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;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">2.11</a><br />
61 <em>20/06/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
68 <!-- JAL-2620 -->Alternative genetic code tables for
69 'Translate as cDNA'</li>
71 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
72 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
75 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
76 shaded according to any associated attributes (e.g. variant
77 attributes from VCF file, or key-value pairs imported from
81 <!-- JAL-2897 -->Show synonymous codon variants on peptide
85 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
89 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
90 algorithm (Z-sort/transparency and filter aware)
93 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
99 <!-- JAL-3141 -->Backup files created when saving Jalview project
102 <li><strong>Principal Components Analysis Viewer</strong>
105 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
106 and Viewer state saved in Jalview Project
108 <li>'Change parameters' option removed from viewer's
111 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
115 <!-- JAL-2965 -->PCA plot is depth cued
120 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
122 <li><strong>Speed and Efficiency</strong>
125 <!-- JAL-3198 -->More efficient creation of selections and
126 multiple groups when working with large alignments
129 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
133 <li><strong>User Interface</strong>
136 <!-- JAL-2933 -->Finder panel remembers last position in each
140 <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
141 what is shown)<br />Only visible region of alignment is shown by
142 default (can be changed in user preferences)
145 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
146 to the Overwrite Dialog
149 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
153 <!-- JAL-1244 -->Status bar shows bounds when dragging a
154 selection region, and gap count when inserting or deleting gaps
157 <!-- JAL-3132 -->Status bar updates over sequence and annotation
161 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
165 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
169 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
172 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
176 <!-- JAL-3181 -->Consistent ordering of links in sequence id
180 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
182 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
186 <li><strong>Java 11 Support</strong>
189 <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
190 and getdown release channels
193 <!-- -->OSX GUI integrations for App menu's 'About' entry and
198 <em>Deprecations</em>
201 <!-- JAL-3035 -->DAS sequence retrieval and annotation
202 capabilities removed from the Jalview Desktop
205 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
206 unmarshalling has been replaced by JAXB for Jalview projects
207 and XML based data retrieval clients</li>
208 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
209 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
210 </ul> <em>Documentation</em>
213 <!-- JAL-3003 -->Added remarks about transparent rendering effects
214 not supported in EPS figure export
216 </ul> <em>Development and Release Processes</em>
219 <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
220 Installers built with Install4j (licensed to the Jalview open
221 source project) rather than InstallAnywhere
224 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
225 settings, receive over the air updates and launch specific
226 versions via (<a href="https://github.com/threerings/getdown">Three
230 <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
233 <!-- JAL-3225 -->Eclipse project configuration managed with
237 Atlassian Bamboo continuous integration for
238 unattended Test Suite execution</li>
240 <!-- JAL-2864 -->Memory test suite to detect leaks in common
243 <!-- JAL-3140 -->IntervalStoreJ (NCList
244 implementation that alows updates) used for Sequence Feature collections</li>
247 <td align="left" valign="top">
250 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
252 <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
254 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
256 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
257 Jalview project involving multiple views</li>
259 <!-- JAL-3164 -->Overview for complementary view in a linked
260 CDS/Protein alignment is not updated when Hide Columns by
261 Annotation dialog hides columns</li>
263 <!-- JAL-3158 -->Selection highlighting in the complement of
264 a CDS/Protein alignment stops working after making a
265 selection in one view, then making another selection in the
268 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
270 <!-- JAL-3154 -->Table Columns could be re-ordered in
271 Feature Settings and Jalview Preferences panels</li>
273 <!-- JAL-2865 -->Jalview hangs when closing windows
274 or the overview updates with large alignments</li>
276 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
277 region if columns were selected by dragging right-to-left
278 and the mouse moved to the left of the first column</li>
280 <!-- JAL-3218 -->Couldn't hide selected columns adjacent
281 to a hidden column marker via scale popup menu</li>
283 <!-- JAL-2846 -->Error message for trying to load in invalid
284 URLs doesn't tell users the invalid URL</li>
286 <!-- JAL-3178 -->Nonpositional features lose feature group
287 on export as Jalview features file</li>
289 <!-- JAL-2060 -->'Graduated colour' option not offered for
290 manually created features (where if feature score is Float.NaN)
