <li>Allow seqspace or Jalview variant of alignment PCA
2835 <li>PCA with either nucleic acid and protein substitution
2837 <li>Allow windows containing HTML reports to be exported
2839 <li>Interactive display and editing of RNA secondary
2840 structure contacts</li>
2841 <li>RNA Helix Alignment Colouring</li>
2842 <li>RNA base pair logo consensus</li>
2843 <li>Parse sequence associated secondary structure
2844 information in Stockholm files</li>
2845 <li>HTML Export database accessions and annotation
2846 information presented in tooltip for sequences</li>
2847 <li>Import secondary structure from LOCARNA clustalw
2848 style RNA alignment files</li>
2849 <li>import and visualise T-COFFEE quality scores for an
2851 <li>'colour by annotation' per sequence option to
2852 shade each sequence according to its associated alignment
2854 <li>New Jalview Logo</li>
2855 </ul> <em>Documentation and Development</em>
2857 <li>documentation for score matrices used in Jalview</li>
2858 <li>New Website!</li>
2860 <td><em>Application</em>
2862 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2863 wsdbfetch REST service</li>
2864 <li>Stop windows being moved outside desktop on OSX</li>
2865 <li>Filetype associations not installed for webstart
2867 <li>Jalview does not always retrieve progress of a JABAWS
2868 job execution in full once it is complete</li>
2869 <li>revise SHMR RSBS definition to ensure alignment is
2870 uploaded via ali_file parameter</li>
2871 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2872 <li>View all structures superposed fails with exception</li>
2873 <li>Jnet job queues forever if a very short sequence is
2874 submitted for prediction</li>
2875 <li>Cut and paste menu not opened when mouse clicked on
2877 <li>Putting fractional value into integer text box in
2878 alignment parameter dialog causes Jalview to hang</li>
2879 <li>Structure view highlighting doesn't work on
2881 <li>View all structures fails with exception shown in
2883 <li>Characters in filename associated with PDBEntry not
2884 escaped in a platform independent way</li>
2885 <li>Jalview desktop fails to launch with exception when
2887 <li>Tree calculation reports 'you must have 2 or more
2888 sequences selected' when selection is empty</li>
2889 <li>Jalview desktop fails to launch with jar signature
2890 failure when java web start temporary file caching is
2892 <li>DAS Sequence retrieval with range qualification
2893 results in sequence xref which includes range qualification</li>
2894 <li>Errors during processing of command line arguments
2895 cause progress bar (JAL-898) to be removed</li>
2896 <li>Replace comma for semi-colon option not disabled for
2897 DAS sources in sequence fetcher</li>
2898 <li>Cannot close news reader when JABAWS server warning
2899 dialog is shown</li>
2900 <li>Option widgets not updated to reflect user settings</li>
2901 <li>Edited sequence not submitted to web service</li>
2902 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2903 <li>InstallAnywhere installer doesn't unpack and run
2904 on OSX Mountain Lion</li>
2905 <li>Annotation panel not given a scroll bar when
2906 sequences with alignment annotation are pasted into the
2908 <li>Sequence associated annotation rows not associated
2909 when loaded from Jalview project</li>
2910 <li>Browser launch fails with NPE on java 1.7</li>
2911 <li>JABAWS alignment marked as finished when job was
2912 cancelled or job failed due to invalid input</li>
2913 <li>NPE with v2.7 example when clicking on Tree
2914 associated with all views</li>
2915 <li>Exceptions when copy/paste sequences with grouped
2916 annotation rows to new window</li>
2917 </ul> <em>Applet</em>
2919 <li>Sequence features are momentarily displayed before
2920 they are hidden using hidefeaturegroups applet parameter</li>
2921 <li>loading features via javascript API automatically
2922 enables feature display</li>
2923 <li>scrollToColumnIn javascript API method doesn't
2925 </ul> <em>General</em>
2927 <li>Redundancy removal fails for rna alignment</li>
2928 <li>PCA calculation fails when sequence has been selected
2929 and then deselected</li>
2930 <li>PCA window shows grey box when first opened on OSX</li>
2931 <li>Letters coloured pink in sequence logo when alignment
2932 coloured with clustalx</li>
2933 <li>Choosing fonts without letter symbols defined causes
2934 exceptions and redraw errors</li>
2935 <li>Initial PCA plot view is not same as manually
2936 reconfigured view</li>
2937 <li>Grouped annotation graph label has incorrect line
2939 <li>Grouped annotation graph label display is corrupted
2940 for lots of labels</li>
2945 <div align="center">
2946 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2949 <td><em>Application</em>
2951 <li>Jalview Desktop News Reader</li>
2952 <li>Tweaked default layout of web services menu</li>
2953 <li>View/alignment association menu to enable user to
2954 easily specify which alignment a multi-structure view takes
2955 its colours/correspondences from</li>
2956 <li>Allow properties file location to be specified as URL</li>
2957 <li>Extend Jalview project to preserve associations
