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.2.11.0">2.11.0</a><br />
74 <em>29/01/2019</em></strong>
77 <td><div align="left">
81 <!-- JAL-3035 -->DAS sequence retrieval and annotation
82 capabilities removed from the Jalview Desktop
85 <em>Release Processes</em>
87 <li>Atlassian Bamboo continuous integration server for unattended Test Suite execution</li>
88 <li><!-- JAL-2864 -->Memory test suite to detect leaks in common operations</li>
91 <td><div align="left">
95 <!-- JAL-2865 -->Jalview hangs when closing windows
96 or the overview updates with large alignments.
99 <!-- JAL-2865 -->Tree and PCA calculation fails for selected
100 region if columns were selected by dragging right-to-left
101 and the mouse moved to the left of the first column.
104 <!-- JAL-2846 -->Error message for trying to load in invalid
105 URLs doesn't tell users the invalid URL
111 <!-- JAL-2822 -->Start and End should be updated when
112 sequence data at beginning or end of alignment added/removed
116 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
117 sequence features correctly when start of sequence is
118 removed (Known defect since 2.10)
124 <em>New Known Defects</em>
127 <!-- JAL-3178 -->Nonpositional features lose feature group
128 on export as jalview features file
134 <td width="60" nowrap>
136 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
139 <td><div align="left">
143 <!-- JAL-3101 -->Default memory for Jalview webstart and
144 InstallAnywhere increased to 1G.
147 <!-- JAL-247 -->Hidden sequence markers and representative
148 sequence bolding included when exporting alignment as EPS,
149 SVG, PNG or HTML. <em>Display is configured via the
150 Format menu, or for command-line use via a jalview
151 properties file.</em>
154 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
155 API and sequence data now imported as JSON.
158 <!-- JAL-3065 -->Change in recommended way of starting
159 Jalview via a Java command line: add jars in lib directory
160 to CLASSPATH, rather than via the deprecated java.ext.dirs
167 <!-- JAL-3047 -->Support added to execute test suite
168 instrumented with <a href="http://openclover.org/">Open
173 <td><div align="left">
177 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
178 row shown in Feredoxin Structure alignment view of example
182 <!-- JAL-2854 -->Annotation obscures sequences if lots of
183 annotation displayed.
186 <!-- JAL-3107 -->Group conservation/consensus not shown
187 for newly created group when 'Apply to all groups'
191 <!-- JAL-3087 -->Corrupted display when switching to
192 wrapped mode when sequence panel's vertical scrollbar is
196 <!-- JAL-3003 -->Alignment is black in exported EPS file
197 when sequences are selected in exported view.</em>
200 <!-- JAL-3059 -->Groups with different coloured borders
201 aren't rendered with correct colour.
204 <!-- JAL-3092 -->Jalview could hang when importing certain
205 types of knotted RNA secondary structure.
208 <!-- JAL-3095 -->Sequence highlight and selection in
209 trimmed VARNA 2D structure is incorrect for sequences that
213 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
214 annotation when columns are inserted into an alignment,
215 and when exporting as Stockholm flatfile.
218 <!-- JAL-3053 -->Jalview annotation rows containing upper
219 and lower-case 'E' and 'H' do not automatically get
220 treated as RNA secondary structure.
223 <!-- JAL-3106 -->.jvp should be used as default extension
224 (not .jar) when saving a jalview project file.
227 <!-- JAL-3105 -->Mac Users: closing a window correctly
228 transfers focus to previous window on OSX
231 <em>Java 10 Issues Resolved</em>
234 <!-- JAL-2988 -->OSX - Can't save new files via the File
235 or export menus by typing in a name into the Save dialog
239 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
240 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
241 'look and feel' which has improved compatibility with the
242 latest version of OSX.
249 <td width="60" nowrap>
251 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
252 <em>7/06/2018</em></strong>
255 <td><div align="left">
259 <!-- JAL-2920 -->Use HGVS nomenclature for variant
260 annotation retrieved from Uniprot
263 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
264 onto the Jalview Desktop
268 <td><div align="left">
272 <!-- JAL-3017 -->Cannot import features with multiple
273 variant elements (blocks import of some Uniprot records)
276 <!-- JAL-2997 -->Clustal files with sequence positions in
277 right-hand column parsed correctly
280 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
281 not alignment area in exported graphic
284 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
285 window has input focus
288 <!-- JAL-2992 -->Annotation panel set too high when
289 annotation added to view (Windows)
292 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
293 network connectivity is poor
296 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
297 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
298 the currently open URL and links from a page viewed in
299 Firefox or Chrome on Windows is now fully supported. If
300 you are using Edge, only links in the page can be
301 dragged, and with Internet Explorer, only the currently
302 open URL in the browser can be dropped onto Jalview.</em>
308 <td width="60" nowrap>
310 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
313 <td><div align="left">
317 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
318 for disabling automatic superposition of multiple
319 structures and open structures in existing views
322 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
323 ID and annotation area margins can be click-dragged to
327 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
331 <!-- JAL-2759 -->Improved performance for large alignments
332 and lots of hidden columns
335 <!-- JAL-2593 -->Improved performance when rendering lots
336 of features (particularly when transparency is disabled)
341 <td><div align="left">
344 <!-- JAL-2899 -->Structure and Overview aren't updated
345 when Colour By Annotation threshold slider is adjusted
348 <!-- JAL-2778 -->Slow redraw when Overview panel shown
349 overlapping alignment panel
352 <!-- JAL-2929 -->Overview doesn't show end of unpadded
356 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
357 improved: CDS not handled correctly if transcript has no
361 <!-- JAL-2321 -->Secondary structure and temperature
362 factor annotation not added to sequence when local PDB
363 file associated with it by drag'n'drop or structure
367 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
368 dialog doesn't import PDB files dropped on an alignment
371 <!-- JAL-2666 -->Linked scrolling via protein horizontal
372 scroll bar doesn't work for some CDS/Protein views
375 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
376 Java 1.8u153 onwards and Java 1.9u4+.
379 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
380 columns in annotation row
383 <!-- JAL-2913 -->Preferences panel's ID Width control is not
384 honored in batch mode
387 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
388 for structures added to existing Jmol view
391 <!-- JAL-2223 -->'View Mappings' includes duplicate
392 entries after importing project with multiple views
395 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
396 protein sequences via SIFTS from associated PDB entries
397 with negative residue numbers or missing residues fails
400 <!-- JAL-2952 -->Exception when shading sequence with negative
401 Temperature Factor values from annotated PDB files (e.g.
402 as generated by CONSURF)
405 <!-- JAL-2920 -->Uniprot 'sequence variant' features
406 tooltip doesn't include a text description of mutation
409 <!-- JAL-2922 -->Invert displayed features very slow when
410 structure and/or overview windows are also shown
413 <!-- JAL-2954 -->Selecting columns from highlighted regions
414 very slow for alignments with large numbers of sequences
417 <!-- JAL-2925 -->Copy Consensus fails for group consensus
418 with 'StringIndexOutOfBounds'
421 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
422 platforms running Java 10
425 <!-- JAL-2960 -->Adding a structure to existing structure
426 view appears to do nothing because the view is hidden behind the alignment view
432 <!-- JAL-2926 -->Copy consensus sequence option in applet
433 should copy the group consensus when popup is opened on it
439 <!-- JAL-2913 -->Fixed ID width preference is not respected
442 <em>New Known Defects</em>
445 <!-- JAL-2973 --> Exceptions occasionally raised when
446 editing a large alignment and overview is displayed
449 <!-- JAL-2974 -->'Overview updating' progress bar is shown
450 repeatedly after a series of edits even when the overview
451 is no longer reflecting updates
454 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
455 structures for protein subsequence (if 'Trim Retrieved
456 Sequences' enabled) or Ensembl isoforms (Workaround in
457 2.10.4 is to fail back to N&W mapping)
464 <td width="60" nowrap>
466 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
469 <td><div align="left">
470 <ul><li>Updated Certum Codesigning Certificate
471 (Valid till 30th November 2018)</li></ul></div></td>
472 <td><div align="left">
475 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
476 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
477 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
478 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
479 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
480 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
481 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
487 <td width="60" nowrap>
489 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
492 <td><div align="left">
496 <!-- JAL-2446 -->Faster and more efficient management and
497 rendering of sequence features
500 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
501 429 rate limit request hander
504 <!-- JAL-2773 -->Structure views don't get updated unless
505 their colours have changed
508 <!-- JAL-2495 -->All linked sequences are highlighted for
509 a structure mousover (Jmol) or selection (Chimera)
512 <!-- JAL-2790 -->'Cancel' button in progress bar for
513 JABAWS AACon, RNAAliFold and Disorder prediction jobs
516 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
517 view from Ensembl locus cross-references
520 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
524 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
525 feature can be disabled
528 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
529 PDB easier retrieval of sequences for lists of IDs
532 <!-- JAL-2758 -->Short names for sequences retrieved from
538 <li>Groovy interpreter updated to 2.4.12</li>
539 <li>Example groovy script for generating a matrix of
540 percent identity scores for current alignment.</li>
542 <em>Testing and Deployment</em>
545 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
549 <td><div align="left">
553 <!-- JAL-2643 -->Pressing tab after updating the colour
554 threshold text field doesn't trigger an update to the
558 <!-- JAL-2682 -->Race condition when parsing sequence ID
562 <!-- JAL-2608 -->Overview windows are also closed when
563 alignment window is closed
566 <!-- JAL-2548 -->Export of features doesn't always respect
570 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
571 takes a long time in Cursor mode
577 <!-- JAL-2777 -->Structures with whitespace chainCode
578 cannot be viewed in Chimera
581 <!-- JAL-2728 -->Protein annotation panel too high in
585 <!-- JAL-2757 -->Can't edit the query after the server
586 error warning icon is shown in Uniprot and PDB Free Text
590 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
593 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
596 <!-- JAL-2739 -->Hidden column marker in last column not
597 rendered when switching back from Wrapped to normal view
600 <!-- JAL-2768 -->Annotation display corrupted when
601 scrolling right in unwapped alignment view
604 <!-- JAL-2542 -->Existing features on subsequence
605 incorrectly relocated when full sequence retrieved from
609 <!-- JAL-2733 -->Last reported memory still shown when
610 Desktop->Show Memory is unticked (OSX only)
613 <!-- JAL-2658 -->Amend Features dialog doesn't allow
614 features of same type and group to be selected for
618 <!-- JAL-2524 -->Jalview becomes sluggish in wide
619 alignments when hidden columns are present
622 <!-- JAL-2392 -->Jalview freezes when loading and
623 displaying several structures
626 <!-- JAL-2732 -->Black outlines left after resizing or
630 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
631 within the Jalview desktop on OSX
634 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
635 when in wrapped alignment mode
638 <!-- JAL-2636 -->Scale mark not shown when close to right
639 hand end of alignment
642 <!-- JAL-2684 -->Pairwise alignment of selected regions of
643 each selected sequence do not have correct start/end
647 <!-- JAL-2793 -->Alignment ruler height set incorrectly
648 after canceling the Alignment Window's Font dialog
651 <!-- JAL-2036 -->Show cross-references not enabled after
652 restoring project until a new view is created
655 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
656 URL links appears when only default EMBL-EBI link is
657 configured (since 2.10.2b2)
660 <!-- JAL-2775 -->Overview redraws whole window when box
664 <!-- JAL-2225 -->Structure viewer doesn't map all chains
665 in a multi-chain structure when viewing alignment
666 involving more than one chain (since 2.10)
669 <!-- JAL-2811 -->Double residue highlights in cursor mode
670 if new selection moves alignment window
673 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
674 arrow key in cursor mode to pass hidden column marker
677 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
678 that produces correctly annotated transcripts and products
681 <!-- JAL-2776 -->Toggling a feature group after first time
682 doesn't update associated structure view
685 <em>Applet</em><br />
688 <!-- JAL-2687 -->Concurrent modification exception when
689 closing alignment panel
692 <em>BioJSON</em><br />
695 <!-- JAL-2546 -->BioJSON export does not preserve
696 non-positional features
699 <em>New Known Issues</em>
702 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
703 sequence features correctly (for many previous versions of
707 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
708 using cursor in wrapped panel other than top
711 <!-- JAL-2791 -->Select columns containing feature ignores
712 graduated colour threshold
715 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
716 always preserve numbering and sequence features
719 <em>Known Java 9 Issues</em>
722 <!-- JAL-2902 -->Groovy Console very slow to open and is
723 not responsive when entering characters (Webstart, Java
730 <td width="60" nowrap>
732 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
733 <em>2/10/2017</em></strong>
736 <td><div align="left">
737 <em>New features in Jalview Desktop</em>
740 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
742 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
746 <td><div align="left">
750 <td width="60" nowrap>
752 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
753 <em>7/9/2017</em></strong>
756 <td><div align="left">
760 <!-- JAL-2588 -->Show gaps in overview window by colouring
761 in grey (sequences used to be coloured grey, and gaps were
765 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
769 <!-- JAL-2587 -->Overview updates immediately on increase
770 in size and progress bar shown as higher resolution
771 overview is recalculated
776 <td><div align="left">
780 <!-- JAL-2664 -->Overview window redraws every hidden
781 column region row by row
784 <!-- JAL-2681 -->duplicate protein sequences shown after
785 retrieving Ensembl crossrefs for sequences from Uniprot
788 <!-- JAL-2603 -->Overview window throws NPE if show boxes
789 format setting is unticked
792 <!-- JAL-2610 -->Groups are coloured wrongly in overview
793 if group has show boxes format setting unticked
796 <!-- JAL-2672,JAL-2665 -->Redraw problems when
797 autoscrolling whilst dragging current selection group to
798 include sequences and columns not currently displayed
801 <!-- JAL-2691 -->Not all chains are mapped when multimeric
802 assemblies are imported via CIF file
805 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
806 displayed when threshold or conservation colouring is also
810 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
814 <!-- JAL-2673 -->Jalview continues to scroll after
815 dragging a selected region off the visible region of the
819 <!-- JAL-2724 -->Cannot apply annotation based
820 colourscheme to all groups in a view
823 <!-- JAL-2511 -->IDs don't line up with sequences
824 initially after font size change using the Font chooser or
831 <td width="60" nowrap>
833 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
836 <td><div align="left">
837 <em>Calculations</em>
841 <!-- JAL-1933 -->Occupancy annotation row shows number of
842 ungapped positions in each column of the alignment.