293 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
294 printed when columns are hidden</li>
296 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
298 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
299 dragging out of Scale or Annotation Panel</li>
301 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
303 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
305 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
307 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
309 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
311 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
313 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
314 opening an alignment</li>
316 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
318 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
319 different groups in the alignment are selected</li>
321 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
323 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
325 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
327 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
329 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
331 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
333 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
335 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
337 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
339 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
341 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
343 <!-- JAL-914 -->Help page can be opened twice</li>
348 <!-- JAL-2822 -->Start and End should be updated when
349 sequence data at beginning or end of alignment added/removed
350 via 'Edit' sequence</li>
352 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
353 sequence features correctly when start of sequence is
354 removed (Known defect since 2.10)</li>
355 </ul><em>New Known Defects</em>
358 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
360 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
362 <!-- JAL-3240 -->Display is incorrect after removing gapped
363 columns within hidden columns
366 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
367 window after dragging left to select columns to left of visible
374 <td width="60" nowrap>
376 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
379 <td><div align="left">
383 <!-- JAL-3101 -->Default memory for Jalview webstart and
384 InstallAnywhere increased to 1G.
387 <!-- JAL-247 -->Hidden sequence markers and representative
388 sequence bolding included when exporting alignment as EPS,
389 SVG, PNG or HTML. <em>Display is configured via the
390 Format menu, or for command-line use via a jalview
391 properties file.</em>
394 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
395 API and sequence data now imported as JSON.
398 <!-- JAL-3065 -->Change in recommended way of starting
399 Jalview via a Java command line: add jars in lib directory
400 to CLASSPATH, rather than via the deprecated java.ext.dirs
407 <!-- JAL-3047 -->Support added to execute test suite
408 instrumented with <a href="http://openclover.org/">Open
413 <td><div align="left">
417 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
418 row shown in Feredoxin Structure alignment view of example
422 <!-- JAL-2854 -->Annotation obscures sequences if lots of
423 annotation displayed.
426 <!-- JAL-3107 -->Group conservation/consensus not shown
427 for newly created group when 'Apply to all groups'
431 <!-- JAL-3087 -->Corrupted display when switching to
432 wrapped mode when sequence panel's vertical scrollbar is
436 <!-- JAL-3003 -->Alignment is black in exported EPS file
437 when sequences are selected in exported view.</em>
440 <!-- JAL-3059 -->Groups with different coloured borders
441 aren't rendered with correct colour.
444 <!-- JAL-3092 -->Jalview could hang when importing certain
445 types of knotted RNA secondary structure.
448 <!-- JAL-3095 -->Sequence highlight and selection in
449 trimmed VARNA 2D structure is incorrect for sequences that
453 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
454 annotation when columns are inserted into an alignment,
455 and when exporting as Stockholm flatfile.
458 <!-- JAL-3053 -->Jalview annotation rows containing upper
459 and lower-case 'E' and 'H' do not automatically get
460 treated as RNA secondary structure.
463 <!-- JAL-3106 -->.jvp should be used as default extension
464 (not .jar) when saving a jalview project file.
467 <!-- JAL-3105 -->Mac Users: closing a window correctly
468 transfers focus to previous window on OSX
471 <em>Java 10 Issues Resolved</em>
474 <!-- JAL-2988 -->OSX - Can't save new files via the File
475 or export menus by typing in a name into the Save dialog
479 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
480 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
481 'look and feel' which has improved compatibility with the
482 latest version of OSX.
489 <td width="60" nowrap>
491 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
492 <em>7/06/2018</em></strong>
495 <td><div align="left">
499 <!-- JAL-2920 -->Use HGVS nomenclature for variant
500 annotation retrieved from Uniprot
503 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
504 onto the Jalview Desktop
508 <td><div align="left">
512 <!-- JAL-3017 -->Cannot import features with multiple
513 variant elements (blocks import of some Uniprot records)
516 <!-- JAL-2997 -->Clustal files with sequence positions in
517 right-hand column parsed correctly
520 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
521 not alignment area in exported graphic
524 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
525 window has input focus
528 <!-- JAL-2992 -->Annotation panel set too high when
529 annotation added to view (Windows)
532 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
533 network connectivity is poor
536 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
537 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
538 the currently open URL and links from a page viewed in
539 Firefox or Chrome on Windows is now fully supported. If
540 you are using Edge, only links in the page can be
541 dragged, and with Internet Explorer, only the currently
542 open URL in the browser can be dropped onto Jalview.</em>
548 <td width="60" nowrap>
550 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
553 <td><div align="left">
557 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
558 for disabling automatic superposition of multiple
559 structures and open structures in existing views
562 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
563 ID and annotation area margins can be click-dragged to
567 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
571 <!-- JAL-2759 -->Improved performance for large alignments
572 and lots of hidden columns
575 <!-- JAL-2593 -->Improved performance when rendering lots
576 of features (particularly when transparency is disabled)
