3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
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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>20/06/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
68 <!-- JAL-2620 -->Alternative genetic code tables for
69 'Translate as cDNA'</li>
71 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
72 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
75 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
76 shaded according to any associated attributes (e.g. variant
77 attributes from VCF file, or key-value pairs imported from
81 <!-- JAL-2897 -->Show synonymous codon variants on peptide
85 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
89 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
90 algorithm (Z-sort/transparency and filter aware)
93 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
99 <!-- JAL-3141 -->Backup files created when saving Jalview project
102 <li><strong>Principal Components Analysis Viewer</strong>
105 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
106 and Viewer state saved in Jalview Project
108 <li>'Change parameters' option removed from viewer's
111 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
115 <!-- JAL-2965 -->PCA plot is depth cued
120 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
122 <li><strong>Speed and Efficiency</strong>
125 <!-- JAL-3198 -->More efficient creation of selections and
126 multiple groups when working with large alignments
129 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
133 <li><strong>User Interface</strong>
136 <!-- JAL-2933 -->Finder panel remembers last position in each
140 <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
141 what is shown)<br />Only visible region of alignment is shown by
142 default (can be changed in user preferences)
145 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
146 to the Overwrite Dialog
149 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
153 <!-- JAL-1244 -->Status bar shows bounds when dragging a
154 selection region, and gap count when inserting or deleting gaps
157 <!-- JAL-3132 -->Status bar updates over sequence and annotation
161 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
165 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
169 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
172 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
176 <!-- JAL-3181 -->Consistent ordering of links in sequence id
180 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
182 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
186 <li><strong>Java 11 Support</strong>
189 <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
190 and getdown release channels
193 <!-- -->OSX GUI integrations for App menu's 'About' entry and
198 <em>Deprecations</em>
201 <!-- JAL-3035 -->DAS sequence retrieval and annotation
202 capabilities removed from the Jalview Desktop
205 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
206 unmarshalling has been replaced by JAXB for Jalview projects
207 and XML based data retrieval clients</li>
208 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
209 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
210 </ul> <em>Documentation</em>
213 <!-- JAL-3003 -->Added remarks about transparent rendering effects
214 not supported in EPS figure export
216 </ul> <em>Development and Release Processes</em>
219 <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
220 Installers built with Install4j (licensed to the Jalview open
221 source project) rather than InstallAnywhere
224 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
225 settings, receive over the air updates and launch specific
226 versions via (<a href="https://github.com/threerings/getdown">Three
230 <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
233 <!-- JAL-3225 -->Eclipse project configuration managed with
237 Atlassian Bamboo continuous integration for
238 unattended Test Suite execution</li>
240 <!-- JAL-2864 -->Memory test suite to detect leaks in common
243 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
244 implementation that alows updates) used for Sequence Feature collections</li>
245 <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
248 <td align="left" valign="top">
251 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
253 <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
255 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
256 structures for sequences with lots of PDB structures
259 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
261 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
262 Jalview project involving multiple views</li>
264 <!-- JAL-3164 -->Overview for complementary view in a linked
265 CDS/Protein alignment is not updated when Hide Columns by
266 Annotation dialog hides columns</li>
268 <!-- JAL-3158 -->Selection highlighting in the complement of
269 a CDS/Protein alignment stops working after making a
270 selection in one view, then making another selection in the
273 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
275 <!-- JAL-3154 -->Table Columns could be re-ordered in
276 Feature Settings and Jalview Preferences panels</li>
278 <!-- JAL-2865 -->Jalview hangs when closing windows
279 or the overview updates with large alignments</li>
281 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
282 region if columns were selected by dragging right-to-left
283 and the mouse moved to the left of the first column</li>
285 <!-- JAL-3218 -->Couldn't hide selected columns adjacent
286 to a hidden column marker via scale popup menu</li>
288 <!-- JAL-2846 -->Error message for trying to load in invalid
289 URLs doesn't tell users the invalid URL</li>
291 <!-- JAL-3178 -->Nonpositional features lose feature group
292 on export as Jalview features file</li>
294 <!-- JAL-2060 -->'Graduated colour' option not offered for
295 manually created features (where if feature score is Float.NaN)
298 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
299 printed when columns are hidden</li>
301 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
303 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
304 dragging out of Scale or Annotation Panel</li>
306 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
308 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
310 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
312 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
314 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
316 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
318 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
319 opening an alignment</li>
321 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
323 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
324 different groups in the alignment are selected</li>
326 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
328 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
330 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
332 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
334 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
336 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
338 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
340 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
342 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
344 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
346 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
348 <!-- JAL-914 -->Help page can be opened twice</li>
353 <!-- JAL-2822 -->Start and End should be updated when
354 sequence data at beginning or end of alignment added/removed
355 via 'Edit' sequence</li>
357 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't relocate
358 sequence features correctly when start of sequence is
359 removed (Known defect since 2.10)</li>
360 </ul><em>New Known Defects</em>
363 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
365 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
367 <!-- JAL-3240 -->Display is incorrect after removing gapped
368 columns within hidden columns
371 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
372 window after dragging left to select columns to left of visible
379 <td width="60" nowrap>
381 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
384 <td><div align="left">
388 <!-- JAL-3101 -->Default memory for Jalview webstart and
389 InstallAnywhere increased to 1G.
392 <!-- JAL-247 -->Hidden sequence markers and representative
393 sequence bolding included when exporting alignment as EPS,
394 SVG, PNG or HTML. <em>Display is configured via the
395 Format menu, or for command-line use via a jalview
396 properties file.</em>
399 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
400 API and sequence data now imported as JSON.
403 <!-- JAL-3065 -->Change in recommended way of starting
404 Jalview via a Java command line: add jars in lib directory
405 to CLASSPATH, rather than via the deprecated java.ext.dirs
412 <!-- JAL-3047 -->Support added to execute test suite
413 instrumented with <a href="http://openclover.org/">Open
418 <td><div align="left">
422 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
423 row shown in Feredoxin Structure alignment view of example
427 <!-- JAL-2854 -->Annotation obscures sequences if lots of
428 annotation displayed.
431 <!-- JAL-3107 -->Group conservation/consensus not shown
432 for newly created group when 'Apply to all groups'
436 <!-- JAL-3087 -->Corrupted display when switching to
437 wrapped mode when sequence panel's vertical scrollbar is
441 <!-- JAL-3003 -->Alignment is black in exported EPS file
442 when sequences are selected in exported view.</em>
445 <!-- JAL-3059 -->Groups with different coloured borders
446 aren't rendered with correct colour.
449 <!-- JAL-3092 -->Jalview could hang when importing certain
450 types of knotted RNA secondary structure.
453 <!-- JAL-3095 -->Sequence highlight and selection in
454 trimmed VARNA 2D structure is incorrect for sequences that
458 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
459 annotation when columns are inserted into an alignment,
460 and when exporting as Stockholm flatfile.
463 <!-- JAL-3053 -->Jalview annotation rows containing upper
464 and lower-case 'E' and 'H' do not automatically get
465 treated as RNA secondary structure.
468 <!-- JAL-3106 -->.jvp should be used as default extension
469 (not .jar) when saving a jalview project file.
472 <!-- JAL-3105 -->Mac Users: closing a window correctly
473 transfers focus to previous window on OSX
476 <em>Java 10 Issues Resolved</em>
479 <!-- JAL-2988 -->OSX - Can't save new files via the File
480 or export menus by typing in a name into the Save dialog
484 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
485 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
486 'look and feel' which has improved compatibility with the
487 latest version of OSX.
494 <td width="60" nowrap>
496 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
497 <em>7/06/2018</em></strong>
500 <td><div align="left">
504 <!-- JAL-2920 -->Use HGVS nomenclature for variant
505 annotation retrieved from Uniprot
508 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
509 onto the Jalview Desktop
513 <td><div align="left">
517 <!-- JAL-3017 -->Cannot import features with multiple
518 variant elements (blocks import of some Uniprot records)
521 <!-- JAL-2997 -->Clustal files with sequence positions in
522 right-hand column parsed correctly
525 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
526 not alignment area in exported graphic
529 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
530 window has input focus
533 <!-- JAL-2992 -->Annotation panel set too high when
534 annotation added to view (Windows)
537 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
538 network connectivity is poor
541 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
542 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
543 the currently open URL and links from a page viewed in
544 Firefox or Chrome on Windows is now fully supported. If
545 you are using Edge, only links in the page can be
546 dragged, and with Internet Explorer, only the currently
547 open URL in the browser can be dropped onto Jalview.</em>
553 <td width="60" nowrap>
555 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
558 <td><div align="left">
562 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
563 for disabling automatic superposition of multiple
564 structures and open structures in existing views
567 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
568 ID and annotation area margins can be click-dragged to
572 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
576 <!-- JAL-2759 -->Improved performance for large alignments
577 and lots of hidden columns
580 <!-- JAL-2593 -->Improved performance when rendering lots
581 of features (particularly when transparency is disabled)
