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 */
41 /* doesnt get processed in javahelp */
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
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 <li><strong>Java 11 Support</strong>
185 <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
186 and getdown release channels
189 <!-- -->OSX GUI integrations for App menu's 'About' entry and
194 <em>Deprecations</em>
197 <!-- JAL-3035 -->DAS sequence retrieval and annotation
198 capabilities removed from the Jalview Desktop
201 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
202 unmarshalling has been replaced by JAXB for Jalview projects
203 and XML based data retrieval clients</li>
204 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
205 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
207 <em>Development and Release Processes</em>
210 <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
211 Installers built with Install4j (licensed to the Jalview open
212 source project) rather than InstallAnywhere
215 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
216 settings, receive over the air updates and launch specific
217 versions via (<a href="https://github.com/threerings/getdown">Three
221 <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
224 <!-- JAL-3225 -->Eclipse project configuration managed with
228 Atlassian Bamboo continuous integration for
229 unattended Test Suite execution</li>
231 <!-- JAL-2864 -->Memory test suite to detect leaks in common
234 <!-- JAL-3140 -->IntervalStoreJ (NCList
235 implementation that alows updates) used for Sequence Feature collections</li>
238 <td align="left" valign="top">
241 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
243 <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
245 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
247 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
248 Jalview project involving multiple views</li>
250 <!-- JAL-3164 -->Overview for complementary view in a linked
251 CDS/Protein alignment is not updated when Hide Columns by
252 Annotation dialog hides columns</li>
254 <!-- JAL-3158 -->Selection highlighting in the complement of
255 a CDS/Protein alignment stops working after making a
256 selection in one view, then making another selection in the
259 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
261 <!-- JAL-3154 -->Table Columns could be re-ordered in
262 Feature Settings and Jalview Preferences panels</li>
264 <!-- JAL-2865 -->Jalview hangs when closing windows
265 or the overview updates with large alignments</li>
267 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
268 region if columns were selected by dragging right-to-left
269 and the mouse moved to the left of the first column</li>
271 <!-- JAL-3218 -->Couldn't hide selected columns adjacent
272 to a hidden column marker via scale popup menu</li>
274 <!-- JAL-2846 -->Error message for trying to load in invalid
275 URLs doesn't tell users the invalid URL</li>
277 <!-- JAL-3178 -->Nonpositional features lose feature group
278 on export as Jalview features file</li>
280 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
281 printed when columns are hidden</li>
283 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
285 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
286 dragging out of Scale or Annotation Panel</li>
288 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
290 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
292 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
294 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
296 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
298 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
300 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
301 opening an alignment</li>
303 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
305 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
306 different groups in the alignment are selected</li>
308 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
310 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
312 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
314 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
316 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
318 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
320 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
322 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
324 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
326 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
328 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
330 <!-- JAL-914 -->Help page can be opened twice</li>
335 <!-- JAL-2822 -->Start and End should be updated when
336 sequence data at beginning or end of alignment added/removed
337 via 'Edit' sequence</li>
339 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
340 sequence features correctly when start of sequence is
341 removed (Known defect since 2.10)</li>
343 <em>New Known Defects</em>
346 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
348 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
350 <!-- JAL-3240 -->Display is incorrect after removing gapped columns within hidden columns</li>
355 <td width="60" nowrap>
357 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
360 <td><div align="left">
364 <!-- JAL-3101 -->Default memory for Jalview webstart and
365 InstallAnywhere increased to 1G.
368 <!-- JAL-247 -->Hidden sequence markers and representative
369 sequence bolding included when exporting alignment as EPS,
370 SVG, PNG or HTML. <em>Display is configured via the
371 Format menu, or for command-line use via a jalview
372 properties file.</em>
375 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
376 API and sequence data now imported as JSON.
379 <!-- JAL-3065 -->Change in recommended way of starting
380 Jalview via a Java command line: add jars in lib directory
381 to CLASSPATH, rather than via the deprecated java.ext.dirs
388 <!-- JAL-3047 -->Support added to execute test suite
389 instrumented with <a href="http://openclover.org/">Open
394 <td><div align="left">
398 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
399 row shown in Feredoxin Structure alignment view of example
403 <!-- JAL-2854 -->Annotation obscures sequences if lots of
404 annotation displayed.
407 <!-- JAL-3107 -->Group conservation/consensus not shown
408 for newly created group when 'Apply to all groups'
412 <!-- JAL-3087 -->Corrupted display when switching to
413 wrapped mode when sequence panel's vertical scrollbar is
417 <!-- JAL-3003 -->Alignment is black in exported EPS file
418 when sequences are selected in exported view.</em>
421 <!-- JAL-3059 -->Groups with different coloured borders
422 aren't rendered with correct colour.
425 <!-- JAL-3092 -->Jalview could hang when importing certain
426 types of knotted RNA secondary structure.
429 <!-- JAL-3095 -->Sequence highlight and selection in
430 trimmed VARNA 2D structure is incorrect for sequences that
434 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
435 annotation when columns are inserted into an alignment,
436 and when exporting as Stockholm flatfile.
439 <!-- JAL-3053 -->Jalview annotation rows containing upper
440 and lower-case 'E' and 'H' do not automatically get
441 treated as RNA secondary structure.
444 <!-- JAL-3106 -->.jvp should be used as default extension
445 (not .jar) when saving a jalview project file.
448 <!-- JAL-3105 -->Mac Users: closing a window correctly
449 transfers focus to previous window on OSX
452 <em>Java 10 Issues Resolved</em>
455 <!-- JAL-2988 -->OSX - Can't save new files via the File
456 or export menus by typing in a name into the Save dialog
460 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
461 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
462 'look and feel' which has improved compatibility with the
463 latest version of OSX.
470 <td width="60" nowrap>
472 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
473 <em>7/06/2018</em></strong>
476 <td><div align="left">
480 <!-- JAL-2920 -->Use HGVS nomenclature for variant
481 annotation retrieved from Uniprot
484 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
485 onto the Jalview Desktop
489 <td><div align="left">
493 <!-- JAL-3017 -->Cannot import features with multiple
494 variant elements (blocks import of some Uniprot records)
497 <!-- JAL-2997 -->Clustal files with sequence positions in
498 right-hand column parsed correctly
501 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
502 not alignment area in exported graphic
505 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
506 window has input focus
509 <!-- JAL-2992 -->Annotation panel set too high when
510 annotation added to view (Windows)
513 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
514 network connectivity is poor
517 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
518 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
519 the currently open URL and links from a page viewed in
520 Firefox or Chrome on Windows is now fully supported. If
521 you are using Edge, only links in the page can be
522 dragged, and with Internet Explorer, only the currently
523 open URL in the browser can be dropped onto Jalview.</em>
529 <td width="60" nowrap>
531 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
534 <td><div align="left">
538 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
539 for disabling automatic superposition of multiple
540 structures and open structures in existing views
543 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
544 ID and annotation area margins can be click-dragged to
548 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
552 <!-- JAL-2759 -->Improved performance for large alignments
553 and lots of hidden columns
556 <!-- JAL-2593 -->Improved performance when rendering lots
557 of features (particularly when transparency is disabled)
562 <td><div align="left">
565 <!-- JAL-2899 -->Structure and Overview aren't updated
566 when Colour By Annotation threshold slider is adjusted
569 <!-- JAL-2778 -->Slow redraw when Overview panel shown
570 overlapping alignment panel
573 <!-- JAL-2929 -->Overview doesn't show end of unpadded
577 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
578 improved: CDS not handled correctly if transcript has no
582 <!-- JAL-2321 -->Secondary structure and temperature
583 factor annotation not added to sequence when local PDB
584 file associated with it by drag'n'drop or structure
588 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
589 dialog doesn't import PDB files dropped on an alignment
592 <!-- JAL-2666 -->Linked scrolling via protein horizontal
593 scroll bar doesn't work for some CDS/Protein views
596 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
597 Java 1.8u153 onwards and Java 1.9u4+.
600 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
601 columns in annotation row
604 <!-- JAL-2913 -->Preferences panel's ID Width control is not
605 honored in batch mode
608 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
609 for structures added to existing Jmol view
612 <!-- JAL-2223 -->'View Mappings' includes duplicate
613 entries after importing project with multiple views
616 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
617 protein sequences via SIFTS from associated PDB entries
618 with negative residue numbers or missing residues fails
621 <!-- JAL-2952 -->Exception when shading sequence with negative
622 Temperature Factor values from annotated PDB files (e.g.
623 as generated by CONSURF)
626 <!-- JAL-2920 -->Uniprot 'sequence variant' features
627 tooltip doesn't include a text description of mutation
630 <!-- JAL-2922 -->Invert displayed features very slow when
631 structure and/or overview windows are also shown
634 <!-- JAL-2954 -->Selecting columns from highlighted regions
635 very slow for alignments with large numbers of sequences
638 <!-- JAL-2925 -->Copy Consensus fails for group consensus
639 with 'StringIndexOutOfBounds'
642 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
643 platforms running Java 10
646 <!-- JAL-2960 -->Adding a structure to existing structure
647 view appears to do nothing because the view is hidden behind the alignment view
653 <!-- JAL-2926 -->Copy consensus sequence option in applet
654 should copy the group consensus when popup is opened on it
660 <!-- JAL-2913 -->Fixed ID width preference is not respected
663 <em>New Known Defects</em>
666 <!-- JAL-2973 --> Exceptions occasionally raised when
667 editing a large alignment and overview is displayed
670 <!-- JAL-2974 -->'Overview updating' progress bar is shown
671 repeatedly after a series of edits even when the overview
672 is no longer reflecting updates
675 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
676 structures for protein subsequence (if 'Trim Retrieved
677 Sequences' enabled) or Ensembl isoforms (Workaround in
678 2.10.4 is to fail back to N&W mapping)
685 <td width="60" nowrap>
687 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
690 <td><div align="left">
691 <ul><li>Updated Certum Codesigning Certificate
692 (Valid till 30th November 2018)</li></ul></div></td>
693 <td><div align="left">
696 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
697 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
698 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
699 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
700 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
701 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
702 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
708 <td width="60" nowrap>
710 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
713 <td><div align="left">
717 <!-- JAL-2446 -->Faster and more efficient management and
718 rendering of sequence features
721 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
722 429 rate limit request hander
725 <!-- JAL-2773 -->Structure views don't get updated unless
726 their colours have changed
729 <!-- JAL-2495 -->All linked sequences are highlighted for
730 a structure mousover (Jmol) or selection (Chimera)
733 <!-- JAL-2790 -->'Cancel' button in progress bar for
734 JABAWS AACon, RNAAliFold and Disorder prediction jobs
737 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
738 view from Ensembl locus cross-references
741 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
745 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
746 feature can be disabled
749 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
750 PDB easier retrieval of sequences for lists of IDs
753 <!-- JAL-2758 -->Short names for sequences retrieved from
759 <li>Groovy interpreter updated to 2.4.12</li>
760 <li>Example groovy script for generating a matrix of
761 percent identity scores for current alignment.</li>
763 <em>Testing and Deployment</em>
766 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
770 <td><div align="left">
774 <!-- JAL-2643 -->Pressing tab after updating the colour
775 threshold text field doesn't trigger an update to the
779 <!-- JAL-2682 -->Race condition when parsing sequence ID
783 <!-- JAL-2608 -->Overview windows are also closed when
784 alignment window is closed
787 <!-- JAL-2548 -->Export of features doesn't always respect
791 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
792 takes a long time in Cursor mode
798 <!-- JAL-2777 -->Structures with whitespace chainCode
799 cannot be viewed in Chimera
802 <!-- JAL-2728 -->Protein annotation panel too high in
806 <!-- JAL-2757 -->Can't edit the query after the server
807 error warning icon is shown in Uniprot and PDB Free Text
811 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
814 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
817 <!-- JAL-2739 -->Hidden column marker in last column not
818 rendered when switching back from Wrapped to normal view
821 <!-- JAL-2768 -->Annotation display corrupted when
822 scrolling right in unwapped alignment view
825 <!-- JAL-2542 -->Existing features on subsequence
826 incorrectly relocated when full sequence retrieved from
830 <!-- JAL-2733 -->Last reported memory still shown when
831 Desktop->Show Memory is unticked (OSX only)
834 <!-- JAL-2658 -->Amend Features dialog doesn't allow
835 features of same type and group to be selected for
839 <!-- JAL-2524 -->Jalview becomes sluggish in wide
840 alignments when hidden columns are present
843 <!-- JAL-2392 -->Jalview freezes when loading and
844 displaying several structures
847 <!-- JAL-2732 -->Black outlines left after resizing or
851 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
852 within the Jalview desktop on OSX
855 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
856 when in wrapped alignment mode
859 <!-- JAL-2636 -->Scale mark not shown when close to right
860 hand end of alignment
863 <!-- JAL-2684 -->Pairwise alignment of selected regions of
864 each selected sequence do not have correct start/end
868 <!-- JAL-2793 -->Alignment ruler height set incorrectly
869 after canceling the Alignment Window's Font dialog
872 <!-- JAL-2036 -->Show cross-references not enabled after
873 restoring project until a new view is created
876 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
877 URL links appears when only default EMBL-EBI link is
878 configured (since 2.10.2b2)
881 <!-- JAL-2775 -->Overview redraws whole window when box
885 <!-- JAL-2225 -->Structure viewer doesn't map all chains
886 in a multi-chain structure when viewing alignment
887 involving more than one chain (since 2.10)
890 <!-- JAL-2811 -->Double residue highlights in cursor mode
891 if new selection moves alignment window
894 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
895 arrow key in cursor mode to pass hidden column marker
898 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
899 that produces correctly annotated transcripts and products
902 <!-- JAL-2776 -->Toggling a feature group after first time
903 doesn't update associated structure view
906 <em>Applet</em><br />
909 <!-- JAL-2687 -->Concurrent modification exception when
910 closing alignment panel
913 <em>BioJSON</em><br />
916 <!-- JAL-2546 -->BioJSON export does not preserve
917 non-positional features
920 <em>New Known Issues</em>
923 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
924 sequence features correctly (for many previous versions of
928 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
929 using cursor in wrapped panel other than top
932 <!-- JAL-2791 -->Select columns containing feature ignores
933 graduated colour threshold
936 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
937 always preserve numbering and sequence features
940 <em>Known Java 9 Issues</em>
943 <!-- JAL-2902 -->Groovy Console very slow to open and is
944 not responsive when entering characters (Webstart, Java
951 <td width="60" nowrap>
953 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
954 <em>2/10/2017</em></strong>
957 <td><div align="left">
958 <em>New features in Jalview Desktop</em>
961 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
963 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
967 <td><div align="left">
971 <td width="60" nowrap>
973 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
974 <em>7/9/2017</em></strong>
977 <td><div align="left">
981 <!-- JAL-2588 -->Show gaps in overview window by colouring
982 in grey (sequences used to be coloured grey, and gaps were
986 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
990 <!-- JAL-2587 -->Overview updates immediately on increase
991 in size and progress bar shown as higher resolution
992 overview is recalculated
997 <td><div align="left">
1001 <!-- JAL-2664 -->Overview window redraws every hidden
1002 column region row by row
1005 <!-- JAL-2681 -->duplicate protein sequences shown after
1006 retrieving Ensembl crossrefs for sequences from Uniprot
1009 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1010 format setting is unticked
1013 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1014 if group has show boxes format setting unticked
1017 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1018 autoscrolling whilst dragging current selection group to
1019 include sequences and columns not currently displayed
1022 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1023 assemblies are imported via CIF file
1026 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1027 displayed when threshold or conservation colouring is also
1031 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1035 <!-- JAL-2673 -->Jalview continues to scroll after
1036 dragging a selected region off the visible region of the
1040 <!-- JAL-2724 -->Cannot apply annotation based
1041 colourscheme to all groups in a view
1044 <!-- JAL-2511 -->IDs don't line up with sequences
1045 initially after font size change using the Font chooser or
1052 <td width="60" nowrap>
1053 <div align="center">
1054 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1057 <td><div align="left">
1058 <em>Calculations</em>
1062 <!-- JAL-1933 -->Occupancy annotation row shows number of
1063 ungapped positions in each column of the alignment.