579 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
580 exchange of Jalview features and Chimera attributes made
586 <td><div align="left">
589 <!-- JAL-2899 -->Structure and Overview aren't updated
590 when Colour By Annotation threshold slider is adjusted
593 <!-- JAL-2778 -->Slow redraw when Overview panel shown
594 overlapping alignment panel
597 <!-- JAL-2929 -->Overview doesn't show end of unpadded
601 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
602 improved: CDS not handled correctly if transcript has no
606 <!-- JAL-2321 -->Secondary structure and temperature
607 factor annotation not added to sequence when local PDB
608 file associated with it by drag'n'drop or structure
612 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
613 dialog doesn't import PDB files dropped on an alignment
616 <!-- JAL-2666 -->Linked scrolling via protein horizontal
617 scroll bar doesn't work for some CDS/Protein views
620 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
621 Java 1.8u153 onwards and Java 1.9u4+.
624 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
625 columns in annotation row
628 <!-- JAL-2913 -->Preferences panel's ID Width control is not
629 honored in batch mode
632 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
633 for structures added to existing Jmol view
636 <!-- JAL-2223 -->'View Mappings' includes duplicate
637 entries after importing project with multiple views
640 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
641 protein sequences via SIFTS from associated PDB entries
642 with negative residue numbers or missing residues fails
645 <!-- JAL-2952 -->Exception when shading sequence with negative
646 Temperature Factor values from annotated PDB files (e.g.
647 as generated by CONSURF)
650 <!-- JAL-2920 -->Uniprot 'sequence variant' features
651 tooltip doesn't include a text description of mutation
654 <!-- JAL-2922 -->Invert displayed features very slow when
655 structure and/or overview windows are also shown
658 <!-- JAL-2954 -->Selecting columns from highlighted regions
659 very slow for alignments with large numbers of sequences
662 <!-- JAL-2925 -->Copy Consensus fails for group consensus
663 with 'StringIndexOutOfBounds'
666 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
667 platforms running Java 10
670 <!-- JAL-2960 -->Adding a structure to existing structure
671 view appears to do nothing because the view is hidden behind the alignment view
677 <!-- JAL-2926 -->Copy consensus sequence option in applet
678 should copy the group consensus when popup is opened on it
684 <!-- JAL-2913 -->Fixed ID width preference is not respected
687 <em>New Known Defects</em>
690 <!-- JAL-2973 --> Exceptions occasionally raised when
691 editing a large alignment and overview is displayed
694 <!-- JAL-2974 -->'Overview updating' progress bar is shown
695 repeatedly after a series of edits even when the overview
696 is no longer reflecting updates
699 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
700 structures for protein subsequence (if 'Trim Retrieved
701 Sequences' enabled) or Ensembl isoforms (Workaround in
702 2.10.4 is to fail back to N&W mapping)
709 <td width="60" nowrap>
711 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
714 <td><div align="left">
715 <ul><li>Updated Certum Codesigning Certificate
716 (Valid till 30th November 2018)</li></ul></div></td>
717 <td><div align="left">
720 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
721 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
722 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
723 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
724 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
725 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
726 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
732 <td width="60" nowrap>
734 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
737 <td><div align="left">
741 <!-- JAL-2446 -->Faster and more efficient management and
742 rendering of sequence features
745 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
746 429 rate limit request hander
749 <!-- JAL-2773 -->Structure views don't get updated unless
750 their colours have changed
753 <!-- JAL-2495 -->All linked sequences are highlighted for
754 a structure mousover (Jmol) or selection (Chimera)
757 <!-- JAL-2790 -->'Cancel' button in progress bar for
758 JABAWS AACon, RNAAliFold and Disorder prediction jobs
761 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
762 view from Ensembl locus cross-references
765 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
769 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
770 feature can be disabled
773 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
774 PDB easier retrieval of sequences for lists of IDs
777 <!-- JAL-2758 -->Short names for sequences retrieved from
783 <li>Groovy interpreter updated to 2.4.12</li>
784 <li>Example groovy script for generating a matrix of
785 percent identity scores for current alignment.</li>
787 <em>Testing and Deployment</em>
790 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
794 <td><div align="left">
798 <!-- JAL-2643 -->Pressing tab after updating the colour
799 threshold text field doesn't trigger an update to the
803 <!-- JAL-2682 -->Race condition when parsing sequence ID
807 <!-- JAL-2608 -->Overview windows are also closed when
808 alignment window is closed
811 <!-- JAL-2548 -->Export of features doesn't always respect
815 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
816 takes a long time in Cursor mode
822 <!-- JAL-2777 -->Structures with whitespace chainCode
823 cannot be viewed in Chimera
