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 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">2.11</a><br />
61 <em>14/05/2019 (final due date !)</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-3141 -->Optional automatic backups when saving
67 Jalview project or alignment files</li>
69 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
70 Viewer state is saved in Jalview Project<br />The 'Change
71 parameters' option has also been removed from the PCA viewer</li>
73 <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
75 <!-- JAL-2620 -->Alternative genetic code tables supported for
76 'Translate as cDNA'</li>
78 <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
80 <!-- JAL-3198 -->More efficient creation of selections and
81 multiple groups when working with large alignments</li>
83 <!-- JAL-3200 -->Speedier import of annotation rows when
84 parsing stockholm files</li>
86 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
88 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
89 shaded according to any associated attributes (e.g. variant
90 attributes from VCF file, or key-value pairs imported from
91 column 9 of GFF file)</li>
93 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
94 algorithm (Z-sort/transparency and filter aware)</li>
96 <!-- JAL-2527 -->Alignment Overview now by default shows
97 only visible region of alignment (this can be changed in
98 user preferences)</li>
100 <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
102 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
103 all sequences are hidden</li>
105 <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
106 region, and gap count when inserting or deleting gaps</li>
108 <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
110 <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
112 <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
114 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
116 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
118 <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
120 <!-- JAL-3203 -->Overview panel default changed to not show hidden regions</li>
122 <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
124 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
126 <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent
127 to a hidden column marker</li>
129 <em>Deprecations</em>
132 <!-- JAL-3035 -->DAS sequence retrieval and annotation
133 capabilities removed from the Jalview Desktop
136 <em>Release Processes</em>
139 Atlassian Bamboo continuous integration server for
140 unattended Test Suite execution</li>
142 <!-- JAL-2864 -->Memory test suite to detect leaks in common
145 <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
146 implementation) used for Sequence Feature collections</li>
148 <!-- JAL-3063 -->Castor library for XML marshalling and
149 unmarshalling has been replaced by JAXB for Jalview projects
150 and XML based data retrieval clients</li>
153 <td align="left" valign="top">
156 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
158 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
159 Jalview project involving multiple views</li>
161 <!-- JAL-3164 -->Overview for complementary view in a linked
162 CDS/Protein alignment is not updated when Hide Columns by
163 Annotation dialog hides columns</li>
165 <!-- JAL-3158 -->Selection highlighting in the complement of
166 a CDS/Protein alignment stops working after making a
167 selection in one view, then making another selection in the
170 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
172 <!-- JAL-3154 -->Table Columns could be re-ordered in
173 Feature Settings and Jalview Preferences panels</li>
175 <!-- JAL-2865 -->Jalview hangs when closing windows
176 or the overview updates with large alignments</li>
178 <!-- JAL-2865 -->Tree and PCA calculation fails for selected
179 region if columns were selected by dragging right-to-left
180 and the mouse moved to the left of the first column</li>
182 <!-- JAL-2846 -->Error message for trying to load in invalid
183 URLs doesn't tell users the invalid URL</li>
185 <!-- JAL-3178 -->Nonpositional features lose feature group
186 on export as Jalview features file</li>
188 <!-- JAL-3161 -->Status bar updates beyond visible columns</li>
190 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
191 printed when columns are hidden</li>
193 <!-- JAL-3082 -->Regular expression error in Select Columns by Annotation description</li>
195 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
196 dragging out of Scale or Annotation Panel</li>
198 <!-- JAL-3002 -->Display is incorrect after Page Down and Up in wrapped mode</li>
200 <!-- JAL-914 -->Help page can be opened twice</li>
202 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
204 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
206 <!-- JAL-2750 -->Tree calculation fails on a selection dragged to left of alignment</li>
208 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
209 opening an alignment</li>
211 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
213 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
214 different groups in the alignment are selected</li>
216 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
221 <!-- JAL-2822 -->Start and End should be updated when
222 sequence data at beginning or end of alignment added/removed
223 via 'Edit' sequence</li>
225 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
226 sequence features correctly when start of sequence is
227 removed (Known defect since 2.10)</li>
229 <em>New Known Defects</em>
232 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
234 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
239 <td width="60" nowrap>
241 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
244 <td><div align="left">
248 <!-- JAL-3101 -->Default memory for Jalview webstart and
249 InstallAnywhere increased to 1G.
252 <!-- JAL-247 -->Hidden sequence markers and representative
253 sequence bolding included when exporting alignment as EPS,
254 SVG, PNG or HTML. <em>Display is configured via the
255 Format menu, or for command-line use via a jalview
256 properties file.</em>
259 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
260 API and sequence data now imported as JSON.
263 <!-- JAL-3065 -->Change in recommended way of starting
264 Jalview via a Java command line: add jars in lib directory
265 to CLASSPATH, rather than via the deprecated java.ext.dirs
272 <!-- JAL-3047 -->Support added to execute test suite
273 instrumented with <a href="http://openclover.org/">Open
278 <td><div align="left">
282 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
283 row shown in Feredoxin Structure alignment view of example
287 <!-- JAL-2854 -->Annotation obscures sequences if lots of
288 annotation displayed.
291 <!-- JAL-3107 -->Group conservation/consensus not shown
292 for newly created group when 'Apply to all groups'
296 <!-- JAL-3087 -->Corrupted display when switching to
297 wrapped mode when sequence panel's vertical scrollbar is
301 <!-- JAL-3003 -->Alignment is black in exported EPS file
302 when sequences are selected in exported view.</em>
305 <!-- JAL-3059 -->Groups with different coloured borders
306 aren't rendered with correct colour.
309 <!-- JAL-3092 -->Jalview could hang when importing certain
310 types of knotted RNA secondary structure.
313 <!-- JAL-3095 -->Sequence highlight and selection in
314 trimmed VARNA 2D structure is incorrect for sequences that
318 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
319 annotation when columns are inserted into an alignment,
320 and when exporting as Stockholm flatfile.
323 <!-- JAL-3053 -->Jalview annotation rows containing upper
324 and lower-case 'E' and 'H' do not automatically get
325 treated as RNA secondary structure.
328 <!-- JAL-3106 -->.jvp should be used as default extension
329 (not .jar) when saving a jalview project file.
332 <!-- JAL-3105 -->Mac Users: closing a window correctly
333 transfers focus to previous window on OSX
336 <em>Java 10 Issues Resolved</em>
339 <!-- JAL-2988 -->OSX - Can't save new files via the File
340 or export menus by typing in a name into the Save dialog
344 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
345 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
346 'look and feel' which has improved compatibility with the
347 latest version of OSX.
354 <td width="60" nowrap>
356 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
357 <em>7/06/2018</em></strong>
360 <td><div align="left">
364 <!-- JAL-2920 -->Use HGVS nomenclature for variant
365 annotation retrieved from Uniprot
368 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
369 onto the Jalview Desktop
373 <td><div align="left">
377 <!-- JAL-3017 -->Cannot import features with multiple
378 variant elements (blocks import of some Uniprot records)
381 <!-- JAL-2997 -->Clustal files with sequence positions in
382 right-hand column parsed correctly
385 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
386 not alignment area in exported graphic
389 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
390 window has input focus
393 <!-- JAL-2992 -->Annotation panel set too high when
394 annotation added to view (Windows)
397 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
398 network connectivity is poor
401 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
402 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
403 the currently open URL and links from a page viewed in
404 Firefox or Chrome on Windows is now fully supported. If
405 you are using Edge, only links in the page can be
406 dragged, and with Internet Explorer, only the currently
407 open URL in the browser can be dropped onto Jalview.</em>
413 <td width="60" nowrap>
415 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
418 <td><div align="left">
422 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
423 for disabling automatic superposition of multiple
424 structures and open structures in existing views
427 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
428 ID and annotation area margins can be click-dragged to
432 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
436 <!-- JAL-2759 -->Improved performance for large alignments
437 and lots of hidden columns
440 <!-- JAL-2593 -->Improved performance when rendering lots
441 of features (particularly when transparency is disabled)
446 <td><div align="left">
449 <!-- JAL-2899 -->Structure and Overview aren't updated
450 when Colour By Annotation threshold slider is adjusted
453 <!-- JAL-2778 -->Slow redraw when Overview panel shown
454 overlapping alignment panel
457 <!-- JAL-2929 -->Overview doesn't show end of unpadded
461 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
462 improved: CDS not handled correctly if transcript has no
466 <!-- JAL-2321 -->Secondary structure and temperature
467 factor annotation not added to sequence when local PDB
468 file associated with it by drag'n'drop or structure
472 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
473 dialog doesn't import PDB files dropped on an alignment
476 <!-- JAL-2666 -->Linked scrolling via protein horizontal
477 scroll bar doesn't work for some CDS/Protein views
480 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
481 Java 1.8u153 onwards and Java 1.9u4+.
484 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
485 columns in annotation row
488 <!-- JAL-2913 -->Preferences panel's ID Width control is not
489 honored in batch mode
492 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
493 for structures added to existing Jmol view
496 <!-- JAL-2223 -->'View Mappings' includes duplicate
497 entries after importing project with multiple views
500 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
501 protein sequences via SIFTS from associated PDB entries
502 with negative residue numbers or missing residues fails
505 <!-- JAL-2952 -->Exception when shading sequence with negative
506 Temperature Factor values from annotated PDB files (e.g.
507 as generated by CONSURF)
510 <!-- JAL-2920 -->Uniprot 'sequence variant' features
511 tooltip doesn't include a text description of mutation
514 <!-- JAL-2922 -->Invert displayed features very slow when
515 structure and/or overview windows are also shown
518 <!-- JAL-2954 -->Selecting columns from highlighted regions
519 very slow for alignments with large numbers of sequences
522 <!-- JAL-2925 -->Copy Consensus fails for group consensus
523 with 'StringIndexOutOfBounds'
526 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
527 platforms running Java 10
530 <!-- JAL-2960 -->Adding a structure to existing structure
531 view appears to do nothing because the view is hidden behind the alignment view
537 <!-- JAL-2926 -->Copy consensus sequence option in applet
538 should copy the group consensus when popup is opened on it
544 <!-- JAL-2913 -->Fixed ID width preference is not respected
547 <em>New Known Defects</em>
550 <!-- JAL-2973 --> Exceptions occasionally raised when
551 editing a large alignment and overview is displayed
554 <!-- JAL-2974 -->'Overview updating' progress bar is shown
555 repeatedly after a series of edits even when the overview
556 is no longer reflecting updates
559 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
560 structures for protein subsequence (if 'Trim Retrieved
561 Sequences' enabled) or Ensembl isoforms (Workaround in
562 2.10.4 is to fail back to N&W mapping)
569 <td width="60" nowrap>
571 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
574 <td><div align="left">
575 <ul><li>Updated Certum Codesigning Certificate
576 (Valid till 30th November 2018)</li></ul></div></td>
577 <td><div align="left">
580 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
581 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
582 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
583 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
584 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
585 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
586 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
592 <td width="60" nowrap>
594 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
597 <td><div align="left">
601 <!-- JAL-2446 -->Faster and more efficient management and
602 rendering of sequence features
605 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
606 429 rate limit request hander
609 <!-- JAL-2773 -->Structure views don't get updated unless
610 their colours have changed
613 <!-- JAL-2495 -->All linked sequences are highlighted for
614 a structure mousover (Jmol) or selection (Chimera)
617 <!-- JAL-2790 -->'Cancel' button in progress bar for
618 JABAWS AACon, RNAAliFold and Disorder prediction jobs
621 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
622 view from Ensembl locus cross-references
625 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
629 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
630 feature can be disabled
633 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
634 PDB easier retrieval of sequences for lists of IDs
637 <!-- JAL-2758 -->Short names for sequences retrieved from
643 <li>Groovy interpreter updated to 2.4.12</li>
644 <li>Example groovy script for generating a matrix of
645 percent identity scores for current alignment.</li>
647 <em>Testing and Deployment</em>
650 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
654 <td><div align="left">
658 <!-- JAL-2643 -->Pressing tab after updating the colour
659 threshold text field doesn't trigger an update to the
663 <!-- JAL-2682 -->Race condition when parsing sequence ID
667 <!-- JAL-2608 -->Overview windows are also closed when
668 alignment window is closed
671 <!-- JAL-2548 -->Export of features doesn't always respect
675 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
676 takes a long time in Cursor mode
682 <!-- JAL-2777 -->Structures with whitespace chainCode
683 cannot be viewed in Chimera
686 <!-- JAL-2728 -->Protein annotation panel too high in
690 <!-- JAL-2757 -->Can't edit the query after the server
691 error warning icon is shown in Uniprot and PDB Free Text
695 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
698 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
701 <!-- JAL-2739 -->Hidden column marker in last column not
702 rendered when switching back from Wrapped to normal view
705 <!-- JAL-2768 -->Annotation display corrupted when
706 scrolling right in unwapped alignment view
709 <!-- JAL-2542 -->Existing features on subsequence
710 incorrectly relocated when full sequence retrieved from
714 <!-- JAL-2733 -->Last reported memory still shown when
715 Desktop->Show Memory is unticked (OSX only)
718 <!-- JAL-2658 -->Amend Features dialog doesn't allow
719 features of same type and group to be selected for
723 <!-- JAL-2524 -->Jalview becomes sluggish in wide
724 alignments when hidden columns are present
727 <!-- JAL-2392 -->Jalview freezes when loading and
728 displaying several structures
731 <!-- JAL-2732 -->Black outlines left after resizing or
735 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
736 within the Jalview desktop on OSX
739 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
740 when in wrapped alignment mode
743 <!-- JAL-2636 -->Scale mark not shown when close to right
744 hand end of alignment
747 <!-- JAL-2684 -->Pairwise alignment of selected regions of
748 each selected sequence do not have correct start/end
752 <!-- JAL-2793 -->Alignment ruler height set incorrectly
753 after canceling the Alignment Window's Font dialog
756 <!-- JAL-2036 -->Show cross-references not enabled after
757 restoring project until a new view is created
760 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
761 URL links appears when only default EMBL-EBI link is
762 configured (since 2.10.2b2)
765 <!-- JAL-2775 -->Overview redraws whole window when box
769 <!-- JAL-2225 -->Structure viewer doesn't map all chains
770 in a multi-chain structure when viewing alignment
771 involving more than one chain (since 2.10)
774 <!-- JAL-2811 -->Double residue highlights in cursor mode
775 if new selection moves alignment window
778 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
779 arrow key in cursor mode to pass hidden column marker
782 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
783 that produces correctly annotated transcripts and products
786 <!-- JAL-2776 -->Toggling a feature group after first time
787 doesn't update associated structure view
790 <em>Applet</em><br />
793 <!-- JAL-2687 -->Concurrent modification exception when
794 closing alignment panel
797 <em>BioJSON</em><br />
800 <!-- JAL-2546 -->BioJSON export does not preserve
801 non-positional features
804 <em>New Known Issues</em>
807 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
808 sequence features correctly (for many previous versions of
812 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
813 using cursor in wrapped panel other than top
816 <!-- JAL-2791 -->Select columns containing feature ignores
817 graduated colour threshold
820 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
821 always preserve numbering and sequence features
824 <em>Known Java 9 Issues</em>
827 <!-- JAL-2902 -->Groovy Console very slow to open and is
828 not responsive when entering characters (Webstart, Java
835 <td width="60" nowrap>
837 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
838 <em>2/10/2017</em></strong>
841 <td><div align="left">
842 <em>New features in Jalview Desktop</em>
845 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
847 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
851 <td><div align="left">
855 <td width="60" nowrap>
857 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
858 <em>7/9/2017</em></strong>
861 <td><div align="left">
865 <!-- JAL-2588 -->Show gaps in overview window by colouring
866 in grey (sequences used to be coloured grey, and gaps were
870 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
874 <!-- JAL-2587 -->Overview updates immediately on increase
875 in size and progress bar shown as higher resolution
876 overview is recalculated
881 <td><div align="left">
885 <!-- JAL-2664 -->Overview window redraws every hidden
886 column region row by row
889 <!-- JAL-2681 -->duplicate protein sequences shown after
890 retrieving Ensembl crossrefs for sequences from Uniprot
893 <!-- JAL-2603 -->Overview window throws NPE if show boxes
894 format setting is unticked
897 <!-- JAL-2610 -->Groups are coloured wrongly in overview
898 if group has show boxes format setting unticked
901 <!-- JAL-2672,JAL-2665 -->Redraw problems when
902 autoscrolling whilst dragging current selection group to
903 include sequences and columns not currently displayed
906 <!-- JAL-2691 -->Not all chains are mapped when multimeric
907 assemblies are imported via CIF file
910 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
911 displayed when threshold or conservation colouring is also
915 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
919 <!-- JAL-2673 -->Jalview continues to scroll after
920 dragging a selected region off the visible region of the
924 <!-- JAL-2724 -->Cannot apply annotation based
925 colourscheme to all groups in a view
928 <!-- JAL-2511 -->IDs don't line up with sequences
929 initially after font size change using the Font chooser or
936 <td width="60" nowrap>
938 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
941 <td><div align="left">
942 <em>Calculations</em>
946 <!-- JAL-1933 -->Occupancy annotation row shows number of
947 ungapped positions in each column of the alignment.