584 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
585 exchange of Jalview features and Chimera attributes made
591 <td><div align="left">
594 <!-- JAL-2899 -->Structure and Overview aren't updated
595 when Colour By Annotation threshold slider is adjusted
598 <!-- JAL-2778 -->Slow redraw when Overview panel shown
599 overlapping alignment panel
602 <!-- JAL-2929 -->Overview doesn't show end of unpadded
606 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
607 improved: CDS not handled correctly if transcript has no
611 <!-- JAL-2321 -->Secondary structure and temperature
612 factor annotation not added to sequence when local PDB
613 file associated with it by drag'n'drop or structure
617 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
618 dialog doesn't import PDB files dropped on an alignment
621 <!-- JAL-2666 -->Linked scrolling via protein horizontal
622 scroll bar doesn't work for some CDS/Protein views
625 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
626 Java 1.8u153 onwards and Java 1.9u4+.
629 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
630 columns in annotation row
633 <!-- JAL-2913 -->Preferences panel's ID Width control is not
634 honored in batch mode
637 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
638 for structures added to existing Jmol view
641 <!-- JAL-2223 -->'View Mappings' includes duplicate
642 entries after importing project with multiple views
645 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
646 protein sequences via SIFTS from associated PDB entries
647 with negative residue numbers or missing residues fails
650 <!-- JAL-2952 -->Exception when shading sequence with negative
651 Temperature Factor values from annotated PDB files (e.g.
652 as generated by CONSURF)
655 <!-- JAL-2920 -->Uniprot 'sequence variant' features
656 tooltip doesn't include a text description of mutation
659 <!-- JAL-2922 -->Invert displayed features very slow when
660 structure and/or overview windows are also shown
663 <!-- JAL-2954 -->Selecting columns from highlighted regions
664 very slow for alignments with large numbers of sequences
667 <!-- JAL-2925 -->Copy Consensus fails for group consensus
668 with 'StringIndexOutOfBounds'
671 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
672 platforms running Java 10
675 <!-- JAL-2960 -->Adding a structure to existing structure
676 view appears to do nothing because the view is hidden behind the alignment view
682 <!-- JAL-2926 -->Copy consensus sequence option in applet
683 should copy the group consensus when popup is opened on it
689 <!-- JAL-2913 -->Fixed ID width preference is not respected
692 <em>New Known Defects</em>
695 <!-- JAL-2973 --> Exceptions occasionally raised when
696 editing a large alignment and overview is displayed
699 <!-- JAL-2974 -->'Overview updating' progress bar is shown
700 repeatedly after a series of edits even when the overview
701 is no longer reflecting updates
704 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
705 structures for protein subsequence (if 'Trim Retrieved
706 Sequences' enabled) or Ensembl isoforms (Workaround in
707 2.10.4 is to fail back to N&W mapping)
714 <td width="60" nowrap>
716 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
719 <td><div align="left">
720 <ul><li>Updated Certum Codesigning Certificate
721 (Valid till 30th November 2018)</li></ul></div></td>
722 <td><div align="left">
725 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
726 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
727 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
728 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
729 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
730 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
731 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
737 <td width="60" nowrap>
739 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
742 <td><div align="left">
746 <!-- JAL-2446 -->Faster and more efficient management and
747 rendering of sequence features
750 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
751 429 rate limit request hander
754 <!-- JAL-2773 -->Structure views don't get updated unless
755 their colours have changed
758 <!-- JAL-2495 -->All linked sequences are highlighted for
759 a structure mousover (Jmol) or selection (Chimera)
762 <!-- JAL-2790 -->'Cancel' button in progress bar for
763 JABAWS AACon, RNAAliFold and Disorder prediction jobs
766 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
767 view from Ensembl locus cross-references
770 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
774 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
775 feature can be disabled
778 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
779 PDB easier retrieval of sequences for lists of IDs
782 <!-- JAL-2758 -->Short names for sequences retrieved from
788 <li>Groovy interpreter updated to 2.4.12</li>
789 <li>Example groovy script for generating a matrix of
790 percent identity scores for current alignment.</li>
792 <em>Testing and Deployment</em>
795 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
799 <td><div align="left">
803 <!-- JAL-2643 -->Pressing tab after updating the colour
804 threshold text field doesn't trigger an update to the
808 <!-- JAL-2682 -->Race condition when parsing sequence ID
812 <!-- JAL-2608 -->Overview windows are also closed when
813 alignment window is closed
816 <!-- JAL-2548 -->Export of features doesn't always respect
820 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
821 takes a long time in Cursor mode
827 <!-- JAL-2777 -->Structures with whitespace chainCode
828 cannot be viewed in Chimera
831 <!-- JAL-2728 -->Protein annotation panel too high in
835 <!-- JAL-2757 -->Can't edit the query after the server
836 error warning icon is shown in Uniprot and PDB Free Text
840 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
843 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
846 <!-- JAL-2739 -->Hidden column marker in last column not
847 rendered when switching back from Wrapped to normal view
850 <!-- JAL-2768 -->Annotation display corrupted when
851 scrolling right in unwapped alignment view
854 <!-- JAL-2542 -->Existing features on subsequence
855 incorrectly relocated when full sequence retrieved from
859 <!-- JAL-2733 -->Last reported memory still shown when
860 Desktop->Show Memory is unticked (OSX only)
863 <!-- JAL-2658 -->Amend Features dialog doesn't allow
864 features of same type and group to be selected for
868 <!-- JAL-2524 -->Jalview becomes sluggish in wide
869 alignments when hidden columns are present
872 <!-- JAL-2392 -->Jalview freezes when loading and
873 displaying several structures
876 <!-- JAL-2732 -->Black outlines left after resizing or
880 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
881 within the Jalview desktop on OSX
884 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
885 when in wrapped alignment mode
888 <!-- JAL-2636 -->Scale mark not shown when close to right
889 hand end of alignment
892 <!-- JAL-2684 -->Pairwise alignment of selected regions of
893 each selected sequence do not have correct start/end
897 <!-- JAL-2793 -->Alignment ruler height set incorrectly
898 after canceling the Alignment Window's Font dialog
901 <!-- JAL-2036 -->Show cross-references not enabled after
902 restoring project until a new view is created
905 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
906 URL links appears when only default EMBL-EBI link is
907 configured (since 2.10.2b2)
910 <!-- JAL-2775 -->Overview redraws whole window when box
914 <!-- JAL-2225 -->Structure viewer doesn't map all chains
915 in a multi-chain structure when viewing alignment
916 involving more than one chain (since 2.10)
919 <!-- JAL-2811 -->Double residue highlights in cursor mode
920 if new selection moves alignment window
923 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
924 arrow key in cursor mode to pass hidden column marker
927 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
928 that produces correctly annotated transcripts and products
931 <!-- JAL-2776 -->Toggling a feature group after first time
932 doesn't update associated structure view
935 <em>Applet</em><br />
938 <!-- JAL-2687 -->Concurrent modification exception when
939 closing alignment panel
942 <em>BioJSON</em><br />
945 <!-- JAL-2546 -->BioJSON export does not preserve
946 non-positional features
949 <em>New Known Issues</em>
952 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
953 sequence features correctly (for many previous versions of
957 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
958 using cursor in wrapped panel other than top
961 <!-- JAL-2791 -->Select columns containing feature ignores
962 graduated colour threshold
965 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
966 always preserve numbering and sequence features
969 <em>Known Java 9 Issues</em>
972 <!-- JAL-2902 -->Groovy Console very slow to open and is
973 not responsive when entering characters (Webstart, Java
980 <td width="60" nowrap>
982 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
983 <em>2/10/2017</em></strong>
986 <td><div align="left">
987 <em>New features in Jalview Desktop</em>
990 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
992 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
996 <td><div align="left">
1000 <td width="60" nowrap>
1001 <div align="center">
1002 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1003 <em>7/9/2017</em></strong>
1006 <td><div align="left">
1010 <!-- JAL-2588 -->Show gaps in overview window by colouring
1011 in grey (sequences used to be coloured grey, and gaps were
1015 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1019 <!-- JAL-2587 -->Overview updates immediately on increase
1020 in size and progress bar shown as higher resolution
1021 overview is recalculated
1026 <td><div align="left">
1030 <!-- JAL-2664 -->Overview window redraws every hidden
1031 column region row by row
1034 <!-- JAL-2681 -->duplicate protein sequences shown after
1035 retrieving Ensembl crossrefs for sequences from Uniprot
1038 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1039 format setting is unticked
1042 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1043 if group has show boxes format setting unticked
1046 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1047 autoscrolling whilst dragging current selection group to
1048 include sequences and columns not currently displayed
1051 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1052 assemblies are imported via CIF file
1055 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1056 displayed when threshold or conservation colouring is also
1060 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1064 <!-- JAL-2673 -->Jalview continues to scroll after
1065 dragging a selected region off the visible region of the
1069 <!-- JAL-2724 -->Cannot apply annotation based
1070 colourscheme to all groups in a view
1073 <!-- JAL-2511 -->IDs don't line up with sequences
1074 initially after font size change using the Font chooser or
1081 <td width="60" nowrap>
1082 <div align="center">
1083 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1086 <td><div align="left">
1087 <em>Calculations</em>
1091 <!-- JAL-1933 -->Occupancy annotation row shows number of
1092 ungapped positions in each column of the alignment.
1095 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1096 a calculation dialog box
1099 <!-- JAL-2379 -->Revised implementation of PCA for speed
1100 and memory efficiency (~30x faster)
1103 <!-- JAL-2403 -->Revised implementation of sequence
1104 similarity scores as used by Tree, PCA, Shading Consensus
1105 and other calculations
1108 <!-- JAL-2416 -->Score matrices are stored as resource
1109 files within the Jalview codebase
1112 <!-- JAL-2500 -->Trees computed on Sequence Feature
1113 Similarity may have different topology due to increased
1120 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1121 model for alignments and groups
1124 <!-- JAL-384 -->Custom shading schemes created via groovy
1131 <!-- JAL-2526 -->Efficiency improvements for interacting
1132 with alignment and overview windows
1135 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1139 <!-- JAL-2388 -->Hidden columns and sequences can be
1143 <!-- JAL-2611 -->Click-drag in visible area allows fine
1144 adjustment of visible position
1148 <em>Data import/export</em>
1151 <!-- JAL-2535 -->Posterior probability annotation from
1152 Stockholm files imported as sequence associated annotation
1155 <!-- JAL-2507 -->More robust per-sequence positional
1156 annotation input/output via stockholm flatfile
1159 <!-- JAL-2533 -->Sequence names don't include file
1160 extension when importing structure files without embedded
1161 names or PDB accessions
1164 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1165 format sequence substitution matrices
1168 <em>User Interface</em>
1171 <!-- JAL-2447 --> Experimental Features Checkbox in
1172 Desktop's Tools menu to hide or show untested features in
1176 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1177 via Overview or sequence motif search operations
1180 <!-- JAL-2547 -->Amend sequence features dialog box can be
1181 opened by double clicking gaps within sequence feature
1185 <!-- JAL-1476 -->Status bar message shown when not enough
1186 aligned positions were available to create a 3D structure
1190 <em>3D Structure</em>
1193 <!-- JAL-2430 -->Hidden regions in alignment views are not
1194 coloured in linked structure views
1197 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1198 file-based command exchange
1201 <!-- JAL-2375 -->Structure chooser automatically shows
1202 Cached Structures rather than querying the PDBe if
1203 structures are already available for sequences
1206 <!-- JAL-2520 -->Structures imported via URL are cached in
1207 the Jalview project rather than downloaded again when the
1208 project is reopened.
1211 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1212 to transfer Chimera's structure attributes as Jalview
1213 features, and vice-versa (<strong>Experimental
1217 <em>Web Services</em>
1220 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1223 <!-- JAL-2335 -->Filter non-standard amino acids and
1224 nucleotides when submitting to AACon and other MSA
1228 <!-- JAL-2316, -->URLs for viewing database
1229 cross-references provided by identifiers.org and the
1230 EMBL-EBI's MIRIAM DB
1237 <!-- JAL-2344 -->FileFormatI interface for describing and
1238 identifying file formats (instead of String constants)
1241 <!-- JAL-2228 -->FeatureCounter script refactored for
1242 efficiency when counting all displayed features (not
1243 backwards compatible with 2.10.1)
1246 <em>Example files</em>
1249 <!-- JAL-2631 -->Graduated feature colour style example
1250 included in the example feature file
1253 <em>Documentation</em>
1256 <!-- JAL-2339 -->Release notes reformatted for readability
1257 with the built-in Java help viewer
1260 <!-- JAL-1644 -->Find documentation updated with 'search
1261 sequence description' option
1267 <!-- JAL-2485, -->External service integration tests for
1268 Uniprot REST Free Text Search Client
1271 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1274 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1279 <td><div align="left">
1280 <em>Calculations</em>
1283 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1284 matrix - C->R should be '-3'<br />Old matrix restored
1285 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1287 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1288 Jalview's treatment of gaps in PCA and substitution matrix
1289 based Tree calculations.<br /> <br />In earlier versions
1290 of Jalview, gaps matching gaps were penalised, and gaps
1291 matching non-gaps penalised even more. In the PCA
1292 calculation, gaps were actually treated as non-gaps - so
1293 different costs were applied, which meant Jalview's PCAs
1294 were different to those produced by SeqSpace.<br />Jalview
1295 now treats gaps in the same way as SeqSpace (ie it scores
1296 them as 0). <br /> <br />Enter the following in the
1297 Groovy console to restore pre-2.10.2 behaviour:<br />
1298 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1299 // for 2.10.1 mode <br />
1300 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1301 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1302 these settings will affect all subsequent tree and PCA
1303 calculations (not recommended)</em></li>
1305 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1306 scaling of branch lengths for trees computed using
1307 Sequence Feature Similarity.
1310 <!-- JAL-2377 -->PCA calculation could hang when
1311 generating output report when working with highly
1312 redundant alignments
1315 <!-- JAL-2544 --> Sort by features includes features to
1316 right of selected region when gaps present on right-hand
1320 <em>User Interface</em>
1323 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1324 doesn't reselect a specific sequence's associated
1325 annotation after it was used for colouring a view
1328 <!-- JAL-2419 -->Current selection lost if popup menu
1329 opened on a region of alignment without groups
1332 <!-- JAL-2374 -->Popup menu not always shown for regions
1333 of an alignment with overlapping groups
1336 <!-- JAL-2310 -->Finder double counts if both a sequence's
1337 name and description match
1340 <!-- JAL-2370 -->Hiding column selection containing two
1341 hidden regions results in incorrect hidden regions
1344 <!-- JAL-2386 -->'Apply to all groups' setting when
1345 changing colour does not apply Conservation slider value
1349 <!-- JAL-2373 -->Percentage identity and conservation menu
1350 items do not show a tick or allow shading to be disabled
1353 <!-- JAL-2385 -->Conservation shading or PID threshold
1354 lost when base colourscheme changed if slider not visible
1357 <!-- JAL-2547 -->Sequence features shown in tooltip for
1358 gaps before start of features
1361 <!-- JAL-2623 -->Graduated feature colour threshold not
1362 restored to UI when feature colour is edited
1365 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1366 a time when scrolling vertically in wrapped mode.
1369 <!-- JAL-2630 -->Structure and alignment overview update
1370 as graduate feature colour settings are modified via the
1374 <!-- JAL-2034 -->Overview window doesn't always update
1375 when a group defined on the alignment is resized
1378 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1379 wrapped view result in positional status updates
1383 <!-- JAL-2563 -->Status bar doesn't show position for
1384 ambiguous amino acid and nucleotide symbols
1387 <!-- JAL-2602 -->Copy consensus sequence failed if
1388 alignment included gapped columns
1391 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1392 widgets don't permanently disappear
1395 <!-- JAL-2503 -->Cannot select or filter quantitative
1396 annotation that are shown only as column labels (e.g.
1397 T-Coffee column reliability scores)
1400 <!-- JAL-2594 -->Exception thrown if trying to create a
1401 sequence feature on gaps only
1404 <!-- JAL-2504 -->Features created with 'New feature'
1405 button from a Find inherit previously defined feature type
1406 rather than the Find query string
1409 <!-- JAL-2423 -->incorrect title in output window when
1410 exporting tree calculated in Jalview
1413 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1414 and then revealing them reorders sequences on the
1418 <!-- JAL-964 -->Group panel in sequence feature settings
1419 doesn't update to reflect available set of groups after
1420 interactively adding or modifying features
1423 <!-- JAL-2225 -->Sequence Database chooser unusable on
1427 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1428 only excluded gaps in current sequence and ignored
1435 <!-- JAL-2421 -->Overview window visible region moves
1436 erratically when hidden rows or columns are present
1439 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1440 Structure Viewer's colour menu don't correspond to
1444 <!-- JAL-2405 -->Protein specific colours only offered in
1445 colour and group colour menu for protein alignments
1448 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1449 reflect currently selected view or group's shading
1453 <!-- JAL-2624 -->Feature colour thresholds not respected
1454 when rendered on overview and structures when opacity at
1458 <!-- JAL-2589 -->User defined gap colour not shown in
1459 overview when features overlaid on alignment
1462 <em>Data import/export</em>
1465 <!-- JAL-2576 -->Very large alignments take a long time to
1469 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1470 added after a sequence was imported are not written to
1474 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1475 when importing RNA secondary structure via Stockholm
1478 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1479 not shown in correct direction for simple pseudoknots
1482 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1483 with lightGray or darkGray via features file (but can
1487 <!-- JAL-2383 -->Above PID colour threshold not recovered
1488 when alignment view imported from project
1491 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1492 structure and sequences extracted from structure files
1493 imported via URL and viewed in Jmol
1496 <!-- JAL-2520 -->Structures loaded via URL are saved in
1497 Jalview Projects rather than fetched via URL again when
1498 the project is loaded and the structure viewed
1501 <em>Web Services</em>
1504 <!-- JAL-2519 -->EnsemblGenomes example failing after
1505 release of Ensembl v.88
1508 <!-- JAL-2366 -->Proxy server address and port always
1509 appear enabled in Preferences->Connections
1512 <!-- JAL-2461 -->DAS registry not found exceptions
1513 removed from console output
1516 <!-- JAL-2582 -->Cannot retrieve protein products from
1517 Ensembl by Peptide ID
1520 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1521 created from SIFTs, and spurious 'Couldn't open structure
1522 in Chimera' errors raised after April 2017 update (problem
1523 due to 'null' string rather than empty string used for
1524 residues with no corresponding PDB mapping).