845 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
846 a calculation dialog box
849 <!-- JAL-2379 -->Revised implementation of PCA for speed
850 and memory efficiency (~30x faster)
853 <!-- JAL-2403 -->Revised implementation of sequence
854 similarity scores as used by Tree, PCA, Shading Consensus
855 and other calculations
858 <!-- JAL-2416 -->Score matrices are stored as resource
859 files within the Jalview codebase
862 <!-- JAL-2500 -->Trees computed on Sequence Feature
863 Similarity may have different topology due to increased
870 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
871 model for alignments and groups
874 <!-- JAL-384 -->Custom shading schemes created via groovy
881 <!-- JAL-2526 -->Efficiency improvements for interacting
882 with alignment and overview windows
885 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
889 <!-- JAL-2388 -->Hidden columns and sequences can be
893 <!-- JAL-2611 -->Click-drag in visible area allows fine
894 adjustment of visible position
898 <em>Data import/export</em>
901 <!-- JAL-2535 -->Posterior probability annotation from
902 Stockholm files imported as sequence associated annotation
905 <!-- JAL-2507 -->More robust per-sequence positional
906 annotation input/output via stockholm flatfile
909 <!-- JAL-2533 -->Sequence names don't include file
910 extension when importing structure files without embedded
911 names or PDB accessions
914 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
915 format sequence substitution matrices
918 <em>User Interface</em>
921 <!-- JAL-2447 --> Experimental Features Checkbox in
922 Desktop's Tools menu to hide or show untested features in
926 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
927 via Overview or sequence motif search operations
930 <!-- JAL-2547 -->Amend sequence features dialog box can be
931 opened by double clicking gaps within sequence feature
935 <!-- JAL-1476 -->Status bar message shown when not enough
936 aligned positions were available to create a 3D structure
940 <em>3D Structure</em>
943 <!-- JAL-2430 -->Hidden regions in alignment views are not
944 coloured in linked structure views
947 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
948 file-based command exchange
951 <!-- JAL-2375 -->Structure chooser automatically shows
952 Cached Structures rather than querying the PDBe if
953 structures are already available for sequences
956 <!-- JAL-2520 -->Structures imported via URL are cached in
957 the Jalview project rather than downloaded again when the
961 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
962 to transfer Chimera's structure attributes as Jalview
963 features, and vice-versa (<strong>Experimental
967 <em>Web Services</em>
970 <!-- JAL-2549 -->Updated JABAWS client to v2.2
973 <!-- JAL-2335 -->Filter non-standard amino acids and
974 nucleotides when submitting to AACon and other MSA
978 <!-- JAL-2316, -->URLs for viewing database
979 cross-references provided by identifiers.org and the
987 <!-- JAL-2344 -->FileFormatI interface for describing and
988 identifying file formats (instead of String constants)
991 <!-- JAL-2228 -->FeatureCounter script refactored for
992 efficiency when counting all displayed features (not
993 backwards compatible with 2.10.1)
996 <em>Example files</em>
999 <!-- JAL-2631 -->Graduated feature colour style example
1000 included in the example feature file
1003 <em>Documentation</em>
1006 <!-- JAL-2339 -->Release notes reformatted for readability
1007 with the built-in Java help viewer
1010 <!-- JAL-1644 -->Find documentation updated with 'search
1011 sequence description' option
1017 <!-- JAL-2485, -->External service integration tests for
1018 Uniprot REST Free Text Search Client
1021 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1024 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1029 <td><div align="left">
1030 <em>Calculations</em>
1033 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1034 matrix - C->R should be '-3'<br />Old matrix restored
1035 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1037 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1038 Jalview's treatment of gaps in PCA and substitution matrix
1039 based Tree calculations.<br /> <br />In earlier versions
1040 of Jalview, gaps matching gaps were penalised, and gaps
1041 matching non-gaps penalised even more. In the PCA
1042 calculation, gaps were actually treated as non-gaps - so
1043 different costs were applied, which meant Jalview's PCAs
1044 were different to those produced by SeqSpace.<br />Jalview
1045 now treats gaps in the same way as SeqSpace (ie it scores
1046 them as 0). <br /> <br />Enter the following in the
1047 Groovy console to restore pre-2.10.2 behaviour:<br />
1048 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1049 // for 2.10.1 mode <br />
1050 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1051 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1052 these settings will affect all subsequent tree and PCA
1053 calculations (not recommended)</em></li>
1055 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1056 scaling of branch lengths for trees computed using
1057 Sequence Feature Similarity.
1060 <!-- JAL-2377 -->PCA calculation could hang when
1061 generating output report when working with highly
1062 redundant alignments
1065 <!-- JAL-2544 --> Sort by features includes features to
1066 right of selected region when gaps present on right-hand
1070 <em>User Interface</em>
1073 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1074 doesn't reselect a specific sequence's associated
1075 annotation after it was used for colouring a view
1078 <!-- JAL-2419 -->Current selection lost if popup menu
1079 opened on a region of alignment without groups
1082 <!-- JAL-2374 -->Popup menu not always shown for regions
1083 of an alignment with overlapping groups
1086 <!-- JAL-2310 -->Finder double counts if both a sequence's
1087 name and description match
1090 <!-- JAL-2370 -->Hiding column selection containing two
1091 hidden regions results in incorrect hidden regions
1094 <!-- JAL-2386 -->'Apply to all groups' setting when
1095 changing colour does not apply Conservation slider value
1099 <!-- JAL-2373 -->Percentage identity and conservation menu
1100 items do not show a tick or allow shading to be disabled
1103 <!-- JAL-2385 -->Conservation shading or PID threshold
1104 lost when base colourscheme changed if slider not visible
1107 <!-- JAL-2547 -->Sequence features shown in tooltip for
1108 gaps before start of features
1111 <!-- JAL-2623 -->Graduated feature colour threshold not
1112 restored to UI when feature colour is edited
1115 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1116 a time when scrolling vertically in wrapped mode.
1119 <!-- JAL-2630 -->Structure and alignment overview update
1120 as graduate feature colour settings are modified via the
1124 <!-- JAL-2034 -->Overview window doesn't always update
1125 when a group defined on the alignment is resized
1128 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1129 wrapped view result in positional status updates
1133 <!-- JAL-2563 -->Status bar doesn't show position for
1134 ambiguous amino acid and nucleotide symbols
1137 <!-- JAL-2602 -->Copy consensus sequence failed if
1138 alignment included gapped columns
1141 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1142 widgets don't permanently disappear
1145 <!-- JAL-2503 -->Cannot select or filter quantitative
1146 annotation that are shown only as column labels (e.g.
1147 T-Coffee column reliability scores)
1150 <!-- JAL-2594 -->Exception thrown if trying to create a
1151 sequence feature on gaps only
1154 <!-- JAL-2504 -->Features created with 'New feature'
1155 button from a Find inherit previously defined feature type
1156 rather than the Find query string
1159 <!-- JAL-2423 -->incorrect title in output window when
1160 exporting tree calculated in Jalview
1163 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1164 and then revealing them reorders sequences on the
1168 <!-- JAL-964 -->Group panel in sequence feature settings
1169 doesn't update to reflect available set of groups after
1170 interactively adding or modifying features
1173 <!-- JAL-2225 -->Sequence Database chooser unusable on
1177 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1178 only excluded gaps in current sequence and ignored
1185 <!-- JAL-2421 -->Overview window visible region moves
1186 erratically when hidden rows or columns are present
1189 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1190 Structure Viewer's colour menu don't correspond to
1194 <!-- JAL-2405 -->Protein specific colours only offered in
1195 colour and group colour menu for protein alignments
1198 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1199 reflect currently selected view or group's shading
1203 <!-- JAL-2624 -->Feature colour thresholds not respected
1204 when rendered on overview and structures when opacity at
1208 <!-- JAL-2589 -->User defined gap colour not shown in
1209 overview when features overlaid on alignment
1212 <em>Data import/export</em>
1215 <!-- JAL-2576 -->Very large alignments take a long time to
1219 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1220 added after a sequence was imported are not written to
1224 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1225 when importing RNA secondary structure via Stockholm
1228 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1229 not shown in correct direction for simple pseudoknots
1232 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1233 with lightGray or darkGray via features file (but can
1237 <!-- JAL-2383 -->Above PID colour threshold not recovered
1238 when alignment view imported from project
1241 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1242 structure and sequences extracted from structure files
1243 imported via URL and viewed in Jmol
1246 <!-- JAL-2520 -->Structures loaded via URL are saved in
1247 Jalview Projects rather than fetched via URL again when
1248 the project is loaded and the structure viewed
1251 <em>Web Services</em>
1254 <!-- JAL-2519 -->EnsemblGenomes example failing after
1255 release of Ensembl v.88
1258 <!-- JAL-2366 -->Proxy server address and port always
1259 appear enabled in Preferences->Connections
1262 <!-- JAL-2461 -->DAS registry not found exceptions
1263 removed from console output
1266 <!-- JAL-2582 -->Cannot retrieve protein products from
1267 Ensembl by Peptide ID
1270 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1271 created from SIFTs, and spurious 'Couldn't open structure
1272 in Chimera' errors raised after April 2017 update (problem
1273 due to 'null' string rather than empty string used for
1274 residues with no corresponding PDB mapping).
1277 <em>Application UI</em>
1280 <!-- JAL-2361 -->User Defined Colours not added to Colour
1284 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1285 case' residues (button in colourscheme editor debugged and
1286 new documentation and tooltips added)
1289 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1290 doesn't restore group-specific text colour thresholds
1293 <!-- JAL-2243 -->Feature settings panel does not update as
1294 new features are added to alignment
1297 <!-- JAL-2532 -->Cancel in feature settings reverts
1298 changes to feature colours via the Amend features dialog
1301 <!-- JAL-2506 -->Null pointer exception when attempting to
1302 edit graduated feature colour via amend features dialog
1306 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1307 selection menu changes colours of alignment views
1310 <!-- JAL-2426 -->Spurious exceptions in console raised
1311 from alignment calculation workers after alignment has
1315 <!-- JAL-1608 -->Typo in selection popup menu - Create
1316 groups now 'Create Group'
1319 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1320 Create/Undefine group doesn't always work
1323 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1324 shown again after pressing 'Cancel'
1327 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1328 adjusts start position in wrap mode
1331 <!-- JAL-2563 -->Status bar doesn't show positions for
1332 ambiguous amino acids
1335 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1336 CDS/Protein view after CDS sequences added for aligned
1340 <!-- JAL-2592 -->User defined colourschemes called 'User
1341 Defined' don't appear in Colours menu
1347 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1348 score models doesn't always result in an updated PCA plot
1351 <!-- JAL-2442 -->Features not rendered as transparent on
1352 overview or linked structure view
1355 <!-- JAL-2372 -->Colour group by conservation doesn't
1359 <!-- JAL-2517 -->Hitting Cancel after applying
1360 user-defined colourscheme doesn't restore original
1367 <!-- JAL-2314 -->Unit test failure:
1368 jalview.ws.jabaws.RNAStructExportImport setup fails
1371 <!-- JAL-2307 -->Unit test failure:
1372 jalview.ws.sifts.SiftsClientTest due to compatibility
1373 problems with deep array comparison equality asserts in
1374 successive versions of TestNG
1377 <!-- JAL-2479 -->Relocated StructureChooserTest and
1378 ParameterUtilsTest Unit tests to Network suite
1381 <em>New Known Issues</em>
1384 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1385 phase after a sequence motif find operation
1388 <!-- JAL-2550 -->Importing annotation file with rows
1389 containing just upper and lower case letters are
1390 interpreted as WUSS RNA secondary structure symbols
1393 <!-- JAL-2590 -->Cannot load and display Newick trees
1394 reliably from eggnog Ortholog database
1397 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1398 containing features of type Highlight' when 'B' is pressed
1399 to mark columns containing highlighted regions.
1402 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1403 doesn't always add secondary structure annotation.
1408 <td width="60" nowrap>
1409 <div align="center">
1410 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1413 <td><div align="left">
1417 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1418 for all consensus calculations
1421 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1424 <li>Updated Jalview's Certum code signing certificate
1427 <em>Application</em>
1430 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1431 set of database cross-references, sorted alphabetically
1434 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1435 from database cross references. Users with custom links
1436 will receive a <a href="webServices/urllinks.html#warning">warning
1437 dialog</a> asking them to update their preferences.