1066 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1067 a calculation dialog box
1070 <!-- JAL-2379 -->Revised implementation of PCA for speed
1071 and memory efficiency (~30x faster)
1074 <!-- JAL-2403 -->Revised implementation of sequence
1075 similarity scores as used by Tree, PCA, Shading Consensus
1076 and other calculations
1079 <!-- JAL-2416 -->Score matrices are stored as resource
1080 files within the Jalview codebase
1083 <!-- JAL-2500 -->Trees computed on Sequence Feature
1084 Similarity may have different topology due to increased
1091 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1092 model for alignments and groups
1095 <!-- JAL-384 -->Custom shading schemes created via groovy
1102 <!-- JAL-2526 -->Efficiency improvements for interacting
1103 with alignment and overview windows
1106 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1110 <!-- JAL-2388 -->Hidden columns and sequences can be
1114 <!-- JAL-2611 -->Click-drag in visible area allows fine
1115 adjustment of visible position
1119 <em>Data import/export</em>
1122 <!-- JAL-2535 -->Posterior probability annotation from
1123 Stockholm files imported as sequence associated annotation
1126 <!-- JAL-2507 -->More robust per-sequence positional
1127 annotation input/output via stockholm flatfile
1130 <!-- JAL-2533 -->Sequence names don't include file
1131 extension when importing structure files without embedded
1132 names or PDB accessions
1135 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1136 format sequence substitution matrices
1139 <em>User Interface</em>
1142 <!-- JAL-2447 --> Experimental Features Checkbox in
1143 Desktop's Tools menu to hide or show untested features in
1147 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1148 via Overview or sequence motif search operations
1151 <!-- JAL-2547 -->Amend sequence features dialog box can be
1152 opened by double clicking gaps within sequence feature
1156 <!-- JAL-1476 -->Status bar message shown when not enough
1157 aligned positions were available to create a 3D structure
1161 <em>3D Structure</em>
1164 <!-- JAL-2430 -->Hidden regions in alignment views are not
1165 coloured in linked structure views
1168 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1169 file-based command exchange
1172 <!-- JAL-2375 -->Structure chooser automatically shows
1173 Cached Structures rather than querying the PDBe if
1174 structures are already available for sequences
1177 <!-- JAL-2520 -->Structures imported via URL are cached in
1178 the Jalview project rather than downloaded again when the
1179 project is reopened.
1182 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1183 to transfer Chimera's structure attributes as Jalview
1184 features, and vice-versa (<strong>Experimental
1188 <em>Web Services</em>
1191 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1194 <!-- JAL-2335 -->Filter non-standard amino acids and
1195 nucleotides when submitting to AACon and other MSA
1199 <!-- JAL-2316, -->URLs for viewing database
1200 cross-references provided by identifiers.org and the
1201 EMBL-EBI's MIRIAM DB
1208 <!-- JAL-2344 -->FileFormatI interface for describing and
1209 identifying file formats (instead of String constants)
1212 <!-- JAL-2228 -->FeatureCounter script refactored for
1213 efficiency when counting all displayed features (not
1214 backwards compatible with 2.10.1)
1217 <em>Example files</em>
1220 <!-- JAL-2631 -->Graduated feature colour style example
1221 included in the example feature file
1224 <em>Documentation</em>
1227 <!-- JAL-2339 -->Release notes reformatted for readability
1228 with the built-in Java help viewer
1231 <!-- JAL-1644 -->Find documentation updated with 'search
1232 sequence description' option
1238 <!-- JAL-2485, -->External service integration tests for
1239 Uniprot REST Free Text Search Client
1242 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1245 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1250 <td><div align="left">
1251 <em>Calculations</em>
1254 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1255 matrix - C->R should be '-3'<br />Old matrix restored
1256 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1258 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1259 Jalview's treatment of gaps in PCA and substitution matrix
1260 based Tree calculations.<br /> <br />In earlier versions
1261 of Jalview, gaps matching gaps were penalised, and gaps
1262 matching non-gaps penalised even more. In the PCA
1263 calculation, gaps were actually treated as non-gaps - so
1264 different costs were applied, which meant Jalview's PCAs
1265 were different to those produced by SeqSpace.<br />Jalview
1266 now treats gaps in the same way as SeqSpace (ie it scores
1267 them as 0). <br /> <br />Enter the following in the
1268 Groovy console to restore pre-2.10.2 behaviour:<br />
1269 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1270 // for 2.10.1 mode <br />
1271 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1272 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1273 these settings will affect all subsequent tree and PCA
1274 calculations (not recommended)</em></li>
1276 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1277 scaling of branch lengths for trees computed using
1278 Sequence Feature Similarity.
1281 <!-- JAL-2377 -->PCA calculation could hang when
1282 generating output report when working with highly
1283 redundant alignments
1286 <!-- JAL-2544 --> Sort by features includes features to
1287 right of selected region when gaps present on right-hand
1291 <em>User Interface</em>
1294 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1295 doesn't reselect a specific sequence's associated
1296 annotation after it was used for colouring a view
1299 <!-- JAL-2419 -->Current selection lost if popup menu
1300 opened on a region of alignment without groups
1303 <!-- JAL-2374 -->Popup menu not always shown for regions
1304 of an alignment with overlapping groups
1307 <!-- JAL-2310 -->Finder double counts if both a sequence's
1308 name and description match
1311 <!-- JAL-2370 -->Hiding column selection containing two
1312 hidden regions results in incorrect hidden regions
1315 <!-- JAL-2386 -->'Apply to all groups' setting when
1316 changing colour does not apply Conservation slider value
1320 <!-- JAL-2373 -->Percentage identity and conservation menu
1321 items do not show a tick or allow shading to be disabled
1324 <!-- JAL-2385 -->Conservation shading or PID threshold
1325 lost when base colourscheme changed if slider not visible
1328 <!-- JAL-2547 -->Sequence features shown in tooltip for
1329 gaps before start of features
1332 <!-- JAL-2623 -->Graduated feature colour threshold not
1333 restored to UI when feature colour is edited
1336 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1337 a time when scrolling vertically in wrapped mode.
1340 <!-- JAL-2630 -->Structure and alignment overview update
1341 as graduate feature colour settings are modified via the
1345 <!-- JAL-2034 -->Overview window doesn't always update
1346 when a group defined on the alignment is resized
1349 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1350 wrapped view result in positional status updates
1354 <!-- JAL-2563 -->Status bar doesn't show position for
1355 ambiguous amino acid and nucleotide symbols
1358 <!-- JAL-2602 -->Copy consensus sequence failed if
1359 alignment included gapped columns
1362 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1363 widgets don't permanently disappear
1366 <!-- JAL-2503 -->Cannot select or filter quantitative
1367 annotation that are shown only as column labels (e.g.
1368 T-Coffee column reliability scores)
1371 <!-- JAL-2594 -->Exception thrown if trying to create a
1372 sequence feature on gaps only
1375 <!-- JAL-2504 -->Features created with 'New feature'
1376 button from a Find inherit previously defined feature type
1377 rather than the Find query string
1380 <!-- JAL-2423 -->incorrect title in output window when
1381 exporting tree calculated in Jalview
1384 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1385 and then revealing them reorders sequences on the
1389 <!-- JAL-964 -->Group panel in sequence feature settings
1390 doesn't update to reflect available set of groups after
1391 interactively adding or modifying features
1394 <!-- JAL-2225 -->Sequence Database chooser unusable on
1398 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1399 only excluded gaps in current sequence and ignored
1406 <!-- JAL-2421 -->Overview window visible region moves
1407 erratically when hidden rows or columns are present
1410 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1411 Structure Viewer's colour menu don't correspond to
1415 <!-- JAL-2405 -->Protein specific colours only offered in
1416 colour and group colour menu for protein alignments
1419 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1420 reflect currently selected view or group's shading
1424 <!-- JAL-2624 -->Feature colour thresholds not respected
1425 when rendered on overview and structures when opacity at
1429 <!-- JAL-2589 -->User defined gap colour not shown in
1430 overview when features overlaid on alignment
1433 <em>Data import/export</em>
1436 <!-- JAL-2576 -->Very large alignments take a long time to
1440 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1441 added after a sequence was imported are not written to
1445 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1446 when importing RNA secondary structure via Stockholm
1449 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1450 not shown in correct direction for simple pseudoknots
1453 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1454 with lightGray or darkGray via features file (but can
1458 <!-- JAL-2383 -->Above PID colour threshold not recovered
1459 when alignment view imported from project
1462 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1463 structure and sequences extracted from structure files
1464 imported via URL and viewed in Jmol
1467 <!-- JAL-2520 -->Structures loaded via URL are saved in
1468 Jalview Projects rather than fetched via URL again when
1469 the project is loaded and the structure viewed
1472 <em>Web Services</em>
1475 <!-- JAL-2519 -->EnsemblGenomes example failing after
1476 release of Ensembl v.88
1479 <!-- JAL-2366 -->Proxy server address and port always
1480 appear enabled in Preferences->Connections
1483 <!-- JAL-2461 -->DAS registry not found exceptions
1484 removed from console output
1487 <!-- JAL-2582 -->Cannot retrieve protein products from
1488 Ensembl by Peptide ID
1491 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1492 created from SIFTs, and spurious 'Couldn't open structure
1493 in Chimera' errors raised after April 2017 update (problem
1494 due to 'null' string rather than empty string used for
1495 residues with no corresponding PDB mapping).
1498 <em>Application UI</em>
1501 <!-- JAL-2361 -->User Defined Colours not added to Colour
1505 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1506 case' residues (button in colourscheme editor debugged and
1507 new documentation and tooltips added)
1510 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1511 doesn't restore group-specific text colour thresholds
1514 <!-- JAL-2243 -->Feature settings panel does not update as
1515 new features are added to alignment
1518 <!-- JAL-2532 -->Cancel in feature settings reverts
1519 changes to feature colours via the Amend features dialog
1522 <!-- JAL-2506 -->Null pointer exception when attempting to
1523 edit graduated feature colour via amend features dialog
1527 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1528 selection menu changes colours of alignment views
1531 <!-- JAL-2426 -->Spurious exceptions in console raised
1532 from alignment calculation workers after alignment has
1536 <!-- JAL-1608 -->Typo in selection popup menu - Create
1537 groups now 'Create Group'
1540 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1541 Create/Undefine group doesn't always work
1544 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1545 shown again after pressing 'Cancel'
1548 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1549 adjusts start position in wrap mode
1552 <!-- JAL-2563 -->Status bar doesn't show positions for
1553 ambiguous amino acids
1556 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1557 CDS/Protein view after CDS sequences added for aligned
1561 <!-- JAL-2592 -->User defined colourschemes called 'User
1562 Defined' don't appear in Colours menu
1568 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1569 score models doesn't always result in an updated PCA plot
1572 <!-- JAL-2442 -->Features not rendered as transparent on
1573 overview or linked structure view
1576 <!-- JAL-2372 -->Colour group by conservation doesn't
1580 <!-- JAL-2517 -->Hitting Cancel after applying
1581 user-defined colourscheme doesn't restore original
1588 <!-- JAL-2314 -->Unit test failure:
1589 jalview.ws.jabaws.RNAStructExportImport setup fails
1592 <!-- JAL-2307 -->Unit test failure:
1593 jalview.ws.sifts.SiftsClientTest due to compatibility
1594 problems with deep array comparison equality asserts in
1595 successive versions of TestNG
1598 <!-- JAL-2479 -->Relocated StructureChooserTest and
1599 ParameterUtilsTest Unit tests to Network suite
1602 <em>New Known Issues</em>
1605 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1606 phase after a sequence motif find operation
1609 <!-- JAL-2550 -->Importing annotation file with rows
1610 containing just upper and lower case letters are
1611 interpreted as WUSS RNA secondary structure symbols
1614 <!-- JAL-2590 -->Cannot load and display Newick trees
1615 reliably from eggnog Ortholog database
1618 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1619 containing features of type Highlight' when 'B' is pressed
1620 to mark columns containing highlighted regions.