826 <!-- JAL-2728 -->Protein annotation panel too high in
830 <!-- JAL-2757 -->Can't edit the query after the server
831 error warning icon is shown in Uniprot and PDB Free Text
835 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
838 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
841 <!-- JAL-2739 -->Hidden column marker in last column not
842 rendered when switching back from Wrapped to normal view
845 <!-- JAL-2768 -->Annotation display corrupted when
846 scrolling right in unwapped alignment view
849 <!-- JAL-2542 -->Existing features on subsequence
850 incorrectly relocated when full sequence retrieved from
854 <!-- JAL-2733 -->Last reported memory still shown when
855 Desktop->Show Memory is unticked (OSX only)
858 <!-- JAL-2658 -->Amend Features dialog doesn't allow
859 features of same type and group to be selected for
863 <!-- JAL-2524 -->Jalview becomes sluggish in wide
864 alignments when hidden columns are present
867 <!-- JAL-2392 -->Jalview freezes when loading and
868 displaying several structures
871 <!-- JAL-2732 -->Black outlines left after resizing or
875 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
876 within the Jalview desktop on OSX
879 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
880 when in wrapped alignment mode
883 <!-- JAL-2636 -->Scale mark not shown when close to right
884 hand end of alignment
887 <!-- JAL-2684 -->Pairwise alignment of selected regions of
888 each selected sequence do not have correct start/end
892 <!-- JAL-2793 -->Alignment ruler height set incorrectly
893 after canceling the Alignment Window's Font dialog
896 <!-- JAL-2036 -->Show cross-references not enabled after
897 restoring project until a new view is created
900 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
901 URL links appears when only default EMBL-EBI link is
902 configured (since 2.10.2b2)
905 <!-- JAL-2775 -->Overview redraws whole window when box
909 <!-- JAL-2225 -->Structure viewer doesn't map all chains
910 in a multi-chain structure when viewing alignment
911 involving more than one chain (since 2.10)
914 <!-- JAL-2811 -->Double residue highlights in cursor mode
915 if new selection moves alignment window
918 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
919 arrow key in cursor mode to pass hidden column marker
922 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
923 that produces correctly annotated transcripts and products
926 <!-- JAL-2776 -->Toggling a feature group after first time
927 doesn't update associated structure view
930 <em>Applet</em><br />
933 <!-- JAL-2687 -->Concurrent modification exception when
934 closing alignment panel
937 <em>BioJSON</em><br />
940 <!-- JAL-2546 -->BioJSON export does not preserve
941 non-positional features
944 <em>New Known Issues</em>
947 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
948 sequence features correctly (for many previous versions of
952 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
953 using cursor in wrapped panel other than top
956 <!-- JAL-2791 -->Select columns containing feature ignores
957 graduated colour threshold
960 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
961 always preserve numbering and sequence features
964 <em>Known Java 9 Issues</em>
967 <!-- JAL-2902 -->Groovy Console very slow to open and is
968 not responsive when entering characters (Webstart, Java
975 <td width="60" nowrap>
977 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
978 <em>2/10/2017</em></strong>
981 <td><div align="left">
982 <em>New features in Jalview Desktop</em>
985 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
987 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
991 <td><div align="left">
995 <td width="60" nowrap>
997 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
998 <em>7/9/2017</em></strong>
1001 <td><div align="left">
1005 <!-- JAL-2588 -->Show gaps in overview window by colouring
1006 in grey (sequences used to be coloured grey, and gaps were
1010 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1014 <!-- JAL-2587 -->Overview updates immediately on increase
1015 in size and progress bar shown as higher resolution
1016 overview is recalculated
1021 <td><div align="left">
1025 <!-- JAL-2664 -->Overview window redraws every hidden
1026 column region row by row
1029 <!-- JAL-2681 -->duplicate protein sequences shown after
1030 retrieving Ensembl crossrefs for sequences from Uniprot
1033 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1034 format setting is unticked
1037 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1038 if group has show boxes format setting unticked
1041 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1042 autoscrolling whilst dragging current selection group to
1043 include sequences and columns not currently displayed
1046 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1047 assemblies are imported via CIF file
1050 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1051 displayed when threshold or conservation colouring is also
1055 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1059 <!-- JAL-2673 -->Jalview continues to scroll after
1060 dragging a selected region off the visible region of the
1064 <!-- JAL-2724 -->Cannot apply annotation based
1065 colourscheme to all groups in a view
1068 <!-- JAL-2511 -->IDs don't line up with sequences
1069 initially after font size change using the Font chooser or
1076 <td width="60" nowrap>
1077 <div align="center">
1078 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1081 <td><div align="left">
1082 <em>Calculations</em>
1086 <!-- JAL-1933 -->Occupancy annotation row shows number of
1087 ungapped positions in each column of the alignment.