1527 <em>Application UI</em>
1530 <!-- JAL-2361 -->User Defined Colours not added to Colour
1534 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1535 case' residues (button in colourscheme editor debugged and
1536 new documentation and tooltips added)
1539 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1540 doesn't restore group-specific text colour thresholds
1543 <!-- JAL-2243 -->Feature settings panel does not update as
1544 new features are added to alignment
1547 <!-- JAL-2532 -->Cancel in feature settings reverts
1548 changes to feature colours via the Amend features dialog
1551 <!-- JAL-2506 -->Null pointer exception when attempting to
1552 edit graduated feature colour via amend features dialog
1556 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1557 selection menu changes colours of alignment views
1560 <!-- JAL-2426 -->Spurious exceptions in console raised
1561 from alignment calculation workers after alignment has
1565 <!-- JAL-1608 -->Typo in selection popup menu - Create
1566 groups now 'Create Group'
1569 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1570 Create/Undefine group doesn't always work
1573 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1574 shown again after pressing 'Cancel'
1577 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1578 adjusts start position in wrap mode
1581 <!-- JAL-2563 -->Status bar doesn't show positions for
1582 ambiguous amino acids
1585 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1586 CDS/Protein view after CDS sequences added for aligned
1590 <!-- JAL-2592 -->User defined colourschemes called 'User
1591 Defined' don't appear in Colours menu
1597 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1598 score models doesn't always result in an updated PCA plot
1601 <!-- JAL-2442 -->Features not rendered as transparent on
1602 overview or linked structure view
1605 <!-- JAL-2372 -->Colour group by conservation doesn't
1609 <!-- JAL-2517 -->Hitting Cancel after applying
1610 user-defined colourscheme doesn't restore original
1617 <!-- JAL-2314 -->Unit test failure:
1618 jalview.ws.jabaws.RNAStructExportImport setup fails
1621 <!-- JAL-2307 -->Unit test failure:
1622 jalview.ws.sifts.SiftsClientTest due to compatibility
1623 problems with deep array comparison equality asserts in
1624 successive versions of TestNG
1627 <!-- JAL-2479 -->Relocated StructureChooserTest and
1628 ParameterUtilsTest Unit tests to Network suite
1631 <em>New Known Issues</em>
1634 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1635 phase after a sequence motif find operation
1638 <!-- JAL-2550 -->Importing annotation file with rows
1639 containing just upper and lower case letters are
1640 interpreted as WUSS RNA secondary structure symbols
1643 <!-- JAL-2590 -->Cannot load and display Newick trees
1644 reliably from eggnog Ortholog database
1647 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1648 containing features of type Highlight' when 'B' is pressed
1649 to mark columns containing highlighted regions.
1652 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1653 doesn't always add secondary structure annotation.
1658 <td width="60" nowrap>
1659 <div align="center">
1660 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1663 <td><div align="left">
1667 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1668 for all consensus calculations
1671 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1674 <li>Updated Jalview's Certum code signing certificate
1677 <em>Application</em>
1680 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1681 set of database cross-references, sorted alphabetically
1684 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1685 from database cross references. Users with custom links
1686 will receive a <a href="webServices/urllinks.html#warning">warning
1687 dialog</a> asking them to update their preferences.
1690 <!-- JAL-2287-->Cancel button and escape listener on
1691 dialog warning user about disconnecting Jalview from a
1695 <!-- JAL-2320-->Jalview's Chimera control window closes if
1696 the Chimera it is connected to is shut down
1699 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1700 columns menu item to mark columns containing highlighted
1701 regions (e.g. from structure selections or results of a
1705 <!-- JAL-2284-->Command line option for batch-generation
1706 of HTML pages rendering alignment data with the BioJS
1716 <!-- JAL-2286 -->Columns with more than one modal residue
1717 are not coloured or thresholded according to percent
1718 identity (first observed in Jalview 2.8.2)
1721 <!-- JAL-2301 -->Threonine incorrectly reported as not
1725 <!-- JAL-2318 -->Updates to documentation pages (above PID
1726 threshold, amino acid properties)
1729 <!-- JAL-2292 -->Lower case residues in sequences are not
1730 reported as mapped to residues in a structure file in the
1734 <!--JAL-2324 -->Identical features with non-numeric scores
1735 could be added multiple times to a sequence
1738 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1739 bond features shown as two highlighted residues rather
1740 than a range in linked structure views, and treated
1741 correctly when selecting and computing trees from features
1744 <!-- JAL-2281-->Custom URL links for database
1745 cross-references are matched to database name regardless
1750 <em>Application</em>
1753 <!-- JAL-2282-->Custom URL links for specific database
1754 names without regular expressions also offer links from
1758 <!-- JAL-2315-->Removing a single configured link in the
1759 URL links pane in Connections preferences doesn't actually
1760 update Jalview configuration
1763 <!-- JAL-2272-->CTRL-Click on a selected region to open
1764 the alignment area popup menu doesn't work on El-Capitan
1767 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1768 files with similarly named sequences if dropped onto the
1772 <!-- JAL-2312 -->Additional mappings are shown for PDB
1773 entries where more chains exist in the PDB accession than
1774 are reported in the SIFTS file
1777 <!-- JAL-2317-->Certain structures do not get mapped to
1778 the structure view when displayed with Chimera
1781 <!-- JAL-2317-->No chains shown in the Chimera view
1782 panel's View->Show Chains submenu
1785 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1786 work for wrapped alignment views
1789 <!--JAL-2197 -->Rename UI components for running JPred
1790 predictions from 'JNet' to 'JPred'
1793 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1794 corrupted when annotation panel vertical scroll is not at
1795 first annotation row
1798 <!--JAL-2332 -->Attempting to view structure for Hen
1799 lysozyme results in a PDB Client error dialog box
1802 <!-- JAL-2319 -->Structure View's mapping report switched
1803 ranges for PDB and sequence for SIFTS
1806 SIFTS 'Not_Observed' residues mapped to non-existant
1810 <!-- <em>New Known Issues</em>
1817 <td width="60" nowrap>
1818 <div align="center">
1819 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1820 <em>25/10/2016</em></strong>
1823 <td><em>Application</em>
1825 <li>3D Structure chooser opens with 'Cached structures'
1826 view if structures already loaded</li>
1827 <li>Progress bar reports models as they are loaded to
1828 structure views</li>
1834 <li>Colour by conservation always enabled and no tick
1835 shown in menu when BLOSUM or PID shading applied</li>
1836 <li>FER1_ARATH and FER2_ARATH labels were switched in
1837 example sequences/projects/trees</li>
1839 <em>Application</em>
1841 <li>Jalview projects with views of local PDB structure
1842 files saved on Windows cannot be opened on OSX</li>
1843 <li>Multiple structure views can be opened and superposed
1844 without timeout for structures with multiple models or
1845 multiple sequences in alignment</li>
1846 <li>Cannot import or associated local PDB files without a
1847 PDB ID HEADER line</li>
1848 <li>RMSD is not output in Jmol console when superposition
1850 <li>Drag and drop of URL from Browser fails for Linux and
1851 OSX versions earlier than El Capitan</li>
1852 <li>ENA client ignores invalid content from ENA server</li>
1853 <li>Exceptions are not raised in console when ENA client
1854 attempts to fetch non-existent IDs via Fetch DB Refs UI
1856 <li>Exceptions are not raised in console when a new view
1857 is created on the alignment</li>
1858 <li>OSX right-click fixed for group selections: CMD-click
1859 to insert/remove gaps in groups and CTRL-click to open group
1862 <em>Build and deployment</em>
1864 <li>URL link checker now copes with multi-line anchor
1867 <em>New Known Issues</em>
1869 <li>Drag and drop from URL links in browsers do not work
1876 <td width="60" nowrap>
1877 <div align="center">
1878 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1881 <td><em>General</em>
1884 <!-- JAL-2124 -->Updated Spanish translations.
1887 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1888 for importing structure data to Jalview. Enables mmCIF and
1892 <!-- JAL-192 --->Alignment ruler shows positions relative to
1896 <!-- JAL-2202 -->Position/residue shown in status bar when
1897 mousing over sequence associated annotation
1900 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1904 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1905 '()', canonical '[]' and invalid '{}' base pair populations
1909 <!-- JAL-2092 -->Feature settings popup menu options for
1910 showing or hiding columns containing a feature
1913 <!-- JAL-1557 -->Edit selected group by double clicking on
1914 group and sequence associated annotation labels
1917 <!-- JAL-2236 -->Sequence name added to annotation label in
1918 select/hide columns by annotation and colour by annotation
1922 </ul> <em>Application</em>
1925 <!-- JAL-2050-->Automatically hide introns when opening a
1926 gene/transcript view
1929 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1933 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1934 structure mappings with the EMBL-EBI PDBe SIFTS database
1937 <!-- JAL-2079 -->Updated download sites used for Rfam and
1938 Pfam sources to xfam.org
1941 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1944 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1945 over sequences in Jalview
1948 <!-- JAL-2027-->Support for reverse-complement coding
1949 regions in ENA and EMBL
1952 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1953 for record retrieval via ENA rest API
1956 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1960 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1961 groovy script execution
1964 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1965 alignment window's Calculate menu
1968 <!-- JAL-1812 -->Allow groovy scripts that call
1969 Jalview.getAlignFrames() to run in headless mode
1972 <!-- JAL-2068 -->Support for creating new alignment
1973 calculation workers from groovy scripts
1976 <!-- JAL-1369 --->Store/restore reference sequence in
1980 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1981 associations are now saved/restored from project
1984 <!-- JAL-1993 -->Database selection dialog always shown
1985 before sequence fetcher is opened
1988 <!-- JAL-2183 -->Double click on an entry in Jalview's
1989 database chooser opens a sequence fetcher
1992 <!-- JAL-1563 -->Free-text search client for UniProt using
1993 the UniProt REST API
1996 <!-- JAL-2168 -->-nonews command line parameter to prevent
1997 the news reader opening
2000 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2001 querying stored in preferences
2004 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2008 <!-- JAL-1977-->Tooltips shown on database chooser
2011 <!-- JAL-391 -->Reverse complement function in calculate
2012 menu for nucleotide sequences
2015 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2016 and feature counts preserves alignment ordering (and
2017 debugged for complex feature sets).
2020 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2021 viewing structures with Jalview 2.10
2024 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2025 genome, transcript CCDS and gene ids via the Ensembl and
2026 Ensembl Genomes REST API
2029 <!-- JAL-2049 -->Protein sequence variant annotation
2030 computed for 'sequence_variant' annotation on CDS regions
2034 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2038 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2039 Ref Fetcher fails to match, or otherwise updates sequence
2040 data from external database records.
2043 <!-- JAL-2154 -->Revised Jalview Project format for
2044 efficient recovery of sequence coding and alignment
2045 annotation relationships.
2047 </ul> <!-- <em>Applet</em>
2058 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2062 <!-- JAL-2018-->Export features in Jalview format (again)
2063 includes graduated colourschemes
2066 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2067 working with big alignments and lots of hidden columns
2070 <!-- JAL-2053-->Hidden column markers not always rendered
2071 at right of alignment window
2074 <!-- JAL-2067 -->Tidied up links in help file table of
2078 <!-- JAL-2072 -->Feature based tree calculation not shown
2082 <!-- JAL-2075 -->Hidden columns ignored during feature
2083 based tree calculation
2086 <!-- JAL-2065 -->Alignment view stops updating when show
2087 unconserved enabled for group on alignment
2090 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2094 <!-- JAL-2146 -->Alignment column in status incorrectly
2095 shown as "Sequence position" when mousing over
2099 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2100 hidden columns present
2103 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2104 user created annotation added to alignment
2107 <!-- JAL-1841 -->RNA Structure consensus only computed for
2108 '()' base pair annotation
2111 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2112 in zero scores for all base pairs in RNA Structure
2116 <!-- JAL-2174-->Extend selection with columns containing
2120 <!-- JAL-2275 -->Pfam format writer puts extra space at
2121 beginning of sequence
2124 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2128 <!-- JAL-2238 -->Cannot create groups on an alignment from
2129 from a tree when t-coffee scores are shown
2132 <!-- JAL-1836,1967 -->Cannot import and view PDB
2133 structures with chains containing negative resnums (4q4h)
2136 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2140 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2141 to Clustal, PIR and PileUp output
2144 <!-- JAL-2008 -->Reordering sequence features that are
2145 not visible causes alignment window to repaint
2148 <!-- JAL-2006 -->Threshold sliders don't work in
2149 graduated colour and colour by annotation row for e-value
2150 scores associated with features and annotation rows
2153 <!-- JAL-1797 -->amino acid physicochemical conservation
2154 calculation should be case independent
2157 <!-- JAL-2173 -->Remove annotation also updates hidden
2161 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2162 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2163 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2166 <!-- JAL-2065 -->Null pointer exceptions and redraw
2167 problems when reference sequence defined and 'show
2168 non-conserved' enabled
2171 <!-- JAL-1306 -->Quality and Conservation are now shown on
2172 load even when Consensus calculation is disabled
2175 <!-- JAL-1932 -->Remove right on penultimate column of
2176 alignment does nothing
2179 <em>Application</em>
2182 <!-- JAL-1552-->URLs and links can't be imported by
2183 drag'n'drop on OSX when launched via webstart (note - not
2184 yet fixed for El Capitan)
2187 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2188 output when running on non-gb/us i18n platforms
2191 <!-- JAL-1944 -->Error thrown when exporting a view with
2192 hidden sequences as flat-file alignment
2195 <!-- JAL-2030-->InstallAnywhere distribution fails when
2199 <!-- JAL-2080-->Jalview very slow to launch via webstart
2200 (also hotfix for 2.9.0b2)
2203 <!-- JAL-2085 -->Cannot save project when view has a
2204 reference sequence defined
2207 <!-- JAL-1011 -->Columns are suddenly selected in other
2208 alignments and views when revealing hidden columns
2211 <!-- JAL-1989 -->Hide columns not mirrored in complement
2212 view in a cDNA/Protein splitframe
2215 <!-- JAL-1369 -->Cannot save/restore representative
2216 sequence from project when only one sequence is
2220 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2221 in Structure Chooser
2224 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2225 structure consensus didn't refresh annotation panel
2228 <!-- JAL-1962 -->View mapping in structure view shows
2229 mappings between sequence and all chains in a PDB file
2232 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2233 dialogs format columns correctly, don't display array
2234 data, sort columns according to type
2237 <!-- JAL-1975 -->Export complete shown after destination
2238 file chooser is cancelled during an image export
2241 <!-- JAL-2025 -->Error when querying PDB Service with
2242 sequence name containing special characters
2245 <!-- JAL-2024 -->Manual PDB structure querying should be
2249 <!-- JAL-2104 -->Large tooltips with broken HTML
2250 formatting don't wrap
2253 <!-- JAL-1128 -->Figures exported from wrapped view are
2254 truncated so L looks like I in consensus annotation
2257 <!-- JAL-2003 -->Export features should only export the
2258 currently displayed features for the current selection or
2262 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2263 after fetching cross-references, and restoring from
2267 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2268 followed in the structure viewer
2271 <!-- JAL-2163 -->Titles for individual alignments in
2272 splitframe not restored from project
2275 <!-- JAL-2145 -->missing autocalculated annotation at
2276 trailing end of protein alignment in transcript/product
2277 splitview when pad-gaps not enabled by default
2280 <!-- JAL-1797 -->amino acid physicochemical conservation
2284 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2285 article has been read (reopened issue due to
2286 internationalisation problems)
2289 <!-- JAL-1960 -->Only offer PDB structures in structure
2290 viewer based on sequence name, PDB and UniProt
2295 <!-- JAL-1976 -->No progress bar shown during export of
2299 <!-- JAL-2213 -->Structures not always superimposed after
2300 multiple structures are shown for one or more sequences.