1623 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1624 doesn't always add secondary structure annotation.
1629 <td width="60" nowrap>
1630 <div align="center">
1631 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1634 <td><div align="left">
1638 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1639 for all consensus calculations
1642 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1645 <li>Updated Jalview's Certum code signing certificate
1648 <em>Application</em>
1651 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1652 set of database cross-references, sorted alphabetically
1655 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1656 from database cross references. Users with custom links
1657 will receive a <a href="webServices/urllinks.html#warning">warning
1658 dialog</a> asking them to update their preferences.
1661 <!-- JAL-2287-->Cancel button and escape listener on
1662 dialog warning user about disconnecting Jalview from a
1666 <!-- JAL-2320-->Jalview's Chimera control window closes if
1667 the Chimera it is connected to is shut down
1670 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1671 columns menu item to mark columns containing highlighted
1672 regions (e.g. from structure selections or results of a
1676 <!-- JAL-2284-->Command line option for batch-generation
1677 of HTML pages rendering alignment data with the BioJS
1687 <!-- JAL-2286 -->Columns with more than one modal residue
1688 are not coloured or thresholded according to percent
1689 identity (first observed in Jalview 2.8.2)
1692 <!-- JAL-2301 -->Threonine incorrectly reported as not
1696 <!-- JAL-2318 -->Updates to documentation pages (above PID
1697 threshold, amino acid properties)
1700 <!-- JAL-2292 -->Lower case residues in sequences are not
1701 reported as mapped to residues in a structure file in the
1705 <!--JAL-2324 -->Identical features with non-numeric scores
1706 could be added multiple times to a sequence
1709 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1710 bond features shown as two highlighted residues rather
1711 than a range in linked structure views, and treated
1712 correctly when selecting and computing trees from features
1715 <!-- JAL-2281-->Custom URL links for database
1716 cross-references are matched to database name regardless
1721 <em>Application</em>
1724 <!-- JAL-2282-->Custom URL links for specific database
1725 names without regular expressions also offer links from
1729 <!-- JAL-2315-->Removing a single configured link in the
1730 URL links pane in Connections preferences doesn't actually
1731 update Jalview configuration
1734 <!-- JAL-2272-->CTRL-Click on a selected region to open
1735 the alignment area popup menu doesn't work on El-Capitan
1738 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1739 files with similarly named sequences if dropped onto the
1743 <!-- JAL-2312 -->Additional mappings are shown for PDB
1744 entries where more chains exist in the PDB accession than
1745 are reported in the SIFTS file
1748 <!-- JAL-2317-->Certain structures do not get mapped to
1749 the structure view when displayed with Chimera
1752 <!-- JAL-2317-->No chains shown in the Chimera view
1753 panel's View->Show Chains submenu
1756 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1757 work for wrapped alignment views
1760 <!--JAL-2197 -->Rename UI components for running JPred
1761 predictions from 'JNet' to 'JPred'
1764 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1765 corrupted when annotation panel vertical scroll is not at
1766 first annotation row
1769 <!--JAL-2332 -->Attempting to view structure for Hen
1770 lysozyme results in a PDB Client error dialog box
1773 <!-- JAL-2319 -->Structure View's mapping report switched
1774 ranges for PDB and sequence for SIFTS
1777 SIFTS 'Not_Observed' residues mapped to non-existant
1781 <!-- <em>New Known Issues</em>
1788 <td width="60" nowrap>
1789 <div align="center">
1790 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1791 <em>25/10/2016</em></strong>
1794 <td><em>Application</em>
1796 <li>3D Structure chooser opens with 'Cached structures'
1797 view if structures already loaded</li>
1798 <li>Progress bar reports models as they are loaded to
1799 structure views</li>
1805 <li>Colour by conservation always enabled and no tick
1806 shown in menu when BLOSUM or PID shading applied</li>
1807 <li>FER1_ARATH and FER2_ARATH labels were switched in
1808 example sequences/projects/trees</li>
1810 <em>Application</em>
1812 <li>Jalview projects with views of local PDB structure
1813 files saved on Windows cannot be opened on OSX</li>
1814 <li>Multiple structure views can be opened and superposed
1815 without timeout for structures with multiple models or
1816 multiple sequences in alignment</li>
1817 <li>Cannot import or associated local PDB files without a
1818 PDB ID HEADER line</li>
1819 <li>RMSD is not output in Jmol console when superposition
1821 <li>Drag and drop of URL from Browser fails for Linux and
1822 OSX versions earlier than El Capitan</li>
1823 <li>ENA client ignores invalid content from ENA server</li>
1824 <li>Exceptions are not raised in console when ENA client
1825 attempts to fetch non-existent IDs via Fetch DB Refs UI
1827 <li>Exceptions are not raised in console when a new view
1828 is created on the alignment</li>
1829 <li>OSX right-click fixed for group selections: CMD-click
1830 to insert/remove gaps in groups and CTRL-click to open group
1833 <em>Build and deployment</em>
1835 <li>URL link checker now copes with multi-line anchor
1838 <em>New Known Issues</em>
1840 <li>Drag and drop from URL links in browsers do not work
1847 <td width="60" nowrap>
1848 <div align="center">
1849 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1852 <td><em>General</em>
1855 <!-- JAL-2124 -->Updated Spanish translations.
1858 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1859 for importing structure data to Jalview. Enables mmCIF and
1863 <!-- JAL-192 --->Alignment ruler shows positions relative to
1867 <!-- JAL-2202 -->Position/residue shown in status bar when
1868 mousing over sequence associated annotation
1871 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1875 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1876 '()', canonical '[]' and invalid '{}' base pair populations
1880 <!-- JAL-2092 -->Feature settings popup menu options for
1881 showing or hiding columns containing a feature
1884 <!-- JAL-1557 -->Edit selected group by double clicking on
1885 group and sequence associated annotation labels
1888 <!-- JAL-2236 -->Sequence name added to annotation label in
1889 select/hide columns by annotation and colour by annotation
1893 </ul> <em>Application</em>
1896 <!-- JAL-2050-->Automatically hide introns when opening a
1897 gene/transcript view
1900 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1904 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1905 structure mappings with the EMBL-EBI PDBe SIFTS database
1908 <!-- JAL-2079 -->Updated download sites used for Rfam and
1909 Pfam sources to xfam.org
1912 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1915 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1916 over sequences in Jalview
1919 <!-- JAL-2027-->Support for reverse-complement coding
1920 regions in ENA and EMBL
1923 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1924 for record retrieval via ENA rest API
1927 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1931 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1932 groovy script execution
1935 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1936 alignment window's Calculate menu
1939 <!-- JAL-1812 -->Allow groovy scripts that call
1940 Jalview.getAlignFrames() to run in headless mode
1943 <!-- JAL-2068 -->Support for creating new alignment
1944 calculation workers from groovy scripts
1947 <!-- JAL-1369 --->Store/restore reference sequence in
1951 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1952 associations are now saved/restored from project
1955 <!-- JAL-1993 -->Database selection dialog always shown
1956 before sequence fetcher is opened
1959 <!-- JAL-2183 -->Double click on an entry in Jalview's
1960 database chooser opens a sequence fetcher
1963 <!-- JAL-1563 -->Free-text search client for UniProt using
1964 the UniProt REST API
1967 <!-- JAL-2168 -->-nonews command line parameter to prevent
1968 the news reader opening
1971 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1972 querying stored in preferences
1975 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1979 <!-- JAL-1977-->Tooltips shown on database chooser
1982 <!-- JAL-391 -->Reverse complement function in calculate
1983 menu for nucleotide sequences
1986 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1987 and feature counts preserves alignment ordering (and
1988 debugged for complex feature sets).
1991 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1992 viewing structures with Jalview 2.10
1995 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1996 genome, transcript CCDS and gene ids via the Ensembl and
1997 Ensembl Genomes REST API
2000 <!-- JAL-2049 -->Protein sequence variant annotation
2001 computed for 'sequence_variant' annotation on CDS regions
2005 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2009 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2010 Ref Fetcher fails to match, or otherwise updates sequence
2011 data from external database records.
2014 <!-- JAL-2154 -->Revised Jalview Project format for
2015 efficient recovery of sequence coding and alignment
2016 annotation relationships.
2018 </ul> <!-- <em>Applet</em>
2029 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2033 <!-- JAL-2018-->Export features in Jalview format (again)
2034 includes graduated colourschemes
2037 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2038 working with big alignments and lots of hidden columns
2041 <!-- JAL-2053-->Hidden column markers not always rendered
2042 at right of alignment window
2045 <!-- JAL-2067 -->Tidied up links in help file table of
2049 <!-- JAL-2072 -->Feature based tree calculation not shown
2053 <!-- JAL-2075 -->Hidden columns ignored during feature
2054 based tree calculation
2057 <!-- JAL-2065 -->Alignment view stops updating when show
2058 unconserved enabled for group on alignment
2061 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2065 <!-- JAL-2146 -->Alignment column in status incorrectly
2066 shown as "Sequence position" when mousing over
2070 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2071 hidden columns present
2074 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2075 user created annotation added to alignment
2078 <!-- JAL-1841 -->RNA Structure consensus only computed for
2079 '()' base pair annotation
2082 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2083 in zero scores for all base pairs in RNA Structure
2087 <!-- JAL-2174-->Extend selection with columns containing
2091 <!-- JAL-2275 -->Pfam format writer puts extra space at
2092 beginning of sequence
2095 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2099 <!-- JAL-2238 -->Cannot create groups on an alignment from
2100 from a tree when t-coffee scores are shown
2103 <!-- JAL-1836,1967 -->Cannot import and view PDB
2104 structures with chains containing negative resnums (4q4h)
2107 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2111 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2112 to Clustal, PIR and PileUp output
2115 <!-- JAL-2008 -->Reordering sequence features that are
2116 not visible causes alignment window to repaint
2119 <!-- JAL-2006 -->Threshold sliders don't work in
2120 graduated colour and colour by annotation row for e-value
2121 scores associated with features and annotation rows
2124 <!-- JAL-1797 -->amino acid physicochemical conservation
2125 calculation should be case independent
2128 <!-- JAL-2173 -->Remove annotation also updates hidden
2132 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2133 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2134 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2137 <!-- JAL-2065 -->Null pointer exceptions and redraw
2138 problems when reference sequence defined and 'show
2139 non-conserved' enabled
2142 <!-- JAL-1306 -->Quality and Conservation are now shown on
2143 load even when Consensus calculation is disabled
2146 <!-- JAL-1932 -->Remove right on penultimate column of
2147 alignment does nothing
2150 <em>Application</em>
2153 <!-- JAL-1552-->URLs and links can't be imported by
2154 drag'n'drop on OSX when launched via webstart (note - not
2155 yet fixed for El Capitan)
2158 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2159 output when running on non-gb/us i18n platforms
2162 <!-- JAL-1944 -->Error thrown when exporting a view with
2163 hidden sequences as flat-file alignment
2166 <!-- JAL-2030-->InstallAnywhere distribution fails when
2170 <!-- JAL-2080-->Jalview very slow to launch via webstart
2171 (also hotfix for 2.9.0b2)
2174 <!-- JAL-2085 -->Cannot save project when view has a
2175 reference sequence defined
2178 <!-- JAL-1011 -->Columns are suddenly selected in other
2179 alignments and views when revealing hidden columns
2182 <!-- JAL-1989 -->Hide columns not mirrored in complement
2183 view in a cDNA/Protein splitframe
2186 <!-- JAL-1369 -->Cannot save/restore representative
2187 sequence from project when only one sequence is
2191 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2192 in Structure Chooser
2195 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2196 structure consensus didn't refresh annotation panel
2199 <!-- JAL-1962 -->View mapping in structure view shows
2200 mappings between sequence and all chains in a PDB file
2203 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2204 dialogs format columns correctly, don't display array
2205 data, sort columns according to type
2208 <!-- JAL-1975 -->Export complete shown after destination
2209 file chooser is cancelled during an image export
2212 <!-- JAL-2025 -->Error when querying PDB Service with
2213 sequence name containing special characters
2216 <!-- JAL-2024 -->Manual PDB structure querying should be
2220 <!-- JAL-2104 -->Large tooltips with broken HTML
2221 formatting don't wrap
2224 <!-- JAL-1128 -->Figures exported from wrapped view are
2225 truncated so L looks like I in consensus annotation
2228 <!-- JAL-2003 -->Export features should only export the
2229 currently displayed features for the current selection or
2233 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2234 after fetching cross-references, and restoring from
2238 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2239 followed in the structure viewer
2242 <!-- JAL-2163 -->Titles for individual alignments in
2243 splitframe not restored from project
2246 <!-- JAL-2145 -->missing autocalculated annotation at
2247 trailing end of protein alignment in transcript/product
2248 splitview when pad-gaps not enabled by default
2251 <!-- JAL-1797 -->amino acid physicochemical conservation
2255 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2256 article has been read (reopened issue due to
2257 internationalisation problems)
2260 <!-- JAL-1960 -->Only offer PDB structures in structure
2261 viewer based on sequence name, PDB and UniProt
2266 <!-- JAL-1976 -->No progress bar shown during export of
2270 <!-- JAL-2213 -->Structures not always superimposed after
2271 multiple structures are shown for one or more sequences.