1090 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1091 a calculation dialog box
1094 <!-- JAL-2379 -->Revised implementation of PCA for speed
1095 and memory efficiency (~30x faster)
1098 <!-- JAL-2403 -->Revised implementation of sequence
1099 similarity scores as used by Tree, PCA, Shading Consensus
1100 and other calculations
1103 <!-- JAL-2416 -->Score matrices are stored as resource
1104 files within the Jalview codebase
1107 <!-- JAL-2500 -->Trees computed on Sequence Feature
1108 Similarity may have different topology due to increased
1115 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1116 model for alignments and groups
1119 <!-- JAL-384 -->Custom shading schemes created via groovy
1126 <!-- JAL-2526 -->Efficiency improvements for interacting
1127 with alignment and overview windows
1130 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1134 <!-- JAL-2388 -->Hidden columns and sequences can be
1138 <!-- JAL-2611 -->Click-drag in visible area allows fine
1139 adjustment of visible position
1143 <em>Data import/export</em>
1146 <!-- JAL-2535 -->Posterior probability annotation from
1147 Stockholm files imported as sequence associated annotation
1150 <!-- JAL-2507 -->More robust per-sequence positional
1151 annotation input/output via stockholm flatfile
1154 <!-- JAL-2533 -->Sequence names don't include file
1155 extension when importing structure files without embedded
1156 names or PDB accessions
1159 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1160 format sequence substitution matrices
1163 <em>User Interface</em>
1166 <!-- JAL-2447 --> Experimental Features Checkbox in
1167 Desktop's Tools menu to hide or show untested features in
1171 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1172 via Overview or sequence motif search operations
1175 <!-- JAL-2547 -->Amend sequence features dialog box can be
1176 opened by double clicking gaps within sequence feature
1180 <!-- JAL-1476 -->Status bar message shown when not enough
1181 aligned positions were available to create a 3D structure
1185 <em>3D Structure</em>
1188 <!-- JAL-2430 -->Hidden regions in alignment views are not
1189 coloured in linked structure views
1192 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1193 file-based command exchange
1196 <!-- JAL-2375 -->Structure chooser automatically shows
1197 Cached Structures rather than querying the PDBe if
1198 structures are already available for sequences
1201 <!-- JAL-2520 -->Structures imported via URL are cached in
1202 the Jalview project rather than downloaded again when the
1203 project is reopened.
1206 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1207 to transfer Chimera's structure attributes as Jalview
1208 features, and vice-versa (<strong>Experimental
1212 <em>Web Services</em>
1215 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1218 <!-- JAL-2335 -->Filter non-standard amino acids and
1219 nucleotides when submitting to AACon and other MSA
1223 <!-- JAL-2316, -->URLs for viewing database
1224 cross-references provided by identifiers.org and the
1225 EMBL-EBI's MIRIAM DB
1232 <!-- JAL-2344 -->FileFormatI interface for describing and
1233 identifying file formats (instead of String constants)
1236 <!-- JAL-2228 -->FeatureCounter script refactored for
1237 efficiency when counting all displayed features (not
1238 backwards compatible with 2.10.1)
1241 <em>Example files</em>
1244 <!-- JAL-2631 -->Graduated feature colour style example
1245 included in the example feature file
1248 <em>Documentation</em>
1251 <!-- JAL-2339 -->Release notes reformatted for readability
1252 with the built-in Java help viewer
1255 <!-- JAL-1644 -->Find documentation updated with 'search
1256 sequence description' option
1262 <!-- JAL-2485, -->External service integration tests for
1263 Uniprot REST Free Text Search Client
1266 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1269 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1274 <td><div align="left">
1275 <em>Calculations</em>
1278 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1279 matrix - C->R should be '-3'<br />Old matrix restored
1280 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1282 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1283 Jalview's treatment of gaps in PCA and substitution matrix
1284 based Tree calculations.<br /> <br />In earlier versions
1285 of Jalview, gaps matching gaps were penalised, and gaps
1286 matching non-gaps penalised even more. In the PCA
1287 calculation, gaps were actually treated as non-gaps - so
1288 different costs were applied, which meant Jalview's PCAs
1289 were different to those produced by SeqSpace.<br />Jalview
1290 now treats gaps in the same way as SeqSpace (ie it scores
1291 them as 0). <br /> <br />Enter the following in the
1292 Groovy console to restore pre-2.10.2 behaviour:<br />
1293 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1294 // for 2.10.1 mode <br />
1295 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1296 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1297 these settings will affect all subsequent tree and PCA
1298 calculations (not recommended)</em></li>
1300 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1301 scaling of branch lengths for trees computed using
1302 Sequence Feature Similarity.
1305 <!-- JAL-2377 -->PCA calculation could hang when
1306 generating output report when working with highly
1307 redundant alignments
1310 <!-- JAL-2544 --> Sort by features includes features to
1311 right of selected region when gaps present on right-hand
1315 <em>User Interface</em>
1318 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1319 doesn't reselect a specific sequence's associated
1320 annotation after it was used for colouring a view
1323 <!-- JAL-2419 -->Current selection lost if popup menu
1324 opened on a region of alignment without groups
1327 <!-- JAL-2374 -->Popup menu not always shown for regions
1328 of an alignment with overlapping groups
1331 <!-- JAL-2310 -->Finder double counts if both a sequence's
1332 name and description match
1335 <!-- JAL-2370 -->Hiding column selection containing two
1336 hidden regions results in incorrect hidden regions
1339 <!-- JAL-2386 -->'Apply to all groups' setting when
1340 changing colour does not apply Conservation slider value
1344 <!-- JAL-2373 -->Percentage identity and conservation menu
1345 items do not show a tick or allow shading to be disabled
1348 <!-- JAL-2385 -->Conservation shading or PID threshold
1349 lost when base colourscheme changed if slider not visible
1352 <!-- JAL-2547 -->Sequence features shown in tooltip for
1353 gaps before start of features
1356 <!-- JAL-2623 -->Graduated feature colour threshold not
1357 restored to UI when feature colour is edited
1360 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1361 a time when scrolling vertically in wrapped mode.