950 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
951 a calculation dialog box
954 <!-- JAL-2379 -->Revised implementation of PCA for speed
955 and memory efficiency (~30x faster)
958 <!-- JAL-2403 -->Revised implementation of sequence
959 similarity scores as used by Tree, PCA, Shading Consensus
960 and other calculations
963 <!-- JAL-2416 -->Score matrices are stored as resource
964 files within the Jalview codebase
967 <!-- JAL-2500 -->Trees computed on Sequence Feature
968 Similarity may have different topology due to increased
975 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
976 model for alignments and groups
979 <!-- JAL-384 -->Custom shading schemes created via groovy
986 <!-- JAL-2526 -->Efficiency improvements for interacting
987 with alignment and overview windows
990 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
994 <!-- JAL-2388 -->Hidden columns and sequences can be
998 <!-- JAL-2611 -->Click-drag in visible area allows fine
999 adjustment of visible position
1003 <em>Data import/export</em>
1006 <!-- JAL-2535 -->Posterior probability annotation from
1007 Stockholm files imported as sequence associated annotation
1010 <!-- JAL-2507 -->More robust per-sequence positional
1011 annotation input/output via stockholm flatfile
1014 <!-- JAL-2533 -->Sequence names don't include file
1015 extension when importing structure files without embedded
1016 names or PDB accessions
1019 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1020 format sequence substitution matrices
1023 <em>User Interface</em>
1026 <!-- JAL-2447 --> Experimental Features Checkbox in
1027 Desktop's Tools menu to hide or show untested features in
1031 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1032 via Overview or sequence motif search operations
1035 <!-- JAL-2547 -->Amend sequence features dialog box can be
1036 opened by double clicking gaps within sequence feature
1040 <!-- JAL-1476 -->Status bar message shown when not enough
1041 aligned positions were available to create a 3D structure
1045 <em>3D Structure</em>
1048 <!-- JAL-2430 -->Hidden regions in alignment views are not
1049 coloured in linked structure views
1052 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1053 file-based command exchange
1056 <!-- JAL-2375 -->Structure chooser automatically shows
1057 Cached Structures rather than querying the PDBe if
1058 structures are already available for sequences
1061 <!-- JAL-2520 -->Structures imported via URL are cached in
1062 the Jalview project rather than downloaded again when the
1063 project is reopened.
1066 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1067 to transfer Chimera's structure attributes as Jalview
1068 features, and vice-versa (<strong>Experimental
1072 <em>Web Services</em>
1075 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1078 <!-- JAL-2335 -->Filter non-standard amino acids and
1079 nucleotides when submitting to AACon and other MSA
1083 <!-- JAL-2316, -->URLs for viewing database
1084 cross-references provided by identifiers.org and the
1085 EMBL-EBI's MIRIAM DB
1092 <!-- JAL-2344 -->FileFormatI interface for describing and
1093 identifying file formats (instead of String constants)
1096 <!-- JAL-2228 -->FeatureCounter script refactored for
1097 efficiency when counting all displayed features (not
1098 backwards compatible with 2.10.1)
1101 <em>Example files</em>
1104 <!-- JAL-2631 -->Graduated feature colour style example
1105 included in the example feature file
1108 <em>Documentation</em>
1111 <!-- JAL-2339 -->Release notes reformatted for readability
1112 with the built-in Java help viewer
1115 <!-- JAL-1644 -->Find documentation updated with 'search
1116 sequence description' option
1122 <!-- JAL-2485, -->External service integration tests for
1123 Uniprot REST Free Text Search Client
1126 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1129 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1134 <td><div align="left">
1135 <em>Calculations</em>
1138 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1139 matrix - C->R should be '-3'<br />Old matrix restored
1140 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1142 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1143 Jalview's treatment of gaps in PCA and substitution matrix
1144 based Tree calculations.<br /> <br />In earlier versions
1145 of Jalview, gaps matching gaps were penalised, and gaps
1146 matching non-gaps penalised even more. In the PCA
1147 calculation, gaps were actually treated as non-gaps - so
1148 different costs were applied, which meant Jalview's PCAs
1149 were different to those produced by SeqSpace.<br />Jalview
1150 now treats gaps in the same way as SeqSpace (ie it scores
1151 them as 0). <br /> <br />Enter the following in the
1152 Groovy console to restore pre-2.10.2 behaviour:<br />
1153 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1154 // for 2.10.1 mode <br />
1155 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1156 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1157 these settings will affect all subsequent tree and PCA
1158 calculations (not recommended)</em></li>
1160 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1161 scaling of branch lengths for trees computed using
1162 Sequence Feature Similarity.
1165 <!-- JAL-2377 -->PCA calculation could hang when
1166 generating output report when working with highly
1167 redundant alignments
1170 <!-- JAL-2544 --> Sort by features includes features to
1171 right of selected region when gaps present on right-hand
1175 <em>User Interface</em>
1178 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1179 doesn't reselect a specific sequence's associated
1180 annotation after it was used for colouring a view
1183 <!-- JAL-2419 -->Current selection lost if popup menu
1184 opened on a region of alignment without groups
1187 <!-- JAL-2374 -->Popup menu not always shown for regions
1188 of an alignment with overlapping groups
1191 <!-- JAL-2310 -->Finder double counts if both a sequence's
1192 name and description match
1195 <!-- JAL-2370 -->Hiding column selection containing two
1196 hidden regions results in incorrect hidden regions
1199 <!-- JAL-2386 -->'Apply to all groups' setting when
1200 changing colour does not apply Conservation slider value
1204 <!-- JAL-2373 -->Percentage identity and conservation menu
1205 items do not show a tick or allow shading to be disabled
1208 <!-- JAL-2385 -->Conservation shading or PID threshold
1209 lost when base colourscheme changed if slider not visible
1212 <!-- JAL-2547 -->Sequence features shown in tooltip for
1213 gaps before start of features
1216 <!-- JAL-2623 -->Graduated feature colour threshold not
1217 restored to UI when feature colour is edited
1220 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1221 a time when scrolling vertically in wrapped mode.
1224 <!-- JAL-2630 -->Structure and alignment overview update
1225 as graduate feature colour settings are modified via the
1229 <!-- JAL-2034 -->Overview window doesn't always update
1230 when a group defined on the alignment is resized
1233 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1234 wrapped view result in positional status updates
1238 <!-- JAL-2563 -->Status bar doesn't show position for
1239 ambiguous amino acid and nucleotide symbols
1242 <!-- JAL-2602 -->Copy consensus sequence failed if
1243 alignment included gapped columns
1246 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1247 widgets don't permanently disappear
1250 <!-- JAL-2503 -->Cannot select or filter quantitative
1251 annotation that are shown only as column labels (e.g.
1252 T-Coffee column reliability scores)
1255 <!-- JAL-2594 -->Exception thrown if trying to create a
1256 sequence feature on gaps only
1259 <!-- JAL-2504 -->Features created with 'New feature'
1260 button from a Find inherit previously defined feature type
1261 rather than the Find query string
1264 <!-- JAL-2423 -->incorrect title in output window when
1265 exporting tree calculated in Jalview
1268 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1269 and then revealing them reorders sequences on the
1273 <!-- JAL-964 -->Group panel in sequence feature settings
1274 doesn't update to reflect available set of groups after
1275 interactively adding or modifying features
1278 <!-- JAL-2225 -->Sequence Database chooser unusable on
1282 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1283 only excluded gaps in current sequence and ignored
1290 <!-- JAL-2421 -->Overview window visible region moves
1291 erratically when hidden rows or columns are present
1294 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1295 Structure Viewer's colour menu don't correspond to
1299 <!-- JAL-2405 -->Protein specific colours only offered in
1300 colour and group colour menu for protein alignments
1303 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1304 reflect currently selected view or group's shading
1308 <!-- JAL-2624 -->Feature colour thresholds not respected
1309 when rendered on overview and structures when opacity at
1313 <!-- JAL-2589 -->User defined gap colour not shown in
1314 overview when features overlaid on alignment
1317 <em>Data import/export</em>
1320 <!-- JAL-2576 -->Very large alignments take a long time to
1324 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1325 added after a sequence was imported are not written to
1329 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1330 when importing RNA secondary structure via Stockholm
1333 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1334 not shown in correct direction for simple pseudoknots
1337 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1338 with lightGray or darkGray via features file (but can
1342 <!-- JAL-2383 -->Above PID colour threshold not recovered
1343 when alignment view imported from project
1346 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1347 structure and sequences extracted from structure files
1348 imported via URL and viewed in Jmol
1351 <!-- JAL-2520 -->Structures loaded via URL are saved in
1352 Jalview Projects rather than fetched via URL again when
1353 the project is loaded and the structure viewed
1356 <em>Web Services</em>
1359 <!-- JAL-2519 -->EnsemblGenomes example failing after
1360 release of Ensembl v.88
1363 <!-- JAL-2366 -->Proxy server address and port always
1364 appear enabled in Preferences->Connections
1367 <!-- JAL-2461 -->DAS registry not found exceptions
1368 removed from console output
1371 <!-- JAL-2582 -->Cannot retrieve protein products from
1372 Ensembl by Peptide ID
1375 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1376 created from SIFTs, and spurious 'Couldn't open structure
1377 in Chimera' errors raised after April 2017 update (problem
1378 due to 'null' string rather than empty string used for
1379 residues with no corresponding PDB mapping).