2274 <!-- JAL-1370 -->Reference sequence characters should not
2275 be replaced with '.' when 'Show unconserved' format option
2279 <!-- JAL-1823 -->Cannot specify chain code when entering
2280 specific PDB id for sequence
2283 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2284 'Export hidden sequences' is enabled, but 'export hidden
2285 columns' is disabled.
2288 <!--JAL-2026-->Best Quality option in structure chooser
2289 selects lowest rather than highest resolution structures
2293 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2294 to sequence mapping in 'View Mappings' report
2297 <!-- JAL-2284 -->Unable to read old Jalview projects that
2298 contain non-XML data added after Jalvew wrote project.
2301 <!-- JAL-2118 -->Newly created annotation row reorders
2302 after clicking on it to create new annotation for a
2306 <!-- JAL-1980 -->Null Pointer Exception raised when
2307 pressing Add on an orphaned cut'n'paste window.
2309 <!-- may exclude, this is an external service stability issue JAL-1941
2310 -- > RNA 3D structure not added via DSSR service</li> -->
2315 <!-- JAL-2151 -->Incorrect columns are selected when
2316 hidden columns present before start of sequence
2319 <!-- JAL-1986 -->Missing dependencies on applet pages
2323 <!-- JAL-1947 -->Overview pixel size changes when
2324 sequences are hidden in applet
2327 <!-- JAL-1996 -->Updated instructions for applet
2328 deployment on examples pages.
2335 <td width="60" nowrap>
2336 <div align="center">
2337 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2338 <em>16/10/2015</em></strong>
2341 <td><em>General</em>
2343 <li>Time stamps for signed Jalview application and applet
2348 <em>Application</em>
2350 <li>Duplicate group consensus and conservation rows
2351 shown when tree is partitioned</li>
2352 <li>Erratic behaviour when tree partitions made with
2353 multiple cDNA/Protein split views</li>
2359 <td width="60" nowrap>
2360 <div align="center">
2361 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2362 <em>8/10/2015</em></strong>
2365 <td><em>General</em>
2367 <li>Updated Spanish translations of localized text for
2369 </ul> <em>Application</em>
2371 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2372 <li>Signed OSX InstallAnywhere installer<br></li>
2373 <li>Support for per-sequence based annotations in BioJSON</li>
2374 </ul> <em>Applet</em>
2376 <li>Split frame example added to applet examples page</li>
2377 </ul> <em>Build and Deployment</em>
2380 <!-- JAL-1888 -->New ant target for running Jalview's test
2388 <li>Mapping of cDNA to protein in split frames
2389 incorrect when sequence start > 1</li>
2390 <li>Broken images in filter column by annotation dialog
2392 <li>Feature colours not parsed from features file</li>
2393 <li>Exceptions and incomplete link URLs recovered when
2394 loading a features file containing HTML tags in feature
2398 <em>Application</em>
2400 <li>Annotations corrupted after BioJS export and
2402 <li>Incorrect sequence limits after Fetch DB References
2403 with 'trim retrieved sequences'</li>
2404 <li>Incorrect warning about deleting all data when
2405 deleting selected columns</li>
2406 <li>Patch to build system for shipping properly signed
2407 JNLP templates for webstart launch</li>
2408 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2409 unreleased structures for download or viewing</li>
2410 <li>Tab/space/return keystroke operation of EMBL-PDBe
2411 fetcher/viewer dialogs works correctly</li>
2412 <li>Disabled 'minimise' button on Jalview windows
2413 running on OSX to workaround redraw hang bug</li>
2414 <li>Split cDNA/Protein view position and geometry not
2415 recovered from jalview project</li>
2416 <li>Initial enabled/disabled state of annotation menu
2417 sorter 'show autocalculated first/last' corresponds to
2419 <li>Restoring of Clustal, RNA Helices and T-Coffee
2420 color schemes from BioJSON</li>
2424 <li>Reorder sequences mirrored in cDNA/Protein split
2426 <li>Applet with Jmol examples not loading correctly</li>
2432 <td><div align="center">
2433 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2435 <td><em>General</em>
2437 <li>Linked visualisation and analysis of DNA and Protein
2440 <li>Translated cDNA alignments shown as split protein
2441 and DNA alignment views</li>
2442 <li>Codon consensus annotation for linked protein and
2443 cDNA alignment views</li>
2444 <li>Link cDNA or Protein product sequences by loading
2445 them onto Protein or cDNA alignments</li>
2446 <li>Reconstruct linked cDNA alignment from aligned
2447 protein sequences</li>
2450 <li>Jmol integration updated to Jmol v14.2.14</li>
2451 <li>Import and export of Jalview alignment views as <a
2452 href="features/bioJsonFormat.html">BioJSON</a></li>
2453 <li>New alignment annotation file statements for
2454 reference sequences and marking hidden columns</li>
2455 <li>Reference sequence based alignment shading to
2456 highlight variation</li>
2457 <li>Select or hide columns according to alignment
2459 <li>Find option for locating sequences by description</li>
2460 <li>Conserved physicochemical properties shown in amino
2461 acid conservation row</li>
2462 <li>Alignments can be sorted by number of RNA helices</li>
2463 </ul> <em>Application</em>
2465 <li>New cDNA/Protein analysis capabilities
2467 <li>Get Cross-References should open a Split Frame
2468 view with cDNA/Protein</li>
2469 <li>Detect when nucleotide sequences and protein
2470 sequences are placed in the same alignment</li>
2471 <li>Split cDNA/Protein views are saved in Jalview
2476 <li>Use REST API to talk to Chimera</li>
2477 <li>Selected regions in Chimera are highlighted in linked
2478 Jalview windows</li>
2480 <li>VARNA RNA viewer updated to v3.93</li>
2481 <li>VARNA views are saved in Jalview Projects</li>
2482 <li>Pseudoknots displayed as Jalview RNA annotation can
2483 be shown in VARNA</li>
2485 <li>Make groups for selection uses marked columns as well
2486 as the active selected region</li>
2488 <li>Calculate UPGMA and NJ trees using sequence feature
2490 <li>New Export options
2492 <li>New Export Settings dialog to control hidden
2493 region export in flat file generation</li>
2495 <li>Export alignment views for display with the <a
2496 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2498 <li>Export scrollable SVG in HTML page</li>
2499 <li>Optional embedding of BioJSON data when exporting
2500 alignment figures to HTML</li>
2502 <li>3D structure retrieval and display
2504 <li>Free text and structured queries with the PDBe
2506 <li>PDBe Search API based discovery and selection of
2507 PDB structures for a sequence set</li>
2511 <li>JPred4 employed for protein secondary structure
2513 <li>Hide Insertions menu option to hide unaligned columns
2514 for one or a group of sequences</li>
2515 <li>Automatically hide insertions in alignments imported
2516 from the JPred4 web server</li>
2517 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2518 system on OSX<br />LGPL libraries courtesy of <a
2519 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2521 <li>changed 'View nucleotide structure' submenu to 'View
2522 VARNA 2D Structure'</li>
2523 <li>change "View protein structure" menu option to "3D
2526 </ul> <em>Applet</em>
2528 <li>New layout for applet example pages</li>
2529 <li>New parameters to enable SplitFrame view
2530 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2531 <li>New example demonstrating linked viewing of cDNA and
2532 Protein alignments</li>
2533 </ul> <em>Development and deployment</em>
2535 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2536 <li>Include installation type and git revision in build
2537 properties and console log output</li>
2538 <li>Jalview Github organisation, and new github site for
2539 storing BioJsMSA Templates</li>
2540 <li>Jalview's unit tests now managed with TestNG</li>
2543 <!-- <em>General</em>
2545 </ul> --> <!-- issues resolved --> <em>Application</em>
2547 <li>Escape should close any open find dialogs</li>
2548 <li>Typo in select-by-features status report</li>
2549 <li>Consensus RNA secondary secondary structure
2550 predictions are not highlighted in amber</li>
2551 <li>Missing gap character in v2.7 example file means
2552 alignment appears unaligned when pad-gaps is not enabled</li>
2553 <li>First switch to RNA Helices colouring doesn't colour
2554 associated structure views</li>
2555 <li>ID width preference option is greyed out when auto
2556 width checkbox not enabled</li>
2557 <li>Stopped a warning dialog from being shown when
2558 creating user defined colours</li>
2559 <li>'View Mapping' in structure viewer shows sequence
2560 mappings for just that viewer's sequences</li>
2561 <li>Workaround for superposing PDB files containing
2562 multiple models in Chimera</li>
2563 <li>Report sequence position in status bar when hovering
2564 over Jmol structure</li>
2565 <li>Cannot output gaps as '.' symbols with Selection ->
2566 output to text box</li>
2567 <li>Flat file exports of alignments with hidden columns
2568 have incorrect sequence start/end</li>
2569 <li>'Aligning' a second chain to a Chimera structure from
2571 <li>Colour schemes applied to structure viewers don't
2572 work for nucleotide</li>
2573 <li>Loading/cut'n'pasting an empty or invalid file leads
2574 to a grey/invisible alignment window</li>
2575 <li>Exported Jpred annotation from a sequence region
2576 imports to different position</li>
2577 <li>Space at beginning of sequence feature tooltips shown
2578 on some platforms</li>
2579 <li>Chimera viewer 'View | Show Chain' menu is not
2581 <li>'New View' fails with a Null Pointer Exception in
2582 console if Chimera has been opened</li>
2583 <li>Mouseover to Chimera not working</li>
2584 <li>Miscellaneous ENA XML feature qualifiers not
2586 <li>NPE in annotation renderer after 'Extract Scores'</li>
2587 <li>If two structures in one Chimera window, mouseover of
2588 either sequence shows on first structure</li>
2589 <li>'Show annotations' options should not make
2590 non-positional annotations visible</li>
2591 <li>Subsequence secondary structure annotation not shown
2592 in right place after 'view flanking regions'</li>
2593 <li>File Save As type unset when current file format is
2595 <li>Save as '.jar' option removed for saving Jalview
2597 <li>Colour by Sequence colouring in Chimera more
2599 <li>Cannot 'add reference annotation' for a sequence in
2600 several views on same alignment</li>
2601 <li>Cannot show linked products for EMBL / ENA records</li>
2602 <li>Jalview's tooltip wraps long texts containing no
2604 </ul> <em>Applet</em>
2606 <li>Jmol to JalviewLite mouseover/link not working</li>
2607 <li>JalviewLite can't import sequences with ID
2608 descriptions containing angle brackets</li>
2609 </ul> <em>General</em>
2611 <li>Cannot export and reimport RNA secondary structure
2612 via jalview annotation file</li>
2613 <li>Random helix colour palette for colour by annotation
2614 with RNA secondary structure</li>
2615 <li>Mouseover to cDNA from STOP residue in protein
2616 translation doesn't work.</li>
2617 <li>hints when using the select by annotation dialog box</li>
2618 <li>Jmol alignment incorrect if PDB file has alternate CA
2620 <li>FontChooser message dialog appears to hang after
2621 choosing 1pt font</li>
2622 <li>Peptide secondary structure incorrectly imported from
2623 annotation file when annotation display text includes 'e' or
2625 <li>Cannot set colour of new feature type whilst creating
2627 <li>cDNA translation alignment should not be sequence
2628 order dependent</li>
2629 <li>'Show unconserved' doesn't work for lower case
2631 <li>Nucleotide ambiguity codes involving R not recognised</li>
2632 </ul> <em>Deployment and Documentation</em>
2634 <li>Applet example pages appear different to the rest of
2635 www.jalview.org</li>
2636 </ul> <em>Application Known issues</em>
2638 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2639 <li>Misleading message appears after trying to delete
2641 <li>Jalview icon not shown in dock after InstallAnywhere
2642 version launches</li>
2643 <li>Fetching EMBL reference for an RNA sequence results
2644 fails with a sequence mismatch</li>
2645 <li>Corrupted or unreadable alignment display when
2646 scrolling alignment to right</li>
2647 <li>ArrayIndexOutOfBoundsException thrown when remove
2648 empty columns called on alignment with ragged gapped ends</li>
2649 <li>auto calculated alignment annotation rows do not get
2650 placed above or below non-autocalculated rows</li>
2651 <li>Jalview dekstop becomes sluggish at full screen in
2652 ultra-high resolution</li>
2653 <li>Cannot disable consensus calculation independently of
2654 quality and conservation</li>
2655 <li>Mouseover highlighting between cDNA and protein can
2656 become sluggish with more than one splitframe shown</li>
2657 </ul> <em>Applet Known Issues</em>
2659 <li>Core PDB parsing code requires Jmol</li>
2660 <li>Sequence canvas panel goes white when alignment
2661 window is being resized</li>
2667 <td><div align="center">
2668 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2670 <td><em>General</em>
2672 <li>Updated Java code signing certificate donated by
2674 <li>Features and annotation preserved when performing
2675 pairwise alignment</li>
2676 <li>RNA pseudoknot annotation can be
2677 imported/exported/displayed</li>
2678 <li>'colour by annotation' can colour by RNA and
2679 protein secondary structure</li>
2680 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2681 post-hoc with 2.9 release</em>)
2684 </ul> <em>Application</em>
2686 <li>Extract and display secondary structure for sequences
2687 with 3D structures</li>
2688 <li>Support for parsing RNAML</li>
2689 <li>Annotations menu for layout
2691 <li>sort sequence annotation rows by alignment</li>
2692 <li>place sequence annotation above/below alignment
2695 <li>Output in Stockholm format</li>
2696 <li>Internationalisation: improved Spanish (es)
2698 <li>Structure viewer preferences tab</li>
2699 <li>Disorder and Secondary Structure annotation tracks
2700 shared between alignments</li>