2958 between many alignment views and a single Jmol display</li>
2959 <li>Store annotation row height in Jalview project file</li>
2960 <li>Annotation row column label formatting attributes
2961 stored in project file</li>
2962 <li>Annotation row order for auto-calculated annotation
2963 rows preserved in Jalview project file</li>
2964 <li>Visual progress indication when Jalview state is
2965 saved using Desktop window menu</li>
2966 <li>Visual indication that command line arguments are
2967 still being processed</li>
2968 <li>Groovy script execution from URL</li>
2969 <li>Colour by annotation default min and max colours in
2971 <li>Automatically associate PDB files dragged onto an
2972 alignment with sequences that have high similarity and
2974 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2975 <li>'view structures' option to open many
2976 structures in same window</li>
2977 <li>Sort associated views menu option for tree panel</li>
2978 <li>Group all JABA and non-JABA services for a particular
2979 analysis function in its own submenu</li>
2980 </ul> <em>Applet</em>
2982 <li>Userdefined and autogenerated annotation rows for
2984 <li>Adjustment of alignment annotation pane height</li>
2985 <li>Annotation scrollbar for annotation panel</li>
2986 <li>Drag to reorder annotation rows in annotation panel</li>
2987 <li>'automaticScrolling' parameter</li>
2988 <li>Allow sequences with partial ID string matches to be
2989 annotated from GFF/Jalview features files</li>
2990 <li>Sequence logo annotation row in applet</li>
2991 <li>Absolute paths relative to host server in applet
2992 parameters are treated as such</li>
2993 <li>New in the JalviewLite javascript API:
2995 <li>JalviewLite.js javascript library</li>
2996 <li>Javascript callbacks for
2998 <li>Applet initialisation</li>
2999 <li>Sequence/alignment mouse-overs and selections</li>
3002 <li>scrollTo row and column alignment scrolling
3004 <li>Select sequence/alignment regions from javascript</li>
3005 <li>javascript structure viewer harness to pass
3006 messages between Jmol and Jalview when running as
3007 distinct applets</li>
3008 <li>sortBy method</li>
3009 <li>Set of applet and application examples shipped
3010 with documentation</li>
3011 <li>New example to demonstrate JalviewLite and Jmol
3012 javascript message exchange</li>
3014 </ul> <em>General</em>
3016 <li>Enable Jmol displays to be associated with multiple
3017 multiple alignments</li>
3018 <li>Option to automatically sort alignment with new tree</li>
3019 <li>User configurable link to enable redirects to a
3020 www.Jalview.org mirror</li>
3021 <li>Jmol colours option for Jmol displays</li>
3022 <li>Configurable newline string when writing alignment
3023 and other flat files</li>
3024 <li>Allow alignment annotation description lines to
3025 contain html tags</li>
3026 </ul> <em>Documentation and Development</em>
3028 <li>Add groovy test harness for bulk load testing to
3030 <li>Groovy script to load and align a set of sequences
3031 using a web service before displaying the result in the
3032 Jalview desktop</li>
3033 <li>Restructured javascript and applet api documentation</li>
3034 <li>Ant target to publish example html files with applet
3036 <li>Netbeans project for building Jalview from source</li>
3037 <li>ant task to create online javadoc for Jalview source</li>
3039 <td><em>Application</em>
3041 <li>User defined colourscheme throws exception when
3042 current built in colourscheme is saved as new scheme</li>
3043 <li>AlignFrame->Save in application pops up save
3044 dialog for valid filename/format</li>
3045 <li>Cannot view associated structure for UniProt sequence</li>
3046 <li>PDB file association breaks for UniProt sequence
3048 <li>Associate PDB from file dialog does not tell you
3049 which sequence is to be associated with the file</li>
3050 <li>Find All raises null pointer exception when query
3051 only matches sequence IDs</li>
3052 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3053 <li>Jalview project with Jmol views created with Jalview
3054 2.4 cannot be loaded</li>
3055 <li>Filetype associations not installed for webstart
3057 <li>Two or more chains in a single PDB file associated
3058 with sequences in different alignments do not get coloured
3059 by their associated sequence</li>
3060 <li>Visibility status of autocalculated annotation row
3061 not preserved when project is loaded</li>
3062 <li>Annotation row height and visibility attributes not
3063 stored in Jalview project</li>
3064 <li>Tree bootstraps are not preserved when saved as a
3065 Jalview project</li>
3066 <li>Envision2 workflow tooltips are corrupted</li>
3067 <li>Enabling show group conservation also enables colour
3068 by conservation</li>
3069 <li>Duplicate group associated conservation or consensus
3070 created on new view</li>
3071 <li>Annotation scrollbar not displayed after 'show
3072 all hidden annotation rows' option selected</li>
3073 <li>Alignment quality not updated after alignment
3074 annotation row is hidden then shown</li>
3075 <li>Preserve colouring of structures coloured by