1440 <!-- JAL-2287-->Cancel button and escape listener on
1441 dialog warning user about disconnecting Jalview from a
1445 <!-- JAL-2320-->Jalview's Chimera control window closes if
1446 the Chimera it is connected to is shut down
1449 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1450 columns menu item to mark columns containing highlighted
1451 regions (e.g. from structure selections or results of a
1455 <!-- JAL-2284-->Command line option for batch-generation
1456 of HTML pages rendering alignment data with the BioJS
1466 <!-- JAL-2286 -->Columns with more than one modal residue
1467 are not coloured or thresholded according to percent
1468 identity (first observed in Jalview 2.8.2)
1471 <!-- JAL-2301 -->Threonine incorrectly reported as not
1475 <!-- JAL-2318 -->Updates to documentation pages (above PID
1476 threshold, amino acid properties)
1479 <!-- JAL-2292 -->Lower case residues in sequences are not
1480 reported as mapped to residues in a structure file in the
1484 <!--JAL-2324 -->Identical features with non-numeric scores
1485 could be added multiple times to a sequence
1488 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1489 bond features shown as two highlighted residues rather
1490 than a range in linked structure views, and treated
1491 correctly when selecting and computing trees from features
1494 <!-- JAL-2281-->Custom URL links for database
1495 cross-references are matched to database name regardless
1500 <em>Application</em>
1503 <!-- JAL-2282-->Custom URL links for specific database
1504 names without regular expressions also offer links from
1508 <!-- JAL-2315-->Removing a single configured link in the
1509 URL links pane in Connections preferences doesn't actually
1510 update Jalview configuration
1513 <!-- JAL-2272-->CTRL-Click on a selected region to open
1514 the alignment area popup menu doesn't work on El-Capitan
1517 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1518 files with similarly named sequences if dropped onto the
1522 <!-- JAL-2312 -->Additional mappings are shown for PDB
1523 entries where more chains exist in the PDB accession than
1524 are reported in the SIFTS file
1527 <!-- JAL-2317-->Certain structures do not get mapped to
1528 the structure view when displayed with Chimera
1531 <!-- JAL-2317-->No chains shown in the Chimera view
1532 panel's View->Show Chains submenu
1535 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1536 work for wrapped alignment views
1539 <!--JAL-2197 -->Rename UI components for running JPred
1540 predictions from 'JNet' to 'JPred'
1543 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1544 corrupted when annotation panel vertical scroll is not at
1545 first annotation row
1548 <!--JAL-2332 -->Attempting to view structure for Hen
1549 lysozyme results in a PDB Client error dialog box
1552 <!-- JAL-2319 -->Structure View's mapping report switched
1553 ranges for PDB and sequence for SIFTS
1556 SIFTS 'Not_Observed' residues mapped to non-existant
1560 <!-- <em>New Known Issues</em>
1567 <td width="60" nowrap>
1568 <div align="center">
1569 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1570 <em>25/10/2016</em></strong>
1573 <td><em>Application</em>
1575 <li>3D Structure chooser opens with 'Cached structures'
1576 view if structures already loaded</li>
1577 <li>Progress bar reports models as they are loaded to
1578 structure views</li>
1584 <li>Colour by conservation always enabled and no tick
1585 shown in menu when BLOSUM or PID shading applied</li>
1586 <li>FER1_ARATH and FER2_ARATH labels were switched in
1587 example sequences/projects/trees</li>
1589 <em>Application</em>
1591 <li>Jalview projects with views of local PDB structure
1592 files saved on Windows cannot be opened on OSX</li>
1593 <li>Multiple structure views can be opened and superposed
1594 without timeout for structures with multiple models or
1595 multiple sequences in alignment</li>
1596 <li>Cannot import or associated local PDB files without a
1597 PDB ID HEADER line</li>
1598 <li>RMSD is not output in Jmol console when superposition
1600 <li>Drag and drop of URL from Browser fails for Linux and
1601 OSX versions earlier than El Capitan</li>
1602 <li>ENA client ignores invalid content from ENA server</li>
1603 <li>Exceptions are not raised in console when ENA client
1604 attempts to fetch non-existent IDs via Fetch DB Refs UI
1606 <li>Exceptions are not raised in console when a new view
1607 is created on the alignment</li>
1608 <li>OSX right-click fixed for group selections: CMD-click
1609 to insert/remove gaps in groups and CTRL-click to open group
1612 <em>Build and deployment</em>
1614 <li>URL link checker now copes with multi-line anchor
1617 <em>New Known Issues</em>
1619 <li>Drag and drop from URL links in browsers do not work
1626 <td width="60" nowrap>
1627 <div align="center">
1628 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1631 <td><em>General</em>
1634 <!-- JAL-2124 -->Updated Spanish translations.
1637 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1638 for importing structure data to Jalview. Enables mmCIF and
1642 <!-- JAL-192 --->Alignment ruler shows positions relative to
1646 <!-- JAL-2202 -->Position/residue shown in status bar when
1647 mousing over sequence associated annotation
1650 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1654 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1655 '()', canonical '[]' and invalid '{}' base pair populations
1659 <!-- JAL-2092 -->Feature settings popup menu options for
1660 showing or hiding columns containing a feature
1663 <!-- JAL-1557 -->Edit selected group by double clicking on
1664 group and sequence associated annotation labels
1667 <!-- JAL-2236 -->Sequence name added to annotation label in
1668 select/hide columns by annotation and colour by annotation
1672 </ul> <em>Application</em>
1675 <!-- JAL-2050-->Automatically hide introns when opening a
1676 gene/transcript view
1679 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1683 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1684 structure mappings with the EMBL-EBI PDBe SIFTS database
1687 <!-- JAL-2079 -->Updated download sites used for Rfam and
1688 Pfam sources to xfam.org
1691 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1694 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1695 over sequences in Jalview
1698 <!-- JAL-2027-->Support for reverse-complement coding
1699 regions in ENA and EMBL
1702 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1703 for record retrieval via ENA rest API
1706 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1710 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1711 groovy script execution
1714 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1715 alignment window's Calculate menu
1718 <!-- JAL-1812 -->Allow groovy scripts that call
1719 Jalview.getAlignFrames() to run in headless mode
1722 <!-- JAL-2068 -->Support for creating new alignment
1723 calculation workers from groovy scripts
1726 <!-- JAL-1369 --->Store/restore reference sequence in
1730 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1731 associations are now saved/restored from project
1734 <!-- JAL-1993 -->Database selection dialog always shown
1735 before sequence fetcher is opened
1738 <!-- JAL-2183 -->Double click on an entry in Jalview's
1739 database chooser opens a sequence fetcher
1742 <!-- JAL-1563 -->Free-text search client for UniProt using
1743 the UniProt REST API
1746 <!-- JAL-2168 -->-nonews command line parameter to prevent
1747 the news reader opening
1750 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1751 querying stored in preferences
1754 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1758 <!-- JAL-1977-->Tooltips shown on database chooser
1761 <!-- JAL-391 -->Reverse complement function in calculate
1762 menu for nucleotide sequences
1765 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1766 and feature counts preserves alignment ordering (and
1767 debugged for complex feature sets).
1770 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1771 viewing structures with Jalview 2.10
1774 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1775 genome, transcript CCDS and gene ids via the Ensembl and
1776 Ensembl Genomes REST API
1779 <!-- JAL-2049 -->Protein sequence variant annotation
1780 computed for 'sequence_variant' annotation on CDS regions
1784 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1788 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1789 Ref Fetcher fails to match, or otherwise updates sequence
1790 data from external database records.
1793 <!-- JAL-2154 -->Revised Jalview Project format for
1794 efficient recovery of sequence coding and alignment
1795 annotation relationships.
1797 </ul> <!-- <em>Applet</em>
1808 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1812 <!-- JAL-2018-->Export features in Jalview format (again)
1813 includes graduated colourschemes
1816 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1817 working with big alignments and lots of hidden columns
1820 <!-- JAL-2053-->Hidden column markers not always rendered
1821 at right of alignment window
1824 <!-- JAL-2067 -->Tidied up links in help file table of
1828 <!-- JAL-2072 -->Feature based tree calculation not shown
1832 <!-- JAL-2075 -->Hidden columns ignored during feature
1833 based tree calculation
1836 <!-- JAL-2065 -->Alignment view stops updating when show
1837 unconserved enabled for group on alignment
1840 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1844 <!-- JAL-2146 -->Alignment column in status incorrectly
1845 shown as "Sequence position" when mousing over
1849 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1850 hidden columns present
1853 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1854 user created annotation added to alignment
1857 <!-- JAL-1841 -->RNA Structure consensus only computed for
1858 '()' base pair annotation
1861 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1862 in zero scores for all base pairs in RNA Structure
1866 <!-- JAL-2174-->Extend selection with columns containing
1870 <!-- JAL-2275 -->Pfam format writer puts extra space at
1871 beginning of sequence
1874 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1878 <!-- JAL-2238 -->Cannot create groups on an alignment from
1879 from a tree when t-coffee scores are shown
1882 <!-- JAL-1836,1967 -->Cannot import and view PDB
1883 structures with chains containing negative resnums (4q4h)
1886 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1890 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1891 to Clustal, PIR and PileUp output
1894 <!-- JAL-2008 -->Reordering sequence features that are
1895 not visible causes alignment window to repaint
1898 <!-- JAL-2006 -->Threshold sliders don't work in
1899 graduated colour and colour by annotation row for e-value
1900 scores associated with features and annotation rows
1903 <!-- JAL-1797 -->amino acid physicochemical conservation
1904 calculation should be case independent
1907 <!-- JAL-2173 -->Remove annotation also updates hidden
1911 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1912 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1913 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1916 <!-- JAL-2065 -->Null pointer exceptions and redraw
1917 problems when reference sequence defined and 'show
1918 non-conserved' enabled
1921 <!-- JAL-1306 -->Quality and Conservation are now shown on
1922 load even when Consensus calculation is disabled
1925 <!-- JAL-1932 -->Remove right on penultimate column of
1926 alignment does nothing
1929 <em>Application</em>
1932 <!-- JAL-1552-->URLs and links can't be imported by
1933 drag'n'drop on OSX when launched via webstart (note - not
1934 yet fixed for El Capitan)
1937 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1938 output when running on non-gb/us i18n platforms
1941 <!-- JAL-1944 -->Error thrown when exporting a view with
1942 hidden sequences as flat-file alignment
1945 <!-- JAL-2030-->InstallAnywhere distribution fails when
1949 <!-- JAL-2080-->Jalview very slow to launch via webstart
1950 (also hotfix for 2.9.0b2)
1953 <!-- JAL-2085 -->Cannot save project when view has a
1954 reference sequence defined
1957 <!-- JAL-1011 -->Columns are suddenly selected in other
1958 alignments and views when revealing hidden columns
1961 <!-- JAL-1989 -->Hide columns not mirrored in complement
1962 view in a cDNA/Protein splitframe
1965 <!-- JAL-1369 -->Cannot save/restore representative
1966 sequence from project when only one sequence is
1970 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1971 in Structure Chooser
1974 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1975 structure consensus didn't refresh annotation panel
1978 <!-- JAL-1962 -->View mapping in structure view shows
1979 mappings between sequence and all chains in a PDB file
1982 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1983 dialogs format columns correctly, don't display array
1984 data, sort columns according to type
1987 <!-- JAL-1975 -->Export complete shown after destination
1988 file chooser is cancelled during an image export
1991 <!-- JAL-2025 -->Error when querying PDB Service with
1992 sequence name containing special characters
1995 <!-- JAL-2024 -->Manual PDB structure querying should be
1999 <!-- JAL-2104 -->Large tooltips with broken HTML
2000 formatting don't wrap
2003 <!-- JAL-1128 -->Figures exported from wrapped view are
2004 truncated so L looks like I in consensus annotation
2007 <!-- JAL-2003 -->Export features should only export the
2008 currently displayed features for the current selection or
2012 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2013 after fetching cross-references, and restoring from
2017 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2018 followed in the structure viewer
2021 <!-- JAL-2163 -->Titles for individual alignments in
2022 splitframe not restored from project
2025 <!-- JAL-2145 -->missing autocalculated annotation at
2026 trailing end of protein alignment in transcript/product
2027 splitview when pad-gaps not enabled by default
2030 <!-- JAL-1797 -->amino acid physicochemical conservation
2034 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2035 article has been read (reopened issue due to
2036 internationalisation problems)
2039 <!-- JAL-1960 -->Only offer PDB structures in structure
2040 viewer based on sequence name, PDB and UniProt
2045 <!-- JAL-1976 -->No progress bar shown during export of
2049 <!-- JAL-2213 -->Structures not always superimposed after
2050 multiple structures are shown for one or more sequences.
2053 <!-- JAL-1370 -->Reference sequence characters should not
2054 be replaced with '.' when 'Show unconserved' format option
2058 <!-- JAL-1823 -->Cannot specify chain code when entering
2059 specific PDB id for sequence
2062 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2063 'Export hidden sequences' is enabled, but 'export hidden
2064 columns' is disabled.
2067 <!--JAL-2026-->Best Quality option in structure chooser
2068 selects lowest rather than highest resolution structures
2072 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2073 to sequence mapping in 'View Mappings' report
2076 <!-- JAL-2284 -->Unable to read old Jalview projects that
2077 contain non-XML data added after Jalvew wrote project.