2701 <li>UCSF Chimera launch and linked highlighting from
2703 <li>Show/hide all sequence associated annotation rows for
2704 all or current selection</li>
2705 <li>disorder and secondary structure predictions
2706 available as dataset annotation</li>
2707 <li>Per-sequence rna helices colouring</li>
2710 <li>Sequence database accessions imported when fetching
2711 alignments from Rfam</li>
2712 <li>update VARNA version to 3.91</li>
2714 <li>New groovy scripts for exporting aligned positions,
2715 conservation values, and calculating sum of pairs scores.</li>
2716 <li>Command line argument to set default JABAWS server</li>
2717 <li>include installation type in build properties and
2718 console log output</li>
2719 <li>Updated Jalview project format to preserve dataset
2723 <!-- issues resolved --> <em>Application</em>
2725 <li>Distinguish alignment and sequence associated RNA
2726 structure in structure->view->VARNA</li>
2727 <li>Raise dialog box if user deletes all sequences in an
2729 <li>Pressing F1 results in documentation opening twice</li>
2730 <li>Sequence feature tooltip is wrapped</li>
2731 <li>Double click on sequence associated annotation
2732 selects only first column</li>
2733 <li>Redundancy removal doesn't result in unlinked
2734 leaves shown in tree</li>
2735 <li>Undos after several redundancy removals don't undo
2737 <li>Hide sequence doesn't hide associated annotation</li>
2738 <li>User defined colours dialog box too big to fit on
2739 screen and buttons not visible</li>
2740 <li>author list isn't updated if already written to
2741 Jalview properties</li>
2742 <li>Popup menu won't open after retrieving sequence
2744 <li>File open window for associate PDB doesn't open</li>
2745 <li>Left-then-right click on a sequence id opens a
2746 browser search window</li>
2747 <li>Cannot open sequence feature shading/sort popup menu
2748 in feature settings dialog</li>
2749 <li>better tooltip placement for some areas of Jalview
2751 <li>Allow addition of JABAWS Server which doesn't
2752 pass validation</li>
2753 <li>Web services parameters dialog box is too large to
2755 <li>Muscle nucleotide alignment preset obscured by
2757 <li>JABAWS preset submenus don't contain newly
2758 defined user preset</li>
2759 <li>MSA web services warns user if they were launched
2760 with invalid input</li>
2761 <li>Jalview cannot contact DAS Registy when running on
2764 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2765 'Superpose with' submenu not shown when new view
2769 </ul> <!-- <em>Applet</em>
2771 </ul> <em>General</em>
2773 </ul>--> <em>Deployment and Documentation</em>
2775 <li>2G and 1G options in launchApp have no effect on
2776 memory allocation</li>
2777 <li>launchApp service doesn't automatically open
2778 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2780 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2781 InstallAnywhere reports cannot find valid JVM when Java
2782 1.7_055 is available
2784 </ul> <em>Application Known issues</em>
2787 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2788 corrupted or unreadable alignment display when scrolling
2792 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2793 retrieval fails but progress bar continues for DAS retrieval
2794 with large number of ID
2797 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2798 flatfile output of visible region has incorrect sequence
2802 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2803 rna structure consensus doesn't update when secondary
2804 structure tracks are rearranged
2807 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2808 invalid rna structure positional highlighting does not
2809 highlight position of invalid base pairs
2812 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2813 out of memory errors are not raised when saving Jalview
2814 project from alignment window file menu
2817 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2818 Switching to RNA Helices colouring doesn't propagate to
2822 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2823 colour by RNA Helices not enabled when user created
2824 annotation added to alignment
2827 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2828 Jalview icon not shown on dock in Mountain Lion/Webstart
2830 </ul> <em>Applet Known Issues</em>
2833 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2834 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2837 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2838 Jalview and Jmol example not compatible with IE9
2841 <li>Sort by annotation score doesn't reverse order
2847 <td><div align="center">
2848 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2851 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2854 <li>Internationalisation of user interface (usually
2855 called i18n support) and translation for Spanish locale</li>
2856 <li>Define/Undefine group on current selection with
2857 Ctrl-G/Shift Ctrl-G</li>
2858 <li>Improved group creation/removal options in
2859 alignment/sequence Popup menu</li>
2860 <li>Sensible precision for symbol distribution
2861 percentages shown in logo tooltip.</li>
2862 <li>Annotation panel height set according to amount of
2863 annotation when alignment first opened</li>
2864 </ul> <em>Application</em>
2866 <li>Interactive consensus RNA secondary structure
2867 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2868 <li>Select columns containing particular features from
2869 Feature Settings dialog</li>
2870 <li>View all 'representative' PDB structures for selected
2872 <li>Update Jalview project format:
2874 <li>New file extension for Jalview projects '.jvp'</li>
2875 <li>Preserve sequence and annotation dataset (to
2876 store secondary structure annotation,etc)</li>
2877 <li>Per group and alignment annotation and RNA helix
2881 <li>New similarity measures for PCA and Tree calculation
2883 <li>Experimental support for retrieval and viewing of
2884 flanking regions for an alignment</li>
2888 <!-- issues resolved --> <em>Application</em>
2890 <li>logo keeps spinning and status remains at queued or
2891 running after job is cancelled</li>
2892 <li>cannot export features from alignments imported from
2893 Jalview/VAMSAS projects</li>
2894 <li>Buggy slider for web service parameters that take
2896 <li>Newly created RNA secondary structure line doesn't
2897 have 'display all symbols' flag set</li>
2898 <li>T-COFFEE alignment score shading scheme and other
2899 annotation shading not saved in Jalview project</li>
2900 <li>Local file cannot be loaded in freshly downloaded
2902 <li>Jalview icon not shown on dock in Mountain
2904 <li>Load file from desktop file browser fails</li>
2905 <li>Occasional NPE thrown when calculating large trees</li>
2906 <li>Cannot reorder or slide sequences after dragging an
2907 alignment onto desktop</li>
2908 <li>Colour by annotation dialog throws NPE after using
2909 'extract scores' function</li>
2910 <li>Loading/cut'n'pasting an empty file leads to a grey
2911 alignment window</li>
2912 <li>Disorder thresholds rendered incorrectly after
2913 performing IUPred disorder prediction</li>
2914 <li>Multiple group annotated consensus rows shown when
2915 changing 'normalise logo' display setting</li>
2916 <li>Find shows blank dialog after 'finished searching' if
2917 nothing matches query</li>
2918 <li>Null Pointer Exceptions raised when sorting by
2919 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2921 <li>Errors in Jmol console when structures in alignment
2922 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2924 <li>Not all working JABAWS services are shown in
2926 <li>JAVAWS version of Jalview fails to launch with
2927 'invalid literal/length code'</li>
2928 <li>Annotation/RNA Helix colourschemes cannot be applied
2929 to alignment with groups (actually fixed in 2.8.0b1)</li>
2930 <li>RNA Helices and T-Coffee Scores available as default
2933 </ul> <em>Applet</em>
2935 <li>Remove group option is shown even when selection is
2937 <li>Apply to all groups ticked but colourscheme changes
2938 don't affect groups</li>
2939 <li>Documented RNA Helices and T-Coffee Scores as valid
2940 colourscheme name</li>
2941 <li>Annotation labels drawn on sequence IDs when
2942 Annotation panel is not displayed</li>
2943 <li>Increased font size for dropdown menus on OSX and
2944 embedded windows</li>
2945 </ul> <em>Other</em>
2947 <li>Consensus sequence for alignments/groups with a
2948 single sequence were not calculated</li>
2949 <li>annotation files that contain only groups imported as
2950 annotation and junk sequences</li>
2951 <li>Fasta files with sequences containing '*' incorrectly
2952 recognised as PFAM or BLC</li>
2953 <li>conservation/PID slider apply all groups option
2954 doesn't affect background (2.8.0b1)
2956 <li>redundancy highlighting is erratic at 0% and 100%</li>
2957 <li>Remove gapped columns fails for sequences with ragged
2959 <li>AMSA annotation row with leading spaces is not
2960 registered correctly on import</li>
2961 <li>Jalview crashes when selecting PCA analysis for
2962 certain alignments</li>
2963 <li>Opening the colour by annotation dialog for an
2964 existing annotation based 'use original colours'
2965 colourscheme loses original colours setting</li>
2970 <td><div align="center">
2971 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2972 <em>30/1/2014</em></strong>
2976 <li>Trusted certificates for JalviewLite applet and
2977 Jalview Desktop application<br />Certificate was donated by
2978 <a href="https://www.certum.eu">Certum</a> to the Jalview
2979 open source project).
2981 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2982 <li>Output in Stockholm format</li>
2983 <li>Allow import of data from gzipped files</li>
2984 <li>Export/import group and sequence associated line
2985 graph thresholds</li>
2986 <li>Nucleotide substitution matrix that supports RNA and
2987 ambiguity codes</li>
2988 <li>Allow disorder predictions to be made on the current
2989 selection (or visible selection) in the same way that JPred
2991 <li>Groovy scripting for headless Jalview operation</li>
2992 </ul> <em>Other improvements</em>
2994 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2995 <li>COMBINE statement uses current SEQUENCE_REF and
2996 GROUP_REF scope to group annotation rows</li>
2997 <li>Support '' style escaping of quotes in Newick
2999 <li>Group options for JABAWS service by command line name</li>
3000 <li>Empty tooltip shown for JABA service options with a
3001 link but no description</li>
3002 <li>Select primary source when selecting authority in
3003 database fetcher GUI</li>
3004 <li>Add .mfa to FASTA file extensions recognised by
3006 <li>Annotation label tooltip text wrap</li>
3011 <li>Slow scrolling when lots of annotation rows are
3013 <li>Lots of NPE (and slowness) after creating RNA
3014 secondary structure annotation line</li>
3015 <li>Sequence database accessions not imported when
3016 fetching alignments from Rfam</li>
3017 <li>Incorrect SHMR submission for sequences with
3019 <li>View all structures does not always superpose
3021 <li>Option widgets in service parameters not updated to
3022 reflect user or preset settings</li>
3023 <li>Null pointer exceptions for some services without
3024 presets or adjustable parameters</li>
3025 <li>Discover PDB IDs entry in structure menu doesn't
3026 discover PDB xRefs</li>
3027 <li>Exception encountered while trying to retrieve
3028 features with DAS</li>
3029 <li>Lowest value in annotation row isn't coloured
3030 when colour by annotation (per sequence) is coloured</li>
3031 <li>Keyboard mode P jumps to start of gapped region when
3032 residue follows a gap</li>
3033 <li>Jalview appears to hang importing an alignment with
3034 Wrap as default or after enabling Wrap</li>
3035 <li>'Right click to add annotations' message
3036 shown in wrap mode when no annotations present</li>
3037 <li>Disorder predictions fail with NPE if no automatic
3038 annotation already exists on alignment</li>
3039 <li>oninit javascript function should be called after
3040 initialisation completes</li>
3041 <li>Remove redundancy after disorder prediction corrupts
3042 alignment window display</li>
3043 <li>Example annotation file in documentation is invalid</li>
3044 <li>Grouped line graph annotation rows are not exported
3045 to annotation file</li>
3046 <li>Multi-harmony analysis cannot be run when only two
3048 <li>Cannot create multiple groups of line graphs with
3049 several 'combine' statements in annotation file</li>
3050 <li>Pressing return several times causes Number Format
3051 exceptions in keyboard mode</li>
3052 <li>Multi-harmony (SHMMR) method doesn't submit
3053 correct partitions for input data</li>
3054 <li>Translation from DNA to Amino Acids fails</li>
3055 <li>Jalview fail to load newick tree with quoted label</li>
3056 <li>--headless flag isn't understood</li>
3057 <li>ClassCastException when generating EPS in headless
3059 <li>Adjusting sequence-associated shading threshold only
3060 changes one row's threshold</li>
3061 <li>Preferences and Feature settings panel panel
3062 doesn't open</li>
3063 <li>hide consensus histogram also hides conservation and
3064 quality histograms</li>
3069 <td><div align="center">
3070 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3072 <td><em>Application</em>
3074 <li>Support for JABAWS 2.0 Services (AACon alignment
3075 conservation, protein disorder and Clustal Omega)</li>
3076 <li>JABAWS server status indicator in Web Services
3078 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3079 in Jalview alignment window</li>
3080 <li>Updated Jalview build and deploy framework for OSX
3081 mountain lion, windows 7, and 8</li>
3082 <li>Nucleotide substitution matrix for PCA that supports
3083 RNA and ambiguity codes</li>
3085 <li>Improved sequence database retrieval GUI</li>
3086 <li>Support fetching and database reference look up
3087 against multiple DAS sources (Fetch all from in 'fetch db
3089 <li>Jalview project improvements
3091 <li>Store and retrieve the 'belowAlignment'
3092 flag for annotation</li>