3076 sequences in pre Jalview 2.7 projects</li>
3077 <li>Web service job parameter dialog is not laid out
3079 <li>Web services menu not refreshed after 'reset
3080 services' button is pressed in preferences</li>
3081 <li>Annotation off by one in Jalview v2_3 example project</li>
3082 <li>Structures imported from file and saved in project
3083 get name like jalview_pdb1234.txt when reloaded</li>
3084 <li>Jalview does not always retrieve progress of a JABAWS
3085 job execution in full once it is complete</li>
3086 </ul> <em>Applet</em>
3088 <li>Alignment height set incorrectly when lots of
3089 annotation rows are displayed</li>
3090 <li>Relative URLs in feature HTML text not resolved to
3092 <li>View follows highlighting does not work for positions
3094 <li><= shown as = in tooltip</li>
3095 <li>Export features raises exception when no features
3097 <li>Separator string used for serialising lists of IDs
3098 for javascript api is modified when separator string
3099 provided as parameter</li>
3100 <li>Null pointer exception when selecting tree leaves for
3101 alignment with no existing selection</li>
3102 <li>Relative URLs for datasources assumed to be relative
3103 to applet's codebase</li>
3104 <li>Status bar not updated after finished searching and
3105 search wraps around to first result</li>
3106 <li>StructureSelectionManager instance shared between
3107 several Jalview applets causes race conditions and memory
3109 <li>Hover tooltip and mouseover of position on structure
3110 not sent from Jmol in applet</li>
3111 <li>Certain sequences of javascript method calls to
3112 applet API fatally hang browser</li>
3113 </ul> <em>General</em>
3115 <li>View follows structure mouseover scrolls beyond
3116 position with wrapped view and hidden regions</li>
3117 <li>Find sequence position moves to wrong residue
3118 with/without hidden columns</li>
3119 <li>Sequence length given in alignment properties window
3121 <li>InvalidNumberFormat exceptions thrown when trying to
3122 import PDB like structure files</li>
3123 <li>Positional search results are only highlighted
3124 between user-supplied sequence start/end bounds</li>
3125 <li>End attribute of sequence is not validated</li>
3126 <li>Find dialog only finds first sequence containing a
3127 given sequence position</li>
3128 <li>Sequence numbering not preserved in MSF alignment
3130 <li>Jalview PDB file reader does not extract sequence
3131 from nucleotide chains correctly</li>
3132 <li>Structure colours not updated when tree partition
3133 changed in alignment</li>
3134 <li>Sequence associated secondary structure not correctly
3135 parsed in interleaved stockholm</li>
3136 <li>Colour by annotation dialog does not restore current
3138 <li>Hiding (nearly) all sequences doesn't work
3140 <li>Sequences containing lowercase letters are not
3141 properly associated with their pdb files</li>
3142 </ul> <em>Documentation and Development</em>
3144 <li>schemas/JalviewWsParamSet.xsd corrupted by
3145 ApplyCopyright tool</li>
3150 <div align="center">
3151 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3154 <td><em>Application</em>
3156 <li>New warning dialog when the Jalview Desktop cannot
3157 contact web services</li>
3158 <li>JABA service parameters for a preset are shown in
3159 service job window</li>
3160 <li>JABA Service menu entries reworded</li>
3164 <li>Modeller PIR IO broken - cannot correctly import a
3165 pir file emitted by Jalview</li>
3166 <li>Existing feature settings transferred to new
3167 alignment view created from cut'n'paste</li>
3168 <li>Improved test for mixed amino/nucleotide chains when
3169 parsing PDB files</li>
3170 <li>Consensus and conservation annotation rows
3171 occasionally become blank for all new windows</li>
3172 <li>Exception raised when right clicking above sequences
3173 in wrapped view mode</li>
3174 </ul> <em>Application</em>
3176 <li>multiple multiply aligned structure views cause cpu
3177 usage to hit 100% and computer to hang</li>
3178 <li>Web Service parameter layout breaks for long user
3179 parameter names</li>
3180 <li>Jaba service discovery hangs desktop if Jaba server
3187 <div align="center">
3188 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3191 <td><em>Application</em>
3193 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3194 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3197 <li>Web Services preference tab</li>
3198 <li>Analysis parameters dialog box and user defined
3200 <li>Improved speed and layout of Envision2 service menu</li>
3201 <li>Superpose structures using associated sequence
3203 <li>Export coordinates and projection as CSV from PCA
3205 </ul> <em>Applet</em>
3207 <li>enable javascript: execution by the applet via the
3208 link out mechanism</li>
3209 </ul> <em>Other</em>
3211 <li>Updated the Jmol Jalview interface to work with Jmol
3213 <li>The Jalview Desktop and JalviewLite applet now
3214 require Java 1.5</li>
3215 <li>Allow Jalview feature colour specification for GFF
3216 sequence annotation files</li>
3217 <li>New 'colour by label' keword in Jalview feature file
3218 type colour specification</li>