1364 <!-- JAL-2630 -->Structure and alignment overview update
1365 as graduate feature colour settings are modified via the
1369 <!-- JAL-2034 -->Overview window doesn't always update
1370 when a group defined on the alignment is resized
1373 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1374 wrapped view result in positional status updates
1378 <!-- JAL-2563 -->Status bar doesn't show position for
1379 ambiguous amino acid and nucleotide symbols
1382 <!-- JAL-2602 -->Copy consensus sequence failed if
1383 alignment included gapped columns
1386 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1387 widgets don't permanently disappear
1390 <!-- JAL-2503 -->Cannot select or filter quantitative
1391 annotation that are shown only as column labels (e.g.
1392 T-Coffee column reliability scores)
1395 <!-- JAL-2594 -->Exception thrown if trying to create a
1396 sequence feature on gaps only
1399 <!-- JAL-2504 -->Features created with 'New feature'
1400 button from a Find inherit previously defined feature type
1401 rather than the Find query string
1404 <!-- JAL-2423 -->incorrect title in output window when
1405 exporting tree calculated in Jalview
1408 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1409 and then revealing them reorders sequences on the
1413 <!-- JAL-964 -->Group panel in sequence feature settings
1414 doesn't update to reflect available set of groups after
1415 interactively adding or modifying features
1418 <!-- JAL-2225 -->Sequence Database chooser unusable on
1422 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1423 only excluded gaps in current sequence and ignored
1430 <!-- JAL-2421 -->Overview window visible region moves
1431 erratically when hidden rows or columns are present
1434 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1435 Structure Viewer's colour menu don't correspond to
1439 <!-- JAL-2405 -->Protein specific colours only offered in
1440 colour and group colour menu for protein alignments
1443 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1444 reflect currently selected view or group's shading
1448 <!-- JAL-2624 -->Feature colour thresholds not respected
1449 when rendered on overview and structures when opacity at
1453 <!-- JAL-2589 -->User defined gap colour not shown in
1454 overview when features overlaid on alignment
1457 <em>Data import/export</em>
1460 <!-- JAL-2576 -->Very large alignments take a long time to
1464 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1465 added after a sequence was imported are not written to
1469 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1470 when importing RNA secondary structure via Stockholm
1473 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1474 not shown in correct direction for simple pseudoknots
1477 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1478 with lightGray or darkGray via features file (but can
1482 <!-- JAL-2383 -->Above PID colour threshold not recovered
1483 when alignment view imported from project
1486 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1487 structure and sequences extracted from structure files
1488 imported via URL and viewed in Jmol
1491 <!-- JAL-2520 -->Structures loaded via URL are saved in
1492 Jalview Projects rather than fetched via URL again when
1493 the project is loaded and the structure viewed
1496 <em>Web Services</em>
1499 <!-- JAL-2519 -->EnsemblGenomes example failing after
1500 release of Ensembl v.88
1503 <!-- JAL-2366 -->Proxy server address and port always
1504 appear enabled in Preferences->Connections
1507 <!-- JAL-2461 -->DAS registry not found exceptions
1508 removed from console output
1511 <!-- JAL-2582 -->Cannot retrieve protein products from
1512 Ensembl by Peptide ID
1515 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1516 created from SIFTs, and spurious 'Couldn't open structure
1517 in Chimera' errors raised after April 2017 update (problem
1518 due to 'null' string rather than empty string used for
1519 residues with no corresponding PDB mapping).