3093 <li>calcId attribute to group annotation rows on the
3095 <li>Store AACon calculation settings for a view in
3096 Jalview project</li>
3100 <li>horizontal scrolling gesture support</li>
3101 <li>Visual progress indicator when PCA calculation is
3103 <li>Simpler JABA web services menus</li>
3104 <li>visual indication that web service results are still
3105 being retrieved from server</li>
3106 <li>Serialise the dialogs that are shown when Jalview
3107 starts up for first time</li>
3108 <li>Jalview user agent string for interacting with HTTP
3110 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3112 <li>Examples directory and Groovy library included in
3113 InstallAnywhere distribution</li>
3114 </ul> <em>Applet</em>
3116 <li>RNA alignment and secondary structure annotation
3117 visualization applet example</li>
3118 </ul> <em>General</em>
3120 <li>Normalise option for consensus sequence logo</li>
3121 <li>Reset button in PCA window to return dimensions to
3123 <li>Allow seqspace or Jalview variant of alignment PCA
3125 <li>PCA with either nucleic acid and protein substitution
3127 <li>Allow windows containing HTML reports to be exported
3129 <li>Interactive display and editing of RNA secondary
3130 structure contacts</li>
3131 <li>RNA Helix Alignment Colouring</li>
3132 <li>RNA base pair logo consensus</li>
3133 <li>Parse sequence associated secondary structure
3134 information in Stockholm files</li>
3135 <li>HTML Export database accessions and annotation
3136 information presented in tooltip for sequences</li>
3137 <li>Import secondary structure from LOCARNA clustalw
3138 style RNA alignment files</li>
3139 <li>import and visualise T-COFFEE quality scores for an
3141 <li>'colour by annotation' per sequence option to
3142 shade each sequence according to its associated alignment
3144 <li>New Jalview Logo</li>
3145 </ul> <em>Documentation and Development</em>
3147 <li>documentation for score matrices used in Jalview</li>
3148 <li>New Website!</li>
3150 <td><em>Application</em>
3152 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3153 wsdbfetch REST service</li>
3154 <li>Stop windows being moved outside desktop on OSX</li>
3155 <li>Filetype associations not installed for webstart
3157 <li>Jalview does not always retrieve progress of a JABAWS
3158 job execution in full once it is complete</li>
3159 <li>revise SHMR RSBS definition to ensure alignment is
3160 uploaded via ali_file parameter</li>
3161 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3162 <li>View all structures superposed fails with exception</li>
3163 <li>Jnet job queues forever if a very short sequence is
3164 submitted for prediction</li>
3165 <li>Cut and paste menu not opened when mouse clicked on
3167 <li>Putting fractional value into integer text box in
3168 alignment parameter dialog causes Jalview to hang</li>
3169 <li>Structure view highlighting doesn't work on
3171 <li>View all structures fails with exception shown in
3173 <li>Characters in filename associated with PDBEntry not
3174 escaped in a platform independent way</li>
3175 <li>Jalview desktop fails to launch with exception when
3177 <li>Tree calculation reports 'you must have 2 or more
3178 sequences selected' when selection is empty</li>
3179 <li>Jalview desktop fails to launch with jar signature
3180 failure when java web start temporary file caching is
3182 <li>DAS Sequence retrieval with range qualification
3183 results in sequence xref which includes range qualification</li>
3184 <li>Errors during processing of command line arguments
3185 cause progress bar (JAL-898) to be removed</li>
3186 <li>Replace comma for semi-colon option not disabled for
3187 DAS sources in sequence fetcher</li>
3188 <li>Cannot close news reader when JABAWS server warning
3189 dialog is shown</li>
3190 <li>Option widgets not updated to reflect user settings</li>
3191 <li>Edited sequence not submitted to web service</li>
3192 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3193 <li>InstallAnywhere installer doesn't unpack and run
3194 on OSX Mountain Lion</li>
3195 <li>Annotation panel not given a scroll bar when
3196 sequences with alignment annotation are pasted into the
3198 <li>Sequence associated annotation rows not associated
3199 when loaded from Jalview project</li>
3200 <li>Browser launch fails with NPE on java 1.7</li>
3201 <li>JABAWS alignment marked as finished when job was
3202 cancelled or job failed due to invalid input</li>
3203 <li>NPE with v2.7 example when clicking on Tree
3204 associated with all views</li>
3205 <li>Exceptions when copy/paste sequences with grouped
3206 annotation rows to new window</li>
3207 </ul> <em>Applet</em>
3209 <li>Sequence features are momentarily displayed before
3210 they are hidden using hidefeaturegroups applet parameter</li>
3211 <li>loading features via javascript API automatically
3212 enables feature display</li>
3213 <li>scrollToColumnIn javascript API method doesn't
3215 </ul> <em>General</em>
3217 <li>Redundancy removal fails for rna alignment</li>
3218 <li>PCA calculation fails when sequence has been selected
3219 and then deselected</li>
3220 <li>PCA window shows grey box when first opened on OSX</li>
3221 <li>Letters coloured pink in sequence logo when alignment
3222 coloured with clustalx</li>
3223 <li>Choosing fonts without letter symbols defined causes
3224 exceptions and redraw errors</li>
3225 <li>Initial PCA plot view is not same as manually
3226 reconfigured view</li>
3227 <li>Grouped annotation graph label has incorrect line
3229 <li>Grouped annotation graph label display is corrupted
3230 for lots of labels</li>
3235 <div align="center">
3236 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3239 <td><em>Application</em>
3241 <li>Jalview Desktop News Reader</li>
3242 <li>Tweaked default layout of web services menu</li>
3243 <li>View/alignment association menu to enable user to
3244 easily specify which alignment a multi-structure view takes
3245 its colours/correspondences from</li>
3246 <li>Allow properties file location to be specified as URL</li>
3247 <li>Extend Jalview project to preserve associations
3248 between many alignment views and a single Jmol display</li>
3249 <li>Store annotation row height in Jalview project file</li>
3250 <li>Annotation row column label formatting attributes
3251 stored in project file</li>
3252 <li>Annotation row order for auto-calculated annotation
3253 rows preserved in Jalview project file</li>
3254 <li>Visual progress indication when Jalview state is
3255 saved using Desktop window menu</li>
3256 <li>Visual indication that command line arguments are
3257 still being processed</li>
3258 <li>Groovy script execution from URL</li>
3259 <li>Colour by annotation default min and max colours in
3261 <li>Automatically associate PDB files dragged onto an
3262 alignment with sequences that have high similarity and
3264 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3265 <li>'view structures' option to open many
3266 structures in same window</li>
3267 <li>Sort associated views menu option for tree panel</li>
3268 <li>Group all JABA and non-JABA services for a particular
3269 analysis function in its own submenu</li>
3270 </ul> <em>Applet</em>
3272 <li>Userdefined and autogenerated annotation rows for
3274 <li>Adjustment of alignment annotation pane height</li>
3275 <li>Annotation scrollbar for annotation panel</li>
3276 <li>Drag to reorder annotation rows in annotation panel</li>
3277 <li>'automaticScrolling' parameter</li>
3278 <li>Allow sequences with partial ID string matches to be
3279 annotated from GFF/Jalview features files</li>
3280 <li>Sequence logo annotation row in applet</li>
3281 <li>Absolute paths relative to host server in applet
3282 parameters are treated as such</li>
3283 <li>New in the JalviewLite javascript API:
3285 <li>JalviewLite.js javascript library</li>
3286 <li>Javascript callbacks for
3288 <li>Applet initialisation</li>
3289 <li>Sequence/alignment mouse-overs and selections</li>
3292 <li>scrollTo row and column alignment scrolling
3294 <li>Select sequence/alignment regions from javascript</li>
3295 <li>javascript structure viewer harness to pass
3296 messages between Jmol and Jalview when running as
3297 distinct applets</li>
3298 <li>sortBy method</li>
3299 <li>Set of applet and application examples shipped
3300 with documentation</li>
3301 <li>New example to demonstrate JalviewLite and Jmol
3302 javascript message exchange</li>
3304 </ul> <em>General</em>
3306 <li>Enable Jmol displays to be associated with multiple
3307 multiple alignments</li>
3308 <li>Option to automatically sort alignment with new tree</li>
3309 <li>User configurable link to enable redirects to a
3310 www.Jalview.org mirror</li>
3311 <li>Jmol colours option for Jmol displays</li>
3312 <li>Configurable newline string when writing alignment
3313 and other flat files</li>
3314 <li>Allow alignment annotation description lines to
3315 contain html tags</li>
3316 </ul> <em>Documentation and Development</em>
3318 <li>Add groovy test harness for bulk load testing to
3320 <li>Groovy script to load and align a set of sequences
3321 using a web service before displaying the result in the
3322 Jalview desktop</li>
3323 <li>Restructured javascript and applet api documentation</li>
3324 <li>Ant target to publish example html files with applet
3326 <li>Netbeans project for building Jalview from source</li>
3327 <li>ant task to create online javadoc for Jalview source</li>
3329 <td><em>Application</em>
3331 <li>User defined colourscheme throws exception when
3332 current built in colourscheme is saved as new scheme</li>
3333 <li>AlignFrame->Save in application pops up save
3334 dialog for valid filename/format</li>
3335 <li>Cannot view associated structure for UniProt sequence</li>
3336 <li>PDB file association breaks for UniProt sequence
3338 <li>Associate PDB from file dialog does not tell you
3339 which sequence is to be associated with the file</li>
3340 <li>Find All raises null pointer exception when query
3341 only matches sequence IDs</li>
3342 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3343 <li>Jalview project with Jmol views created with Jalview
3344 2.4 cannot be loaded</li>
3345 <li>Filetype associations not installed for webstart
3347 <li>Two or more chains in a single PDB file associated
3348 with sequences in different alignments do not get coloured
3349 by their associated sequence</li>
3350 <li>Visibility status of autocalculated annotation row
3351 not preserved when project is loaded</li>
3352 <li>Annotation row height and visibility attributes not
3353 stored in Jalview project</li>
3354 <li>Tree bootstraps are not preserved when saved as a
3355 Jalview project</li>
3356 <li>Envision2 workflow tooltips are corrupted</li>
3357 <li>Enabling show group conservation also enables colour
3358 by conservation</li>
3359 <li>Duplicate group associated conservation or consensus
3360 created on new view</li>
3361 <li>Annotation scrollbar not displayed after 'show
3362 all hidden annotation rows' option selected</li>
3363 <li>Alignment quality not updated after alignment
3364 annotation row is hidden then shown</li>
3365 <li>Preserve colouring of structures coloured by
3366 sequences in pre Jalview 2.7 projects</li>
3367 <li>Web service job parameter dialog is not laid out
3369 <li>Web services menu not refreshed after 'reset
3370 services' button is pressed in preferences</li>
3371 <li>Annotation off by one in Jalview v2_3 example project</li>
3372 <li>Structures imported from file and saved in project
3373 get name like jalview_pdb1234.txt when reloaded</li>
3374 <li>Jalview does not always retrieve progress of a JABAWS
3375 job execution in full once it is complete</li>
3376 </ul> <em>Applet</em>
3378 <li>Alignment height set incorrectly when lots of
3379 annotation rows are displayed</li>
3380 <li>Relative URLs in feature HTML text not resolved to
3382 <li>View follows highlighting does not work for positions
3384 <li><= shown as = in tooltip</li>
3385 <li>Export features raises exception when no features
3387 <li>Separator string used for serialising lists of IDs
3388 for javascript api is modified when separator string
3389 provided as parameter</li>
3390 <li>Null pointer exception when selecting tree leaves for
3391 alignment with no existing selection</li>
3392 <li>Relative URLs for datasources assumed to be relative
3393 to applet's codebase</li>
3394 <li>Status bar not updated after finished searching and
3395 search wraps around to first result</li>
3396 <li>StructureSelectionManager instance shared between
3397 several Jalview applets causes race conditions and memory
3399 <li>Hover tooltip and mouseover of position on structure
3400 not sent from Jmol in applet</li>
3401 <li>Certain sequences of javascript method calls to
3402 applet API fatally hang browser</li>
3403 </ul> <em>General</em>
3405 <li>View follows structure mouseover scrolls beyond
3406 position with wrapped view and hidden regions</li>
3407 <li>Find sequence position moves to wrong residue
3408 with/without hidden columns</li>
3409 <li>Sequence length given in alignment properties window
3411 <li>InvalidNumberFormat exceptions thrown when trying to
3412 import PDB like structure files</li>
3413 <li>Positional search results are only highlighted
3414 between user-supplied sequence start/end bounds</li>
3415 <li>End attribute of sequence is not validated</li>
3416 <li>Find dialog only finds first sequence containing a
3417 given sequence position</li>
3418 <li>Sequence numbering not preserved in MSF alignment
3420 <li>Jalview PDB file reader does not extract sequence
3421 from nucleotide chains correctly</li>
3422 <li>Structure colours not updated when tree partition
3423 changed in alignment</li>
3424 <li>Sequence associated secondary structure not correctly
3425 parsed in interleaved stockholm</li>
3426 <li>Colour by annotation dialog does not restore current
3428 <li>Hiding (nearly) all sequences doesn't work
3430 <li>Sequences containing lowercase letters are not
3431 properly associated with their pdb files</li>