3219 <li>New Jalview Desktop Groovy API method that allows a
3220 script to check if it being run in an interactive session or
3221 in a batch operation from the Jalview command line</li>
3225 <li>clustalx colourscheme colours Ds preferentially when
3226 both D+E are present in over 50% of the column</li>
3227 </ul> <em>Application</em>
3229 <li>typo in AlignmentFrame->View->Hide->all but
3230 selected Regions menu item</li>
3231 <li>sequence fetcher replaces ',' for ';' when the ',' is
3232 part of a valid accession ID</li>
3233 <li>fatal OOM if object retrieved by sequence fetcher
3234 runs out of memory</li>
3235 <li>unhandled Out of Memory Error when viewing pca
3236 analysis results</li>
3237 <li>InstallAnywhere builds fail to launch on OS X java
3238 10.5 update 4 (due to apple Java 1.6 update)</li>
3239 <li>Installanywhere Jalview silently fails to launch</li>
3240 </ul> <em>Applet</em>
3242 <li>Jalview.getFeatureGroups() raises an
3243 ArrayIndexOutOfBoundsException if no feature groups are
3250 <div align="center">
3251 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3257 <li>Alignment prettyprinter doesn't cope with long
3259 <li>clustalx colourscheme colours Ds preferentially when
3260 both D+E are present in over 50% of the column</li>
3261 <li>nucleic acid structures retrieved from PDB do not
3262 import correctly</li>
3263 <li>More columns get selected than were clicked on when a
3264 number of columns are hidden</li>
3265 <li>annotation label popup menu not providing correct
3266 add/hide/show options when rows are hidden or none are
3268 <li>Stockholm format shown in list of readable formats,
3269 and parser copes better with alignments from RFAM.</li>
3270 <li>CSV output of consensus only includes the percentage
3271 of all symbols if sequence logo display is enabled</li>
3273 </ul> <em>Applet</em>
3275 <li>annotation panel disappears when annotation is
3277 </ul> <em>Application</em>
3279 <li>Alignment view not redrawn properly when new
3280 alignment opened where annotation panel is visible but no
3281 annotations are present on alignment</li>
3282 <li>pasted region containing hidden columns is
3283 incorrectly displayed in new alignment window</li>
3284 <li>Jalview slow to complete operations when stdout is
3285 flooded (fix is to close the Jalview console)</li>
3286 <li>typo in AlignmentFrame->View->Hide->all but
3287 selected Rregions menu item.</li>
3288 <li>inconsistent group submenu and Format submenu entry
3289 'Un' or 'Non'conserved</li>
3290 <li>Sequence feature settings are being shared by
3291 multiple distinct alignments</li>
3292 <li>group annotation not recreated when tree partition is
3294 <li>double click on group annotation to select sequences
3295 does not propagate to associated trees</li>
3296 <li>Mac OSX specific issues:
3298 <li>exception raised when mouse clicked on desktop
3299 window background</li>
3300 <li>Desktop menu placed on menu bar and application
3301 name set correctly</li>
3302 <li>sequence feature settings not wide enough for the
3303 save feature colourscheme button</li>
3312 <div align="center">
3313 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3316 <td><em>New Capabilities</em>
3318 <li>URL links generated from description line for
3319 regular-expression based URL links (applet and application)
3321 <li>Non-positional feature URL links are shown in link
3323 <li>Linked viewing of nucleic acid sequences and
3325 <li>Automatic Scrolling option in View menu to display
3326 the currently highlighted region of an alignment.</li>
3327 <li>Order an alignment by sequence length, or using the
3328 average score or total feature count for each sequence.</li>
3329 <li>Shading features by score or associated description</li>
3330 <li>Subdivide alignment and groups based on identity of
3331 selected subsequence (Make Groups from Selection).</li>
3332 <li>New hide/show options including Shift+Control+H to
3333 hide everything but the currently selected region.</li>
3334 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3335 </ul> <em>Application</em>
3337 <li>Fetch DB References capabilities and UI expanded to
3338 support retrieval from DAS sequence sources</li>
3339 <li>Local DAS Sequence sources can be added via the
3340 command line or via the Add local source dialog box.</li>
3341 <li>DAS Dbref and DbxRef feature types are parsed as
3342 database references and protein_name is parsed as
3343 description line (BioSapiens terms).</li>
3344 <li>Enable or disable non-positional feature and database
3345 references in sequence ID tooltip from View menu in
3347 <!-- <li>New hidden columns and rows and representatives capabilities
3348 in annotations file (in progress - not yet fully implemented)</li> -->
3349 <li>Group-associated consensus, sequence logos and
3350 conservation plots</li>
3351 <li>Symbol distributions for each column can be exported
3352 and visualized as sequence logos</li>
3353 <li>Optionally scale multi-character column labels to fit
3354 within each column of annotation row<!-- todo for applet -->
3356 <li>Optional automatic sort of associated alignment view