2080 <!-- JAL-2118 -->Newly created annotation row reorders
2081 after clicking on it to create new annotation for a
2085 <!-- JAL-1980 -->Null Pointer Exception raised when
2086 pressing Add on an orphaned cut'n'paste window.
2088 <!-- may exclude, this is an external service stability issue JAL-1941
2089 -- > RNA 3D structure not added via DSSR service</li> -->
2094 <!-- JAL-2151 -->Incorrect columns are selected when
2095 hidden columns present before start of sequence
2098 <!-- JAL-1986 -->Missing dependencies on applet pages
2102 <!-- JAL-1947 -->Overview pixel size changes when
2103 sequences are hidden in applet
2106 <!-- JAL-1996 -->Updated instructions for applet
2107 deployment on examples pages.
2114 <td width="60" nowrap>
2115 <div align="center">
2116 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2117 <em>16/10/2015</em></strong>
2120 <td><em>General</em>
2122 <li>Time stamps for signed Jalview application and applet
2127 <em>Application</em>
2129 <li>Duplicate group consensus and conservation rows
2130 shown when tree is partitioned</li>
2131 <li>Erratic behaviour when tree partitions made with
2132 multiple cDNA/Protein split views</li>
2138 <td width="60" nowrap>
2139 <div align="center">
2140 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2141 <em>8/10/2015</em></strong>
2144 <td><em>General</em>
2146 <li>Updated Spanish translations of localized text for
2148 </ul> <em>Application</em>
2150 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2151 <li>Signed OSX InstallAnywhere installer<br></li>
2152 <li>Support for per-sequence based annotations in BioJSON</li>
2153 </ul> <em>Applet</em>
2155 <li>Split frame example added to applet examples page</li>
2156 </ul> <em>Build and Deployment</em>
2159 <!-- JAL-1888 -->New ant target for running Jalview's test
2167 <li>Mapping of cDNA to protein in split frames
2168 incorrect when sequence start > 1</li>
2169 <li>Broken images in filter column by annotation dialog
2171 <li>Feature colours not parsed from features file</li>
2172 <li>Exceptions and incomplete link URLs recovered when
2173 loading a features file containing HTML tags in feature
2177 <em>Application</em>
2179 <li>Annotations corrupted after BioJS export and
2181 <li>Incorrect sequence limits after Fetch DB References
2182 with 'trim retrieved sequences'</li>
2183 <li>Incorrect warning about deleting all data when
2184 deleting selected columns</li>
2185 <li>Patch to build system for shipping properly signed
2186 JNLP templates for webstart launch</li>
2187 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2188 unreleased structures for download or viewing</li>
2189 <li>Tab/space/return keystroke operation of EMBL-PDBe
2190 fetcher/viewer dialogs works correctly</li>
2191 <li>Disabled 'minimise' button on Jalview windows
2192 running on OSX to workaround redraw hang bug</li>
2193 <li>Split cDNA/Protein view position and geometry not
2194 recovered from jalview project</li>
2195 <li>Initial enabled/disabled state of annotation menu
2196 sorter 'show autocalculated first/last' corresponds to
2198 <li>Restoring of Clustal, RNA Helices and T-Coffee
2199 color schemes from BioJSON</li>
2203 <li>Reorder sequences mirrored in cDNA/Protein split
2205 <li>Applet with Jmol examples not loading correctly</li>
2211 <td><div align="center">
2212 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2214 <td><em>General</em>
2216 <li>Linked visualisation and analysis of DNA and Protein
2219 <li>Translated cDNA alignments shown as split protein
2220 and DNA alignment views</li>
2221 <li>Codon consensus annotation for linked protein and
2222 cDNA alignment views</li>
2223 <li>Link cDNA or Protein product sequences by loading
2224 them onto Protein or cDNA alignments</li>
2225 <li>Reconstruct linked cDNA alignment from aligned
2226 protein sequences</li>
2229 <li>Jmol integration updated to Jmol v14.2.14</li>
2230 <li>Import and export of Jalview alignment views as <a
2231 href="features/bioJsonFormat.html">BioJSON</a></li>
2232 <li>New alignment annotation file statements for
2233 reference sequences and marking hidden columns</li>
2234 <li>Reference sequence based alignment shading to
2235 highlight variation</li>
2236 <li>Select or hide columns according to alignment
2238 <li>Find option for locating sequences by description</li>
2239 <li>Conserved physicochemical properties shown in amino
2240 acid conservation row</li>
2241 <li>Alignments can be sorted by number of RNA helices</li>
2242 </ul> <em>Application</em>
2244 <li>New cDNA/Protein analysis capabilities
2246 <li>Get Cross-References should open a Split Frame
2247 view with cDNA/Protein</li>
2248 <li>Detect when nucleotide sequences and protein
2249 sequences are placed in the same alignment</li>
2250 <li>Split cDNA/Protein views are saved in Jalview
2255 <li>Use REST API to talk to Chimera</li>
2256 <li>Selected regions in Chimera are highlighted in linked
2257 Jalview windows</li>
2259 <li>VARNA RNA viewer updated to v3.93</li>
2260 <li>VARNA views are saved in Jalview Projects</li>
2261 <li>Pseudoknots displayed as Jalview RNA annotation can
2262 be shown in VARNA</li>
2264 <li>Make groups for selection uses marked columns as well
2265 as the active selected region</li>
2267 <li>Calculate UPGMA and NJ trees using sequence feature
2269 <li>New Export options
2271 <li>New Export Settings dialog to control hidden
2272 region export in flat file generation</li>
2274 <li>Export alignment views for display with the <a
2275 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2277 <li>Export scrollable SVG in HTML page</li>
2278 <li>Optional embedding of BioJSON data when exporting
2279 alignment figures to HTML</li>
2281 <li>3D structure retrieval and display
2283 <li>Free text and structured queries with the PDBe
2285 <li>PDBe Search API based discovery and selection of
2286 PDB structures for a sequence set</li>
2290 <li>JPred4 employed for protein secondary structure
2292 <li>Hide Insertions menu option to hide unaligned columns
2293 for one or a group of sequences</li>
2294 <li>Automatically hide insertions in alignments imported
2295 from the JPred4 web server</li>
2296 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2297 system on OSX<br />LGPL libraries courtesy of <a
2298 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2300 <li>changed 'View nucleotide structure' submenu to 'View
2301 VARNA 2D Structure'</li>
2302 <li>change "View protein structure" menu option to "3D
2305 </ul> <em>Applet</em>
2307 <li>New layout for applet example pages</li>
2308 <li>New parameters to enable SplitFrame view
2309 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2310 <li>New example demonstrating linked viewing of cDNA and
2311 Protein alignments</li>
2312 </ul> <em>Development and deployment</em>
2314 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2315 <li>Include installation type and git revision in build
2316 properties and console log output</li>
2317 <li>Jalview Github organisation, and new github site for
2318 storing BioJsMSA Templates</li>
2319 <li>Jalview's unit tests now managed with TestNG</li>
2322 <!-- <em>General</em>
2324 </ul> --> <!-- issues resolved --> <em>Application</em>
2326 <li>Escape should close any open find dialogs</li>
2327 <li>Typo in select-by-features status report</li>
2328 <li>Consensus RNA secondary secondary structure
2329 predictions are not highlighted in amber</li>
2330 <li>Missing gap character in v2.7 example file means
2331 alignment appears unaligned when pad-gaps is not enabled</li>
2332 <li>First switch to RNA Helices colouring doesn't colour
2333 associated structure views</li>
2334 <li>ID width preference option is greyed out when auto
2335 width checkbox not enabled</li>
2336 <li>Stopped a warning dialog from being shown when
2337 creating user defined colours</li>
2338 <li>'View Mapping' in structure viewer shows sequence
2339 mappings for just that viewer's sequences</li>
2340 <li>Workaround for superposing PDB files containing
2341 multiple models in Chimera</li>
2342 <li>Report sequence position in status bar when hovering
2343 over Jmol structure</li>
2344 <li>Cannot output gaps as '.' symbols with Selection ->
2345 output to text box</li>
2346 <li>Flat file exports of alignments with hidden columns
2347 have incorrect sequence start/end</li>
2348 <li>'Aligning' a second chain to a Chimera structure from
2350 <li>Colour schemes applied to structure viewers don't
2351 work for nucleotide</li>
2352 <li>Loading/cut'n'pasting an empty or invalid file leads
2353 to a grey/invisible alignment window</li>
2354 <li>Exported Jpred annotation from a sequence region
2355 imports to different position</li>
2356 <li>Space at beginning of sequence feature tooltips shown
2357 on some platforms</li>
2358 <li>Chimera viewer 'View | Show Chain' menu is not
2360 <li>'New View' fails with a Null Pointer Exception in
2361 console if Chimera has been opened</li>
2362 <li>Mouseover to Chimera not working</li>
2363 <li>Miscellaneous ENA XML feature qualifiers not
2365 <li>NPE in annotation renderer after 'Extract Scores'</li>
2366 <li>If two structures in one Chimera window, mouseover of
2367 either sequence shows on first structure</li>
2368 <li>'Show annotations' options should not make
2369 non-positional annotations visible</li>
2370 <li>Subsequence secondary structure annotation not shown
2371 in right place after 'view flanking regions'</li>
2372 <li>File Save As type unset when current file format is
2374 <li>Save as '.jar' option removed for saving Jalview
2376 <li>Colour by Sequence colouring in Chimera more
2378 <li>Cannot 'add reference annotation' for a sequence in
2379 several views on same alignment</li>
2380 <li>Cannot show linked products for EMBL / ENA records</li>
2381 <li>Jalview's tooltip wraps long texts containing no
2383 </ul> <em>Applet</em>
2385 <li>Jmol to JalviewLite mouseover/link not working</li>
2386 <li>JalviewLite can't import sequences with ID
2387 descriptions containing angle brackets</li>
2388 </ul> <em>General</em>
2390 <li>Cannot export and reimport RNA secondary structure
2391 via jalview annotation file</li>
2392 <li>Random helix colour palette for colour by annotation
2393 with RNA secondary structure</li>
2394 <li>Mouseover to cDNA from STOP residue in protein
2395 translation doesn't work.</li>
2396 <li>hints when using the select by annotation dialog box</li>
2397 <li>Jmol alignment incorrect if PDB file has alternate CA
2399 <li>FontChooser message dialog appears to hang after
2400 choosing 1pt font</li>
2401 <li>Peptide secondary structure incorrectly imported from
2402 annotation file when annotation display text includes 'e' or
2404 <li>Cannot set colour of new feature type whilst creating
2406 <li>cDNA translation alignment should not be sequence
2407 order dependent</li>
2408 <li>'Show unconserved' doesn't work for lower case
2410 <li>Nucleotide ambiguity codes involving R not recognised</li>
2411 </ul> <em>Deployment and Documentation</em>
2413 <li>Applet example pages appear different to the rest of
2414 www.jalview.org</li>
2415 </ul> <em>Application Known issues</em>
2417 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2418 <li>Misleading message appears after trying to delete
2420 <li>Jalview icon not shown in dock after InstallAnywhere
2421 version launches</li>
2422 <li>Fetching EMBL reference for an RNA sequence results
2423 fails with a sequence mismatch</li>
2424 <li>Corrupted or unreadable alignment display when
2425 scrolling alignment to right</li>
2426 <li>ArrayIndexOutOfBoundsException thrown when remove
2427 empty columns called on alignment with ragged gapped ends</li>
2428 <li>auto calculated alignment annotation rows do not get
2429 placed above or below non-autocalculated rows</li>
2430 <li>Jalview dekstop becomes sluggish at full screen in
2431 ultra-high resolution</li>
2432 <li>Cannot disable consensus calculation independently of
2433 quality and conservation</li>
2434 <li>Mouseover highlighting between cDNA and protein can
2435 become sluggish with more than one splitframe shown</li>
2436 </ul> <em>Applet Known Issues</em>
2438 <li>Core PDB parsing code requires Jmol</li>
2439 <li>Sequence canvas panel goes white when alignment
2440 window is being resized</li>
2446 <td><div align="center">
2447 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2449 <td><em>General</em>
2451 <li>Updated Java code signing certificate donated by
2453 <li>Features and annotation preserved when performing
2454 pairwise alignment</li>
2455 <li>RNA pseudoknot annotation can be
2456 imported/exported/displayed</li>
2457 <li>'colour by annotation' can colour by RNA and
2458 protein secondary structure</li>
2459 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2460 post-hoc with 2.9 release</em>)
2463 </ul> <em>Application</em>
2465 <li>Extract and display secondary structure for sequences
2466 with 3D structures</li>
2467 <li>Support for parsing RNAML</li>
2468 <li>Annotations menu for layout
2470 <li>sort sequence annotation rows by alignment</li>
2471 <li>place sequence annotation above/below alignment
2474 <li>Output in Stockholm format</li>
2475 <li>Internationalisation: improved Spanish (es)
2477 <li>Structure viewer preferences tab</li>
2478 <li>Disorder and Secondary Structure annotation tracks
2479 shared between alignments</li>
2480 <li>UCSF Chimera launch and linked highlighting from
2482 <li>Show/hide all sequence associated annotation rows for
2483 all or current selection</li>
2484 <li>disorder and secondary structure predictions
2485 available as dataset annotation</li>
2486 <li>Per-sequence rna helices colouring</li>
2489 <li>Sequence database accessions imported when fetching
2490 alignments from Rfam</li>
2491 <li>update VARNA version to 3.91</li>
2493 <li>New groovy scripts for exporting aligned positions,
2494 conservation values, and calculating sum of pairs scores.</li>