2303 <!-- JAL-1370 -->Reference sequence characters should not
2304 be replaced with '.' when 'Show unconserved' format option
2308 <!-- JAL-1823 -->Cannot specify chain code when entering
2309 specific PDB id for sequence
2312 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2313 'Export hidden sequences' is enabled, but 'export hidden
2314 columns' is disabled.
2317 <!--JAL-2026-->Best Quality option in structure chooser
2318 selects lowest rather than highest resolution structures
2322 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2323 to sequence mapping in 'View Mappings' report
2326 <!-- JAL-2284 -->Unable to read old Jalview projects that
2327 contain non-XML data added after Jalvew wrote project.
2330 <!-- JAL-2118 -->Newly created annotation row reorders
2331 after clicking on it to create new annotation for a
2335 <!-- JAL-1980 -->Null Pointer Exception raised when
2336 pressing Add on an orphaned cut'n'paste window.
2338 <!-- may exclude, this is an external service stability issue JAL-1941
2339 -- > RNA 3D structure not added via DSSR service</li> -->
2344 <!-- JAL-2151 -->Incorrect columns are selected when
2345 hidden columns present before start of sequence
2348 <!-- JAL-1986 -->Missing dependencies on applet pages
2352 <!-- JAL-1947 -->Overview pixel size changes when
2353 sequences are hidden in applet
2356 <!-- JAL-1996 -->Updated instructions for applet
2357 deployment on examples pages.
2364 <td width="60" nowrap>
2365 <div align="center">
2366 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2367 <em>16/10/2015</em></strong>
2370 <td><em>General</em>
2372 <li>Time stamps for signed Jalview application and applet
2377 <em>Application</em>
2379 <li>Duplicate group consensus and conservation rows
2380 shown when tree is partitioned</li>
2381 <li>Erratic behaviour when tree partitions made with
2382 multiple cDNA/Protein split views</li>
2388 <td width="60" nowrap>
2389 <div align="center">
2390 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2391 <em>8/10/2015</em></strong>
2394 <td><em>General</em>
2396 <li>Updated Spanish translations of localized text for
2398 </ul> <em>Application</em>
2400 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2401 <li>Signed OSX InstallAnywhere installer<br></li>
2402 <li>Support for per-sequence based annotations in BioJSON</li>
2403 </ul> <em>Applet</em>
2405 <li>Split frame example added to applet examples page</li>
2406 </ul> <em>Build and Deployment</em>
2409 <!-- JAL-1888 -->New ant target for running Jalview's test
2417 <li>Mapping of cDNA to protein in split frames
2418 incorrect when sequence start > 1</li>
2419 <li>Broken images in filter column by annotation dialog
2421 <li>Feature colours not parsed from features file</li>
2422 <li>Exceptions and incomplete link URLs recovered when
2423 loading a features file containing HTML tags in feature
2427 <em>Application</em>
2429 <li>Annotations corrupted after BioJS export and
2431 <li>Incorrect sequence limits after Fetch DB References
2432 with 'trim retrieved sequences'</li>
2433 <li>Incorrect warning about deleting all data when
2434 deleting selected columns</li>
2435 <li>Patch to build system for shipping properly signed
2436 JNLP templates for webstart launch</li>
2437 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2438 unreleased structures for download or viewing</li>
2439 <li>Tab/space/return keystroke operation of EMBL-PDBe
2440 fetcher/viewer dialogs works correctly</li>
2441 <li>Disabled 'minimise' button on Jalview windows
2442 running on OSX to workaround redraw hang bug</li>
2443 <li>Split cDNA/Protein view position and geometry not
2444 recovered from jalview project</li>
2445 <li>Initial enabled/disabled state of annotation menu
2446 sorter 'show autocalculated first/last' corresponds to
2448 <li>Restoring of Clustal, RNA Helices and T-Coffee
2449 color schemes from BioJSON</li>
2453 <li>Reorder sequences mirrored in cDNA/Protein split
2455 <li>Applet with Jmol examples not loading correctly</li>
2461 <td><div align="center">
2462 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2464 <td><em>General</em>
2466 <li>Linked visualisation and analysis of DNA and Protein
2469 <li>Translated cDNA alignments shown as split protein
2470 and DNA alignment views</li>
2471 <li>Codon consensus annotation for linked protein and
2472 cDNA alignment views</li>
2473 <li>Link cDNA or Protein product sequences by loading
2474 them onto Protein or cDNA alignments</li>
2475 <li>Reconstruct linked cDNA alignment from aligned
2476 protein sequences</li>
2479 <li>Jmol integration updated to Jmol v14.2.14</li>
2480 <li>Import and export of Jalview alignment views as <a
2481 href="features/bioJsonFormat.html">BioJSON</a></li>
2482 <li>New alignment annotation file statements for
2483 reference sequences and marking hidden columns</li>
2484 <li>Reference sequence based alignment shading to
2485 highlight variation</li>
2486 <li>Select or hide columns according to alignment
2488 <li>Find option for locating sequences by description</li>
2489 <li>Conserved physicochemical properties shown in amino
2490 acid conservation row</li>
2491 <li>Alignments can be sorted by number of RNA helices</li>
2492 </ul> <em>Application</em>
2494 <li>New cDNA/Protein analysis capabilities
2496 <li>Get Cross-References should open a Split Frame
2497 view with cDNA/Protein</li>
2498 <li>Detect when nucleotide sequences and protein
2499 sequences are placed in the same alignment</li>
2500 <li>Split cDNA/Protein views are saved in Jalview
2505 <li>Use REST API to talk to Chimera</li>
2506 <li>Selected regions in Chimera are highlighted in linked
2507 Jalview windows</li>
2509 <li>VARNA RNA viewer updated to v3.93</li>
2510 <li>VARNA views are saved in Jalview Projects</li>
2511 <li>Pseudoknots displayed as Jalview RNA annotation can
2512 be shown in VARNA</li>
2514 <li>Make groups for selection uses marked columns as well
2515 as the active selected region</li>
2517 <li>Calculate UPGMA and NJ trees using sequence feature
2519 <li>New Export options
2521 <li>New Export Settings dialog to control hidden
2522 region export in flat file generation</li>
2524 <li>Export alignment views for display with the <a
2525 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2527 <li>Export scrollable SVG in HTML page</li>
2528 <li>Optional embedding of BioJSON data when exporting
2529 alignment figures to HTML</li>
2531 <li>3D structure retrieval and display
2533 <li>Free text and structured queries with the PDBe
2535 <li>PDBe Search API based discovery and selection of
2536 PDB structures for a sequence set</li>
2540 <li>JPred4 employed for protein secondary structure
2542 <li>Hide Insertions menu option to hide unaligned columns
2543 for one or a group of sequences</li>
2544 <li>Automatically hide insertions in alignments imported
2545 from the JPred4 web server</li>
2546 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2547 system on OSX<br />LGPL libraries courtesy of <a
2548 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2550 <li>changed 'View nucleotide structure' submenu to 'View
2551 VARNA 2D Structure'</li>
2552 <li>change "View protein structure" menu option to "3D
2555 </ul> <em>Applet</em>
2557 <li>New layout for applet example pages</li>
2558 <li>New parameters to enable SplitFrame view
2559 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2560 <li>New example demonstrating linked viewing of cDNA and
2561 Protein alignments</li>
2562 </ul> <em>Development and deployment</em>
2564 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2565 <li>Include installation type and git revision in build
2566 properties and console log output</li>
2567 <li>Jalview Github organisation, and new github site for
2568 storing BioJsMSA Templates</li>
2569 <li>Jalview's unit tests now managed with TestNG</li>
2572 <!-- <em>General</em>
2574 </ul> --> <!-- issues resolved --> <em>Application</em>
2576 <li>Escape should close any open find dialogs</li>
2577 <li>Typo in select-by-features status report</li>
2578 <li>Consensus RNA secondary secondary structure
2579 predictions are not highlighted in amber</li>
2580 <li>Missing gap character in v2.7 example file means
2581 alignment appears unaligned when pad-gaps is not enabled</li>
2582 <li>First switch to RNA Helices colouring doesn't colour
2583 associated structure views</li>
2584 <li>ID width preference option is greyed out when auto
2585 width checkbox not enabled</li>
2586 <li>Stopped a warning dialog from being shown when
2587 creating user defined colours</li>
2588 <li>'View Mapping' in structure viewer shows sequence
2589 mappings for just that viewer's sequences</li>
2590 <li>Workaround for superposing PDB files containing
2591 multiple models in Chimera</li>
2592 <li>Report sequence position in status bar when hovering
2593 over Jmol structure</li>
2594 <li>Cannot output gaps as '.' symbols with Selection ->
2595 output to text box</li>
2596 <li>Flat file exports of alignments with hidden columns
2597 have incorrect sequence start/end</li>
2598 <li>'Aligning' a second chain to a Chimera structure from
2600 <li>Colour schemes applied to structure viewers don't
2601 work for nucleotide</li>
2602 <li>Loading/cut'n'pasting an empty or invalid file leads
2603 to a grey/invisible alignment window</li>
2604 <li>Exported Jpred annotation from a sequence region
2605 imports to different position</li>
2606 <li>Space at beginning of sequence feature tooltips shown
2607 on some platforms</li>
2608 <li>Chimera viewer 'View | Show Chain' menu is not
2610 <li>'New View' fails with a Null Pointer Exception in
2611 console if Chimera has been opened</li>
2612 <li>Mouseover to Chimera not working</li>
2613 <li>Miscellaneous ENA XML feature qualifiers not
2615 <li>NPE in annotation renderer after 'Extract Scores'</li>
2616 <li>If two structures in one Chimera window, mouseover of
2617 either sequence shows on first structure</li>
2618 <li>'Show annotations' options should not make
2619 non-positional annotations visible</li>
2620 <li>Subsequence secondary structure annotation not shown
2621 in right place after 'view flanking regions'</li>
2622 <li>File Save As type unset when current file format is
2624 <li>Save as '.jar' option removed for saving Jalview
2626 <li>Colour by Sequence colouring in Chimera more
2628 <li>Cannot 'add reference annotation' for a sequence in
2629 several views on same alignment</li>
2630 <li>Cannot show linked products for EMBL / ENA records</li>
2631 <li>Jalview's tooltip wraps long texts containing no
2633 </ul> <em>Applet</em>
2635 <li>Jmol to JalviewLite mouseover/link not working</li>
2636 <li>JalviewLite can't import sequences with ID
2637 descriptions containing angle brackets</li>
2638 </ul> <em>General</em>
2640 <li>Cannot export and reimport RNA secondary structure
2641 via jalview annotation file</li>
2642 <li>Random helix colour palette for colour by annotation
2643 with RNA secondary structure</li>
2644 <li>Mouseover to cDNA from STOP residue in protein
2645 translation doesn't work.</li>
2646 <li>hints when using the select by annotation dialog box</li>
2647 <li>Jmol alignment incorrect if PDB file has alternate CA
2649 <li>FontChooser message dialog appears to hang after
2650 choosing 1pt font</li>
2651 <li>Peptide secondary structure incorrectly imported from
2652 annotation file when annotation display text includes 'e' or
2654 <li>Cannot set colour of new feature type whilst creating
2656 <li>cDNA translation alignment should not be sequence
2657 order dependent</li>
2658 <li>'Show unconserved' doesn't work for lower case
2660 <li>Nucleotide ambiguity codes involving R not recognised</li>
2661 </ul> <em>Deployment and Documentation</em>
2663 <li>Applet example pages appear different to the rest of
2664 www.jalview.org</li>