3357 when a new tree is opened.</li>
3358 <li>Jalview Java Console</li>
3359 <li>Better placement of desktop window when moving
3360 between different screens.</li>
3361 <li>New preference items for sequence ID tooltip and
3362 consensus annotation</li>
3363 <li>Client to submit sequences and IDs to Envision2
3365 <li><em>Vamsas Capabilities</em>
3367 <li>Improved VAMSAS synchronization (Jalview archive
3368 used to preserve views, structures, and tree display
3370 <li>Import of vamsas documents from disk or URL via
3372 <li>Sharing of selected regions between views and
3373 with other VAMSAS applications (Experimental feature!)</li>
3374 <li>Updated API to VAMSAS version 0.2</li>
3376 </ul> <em>Applet</em>
3378 <li>Middle button resizes annotation row height</li>
3381 <li>sortByTree (true/false) - automatically sort the
3382 associated alignment view by the tree when a new tree is
3384 <li>showTreeBootstraps (true/false) - show or hide
3385 branch bootstraps (default is to show them if available)</li>
3386 <li>showTreeDistances (true/false) - show or hide
3387 branch lengths (default is to show them if available)</li>
3388 <li>showUnlinkedTreeNodes (true/false) - indicate if
3389 unassociated nodes should be highlighted in the tree
3391 <li>heightScale and widthScale (1.0 or more) -
3392 increase the height or width of a cell in the alignment
3393 grid relative to the current font size.</li>
3396 <li>Non-positional features displayed in sequence ID
3398 </ul> <em>Other</em>
3400 <li>Features format: graduated colour definitions and
3401 specification of feature scores</li>
3402 <li>Alignment Annotations format: new keywords for group
3403 associated annotation (GROUP_REF) and annotation row display
3404 properties (ROW_PROPERTIES)</li>
3405 <li>XML formats extended to support graduated feature
3406 colourschemes, group associated annotation, and profile
3407 visualization settings.</li></td>
3410 <li>Source field in GFF files parsed as feature source
3411 rather than description</li>
3412 <li>Non-positional features are now included in sequence
3413 feature and gff files (controlled via non-positional feature
3414 visibility in tooltip).</li>
3415 <li>URL links generated for all feature links (bugfix)</li>
3416 <li>Added URL embedding instructions to features file
3418 <li>Codons containing ambiguous nucleotides translated as
3419 'X' in peptide product</li>
3420 <li>Match case switch in find dialog box works for both
3421 sequence ID and sequence string and query strings do not
3422 have to be in upper case to match case-insensitively.</li>
3423 <li>AMSA files only contain first column of
3424 multi-character column annotation labels</li>
3425 <li>Jalview Annotation File generation/parsing consistent
3426 with documentation (e.g. Stockholm annotation can be
3427 exported and re-imported)</li>
3428 <li>PDB files without embedded PDB IDs given a friendly
3430 <li>Find incrementally searches ID string matches as well
3431 as subsequence matches, and correctly reports total number
3435 <li>Better handling of exceptions during sequence
3437 <li>Dasobert generated non-positional feature URL
3438 link text excludes the start_end suffix</li>
3439 <li>DAS feature and source retrieval buttons disabled
3440 when fetch or registry operations in progress.</li>
3441 <li>PDB files retrieved from URLs are cached properly</li>
3442 <li>Sequence description lines properly shared via
3444 <li>Sequence fetcher fetches multiple records for all
3446 <li>Ensured that command line das feature retrieval
3447 completes before alignment figures are generated.</li>
3448 <li>Reduced time taken when opening file browser for
3450 <li>isAligned check prior to calculating tree, PCA or
3451 submitting an MSA to JNet now excludes hidden sequences.</li>
3452 <li>User defined group colours properly recovered
3453 from Jalview projects.</li>
3462 <div align="center">
3463 <strong>2.4.0.b2</strong><br> 28/10/2009
3468 <li>Experimental support for google analytics usage
3470 <li>Jalview privacy settings (user preferences and docs).</li>
3475 <li>Race condition in applet preventing startup in
3477 <li>Exception when feature created from selection beyond
3478 length of sequence.</li>
3479 <li>Allow synthetic PDB files to be imported gracefully</li>
3480 <li>Sequence associated annotation rows associate with
3481 all sequences with a given id</li>
3482 <li>Find function matches case-insensitively for sequence
3483 ID string searches</li>
3484 <li>Non-standard characters do not cause pairwise
3485 alignment to fail with exception</li>
3486 </ul> <em>Application Issues</em>
3488 <li>Sequences are now validated against EMBL database</li>
3489 <li>Sequence fetcher fetches multiple records for all
3491 </ul> <em>InstallAnywhere Issues</em>
3493 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3494 issue with installAnywhere mechanism)</li>
3495 <li>Command line launching of JARs from InstallAnywhere
3496 version (java class versioning error fixed)</li>
3503 <div align="center">
3504 <strong>2.4</strong><br> 27/8/2008
3507 <td><em>User Interface</em>