1382 <em>Application UI</em>
1385 <!-- JAL-2361 -->User Defined Colours not added to Colour
1389 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1390 case' residues (button in colourscheme editor debugged and
1391 new documentation and tooltips added)
1394 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1395 doesn't restore group-specific text colour thresholds
1398 <!-- JAL-2243 -->Feature settings panel does not update as
1399 new features are added to alignment
1402 <!-- JAL-2532 -->Cancel in feature settings reverts
1403 changes to feature colours via the Amend features dialog
1406 <!-- JAL-2506 -->Null pointer exception when attempting to
1407 edit graduated feature colour via amend features dialog
1411 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1412 selection menu changes colours of alignment views
1415 <!-- JAL-2426 -->Spurious exceptions in console raised
1416 from alignment calculation workers after alignment has
1420 <!-- JAL-1608 -->Typo in selection popup menu - Create
1421 groups now 'Create Group'
1424 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1425 Create/Undefine group doesn't always work
1428 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1429 shown again after pressing 'Cancel'
1432 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1433 adjusts start position in wrap mode
1436 <!-- JAL-2563 -->Status bar doesn't show positions for
1437 ambiguous amino acids
1440 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1441 CDS/Protein view after CDS sequences added for aligned
1445 <!-- JAL-2592 -->User defined colourschemes called 'User
1446 Defined' don't appear in Colours menu
1452 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1453 score models doesn't always result in an updated PCA plot
1456 <!-- JAL-2442 -->Features not rendered as transparent on
1457 overview or linked structure view
1460 <!-- JAL-2372 -->Colour group by conservation doesn't
1464 <!-- JAL-2517 -->Hitting Cancel after applying
1465 user-defined colourscheme doesn't restore original
1472 <!-- JAL-2314 -->Unit test failure:
1473 jalview.ws.jabaws.RNAStructExportImport setup fails
1476 <!-- JAL-2307 -->Unit test failure:
1477 jalview.ws.sifts.SiftsClientTest due to compatibility
1478 problems with deep array comparison equality asserts in
1479 successive versions of TestNG
1482 <!-- JAL-2479 -->Relocated StructureChooserTest and
1483 ParameterUtilsTest Unit tests to Network suite
1486 <em>New Known Issues</em>
1489 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1490 phase after a sequence motif find operation
1493 <!-- JAL-2550 -->Importing annotation file with rows
1494 containing just upper and lower case letters are
1495 interpreted as WUSS RNA secondary structure symbols
1498 <!-- JAL-2590 -->Cannot load and display Newick trees
1499 reliably from eggnog Ortholog database
1502 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1503 containing features of type Highlight' when 'B' is pressed
1504 to mark columns containing highlighted regions.
1507 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1508 doesn't always add secondary structure annotation.
1513 <td width="60" nowrap>
1514 <div align="center">
1515 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1518 <td><div align="left">
1522 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1523 for all consensus calculations
1526 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1529 <li>Updated Jalview's Certum code signing certificate
1532 <em>Application</em>
1535 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1536 set of database cross-references, sorted alphabetically
1539 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1540 from database cross references. Users with custom links
1541 will receive a <a href="webServices/urllinks.html#warning">warning
1542 dialog</a> asking them to update their preferences.
1545 <!-- JAL-2287-->Cancel button and escape listener on
1546 dialog warning user about disconnecting Jalview from a
1550 <!-- JAL-2320-->Jalview's Chimera control window closes if
1551 the Chimera it is connected to is shut down
1554 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1555 columns menu item to mark columns containing highlighted
1556 regions (e.g. from structure selections or results of a
1560 <!-- JAL-2284-->Command line option for batch-generation
1561 of HTML pages rendering alignment data with the BioJS
1571 <!-- JAL-2286 -->Columns with more than one modal residue
1572 are not coloured or thresholded according to percent
1573 identity (first observed in Jalview 2.8.2)
1576 <!-- JAL-2301 -->Threonine incorrectly reported as not
1580 <!-- JAL-2318 -->Updates to documentation pages (above PID
1581 threshold, amino acid properties)
1584 <!-- JAL-2292 -->Lower case residues in sequences are not
1585 reported as mapped to residues in a structure file in the
1589 <!--JAL-2324 -->Identical features with non-numeric scores
1590 could be added multiple times to a sequence
1593 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1594 bond features shown as two highlighted residues rather
1595 than a range in linked structure views, and treated
1596 correctly when selecting and computing trees from features
1599 <!-- JAL-2281-->Custom URL links for database
1600 cross-references are matched to database name regardless
1605 <em>Application</em>
1608 <!-- JAL-2282-->Custom URL links for specific database
1609 names without regular expressions also offer links from
1613 <!-- JAL-2315-->Removing a single configured link in the
1614 URL links pane in Connections preferences doesn't actually
1615 update Jalview configuration
1618 <!-- JAL-2272-->CTRL-Click on a selected region to open
1619 the alignment area popup menu doesn't work on El-Capitan
1622 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1623 files with similarly named sequences if dropped onto the
1627 <!-- JAL-2312 -->Additional mappings are shown for PDB
1628 entries where more chains exist in the PDB accession than
1629 are reported in the SIFTS file
1632 <!-- JAL-2317-->Certain structures do not get mapped to
1633 the structure view when displayed with Chimera
1636 <!-- JAL-2317-->No chains shown in the Chimera view
1637 panel's View->Show Chains submenu
1640 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1641 work for wrapped alignment views
1644 <!--JAL-2197 -->Rename UI components for running JPred
1645 predictions from 'JNet' to 'JPred'
1648 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1649 corrupted when annotation panel vertical scroll is not at
1650 first annotation row
1653 <!--JAL-2332 -->Attempting to view structure for Hen
1654 lysozyme results in a PDB Client error dialog box
1657 <!-- JAL-2319 -->Structure View's mapping report switched
1658 ranges for PDB and sequence for SIFTS
1661 SIFTS 'Not_Observed' residues mapped to non-existant
1665 <!-- <em>New Known Issues</em>
1672 <td width="60" nowrap>
1673 <div align="center">
1674 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1675 <em>25/10/2016</em></strong>
1678 <td><em>Application</em>
1680 <li>3D Structure chooser opens with 'Cached structures'
1681 view if structures already loaded</li>
1682 <li>Progress bar reports models as they are loaded to
1683 structure views</li>
1689 <li>Colour by conservation always enabled and no tick
1690 shown in menu when BLOSUM or PID shading applied</li>
1691 <li>FER1_ARATH and FER2_ARATH labels were switched in
1692 example sequences/projects/trees</li>
1694 <em>Application</em>
1696 <li>Jalview projects with views of local PDB structure
1697 files saved on Windows cannot be opened on OSX</li>
1698 <li>Multiple structure views can be opened and superposed
1699 without timeout for structures with multiple models or
1700 multiple sequences in alignment</li>
1701 <li>Cannot import or associated local PDB files without a
1702 PDB ID HEADER line</li>
1703 <li>RMSD is not output in Jmol console when superposition
1705 <li>Drag and drop of URL from Browser fails for Linux and
1706 OSX versions earlier than El Capitan</li>
1707 <li>ENA client ignores invalid content from ENA server</li>
1708 <li>Exceptions are not raised in console when ENA client
1709 attempts to fetch non-existent IDs via Fetch DB Refs UI
1711 <li>Exceptions are not raised in console when a new view
1712 is created on the alignment</li>
1713 <li>OSX right-click fixed for group selections: CMD-click
1714 to insert/remove gaps in groups and CTRL-click to open group
1717 <em>Build and deployment</em>
1719 <li>URL link checker now copes with multi-line anchor
1722 <em>New Known Issues</em>
1724 <li>Drag and drop from URL links in browsers do not work
1731 <td width="60" nowrap>
1732 <div align="center">
1733 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1736 <td><em>General</em>
1739 <!-- JAL-2124 -->Updated Spanish translations.
1742 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1743 for importing structure data to Jalview. Enables mmCIF and
1747 <!-- JAL-192 --->Alignment ruler shows positions relative to
1751 <!-- JAL-2202 -->Position/residue shown in status bar when
1752 mousing over sequence associated annotation
1755 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1759 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1760 '()', canonical '[]' and invalid '{}' base pair populations
1764 <!-- JAL-2092 -->Feature settings popup menu options for
1765 showing or hiding columns containing a feature
1768 <!-- JAL-1557 -->Edit selected group by double clicking on
1769 group and sequence associated annotation labels
1772 <!-- JAL-2236 -->Sequence name added to annotation label in
1773 select/hide columns by annotation and colour by annotation
1777 </ul> <em>Application</em>
1780 <!-- JAL-2050-->Automatically hide introns when opening a
1781 gene/transcript view
1784 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1788 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1789 structure mappings with the EMBL-EBI PDBe SIFTS database
1792 <!-- JAL-2079 -->Updated download sites used for Rfam and
1793 Pfam sources to xfam.org
1796 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1799 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1800 over sequences in Jalview
1803 <!-- JAL-2027-->Support for reverse-complement coding
1804 regions in ENA and EMBL
1807 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1808 for record retrieval via ENA rest API
1811 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1815 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1816 groovy script execution
1819 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1820 alignment window's Calculate menu
1823 <!-- JAL-1812 -->Allow groovy scripts that call
1824 Jalview.getAlignFrames() to run in headless mode
1827 <!-- JAL-2068 -->Support for creating new alignment
1828 calculation workers from groovy scripts
1831 <!-- JAL-1369 --->Store/restore reference sequence in
1835 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1836 associations are now saved/restored from project
1839 <!-- JAL-1993 -->Database selection dialog always shown
1840 before sequence fetcher is opened
1843 <!-- JAL-2183 -->Double click on an entry in Jalview's
1844 database chooser opens a sequence fetcher
1847 <!-- JAL-1563 -->Free-text search client for UniProt using
1848 the UniProt REST API
1851 <!-- JAL-2168 -->-nonews command line parameter to prevent
1852 the news reader opening
1855 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1856 querying stored in preferences
1859 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1863 <!-- JAL-1977-->Tooltips shown on database chooser
1866 <!-- JAL-391 -->Reverse complement function in calculate
1867 menu for nucleotide sequences
1870 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1871 and feature counts preserves alignment ordering (and
1872 debugged for complex feature sets).
1875 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1876 viewing structures with Jalview 2.10
1879 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1880 genome, transcript CCDS and gene ids via the Ensembl and
1881 Ensembl Genomes REST API
1884 <!-- JAL-2049 -->Protein sequence variant annotation
1885 computed for 'sequence_variant' annotation on CDS regions
1889 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1893 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1894 Ref Fetcher fails to match, or otherwise updates sequence
1895 data from external database records.
1898 <!-- JAL-2154 -->Revised Jalview Project format for
1899 efficient recovery of sequence coding and alignment
1900 annotation relationships.
1902 </ul> <!-- <em>Applet</em>
1913 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1917 <!-- JAL-2018-->Export features in Jalview format (again)
1918 includes graduated colourschemes
1921 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1922 working with big alignments and lots of hidden columns
1925 <!-- JAL-2053-->Hidden column markers not always rendered
1926 at right of alignment window
1929 <!-- JAL-2067 -->Tidied up links in help file table of
1933 <!-- JAL-2072 -->Feature based tree calculation not shown
1937 <!-- JAL-2075 -->Hidden columns ignored during feature
1938 based tree calculation
1941 <!-- JAL-2065 -->Alignment view stops updating when show
1942 unconserved enabled for group on alignment
1945 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1949 <!-- JAL-2146 -->Alignment column in status incorrectly
1950 shown as "Sequence position" when mousing over
1954 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1955 hidden columns present
1958 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1959 user created annotation added to alignment
1962 <!-- JAL-1841 -->RNA Structure consensus only computed for
1963 '()' base pair annotation
1966 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1967 in zero scores for all base pairs in RNA Structure
1971 <!-- JAL-2174-->Extend selection with columns containing
1975 <!-- JAL-2275 -->Pfam format writer puts extra space at
1976 beginning of sequence
1979 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1983 <!-- JAL-2238 -->Cannot create groups on an alignment from
1984 from a tree when t-coffee scores are shown
1987 <!-- JAL-1836,1967 -->Cannot import and view PDB
1988 structures with chains containing negative resnums (4q4h)
1991 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1995 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1996 to Clustal, PIR and PileUp output
1999 <!-- JAL-2008 -->Reordering sequence features that are
2000 not visible causes alignment window to repaint
2003 <!-- JAL-2006 -->Threshold sliders don't work in
2004 graduated colour and colour by annotation row for e-value
2005 scores associated with features and annotation rows
2008 <!-- JAL-1797 -->amino acid physicochemical conservation
2009 calculation should be case independent
2012 <!-- JAL-2173 -->Remove annotation also updates hidden
2016 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2017 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2018 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2021 <!-- JAL-2065 -->Null pointer exceptions and redraw
2022 problems when reference sequence defined and 'show
2023 non-conserved' enabled
2026 <!-- JAL-1306 -->Quality and Conservation are now shown on
2027 load even when Consensus calculation is disabled
2030 <!-- JAL-1932 -->Remove right on penultimate column of
2031 alignment does nothing
2034 <em>Application</em>
2037 <!-- JAL-1552-->URLs and links can't be imported by
2038 drag'n'drop on OSX when launched via webstart (note - not
2039 yet fixed for El Capitan)
2042 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2043 output when running on non-gb/us i18n platforms
2046 <!-- JAL-1944 -->Error thrown when exporting a view with
2047 hidden sequences as flat-file alignment
2050 <!-- JAL-2030-->InstallAnywhere distribution fails when
2054 <!-- JAL-2080-->Jalview very slow to launch via webstart
2055 (also hotfix for 2.9.0b2)
2058 <!-- JAL-2085 -->Cannot save project when view has a
2059 reference sequence defined
2062 <!-- JAL-1011 -->Columns are suddenly selected in other
2063 alignments and views when revealing hidden columns
2066 <!-- JAL-1989 -->Hide columns not mirrored in complement
2067 view in a cDNA/Protein splitframe
2070 <!-- JAL-1369 -->Cannot save/restore representative
2071 sequence from project when only one sequence is
2075 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2076 in Structure Chooser
2079 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2080 structure consensus didn't refresh annotation panel
2083 <!-- JAL-1962 -->View mapping in structure view shows
2084 mappings between sequence and all chains in a PDB file
2087 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2088 dialogs format columns correctly, don't display array
2089 data, sort columns according to type
2092 <!-- JAL-1975 -->Export complete shown after destination
2093 file chooser is cancelled during an image export
2096 <!-- JAL-2025 -->Error when querying PDB Service with
2097 sequence name containing special characters
2100 <!-- JAL-2024 -->Manual PDB structure querying should be
2104 <!-- JAL-2104 -->Large tooltips with broken HTML
2105 formatting don't wrap
2108 <!-- JAL-1128 -->Figures exported from wrapped view are
2109 truncated so L looks like I in consensus annotation
2112 <!-- JAL-2003 -->Export features should only export the
2113 currently displayed features for the current selection or
2117 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2118 after fetching cross-references, and restoring from
2122 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2123 followed in the structure viewer
2126 <!-- JAL-2163 -->Titles for individual alignments in
2127 splitframe not restored from project
2130 <!-- JAL-2145 -->missing autocalculated annotation at
2131 trailing end of protein alignment in transcript/product
2132 splitview when pad-gaps not enabled by default
2135 <!-- JAL-1797 -->amino acid physicochemical conservation
2139 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2140 article has been read (reopened issue due to
2141 internationalisation problems)
2144 <!-- JAL-1960 -->Only offer PDB structures in structure
2145 viewer based on sequence name, PDB and UniProt
2150 <!-- JAL-1976 -->No progress bar shown during export of
2154 <!-- JAL-2213 -->Structures not always superimposed after
2155 multiple structures are shown for one or more sequences.