2665 </ul> <em>Application Known issues</em>
2667 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2668 <li>Misleading message appears after trying to delete
2670 <li>Jalview icon not shown in dock after InstallAnywhere
2671 version launches</li>
2672 <li>Fetching EMBL reference for an RNA sequence results
2673 fails with a sequence mismatch</li>
2674 <li>Corrupted or unreadable alignment display when
2675 scrolling alignment to right</li>
2676 <li>ArrayIndexOutOfBoundsException thrown when remove
2677 empty columns called on alignment with ragged gapped ends</li>
2678 <li>auto calculated alignment annotation rows do not get
2679 placed above or below non-autocalculated rows</li>
2680 <li>Jalview dekstop becomes sluggish at full screen in
2681 ultra-high resolution</li>
2682 <li>Cannot disable consensus calculation independently of
2683 quality and conservation</li>
2684 <li>Mouseover highlighting between cDNA and protein can
2685 become sluggish with more than one splitframe shown</li>
2686 </ul> <em>Applet Known Issues</em>
2688 <li>Core PDB parsing code requires Jmol</li>
2689 <li>Sequence canvas panel goes white when alignment
2690 window is being resized</li>
2696 <td><div align="center">
2697 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2699 <td><em>General</em>
2701 <li>Updated Java code signing certificate donated by
2703 <li>Features and annotation preserved when performing
2704 pairwise alignment</li>
2705 <li>RNA pseudoknot annotation can be
2706 imported/exported/displayed</li>
2707 <li>'colour by annotation' can colour by RNA and
2708 protein secondary structure</li>
2709 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2710 post-hoc with 2.9 release</em>)
2713 </ul> <em>Application</em>
2715 <li>Extract and display secondary structure for sequences
2716 with 3D structures</li>
2717 <li>Support for parsing RNAML</li>
2718 <li>Annotations menu for layout
2720 <li>sort sequence annotation rows by alignment</li>
2721 <li>place sequence annotation above/below alignment
2724 <li>Output in Stockholm format</li>
2725 <li>Internationalisation: improved Spanish (es)
2727 <li>Structure viewer preferences tab</li>
2728 <li>Disorder and Secondary Structure annotation tracks
2729 shared between alignments</li>
2730 <li>UCSF Chimera launch and linked highlighting from
2732 <li>Show/hide all sequence associated annotation rows for
2733 all or current selection</li>
2734 <li>disorder and secondary structure predictions
2735 available as dataset annotation</li>
2736 <li>Per-sequence rna helices colouring</li>
2739 <li>Sequence database accessions imported when fetching
2740 alignments from Rfam</li>
2741 <li>update VARNA version to 3.91</li>
2743 <li>New groovy scripts for exporting aligned positions,
2744 conservation values, and calculating sum of pairs scores.</li>
2745 <li>Command line argument to set default JABAWS server</li>
2746 <li>include installation type in build properties and
2747 console log output</li>
2748 <li>Updated Jalview project format to preserve dataset
2752 <!-- issues resolved --> <em>Application</em>
2754 <li>Distinguish alignment and sequence associated RNA
2755 structure in structure->view->VARNA</li>
2756 <li>Raise dialog box if user deletes all sequences in an
2758 <li>Pressing F1 results in documentation opening twice</li>
2759 <li>Sequence feature tooltip is wrapped</li>
2760 <li>Double click on sequence associated annotation
2761 selects only first column</li>
2762 <li>Redundancy removal doesn't result in unlinked
2763 leaves shown in tree</li>
2764 <li>Undos after several redundancy removals don't undo
2766 <li>Hide sequence doesn't hide associated annotation</li>
2767 <li>User defined colours dialog box too big to fit on
2768 screen and buttons not visible</li>
2769 <li>author list isn't updated if already written to
2770 Jalview properties</li>
2771 <li>Popup menu won't open after retrieving sequence
2773 <li>File open window for associate PDB doesn't open</li>
2774 <li>Left-then-right click on a sequence id opens a
2775 browser search window</li>
2776 <li>Cannot open sequence feature shading/sort popup menu
2777 in feature settings dialog</li>
2778 <li>better tooltip placement for some areas of Jalview
2780 <li>Allow addition of JABAWS Server which doesn't
2781 pass validation</li>
2782 <li>Web services parameters dialog box is too large to
2784 <li>Muscle nucleotide alignment preset obscured by
2786 <li>JABAWS preset submenus don't contain newly
2787 defined user preset</li>
2788 <li>MSA web services warns user if they were launched
2789 with invalid input</li>
2790 <li>Jalview cannot contact DAS Registy when running on
2793 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2794 'Superpose with' submenu not shown when new view
2798 </ul> <!-- <em>Applet</em>
2800 </ul> <em>General</em>
2802 </ul>--> <em>Deployment and Documentation</em>
2804 <li>2G and 1G options in launchApp have no effect on
2805 memory allocation</li>
2806 <li>launchApp service doesn't automatically open
2807 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2809 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2810 InstallAnywhere reports cannot find valid JVM when Java
2811 1.7_055 is available
2813 </ul> <em>Application Known issues</em>
2816 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2817 corrupted or unreadable alignment display when scrolling
2821 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2822 retrieval fails but progress bar continues for DAS retrieval
2823 with large number of ID
2826 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2827 flatfile output of visible region has incorrect sequence
2831 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2832 rna structure consensus doesn't update when secondary
2833 structure tracks are rearranged
2836 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2837 invalid rna structure positional highlighting does not
2838 highlight position of invalid base pairs
2841 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2842 out of memory errors are not raised when saving Jalview
2843 project from alignment window file menu
2846 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2847 Switching to RNA Helices colouring doesn't propagate to
2851 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2852 colour by RNA Helices not enabled when user created
2853 annotation added to alignment
2856 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2857 Jalview icon not shown on dock in Mountain Lion/Webstart
2859 </ul> <em>Applet Known Issues</em>
2862 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2863 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2866 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2867 Jalview and Jmol example not compatible with IE9
2870 <li>Sort by annotation score doesn't reverse order
2876 <td><div align="center">
2877 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2880 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2883 <li>Internationalisation of user interface (usually
2884 called i18n support) and translation for Spanish locale</li>
2885 <li>Define/Undefine group on current selection with
2886 Ctrl-G/Shift Ctrl-G</li>
2887 <li>Improved group creation/removal options in
2888 alignment/sequence Popup menu</li>
2889 <li>Sensible precision for symbol distribution
2890 percentages shown in logo tooltip.</li>
2891 <li>Annotation panel height set according to amount of
2892 annotation when alignment first opened</li>
2893 </ul> <em>Application</em>
2895 <li>Interactive consensus RNA secondary structure
2896 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2897 <li>Select columns containing particular features from
2898 Feature Settings dialog</li>
2899 <li>View all 'representative' PDB structures for selected
2901 <li>Update Jalview project format:
2903 <li>New file extension for Jalview projects '.jvp'</li>
2904 <li>Preserve sequence and annotation dataset (to
2905 store secondary structure annotation,etc)</li>
2906 <li>Per group and alignment annotation and RNA helix
2910 <li>New similarity measures for PCA and Tree calculation
2912 <li>Experimental support for retrieval and viewing of
2913 flanking regions for an alignment</li>
2917 <!-- issues resolved --> <em>Application</em>
2919 <li>logo keeps spinning and status remains at queued or
2920 running after job is cancelled</li>
2921 <li>cannot export features from alignments imported from
2922 Jalview/VAMSAS projects</li>
2923 <li>Buggy slider for web service parameters that take
2925 <li>Newly created RNA secondary structure line doesn't
2926 have 'display all symbols' flag set</li>
2927 <li>T-COFFEE alignment score shading scheme and other
2928 annotation shading not saved in Jalview project</li>
2929 <li>Local file cannot be loaded in freshly downloaded
2931 <li>Jalview icon not shown on dock in Mountain
2933 <li>Load file from desktop file browser fails</li>
2934 <li>Occasional NPE thrown when calculating large trees</li>
2935 <li>Cannot reorder or slide sequences after dragging an
2936 alignment onto desktop</li>
2937 <li>Colour by annotation dialog throws NPE after using
2938 'extract scores' function</li>
2939 <li>Loading/cut'n'pasting an empty file leads to a grey
2940 alignment window</li>
2941 <li>Disorder thresholds rendered incorrectly after
2942 performing IUPred disorder prediction</li>
2943 <li>Multiple group annotated consensus rows shown when
2944 changing 'normalise logo' display setting</li>
2945 <li>Find shows blank dialog after 'finished searching' if
2946 nothing matches query</li>
2947 <li>Null Pointer Exceptions raised when sorting by
2948 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2950 <li>Errors in Jmol console when structures in alignment
2951 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2953 <li>Not all working JABAWS services are shown in
2955 <li>JAVAWS version of Jalview fails to launch with
2956 'invalid literal/length code'</li>
2957 <li>Annotation/RNA Helix colourschemes cannot be applied
2958 to alignment with groups (actually fixed in 2.8.0b1)</li>
2959 <li>RNA Helices and T-Coffee Scores available as default
2962 </ul> <em>Applet</em>
2964 <li>Remove group option is shown even when selection is
2966 <li>Apply to all groups ticked but colourscheme changes
2967 don't affect groups</li>
2968 <li>Documented RNA Helices and T-Coffee Scores as valid
2969 colourscheme name</li>
2970 <li>Annotation labels drawn on sequence IDs when
2971 Annotation panel is not displayed</li>
2972 <li>Increased font size for dropdown menus on OSX and
2973 embedded windows</li>
2974 </ul> <em>Other</em>
2976 <li>Consensus sequence for alignments/groups with a
2977 single sequence were not calculated</li>
2978 <li>annotation files that contain only groups imported as
2979 annotation and junk sequences</li>
2980 <li>Fasta files with sequences containing '*' incorrectly
2981 recognised as PFAM or BLC</li>
2982 <li>conservation/PID slider apply all groups option
2983 doesn't affect background (2.8.0b1)
2985 <li>redundancy highlighting is erratic at 0% and 100%</li>
2986 <li>Remove gapped columns fails for sequences with ragged
2988 <li>AMSA annotation row with leading spaces is not
2989 registered correctly on import</li>
2990 <li>Jalview crashes when selecting PCA analysis for
2991 certain alignments</li>
2992 <li>Opening the colour by annotation dialog for an
2993 existing annotation based 'use original colours'
2994 colourscheme loses original colours setting</li>
2999 <td><div align="center">
3000 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3001 <em>30/1/2014</em></strong>
3005 <li>Trusted certificates for JalviewLite applet and
3006 Jalview Desktop application<br />Certificate was donated by
3007 <a href="https://www.certum.eu">Certum</a> to the Jalview
3008 open source project).