1522 <em>Application UI</em>
1525 <!-- JAL-2361 -->User Defined Colours not added to Colour
1529 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1530 case' residues (button in colourscheme editor debugged and
1531 new documentation and tooltips added)
1534 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1535 doesn't restore group-specific text colour thresholds
1538 <!-- JAL-2243 -->Feature settings panel does not update as
1539 new features are added to alignment
1542 <!-- JAL-2532 -->Cancel in feature settings reverts
1543 changes to feature colours via the Amend features dialog
1546 <!-- JAL-2506 -->Null pointer exception when attempting to
1547 edit graduated feature colour via amend features dialog
1551 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1552 selection menu changes colours of alignment views
1555 <!-- JAL-2426 -->Spurious exceptions in console raised
1556 from alignment calculation workers after alignment has
1560 <!-- JAL-1608 -->Typo in selection popup menu - Create
1561 groups now 'Create Group'
1564 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1565 Create/Undefine group doesn't always work
1568 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1569 shown again after pressing 'Cancel'
1572 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1573 adjusts start position in wrap mode
1576 <!-- JAL-2563 -->Status bar doesn't show positions for
1577 ambiguous amino acids
1580 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1581 CDS/Protein view after CDS sequences added for aligned
1585 <!-- JAL-2592 -->User defined colourschemes called 'User
1586 Defined' don't appear in Colours menu
1592 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1593 score models doesn't always result in an updated PCA plot
1596 <!-- JAL-2442 -->Features not rendered as transparent on
1597 overview or linked structure view
1600 <!-- JAL-2372 -->Colour group by conservation doesn't
1604 <!-- JAL-2517 -->Hitting Cancel after applying
1605 user-defined colourscheme doesn't restore original
1612 <!-- JAL-2314 -->Unit test failure:
1613 jalview.ws.jabaws.RNAStructExportImport setup fails
1616 <!-- JAL-2307 -->Unit test failure:
1617 jalview.ws.sifts.SiftsClientTest due to compatibility
1618 problems with deep array comparison equality asserts in
1619 successive versions of TestNG
1622 <!-- JAL-2479 -->Relocated StructureChooserTest and
1623 ParameterUtilsTest Unit tests to Network suite
1626 <em>New Known Issues</em>
1629 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1630 phase after a sequence motif find operation
1633 <!-- JAL-2550 -->Importing annotation file with rows
1634 containing just upper and lower case letters are
1635 interpreted as WUSS RNA secondary structure symbols
1638 <!-- JAL-2590 -->Cannot load and display Newick trees
1639 reliably from eggnog Ortholog database
1642 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1643 containing features of type Highlight' when 'B' is pressed
1644 to mark columns containing highlighted regions.
1647 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1648 doesn't always add secondary structure annotation.
1653 <td width="60" nowrap>
1654 <div align="center">
1655 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1658 <td><div align="left">
1662 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1663 for all consensus calculations
1666 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1669 <li>Updated Jalview's Certum code signing certificate
1672 <em>Application</em>
1675 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1676 set of database cross-references, sorted alphabetically
1679 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1680 from database cross references. Users with custom links
1681 will receive a <a href="webServices/urllinks.html#warning">warning
1682 dialog</a> asking them to update their preferences.
1685 <!-- JAL-2287-->Cancel button and escape listener on
1686 dialog warning user about disconnecting Jalview from a
1690 <!-- JAL-2320-->Jalview's Chimera control window closes if
1691 the Chimera it is connected to is shut down
1694 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1695 columns menu item to mark columns containing highlighted
1696 regions (e.g. from structure selections or results of a
1700 <!-- JAL-2284-->Command line option for batch-generation
1701 of HTML pages rendering alignment data with the BioJS
1711 <!-- JAL-2286 -->Columns with more than one modal residue
1712 are not coloured or thresholded according to percent
1713 identity (first observed in Jalview 2.8.2)
1716 <!-- JAL-2301 -->Threonine incorrectly reported as not
1720 <!-- JAL-2318 -->Updates to documentation pages (above PID
1721 threshold, amino acid properties)
1724 <!-- JAL-2292 -->Lower case residues in sequences are not
1725 reported as mapped to residues in a structure file in the
1729 <!--JAL-2324 -->Identical features with non-numeric scores
1730 could be added multiple times to a sequence
1733 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1734 bond features shown as two highlighted residues rather
1735 than a range in linked structure views, and treated
1736 correctly when selecting and computing trees from features
1739 <!-- JAL-2281-->Custom URL links for database
1740 cross-references are matched to database name regardless
1745 <em>Application</em>
1748 <!-- JAL-2282-->Custom URL links for specific database
1749 names without regular expressions also offer links from
1753 <!-- JAL-2315-->Removing a single configured link in the
1754 URL links pane in Connections preferences doesn't actually
1755 update Jalview configuration
1758 <!-- JAL-2272-->CTRL-Click on a selected region to open
1759 the alignment area popup menu doesn't work on El-Capitan
1762 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1763 files with similarly named sequences if dropped onto the
1767 <!-- JAL-2312 -->Additional mappings are shown for PDB
1768 entries where more chains exist in the PDB accession than
1769 are reported in the SIFTS file
1772 <!-- JAL-2317-->Certain structures do not get mapped to
1773 the structure view when displayed with Chimera
1776 <!-- JAL-2317-->No chains shown in the Chimera view
1777 panel's View->Show Chains submenu
1780 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1781 work for wrapped alignment views