2158 <!-- JAL-1370 -->Reference sequence characters should not
2159 be replaced with '.' when 'Show unconserved' format option
2163 <!-- JAL-1823 -->Cannot specify chain code when entering
2164 specific PDB id for sequence
2167 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2168 'Export hidden sequences' is enabled, but 'export hidden
2169 columns' is disabled.
2172 <!--JAL-2026-->Best Quality option in structure chooser
2173 selects lowest rather than highest resolution structures
2177 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2178 to sequence mapping in 'View Mappings' report
2181 <!-- JAL-2284 -->Unable to read old Jalview projects that
2182 contain non-XML data added after Jalvew wrote project.
2185 <!-- JAL-2118 -->Newly created annotation row reorders
2186 after clicking on it to create new annotation for a
2190 <!-- JAL-1980 -->Null Pointer Exception raised when
2191 pressing Add on an orphaned cut'n'paste window.
2193 <!-- may exclude, this is an external service stability issue JAL-1941
2194 -- > RNA 3D structure not added via DSSR service</li> -->
2199 <!-- JAL-2151 -->Incorrect columns are selected when
2200 hidden columns present before start of sequence
2203 <!-- JAL-1986 -->Missing dependencies on applet pages
2207 <!-- JAL-1947 -->Overview pixel size changes when
2208 sequences are hidden in applet
2211 <!-- JAL-1996 -->Updated instructions for applet
2212 deployment on examples pages.
2219 <td width="60" nowrap>
2220 <div align="center">
2221 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2222 <em>16/10/2015</em></strong>
2225 <td><em>General</em>
2227 <li>Time stamps for signed Jalview application and applet
2232 <em>Application</em>
2234 <li>Duplicate group consensus and conservation rows
2235 shown when tree is partitioned</li>
2236 <li>Erratic behaviour when tree partitions made with
2237 multiple cDNA/Protein split views</li>
2243 <td width="60" nowrap>
2244 <div align="center">
2245 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2246 <em>8/10/2015</em></strong>
2249 <td><em>General</em>
2251 <li>Updated Spanish translations of localized text for
2253 </ul> <em>Application</em>
2255 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2256 <li>Signed OSX InstallAnywhere installer<br></li>
2257 <li>Support for per-sequence based annotations in BioJSON</li>
2258 </ul> <em>Applet</em>
2260 <li>Split frame example added to applet examples page</li>
2261 </ul> <em>Build and Deployment</em>
2264 <!-- JAL-1888 -->New ant target for running Jalview's test
2272 <li>Mapping of cDNA to protein in split frames
2273 incorrect when sequence start > 1</li>
2274 <li>Broken images in filter column by annotation dialog
2276 <li>Feature colours not parsed from features file</li>
2277 <li>Exceptions and incomplete link URLs recovered when
2278 loading a features file containing HTML tags in feature
2282 <em>Application</em>
2284 <li>Annotations corrupted after BioJS export and
2286 <li>Incorrect sequence limits after Fetch DB References
2287 with 'trim retrieved sequences'</li>
2288 <li>Incorrect warning about deleting all data when
2289 deleting selected columns</li>
2290 <li>Patch to build system for shipping properly signed
2291 JNLP templates for webstart launch</li>
2292 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2293 unreleased structures for download or viewing</li>
2294 <li>Tab/space/return keystroke operation of EMBL-PDBe
2295 fetcher/viewer dialogs works correctly</li>
2296 <li>Disabled 'minimise' button on Jalview windows
2297 running on OSX to workaround redraw hang bug</li>
2298 <li>Split cDNA/Protein view position and geometry not
2299 recovered from jalview project</li>
2300 <li>Initial enabled/disabled state of annotation menu
2301 sorter 'show autocalculated first/last' corresponds to
2303 <li>Restoring of Clustal, RNA Helices and T-Coffee
2304 color schemes from BioJSON</li>
2308 <li>Reorder sequences mirrored in cDNA/Protein split
2310 <li>Applet with Jmol examples not loading correctly</li>
2316 <td><div align="center">
2317 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2319 <td><em>General</em>
2321 <li>Linked visualisation and analysis of DNA and Protein
2324 <li>Translated cDNA alignments shown as split protein
2325 and DNA alignment views</li>
2326 <li>Codon consensus annotation for linked protein and
2327 cDNA alignment views</li>
2328 <li>Link cDNA or Protein product sequences by loading
2329 them onto Protein or cDNA alignments</li>
2330 <li>Reconstruct linked cDNA alignment from aligned
2331 protein sequences</li>
2334 <li>Jmol integration updated to Jmol v14.2.14</li>
2335 <li>Import and export of Jalview alignment views as <a
2336 href="features/bioJsonFormat.html">BioJSON</a></li>
2337 <li>New alignment annotation file statements for
2338 reference sequences and marking hidden columns</li>
2339 <li>Reference sequence based alignment shading to
2340 highlight variation</li>
2341 <li>Select or hide columns according to alignment
2343 <li>Find option for locating sequences by description</li>
2344 <li>Conserved physicochemical properties shown in amino
2345 acid conservation row</li>
2346 <li>Alignments can be sorted by number of RNA helices</li>
2347 </ul> <em>Application</em>
2349 <li>New cDNA/Protein analysis capabilities
2351 <li>Get Cross-References should open a Split Frame
2352 view with cDNA/Protein</li>
2353 <li>Detect when nucleotide sequences and protein
2354 sequences are placed in the same alignment</li>
2355 <li>Split cDNA/Protein views are saved in Jalview
2360 <li>Use REST API to talk to Chimera</li>
2361 <li>Selected regions in Chimera are highlighted in linked
2362 Jalview windows</li>
2364 <li>VARNA RNA viewer updated to v3.93</li>
2365 <li>VARNA views are saved in Jalview Projects</li>
2366 <li>Pseudoknots displayed as Jalview RNA annotation can
2367 be shown in VARNA</li>
2369 <li>Make groups for selection uses marked columns as well
2370 as the active selected region</li>
2372 <li>Calculate UPGMA and NJ trees using sequence feature
2374 <li>New Export options
2376 <li>New Export Settings dialog to control hidden
2377 region export in flat file generation</li>
2379 <li>Export alignment views for display with the <a
2380 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2382 <li>Export scrollable SVG in HTML page</li>
2383 <li>Optional embedding of BioJSON data when exporting
2384 alignment figures to HTML</li>
2386 <li>3D structure retrieval and display
2388 <li>Free text and structured queries with the PDBe
2390 <li>PDBe Search API based discovery and selection of
2391 PDB structures for a sequence set</li>
2395 <li>JPred4 employed for protein secondary structure
2397 <li>Hide Insertions menu option to hide unaligned columns
2398 for one or a group of sequences</li>
2399 <li>Automatically hide insertions in alignments imported
2400 from the JPred4 web server</li>
2401 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2402 system on OSX<br />LGPL libraries courtesy of <a
2403 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2405 <li>changed 'View nucleotide structure' submenu to 'View
2406 VARNA 2D Structure'</li>
2407 <li>change "View protein structure" menu option to "3D
2410 </ul> <em>Applet</em>
2412 <li>New layout for applet example pages</li>
2413 <li>New parameters to enable SplitFrame view
2414 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2415 <li>New example demonstrating linked viewing of cDNA and
2416 Protein alignments</li>
2417 </ul> <em>Development and deployment</em>
2419 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2420 <li>Include installation type and git revision in build
2421 properties and console log output</li>
2422 <li>Jalview Github organisation, and new github site for
2423 storing BioJsMSA Templates</li>
2424 <li>Jalview's unit tests now managed with TestNG</li>
2427 <!-- <em>General</em>
2429 </ul> --> <!-- issues resolved --> <em>Application</em>
2431 <li>Escape should close any open find dialogs</li>
2432 <li>Typo in select-by-features status report</li>
2433 <li>Consensus RNA secondary secondary structure
2434 predictions are not highlighted in amber</li>
2435 <li>Missing gap character in v2.7 example file means
2436 alignment appears unaligned when pad-gaps is not enabled</li>
2437 <li>First switch to RNA Helices colouring doesn't colour
2438 associated structure views</li>
2439 <li>ID width preference option is greyed out when auto
2440 width checkbox not enabled</li>
2441 <li>Stopped a warning dialog from being shown when
2442 creating user defined colours</li>
2443 <li>'View Mapping' in structure viewer shows sequence
2444 mappings for just that viewer's sequences</li>
2445 <li>Workaround for superposing PDB files containing
2446 multiple models in Chimera</li>
2447 <li>Report sequence position in status bar when hovering
2448 over Jmol structure</li>
2449 <li>Cannot output gaps as '.' symbols with Selection ->
2450 output to text box</li>
2451 <li>Flat file exports of alignments with hidden columns
2452 have incorrect sequence start/end</li>
2453 <li>'Aligning' a second chain to a Chimera structure from
2455 <li>Colour schemes applied to structure viewers don't
2456 work for nucleotide</li>
2457 <li>Loading/cut'n'pasting an empty or invalid file leads
2458 to a grey/invisible alignment window</li>
2459 <li>Exported Jpred annotation from a sequence region
2460 imports to different position</li>
2461 <li>Space at beginning of sequence feature tooltips shown
2462 on some platforms</li>
2463 <li>Chimera viewer 'View | Show Chain' menu is not
2465 <li>'New View' fails with a Null Pointer Exception in
2466 console if Chimera has been opened</li>
2467 <li>Mouseover to Chimera not working</li>
2468 <li>Miscellaneous ENA XML feature qualifiers not
2470 <li>NPE in annotation renderer after 'Extract Scores'</li>
2471 <li>If two structures in one Chimera window, mouseover of
2472 either sequence shows on first structure</li>
2473 <li>'Show annotations' options should not make
2474 non-positional annotations visible</li>
2475 <li>Subsequence secondary structure annotation not shown
2476 in right place after 'view flanking regions'</li>
2477 <li>File Save As type unset when current file format is
2479 <li>Save as '.jar' option removed for saving Jalview
2481 <li>Colour by Sequence colouring in Chimera more
2483 <li>Cannot 'add reference annotation' for a sequence in
2484 several views on same alignment</li>
2485 <li>Cannot show linked products for EMBL / ENA records</li>
2486 <li>Jalview's tooltip wraps long texts containing no
2488 </ul> <em>Applet</em>
2490 <li>Jmol to JalviewLite mouseover/link not working</li>
2491 <li>JalviewLite can't import sequences with ID
2492 descriptions containing angle brackets</li>
2493 </ul> <em>General</em>
2495 <li>Cannot export and reimport RNA secondary structure
2496 via jalview annotation file</li>
2497 <li>Random helix colour palette for colour by annotation
2498 with RNA secondary structure</li>
2499 <li>Mouseover to cDNA from STOP residue in protein
2500 translation doesn't work.</li>
2501 <li>hints when using the select by annotation dialog box</li>
2502 <li>Jmol alignment incorrect if PDB file has alternate CA
2504 <li>FontChooser message dialog appears to hang after
2505 choosing 1pt font</li>
2506 <li>Peptide secondary structure incorrectly imported from
2507 annotation file when annotation display text includes 'e' or
2509 <li>Cannot set colour of new feature type whilst creating
2511 <li>cDNA translation alignment should not be sequence
2512 order dependent</li>
2513 <li>'Show unconserved' doesn't work for lower case
2515 <li>Nucleotide ambiguity codes involving R not recognised</li>
2516 </ul> <em>Deployment and Documentation</em>
2518 <li>Applet example pages appear different to the rest of
2519 www.jalview.org</li>