3432 </ul> <em>Documentation and Development</em>
3434 <li>schemas/JalviewWsParamSet.xsd corrupted by
3435 ApplyCopyright tool</li>
3440 <div align="center">
3441 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3444 <td><em>Application</em>
3446 <li>New warning dialog when the Jalview Desktop cannot
3447 contact web services</li>
3448 <li>JABA service parameters for a preset are shown in
3449 service job window</li>
3450 <li>JABA Service menu entries reworded</li>
3454 <li>Modeller PIR IO broken - cannot correctly import a
3455 pir file emitted by Jalview</li>
3456 <li>Existing feature settings transferred to new
3457 alignment view created from cut'n'paste</li>
3458 <li>Improved test for mixed amino/nucleotide chains when
3459 parsing PDB files</li>
3460 <li>Consensus and conservation annotation rows
3461 occasionally become blank for all new windows</li>
3462 <li>Exception raised when right clicking above sequences
3463 in wrapped view mode</li>
3464 </ul> <em>Application</em>
3466 <li>multiple multiply aligned structure views cause cpu
3467 usage to hit 100% and computer to hang</li>
3468 <li>Web Service parameter layout breaks for long user
3469 parameter names</li>
3470 <li>Jaba service discovery hangs desktop if Jaba server
3477 <div align="center">
3478 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3481 <td><em>Application</em>
3483 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3484 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3487 <li>Web Services preference tab</li>
3488 <li>Analysis parameters dialog box and user defined
3490 <li>Improved speed and layout of Envision2 service menu</li>
3491 <li>Superpose structures using associated sequence
3493 <li>Export coordinates and projection as CSV from PCA
3495 </ul> <em>Applet</em>
3497 <li>enable javascript: execution by the applet via the
3498 link out mechanism</li>
3499 </ul> <em>Other</em>
3501 <li>Updated the Jmol Jalview interface to work with Jmol
3503 <li>The Jalview Desktop and JalviewLite applet now
3504 require Java 1.5</li>
3505 <li>Allow Jalview feature colour specification for GFF
3506 sequence annotation files</li>
3507 <li>New 'colour by label' keword in Jalview feature file
3508 type colour specification</li>
3509 <li>New Jalview Desktop Groovy API method that allows a
3510 script to check if it being run in an interactive session or
3511 in a batch operation from the Jalview command line</li>
3515 <li>clustalx colourscheme colours Ds preferentially when
3516 both D+E are present in over 50% of the column</li>
3517 </ul> <em>Application</em>
3519 <li>typo in AlignmentFrame->View->Hide->all but
3520 selected Regions menu item</li>
3521 <li>sequence fetcher replaces ',' for ';' when the ',' is
3522 part of a valid accession ID</li>
3523 <li>fatal OOM if object retrieved by sequence fetcher
3524 runs out of memory</li>
3525 <li>unhandled Out of Memory Error when viewing pca
3526 analysis results</li>
3527 <li>InstallAnywhere builds fail to launch on OS X java
3528 10.5 update 4 (due to apple Java 1.6 update)</li>
3529 <li>Installanywhere Jalview silently fails to launch</li>
3530 </ul> <em>Applet</em>
3532 <li>Jalview.getFeatureGroups() raises an
3533 ArrayIndexOutOfBoundsException if no feature groups are
3540 <div align="center">
3541 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3547 <li>Alignment prettyprinter doesn't cope with long
3549 <li>clustalx colourscheme colours Ds preferentially when
3550 both D+E are present in over 50% of the column</li>
3551 <li>nucleic acid structures retrieved from PDB do not
3552 import correctly</li>
3553 <li>More columns get selected than were clicked on when a
3554 number of columns are hidden</li>
3555 <li>annotation label popup menu not providing correct
3556 add/hide/show options when rows are hidden or none are
3558 <li>Stockholm format shown in list of readable formats,
3559 and parser copes better with alignments from RFAM.</li>
3560 <li>CSV output of consensus only includes the percentage
3561 of all symbols if sequence logo display is enabled</li>
3563 </ul> <em>Applet</em>
3565 <li>annotation panel disappears when annotation is
3567 </ul> <em>Application</em>
3569 <li>Alignment view not redrawn properly when new
3570 alignment opened where annotation panel is visible but no
3571 annotations are present on alignment</li>
3572 <li>pasted region containing hidden columns is
3573 incorrectly displayed in new alignment window</li>
3574 <li>Jalview slow to complete operations when stdout is
3575 flooded (fix is to close the Jalview console)</li>
3576 <li>typo in AlignmentFrame->View->Hide->all but
3577 selected Rregions menu item.</li>
3578 <li>inconsistent group submenu and Format submenu entry
3579 'Un' or 'Non'conserved</li>
3580 <li>Sequence feature settings are being shared by
3581 multiple distinct alignments</li>
3582 <li>group annotation not recreated when tree partition is
3584 <li>double click on group annotation to select sequences
3585 does not propagate to associated trees</li>
3586 <li>Mac OSX specific issues:
3588 <li>exception raised when mouse clicked on desktop
3589 window background</li>
3590 <li>Desktop menu placed on menu bar and application
3591 name set correctly</li>
3592 <li>sequence feature settings not wide enough for the
3593 save feature colourscheme button</li>
3602 <div align="center">
3603 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3606 <td><em>New Capabilities</em>
3608 <li>URL links generated from description line for
3609 regular-expression based URL links (applet and application)
3611 <li>Non-positional feature URL links are shown in link
3613 <li>Linked viewing of nucleic acid sequences and
3615 <li>Automatic Scrolling option in View menu to display
3616 the currently highlighted region of an alignment.</li>
3617 <li>Order an alignment by sequence length, or using the
3618 average score or total feature count for each sequence.</li>
3619 <li>Shading features by score or associated description</li>
3620 <li>Subdivide alignment and groups based on identity of
3621 selected subsequence (Make Groups from Selection).</li>
3622 <li>New hide/show options including Shift+Control+H to
3623 hide everything but the currently selected region.</li>
3624 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3625 </ul> <em>Application</em>
3627 <li>Fetch DB References capabilities and UI expanded to
3628 support retrieval from DAS sequence sources</li>
3629 <li>Local DAS Sequence sources can be added via the
3630 command line or via the Add local source dialog box.</li>
3631 <li>DAS Dbref and DbxRef feature types are parsed as
3632 database references and protein_name is parsed as
3633 description line (BioSapiens terms).</li>
3634 <li>Enable or disable non-positional feature and database
3635 references in sequence ID tooltip from View menu in
3637 <!-- <li>New hidden columns and rows and representatives capabilities
3638 in annotations file (in progress - not yet fully implemented)</li> -->
3639 <li>Group-associated consensus, sequence logos and
3640 conservation plots</li>
3641 <li>Symbol distributions for each column can be exported
3642 and visualized as sequence logos</li>
3643 <li>Optionally scale multi-character column labels to fit
3644 within each column of annotation row<!-- todo for applet -->
3646 <li>Optional automatic sort of associated alignment view
3647 when a new tree is opened.</li>
3648 <li>Jalview Java Console</li>
3649 <li>Better placement of desktop window when moving
3650 between different screens.</li>
3651 <li>New preference items for sequence ID tooltip and
3652 consensus annotation</li>
3653 <li>Client to submit sequences and IDs to Envision2
3655 <li><em>Vamsas Capabilities</em>
3657 <li>Improved VAMSAS synchronization (Jalview archive
3658 used to preserve views, structures, and tree display
3660 <li>Import of vamsas documents from disk or URL via
3662 <li>Sharing of selected regions between views and
3663 with other VAMSAS applications (Experimental feature!)</li>
3664 <li>Updated API to VAMSAS version 0.2</li>
3666 </ul> <em>Applet</em>
3668 <li>Middle button resizes annotation row height</li>
3671 <li>sortByTree (true/false) - automatically sort the
3672 associated alignment view by the tree when a new tree is
3674 <li>showTreeBootstraps (true/false) - show or hide
3675 branch bootstraps (default is to show them if available)</li>
3676 <li>showTreeDistances (true/false) - show or hide
3677 branch lengths (default is to show them if available)</li>
3678 <li>showUnlinkedTreeNodes (true/false) - indicate if
3679 unassociated nodes should be highlighted in the tree
3681 <li>heightScale and widthScale (1.0 or more) -
3682 increase the height or width of a cell in the alignment
3683 grid relative to the current font size.</li>
3686 <li>Non-positional features displayed in sequence ID
3688 </ul> <em>Other</em>
3690 <li>Features format: graduated colour definitions and
3691 specification of feature scores</li>
3692 <li>Alignment Annotations format: new keywords for group
3693 associated annotation (GROUP_REF) and annotation row display
3694 properties (ROW_PROPERTIES)</li>
3695 <li>XML formats extended to support graduated feature
3696 colourschemes, group associated annotation, and profile
3697 visualization settings.</li></td>
3700 <li>Source field in GFF files parsed as feature source
3701 rather than description</li>
3702 <li>Non-positional features are now included in sequence
3703 feature and gff files (controlled via non-positional feature
3704 visibility in tooltip).</li>
3705 <li>URL links generated for all feature links (bugfix)</li>
3706 <li>Added URL embedding instructions to features file
3708 <li>Codons containing ambiguous nucleotides translated as
3709 'X' in peptide product</li>
3710 <li>Match case switch in find dialog box works for both
3711 sequence ID and sequence string and query strings do not
3712 have to be in upper case to match case-insensitively.</li>
3713 <li>AMSA files only contain first column of
3714 multi-character column annotation labels</li>
3715 <li>Jalview Annotation File generation/parsing consistent
3716 with documentation (e.g. Stockholm annotation can be
3717 exported and re-imported)</li>
3718 <li>PDB files without embedded PDB IDs given a friendly
3720 <li>Find incrementally searches ID string matches as well
3721 as subsequence matches, and correctly reports total number
3725 <li>Better handling of exceptions during sequence
3727 <li>Dasobert generated non-positional feature URL
3728 link text excludes the start_end suffix</li>
3729 <li>DAS feature and source retrieval buttons disabled
3730 when fetch or registry operations in progress.</li>
3731 <li>PDB files retrieved from URLs are cached properly</li>
3732 <li>Sequence description lines properly shared via
3734 <li>Sequence fetcher fetches multiple records for all
3736 <li>Ensured that command line das feature retrieval
3737 completes before alignment figures are generated.</li>
3738 <li>Reduced time taken when opening file browser for
3740 <li>isAligned check prior to calculating tree, PCA or
3741 submitting an MSA to JNet now excludes hidden sequences.</li>
3742 <li>User defined group colours properly recovered
3743 from Jalview projects.</li>
3752 <div align="center">
3753 <strong>2.4.0.b2</strong><br> 28/10/2009
3758 <li>Experimental support for google analytics usage
3760 <li>Jalview privacy settings (user preferences and docs).</li>
3765 <li>Race condition in applet preventing startup in
3767 <li>Exception when feature created from selection beyond
3768 length of sequence.</li>
3769 <li>Allow synthetic PDB files to be imported gracefully</li>
3770 <li>Sequence associated annotation rows associate with
3771 all sequences with a given id</li>
3772 <li>Find function matches case-insensitively for sequence
3773 ID string searches</li>
3774 <li>Non-standard characters do not cause pairwise
3775 alignment to fail with exception</li>
3776 </ul> <em>Application Issues</em>
3778 <li>Sequences are now validated against EMBL database</li>
3779 <li>Sequence fetcher fetches multiple records for all
3781 </ul> <em>InstallAnywhere Issues</em>
3783 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3784 issue with installAnywhere mechanism)</li>
3785 <li>Command line launching of JARs from InstallAnywhere
3786 version (java class versioning error fixed)</li>
3793 <div align="center">
3794 <strong>2.4</strong><br> 27/8/2008
3797 <td><em>User Interface</em>
3799 <li>Linked highlighting of codon and amino acid from
3800 translation and protein products</li>
3801 <li>Linked highlighting of structure associated with
3802 residue mapping to codon position</li>
3803 <li>Sequence Fetcher provides example accession numbers
3804 and 'clear' button</li>
3805 <li>MemoryMonitor added as an option under Desktop's
3807 <li>Extract score function to parse whitespace separated
3808 numeric data in description line</li>
3809 <li>Column labels in alignment annotation can be centred.</li>
3810 <li>Tooltip for sequence associated annotation give name
3812 </ul> <em>Web Services and URL fetching</em>
3814 <li>JPred3 web service</li>
3815 <li>Prototype sequence search client (no public services
3817 <li>Fetch either seed alignment or full alignment from
3819 <li>URL Links created for matching database cross
3820 references as well as sequence ID</li>
3821 <li>URL Links can be created using regular-expressions</li>
3822 </ul> <em>Sequence Database Connectivity</em>
3824 <li>Retrieval of cross-referenced sequences from other
3826 <li>Generalised database reference retrieval and
3827 validation to all fetchable databases</li>
3828 <li>Fetch sequences from DAS sources supporting the
3829 sequence command</li>
3830 </ul> <em>Import and Export</em>
3831 <li>export annotation rows as CSV for spreadsheet import</li>
3832 <li>Jalview projects record alignment dataset associations,
3833 EMBL products, and cDNA sequence mappings</li>
3834 <li>Sequence Group colour can be specified in Annotation
3836 <li>Ad-hoc colouring of group in Annotation File using RGB