3509 <li>Linked highlighting of codon and amino acid from
3510 translation and protein products</li>
3511 <li>Linked highlighting of structure associated with
3512 residue mapping to codon position</li>
3513 <li>Sequence Fetcher provides example accession numbers
3514 and 'clear' button</li>
3515 <li>MemoryMonitor added as an option under Desktop's
3517 <li>Extract score function to parse whitespace separated
3518 numeric data in description line</li>
3519 <li>Column labels in alignment annotation can be centred.</li>
3520 <li>Tooltip for sequence associated annotation give name
3522 </ul> <em>Web Services and URL fetching</em>
3524 <li>JPred3 web service</li>
3525 <li>Prototype sequence search client (no public services
3527 <li>Fetch either seed alignment or full alignment from
3529 <li>URL Links created for matching database cross
3530 references as well as sequence ID</li>
3531 <li>URL Links can be created using regular-expressions</li>
3532 </ul> <em>Sequence Database Connectivity</em>
3534 <li>Retrieval of cross-referenced sequences from other
3536 <li>Generalised database reference retrieval and
3537 validation to all fetchable databases</li>
3538 <li>Fetch sequences from DAS sources supporting the
3539 sequence command</li>
3540 </ul> <em>Import and Export</em>
3541 <li>export annotation rows as CSV for spreadsheet import</li>
3542 <li>Jalview projects record alignment dataset associations,
3543 EMBL products, and cDNA sequence mappings</li>
3544 <li>Sequence Group colour can be specified in Annotation
3546 <li>Ad-hoc colouring of group in Annotation File using RGB
3547 triplet as name of colourscheme</li>
3548 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3550 <li>treenode binding for VAMSAS tree exchange</li>
3551 <li>local editing and update of sequences in VAMSAS
3552 alignments (experimental)</li>
3553 <li>Create new or select existing session to join</li>
3554 <li>load and save of vamsas documents</li>
3555 </ul> <em>Application command line</em>
3557 <li>-tree parameter to open trees (introduced for passing
3559 <li>-fetchfrom command line argument to specify nicknames
3560 of DAS servers to query for alignment features</li>
3561 <li>-dasserver command line argument to add new servers
3562 that are also automatically queried for features</li>
3563 <li>-groovy command line argument executes a given groovy
3564 script after all input data has been loaded and parsed</li>
3565 </ul> <em>Applet-Application data exchange</em>
3567 <li>Trees passed as applet parameters can be passed to
3568 application (when using "View in full
3569 application")</li>
3570 </ul> <em>Applet Parameters</em>
3572 <li>feature group display control parameter</li>
3573 <li>debug parameter</li>
3574 <li>showbutton parameter</li>
3575 </ul> <em>Applet API methods</em>
3577 <li>newView public method</li>
3578 <li>Window (current view) specific get/set public methods</li>
3579 <li>Feature display control methods</li>
3580 <li>get list of currently selected sequences</li>
3581 </ul> <em>New Jalview distribution features</em>
3583 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3584 <li>RELEASE file gives build properties for the latest
3585 Jalview release.</li>
3586 <li>Java 1.1 Applet build made easier and donotobfuscate
3587 property controls execution of obfuscator</li>
3588 <li>Build target for generating source distribution</li>
3589 <li>Debug flag for javacc</li>
3590 <li>.jalview_properties file is documented (slightly) in
3591 jalview.bin.Cache</li>
3592 <li>Continuous Build Integration for stable and
3593 development version of Application, Applet and source
3598 <li>selected region output includes visible annotations
3599 (for certain formats)</li>
3600 <li>edit label/displaychar contains existing label/char
3602 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3603 <li>shorter peptide product names from EMBL records</li>
3604 <li>Newick string generator makes compact representations</li>
3605 <li>bootstrap values parsed correctly for tree files with
3607 <li>pathological filechooser bug avoided by not allowing
3608 filenames containing a ':'</li>
3609 <li>Fixed exception when parsing GFF files containing
3610 global sequence features</li>
3611 <li>Alignment datasets are finalized only when number of
3612 references from alignment sequences goes to zero</li>
3613 <li>Close of tree branch colour box without colour
3614 selection causes cascading exceptions</li>
3615 <li>occasional negative imgwidth exceptions</li>
3616 <li>better reporting of non-fatal warnings to user when
3617 file parsing fails.</li>
3618 <li>Save works when Jalview project is default format</li>
3619 <li>Save as dialog opened if current alignment format is
3620 not a valid output format</li>
3621 <li>UniProt canonical names introduced for both das and
3623 <li>Histidine should be midblue (not pink!) in Zappo</li>
3624 <li>error messages passed up and output when data read
3626 <li>edit undo recovers previous dataset sequence when
3627 sequence is edited</li>
3628 <li>allow PDB files without pdb ID HEADER lines (like
3629 those generated by MODELLER) to be read in properly</li>