2520 </ul> <em>Application Known issues</em>
2522 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2523 <li>Misleading message appears after trying to delete
2525 <li>Jalview icon not shown in dock after InstallAnywhere
2526 version launches</li>
2527 <li>Fetching EMBL reference for an RNA sequence results
2528 fails with a sequence mismatch</li>
2529 <li>Corrupted or unreadable alignment display when
2530 scrolling alignment to right</li>
2531 <li>ArrayIndexOutOfBoundsException thrown when remove
2532 empty columns called on alignment with ragged gapped ends</li>
2533 <li>auto calculated alignment annotation rows do not get
2534 placed above or below non-autocalculated rows</li>
2535 <li>Jalview dekstop becomes sluggish at full screen in
2536 ultra-high resolution</li>
2537 <li>Cannot disable consensus calculation independently of
2538 quality and conservation</li>
2539 <li>Mouseover highlighting between cDNA and protein can
2540 become sluggish with more than one splitframe shown</li>
2541 </ul> <em>Applet Known Issues</em>
2543 <li>Core PDB parsing code requires Jmol</li>
2544 <li>Sequence canvas panel goes white when alignment
2545 window is being resized</li>
2551 <td><div align="center">
2552 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2554 <td><em>General</em>
2556 <li>Updated Java code signing certificate donated by
2558 <li>Features and annotation preserved when performing
2559 pairwise alignment</li>
2560 <li>RNA pseudoknot annotation can be
2561 imported/exported/displayed</li>
2562 <li>'colour by annotation' can colour by RNA and
2563 protein secondary structure</li>
2564 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2565 post-hoc with 2.9 release</em>)
2568 </ul> <em>Application</em>
2570 <li>Extract and display secondary structure for sequences
2571 with 3D structures</li>
2572 <li>Support for parsing RNAML</li>
2573 <li>Annotations menu for layout
2575 <li>sort sequence annotation rows by alignment</li>
2576 <li>place sequence annotation above/below alignment
2579 <li>Output in Stockholm format</li>
2580 <li>Internationalisation: improved Spanish (es)
2582 <li>Structure viewer preferences tab</li>
2583 <li>Disorder and Secondary Structure annotation tracks
2584 shared between alignments</li>
2585 <li>UCSF Chimera launch and linked highlighting from
2587 <li>Show/hide all sequence associated annotation rows for
2588 all or current selection</li>
2589 <li>disorder and secondary structure predictions
2590 available as dataset annotation</li>
2591 <li>Per-sequence rna helices colouring</li>
2594 <li>Sequence database accessions imported when fetching
2595 alignments from Rfam</li>
2596 <li>update VARNA version to 3.91</li>
2598 <li>New groovy scripts for exporting aligned positions,
2599 conservation values, and calculating sum of pairs scores.</li>
2600 <li>Command line argument to set default JABAWS server</li>
2601 <li>include installation type in build properties and
2602 console log output</li>
2603 <li>Updated Jalview project format to preserve dataset
2607 <!-- issues resolved --> <em>Application</em>
2609 <li>Distinguish alignment and sequence associated RNA
2610 structure in structure->view->VARNA</li>
2611 <li>Raise dialog box if user deletes all sequences in an
2613 <li>Pressing F1 results in documentation opening twice</li>
2614 <li>Sequence feature tooltip is wrapped</li>
2615 <li>Double click on sequence associated annotation
2616 selects only first column</li>
2617 <li>Redundancy removal doesn't result in unlinked
2618 leaves shown in tree</li>
2619 <li>Undos after several redundancy removals don't undo
2621 <li>Hide sequence doesn't hide associated annotation</li>
2622 <li>User defined colours dialog box too big to fit on
2623 screen and buttons not visible</li>
2624 <li>author list isn't updated if already written to
2625 Jalview properties</li>
2626 <li>Popup menu won't open after retrieving sequence
2628 <li>File open window for associate PDB doesn't open</li>
2629 <li>Left-then-right click on a sequence id opens a
2630 browser search window</li>
2631 <li>Cannot open sequence feature shading/sort popup menu
2632 in feature settings dialog</li>
2633 <li>better tooltip placement for some areas of Jalview
2635 <li>Allow addition of JABAWS Server which doesn't
2636 pass validation</li>
2637 <li>Web services parameters dialog box is too large to
2639 <li>Muscle nucleotide alignment preset obscured by
2641 <li>JABAWS preset submenus don't contain newly
2642 defined user preset</li>
2643 <li>MSA web services warns user if they were launched
2644 with invalid input</li>
2645 <li>Jalview cannot contact DAS Registy when running on
2648 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2649 'Superpose with' submenu not shown when new view
2653 </ul> <!-- <em>Applet</em>
2655 </ul> <em>General</em>
2657 </ul>--> <em>Deployment and Documentation</em>
2659 <li>2G and 1G options in launchApp have no effect on
2660 memory allocation</li>
2661 <li>launchApp service doesn't automatically open
2662 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2664 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2665 InstallAnywhere reports cannot find valid JVM when Java
2666 1.7_055 is available
2668 </ul> <em>Application Known issues</em>
2671 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2672 corrupted or unreadable alignment display when scrolling
2676 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2677 retrieval fails but progress bar continues for DAS retrieval
2678 with large number of ID
2681 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2682 flatfile output of visible region has incorrect sequence
2686 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2687 rna structure consensus doesn't update when secondary
2688 structure tracks are rearranged
2691 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2692 invalid rna structure positional highlighting does not
2693 highlight position of invalid base pairs
2696 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2697 out of memory errors are not raised when saving Jalview
2698 project from alignment window file menu
2701 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2702 Switching to RNA Helices colouring doesn't propagate to
2706 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2707 colour by RNA Helices not enabled when user created
2708 annotation added to alignment
2711 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2712 Jalview icon not shown on dock in Mountain Lion/Webstart
2714 </ul> <em>Applet Known Issues</em>
2717 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2718 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2721 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2722 Jalview and Jmol example not compatible with IE9
2725 <li>Sort by annotation score doesn't reverse order
2731 <td><div align="center">
2732 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2735 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2738 <li>Internationalisation of user interface (usually
2739 called i18n support) and translation for Spanish locale</li>
2740 <li>Define/Undefine group on current selection with
2741 Ctrl-G/Shift Ctrl-G</li>
2742 <li>Improved group creation/removal options in
2743 alignment/sequence Popup menu</li>
2744 <li>Sensible precision for symbol distribution
2745 percentages shown in logo tooltip.</li>
2746 <li>Annotation panel height set according to amount of
2747 annotation when alignment first opened</li>
2748 </ul> <em>Application</em>
2750 <li>Interactive consensus RNA secondary structure
2751 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2752 <li>Select columns containing particular features from
2753 Feature Settings dialog</li>
2754 <li>View all 'representative' PDB structures for selected
2756 <li>Update Jalview project format:
2758 <li>New file extension for Jalview projects '.jvp'</li>
2759 <li>Preserve sequence and annotation dataset (to
2760 store secondary structure annotation,etc)</li>
2761 <li>Per group and alignment annotation and RNA helix
2765 <li>New similarity measures for PCA and Tree calculation
2767 <li>Experimental support for retrieval and viewing of
2768 flanking regions for an alignment</li>
2772 <!-- issues resolved --> <em>Application</em>
2774 <li>logo keeps spinning and status remains at queued or
2775 running after job is cancelled</li>
2776 <li>cannot export features from alignments imported from
2777 Jalview/VAMSAS projects</li>
2778 <li>Buggy slider for web service parameters that take
2780 <li>Newly created RNA secondary structure line doesn't
2781 have 'display all symbols' flag set</li>
2782 <li>T-COFFEE alignment score shading scheme and other
2783 annotation shading not saved in Jalview project</li>
2784 <li>Local file cannot be loaded in freshly downloaded
2786 <li>Jalview icon not shown on dock in Mountain
2788 <li>Load file from desktop file browser fails</li>
2789 <li>Occasional NPE thrown when calculating large trees</li>
2790 <li>Cannot reorder or slide sequences after dragging an
2791 alignment onto desktop</li>
2792 <li>Colour by annotation dialog throws NPE after using
2793 'extract scores' function</li>
2794 <li>Loading/cut'n'pasting an empty file leads to a grey
2795 alignment window</li>
2796 <li>Disorder thresholds rendered incorrectly after
2797 performing IUPred disorder prediction</li>
2798 <li>Multiple group annotated consensus rows shown when
2799 changing 'normalise logo' display setting</li>
2800 <li>Find shows blank dialog after 'finished searching' if
2801 nothing matches query</li>
2802 <li>Null Pointer Exceptions raised when sorting by
2803 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2805 <li>Errors in Jmol console when structures in alignment
2806 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2808 <li>Not all working JABAWS services are shown in
2810 <li>JAVAWS version of Jalview fails to launch with
2811 'invalid literal/length code'</li>
2812 <li>Annotation/RNA Helix colourschemes cannot be applied
2813 to alignment with groups (actually fixed in 2.8.0b1)</li>
2814 <li>RNA Helices and T-Coffee Scores available as default
2817 </ul> <em>Applet</em>
2819 <li>Remove group option is shown even when selection is
2821 <li>Apply to all groups ticked but colourscheme changes
2822 don't affect groups</li>
2823 <li>Documented RNA Helices and T-Coffee Scores as valid
2824 colourscheme name</li>
2825 <li>Annotation labels drawn on sequence IDs when
2826 Annotation panel is not displayed</li>
2827 <li>Increased font size for dropdown menus on OSX and
2828 embedded windows</li>
2829 </ul> <em>Other</em>
2831 <li>Consensus sequence for alignments/groups with a
2832 single sequence were not calculated</li>
2833 <li>annotation files that contain only groups imported as
2834 annotation and junk sequences</li>
2835 <li>Fasta files with sequences containing '*' incorrectly
2836 recognised as PFAM or BLC</li>
2837 <li>conservation/PID slider apply all groups option
2838 doesn't affect background (2.8.0b1)
2840 <li>redundancy highlighting is erratic at 0% and 100%</li>
2841 <li>Remove gapped columns fails for sequences with ragged
2843 <li>AMSA annotation row with leading spaces is not
2844 registered correctly on import</li>
2845 <li>Jalview crashes when selecting PCA analysis for
2846 certain alignments</li>
2847 <li>Opening the colour by annotation dialog for an
2848 existing annotation based 'use original colours'
2849 colourscheme loses original colours setting</li>
2854 <td><div align="center">
2855 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2856 <em>30/1/2014</em></strong>
2860 <li>Trusted certificates for JalviewLite applet and
2861 Jalview Desktop application<br />Certificate was donated by
2862 <a href="https://www.certum.eu">Certum</a> to the Jalview
2863 open source project).