2495 <li>Command line argument to set default JABAWS server</li>
2496 <li>include installation type in build properties and
2497 console log output</li>
2498 <li>Updated Jalview project format to preserve dataset
2502 <!-- issues resolved --> <em>Application</em>
2504 <li>Distinguish alignment and sequence associated RNA
2505 structure in structure->view->VARNA</li>
2506 <li>Raise dialog box if user deletes all sequences in an
2508 <li>Pressing F1 results in documentation opening twice</li>
2509 <li>Sequence feature tooltip is wrapped</li>
2510 <li>Double click on sequence associated annotation
2511 selects only first column</li>
2512 <li>Redundancy removal doesn't result in unlinked
2513 leaves shown in tree</li>
2514 <li>Undos after several redundancy removals don't undo
2516 <li>Hide sequence doesn't hide associated annotation</li>
2517 <li>User defined colours dialog box too big to fit on
2518 screen and buttons not visible</li>
2519 <li>author list isn't updated if already written to
2520 Jalview properties</li>
2521 <li>Popup menu won't open after retrieving sequence
2523 <li>File open window for associate PDB doesn't open</li>
2524 <li>Left-then-right click on a sequence id opens a
2525 browser search window</li>
2526 <li>Cannot open sequence feature shading/sort popup menu
2527 in feature settings dialog</li>
2528 <li>better tooltip placement for some areas of Jalview
2530 <li>Allow addition of JABAWS Server which doesn't
2531 pass validation</li>
2532 <li>Web services parameters dialog box is too large to
2534 <li>Muscle nucleotide alignment preset obscured by
2536 <li>JABAWS preset submenus don't contain newly
2537 defined user preset</li>
2538 <li>MSA web services warns user if they were launched
2539 with invalid input</li>
2540 <li>Jalview cannot contact DAS Registy when running on
2543 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2544 'Superpose with' submenu not shown when new view
2548 </ul> <!-- <em>Applet</em>
2550 </ul> <em>General</em>
2552 </ul>--> <em>Deployment and Documentation</em>
2554 <li>2G and 1G options in launchApp have no effect on
2555 memory allocation</li>
2556 <li>launchApp service doesn't automatically open
2557 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2559 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2560 InstallAnywhere reports cannot find valid JVM when Java
2561 1.7_055 is available
2563 </ul> <em>Application Known issues</em>
2566 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2567 corrupted or unreadable alignment display when scrolling
2571 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2572 retrieval fails but progress bar continues for DAS retrieval
2573 with large number of ID
2576 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2577 flatfile output of visible region has incorrect sequence
2581 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2582 rna structure consensus doesn't update when secondary
2583 structure tracks are rearranged
2586 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2587 invalid rna structure positional highlighting does not
2588 highlight position of invalid base pairs
2591 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2592 out of memory errors are not raised when saving Jalview
2593 project from alignment window file menu
2596 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2597 Switching to RNA Helices colouring doesn't propagate to
2601 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2602 colour by RNA Helices not enabled when user created
2603 annotation added to alignment
2606 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2607 Jalview icon not shown on dock in Mountain Lion/Webstart
2609 </ul> <em>Applet Known Issues</em>
2612 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2613 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2616 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2617 Jalview and Jmol example not compatible with IE9
2620 <li>Sort by annotation score doesn't reverse order
2626 <td><div align="center">
2627 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2630 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2633 <li>Internationalisation of user interface (usually
2634 called i18n support) and translation for Spanish locale</li>
2635 <li>Define/Undefine group on current selection with
2636 Ctrl-G/Shift Ctrl-G</li>
2637 <li>Improved group creation/removal options in
2638 alignment/sequence Popup menu</li>
2639 <li>Sensible precision for symbol distribution
2640 percentages shown in logo tooltip.</li>
2641 <li>Annotation panel height set according to amount of
2642 annotation when alignment first opened</li>
2643 </ul> <em>Application</em>
2645 <li>Interactive consensus RNA secondary structure
2646 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2647 <li>Select columns containing particular features from
2648 Feature Settings dialog</li>
2649 <li>View all 'representative' PDB structures for selected
2651 <li>Update Jalview project format:
2653 <li>New file extension for Jalview projects '.jvp'</li>
2654 <li>Preserve sequence and annotation dataset (to
2655 store secondary structure annotation,etc)</li>
2656 <li>Per group and alignment annotation and RNA helix
2660 <li>New similarity measures for PCA and Tree calculation
2662 <li>Experimental support for retrieval and viewing of
2663 flanking regions for an alignment</li>
2667 <!-- issues resolved --> <em>Application</em>
2669 <li>logo keeps spinning and status remains at queued or
2670 running after job is cancelled</li>
2671 <li>cannot export features from alignments imported from
2672 Jalview/VAMSAS projects</li>
2673 <li>Buggy slider for web service parameters that take
2675 <li>Newly created RNA secondary structure line doesn't
2676 have 'display all symbols' flag set</li>
2677 <li>T-COFFEE alignment score shading scheme and other
2678 annotation shading not saved in Jalview project</li>
2679 <li>Local file cannot be loaded in freshly downloaded
2681 <li>Jalview icon not shown on dock in Mountain
2683 <li>Load file from desktop file browser fails</li>
2684 <li>Occasional NPE thrown when calculating large trees</li>
2685 <li>Cannot reorder or slide sequences after dragging an
2686 alignment onto desktop</li>
2687 <li>Colour by annotation dialog throws NPE after using
2688 'extract scores' function</li>
2689 <li>Loading/cut'n'pasting an empty file leads to a grey
2690 alignment window</li>
2691 <li>Disorder thresholds rendered incorrectly after
2692 performing IUPred disorder prediction</li>
2693 <li>Multiple group annotated consensus rows shown when
2694 changing 'normalise logo' display setting</li>
2695 <li>Find shows blank dialog after 'finished searching' if
2696 nothing matches query</li>
2697 <li>Null Pointer Exceptions raised when sorting by
2698 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2700 <li>Errors in Jmol console when structures in alignment
2701 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2703 <li>Not all working JABAWS services are shown in
2705 <li>JAVAWS version of Jalview fails to launch with
2706 'invalid literal/length code'</li>
2707 <li>Annotation/RNA Helix colourschemes cannot be applied
2708 to alignment with groups (actually fixed in 2.8.0b1)</li>
2709 <li>RNA Helices and T-Coffee Scores available as default
2712 </ul> <em>Applet</em>
2714 <li>Remove group option is shown even when selection is
2716 <li>Apply to all groups ticked but colourscheme changes
2717 don't affect groups</li>
2718 <li>Documented RNA Helices and T-Coffee Scores as valid
2719 colourscheme name</li>
2720 <li>Annotation labels drawn on sequence IDs when
2721 Annotation panel is not displayed</li>
2722 <li>Increased font size for dropdown menus on OSX and
2723 embedded windows</li>
2724 </ul> <em>Other</em>
2726 <li>Consensus sequence for alignments/groups with a
2727 single sequence were not calculated</li>
2728 <li>annotation files that contain only groups imported as
2729 annotation and junk sequences</li>
2730 <li>Fasta files with sequences containing '*' incorrectly
2731 recognised as PFAM or BLC</li>
2732 <li>conservation/PID slider apply all groups option
2733 doesn't affect background (2.8.0b1)
2735 <li>redundancy highlighting is erratic at 0% and 100%</li>
2736 <li>Remove gapped columns fails for sequences with ragged
2738 <li>AMSA annotation row with leading spaces is not
2739 registered correctly on import</li>
2740 <li>Jalview crashes when selecting PCA analysis for
2741 certain alignments</li>
2742 <li>Opening the colour by annotation dialog for an
2743 existing annotation based 'use original colours'
2744 colourscheme loses original colours setting</li>
2749 <td><div align="center">
2750 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2751 <em>30/1/2014</em></strong>
2755 <li>Trusted certificates for JalviewLite applet and
2756 Jalview Desktop application<br />Certificate was donated by
2757 <a href="https://www.certum.eu">Certum</a> to the Jalview
2758 open source project).
2760 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2761 <li>Output in Stockholm format</li>
2762 <li>Allow import of data from gzipped files</li>
2763 <li>Export/import group and sequence associated line
2764 graph thresholds</li>
2765 <li>Nucleotide substitution matrix that supports RNA and
2766 ambiguity codes</li>
2767 <li>Allow disorder predictions to be made on the current
2768 selection (or visible selection) in the same way that JPred
2770 <li>Groovy scripting for headless Jalview operation</li>
2771 </ul> <em>Other improvements</em>
2773 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2774 <li>COMBINE statement uses current SEQUENCE_REF and
2775 GROUP_REF scope to group annotation rows</li>
2776 <li>Support '' style escaping of quotes in Newick
2778 <li>Group options for JABAWS service by command line name</li>
2779 <li>Empty tooltip shown for JABA service options with a
2780 link but no description</li>
2781 <li>Select primary source when selecting authority in
2782 database fetcher GUI</li>
2783 <li>Add .mfa to FASTA file extensions recognised by
2785 <li>Annotation label tooltip text wrap</li>
2790 <li>Slow scrolling when lots of annotation rows are
2792 <li>Lots of NPE (and slowness) after creating RNA
2793 secondary structure annotation line</li>
2794 <li>Sequence database accessions not imported when
2795 fetching alignments from Rfam</li>
2796 <li>Incorrect SHMR submission for sequences with
2798 <li>View all structures does not always superpose
2800 <li>Option widgets in service parameters not updated to
2801 reflect user or preset settings</li>
2802 <li>Null pointer exceptions for some services without
2803 presets or adjustable parameters</li>
2804 <li>Discover PDB IDs entry in structure menu doesn't
2805 discover PDB xRefs</li>
2806 <li>Exception encountered while trying to retrieve
2807 features with DAS</li>
2808 <li>Lowest value in annotation row isn't coloured
2809 when colour by annotation (per sequence) is coloured</li>
2810 <li>Keyboard mode P jumps to start of gapped region when
2811 residue follows a gap</li>
2812 <li>Jalview appears to hang importing an alignment with
2813 Wrap as default or after enabling Wrap</li>
2814 <li>'Right click to add annotations' message
2815 shown in wrap mode when no annotations present</li>
2816 <li>Disorder predictions fail with NPE if no automatic
2817 annotation already exists on alignment</li>
2818 <li>oninit javascript function should be called after
2819 initialisation completes</li>
2820 <li>Remove redundancy after disorder prediction corrupts
2821 alignment window display</li>
2822 <li>Example annotation file in documentation is invalid</li>
2823 <li>Grouped line graph annotation rows are not exported
2824 to annotation file</li>
2825 <li>Multi-harmony analysis cannot be run when only two
2827 <li>Cannot create multiple groups of line graphs with
2828 several 'combine' statements in annotation file</li>
2829 <li>Pressing return several times causes Number Format
2830 exceptions in keyboard mode</li>
2831 <li>Multi-harmony (SHMMR) method doesn't submit
2832 correct partitions for input data</li>
2833 <li>Translation from DNA to Amino Acids fails</li>
2834 <li>Jalview fail to load newick tree with quoted label</li>
2835 <li>--headless flag isn't understood</li>
2836 <li>ClassCastException when generating EPS in headless
2838 <li>Adjusting sequence-associated shading threshold only
2839 changes one row's threshold</li>
2840 <li>Preferences and Feature settings panel panel
2841 doesn't open</li>
2842 <li>hide consensus histogram also hides conservation and
2843 quality histograms</li>
2848 <td><div align="center">
2849 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2851 <td><em>Application</em>
2853 <li>Support for JABAWS 2.0 Services (AACon alignment
2854 conservation, protein disorder and Clustal Omega)</li>
2855 <li>JABAWS server status indicator in Web Services
2857 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2858 in Jalview alignment window</li>
2859 <li>Updated Jalview build and deploy framework for OSX
2860 mountain lion, windows 7, and 8</li>
2861 <li>Nucleotide substitution matrix for PCA that supports
2862 RNA and ambiguity codes</li>
2864 <li>Improved sequence database retrieval GUI</li>
2865 <li>Support fetching and database reference look up
2866 against multiple DAS sources (Fetch all from in 'fetch db
2868 <li>Jalview project improvements
2870 <li>Store and retrieve the 'belowAlignment'
2871 flag for annotation</li>
2872 <li>calcId attribute to group annotation rows on the
2874 <li>Store AACon calculation settings for a view in
2875 Jalview project</li>
2879 <li>horizontal scrolling gesture support</li>
2880 <li>Visual progress indicator when PCA calculation is
2882 <li>Simpler JABA web services menus</li>
2883 <li>visual indication that web service results are still
2884 being retrieved from server</li>
2885 <li>Serialise the dialogs that are shown when Jalview