3010 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3011 <li>Output in Stockholm format</li>
3012 <li>Allow import of data from gzipped files</li>
3013 <li>Export/import group and sequence associated line
3014 graph thresholds</li>
3015 <li>Nucleotide substitution matrix that supports RNA and
3016 ambiguity codes</li>
3017 <li>Allow disorder predictions to be made on the current
3018 selection (or visible selection) in the same way that JPred
3020 <li>Groovy scripting for headless Jalview operation</li>
3021 </ul> <em>Other improvements</em>
3023 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3024 <li>COMBINE statement uses current SEQUENCE_REF and
3025 GROUP_REF scope to group annotation rows</li>
3026 <li>Support '' style escaping of quotes in Newick
3028 <li>Group options for JABAWS service by command line name</li>
3029 <li>Empty tooltip shown for JABA service options with a
3030 link but no description</li>
3031 <li>Select primary source when selecting authority in
3032 database fetcher GUI</li>
3033 <li>Add .mfa to FASTA file extensions recognised by
3035 <li>Annotation label tooltip text wrap</li>
3040 <li>Slow scrolling when lots of annotation rows are
3042 <li>Lots of NPE (and slowness) after creating RNA
3043 secondary structure annotation line</li>
3044 <li>Sequence database accessions not imported when
3045 fetching alignments from Rfam</li>
3046 <li>Incorrect SHMR submission for sequences with
3048 <li>View all structures does not always superpose
3050 <li>Option widgets in service parameters not updated to
3051 reflect user or preset settings</li>
3052 <li>Null pointer exceptions for some services without
3053 presets or adjustable parameters</li>
3054 <li>Discover PDB IDs entry in structure menu doesn't
3055 discover PDB xRefs</li>
3056 <li>Exception encountered while trying to retrieve
3057 features with DAS</li>
3058 <li>Lowest value in annotation row isn't coloured
3059 when colour by annotation (per sequence) is coloured</li>
3060 <li>Keyboard mode P jumps to start of gapped region when
3061 residue follows a gap</li>
3062 <li>Jalview appears to hang importing an alignment with
3063 Wrap as default or after enabling Wrap</li>
3064 <li>'Right click to add annotations' message
3065 shown in wrap mode when no annotations present</li>
3066 <li>Disorder predictions fail with NPE if no automatic
3067 annotation already exists on alignment</li>
3068 <li>oninit javascript function should be called after
3069 initialisation completes</li>
3070 <li>Remove redundancy after disorder prediction corrupts
3071 alignment window display</li>
3072 <li>Example annotation file in documentation is invalid</li>
3073 <li>Grouped line graph annotation rows are not exported
3074 to annotation file</li>
3075 <li>Multi-harmony analysis cannot be run when only two
3077 <li>Cannot create multiple groups of line graphs with
3078 several 'combine' statements in annotation file</li>
3079 <li>Pressing return several times causes Number Format
3080 exceptions in keyboard mode</li>
3081 <li>Multi-harmony (SHMMR) method doesn't submit
3082 correct partitions for input data</li>
3083 <li>Translation from DNA to Amino Acids fails</li>
3084 <li>Jalview fail to load newick tree with quoted label</li>
3085 <li>--headless flag isn't understood</li>
3086 <li>ClassCastException when generating EPS in headless
3088 <li>Adjusting sequence-associated shading threshold only
3089 changes one row's threshold</li>
3090 <li>Preferences and Feature settings panel panel
3091 doesn't open</li>
3092 <li>hide consensus histogram also hides conservation and
3093 quality histograms</li>
3098 <td><div align="center">
3099 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3101 <td><em>Application</em>
3103 <li>Support for JABAWS 2.0 Services (AACon alignment
3104 conservation, protein disorder and Clustal Omega)</li>
3105 <li>JABAWS server status indicator in Web Services
3107 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3108 in Jalview alignment window</li>
3109 <li>Updated Jalview build and deploy framework for OSX
3110 mountain lion, windows 7, and 8</li>
3111 <li>Nucleotide substitution matrix for PCA that supports
3112 RNA and ambiguity codes</li>
3114 <li>Improved sequence database retrieval GUI</li>
3115 <li>Support fetching and database reference look up
3116 against multiple DAS sources (Fetch all from in 'fetch db
3118 <li>Jalview project improvements
3120 <li>Store and retrieve the 'belowAlignment'
3121 flag for annotation</li>
3122 <li>calcId attribute to group annotation rows on the
3124 <li>Store AACon calculation settings for a view in
3125 Jalview project</li>
3129 <li>horizontal scrolling gesture support</li>
3130 <li>Visual progress indicator when PCA calculation is
3132 <li>Simpler JABA web services menus</li>
3133 <li>visual indication that web service results are still
3134 being retrieved from server</li>
3135 <li>Serialise the dialogs that are shown when Jalview
3136 starts up for first time</li>
3137 <li>Jalview user agent string for interacting with HTTP
3139 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3141 <li>Examples directory and Groovy library included in
3142 InstallAnywhere distribution</li>
3143 </ul> <em>Applet</em>
3145 <li>RNA alignment and secondary structure annotation
3146 visualization applet example</li>
3147 </ul> <em>General</em>
3149 <li>Normalise option for consensus sequence logo</li>
3150 <li>Reset button in PCA window to return dimensions to
3152 <li>Allow seqspace or Jalview variant of alignment PCA
3154 <li>PCA with either nucleic acid and protein substitution
3156 <li>Allow windows containing HTML reports to be exported
3158 <li>Interactive display and editing of RNA secondary
3159 structure contacts</li>
3160 <li>RNA Helix Alignment Colouring</li>
3161 <li>RNA base pair logo consensus</li>
3162 <li>Parse sequence associated secondary structure
3163 information in Stockholm files</li>
3164 <li>HTML Export database accessions and annotation
3165 information presented in tooltip for sequences</li>
3166 <li>Import secondary structure from LOCARNA clustalw
3167 style RNA alignment files</li>
3168 <li>import and visualise T-COFFEE quality scores for an
3170 <li>'colour by annotation' per sequence option to
3171 shade each sequence according to its associated alignment
3173 <li>New Jalview Logo</li>
3174 </ul> <em>Documentation and Development</em>
3176 <li>documentation for score matrices used in Jalview</li>
3177 <li>New Website!</li>
3179 <td><em>Application</em>
3181 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3182 wsdbfetch REST service</li>
3183 <li>Stop windows being moved outside desktop on OSX</li>
3184 <li>Filetype associations not installed for webstart
3186 <li>Jalview does not always retrieve progress of a JABAWS
3187 job execution in full once it is complete</li>
3188 <li>revise SHMR RSBS definition to ensure alignment is
3189 uploaded via ali_file parameter</li>
3190 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3191 <li>View all structures superposed fails with exception</li>
3192 <li>Jnet job queues forever if a very short sequence is
3193 submitted for prediction</li>
3194 <li>Cut and paste menu not opened when mouse clicked on
3196 <li>Putting fractional value into integer text box in
3197 alignment parameter dialog causes Jalview to hang</li>
3198 <li>Structure view highlighting doesn't work on
3200 <li>View all structures fails with exception shown in
3202 <li>Characters in filename associated with PDBEntry not
3203 escaped in a platform independent way</li>
3204 <li>Jalview desktop fails to launch with exception when
3206 <li>Tree calculation reports 'you must have 2 or more
3207 sequences selected' when selection is empty</li>
3208 <li>Jalview desktop fails to launch with jar signature
3209 failure when java web start temporary file caching is
3211 <li>DAS Sequence retrieval with range qualification
3212 results in sequence xref which includes range qualification</li>
3213 <li>Errors during processing of command line arguments
3214 cause progress bar (JAL-898) to be removed</li>
3215 <li>Replace comma for semi-colon option not disabled for
3216 DAS sources in sequence fetcher</li>
3217 <li>Cannot close news reader when JABAWS server warning
3218 dialog is shown</li>
3219 <li>Option widgets not updated to reflect user settings</li>
3220 <li>Edited sequence not submitted to web service</li>
3221 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3222 <li>InstallAnywhere installer doesn't unpack and run
3223 on OSX Mountain Lion</li>
3224 <li>Annotation panel not given a scroll bar when
3225 sequences with alignment annotation are pasted into the
3227 <li>Sequence associated annotation rows not associated
3228 when loaded from Jalview project</li>
3229 <li>Browser launch fails with NPE on java 1.7</li>
3230 <li>JABAWS alignment marked as finished when job was
3231 cancelled or job failed due to invalid input</li>
3232 <li>NPE with v2.7 example when clicking on Tree
3233 associated with all views</li>
3234 <li>Exceptions when copy/paste sequences with grouped
3235 annotation rows to new window</li>
3236 </ul> <em>Applet</em>
3238 <li>Sequence features are momentarily displayed before
3239 they are hidden using hidefeaturegroups applet parameter</li>
3240 <li>loading features via javascript API automatically
3241 enables feature display</li>
3242 <li>scrollToColumnIn javascript API method doesn't
3244 </ul> <em>General</em>
3246 <li>Redundancy removal fails for rna alignment</li>
3247 <li>PCA calculation fails when sequence has been selected
3248 and then deselected</li>
3249 <li>PCA window shows grey box when first opened on OSX</li>
3250 <li>Letters coloured pink in sequence logo when alignment
3251 coloured with clustalx</li>
3252 <li>Choosing fonts without letter symbols defined causes
3253 exceptions and redraw errors</li>
3254 <li>Initial PCA plot view is not same as manually
3255 reconfigured view</li>
3256 <li>Grouped annotation graph label has incorrect line
3258 <li>Grouped annotation graph label display is corrupted
3259 for lots of labels</li>
3264 <div align="center">
3265 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3268 <td><em>Application</em>
3270 <li>Jalview Desktop News Reader</li>
3271 <li>Tweaked default layout of web services menu</li>
3272 <li>View/alignment association menu to enable user to
3273 easily specify which alignment a multi-structure view takes
3274 its colours/correspondences from</li>
3275 <li>Allow properties file location to be specified as URL</li>
3276 <li>Extend Jalview project to preserve associations
3277 between many alignment views and a single Jmol display</li>
3278 <li>Store annotation row height in Jalview project file</li>
3279 <li>Annotation row column label formatting attributes
3280 stored in project file</li>
3281 <li>Annotation row order for auto-calculated annotation
3282 rows preserved in Jalview project file</li>
3283 <li>Visual progress indication when Jalview state is
3284 saved using Desktop window menu</li>
3285 <li>Visual indication that command line arguments are
3286 still being processed</li>
3287 <li>Groovy script execution from URL</li>
3288 <li>Colour by annotation default min and max colours in
3290 <li>Automatically associate PDB files dragged onto an
3291 alignment with sequences that have high similarity and
3293 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3294 <li>'view structures' option to open many
3295 structures in same window</li>
3296 <li>Sort associated views menu option for tree panel</li>
3297 <li>Group all JABA and non-JABA services for a particular
3298 analysis function in its own submenu</li>
3299 </ul> <em>Applet</em>
3301 <li>Userdefined and autogenerated annotation rows for
3303 <li>Adjustment of alignment annotation pane height</li>
3304 <li>Annotation scrollbar for annotation panel</li>
3305 <li>Drag to reorder annotation rows in annotation panel</li>
3306 <li>'automaticScrolling' parameter</li>
3307 <li>Allow sequences with partial ID string matches to be
3308 annotated from GFF/Jalview features files</li>
3309 <li>Sequence logo annotation row in applet</li>
3310 <li>Absolute paths relative to host server in applet
3311 parameters are treated as such</li>
3312 <li>New in the JalviewLite javascript API:
3314 <li>JalviewLite.js javascript library</li>
3315 <li>Javascript callbacks for
3317 <li>Applet initialisation</li>
3318 <li>Sequence/alignment mouse-overs and selections</li>
3321 <li>scrollTo row and column alignment scrolling
3323 <li>Select sequence/alignment regions from javascript</li>
3324 <li>javascript structure viewer harness to pass
3325 messages between Jmol and Jalview when running as
3326 distinct applets</li>
3327 <li>sortBy method</li>
3328 <li>Set of applet and application examples shipped
3329 with documentation</li>
3330 <li>New example to demonstrate JalviewLite and Jmol
3331 javascript message exchange</li>
3333 </ul> <em>General</em>
3335 <li>Enable Jmol displays to be associated with multiple
3336 multiple alignments</li>
3337 <li>Option to automatically sort alignment with new tree</li>
3338 <li>User configurable link to enable redirects to a
3339 www.Jalview.org mirror</li>
3340 <li>Jmol colours option for Jmol displays</li>
3341 <li>Configurable newline string when writing alignment
3342 and other flat files</li>
3343 <li>Allow alignment annotation description lines to
3344 contain html tags</li>
3345 </ul> <em>Documentation and Development</em>
3347 <li>Add groovy test harness for bulk load testing to
3349 <li>Groovy script to load and align a set of sequences
3350 using a web service before displaying the result in the
3351 Jalview desktop</li>
3352 <li>Restructured javascript and applet api documentation</li>
3353 <li>Ant target to publish example html files with applet
3355 <li>Netbeans project for building Jalview from source</li>
3356 <li>ant task to create online javadoc for Jalview source</li>
3358 <td><em>Application</em>
3360 <li>User defined colourscheme throws exception when
3361 current built in colourscheme is saved as new scheme</li>
3362 <li>AlignFrame->Save in application pops up save
3363 dialog for valid filename/format</li>
3364 <li>Cannot view associated structure for UniProt sequence</li>
3365 <li>PDB file association breaks for UniProt sequence
3367 <li>Associate PDB from file dialog does not tell you
3368 which sequence is to be associated with the file</li>
3369 <li>Find All raises null pointer exception when query
3370 only matches sequence IDs</li>
3371 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3372 <li>Jalview project with Jmol views created with Jalview
3373 2.4 cannot be loaded</li>
3374 <li>Filetype associations not installed for webstart
3376 <li>Two or more chains in a single PDB file associated
3377 with sequences in different alignments do not get coloured
3378 by their associated sequence</li>
3379 <li>Visibility status of autocalculated annotation row
3380 not preserved when project is loaded</li>
3381 <li>Annotation row height and visibility attributes not
3382 stored in Jalview project</li>
3383 <li>Tree bootstraps are not preserved when saved as a
3384 Jalview project</li>
3385 <li>Envision2 workflow tooltips are corrupted</li>
3386 <li>Enabling show group conservation also enables colour
3387 by conservation</li>
3388 <li>Duplicate group associated conservation or consensus
3389 created on new view</li>
3390 <li>Annotation scrollbar not displayed after 'show
3391 all hidden annotation rows' option selected</li>