3630 <li>allow reading of JPred concise files as a normal
3632 <li>Stockholm annotation parsing and alignment properties
3633 import fixed for PFAM records</li>
3634 <li>Structure view windows have correct name in Desktop
3636 <li>annotation consisting of sequence associated scores
3637 can be read and written correctly to annotation file</li>
3638 <li>Aligned cDNA translation to aligned peptide works
3640 <li>Fixed display of hidden sequence markers and
3641 non-italic font for representatives in Applet</li>
3642 <li>Applet Menus are always embedded in applet window on
3644 <li>Newly shown features appear at top of stack (in
3646 <li>Annotations added via parameter not drawn properly
3647 due to null pointer exceptions</li>
3648 <li>Secondary structure lines are drawn starting from
3649 first column of alignment</li>
3650 <li>UniProt XML import updated for new schema release in
3652 <li>Sequence feature to sequence ID match for Features
3653 file is case-insensitive</li>
3654 <li>Sequence features read from Features file appended to
3655 all sequences with matching IDs</li>
3656 <li>PDB structure coloured correctly for associated views
3657 containing a sub-sequence</li>
3658 <li>PDB files can be retrieved by applet from Jar files</li>
3659 <li>feature and annotation file applet parameters
3660 referring to different directories are retrieved correctly</li>
3661 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3662 <li>Fixed application hang whilst waiting for
3663 splash-screen version check to complete</li>
3664 <li>Applet properly URLencodes input parameter values
3665 when passing them to the launchApp service</li>
3666 <li>display name and local features preserved in results
3667 retrieved from web service</li>
3668 <li>Visual delay indication for sequence retrieval and
3669 sequence fetcher initialisation</li>
3670 <li>updated Application to use DAS 1.53e version of
3671 dasobert DAS client</li>
3672 <li>Re-instated Full AMSA support and .amsa file
3674 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3682 <div align="center">
3683 <strong>2.3</strong><br> 9/5/07
3688 <li>Jmol 11.0.2 integration</li>
3689 <li>PDB views stored in Jalview XML files</li>
3690 <li>Slide sequences</li>
3691 <li>Edit sequence in place</li>
3692 <li>EMBL CDS features</li>
3693 <li>DAS Feature mapping</li>
3694 <li>Feature ordering</li>
3695 <li>Alignment Properties</li>
3696 <li>Annotation Scores</li>
3697 <li>Sort by scores</li>
3698 <li>Feature/annotation editing in applet</li>
3703 <li>Headless state operation in 2.2.1</li>
3704 <li>Incorrect and unstable DNA pairwise alignment</li>
3705 <li>Cut and paste of sequences with annotation</li>
3706 <li>Feature group display state in XML</li>
3707 <li>Feature ordering in XML</li>
3708 <li>blc file iteration selection using filename # suffix</li>
3709 <li>Stockholm alignment properties</li>
3710 <li>Stockhom alignment secondary structure annotation</li>
3711 <li>2.2.1 applet had no feature transparency</li>
3712 <li>Number pad keys can be used in cursor mode</li>
3713 <li>Structure Viewer mirror image resolved</li>
3720 <div align="center">
3721 <strong>2.2.1</strong><br> 12/2/07
3726 <li>Non standard characters can be read and displayed
3727 <li>Annotations/Features can be imported/exported to the
3729 <li>Applet allows editing of sequence/annotation/group
3730 name & description
3731 <li>Preference setting to display sequence name in
3733 <li>Annotation file format extended to allow
3734 Sequence_groups to be defined
3735 <li>Default opening of alignment overview panel can be
3736 specified in preferences
3737 <li>PDB residue numbering annotation added to associated
3743 <li>Applet crash under certain Linux OS with Java 1.6
3745 <li>Annotation file export / import bugs fixed
3746 <li>PNG / EPS image output bugs fixed
3752 <div align="center">
3753 <strong>2.2</strong><br> 27/11/06
3758 <li>Multiple views on alignment
3759 <li>Sequence feature editing
3760 <li>"Reload" alignment
3761 <li>"Save" to current filename
3762 <li>Background dependent text colour
3763 <li>Right align sequence ids
3764 <li>User-defined lower case residue colours
3767 <li>Menu item accelerator keys
3768 <li>Control-V pastes to current alignment
3769 <li>Cancel button for DAS Feature Fetching
3770 <li>PCA and PDB Viewers zoom via mouse roller
3771 <li>User-defined sub-tree colours and sub-tree selection
3773 <li>'New Window' button on the 'Output to Text box'
3778 <li>New memory efficient Undo/Redo System
3779 <li>Optimised symbol lookups and conservation/consensus
3781 <li>Region Conservation/Consensus recalculated after
3783 <li>Fixed Remove Empty Columns Bug (empty columns at end
3785 <li>Slowed DAS Feature Fetching for increased robustness.
3787 <li>Made angle brackets in ASCII feature descriptions
3789 <li>Re-instated Zoom function for PCA
3790 <li>Sequence descriptions conserved in web service
3792 <li>UniProt ID discoverer uses any word separated by
3794 <li>WsDbFetch query/result association resolved
3795 <li>Tree leaf to sequence mapping improved
3796 <li>Smooth fonts switch moved to FontChooser dialog box.