2886 starts up for first time</li>
2887 <li>Jalview user agent string for interacting with HTTP
2889 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2891 <li>Examples directory and Groovy library included in
2892 InstallAnywhere distribution</li>
2893 </ul> <em>Applet</em>
2895 <li>RNA alignment and secondary structure annotation
2896 visualization applet example</li>
2897 </ul> <em>General</em>
2899 <li>Normalise option for consensus sequence logo</li>
2900 <li>Reset button in PCA window to return dimensions to
2902 <li>Allow seqspace or Jalview variant of alignment PCA
2904 <li>PCA with either nucleic acid and protein substitution
2906 <li>Allow windows containing HTML reports to be exported
2908 <li>Interactive display and editing of RNA secondary
2909 structure contacts</li>
2910 <li>RNA Helix Alignment Colouring</li>
2911 <li>RNA base pair logo consensus</li>
2912 <li>Parse sequence associated secondary structure
2913 information in Stockholm files</li>
2914 <li>HTML Export database accessions and annotation
2915 information presented in tooltip for sequences</li>
2916 <li>Import secondary structure from LOCARNA clustalw
2917 style RNA alignment files</li>
2918 <li>import and visualise T-COFFEE quality scores for an
2920 <li>'colour by annotation' per sequence option to
2921 shade each sequence according to its associated alignment
2923 <li>New Jalview Logo</li>
2924 </ul> <em>Documentation and Development</em>
2926 <li>documentation for score matrices used in Jalview</li>
2927 <li>New Website!</li>
2929 <td><em>Application</em>
2931 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2932 wsdbfetch REST service</li>
2933 <li>Stop windows being moved outside desktop on OSX</li>
2934 <li>Filetype associations not installed for webstart
2936 <li>Jalview does not always retrieve progress of a JABAWS
2937 job execution in full once it is complete</li>
2938 <li>revise SHMR RSBS definition to ensure alignment is
2939 uploaded via ali_file parameter</li>
2940 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2941 <li>View all structures superposed fails with exception</li>
2942 <li>Jnet job queues forever if a very short sequence is
2943 submitted for prediction</li>
2944 <li>Cut and paste menu not opened when mouse clicked on
2946 <li>Putting fractional value into integer text box in
2947 alignment parameter dialog causes Jalview to hang</li>
2948 <li>Structure view highlighting doesn't work on
2950 <li>View all structures fails with exception shown in
2952 <li>Characters in filename associated with PDBEntry not
2953 escaped in a platform independent way</li>
2954 <li>Jalview desktop fails to launch with exception when
2956 <li>Tree calculation reports 'you must have 2 or more
2957 sequences selected' when selection is empty</li>
2958 <li>Jalview desktop fails to launch with jar signature
2959 failure when java web start temporary file caching is
2961 <li>DAS Sequence retrieval with range qualification
2962 results in sequence xref which includes range qualification</li>
2963 <li>Errors during processing of command line arguments
2964 cause progress bar (JAL-898) to be removed</li>
2965 <li>Replace comma for semi-colon option not disabled for
2966 DAS sources in sequence fetcher</li>
2967 <li>Cannot close news reader when JABAWS server warning
2968 dialog is shown</li>
2969 <li>Option widgets not updated to reflect user settings</li>
2970 <li>Edited sequence not submitted to web service</li>
2971 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2972 <li>InstallAnywhere installer doesn't unpack and run
2973 on OSX Mountain Lion</li>
2974 <li>Annotation panel not given a scroll bar when
2975 sequences with alignment annotation are pasted into the
2977 <li>Sequence associated annotation rows not associated
2978 when loaded from Jalview project</li>
2979 <li>Browser launch fails with NPE on java 1.7</li>
2980 <li>JABAWS alignment marked as finished when job was
2981 cancelled or job failed due to invalid input</li>
2982 <li>NPE with v2.7 example when clicking on Tree
2983 associated with all views</li>
2984 <li>Exceptions when copy/paste sequences with grouped
2985 annotation rows to new window</li>
2986 </ul> <em>Applet</em>
2988 <li>Sequence features are momentarily displayed before
2989 they are hidden using hidefeaturegroups applet parameter</li>
2990 <li>loading features via javascript API automatically
2991 enables feature display</li>
2992 <li>scrollToColumnIn javascript API method doesn't
2994 </ul> <em>General</em>
2996 <li>Redundancy removal fails for rna alignment</li>
2997 <li>PCA calculation fails when sequence has been selected
2998 and then deselected</li>
2999 <li>PCA window shows grey box when first opened on OSX</li>
3000 <li>Letters coloured pink in sequence logo when alignment
3001 coloured with clustalx</li>
3002 <li>Choosing fonts without letter symbols defined causes
3003 exceptions and redraw errors</li>
3004 <li>Initial PCA plot view is not same as manually
3005 reconfigured view</li>
3006 <li>Grouped annotation graph label has incorrect line
3008 <li>Grouped annotation graph label display is corrupted
3009 for lots of labels</li>
3014 <div align="center">
3015 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3018 <td><em>Application</em>
3020 <li>Jalview Desktop News Reader</li>
3021 <li>Tweaked default layout of web services menu</li>
3022 <li>View/alignment association menu to enable user to
3023 easily specify which alignment a multi-structure view takes
3024 its colours/correspondences from</li>
3025 <li>Allow properties file location to be specified as URL</li>
3026 <li>Extend Jalview project to preserve associations
3027 between many alignment views and a single Jmol display</li>
3028 <li>Store annotation row height in Jalview project file</li>
3029 <li>Annotation row column label formatting attributes
3030 stored in project file</li>
3031 <li>Annotation row order for auto-calculated annotation
3032 rows preserved in Jalview project file</li>
3033 <li>Visual progress indication when Jalview state is
3034 saved using Desktop window menu</li>
3035 <li>Visual indication that command line arguments are
3036 still being processed</li>
3037 <li>Groovy script execution from URL</li>
3038 <li>Colour by annotation default min and max colours in
3040 <li>Automatically associate PDB files dragged onto an
3041 alignment with sequences that have high similarity and
3043 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3044 <li>'view structures' option to open many
3045 structures in same window</li>
3046 <li>Sort associated views menu option for tree panel</li>
3047 <li>Group all JABA and non-JABA services for a particular
3048 analysis function in its own submenu</li>
3049 </ul> <em>Applet</em>
3051 <li>Userdefined and autogenerated annotation rows for
3053 <li>Adjustment of alignment annotation pane height</li>
3054 <li>Annotation scrollbar for annotation panel</li>
3055 <li>Drag to reorder annotation rows in annotation panel</li>
3056 <li>'automaticScrolling' parameter</li>
3057 <li>Allow sequences with partial ID string matches to be
3058 annotated from GFF/Jalview features files</li>
3059 <li>Sequence logo annotation row in applet</li>
3060 <li>Absolute paths relative to host server in applet
3061 parameters are treated as such</li>
3062 <li>New in the JalviewLite javascript API:
3064 <li>JalviewLite.js javascript library</li>
3065 <li>Javascript callbacks for
3067 <li>Applet initialisation</li>
3068 <li>Sequence/alignment mouse-overs and selections</li>
3071 <li>scrollTo row and column alignment scrolling
3073 <li>Select sequence/alignment regions from javascript</li>
3074 <li>javascript structure viewer harness to pass
3075 messages between Jmol and Jalview when running as
3076 distinct applets</li>
3077 <li>sortBy method</li>
3078 <li>Set of applet and application examples shipped
3079 with documentation</li>
3080 <li>New example to demonstrate JalviewLite and Jmol
3081 javascript message exchange</li>
3083 </ul> <em>General</em>
3085 <li>Enable Jmol displays to be associated with multiple
3086 multiple alignments</li>
3087 <li>Option to automatically sort alignment with new tree</li>
3088 <li>User configurable link to enable redirects to a
3089 www.Jalview.org mirror</li>
3090 <li>Jmol colours option for Jmol displays</li>
3091 <li>Configurable newline string when writing alignment
3092 and other flat files</li>
3093 <li>Allow alignment annotation description lines to
3094 contain html tags</li>
3095 </ul> <em>Documentation and Development</em>
3097 <li>Add groovy test harness for bulk load testing to
3099 <li>Groovy script to load and align a set of sequences
3100 using a web service before displaying the result in the
3101 Jalview desktop</li>
3102 <li>Restructured javascript and applet api documentation</li>
3103 <li>Ant target to publish example html files with applet
3105 <li>Netbeans project for building Jalview from source</li>
3106 <li>ant task to create online javadoc for Jalview source</li>
3108 <td><em>Application</em>
3110 <li>User defined colourscheme throws exception when
3111 current built in colourscheme is saved as new scheme</li>
3112 <li>AlignFrame->Save in application pops up save
3113 dialog for valid filename/format</li>
3114 <li>Cannot view associated structure for UniProt sequence</li>
3115 <li>PDB file association breaks for UniProt sequence
3117 <li>Associate PDB from file dialog does not tell you
3118 which sequence is to be associated with the file</li>
3119 <li>Find All raises null pointer exception when query
3120 only matches sequence IDs</li>
3121 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3122 <li>Jalview project with Jmol views created with Jalview
3123 2.4 cannot be loaded</li>
3124 <li>Filetype associations not installed for webstart
3126 <li>Two or more chains in a single PDB file associated
3127 with sequences in different alignments do not get coloured
3128 by their associated sequence</li>
3129 <li>Visibility status of autocalculated annotation row
3130 not preserved when project is loaded</li>
3131 <li>Annotation row height and visibility attributes not
3132 stored in Jalview project</li>
3133 <li>Tree bootstraps are not preserved when saved as a
3134 Jalview project</li>
3135 <li>Envision2 workflow tooltips are corrupted</li>
3136 <li>Enabling show group conservation also enables colour
3137 by conservation</li>
3138 <li>Duplicate group associated conservation or consensus
3139 created on new view</li>
3140 <li>Annotation scrollbar not displayed after 'show
3141 all hidden annotation rows' option selected</li>
3142 <li>Alignment quality not updated after alignment
3143 annotation row is hidden then shown</li>
3144 <li>Preserve colouring of structures coloured by
3145 sequences in pre Jalview 2.7 projects</li>
3146 <li>Web service job parameter dialog is not laid out
3148 <li>Web services menu not refreshed after 'reset
3149 services' button is pressed in preferences</li>
3150 <li>Annotation off by one in Jalview v2_3 example project</li>
3151 <li>Structures imported from file and saved in project
3152 get name like jalview_pdb1234.txt when reloaded</li>
3153 <li>Jalview does not always retrieve progress of a JABAWS
3154 job execution in full once it is complete</li>
3155 </ul> <em>Applet</em>
3157 <li>Alignment height set incorrectly when lots of
3158 annotation rows are displayed</li>
3159 <li>Relative URLs in feature HTML text not resolved to
3161 <li>View follows highlighting does not work for positions
3163 <li><= shown as = in tooltip</li>
3164 <li>Export features raises exception when no features
3166 <li>Separator string used for serialising lists of IDs
3167 for javascript api is modified when separator string
3168 provided as parameter</li>
3169 <li>Null pointer exception when selecting tree leaves for
3170 alignment with no existing selection</li>
3171 <li>Relative URLs for datasources assumed to be relative
3172 to applet's codebase</li>
3173 <li>Status bar not updated after finished searching and
3174 search wraps around to first result</li>
3175 <li>StructureSelectionManager instance shared between
3176 several Jalview applets causes race conditions and memory
3178 <li>Hover tooltip and mouseover of position on structure
3179 not sent from Jmol in applet</li>
3180 <li>Certain sequences of javascript method calls to
3181 applet API fatally hang browser</li>
3182 </ul> <em>General</em>
3184 <li>View follows structure mouseover scrolls beyond
3185 position with wrapped view and hidden regions</li>
3186 <li>Find sequence position moves to wrong residue
3187 with/without hidden columns</li>
3188 <li>Sequence length given in alignment properties window
3190 <li>InvalidNumberFormat exceptions thrown when trying to
3191 import PDB like structure files</li>
3192 <li>Positional search results are only highlighted
3193 between user-supplied sequence start/end bounds</li>
3194 <li>End attribute of sequence is not validated</li>
3195 <li>Find dialog only finds first sequence containing a
3196 given sequence position</li>
3197 <li>Sequence numbering not preserved in MSF alignment
3199 <li>Jalview PDB file reader does not extract sequence
3200 from nucleotide chains correctly</li>
3201 <li>Structure colours not updated when tree partition
3202 changed in alignment</li>
3203 <li>Sequence associated secondary structure not correctly
3204 parsed in interleaved stockholm</li>
3205 <li>Colour by annotation dialog does not restore current
3207 <li>Hiding (nearly) all sequences doesn't work
3209 <li>Sequences containing lowercase letters are not
3210 properly associated with their pdb files</li>
3211 </ul> <em>Documentation and Development</em>
3213 <li>schemas/JalviewWsParamSet.xsd corrupted by
3214 ApplyCopyright tool</li>
3219 <div align="center">
3220 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3223 <td><em>Application</em>
3225 <li>New warning dialog when the Jalview Desktop cannot