3392 <li>Alignment quality not updated after alignment
3393 annotation row is hidden then shown</li>
3394 <li>Preserve colouring of structures coloured by
3395 sequences in pre Jalview 2.7 projects</li>
3396 <li>Web service job parameter dialog is not laid out
3398 <li>Web services menu not refreshed after 'reset
3399 services' button is pressed in preferences</li>
3400 <li>Annotation off by one in Jalview v2_3 example project</li>
3401 <li>Structures imported from file and saved in project
3402 get name like jalview_pdb1234.txt when reloaded</li>
3403 <li>Jalview does not always retrieve progress of a JABAWS
3404 job execution in full once it is complete</li>
3405 </ul> <em>Applet</em>
3407 <li>Alignment height set incorrectly when lots of
3408 annotation rows are displayed</li>
3409 <li>Relative URLs in feature HTML text not resolved to
3411 <li>View follows highlighting does not work for positions
3413 <li><= shown as = in tooltip</li>
3414 <li>Export features raises exception when no features
3416 <li>Separator string used for serialising lists of IDs
3417 for javascript api is modified when separator string
3418 provided as parameter</li>
3419 <li>Null pointer exception when selecting tree leaves for
3420 alignment with no existing selection</li>
3421 <li>Relative URLs for datasources assumed to be relative
3422 to applet's codebase</li>
3423 <li>Status bar not updated after finished searching and
3424 search wraps around to first result</li>
3425 <li>StructureSelectionManager instance shared between
3426 several Jalview applets causes race conditions and memory
3428 <li>Hover tooltip and mouseover of position on structure
3429 not sent from Jmol in applet</li>
3430 <li>Certain sequences of javascript method calls to
3431 applet API fatally hang browser</li>
3432 </ul> <em>General</em>
3434 <li>View follows structure mouseover scrolls beyond
3435 position with wrapped view and hidden regions</li>
3436 <li>Find sequence position moves to wrong residue
3437 with/without hidden columns</li>
3438 <li>Sequence length given in alignment properties window
3440 <li>InvalidNumberFormat exceptions thrown when trying to
3441 import PDB like structure files</li>
3442 <li>Positional search results are only highlighted
3443 between user-supplied sequence start/end bounds</li>
3444 <li>End attribute of sequence is not validated</li>
3445 <li>Find dialog only finds first sequence containing a
3446 given sequence position</li>
3447 <li>Sequence numbering not preserved in MSF alignment
3449 <li>Jalview PDB file reader does not extract sequence
3450 from nucleotide chains correctly</li>
3451 <li>Structure colours not updated when tree partition
3452 changed in alignment</li>
3453 <li>Sequence associated secondary structure not correctly
3454 parsed in interleaved stockholm</li>
3455 <li>Colour by annotation dialog does not restore current
3457 <li>Hiding (nearly) all sequences doesn't work
3459 <li>Sequences containing lowercase letters are not
3460 properly associated with their pdb files</li>
3461 </ul> <em>Documentation and Development</em>
3463 <li>schemas/JalviewWsParamSet.xsd corrupted by
3464 ApplyCopyright tool</li>
3469 <div align="center">
3470 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3473 <td><em>Application</em>
3475 <li>New warning dialog when the Jalview Desktop cannot
3476 contact web services</li>
3477 <li>JABA service parameters for a preset are shown in
3478 service job window</li>
3479 <li>JABA Service menu entries reworded</li>
3483 <li>Modeller PIR IO broken - cannot correctly import a
3484 pir file emitted by Jalview</li>
3485 <li>Existing feature settings transferred to new
3486 alignment view created from cut'n'paste</li>
3487 <li>Improved test for mixed amino/nucleotide chains when
3488 parsing PDB files</li>
3489 <li>Consensus and conservation annotation rows
3490 occasionally become blank for all new windows</li>
3491 <li>Exception raised when right clicking above sequences
3492 in wrapped view mode</li>
3493 </ul> <em>Application</em>
3495 <li>multiple multiply aligned structure views cause cpu
3496 usage to hit 100% and computer to hang</li>
3497 <li>Web Service parameter layout breaks for long user
3498 parameter names</li>
3499 <li>Jaba service discovery hangs desktop if Jaba server
3506 <div align="center">
3507 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3510 <td><em>Application</em>
3512 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3513 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3516 <li>Web Services preference tab</li>
3517 <li>Analysis parameters dialog box and user defined
3519 <li>Improved speed and layout of Envision2 service menu</li>
3520 <li>Superpose structures using associated sequence
3522 <li>Export coordinates and projection as CSV from PCA
3524 </ul> <em>Applet</em>
3526 <li>enable javascript: execution by the applet via the
3527 link out mechanism</li>
3528 </ul> <em>Other</em>
3530 <li>Updated the Jmol Jalview interface to work with Jmol
3532 <li>The Jalview Desktop and JalviewLite applet now
3533 require Java 1.5</li>
3534 <li>Allow Jalview feature colour specification for GFF
3535 sequence annotation files</li>
3536 <li>New 'colour by label' keword in Jalview feature file
3537 type colour specification</li>
3538 <li>New Jalview Desktop Groovy API method that allows a
3539 script to check if it being run in an interactive session or
3540 in a batch operation from the Jalview command line</li>
3544 <li>clustalx colourscheme colours Ds preferentially when
3545 both D+E are present in over 50% of the column</li>
3546 </ul> <em>Application</em>
3548 <li>typo in AlignmentFrame->View->Hide->all but
3549 selected Regions menu item</li>
3550 <li>sequence fetcher replaces ',' for ';' when the ',' is
3551 part of a valid accession ID</li>
3552 <li>fatal OOM if object retrieved by sequence fetcher
3553 runs out of memory</li>
3554 <li>unhandled Out of Memory Error when viewing pca
3555 analysis results</li>
3556 <li>InstallAnywhere builds fail to launch on OS X java
3557 10.5 update 4 (due to apple Java 1.6 update)</li>
3558 <li>Installanywhere Jalview silently fails to launch</li>
3559 </ul> <em>Applet</em>
3561 <li>Jalview.getFeatureGroups() raises an
3562 ArrayIndexOutOfBoundsException if no feature groups are
3569 <div align="center">
3570 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3576 <li>Alignment prettyprinter doesn't cope with long
3578 <li>clustalx colourscheme colours Ds preferentially when
3579 both D+E are present in over 50% of the column</li>
3580 <li>nucleic acid structures retrieved from PDB do not
3581 import correctly</li>
3582 <li>More columns get selected than were clicked on when a
3583 number of columns are hidden</li>
3584 <li>annotation label popup menu not providing correct
3585 add/hide/show options when rows are hidden or none are
3587 <li>Stockholm format shown in list of readable formats,
3588 and parser copes better with alignments from RFAM.</li>
3589 <li>CSV output of consensus only includes the percentage
3590 of all symbols if sequence logo display is enabled</li>
3592 </ul> <em>Applet</em>
3594 <li>annotation panel disappears when annotation is
3596 </ul> <em>Application</em>
3598 <li>Alignment view not redrawn properly when new
3599 alignment opened where annotation panel is visible but no
3600 annotations are present on alignment</li>
3601 <li>pasted region containing hidden columns is
3602 incorrectly displayed in new alignment window</li>
3603 <li>Jalview slow to complete operations when stdout is
3604 flooded (fix is to close the Jalview console)</li>
3605 <li>typo in AlignmentFrame->View->Hide->all but
3606 selected Rregions menu item.</li>
3607 <li>inconsistent group submenu and Format submenu entry
3608 'Un' or 'Non'conserved</li>
3609 <li>Sequence feature settings are being shared by
3610 multiple distinct alignments</li>
3611 <li>group annotation not recreated when tree partition is
3613 <li>double click on group annotation to select sequences
3614 does not propagate to associated trees</li>
3615 <li>Mac OSX specific issues:
3617 <li>exception raised when mouse clicked on desktop
3618 window background</li>
3619 <li>Desktop menu placed on menu bar and application
3620 name set correctly</li>
3621 <li>sequence feature settings not wide enough for the
3622 save feature colourscheme button</li>
3631 <div align="center">
3632 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3635 <td><em>New Capabilities</em>
3637 <li>URL links generated from description line for
3638 regular-expression based URL links (applet and application)
3640 <li>Non-positional feature URL links are shown in link
3642 <li>Linked viewing of nucleic acid sequences and
3644 <li>Automatic Scrolling option in View menu to display
3645 the currently highlighted region of an alignment.</li>
3646 <li>Order an alignment by sequence length, or using the
3647 average score or total feature count for each sequence.</li>
3648 <li>Shading features by score or associated description</li>
3649 <li>Subdivide alignment and groups based on identity of
3650 selected subsequence (Make Groups from Selection).</li>
3651 <li>New hide/show options including Shift+Control+H to
3652 hide everything but the currently selected region.</li>
3653 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3654 </ul> <em>Application</em>
3656 <li>Fetch DB References capabilities and UI expanded to
3657 support retrieval from DAS sequence sources</li>
3658 <li>Local DAS Sequence sources can be added via the
3659 command line or via the Add local source dialog box.</li>
3660 <li>DAS Dbref and DbxRef feature types are parsed as
3661 database references and protein_name is parsed as
3662 description line (BioSapiens terms).</li>
3663 <li>Enable or disable non-positional feature and database
3664 references in sequence ID tooltip from View menu in
3666 <!-- <li>New hidden columns and rows and representatives capabilities
3667 in annotations file (in progress - not yet fully implemented)</li> -->
3668 <li>Group-associated consensus, sequence logos and
3669 conservation plots</li>
3670 <li>Symbol distributions for each column can be exported
3671 and visualized as sequence logos</li>
3672 <li>Optionally scale multi-character column labels to fit
3673 within each column of annotation row<!-- todo for applet -->
3675 <li>Optional automatic sort of associated alignment view
3676 when a new tree is opened.</li>
3677 <li>Jalview Java Console</li>
3678 <li>Better placement of desktop window when moving
3679 between different screens.</li>
3680 <li>New preference items for sequence ID tooltip and
3681 consensus annotation</li>
3682 <li>Client to submit sequences and IDs to Envision2
3684 <li><em>Vamsas Capabilities</em>
3686 <li>Improved VAMSAS synchronization (Jalview archive
3687 used to preserve views, structures, and tree display
3689 <li>Import of vamsas documents from disk or URL via
3691 <li>Sharing of selected regions between views and
3692 with other VAMSAS applications (Experimental feature!)</li>
3693 <li>Updated API to VAMSAS version 0.2</li>
3695 </ul> <em>Applet</em>
3697 <li>Middle button resizes annotation row height</li>
3700 <li>sortByTree (true/false) - automatically sort the
3701 associated alignment view by the tree when a new tree is
3703 <li>showTreeBootstraps (true/false) - show or hide
3704 branch bootstraps (default is to show them if available)</li>
3705 <li>showTreeDistances (true/false) - show or hide
3706 branch lengths (default is to show them if available)</li>
3707 <li>showUnlinkedTreeNodes (true/false) - indicate if
3708 unassociated nodes should be highlighted in the tree
3710 <li>heightScale and widthScale (1.0 or more) -
3711 increase the height or width of a cell in the alignment
3712 grid relative to the current font size.</li>
3715 <li>Non-positional features displayed in sequence ID
3717 </ul> <em>Other</em>
3719 <li>Features format: graduated colour definitions and
3720 specification of feature scores</li>
3721 <li>Alignment Annotations format: new keywords for group
3722 associated annotation (GROUP_REF) and annotation row display
3723 properties (ROW_PROPERTIES)</li>
3724 <li>XML formats extended to support graduated feature
3725 colourschemes, group associated annotation, and profile
3726 visualization settings.</li></td>
3729 <li>Source field in GFF files parsed as feature source
3730 rather than description</li>
3731 <li>Non-positional features are now included in sequence
3732 feature and gff files (controlled via non-positional feature
3733 visibility in tooltip).</li>
3734 <li>URL links generated for all feature links (bugfix)</li>
3735 <li>Added URL embedding instructions to features file
3737 <li>Codons containing ambiguous nucleotides translated as
3738 'X' in peptide product</li>
3739 <li>Match case switch in find dialog box works for both
3740 sequence ID and sequence string and query strings do not
3741 have to be in upper case to match case-insensitively.</li>
3742 <li>AMSA files only contain first column of
3743 multi-character column annotation labels</li>
3744 <li>Jalview Annotation File generation/parsing consistent
3745 with documentation (e.g. Stockholm annotation can be
3746 exported and re-imported)</li>
3747 <li>PDB files without embedded PDB IDs given a friendly
3749 <li>Find incrementally searches ID string matches as well
3750 as subsequence matches, and correctly reports total number
3754 <li>Better handling of exceptions during sequence
3756 <li>Dasobert generated non-positional feature URL
3757 link text excludes the start_end suffix</li>
3758 <li>DAS feature and source retrieval buttons disabled
3759 when fetch or registry operations in progress.</li>
3760 <li>PDB files retrieved from URLs are cached properly</li>
3761 <li>Sequence description lines properly shared via
3763 <li>Sequence fetcher fetches multiple records for all
3765 <li>Ensured that command line das feature retrieval
3766 completes before alignment figures are generated.</li>
3767 <li>Reduced time taken when opening file browser for
3769 <li>isAligned check prior to calculating tree, PCA or
3770 submitting an MSA to JNet now excludes hidden sequences.</li>
3771 <li>User defined group colours properly recovered
3772 from Jalview projects.</li>
3781 <div align="center">
3782 <strong>2.4.0.b2</strong><br> 28/10/2009
3787 <li>Experimental support for google analytics usage
3789 <li>Jalview privacy settings (user preferences and docs).</li>
3794 <li>Race condition in applet preventing startup in
3796 <li>Exception when feature created from selection beyond
3797 length of sequence.</li>
3798 <li>Allow synthetic PDB files to be imported gracefully</li>
3799 <li>Sequence associated annotation rows associate with
3800 all sequences with a given id</li>
3801 <li>Find function matches case-insensitively for sequence
3802 ID string searches</li>
3803 <li>Non-standard characters do not cause pairwise
3804 alignment to fail with exception</li>
3805 </ul> <em>Application Issues</em>
3807 <li>Sequences are now validated against EMBL database</li>
3808 <li>Sequence fetcher fetches multiple records for all
3810 </ul> <em>InstallAnywhere Issues</em>
3812 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3813 issue with installAnywhere mechanism)</li>
3814 <li>Command line launching of JARs from InstallAnywhere
3815 version (java class versioning error fixed)</li>
3822 <div align="center">
3823 <strong>2.4</strong><br> 27/8/2008
3826 <td><em>User Interface</em>
3828 <li>Linked highlighting of codon and amino acid from
3829 translation and protein products</li>