3837 triplet as name of colourscheme</li>
3838 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3840 <li>treenode binding for VAMSAS tree exchange</li>
3841 <li>local editing and update of sequences in VAMSAS
3842 alignments (experimental)</li>
3843 <li>Create new or select existing session to join</li>
3844 <li>load and save of vamsas documents</li>
3845 </ul> <em>Application command line</em>
3847 <li>-tree parameter to open trees (introduced for passing
3849 <li>-fetchfrom command line argument to specify nicknames
3850 of DAS servers to query for alignment features</li>
3851 <li>-dasserver command line argument to add new servers
3852 that are also automatically queried for features</li>
3853 <li>-groovy command line argument executes a given groovy
3854 script after all input data has been loaded and parsed</li>
3855 </ul> <em>Applet-Application data exchange</em>
3857 <li>Trees passed as applet parameters can be passed to
3858 application (when using "View in full
3859 application")</li>
3860 </ul> <em>Applet Parameters</em>
3862 <li>feature group display control parameter</li>
3863 <li>debug parameter</li>
3864 <li>showbutton parameter</li>
3865 </ul> <em>Applet API methods</em>
3867 <li>newView public method</li>
3868 <li>Window (current view) specific get/set public methods</li>
3869 <li>Feature display control methods</li>
3870 <li>get list of currently selected sequences</li>
3871 </ul> <em>New Jalview distribution features</em>
3873 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3874 <li>RELEASE file gives build properties for the latest
3875 Jalview release.</li>
3876 <li>Java 1.1 Applet build made easier and donotobfuscate
3877 property controls execution of obfuscator</li>
3878 <li>Build target for generating source distribution</li>
3879 <li>Debug flag for javacc</li>
3880 <li>.jalview_properties file is documented (slightly) in
3881 jalview.bin.Cache</li>
3882 <li>Continuous Build Integration for stable and
3883 development version of Application, Applet and source
3888 <li>selected region output includes visible annotations
3889 (for certain formats)</li>
3890 <li>edit label/displaychar contains existing label/char
3892 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3893 <li>shorter peptide product names from EMBL records</li>
3894 <li>Newick string generator makes compact representations</li>
3895 <li>bootstrap values parsed correctly for tree files with
3897 <li>pathological filechooser bug avoided by not allowing
3898 filenames containing a ':'</li>
3899 <li>Fixed exception when parsing GFF files containing
3900 global sequence features</li>
3901 <li>Alignment datasets are finalized only when number of
3902 references from alignment sequences goes to zero</li>
3903 <li>Close of tree branch colour box without colour
3904 selection causes cascading exceptions</li>
3905 <li>occasional negative imgwidth exceptions</li>
3906 <li>better reporting of non-fatal warnings to user when
3907 file parsing fails.</li>
3908 <li>Save works when Jalview project is default format</li>
3909 <li>Save as dialog opened if current alignment format is
3910 not a valid output format</li>
3911 <li>UniProt canonical names introduced for both das and
3913 <li>Histidine should be midblue (not pink!) in Zappo</li>
3914 <li>error messages passed up and output when data read
3916 <li>edit undo recovers previous dataset sequence when
3917 sequence is edited</li>
3918 <li>allow PDB files without pdb ID HEADER lines (like
3919 those generated by MODELLER) to be read in properly</li>
3920 <li>allow reading of JPred concise files as a normal
3922 <li>Stockholm annotation parsing and alignment properties
3923 import fixed for PFAM records</li>
3924 <li>Structure view windows have correct name in Desktop
3926 <li>annotation consisting of sequence associated scores
3927 can be read and written correctly to annotation file</li>
3928 <li>Aligned cDNA translation to aligned peptide works
3930 <li>Fixed display of hidden sequence markers and
3931 non-italic font for representatives in Applet</li>
3932 <li>Applet Menus are always embedded in applet window on
3934 <li>Newly shown features appear at top of stack (in
3936 <li>Annotations added via parameter not drawn properly
3937 due to null pointer exceptions</li>
3938 <li>Secondary structure lines are drawn starting from
3939 first column of alignment</li>
3940 <li>UniProt XML import updated for new schema release in
3942 <li>Sequence feature to sequence ID match for Features
3943 file is case-insensitive</li>
3944 <li>Sequence features read from Features file appended to
3945 all sequences with matching IDs</li>
3946 <li>PDB structure coloured correctly for associated views
3947 containing a sub-sequence</li>
3948 <li>PDB files can be retrieved by applet from Jar files</li>
3949 <li>feature and annotation file applet parameters
3950 referring to different directories are retrieved correctly</li>
3951 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3952 <li>Fixed application hang whilst waiting for
3953 splash-screen version check to complete</li>
3954 <li>Applet properly URLencodes input parameter values
3955 when passing them to the launchApp service</li>
3956 <li>display name and local features preserved in results
3957 retrieved from web service</li>
3958 <li>Visual delay indication for sequence retrieval and
3959 sequence fetcher initialisation</li>
3960 <li>updated Application to use DAS 1.53e version of
3961 dasobert DAS client</li>
3962 <li>Re-instated Full AMSA support and .amsa file
3964 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3972 <div align="center">
3973 <strong>2.3</strong><br> 9/5/07
3978 <li>Jmol 11.0.2 integration</li>
3979 <li>PDB views stored in Jalview XML files</li>
3980 <li>Slide sequences</li>
3981 <li>Edit sequence in place</li>
3982 <li>EMBL CDS features</li>
3983 <li>DAS Feature mapping</li>
3984 <li>Feature ordering</li>
3985 <li>Alignment Properties</li>
3986 <li>Annotation Scores</li>
3987 <li>Sort by scores</li>
3988 <li>Feature/annotation editing in applet</li>
3993 <li>Headless state operation in 2.2.1</li>
3994 <li>Incorrect and unstable DNA pairwise alignment</li>
3995 <li>Cut and paste of sequences with annotation</li>
3996 <li>Feature group display state in XML</li>
3997 <li>Feature ordering in XML</li>
3998 <li>blc file iteration selection using filename # suffix</li>
3999 <li>Stockholm alignment properties</li>
4000 <li>Stockhom alignment secondary structure annotation</li>
4001 <li>2.2.1 applet had no feature transparency</li>
4002 <li>Number pad keys can be used in cursor mode</li>
4003 <li>Structure Viewer mirror image resolved</li>
4010 <div align="center">
4011 <strong>2.2.1</strong><br> 12/2/07
4016 <li>Non standard characters can be read and displayed
4017 <li>Annotations/Features can be imported/exported to the
4019 <li>Applet allows editing of sequence/annotation/group
4020 name & description
4021 <li>Preference setting to display sequence name in
4023 <li>Annotation file format extended to allow
4024 Sequence_groups to be defined
4025 <li>Default opening of alignment overview panel can be
4026 specified in preferences
4027 <li>PDB residue numbering annotation added to associated
4033 <li>Applet crash under certain Linux OS with Java 1.6
4035 <li>Annotation file export / import bugs fixed
4036 <li>PNG / EPS image output bugs fixed
4042 <div align="center">
4043 <strong>2.2</strong><br> 27/11/06
4048 <li>Multiple views on alignment
4049 <li>Sequence feature editing
4050 <li>"Reload" alignment
4051 <li>"Save" to current filename
4052 <li>Background dependent text colour
4053 <li>Right align sequence ids
4054 <li>User-defined lower case residue colours
4057 <li>Menu item accelerator keys
4058 <li>Control-V pastes to current alignment
4059 <li>Cancel button for DAS Feature Fetching
4060 <li>PCA and PDB Viewers zoom via mouse roller
4061 <li>User-defined sub-tree colours and sub-tree selection
4063 <li>'New Window' button on the 'Output to Text box'
4068 <li>New memory efficient Undo/Redo System
4069 <li>Optimised symbol lookups and conservation/consensus
4071 <li>Region Conservation/Consensus recalculated after
4073 <li>Fixed Remove Empty Columns Bug (empty columns at end
4075 <li>Slowed DAS Feature Fetching for increased robustness.
4077 <li>Made angle brackets in ASCII feature descriptions
4079 <li>Re-instated Zoom function for PCA
4080 <li>Sequence descriptions conserved in web service
4082 <li>UniProt ID discoverer uses any word separated by
4084 <li>WsDbFetch query/result association resolved
4085 <li>Tree leaf to sequence mapping improved
4086 <li>Smooth fonts switch moved to FontChooser dialog box.
4093 <div align="center">
4094 <strong>2.1.1</strong><br> 12/9/06
4099 <li>Copy consensus sequence to clipboard</li>
4104 <li>Image output - rightmost residues are rendered if
4105 sequence id panel has been resized</li>
4106 <li>Image output - all offscreen group boundaries are
4108 <li>Annotation files with sequence references - all
4109 elements in file are relative to sequence position</li>
4110 <li>Mac Applet users can use Alt key for group editing</li>
4116 <div align="center">
4117 <strong>2.1</strong><br> 22/8/06
4122 <li>MAFFT Multiple Alignment in default Web Service list</li>
4123 <li>DAS Feature fetching</li>
4124 <li>Hide sequences and columns</li>
4125 <li>Export Annotations and Features</li>
4126 <li>GFF file reading / writing</li>
4127 <li>Associate structures with sequences from local PDB
4129 <li>Add sequences to exisiting alignment</li>
4130 <li>Recently opened files / URL lists</li>
4131 <li>Applet can launch the full application</li>
4132 <li>Applet has transparency for features (Java 1.2
4134 <li>Applet has user defined colours parameter</li>
4135 <li>Applet can load sequences from parameter
4136 "sequence<em>x</em>"
4142 <li>Redundancy Panel reinstalled in the Applet</li>
4143 <li>Monospaced font - EPS / rescaling bug fixed</li>
4144 <li>Annotation files with sequence references bug fixed</li>
4150 <div align="center">
4151 <strong>2.08.1</strong><br> 2/5/06
4156 <li>Change case of selected region from Popup menu</li>
4157 <li>Choose to match case when searching</li>
4158 <li>Middle mouse button and mouse movement can compress /
4159 expand the visible width and height of the alignment</li>
4164 <li>Annotation Panel displays complete JNet results</li>
4170 <div align="center">
4171 <strong>2.08b</strong><br> 18/4/06
4177 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4178 <li>Righthand label on wrapped alignments shows correct
4185 <div align="center">
4186 <strong>2.08</strong><br> 10/4/06
4191 <li>Editing can be locked to the selection area</li>
4192 <li>Keyboard editing</li>
4193 <li>Create sequence features from searches</li>
4194 <li>Precalculated annotations can be loaded onto
4196 <li>Features file allows grouping of features</li>
4197 <li>Annotation Colouring scheme added</li>
4198 <li>Smooth fonts off by default - Faster rendering</li>
4199 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4204 <li>Drag & Drop fixed on Linux</li>
4205 <li>Jalview Archive file faster to load/save, sequence
4206 descriptions saved.</li>
4212 <div align="center">
4213 <strong>2.07</strong><br> 12/12/05
4218 <li>PDB Structure Viewer enhanced</li>
4219 <li>Sequence Feature retrieval and display enhanced</li>
4220 <li>Choose to output sequence start-end after sequence
4221 name for file output</li>
4222 <li>Sequence Fetcher WSDBFetch@EBI</li>
4223 <li>Applet can read feature files, PDB files and can be
4224 used for HTML form input</li>
4229 <li>HTML output writes groups and features</li>
4230 <li>Group editing is Control and mouse click</li>
4231 <li>File IO bugs</li>
4237 <div align="center">
4238 <strong>2.06</strong><br> 28/9/05
4243 <li>View annotations in wrapped mode</li>
4244 <li>More options for PCA viewer</li>
4249 <li>GUI bugs resolved</li>
4250 <li>Runs with -nodisplay from command line</li>
4256 <div align="center">
4257 <strong>2.05b</strong><br> 15/9/05
4262 <li>Choose EPS export as lineart or text</li>
4263 <li>Jar files are executable</li>
4264 <li>Can read in Uracil - maps to unknown residue</li>
4269 <li>Known OutOfMemory errors give warning message</li>
4270 <li>Overview window calculated more efficiently</li>
4271 <li>Several GUI bugs resolved</li>
4277 <div align="center">
4278 <strong>2.05</strong><br> 30/8/05
4283 <li>Edit and annotate in "Wrapped" view</li>
4288 <li>Several GUI bugs resolved</li>
4294 <div align="center">
4295 <strong>2.04</strong><br> 24/8/05
4300 <li>Hold down mouse wheel & scroll to change font
4306 <li>Improved JPred client reliability</li>
4307 <li>Improved loading of Jalview files</li>
4313 <div align="center">
4314 <strong>2.03</strong><br> 18/8/05
4319 <li>Set Proxy server name and port in preferences</li>
4320 <li>Multiple URL links from sequence ids</li>
4321 <li>User Defined Colours can have a scheme name and added
4323 <li>Choose to ignore gaps in consensus calculation</li>
4324 <li>Unix users can set default web browser</li>
4325 <li>Runs without GUI for batch processing</li>
4326 <li>Dynamically generated Web Service Menus</li>
4331 <li>InstallAnywhere download for Sparc Solaris</li>
4337 <div align="center">
4338 <strong>2.02</strong><br> 18/7/05
4344 <li>Copy & Paste order of sequences maintains
4345 alignment order.</li>
4351 <div align="center">
4352 <strong>2.01</strong><br> 12/7/05
4357 <li>Use delete key for deleting selection.</li>
4358 <li>Use Mouse wheel to scroll sequences.</li>
4359 <li>Help file updated to describe how to add alignment
4361 <li>Version and build date written to build properties
4363 <li>InstallAnywhere installation will check for updates
4364 at launch of Jalview.</li>
4369 <li>Delete gaps bug fixed.</li>
4370 <li>FileChooser sorts columns.</li>
4371 <li>Can remove groups one by one.</li>
4372 <li>Filechooser icons installed.</li>
4373 <li>Finder ignores return character when searching.
4374 Return key will initiate a search.<br>
4381 <div align="center">
4382 <strong>2.0</strong><br> 20/6/05
4387 <li>New codebase</li>