3226 contact web services</li>
3227 <li>JABA service parameters for a preset are shown in
3228 service job window</li>
3229 <li>JABA Service menu entries reworded</li>
3233 <li>Modeller PIR IO broken - cannot correctly import a
3234 pir file emitted by Jalview</li>
3235 <li>Existing feature settings transferred to new
3236 alignment view created from cut'n'paste</li>
3237 <li>Improved test for mixed amino/nucleotide chains when
3238 parsing PDB files</li>
3239 <li>Consensus and conservation annotation rows
3240 occasionally become blank for all new windows</li>
3241 <li>Exception raised when right clicking above sequences
3242 in wrapped view mode</li>
3243 </ul> <em>Application</em>
3245 <li>multiple multiply aligned structure views cause cpu
3246 usage to hit 100% and computer to hang</li>
3247 <li>Web Service parameter layout breaks for long user
3248 parameter names</li>
3249 <li>Jaba service discovery hangs desktop if Jaba server
3256 <div align="center">
3257 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3260 <td><em>Application</em>
3262 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3263 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3266 <li>Web Services preference tab</li>
3267 <li>Analysis parameters dialog box and user defined
3269 <li>Improved speed and layout of Envision2 service menu</li>
3270 <li>Superpose structures using associated sequence
3272 <li>Export coordinates and projection as CSV from PCA
3274 </ul> <em>Applet</em>
3276 <li>enable javascript: execution by the applet via the
3277 link out mechanism</li>
3278 </ul> <em>Other</em>
3280 <li>Updated the Jmol Jalview interface to work with Jmol
3282 <li>The Jalview Desktop and JalviewLite applet now
3283 require Java 1.5</li>
3284 <li>Allow Jalview feature colour specification for GFF
3285 sequence annotation files</li>
3286 <li>New 'colour by label' keword in Jalview feature file
3287 type colour specification</li>
3288 <li>New Jalview Desktop Groovy API method that allows a
3289 script to check if it being run in an interactive session or
3290 in a batch operation from the Jalview command line</li>
3294 <li>clustalx colourscheme colours Ds preferentially when
3295 both D+E are present in over 50% of the column</li>
3296 </ul> <em>Application</em>
3298 <li>typo in AlignmentFrame->View->Hide->all but
3299 selected Regions menu item</li>
3300 <li>sequence fetcher replaces ',' for ';' when the ',' is
3301 part of a valid accession ID</li>
3302 <li>fatal OOM if object retrieved by sequence fetcher
3303 runs out of memory</li>
3304 <li>unhandled Out of Memory Error when viewing pca
3305 analysis results</li>
3306 <li>InstallAnywhere builds fail to launch on OS X java
3307 10.5 update 4 (due to apple Java 1.6 update)</li>
3308 <li>Installanywhere Jalview silently fails to launch</li>
3309 </ul> <em>Applet</em>
3311 <li>Jalview.getFeatureGroups() raises an
3312 ArrayIndexOutOfBoundsException if no feature groups are
3319 <div align="center">
3320 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3326 <li>Alignment prettyprinter doesn't cope with long
3328 <li>clustalx colourscheme colours Ds preferentially when
3329 both D+E are present in over 50% of the column</li>
3330 <li>nucleic acid structures retrieved from PDB do not
3331 import correctly</li>
3332 <li>More columns get selected than were clicked on when a
3333 number of columns are hidden</li>
3334 <li>annotation label popup menu not providing correct
3335 add/hide/show options when rows are hidden or none are
3337 <li>Stockholm format shown in list of readable formats,
3338 and parser copes better with alignments from RFAM.</li>
3339 <li>CSV output of consensus only includes the percentage
3340 of all symbols if sequence logo display is enabled</li>
3342 </ul> <em>Applet</em>
3344 <li>annotation panel disappears when annotation is
3346 </ul> <em>Application</em>
3348 <li>Alignment view not redrawn properly when new
3349 alignment opened where annotation panel is visible but no
3350 annotations are present on alignment</li>
3351 <li>pasted region containing hidden columns is
3352 incorrectly displayed in new alignment window</li>
3353 <li>Jalview slow to complete operations when stdout is
3354 flooded (fix is to close the Jalview console)</li>
3355 <li>typo in AlignmentFrame->View->Hide->all but
3356 selected Rregions menu item.</li>
3357 <li>inconsistent group submenu and Format submenu entry
3358 'Un' or 'Non'conserved</li>
3359 <li>Sequence feature settings are being shared by
3360 multiple distinct alignments</li>
3361 <li>group annotation not recreated when tree partition is
3363 <li>double click on group annotation to select sequences
3364 does not propagate to associated trees</li>
3365 <li>Mac OSX specific issues:
3367 <li>exception raised when mouse clicked on desktop
3368 window background</li>
3369 <li>Desktop menu placed on menu bar and application
3370 name set correctly</li>
3371 <li>sequence feature settings not wide enough for the
3372 save feature colourscheme button</li>
3381 <div align="center">
3382 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3385 <td><em>New Capabilities</em>
3387 <li>URL links generated from description line for
3388 regular-expression based URL links (applet and application)
3390 <li>Non-positional feature URL links are shown in link
3392 <li>Linked viewing of nucleic acid sequences and
3394 <li>Automatic Scrolling option in View menu to display
3395 the currently highlighted region of an alignment.</li>
3396 <li>Order an alignment by sequence length, or using the
3397 average score or total feature count for each sequence.</li>
3398 <li>Shading features by score or associated description</li>
3399 <li>Subdivide alignment and groups based on identity of
3400 selected subsequence (Make Groups from Selection).</li>
3401 <li>New hide/show options including Shift+Control+H to
3402 hide everything but the currently selected region.</li>
3403 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3404 </ul> <em>Application</em>
3406 <li>Fetch DB References capabilities and UI expanded to
3407 support retrieval from DAS sequence sources</li>
3408 <li>Local DAS Sequence sources can be added via the
3409 command line or via the Add local source dialog box.</li>
3410 <li>DAS Dbref and DbxRef feature types are parsed as
3411 database references and protein_name is parsed as
3412 description line (BioSapiens terms).</li>
3413 <li>Enable or disable non-positional feature and database
3414 references in sequence ID tooltip from View menu in
3416 <!-- <li>New hidden columns and rows and representatives capabilities
3417 in annotations file (in progress - not yet fully implemented)</li> -->
3418 <li>Group-associated consensus, sequence logos and
3419 conservation plots</li>
3420 <li>Symbol distributions for each column can be exported
3421 and visualized as sequence logos</li>
3422 <li>Optionally scale multi-character column labels to fit
3423 within each column of annotation row<!-- todo for applet -->
3425 <li>Optional automatic sort of associated alignment view
3426 when a new tree is opened.</li>
3427 <li>Jalview Java Console</li>
3428 <li>Better placement of desktop window when moving
3429 between different screens.</li>
3430 <li>New preference items for sequence ID tooltip and
3431 consensus annotation</li>
3432 <li>Client to submit sequences and IDs to Envision2
3434 <li><em>Vamsas Capabilities</em>
3436 <li>Improved VAMSAS synchronization (Jalview archive
3437 used to preserve views, structures, and tree display
3439 <li>Import of vamsas documents from disk or URL via
3441 <li>Sharing of selected regions between views and
3442 with other VAMSAS applications (Experimental feature!)</li>
3443 <li>Updated API to VAMSAS version 0.2</li>
3445 </ul> <em>Applet</em>
3447 <li>Middle button resizes annotation row height</li>
3450 <li>sortByTree (true/false) - automatically sort the
3451 associated alignment view by the tree when a new tree is
3453 <li>showTreeBootstraps (true/false) - show or hide
3454 branch bootstraps (default is to show them if available)</li>
3455 <li>showTreeDistances (true/false) - show or hide
3456 branch lengths (default is to show them if available)</li>
3457 <li>showUnlinkedTreeNodes (true/false) - indicate if
3458 unassociated nodes should be highlighted in the tree
3460 <li>heightScale and widthScale (1.0 or more) -
3461 increase the height or width of a cell in the alignment
3462 grid relative to the current font size.</li>
3465 <li>Non-positional features displayed in sequence ID
3467 </ul> <em>Other</em>
3469 <li>Features format: graduated colour definitions and
3470 specification of feature scores</li>
3471 <li>Alignment Annotations format: new keywords for group
3472 associated annotation (GROUP_REF) and annotation row display
3473 properties (ROW_PROPERTIES)</li>
3474 <li>XML formats extended to support graduated feature
3475 colourschemes, group associated annotation, and profile
3476 visualization settings.</li></td>
3479 <li>Source field in GFF files parsed as feature source
3480 rather than description</li>
3481 <li>Non-positional features are now included in sequence
3482 feature and gff files (controlled via non-positional feature
3483 visibility in tooltip).</li>
3484 <li>URL links generated for all feature links (bugfix)</li>
3485 <li>Added URL embedding instructions to features file
3487 <li>Codons containing ambiguous nucleotides translated as
3488 'X' in peptide product</li>
3489 <li>Match case switch in find dialog box works for both
3490 sequence ID and sequence string and query strings do not
3491 have to be in upper case to match case-insensitively.</li>
3492 <li>AMSA files only contain first column of
3493 multi-character column annotation labels</li>
3494 <li>Jalview Annotation File generation/parsing consistent
3495 with documentation (e.g. Stockholm annotation can be
3496 exported and re-imported)</li>
3497 <li>PDB files without embedded PDB IDs given a friendly
3499 <li>Find incrementally searches ID string matches as well
3500 as subsequence matches, and correctly reports total number
3504 <li>Better handling of exceptions during sequence
3506 <li>Dasobert generated non-positional feature URL
3507 link text excludes the start_end suffix</li>
3508 <li>DAS feature and source retrieval buttons disabled
3509 when fetch or registry operations in progress.</li>
3510 <li>PDB files retrieved from URLs are cached properly</li>
3511 <li>Sequence description lines properly shared via
3513 <li>Sequence fetcher fetches multiple records for all
3515 <li>Ensured that command line das feature retrieval
3516 completes before alignment figures are generated.</li>
3517 <li>Reduced time taken when opening file browser for
3519 <li>isAligned check prior to calculating tree, PCA or
3520 submitting an MSA to JNet now excludes hidden sequences.</li>
3521 <li>User defined group colours properly recovered
3522 from Jalview projects.</li>
3531 <div align="center">
3532 <strong>2.4.0.b2</strong><br> 28/10/2009
3537 <li>Experimental support for google analytics usage
3539 <li>Jalview privacy settings (user preferences and docs).</li>
3544 <li>Race condition in applet preventing startup in
3546 <li>Exception when feature created from selection beyond
3547 length of sequence.</li>
3548 <li>Allow synthetic PDB files to be imported gracefully</li>
3549 <li>Sequence associated annotation rows associate with
3550 all sequences with a given id</li>
3551 <li>Find function matches case-insensitively for sequence
3552 ID string searches</li>
3553 <li>Non-standard characters do not cause pairwise
3554 alignment to fail with exception</li>
3555 </ul> <em>Application Issues</em>
3557 <li>Sequences are now validated against EMBL database</li>
3558 <li>Sequence fetcher fetches multiple records for all
3560 </ul> <em>InstallAnywhere Issues</em>
3562 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3563 issue with installAnywhere mechanism)</li>
3564 <li>Command line launching of JARs from InstallAnywhere
3565 version (java class versioning error fixed)</li>
3572 <div align="center">
3573 <strong>2.4</strong><br> 27/8/2008
3576 <td><em>User Interface</em>
3578 <li>Linked highlighting of codon and amino acid from
3579 translation and protein products</li>
3580 <li>Linked highlighting of structure associated with
3581 residue mapping to codon position</li>
3582 <li>Sequence Fetcher provides example accession numbers
3583 and 'clear' button</li>
3584 <li>MemoryMonitor added as an option under Desktop's
3586 <li>Extract score function to parse whitespace separated
3587 numeric data in description line</li>
3588 <li>Column labels in alignment annotation can be centred.</li>
3589 <li>Tooltip for sequence associated annotation give name
3591 </ul> <em>Web Services and URL fetching</em>
3593 <li>JPred3 web service</li>
3594 <li>Prototype sequence search client (no public services
3596 <li>Fetch either seed alignment or full alignment from
3598 <li>URL Links created for matching database cross
3599 references as well as sequence ID</li>
3600 <li>URL Links can be created using regular-expressions</li>
3601 </ul> <em>Sequence Database Connectivity</em>
3603 <li>Retrieval of cross-referenced sequences from other
3605 <li>Generalised database reference retrieval and
3606 validation to all fetchable databases</li>
3607 <li>Fetch sequences from DAS sources supporting the
3608 sequence command</li>
3609 </ul> <em>Import and Export</em>
3610 <li>export annotation rows as CSV for spreadsheet import</li>
3611 <li>Jalview projects record alignment dataset associations,
3612 EMBL products, and cDNA sequence mappings</li>
3613 <li>Sequence Group colour can be specified in Annotation
3615 <li>Ad-hoc colouring of group in Annotation File using RGB
3616 triplet as name of colourscheme</li>
3617 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3619 <li>treenode binding for VAMSAS tree exchange</li>