2865 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2866 <li>Output in Stockholm format</li>
2867 <li>Allow import of data from gzipped files</li>
2868 <li>Export/import group and sequence associated line
2869 graph thresholds</li>
2870 <li>Nucleotide substitution matrix that supports RNA and
2871 ambiguity codes</li>
2872 <li>Allow disorder predictions to be made on the current
2873 selection (or visible selection) in the same way that JPred
2875 <li>Groovy scripting for headless Jalview operation</li>
2876 </ul> <em>Other improvements</em>
2878 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2879 <li>COMBINE statement uses current SEQUENCE_REF and
2880 GROUP_REF scope to group annotation rows</li>
2881 <li>Support '' style escaping of quotes in Newick
2883 <li>Group options for JABAWS service by command line name</li>
2884 <li>Empty tooltip shown for JABA service options with a
2885 link but no description</li>
2886 <li>Select primary source when selecting authority in
2887 database fetcher GUI</li>
2888 <li>Add .mfa to FASTA file extensions recognised by
2890 <li>Annotation label tooltip text wrap</li>
2895 <li>Slow scrolling when lots of annotation rows are
2897 <li>Lots of NPE (and slowness) after creating RNA
2898 secondary structure annotation line</li>
2899 <li>Sequence database accessions not imported when
2900 fetching alignments from Rfam</li>
2901 <li>Incorrect SHMR submission for sequences with
2903 <li>View all structures does not always superpose
2905 <li>Option widgets in service parameters not updated to
2906 reflect user or preset settings</li>
2907 <li>Null pointer exceptions for some services without
2908 presets or adjustable parameters</li>
2909 <li>Discover PDB IDs entry in structure menu doesn't
2910 discover PDB xRefs</li>
2911 <li>Exception encountered while trying to retrieve
2912 features with DAS</li>
2913 <li>Lowest value in annotation row isn't coloured
2914 when colour by annotation (per sequence) is coloured</li>
2915 <li>Keyboard mode P jumps to start of gapped region when
2916 residue follows a gap</li>
2917 <li>Jalview appears to hang importing an alignment with
2918 Wrap as default or after enabling Wrap</li>
2919 <li>'Right click to add annotations' message
2920 shown in wrap mode when no annotations present</li>
2921 <li>Disorder predictions fail with NPE if no automatic
2922 annotation already exists on alignment</li>
2923 <li>oninit javascript function should be called after
2924 initialisation completes</li>
2925 <li>Remove redundancy after disorder prediction corrupts
2926 alignment window display</li>
2927 <li>Example annotation file in documentation is invalid</li>
2928 <li>Grouped line graph annotation rows are not exported
2929 to annotation file</li>
2930 <li>Multi-harmony analysis cannot be run when only two
2932 <li>Cannot create multiple groups of line graphs with
2933 several 'combine' statements in annotation file</li>
2934 <li>Pressing return several times causes Number Format
2935 exceptions in keyboard mode</li>
2936 <li>Multi-harmony (SHMMR) method doesn't submit
2937 correct partitions for input data</li>
2938 <li>Translation from DNA to Amino Acids fails</li>
2939 <li>Jalview fail to load newick tree with quoted label</li>
2940 <li>--headless flag isn't understood</li>
2941 <li>ClassCastException when generating EPS in headless
2943 <li>Adjusting sequence-associated shading threshold only
2944 changes one row's threshold</li>
2945 <li>Preferences and Feature settings panel panel
2946 doesn't open</li>
2947 <li>hide consensus histogram also hides conservation and
2948 quality histograms</li>
2953 <td><div align="center">
2954 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2956 <td><em>Application</em>
2958 <li>Support for JABAWS 2.0 Services (AACon alignment
2959 conservation, protein disorder and Clustal Omega)</li>
2960 <li>JABAWS server status indicator in Web Services
2962 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2963 in Jalview alignment window</li>
2964 <li>Updated Jalview build and deploy framework for OSX
2965 mountain lion, windows 7, and 8</li>
2966 <li>Nucleotide substitution matrix for PCA that supports
2967 RNA and ambiguity codes</li>
2969 <li>Improved sequence database retrieval GUI</li>
2970 <li>Support fetching and database reference look up
2971 against multiple DAS sources (Fetch all from in 'fetch db
2973 <li>Jalview project improvements
2975 <li>Store and retrieve the 'belowAlignment'
2976 flag for annotation</li>
2977 <li>calcId attribute to group annotation rows on the
2979 <li>Store AACon calculation settings for a view in
2980 Jalview project</li>
2984 <li>horizontal scrolling gesture support</li>
2985 <li>Visual progress indicator when PCA calculation is
2987 <li>Simpler JABA web services menus</li>
2988 <li>visual indication that web service results are still
2989 being retrieved from server</li>
2990 <li>Serialise the dialogs that are shown when Jalview
2991 starts up for first time</li>
2992 <li>Jalview user agent string for interacting with HTTP
2994 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2996 <li>Examples directory and Groovy library included in
2997 InstallAnywhere distribution</li>
2998 </ul> <em>Applet</em>
3000 <li>RNA alignment and secondary structure annotation
3001 visualization applet example</li>
3002 </ul> <em>General</em>
3004 <li>Normalise option for consensus sequence logo</li>
3005 <li>Reset button in PCA window to return dimensions to
3007 <li>Allow seqspace or Jalview variant of alignment PCA
3009 <li>PCA with either nucleic acid and protein substitution
3011 <li>Allow windows containing HTML reports to be exported
3013 <li>Interactive display and editing of RNA secondary
3014 structure contacts</li>
3015 <li>RNA Helix Alignment Colouring</li>
3016 <li>RNA base pair logo consensus</li>
3017 <li>Parse sequence associated secondary structure
3018 information in Stockholm files</li>
3019 <li>HTML Export database accessions and annotation
3020 information presented in tooltip for sequences</li>
3021 <li>Import secondary structure from LOCARNA clustalw
3022 style RNA alignment files</li>
3023 <li>import and visualise T-COFFEE quality scores for an
3025 <li>'colour by annotation' per sequence option to
3026 shade each sequence according to its associated alignment
3028 <li>New Jalview Logo</li>
3029 </ul> <em>Documentation and Development</em>
3031 <li>documentation for score matrices used in Jalview</li>
3032 <li>New Website!</li>
3034 <td><em>Application</em>
3036 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3037 wsdbfetch REST service</li>
3038 <li>Stop windows being moved outside desktop on OSX</li>
3039 <li>Filetype associations not installed for webstart
3041 <li>Jalview does not always retrieve progress of a JABAWS
3042 job execution in full once it is complete</li>
3043 <li>revise SHMR RSBS definition to ensure alignment is
3044 uploaded via ali_file parameter</li>
3045 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3046 <li>View all structures superposed fails with exception</li>
3047 <li>Jnet job queues forever if a very short sequence is
3048 submitted for prediction</li>
3049 <li>Cut and paste menu not opened when mouse clicked on
3051 <li>Putting fractional value into integer text box in
3052 alignment parameter dialog causes Jalview to hang</li>
3053 <li>Structure view highlighting doesn't work on
3055 <li>View all structures fails with exception shown in
3057 <li>Characters in filename associated with PDBEntry not
3058 escaped in a platform independent way</li>
3059 <li>Jalview desktop fails to launch with exception when
3061 <li>Tree calculation reports 'you must have 2 or more
3062 sequences selected' when selection is empty</li>
3063 <li>Jalview desktop fails to launch with jar signature
3064 failure when java web start temporary file caching is
3066 <li>DAS Sequence retrieval with range qualification
3067 results in sequence xref which includes range qualification</li>
3068 <li>Errors during processing of command line arguments
3069 cause progress bar (JAL-898) to be removed</li>
3070 <li>Replace comma for semi-colon option not disabled for
3071 DAS sources in sequence fetcher</li>
3072 <li>Cannot close news reader when JABAWS server warning
3073 dialog is shown</li>
3074 <li>Option widgets not updated to reflect user settings</li>
3075 <li>Edited sequence not submitted to web service</li>
3076 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3077 <li>InstallAnywhere installer doesn't unpack and run
3078 on OSX Mountain Lion</li>
3079 <li>Annotation panel not given a scroll bar when
3080 sequences with alignment annotation are pasted into the
3082 <li>Sequence associated annotation rows not associated
3083 when loaded from Jalview project</li>
3084 <li>Browser launch fails with NPE on java 1.7</li>
3085 <li>JABAWS alignment marked as finished when job was
3086 cancelled or job failed due to invalid input</li>
3087 <li>NPE with v2.7 example when clicking on Tree
3088 associated with all views</li>
3089 <li>Exceptions when copy/paste sequences with grouped
3090 annotation rows to new window</li>
3091 </ul> <em>Applet</em>
3093 <li>Sequence features are momentarily displayed before
3094 they are hidden using hidefeaturegroups applet parameter</li>
3095 <li>loading features via javascript API automatically
3096 enables feature display</li>
3097 <li>scrollToColumnIn javascript API method doesn't
3099 </ul> <em>General</em>
3101 <li>Redundancy removal fails for rna alignment</li>
3102 <li>PCA calculation fails when sequence has been selected
3103 and then deselected</li>
3104 <li>PCA window shows grey box when first opened on OSX</li>
3105 <li>Letters coloured pink in sequence logo when alignment
3106 coloured with clustalx</li>
3107 <li>Choosing fonts without letter symbols defined causes
3108 exceptions and redraw errors</li>
3109 <li>Initial PCA plot view is not same as manually
3110 reconfigured view</li>
3111 <li>Grouped annotation graph label has incorrect line
3113 <li>Grouped annotation graph label display is corrupted
3114 for lots of labels</li>
3119 <div align="center">
3120 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3123 <td><em>Application</em>
3125 <li>Jalview Desktop News Reader</li>
3126 <li>Tweaked default layout of web services menu</li>
3127 <li>View/alignment association menu to enable user to
3128 easily specify which alignment a multi-structure view takes
3129 its colours/correspondences from</li>
3130 <li>Allow properties file location to be specified as URL</li>
3131 <li>Extend Jalview project to preserve associations
3132 between many alignment views and a single Jmol display</li>
3133 <li>Store annotation row height in Jalview project file</li>
3134 <li>Annotation row column label formatting attributes
3135 stored in project file</li>
3136 <li>Annotation row order for auto-calculated annotation
3137 rows preserved in Jalview project file</li>
3138 <li>Visual progress indication when Jalview state is
3139 saved using Desktop window menu</li>
3140 <li>Visual indication that command line arguments are
3141 still being processed</li>
3142 <li>Groovy script execution from URL</li>
3143 <li>Colour by annotation default min and max colours in
3145 <li>Automatically associate PDB files dragged onto an
3146 alignment with sequences that have high similarity and
3148 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3149 <li>'view structures' option to open many
3150 structures in same window</li>
3151 <li>Sort associated views menu option for tree panel</li>
3152 <li>Group all JABA and non-JABA services for a particular
3153 analysis function in its own submenu</li>
3154 </ul> <em>Applet</em>
3156 <li>Userdefined and autogenerated annotation rows for
3158 <li>Adjustment of alignment annotation pane height</li>
3159 <li>Annotation scrollbar for annotation panel</li>
3160 <li>Drag to reorder annotation rows in annotation panel</li>
3161 <li>'automaticScrolling' parameter</li>
3162 <li>Allow sequences with partial ID string matches to be
3163 annotated from GFF/Jalview features files</li>
3164 <li>Sequence logo annotation row in applet</li>
3165 <li>Absolute paths relative to host server in applet
3166 parameters are treated as such</li>
3167 <li>New in the JalviewLite javascript API:
3169 <li>JalviewLite.js javascript library</li>
3170 <li>Javascript callbacks for
3172 <li>Applet initialisation</li>
3173 <li>Sequence/alignment mouse-overs and selections</li>
3176 <li>scrollTo row and column alignment scrolling
3178 <li>Select sequence/alignment regions from javascript</li>
3179 <li>javascript structure viewer harness to pass
3180 messages between Jmol and Jalview when running as
3181 distinct applets</li>
3182 <li>sortBy method</li>
3183 <li>Set of applet and application examples shipped
3184 with documentation</li>
3185 <li>New example to demonstrate JalviewLite and Jmol
3186 javascript message exchange</li>
3188 </ul> <em>General</em>
3190 <li>Enable Jmol displays to be associated with multiple
3191 multiple alignments</li>
3192 <li>Option to automatically sort alignment with new tree</li>
3193 <li>User configurable link to enable redirects to a
3194 www.Jalview.org mirror</li>
3195 <li>Jmol colours option for Jmol displays</li>
3196 <li>Configurable newline string when writing alignment
3197 and other flat files</li>
3198 <li>Allow alignment annotation description lines to
3199 contain html tags</li>
3200 </ul> <em>Documentation and Development</em>
3202 <li>Add groovy test harness for bulk load testing to
3204 <li>Groovy script to load and align a set of sequences
3205 using a web service before displaying the result in the
3206 Jalview desktop</li>
3207 <li>Restructured javascript and applet api documentation</li>
3208 <li>Ant target to publish example html files with applet
3210 <li>Netbeans project for building Jalview from source</li>
3211 <li>ant task to create online javadoc for Jalview source</li>
3213 <td><em>Application</em>
3215 <li>User defined colourscheme throws exception when
3216 current built in colourscheme is saved as new scheme</li>
3217 <li>AlignFrame->Save in application pops up save
3218 dialog for valid filename/format</li>
3219 <li>Cannot view associated structure for UniProt sequence</li>
3220 <li>PDB file association breaks for UniProt sequence
3222 <li>Associate PDB from file dialog does not tell you
3223 which sequence is to be associated with the file</li>
3224 <li>Find All raises null pointer exception when query
3225 only matches sequence IDs</li>
3226 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3227 <li>Jalview project with Jmol views created with Jalview
3228 2.4 cannot be loaded</li>
3229 <li>Filetype associations not installed for webstart
3231 <li>Two or more chains in a single PDB file associated
3232 with sequences in different alignments do not get coloured
3233 by their associated sequence</li>
3234 <li>Visibility status of autocalculated annotation row
3235 not preserved when project is loaded</li>
3236 <li>Annotation row height and visibility attributes not
3237 stored in Jalview project</li>
3238 <li>Tree bootstraps are not preserved when saved as a
3239 Jalview project</li>
3240 <li>Envision2 workflow tooltips are corrupted</li>
3241 <li>Enabling show group conservation also enables colour
3242 by conservation</li>
3243 <li>Duplicate group associated conservation or consensus
3244 created on new view</li>
3245 <li>Annotation scrollbar not displayed after 'show
3246 all hidden annotation rows' option selected</li>