3803 <div align="center">
3804 <strong>2.1.1</strong><br> 12/9/06
3809 <li>Copy consensus sequence to clipboard</li>
3814 <li>Image output - rightmost residues are rendered if
3815 sequence id panel has been resized</li>
3816 <li>Image output - all offscreen group boundaries are
3818 <li>Annotation files with sequence references - all
3819 elements in file are relative to sequence position</li>
3820 <li>Mac Applet users can use Alt key for group editing</li>
3826 <div align="center">
3827 <strong>2.1</strong><br> 22/8/06
3832 <li>MAFFT Multiple Alignment in default Web Service list</li>
3833 <li>DAS Feature fetching</li>
3834 <li>Hide sequences and columns</li>
3835 <li>Export Annotations and Features</li>
3836 <li>GFF file reading / writing</li>
3837 <li>Associate structures with sequences from local PDB
3839 <li>Add sequences to exisiting alignment</li>
3840 <li>Recently opened files / URL lists</li>
3841 <li>Applet can launch the full application</li>
3842 <li>Applet has transparency for features (Java 1.2
3844 <li>Applet has user defined colours parameter</li>
3845 <li>Applet can load sequences from parameter
3846 "sequence<em>x</em>"
3852 <li>Redundancy Panel reinstalled in the Applet</li>
3853 <li>Monospaced font - EPS / rescaling bug fixed</li>
3854 <li>Annotation files with sequence references bug fixed</li>
3860 <div align="center">
3861 <strong>2.08.1</strong><br> 2/5/06
3866 <li>Change case of selected region from Popup menu</li>
3867 <li>Choose to match case when searching</li>
3868 <li>Middle mouse button and mouse movement can compress /
3869 expand the visible width and height of the alignment</li>
3874 <li>Annotation Panel displays complete JNet results</li>
3880 <div align="center">
3881 <strong>2.08b</strong><br> 18/4/06
3887 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3888 <li>Righthand label on wrapped alignments shows correct
3895 <div align="center">
3896 <strong>2.08</strong><br> 10/4/06
3901 <li>Editing can be locked to the selection area</li>
3902 <li>Keyboard editing</li>
3903 <li>Create sequence features from searches</li>
3904 <li>Precalculated annotations can be loaded onto
3906 <li>Features file allows grouping of features</li>
3907 <li>Annotation Colouring scheme added</li>
3908 <li>Smooth fonts off by default - Faster rendering</li>
3909 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3914 <li>Drag & Drop fixed on Linux</li>
3915 <li>Jalview Archive file faster to load/save, sequence
3916 descriptions saved.</li>
3922 <div align="center">
3923 <strong>2.07</strong><br> 12/12/05
3928 <li>PDB Structure Viewer enhanced</li>
3929 <li>Sequence Feature retrieval and display enhanced</li>
3930 <li>Choose to output sequence start-end after sequence
3931 name for file output</li>
3932 <li>Sequence Fetcher WSDBFetch@EBI</li>
3933 <li>Applet can read feature files, PDB files and can be
3934 used for HTML form input</li>
3939 <li>HTML output writes groups and features</li>
3940 <li>Group editing is Control and mouse click</li>
3941 <li>File IO bugs</li>
3947 <div align="center">
3948 <strong>2.06</strong><br> 28/9/05
3953 <li>View annotations in wrapped mode</li>
3954 <li>More options for PCA viewer</li>
3959 <li>GUI bugs resolved</li>
3960 <li>Runs with -nodisplay from command line</li>
3966 <div align="center">
3967 <strong>2.05b</strong><br> 15/9/05
3972 <li>Choose EPS export as lineart or text</li>
3973 <li>Jar files are executable</li>
3974 <li>Can read in Uracil - maps to unknown residue</li>
3979 <li>Known OutOfMemory errors give warning message</li>
3980 <li>Overview window calculated more efficiently</li>
3981 <li>Several GUI bugs resolved</li>
3987 <div align="center">
3988 <strong>2.05</strong><br> 30/8/05
3993 <li>Edit and annotate in "Wrapped" view</li>
3998 <li>Several GUI bugs resolved</li>
4004 <div align="center">
4005 <strong>2.04</strong><br> 24/8/05
4010 <li>Hold down mouse wheel & scroll to change font
4016 <li>Improved JPred client reliability</li>
4017 <li>Improved loading of Jalview files</li>
4023 <div align="center">
4024 <strong>2.03</strong><br> 18/8/05
4029 <li>Set Proxy server name and port in preferences</li>
4030 <li>Multiple URL links from sequence ids</li>
4031 <li>User Defined Colours can have a scheme name and added
4033 <li>Choose to ignore gaps in consensus calculation</li>
4034 <li>Unix users can set default web browser</li>
4035 <li>Runs without GUI for batch processing</li>
4036 <li>Dynamically generated Web Service Menus</li>
4041 <li>InstallAnywhere download for Sparc Solaris</li>
4047 <div align="center">
4048 <strong>2.02</strong><br> 18/7/05
4054 <li>Copy & Paste order of sequences maintains
4055 alignment order.</li>
4061 <div align="center">
4062 <strong>2.01</strong><br> 12/7/05
4067 <li>Use delete key for deleting selection.</li>
4068 <li>Use Mouse wheel to scroll sequences.</li>
4069 <li>Help file updated to describe how to add alignment
4071 <li>Version and build date written to build properties
4073 <li>InstallAnywhere installation will check for updates
4074 at launch of Jalview.</li>
4079 <li>Delete gaps bug fixed.</li>
4080 <li>FileChooser sorts columns.</li>
4081 <li>Can remove groups one by one.</li>
4082 <li>Filechooser icons installed.</li>
4083 <li>Finder ignores return character when searching.
4084 Return key will initiate a search.<br>
4091 <div align="center">
4092 <strong>2.0</strong><br> 20/6/05
4097 <li>New codebase</li>