3620 <li>local editing and update of sequences in VAMSAS
3621 alignments (experimental)</li>
3622 <li>Create new or select existing session to join</li>
3623 <li>load and save of vamsas documents</li>
3624 </ul> <em>Application command line</em>
3626 <li>-tree parameter to open trees (introduced for passing
3628 <li>-fetchfrom command line argument to specify nicknames
3629 of DAS servers to query for alignment features</li>
3630 <li>-dasserver command line argument to add new servers
3631 that are also automatically queried for features</li>
3632 <li>-groovy command line argument executes a given groovy
3633 script after all input data has been loaded and parsed</li>
3634 </ul> <em>Applet-Application data exchange</em>
3636 <li>Trees passed as applet parameters can be passed to
3637 application (when using "View in full
3638 application")</li>
3639 </ul> <em>Applet Parameters</em>
3641 <li>feature group display control parameter</li>
3642 <li>debug parameter</li>
3643 <li>showbutton parameter</li>
3644 </ul> <em>Applet API methods</em>
3646 <li>newView public method</li>
3647 <li>Window (current view) specific get/set public methods</li>
3648 <li>Feature display control methods</li>
3649 <li>get list of currently selected sequences</li>
3650 </ul> <em>New Jalview distribution features</em>
3652 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3653 <li>RELEASE file gives build properties for the latest
3654 Jalview release.</li>
3655 <li>Java 1.1 Applet build made easier and donotobfuscate
3656 property controls execution of obfuscator</li>
3657 <li>Build target for generating source distribution</li>
3658 <li>Debug flag for javacc</li>
3659 <li>.jalview_properties file is documented (slightly) in
3660 jalview.bin.Cache</li>
3661 <li>Continuous Build Integration for stable and
3662 development version of Application, Applet and source
3667 <li>selected region output includes visible annotations
3668 (for certain formats)</li>
3669 <li>edit label/displaychar contains existing label/char
3671 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3672 <li>shorter peptide product names from EMBL records</li>
3673 <li>Newick string generator makes compact representations</li>
3674 <li>bootstrap values parsed correctly for tree files with
3676 <li>pathological filechooser bug avoided by not allowing
3677 filenames containing a ':'</li>
3678 <li>Fixed exception when parsing GFF files containing
3679 global sequence features</li>
3680 <li>Alignment datasets are finalized only when number of
3681 references from alignment sequences goes to zero</li>
3682 <li>Close of tree branch colour box without colour
3683 selection causes cascading exceptions</li>
3684 <li>occasional negative imgwidth exceptions</li>
3685 <li>better reporting of non-fatal warnings to user when
3686 file parsing fails.</li>
3687 <li>Save works when Jalview project is default format</li>
3688 <li>Save as dialog opened if current alignment format is
3689 not a valid output format</li>
3690 <li>UniProt canonical names introduced for both das and
3692 <li>Histidine should be midblue (not pink!) in Zappo</li>
3693 <li>error messages passed up and output when data read
3695 <li>edit undo recovers previous dataset sequence when
3696 sequence is edited</li>
3697 <li>allow PDB files without pdb ID HEADER lines (like
3698 those generated by MODELLER) to be read in properly</li>
3699 <li>allow reading of JPred concise files as a normal
3701 <li>Stockholm annotation parsing and alignment properties
3702 import fixed for PFAM records</li>
3703 <li>Structure view windows have correct name in Desktop
3705 <li>annotation consisting of sequence associated scores
3706 can be read and written correctly to annotation file</li>
3707 <li>Aligned cDNA translation to aligned peptide works
3709 <li>Fixed display of hidden sequence markers and
3710 non-italic font for representatives in Applet</li>
3711 <li>Applet Menus are always embedded in applet window on
3713 <li>Newly shown features appear at top of stack (in
3715 <li>Annotations added via parameter not drawn properly
3716 due to null pointer exceptions</li>
3717 <li>Secondary structure lines are drawn starting from
3718 first column of alignment</li>
3719 <li>UniProt XML import updated for new schema release in
3721 <li>Sequence feature to sequence ID match for Features
3722 file is case-insensitive</li>
3723 <li>Sequence features read from Features file appended to
3724 all sequences with matching IDs</li>
3725 <li>PDB structure coloured correctly for associated views
3726 containing a sub-sequence</li>
3727 <li>PDB files can be retrieved by applet from Jar files</li>
3728 <li>feature and annotation file applet parameters
3729 referring to different directories are retrieved correctly</li>
3730 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3731 <li>Fixed application hang whilst waiting for
3732 splash-screen version check to complete</li>
3733 <li>Applet properly URLencodes input parameter values
3734 when passing them to the launchApp service</li>
3735 <li>display name and local features preserved in results
3736 retrieved from web service</li>
3737 <li>Visual delay indication for sequence retrieval and
3738 sequence fetcher initialisation</li>
3739 <li>updated Application to use DAS 1.53e version of
3740 dasobert DAS client</li>
3741 <li>Re-instated Full AMSA support and .amsa file
3743 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3751 <div align="center">
3752 <strong>2.3</strong><br> 9/5/07
3757 <li>Jmol 11.0.2 integration</li>
3758 <li>PDB views stored in Jalview XML files</li>
3759 <li>Slide sequences</li>
3760 <li>Edit sequence in place</li>
3761 <li>EMBL CDS features</li>
3762 <li>DAS Feature mapping</li>
3763 <li>Feature ordering</li>
3764 <li>Alignment Properties</li>
3765 <li>Annotation Scores</li>
3766 <li>Sort by scores</li>
3767 <li>Feature/annotation editing in applet</li>
3772 <li>Headless state operation in 2.2.1</li>
3773 <li>Incorrect and unstable DNA pairwise alignment</li>
3774 <li>Cut and paste of sequences with annotation</li>
3775 <li>Feature group display state in XML</li>
3776 <li>Feature ordering in XML</li>
3777 <li>blc file iteration selection using filename # suffix</li>
3778 <li>Stockholm alignment properties</li>
3779 <li>Stockhom alignment secondary structure annotation</li>
3780 <li>2.2.1 applet had no feature transparency</li>
3781 <li>Number pad keys can be used in cursor mode</li>
3782 <li>Structure Viewer mirror image resolved</li>
3789 <div align="center">
3790 <strong>2.2.1</strong><br> 12/2/07
3795 <li>Non standard characters can be read and displayed
3796 <li>Annotations/Features can be imported/exported to the
3798 <li>Applet allows editing of sequence/annotation/group
3799 name & description
3800 <li>Preference setting to display sequence name in
3802 <li>Annotation file format extended to allow
3803 Sequence_groups to be defined
3804 <li>Default opening of alignment overview panel can be
3805 specified in preferences
3806 <li>PDB residue numbering annotation added to associated
3812 <li>Applet crash under certain Linux OS with Java 1.6
3814 <li>Annotation file export / import bugs fixed
3815 <li>PNG / EPS image output bugs fixed
3821 <div align="center">
3822 <strong>2.2</strong><br> 27/11/06
3827 <li>Multiple views on alignment
3828 <li>Sequence feature editing
3829 <li>"Reload" alignment
3830 <li>"Save" to current filename
3831 <li>Background dependent text colour
3832 <li>Right align sequence ids
3833 <li>User-defined lower case residue colours
3836 <li>Menu item accelerator keys
3837 <li>Control-V pastes to current alignment
3838 <li>Cancel button for DAS Feature Fetching
3839 <li>PCA and PDB Viewers zoom via mouse roller
3840 <li>User-defined sub-tree colours and sub-tree selection
3842 <li>'New Window' button on the 'Output to Text box'
3847 <li>New memory efficient Undo/Redo System
3848 <li>Optimised symbol lookups and conservation/consensus
3850 <li>Region Conservation/Consensus recalculated after
3852 <li>Fixed Remove Empty Columns Bug (empty columns at end
3854 <li>Slowed DAS Feature Fetching for increased robustness.
3856 <li>Made angle brackets in ASCII feature descriptions
3858 <li>Re-instated Zoom function for PCA
3859 <li>Sequence descriptions conserved in web service
3861 <li>UniProt ID discoverer uses any word separated by
3863 <li>WsDbFetch query/result association resolved
3864 <li>Tree leaf to sequence mapping improved
3865 <li>Smooth fonts switch moved to FontChooser dialog box.
3872 <div align="center">
3873 <strong>2.1.1</strong><br> 12/9/06
3878 <li>Copy consensus sequence to clipboard</li>
3883 <li>Image output - rightmost residues are rendered if
3884 sequence id panel has been resized</li>
3885 <li>Image output - all offscreen group boundaries are
3887 <li>Annotation files with sequence references - all
3888 elements in file are relative to sequence position</li>
3889 <li>Mac Applet users can use Alt key for group editing</li>
3895 <div align="center">
3896 <strong>2.1</strong><br> 22/8/06
3901 <li>MAFFT Multiple Alignment in default Web Service list</li>
3902 <li>DAS Feature fetching</li>
3903 <li>Hide sequences and columns</li>
3904 <li>Export Annotations and Features</li>
3905 <li>GFF file reading / writing</li>
3906 <li>Associate structures with sequences from local PDB
3908 <li>Add sequences to exisiting alignment</li>
3909 <li>Recently opened files / URL lists</li>
3910 <li>Applet can launch the full application</li>
3911 <li>Applet has transparency for features (Java 1.2
3913 <li>Applet has user defined colours parameter</li>
3914 <li>Applet can load sequences from parameter
3915 "sequence<em>x</em>"
3921 <li>Redundancy Panel reinstalled in the Applet</li>
3922 <li>Monospaced font - EPS / rescaling bug fixed</li>
3923 <li>Annotation files with sequence references bug fixed</li>
3929 <div align="center">
3930 <strong>2.08.1</strong><br> 2/5/06
3935 <li>Change case of selected region from Popup menu</li>
3936 <li>Choose to match case when searching</li>
3937 <li>Middle mouse button and mouse movement can compress /
3938 expand the visible width and height of the alignment</li>
3943 <li>Annotation Panel displays complete JNet results</li>
3949 <div align="center">
3950 <strong>2.08b</strong><br> 18/4/06
3956 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3957 <li>Righthand label on wrapped alignments shows correct
3964 <div align="center">
3965 <strong>2.08</strong><br> 10/4/06
3970 <li>Editing can be locked to the selection area</li>
3971 <li>Keyboard editing</li>
3972 <li>Create sequence features from searches</li>
3973 <li>Precalculated annotations can be loaded onto
3975 <li>Features file allows grouping of features</li>
3976 <li>Annotation Colouring scheme added</li>
3977 <li>Smooth fonts off by default - Faster rendering</li>
3978 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3983 <li>Drag & Drop fixed on Linux</li>
3984 <li>Jalview Archive file faster to load/save, sequence
3985 descriptions saved.</li>
3991 <div align="center">
3992 <strong>2.07</strong><br> 12/12/05
3997 <li>PDB Structure Viewer enhanced</li>
3998 <li>Sequence Feature retrieval and display enhanced</li>
3999 <li>Choose to output sequence start-end after sequence
4000 name for file output</li>
4001 <li>Sequence Fetcher WSDBFetch@EBI</li>
4002 <li>Applet can read feature files, PDB files and can be
4003 used for HTML form input</li>
4008 <li>HTML output writes groups and features</li>
4009 <li>Group editing is Control and mouse click</li>
4010 <li>File IO bugs</li>
4016 <div align="center">
4017 <strong>2.06</strong><br> 28/9/05
4022 <li>View annotations in wrapped mode</li>
4023 <li>More options for PCA viewer</li>
4028 <li>GUI bugs resolved</li>
4029 <li>Runs with -nodisplay from command line</li>
4035 <div align="center">
4036 <strong>2.05b</strong><br> 15/9/05
4041 <li>Choose EPS export as lineart or text</li>
4042 <li>Jar files are executable</li>
4043 <li>Can read in Uracil - maps to unknown residue</li>
4048 <li>Known OutOfMemory errors give warning message</li>
4049 <li>Overview window calculated more efficiently</li>
4050 <li>Several GUI bugs resolved</li>
4056 <div align="center">
4057 <strong>2.05</strong><br> 30/8/05
4062 <li>Edit and annotate in "Wrapped" view</li>
4067 <li>Several GUI bugs resolved</li>
4073 <div align="center">
4074 <strong>2.04</strong><br> 24/8/05
4079 <li>Hold down mouse wheel & scroll to change font
4085 <li>Improved JPred client reliability</li>
4086 <li>Improved loading of Jalview files</li>
4092 <div align="center">
4093 <strong>2.03</strong><br> 18/8/05
4098 <li>Set Proxy server name and port in preferences</li>
4099 <li>Multiple URL links from sequence ids</li>
4100 <li>User Defined Colours can have a scheme name and added
4102 <li>Choose to ignore gaps in consensus calculation</li>
4103 <li>Unix users can set default web browser</li>
4104 <li>Runs without GUI for batch processing</li>
4105 <li>Dynamically generated Web Service Menus</li>
4110 <li>InstallAnywhere download for Sparc Solaris</li>
4116 <div align="center">
4117 <strong>2.02</strong><br> 18/7/05
4123 <li>Copy & Paste order of sequences maintains
4124 alignment order.</li>
4130 <div align="center">
4131 <strong>2.01</strong><br> 12/7/05
4136 <li>Use delete key for deleting selection.</li>
4137 <li>Use Mouse wheel to scroll sequences.</li>
4138 <li>Help file updated to describe how to add alignment
4140 <li>Version and build date written to build properties
4142 <li>InstallAnywhere installation will check for updates
4143 at launch of Jalview.</li>
4148 <li>Delete gaps bug fixed.</li>
4149 <li>FileChooser sorts columns.</li>
4150 <li>Can remove groups one by one.</li>
4151 <li>Filechooser icons installed.</li>
4152 <li>Finder ignores return character when searching.
4153 Return key will initiate a search.<br>
4160 <div align="center">
4161 <strong>2.0</strong><br> 20/6/05
4166 <li>New codebase</li>