3830 <li>Linked highlighting of structure associated with
3831 residue mapping to codon position</li>
3832 <li>Sequence Fetcher provides example accession numbers
3833 and 'clear' button</li>
3834 <li>MemoryMonitor added as an option under Desktop's
3836 <li>Extract score function to parse whitespace separated
3837 numeric data in description line</li>
3838 <li>Column labels in alignment annotation can be centred.</li>
3839 <li>Tooltip for sequence associated annotation give name
3841 </ul> <em>Web Services and URL fetching</em>
3843 <li>JPred3 web service</li>
3844 <li>Prototype sequence search client (no public services
3846 <li>Fetch either seed alignment or full alignment from
3848 <li>URL Links created for matching database cross
3849 references as well as sequence ID</li>
3850 <li>URL Links can be created using regular-expressions</li>
3851 </ul> <em>Sequence Database Connectivity</em>
3853 <li>Retrieval of cross-referenced sequences from other
3855 <li>Generalised database reference retrieval and
3856 validation to all fetchable databases</li>
3857 <li>Fetch sequences from DAS sources supporting the
3858 sequence command</li>
3859 </ul> <em>Import and Export</em>
3860 <li>export annotation rows as CSV for spreadsheet import</li>
3861 <li>Jalview projects record alignment dataset associations,
3862 EMBL products, and cDNA sequence mappings</li>
3863 <li>Sequence Group colour can be specified in Annotation
3865 <li>Ad-hoc colouring of group in Annotation File using RGB
3866 triplet as name of colourscheme</li>
3867 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3869 <li>treenode binding for VAMSAS tree exchange</li>
3870 <li>local editing and update of sequences in VAMSAS
3871 alignments (experimental)</li>
3872 <li>Create new or select existing session to join</li>
3873 <li>load and save of vamsas documents</li>
3874 </ul> <em>Application command line</em>
3876 <li>-tree parameter to open trees (introduced for passing
3878 <li>-fetchfrom command line argument to specify nicknames
3879 of DAS servers to query for alignment features</li>
3880 <li>-dasserver command line argument to add new servers
3881 that are also automatically queried for features</li>
3882 <li>-groovy command line argument executes a given groovy
3883 script after all input data has been loaded and parsed</li>
3884 </ul> <em>Applet-Application data exchange</em>
3886 <li>Trees passed as applet parameters can be passed to
3887 application (when using "View in full
3888 application")</li>
3889 </ul> <em>Applet Parameters</em>
3891 <li>feature group display control parameter</li>
3892 <li>debug parameter</li>
3893 <li>showbutton parameter</li>
3894 </ul> <em>Applet API methods</em>
3896 <li>newView public method</li>
3897 <li>Window (current view) specific get/set public methods</li>
3898 <li>Feature display control methods</li>
3899 <li>get list of currently selected sequences</li>
3900 </ul> <em>New Jalview distribution features</em>
3902 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3903 <li>RELEASE file gives build properties for the latest
3904 Jalview release.</li>
3905 <li>Java 1.1 Applet build made easier and donotobfuscate
3906 property controls execution of obfuscator</li>
3907 <li>Build target for generating source distribution</li>
3908 <li>Debug flag for javacc</li>
3909 <li>.jalview_properties file is documented (slightly) in
3910 jalview.bin.Cache</li>
3911 <li>Continuous Build Integration for stable and
3912 development version of Application, Applet and source
3917 <li>selected region output includes visible annotations
3918 (for certain formats)</li>
3919 <li>edit label/displaychar contains existing label/char
3921 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3922 <li>shorter peptide product names from EMBL records</li>
3923 <li>Newick string generator makes compact representations</li>
3924 <li>bootstrap values parsed correctly for tree files with
3926 <li>pathological filechooser bug avoided by not allowing
3927 filenames containing a ':'</li>
3928 <li>Fixed exception when parsing GFF files containing
3929 global sequence features</li>
3930 <li>Alignment datasets are finalized only when number of
3931 references from alignment sequences goes to zero</li>
3932 <li>Close of tree branch colour box without colour
3933 selection causes cascading exceptions</li>
3934 <li>occasional negative imgwidth exceptions</li>
3935 <li>better reporting of non-fatal warnings to user when
3936 file parsing fails.</li>
3937 <li>Save works when Jalview project is default format</li>
3938 <li>Save as dialog opened if current alignment format is
3939 not a valid output format</li>
3940 <li>UniProt canonical names introduced for both das and
3942 <li>Histidine should be midblue (not pink!) in Zappo</li>
3943 <li>error messages passed up and output when data read
3945 <li>edit undo recovers previous dataset sequence when
3946 sequence is edited</li>
3947 <li>allow PDB files without pdb ID HEADER lines (like
3948 those generated by MODELLER) to be read in properly</li>
3949 <li>allow reading of JPred concise files as a normal
3951 <li>Stockholm annotation parsing and alignment properties
3952 import fixed for PFAM records</li>
3953 <li>Structure view windows have correct name in Desktop
3955 <li>annotation consisting of sequence associated scores
3956 can be read and written correctly to annotation file</li>
3957 <li>Aligned cDNA translation to aligned peptide works
3959 <li>Fixed display of hidden sequence markers and
3960 non-italic font for representatives in Applet</li>
3961 <li>Applet Menus are always embedded in applet window on
3963 <li>Newly shown features appear at top of stack (in
3965 <li>Annotations added via parameter not drawn properly
3966 due to null pointer exceptions</li>
3967 <li>Secondary structure lines are drawn starting from
3968 first column of alignment</li>
3969 <li>UniProt XML import updated for new schema release in
3971 <li>Sequence feature to sequence ID match for Features
3972 file is case-insensitive</li>
3973 <li>Sequence features read from Features file appended to
3974 all sequences with matching IDs</li>
3975 <li>PDB structure coloured correctly for associated views
3976 containing a sub-sequence</li>
3977 <li>PDB files can be retrieved by applet from Jar files</li>
3978 <li>feature and annotation file applet parameters
3979 referring to different directories are retrieved correctly</li>
3980 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3981 <li>Fixed application hang whilst waiting for
3982 splash-screen version check to complete</li>
3983 <li>Applet properly URLencodes input parameter values
3984 when passing them to the launchApp service</li>
3985 <li>display name and local features preserved in results
3986 retrieved from web service</li>
3987 <li>Visual delay indication for sequence retrieval and
3988 sequence fetcher initialisation</li>
3989 <li>updated Application to use DAS 1.53e version of
3990 dasobert DAS client</li>
3991 <li>Re-instated Full AMSA support and .amsa file
3993 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4001 <div align="center">
4002 <strong>2.3</strong><br> 9/5/07
4007 <li>Jmol 11.0.2 integration</li>
4008 <li>PDB views stored in Jalview XML files</li>
4009 <li>Slide sequences</li>
4010 <li>Edit sequence in place</li>
4011 <li>EMBL CDS features</li>
4012 <li>DAS Feature mapping</li>
4013 <li>Feature ordering</li>
4014 <li>Alignment Properties</li>
4015 <li>Annotation Scores</li>
4016 <li>Sort by scores</li>
4017 <li>Feature/annotation editing in applet</li>
4022 <li>Headless state operation in 2.2.1</li>
4023 <li>Incorrect and unstable DNA pairwise alignment</li>
4024 <li>Cut and paste of sequences with annotation</li>
4025 <li>Feature group display state in XML</li>
4026 <li>Feature ordering in XML</li>
4027 <li>blc file iteration selection using filename # suffix</li>
4028 <li>Stockholm alignment properties</li>
4029 <li>Stockhom alignment secondary structure annotation</li>
4030 <li>2.2.1 applet had no feature transparency</li>
4031 <li>Number pad keys can be used in cursor mode</li>
4032 <li>Structure Viewer mirror image resolved</li>
4039 <div align="center">
4040 <strong>2.2.1</strong><br> 12/2/07
4045 <li>Non standard characters can be read and displayed
4046 <li>Annotations/Features can be imported/exported to the
4048 <li>Applet allows editing of sequence/annotation/group
4049 name & description
4050 <li>Preference setting to display sequence name in
4052 <li>Annotation file format extended to allow
4053 Sequence_groups to be defined
4054 <li>Default opening of alignment overview panel can be
4055 specified in preferences
4056 <li>PDB residue numbering annotation added to associated
4062 <li>Applet crash under certain Linux OS with Java 1.6
4064 <li>Annotation file export / import bugs fixed
4065 <li>PNG / EPS image output bugs fixed
4071 <div align="center">
4072 <strong>2.2</strong><br> 27/11/06
4077 <li>Multiple views on alignment
4078 <li>Sequence feature editing
4079 <li>"Reload" alignment
4080 <li>"Save" to current filename
4081 <li>Background dependent text colour
4082 <li>Right align sequence ids
4083 <li>User-defined lower case residue colours
4086 <li>Menu item accelerator keys
4087 <li>Control-V pastes to current alignment
4088 <li>Cancel button for DAS Feature Fetching
4089 <li>PCA and PDB Viewers zoom via mouse roller
4090 <li>User-defined sub-tree colours and sub-tree selection
4092 <li>'New Window' button on the 'Output to Text box'
4097 <li>New memory efficient Undo/Redo System
4098 <li>Optimised symbol lookups and conservation/consensus
4100 <li>Region Conservation/Consensus recalculated after
4102 <li>Fixed Remove Empty Columns Bug (empty columns at end
4104 <li>Slowed DAS Feature Fetching for increased robustness.
4106 <li>Made angle brackets in ASCII feature descriptions
4108 <li>Re-instated Zoom function for PCA
4109 <li>Sequence descriptions conserved in web service
4111 <li>UniProt ID discoverer uses any word separated by
4113 <li>WsDbFetch query/result association resolved
4114 <li>Tree leaf to sequence mapping improved
4115 <li>Smooth fonts switch moved to FontChooser dialog box.
4122 <div align="center">
4123 <strong>2.1.1</strong><br> 12/9/06
4128 <li>Copy consensus sequence to clipboard</li>
4133 <li>Image output - rightmost residues are rendered if
4134 sequence id panel has been resized</li>
4135 <li>Image output - all offscreen group boundaries are
4137 <li>Annotation files with sequence references - all
4138 elements in file are relative to sequence position</li>
4139 <li>Mac Applet users can use Alt key for group editing</li>
4145 <div align="center">
4146 <strong>2.1</strong><br> 22/8/06
4151 <li>MAFFT Multiple Alignment in default Web Service list</li>
4152 <li>DAS Feature fetching</li>
4153 <li>Hide sequences and columns</li>
4154 <li>Export Annotations and Features</li>
4155 <li>GFF file reading / writing</li>
4156 <li>Associate structures with sequences from local PDB
4158 <li>Add sequences to exisiting alignment</li>
4159 <li>Recently opened files / URL lists</li>
4160 <li>Applet can launch the full application</li>
4161 <li>Applet has transparency for features (Java 1.2
4163 <li>Applet has user defined colours parameter</li>
4164 <li>Applet can load sequences from parameter
4165 "sequence<em>x</em>"
4171 <li>Redundancy Panel reinstalled in the Applet</li>
4172 <li>Monospaced font - EPS / rescaling bug fixed</li>
4173 <li>Annotation files with sequence references bug fixed</li>
4179 <div align="center">
4180 <strong>2.08.1</strong><br> 2/5/06
4185 <li>Change case of selected region from Popup menu</li>
4186 <li>Choose to match case when searching</li>
4187 <li>Middle mouse button and mouse movement can compress /
4188 expand the visible width and height of the alignment</li>
4193 <li>Annotation Panel displays complete JNet results</li>
4199 <div align="center">
4200 <strong>2.08b</strong><br> 18/4/06
4206 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4207 <li>Righthand label on wrapped alignments shows correct
4214 <div align="center">
4215 <strong>2.08</strong><br> 10/4/06
4220 <li>Editing can be locked to the selection area</li>
4221 <li>Keyboard editing</li>
4222 <li>Create sequence features from searches</li>
4223 <li>Precalculated annotations can be loaded onto
4225 <li>Features file allows grouping of features</li>
4226 <li>Annotation Colouring scheme added</li>
4227 <li>Smooth fonts off by default - Faster rendering</li>
4228 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4233 <li>Drag & Drop fixed on Linux</li>
4234 <li>Jalview Archive file faster to load/save, sequence
4235 descriptions saved.</li>
4241 <div align="center">
4242 <strong>2.07</strong><br> 12/12/05
4247 <li>PDB Structure Viewer enhanced</li>
4248 <li>Sequence Feature retrieval and display enhanced</li>
4249 <li>Choose to output sequence start-end after sequence
4250 name for file output</li>
4251 <li>Sequence Fetcher WSDBFetch@EBI</li>
4252 <li>Applet can read feature files, PDB files and can be
4253 used for HTML form input</li>
4258 <li>HTML output writes groups and features</li>
4259 <li>Group editing is Control and mouse click</li>
4260 <li>File IO bugs</li>
4266 <div align="center">
4267 <strong>2.06</strong><br> 28/9/05
4272 <li>View annotations in wrapped mode</li>
4273 <li>More options for PCA viewer</li>
4278 <li>GUI bugs resolved</li>
4279 <li>Runs with -nodisplay from command line</li>
4285 <div align="center">
4286 <strong>2.05b</strong><br> 15/9/05
4291 <li>Choose EPS export as lineart or text</li>
4292 <li>Jar files are executable</li>
4293 <li>Can read in Uracil - maps to unknown residue</li>
4298 <li>Known OutOfMemory errors give warning message</li>
4299 <li>Overview window calculated more efficiently</li>
4300 <li>Several GUI bugs resolved</li>
4306 <div align="center">
4307 <strong>2.05</strong><br> 30/8/05
4312 <li>Edit and annotate in "Wrapped" view</li>
4317 <li>Several GUI bugs resolved</li>
4323 <div align="center">
4324 <strong>2.04</strong><br> 24/8/05
4329 <li>Hold down mouse wheel & scroll to change font
4335 <li>Improved JPred client reliability</li>
4336 <li>Improved loading of Jalview files</li>
4342 <div align="center">
4343 <strong>2.03</strong><br> 18/8/05
4348 <li>Set Proxy server name and port in preferences</li>
4349 <li>Multiple URL links from sequence ids</li>
4350 <li>User Defined Colours can have a scheme name and added
4352 <li>Choose to ignore gaps in consensus calculation</li>
4353 <li>Unix users can set default web browser</li>
4354 <li>Runs without GUI for batch processing</li>
4355 <li>Dynamically generated Web Service Menus</li>
4360 <li>InstallAnywhere download for Sparc Solaris</li>
4366 <div align="center">
4367 <strong>2.02</strong><br> 18/7/05
4373 <li>Copy & Paste order of sequences maintains
4374 alignment order.</li>
4380 <div align="center">
4381 <strong>2.01</strong><br> 12/7/05
4386 <li>Use delete key for deleting selection.</li>
4387 <li>Use Mouse wheel to scroll sequences.</li>
4388 <li>Help file updated to describe how to add alignment
4390 <li>Version and build date written to build properties
4392 <li>InstallAnywhere installation will check for updates
4393 at launch of Jalview.</li>
4398 <li>Delete gaps bug fixed.</li>
4399 <li>FileChooser sorts columns.</li>
4400 <li>Can remove groups one by one.</li>
4401 <li>Filechooser icons installed.</li>
4402 <li>Finder ignores return character when searching.
4403 Return key will initiate a search.<br>
4410 <div align="center">
4411 <strong>2.0</strong><br> 20/6/05
4416 <li>New codebase</li>