3247 <li>Alignment quality not updated after alignment
3248 annotation row is hidden then shown</li>
3249 <li>Preserve colouring of structures coloured by
3250 sequences in pre Jalview 2.7 projects</li>
3251 <li>Web service job parameter dialog is not laid out
3253 <li>Web services menu not refreshed after 'reset
3254 services' button is pressed in preferences</li>
3255 <li>Annotation off by one in Jalview v2_3 example project</li>
3256 <li>Structures imported from file and saved in project
3257 get name like jalview_pdb1234.txt when reloaded</li>
3258 <li>Jalview does not always retrieve progress of a JABAWS
3259 job execution in full once it is complete</li>
3260 </ul> <em>Applet</em>
3262 <li>Alignment height set incorrectly when lots of
3263 annotation rows are displayed</li>
3264 <li>Relative URLs in feature HTML text not resolved to
3266 <li>View follows highlighting does not work for positions
3268 <li><= shown as = in tooltip</li>
3269 <li>Export features raises exception when no features
3271 <li>Separator string used for serialising lists of IDs
3272 for javascript api is modified when separator string
3273 provided as parameter</li>
3274 <li>Null pointer exception when selecting tree leaves for
3275 alignment with no existing selection</li>
3276 <li>Relative URLs for datasources assumed to be relative
3277 to applet's codebase</li>
3278 <li>Status bar not updated after finished searching and
3279 search wraps around to first result</li>
3280 <li>StructureSelectionManager instance shared between
3281 several Jalview applets causes race conditions and memory
3283 <li>Hover tooltip and mouseover of position on structure
3284 not sent from Jmol in applet</li>
3285 <li>Certain sequences of javascript method calls to
3286 applet API fatally hang browser</li>
3287 </ul> <em>General</em>
3289 <li>View follows structure mouseover scrolls beyond
3290 position with wrapped view and hidden regions</li>
3291 <li>Find sequence position moves to wrong residue
3292 with/without hidden columns</li>
3293 <li>Sequence length given in alignment properties window
3295 <li>InvalidNumberFormat exceptions thrown when trying to
3296 import PDB like structure files</li>
3297 <li>Positional search results are only highlighted
3298 between user-supplied sequence start/end bounds</li>
3299 <li>End attribute of sequence is not validated</li>
3300 <li>Find dialog only finds first sequence containing a
3301 given sequence position</li>
3302 <li>Sequence numbering not preserved in MSF alignment
3304 <li>Jalview PDB file reader does not extract sequence
3305 from nucleotide chains correctly</li>
3306 <li>Structure colours not updated when tree partition
3307 changed in alignment</li>
3308 <li>Sequence associated secondary structure not correctly
3309 parsed in interleaved stockholm</li>
3310 <li>Colour by annotation dialog does not restore current
3312 <li>Hiding (nearly) all sequences doesn't work
3314 <li>Sequences containing lowercase letters are not
3315 properly associated with their pdb files</li>
3316 </ul> <em>Documentation and Development</em>
3318 <li>schemas/JalviewWsParamSet.xsd corrupted by
3319 ApplyCopyright tool</li>
3324 <div align="center">
3325 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3328 <td><em>Application</em>
3330 <li>New warning dialog when the Jalview Desktop cannot
3331 contact web services</li>
3332 <li>JABA service parameters for a preset are shown in
3333 service job window</li>
3334 <li>JABA Service menu entries reworded</li>
3338 <li>Modeller PIR IO broken - cannot correctly import a
3339 pir file emitted by Jalview</li>
3340 <li>Existing feature settings transferred to new
3341 alignment view created from cut'n'paste</li>
3342 <li>Improved test for mixed amino/nucleotide chains when
3343 parsing PDB files</li>
3344 <li>Consensus and conservation annotation rows
3345 occasionally become blank for all new windows</li>
3346 <li>Exception raised when right clicking above sequences
3347 in wrapped view mode</li>
3348 </ul> <em>Application</em>
3350 <li>multiple multiply aligned structure views cause cpu
3351 usage to hit 100% and computer to hang</li>
3352 <li>Web Service parameter layout breaks for long user
3353 parameter names</li>
3354 <li>Jaba service discovery hangs desktop if Jaba server
3361 <div align="center">
3362 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3365 <td><em>Application</em>
3367 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3368 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3371 <li>Web Services preference tab</li>
3372 <li>Analysis parameters dialog box and user defined
3374 <li>Improved speed and layout of Envision2 service menu</li>
3375 <li>Superpose structures using associated sequence
3377 <li>Export coordinates and projection as CSV from PCA
3379 </ul> <em>Applet</em>
3381 <li>enable javascript: execution by the applet via the
3382 link out mechanism</li>
3383 </ul> <em>Other</em>
3385 <li>Updated the Jmol Jalview interface to work with Jmol
3387 <li>The Jalview Desktop and JalviewLite applet now
3388 require Java 1.5</li>
3389 <li>Allow Jalview feature colour specification for GFF
3390 sequence annotation files</li>
3391 <li>New 'colour by label' keword in Jalview feature file
3392 type colour specification</li>
3393 <li>New Jalview Desktop Groovy API method that allows a
3394 script to check if it being run in an interactive session or
3395 in a batch operation from the Jalview command line</li>
3399 <li>clustalx colourscheme colours Ds preferentially when
3400 both D+E are present in over 50% of the column</li>
3401 </ul> <em>Application</em>
3403 <li>typo in AlignmentFrame->View->Hide->all but
3404 selected Regions menu item</li>
3405 <li>sequence fetcher replaces ',' for ';' when the ',' is
3406 part of a valid accession ID</li>
3407 <li>fatal OOM if object retrieved by sequence fetcher
3408 runs out of memory</li>
3409 <li>unhandled Out of Memory Error when viewing pca
3410 analysis results</li>
3411 <li>InstallAnywhere builds fail to launch on OS X java
3412 10.5 update 4 (due to apple Java 1.6 update)</li>
3413 <li>Installanywhere Jalview silently fails to launch</li>
3414 </ul> <em>Applet</em>
3416 <li>Jalview.getFeatureGroups() raises an
3417 ArrayIndexOutOfBoundsException if no feature groups are
3424 <div align="center">
3425 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3431 <li>Alignment prettyprinter doesn't cope with long
3433 <li>clustalx colourscheme colours Ds preferentially when
3434 both D+E are present in over 50% of the column</li>
3435 <li>nucleic acid structures retrieved from PDB do not
3436 import correctly</li>
3437 <li>More columns get selected than were clicked on when a
3438 number of columns are hidden</li>
3439 <li>annotation label popup menu not providing correct
3440 add/hide/show options when rows are hidden or none are
3442 <li>Stockholm format shown in list of readable formats,
3443 and parser copes better with alignments from RFAM.</li>
3444 <li>CSV output of consensus only includes the percentage
3445 of all symbols if sequence logo display is enabled</li>
3447 </ul> <em>Applet</em>
3449 <li>annotation panel disappears when annotation is
3451 </ul> <em>Application</em>
3453 <li>Alignment view not redrawn properly when new
3454 alignment opened where annotation panel is visible but no
3455 annotations are present on alignment</li>
3456 <li>pasted region containing hidden columns is
3457 incorrectly displayed in new alignment window</li>
3458 <li>Jalview slow to complete operations when stdout is
3459 flooded (fix is to close the Jalview console)</li>
3460 <li>typo in AlignmentFrame->View->Hide->all but
3461 selected Rregions menu item.</li>
3462 <li>inconsistent group submenu and Format submenu entry
3463 'Un' or 'Non'conserved</li>
3464 <li>Sequence feature settings are being shared by
3465 multiple distinct alignments</li>
3466 <li>group annotation not recreated when tree partition is
3468 <li>double click on group annotation to select sequences
3469 does not propagate to associated trees</li>
3470 <li>Mac OSX specific issues:
3472 <li>exception raised when mouse clicked on desktop
3473 window background</li>
3474 <li>Desktop menu placed on menu bar and application
3475 name set correctly</li>
3476 <li>sequence feature settings not wide enough for the
3477 save feature colourscheme button</li>
3486 <div align="center">
3487 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3490 <td><em>New Capabilities</em>
3492 <li>URL links generated from description line for
3493 regular-expression based URL links (applet and application)
3495 <li>Non-positional feature URL links are shown in link
3497 <li>Linked viewing of nucleic acid sequences and
3499 <li>Automatic Scrolling option in View menu to display
3500 the currently highlighted region of an alignment.</li>
3501 <li>Order an alignment by sequence length, or using the
3502 average score or total feature count for each sequence.</li>
3503 <li>Shading features by score or associated description</li>
3504 <li>Subdivide alignment and groups based on identity of
3505 selected subsequence (Make Groups from Selection).</li>
3506 <li>New hide/show options including Shift+Control+H to
3507 hide everything but the currently selected region.</li>
3508 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3509 </ul> <em>Application</em>
3511 <li>Fetch DB References capabilities and UI expanded to
3512 support retrieval from DAS sequence sources</li>
3513 <li>Local DAS Sequence sources can be added via the
3514 command line or via the Add local source dialog box.</li>
3515 <li>DAS Dbref and DbxRef feature types are parsed as
3516 database references and protein_name is parsed as
3517 description line (BioSapiens terms).</li>
3518 <li>Enable or disable non-positional feature and database
3519 references in sequence ID tooltip from View menu in
3521 <!-- <li>New hidden columns and rows and representatives capabilities
3522 in annotations file (in progress - not yet fully implemented)</li> -->
3523 <li>Group-associated consensus, sequence logos and
3524 conservation plots</li>
3525 <li>Symbol distributions for each column can be exported
3526 and visualized as sequence logos</li>
3527 <li>Optionally scale multi-character column labels to fit
3528 within each column of annotation row<!-- todo for applet -->
3530 <li>Optional automatic sort of associated alignment view
3531 when a new tree is opened.</li>
3532 <li>Jalview Java Console</li>
3533 <li>Better placement of desktop window when moving
3534 between different screens.</li>
3535 <li>New preference items for sequence ID tooltip and
3536 consensus annotation</li>
3537 <li>Client to submit sequences and IDs to Envision2
3539 <li><em>Vamsas Capabilities</em>
3541 <li>Improved VAMSAS synchronization (Jalview archive
3542 used to preserve views, structures, and tree display
3544 <li>Import of vamsas documents from disk or URL via
3546 <li>Sharing of selected regions between views and
3547 with other VAMSAS applications (Experimental feature!)</li>
3548 <li>Updated API to VAMSAS version 0.2</li>
3550 </ul> <em>Applet</em>
3552 <li>Middle button resizes annotation row height</li>
3555 <li>sortByTree (true/false) - automatically sort the
3556 associated alignment view by the tree when a new tree is
3558 <li>showTreeBootstraps (true/false) - show or hide
3559 branch bootstraps (default is to show them if available)</li>
3560 <li>showTreeDistances (true/false) - show or hide
3561 branch lengths (default is to show them if available)</li>
3562 <li>showUnlinkedTreeNodes (true/false) - indicate if
3563 unassociated nodes should be highlighted in the tree
3565 <li>heightScale and widthScale (1.0 or more) -
3566 increase the height or width of a cell in the alignment
3567 grid relative to the current font size.</li>
3570 <li>Non-positional features displayed in sequence ID
3572 </ul> <em>Other</em>
3574 <li>Features format: graduated colour definitions and
3575 specification of feature scores</li>
3576 <li>Alignment Annotations format: new keywords for group
3577 associated annotation (GROUP_REF) and annotation row display
3578 properties (ROW_PROPERTIES)</li>
3579 <li>XML formats extended to support graduated feature
3580 colourschemes, group associated annotation, and profile
3581 visualization settings.</li></td>
3584 <li>Source field in GFF files parsed as feature source
3585 rather than description</li>
3586 <li>Non-positional features are now included in sequence
3587 feature and gff files (controlled via non-positional feature
3588 visibility in tooltip).</li>
3589 <li>URL links generated for all feature links (bugfix)</li>
3590 <li>Added URL embedding instructions to features file
3592 <li>Codons containing ambiguous nucleotides translated as
3593 'X' in peptide product</li>
3594 <li>Match case switch in find dialog box works for both
3595 sequence ID and sequence string and query strings do not
3596 have to be in upper case to match case-insensitively.</li>
3597 <li>AMSA files only contain first column of
3598 multi-character column annotation labels</li>
3599 <li>Jalview Annotation File generation/parsing consistent
3600 with documentation (e.g. Stockholm annotation can be
3601 exported and re-imported)</li>
3602 <li>PDB files without embedded PDB IDs given a friendly
3604 <li>Find incrementally searches ID string matches as well
3605 as subsequence matches, and correctly reports total number
3609 <li>Better handling of exceptions during sequence
3611 <li>Dasobert generated non-positional feature URL
3612 link text excludes the start_end suffix</li>
3613 <li>DAS feature and source retrieval buttons disabled
3614 when fetch or registry operations in progress.</li>
3615 <li>PDB files retrieved from URLs are cached properly</li>
3616 <li>Sequence description lines properly shared via
3618 <li>Sequence fetcher fetches multiple records for all
3620 <li>Ensured that command line das feature retrieval
3621 completes before alignment figures are generated.</li>
3622 <li>Reduced time taken when opening file browser for
3624 <li>isAligned check prior to calculating tree, PCA or
3625 submitting an MSA to JNet now excludes hidden sequences.</li>
3626 <li>User defined group colours properly recovered
3627 from Jalview projects.</li>
3636 <div align="center">
3637 <strong>2.4.0.b2</strong><br> 28/10/2009
3642 <li>Experimental support for google analytics usage
3644 <li>Jalview privacy settings (user preferences and docs).</li>
3649 <li>Race condition in applet preventing startup in
3651 <li>Exception when feature created from selection beyond
3652 length of sequence.</li>
3653 <li>Allow synthetic PDB files to be imported gracefully</li>
3654 <li>Sequence associated annotation rows associate with
3655 all sequences with a given id</li>
3656 <li>Find function matches case-insensitively for sequence
3657 ID string searches</li>
3658 <li>Non-standard characters do not cause pairwise
3659 alignment to fail with exception</li>
3660 </ul> <em>Application Issues</em>
3662 <li>Sequences are now validated against EMBL database</li>
3663 <li>Sequence fetcher fetches multiple records for all
3665 </ul> <em>InstallAnywhere Issues</em>
3667 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3668 issue with installAnywhere mechanism)</li>
3669 <li>Command line launching of JARs from InstallAnywhere
3670 version (java class versioning error fixed)</li>
3677 <div align="center">
3678 <strong>2.4</strong><br> 27/8/2008
3681 <td><em>User Interface</em>
3683 <li>Linked highlighting of codon and amino acid from
3684 translation and protein products</li>
3685 <li>Linked highlighting of structure associated with
3686 residue mapping to codon position</li>
3687 <li>Sequence Fetcher provides example accession numbers
3688 and 'clear' button</li>
3689 <li>MemoryMonitor added as an option under Desktop's
3691 <li>Extract score function to parse whitespace separated
3692 numeric data in description line</li>
3693 <li>Column labels in alignment annotation can be centred.</li>
3694 <li>Tooltip for sequence associated annotation give name
3696 </ul> <em>Web Services and URL fetching</em>
3698 <li>JPred3 web service</li>
3699 <li>Prototype sequence search client (no public services
3701 <li>Fetch either seed alignment or full alignment from
3703 <li>URL Links created for matching database cross
3704 references as well as sequence ID</li>
3705 <li>URL Links can be created using regular-expressions</li>
3706 </ul> <em>Sequence Database Connectivity</em>
3708 <li>Retrieval of cross-referenced sequences from other
3710 <li>Generalised database reference retrieval and
3711 validation to all fetchable databases</li>
3712 <li>Fetch sequences from DAS sources supporting the
3713 sequence command</li>
3714 </ul> <em>Import and Export</em>
3715 <li>export annotation rows as CSV for spreadsheet import</li>
3716 <li>Jalview projects record alignment dataset associations,
3717 EMBL products, and cDNA sequence mappings</li>
3718 <li>Sequence Group colour can be specified in Annotation
3720 <li>Ad-hoc colouring of group in Annotation File using RGB
3721 triplet as name of colourscheme</li>
3722 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3724 <li>treenode binding for VAMSAS tree exchange</li>
3725 <li>local editing and update of sequences in VAMSAS
3726 alignments (experimental)</li>
3727 <li>Create new or select existing session to join</li>
3728 <li>load and save of vamsas documents</li>
3729 </ul> <em>Application command line</em>
3731 <li>-tree parameter to open trees (introduced for passing
3733 <li>-fetchfrom command line argument to specify nicknames
3734 of DAS servers to query for alignment features</li>
3735 <li>-dasserver command line argument to add new servers
3736 that are also automatically queried for features</li>
3737 <li>-groovy command line argument executes a given groovy
3738 script after all input data has been loaded and parsed</li>
3739 </ul> <em>Applet-Application data exchange</em>
3741 <li>Trees passed as applet parameters can be passed to
3742 application (when using "View in full
3743 application")</li>
3744 </ul> <em>Applet Parameters</em>
3746 <li>feature group display control parameter</li>
3747 <li>debug parameter</li>
3748 <li>showbutton parameter</li>
3749 </ul> <em>Applet API methods</em>
3751 <li>newView public method</li>
3752 <li>Window (current view) specific get/set public methods</li>
3753 <li>Feature display control methods</li>
3754 <li>get list of currently selected sequences</li>
3755 </ul> <em>New Jalview distribution features</em>
3757 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3758 <li>RELEASE file gives build properties for the latest
3759 Jalview release.</li>
3760 <li>Java 1.1 Applet build made easier and donotobfuscate
3761 property controls execution of obfuscator</li>
3762 <li>Build target for generating source distribution</li>
3763 <li>Debug flag for javacc</li>
3764 <li>.jalview_properties file is documented (slightly) in
3765 jalview.bin.Cache</li>
3766 <li>Continuous Build Integration for stable and
3767 development version of Application, Applet and source
3772 <li>selected region output includes visible annotations
3773 (for certain formats)</li>
3774 <li>edit label/displaychar contains existing label/char
3776 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3777 <li>shorter peptide product names from EMBL records</li>
3778 <li>Newick string generator makes compact representations</li>
3779 <li>bootstrap values parsed correctly for tree files with
3781 <li>pathological filechooser bug avoided by not allowing
3782 filenames containing a ':'</li>
3783 <li>Fixed exception when parsing GFF files containing
3784 global sequence features</li>
3785 <li>Alignment datasets are finalized only when number of
3786 references from alignment sequences goes to zero</li>
3787 <li>Close of tree branch colour box without colour
3788 selection causes cascading exceptions</li>
3789 <li>occasional negative imgwidth exceptions</li>
3790 <li>better reporting of non-fatal warnings to user when
3791 file parsing fails.</li>
3792 <li>Save works when Jalview project is default format</li>
3793 <li>Save as dialog opened if current alignment format is
3794 not a valid output format</li>
3795 <li>UniProt canonical names introduced for both das and
3797 <li>Histidine should be midblue (not pink!) in Zappo</li>
3798 <li>error messages passed up and output when data read
3800 <li>edit undo recovers previous dataset sequence when
3801 sequence is edited</li>
3802 <li>allow PDB files without pdb ID HEADER lines (like
3803 those generated by MODELLER) to be read in properly</li>
3804 <li>allow reading of JPred concise files as a normal
3806 <li>Stockholm annotation parsing and alignment properties
3807 import fixed for PFAM records</li>
3808 <li>Structure view windows have correct name in Desktop
3810 <li>annotation consisting of sequence associated scores
3811 can be read and written correctly to annotation file</li>
3812 <li>Aligned cDNA translation to aligned peptide works
3814 <li>Fixed display of hidden sequence markers and
3815 non-italic font for representatives in Applet</li>
3816 <li>Applet Menus are always embedded in applet window on
3818 <li>Newly shown features appear at top of stack (in
3820 <li>Annotations added via parameter not drawn properly
3821 due to null pointer exceptions</li>
3822 <li>Secondary structure lines are drawn starting from
3823 first column of alignment</li>
3824 <li>UniProt XML import updated for new schema release in
3826 <li>Sequence feature to sequence ID match for Features
3827 file is case-insensitive</li>
3828 <li>Sequence features read from Features file appended to
3829 all sequences with matching IDs</li>
3830 <li>PDB structure coloured correctly for associated views
3831 containing a sub-sequence</li>
3832 <li>PDB files can be retrieved by applet from Jar files</li>
3833 <li>feature and annotation file applet parameters
3834 referring to different directories are retrieved correctly</li>
3835 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3836 <li>Fixed application hang whilst waiting for
3837 splash-screen version check to complete</li>
3838 <li>Applet properly URLencodes input parameter values
3839 when passing them to the launchApp service</li>
3840 <li>display name and local features preserved in results
3841 retrieved from web service</li>
3842 <li>Visual delay indication for sequence retrieval and
3843 sequence fetcher initialisation</li>
3844 <li>updated Application to use DAS 1.53e version of
3845 dasobert DAS client</li>
3846 <li>Re-instated Full AMSA support and .amsa file
3848 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3856 <div align="center">
3857 <strong>2.3</strong><br> 9/5/07
3862 <li>Jmol 11.0.2 integration</li>
3863 <li>PDB views stored in Jalview XML files</li>
3864 <li>Slide sequences</li>
3865 <li>Edit sequence in place</li>
3866 <li>EMBL CDS features</li>
3867 <li>DAS Feature mapping</li>
3868 <li>Feature ordering</li>
3869 <li>Alignment Properties</li>
3870 <li>Annotation Scores</li>
3871 <li>Sort by scores</li>
3872 <li>Feature/annotation editing in applet</li>
3877 <li>Headless state operation in 2.2.1</li>
3878 <li>Incorrect and unstable DNA pairwise alignment</li>
3879 <li>Cut and paste of sequences with annotation</li>
3880 <li>Feature group display state in XML</li>
3881 <li>Feature ordering in XML</li>
3882 <li>blc file iteration selection using filename # suffix</li>
3883 <li>Stockholm alignment properties</li>
3884 <li>Stockhom alignment secondary structure annotation</li>
3885 <li>2.2.1 applet had no feature transparency</li>
3886 <li>Number pad keys can be used in cursor mode</li>
3887 <li>Structure Viewer mirror image resolved</li>
3894 <div align="center">
3895 <strong>2.2.1</strong><br> 12/2/07
3900 <li>Non standard characters can be read and displayed
3901 <li>Annotations/Features can be imported/exported to the
3903 <li>Applet allows editing of sequence/annotation/group
3904 name & description
3905 <li>Preference setting to display sequence name in
3907 <li>Annotation file format extended to allow
3908 Sequence_groups to be defined
3909 <li>Default opening of alignment overview panel can be
3910 specified in preferences
3911 <li>PDB residue numbering annotation added to associated
3917 <li>Applet crash under certain Linux OS with Java 1.6
3919 <li>Annotation file export / import bugs fixed
3920 <li>PNG / EPS image output bugs fixed
3926 <div align="center">
3927 <strong>2.2</strong><br> 27/11/06
3932 <li>Multiple views on alignment
3933 <li>Sequence feature editing
3934 <li>"Reload" alignment
3935 <li>"Save" to current filename
3936 <li>Background dependent text colour
3937 <li>Right align sequence ids
3938 <li>User-defined lower case residue colours
3941 <li>Menu item accelerator keys
3942 <li>Control-V pastes to current alignment
3943 <li>Cancel button for DAS Feature Fetching
3944 <li>PCA and PDB Viewers zoom via mouse roller
3945 <li>User-defined sub-tree colours and sub-tree selection
3947 <li>'New Window' button on the 'Output to Text box'
3952 <li>New memory efficient Undo/Redo System
3953 <li>Optimised symbol lookups and conservation/consensus
3955 <li>Region Conservation/Consensus recalculated after
3957 <li>Fixed Remove Empty Columns Bug (empty columns at end
3959 <li>Slowed DAS Feature Fetching for increased robustness.
3961 <li>Made angle brackets in ASCII feature descriptions
3963 <li>Re-instated Zoom function for PCA
3964 <li>Sequence descriptions conserved in web service
3966 <li>UniProt ID discoverer uses any word separated by
3968 <li>WsDbFetch query/result association resolved
3969 <li>Tree leaf to sequence mapping improved
3970 <li>Smooth fonts switch moved to FontChooser dialog box.
3977 <div align="center">
3978 <strong>2.1.1</strong><br> 12/9/06
3983 <li>Copy consensus sequence to clipboard</li>
3988 <li>Image output - rightmost residues are rendered if
3989 sequence id panel has been resized</li>
3990 <li>Image output - all offscreen group boundaries are
3992 <li>Annotation files with sequence references - all
3993 elements in file are relative to sequence position</li>
3994 <li>Mac Applet users can use Alt key for group editing</li>
4000 <div align="center">
4001 <strong>2.1</strong><br> 22/8/06
4006 <li>MAFFT Multiple Alignment in default Web Service list</li>
4007 <li>DAS Feature fetching</li>
4008 <li>Hide sequences and columns</li>
4009 <li>Export Annotations and Features</li>
4010 <li>GFF file reading / writing</li>
4011 <li>Associate structures with sequences from local PDB
4013 <li>Add sequences to exisiting alignment</li>
4014 <li>Recently opened files / URL lists</li>
4015 <li>Applet can launch the full application</li>
4016 <li>Applet has transparency for features (Java 1.2
4018 <li>Applet has user defined colours parameter</li>
4019 <li>Applet can load sequences from parameter
4020 "sequence<em>x</em>"
4026 <li>Redundancy Panel reinstalled in the Applet</li>
4027 <li>Monospaced font - EPS / rescaling bug fixed</li>
4028 <li>Annotation files with sequence references bug fixed</li>
4034 <div align="center">
4035 <strong>2.08.1</strong><br> 2/5/06
4040 <li>Change case of selected region from Popup menu</li>
4041 <li>Choose to match case when searching</li>
4042 <li>Middle mouse button and mouse movement can compress /
4043 expand the visible width and height of the alignment</li>
4048 <li>Annotation Panel displays complete JNet results</li>
4054 <div align="center">
4055 <strong>2.08b</strong><br> 18/4/06
4061 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4062 <li>Righthand label on wrapped alignments shows correct
4069 <div align="center">
4070 <strong>2.08</strong><br> 10/4/06
4075 <li>Editing can be locked to the selection area</li>
4076 <li>Keyboard editing</li>
4077 <li>Create sequence features from searches</li>
4078 <li>Precalculated annotations can be loaded onto
4080 <li>Features file allows grouping of features</li>
4081 <li>Annotation Colouring scheme added</li>
4082 <li>Smooth fonts off by default - Faster rendering</li>
4083 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4088 <li>Drag & Drop fixed on Linux</li>
4089 <li>Jalview Archive file faster to load/save, sequence
4090 descriptions saved.</li>
4096 <div align="center">
4097 <strong>2.07</strong><br> 12/12/05
4102 <li>PDB Structure Viewer enhanced</li>
4103 <li>Sequence Feature retrieval and display enhanced</li>
4104 <li>Choose to output sequence start-end after sequence
4105 name for file output</li>
4106 <li>Sequence Fetcher WSDBFetch@EBI</li>
4107 <li>Applet can read feature files, PDB files and can be
4108 used for HTML form input</li>
4113 <li>HTML output writes groups and features</li>
4114 <li>Group editing is Control and mouse click</li>
4115 <li>File IO bugs</li>
4121 <div align="center">
4122 <strong>2.06</strong><br> 28/9/05
4127 <li>View annotations in wrapped mode</li>
4128 <li>More options for PCA viewer</li>
4133 <li>GUI bugs resolved</li>
4134 <li>Runs with -nodisplay from command line</li>
4140 <div align="center">
4141 <strong>2.05b</strong><br> 15/9/05
4146 <li>Choose EPS export as lineart or text</li>
4147 <li>Jar files are executable</li>
4148 <li>Can read in Uracil - maps to unknown residue</li>
4153 <li>Known OutOfMemory errors give warning message</li>
4154 <li>Overview window calculated more efficiently</li>
4155 <li>Several GUI bugs resolved</li>
4161 <div align="center">
4162 <strong>2.05</strong><br> 30/8/05
4167 <li>Edit and annotate in "Wrapped" view</li>
4172 <li>Several GUI bugs resolved</li>
4178 <div align="center">
4179 <strong>2.04</strong><br> 24/8/05
4184 <li>Hold down mouse wheel & scroll to change font
4190 <li>Improved JPred client reliability</li>
4191 <li>Improved loading of Jalview files</li>
4197 <div align="center">
4198 <strong>2.03</strong><br> 18/8/05
4203 <li>Set Proxy server name and port in preferences</li>
4204 <li>Multiple URL links from sequence ids</li>
4205 <li>User Defined Colours can have a scheme name and added
4207 <li>Choose to ignore gaps in consensus calculation</li>
4208 <li>Unix users can set default web browser</li>
4209 <li>Runs without GUI for batch processing</li>
4210 <li>Dynamically generated Web Service Menus</li>
4215 <li>InstallAnywhere download for Sparc Solaris</li>
4221 <div align="center">
4222 <strong>2.02</strong><br> 18/7/05
4228 <li>Copy & Paste order of sequences maintains
4229 alignment order.</li>
4235 <div align="center">
4236 <strong>2.01</strong><br> 12/7/05
4241 <li>Use delete key for deleting selection.</li>
4242 <li>Use Mouse wheel to scroll sequences.</li>
4243 <li>Help file updated to describe how to add alignment
4245 <li>Version and build date written to build properties
4247 <li>InstallAnywhere installation will check for updates
4248 at launch of Jalview.</li>
4253 <li>Delete gaps bug fixed.</li>
4254 <li>FileChooser sorts columns.</li>
4255 <li>Can remove groups one by one.</li>
4256 <li>Filechooser icons installed.</li>
4257 <li>Finder ignores return character when searching.
4258 Return key will initiate a search.<br>
4265 <div align="center">
4266 <strong>2.0</strong><br> 20/6/05
4271 <li>New codebase</li>