1784 <!--JAL-2197 -->Rename UI components for running JPred
1785 predictions from 'JNet' to 'JPred'
1788 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1789 corrupted when annotation panel vertical scroll is not at
1790 first annotation row
1793 <!--JAL-2332 -->Attempting to view structure for Hen
1794 lysozyme results in a PDB Client error dialog box
1797 <!-- JAL-2319 -->Structure View's mapping report switched
1798 ranges for PDB and sequence for SIFTS
1801 SIFTS 'Not_Observed' residues mapped to non-existant
1805 <!-- <em>New Known Issues</em>
1812 <td width="60" nowrap>
1813 <div align="center">
1814 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1815 <em>25/10/2016</em></strong>
1818 <td><em>Application</em>
1820 <li>3D Structure chooser opens with 'Cached structures'
1821 view if structures already loaded</li>
1822 <li>Progress bar reports models as they are loaded to
1823 structure views</li>
1829 <li>Colour by conservation always enabled and no tick
1830 shown in menu when BLOSUM or PID shading applied</li>
1831 <li>FER1_ARATH and FER2_ARATH labels were switched in
1832 example sequences/projects/trees</li>
1834 <em>Application</em>
1836 <li>Jalview projects with views of local PDB structure
1837 files saved on Windows cannot be opened on OSX</li>
1838 <li>Multiple structure views can be opened and superposed
1839 without timeout for structures with multiple models or
1840 multiple sequences in alignment</li>
1841 <li>Cannot import or associated local PDB files without a
1842 PDB ID HEADER line</li>
1843 <li>RMSD is not output in Jmol console when superposition
1845 <li>Drag and drop of URL from Browser fails for Linux and
1846 OSX versions earlier than El Capitan</li>
1847 <li>ENA client ignores invalid content from ENA server</li>
1848 <li>Exceptions are not raised in console when ENA client
1849 attempts to fetch non-existent IDs via Fetch DB Refs UI
1851 <li>Exceptions are not raised in console when a new view
1852 is created on the alignment</li>
1853 <li>OSX right-click fixed for group selections: CMD-click
1854 to insert/remove gaps in groups and CTRL-click to open group
1857 <em>Build and deployment</em>
1859 <li>URL link checker now copes with multi-line anchor
1862 <em>New Known Issues</em>
1864 <li>Drag and drop from URL links in browsers do not work
1871 <td width="60" nowrap>
1872 <div align="center">
1873 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1876 <td><em>General</em>
1879 <!-- JAL-2124 -->Updated Spanish translations.
1882 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1883 for importing structure data to Jalview. Enables mmCIF and
1887 <!-- JAL-192 --->Alignment ruler shows positions relative to
1891 <!-- JAL-2202 -->Position/residue shown in status bar when
1892 mousing over sequence associated annotation
1895 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1899 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1900 '()', canonical '[]' and invalid '{}' base pair populations
1904 <!-- JAL-2092 -->Feature settings popup menu options for
1905 showing or hiding columns containing a feature
1908 <!-- JAL-1557 -->Edit selected group by double clicking on
1909 group and sequence associated annotation labels
1912 <!-- JAL-2236 -->Sequence name added to annotation label in
1913 select/hide columns by annotation and colour by annotation
1917 </ul> <em>Application</em>
1920 <!-- JAL-2050-->Automatically hide introns when opening a
1921 gene/transcript view
1924 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1928 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1929 structure mappings with the EMBL-EBI PDBe SIFTS database
1932 <!-- JAL-2079 -->Updated download sites used for Rfam and
1933 Pfam sources to xfam.org
1936 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1939 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1940 over sequences in Jalview
1943 <!-- JAL-2027-->Support for reverse-complement coding
1944 regions in ENA and EMBL
1947 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1948 for record retrieval via ENA rest API
1951 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1955 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1956 groovy script execution
1959 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1960 alignment window's Calculate menu
1963 <!-- JAL-1812 -->Allow groovy scripts that call
1964 Jalview.getAlignFrames() to run in headless mode
1967 <!-- JAL-2068 -->Support for creating new alignment
1968 calculation workers from groovy scripts
1971 <!-- JAL-1369 --->Store/restore reference sequence in
1975 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1976 associations are now saved/restored from project
1979 <!-- JAL-1993 -->Database selection dialog always shown
1980 before sequence fetcher is opened
1983 <!-- JAL-2183 -->Double click on an entry in Jalview's
1984 database chooser opens a sequence fetcher
1987 <!-- JAL-1563 -->Free-text search client for UniProt using
1988 the UniProt REST API
1991 <!-- JAL-2168 -->-nonews command line parameter to prevent
1992 the news reader opening
1995 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1996 querying stored in preferences
1999 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2003 <!-- JAL-1977-->Tooltips shown on database chooser
2006 <!-- JAL-391 -->Reverse complement function in calculate
2007 menu for nucleotide sequences
2010 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2011 and feature counts preserves alignment ordering (and
2012 debugged for complex feature sets).
2015 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2016 viewing structures with Jalview 2.10
2019 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2020 genome, transcript CCDS and gene ids via the Ensembl and
2021 Ensembl Genomes REST API
2024 <!-- JAL-2049 -->Protein sequence variant annotation
2025 computed for 'sequence_variant' annotation on CDS regions
2029 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2033 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2034 Ref Fetcher fails to match, or otherwise updates sequence
2035 data from external database records.
2038 <!-- JAL-2154 -->Revised Jalview Project format for
2039 efficient recovery of sequence coding and alignment
2040 annotation relationships.
2042 </ul> <!-- <em>Applet</em>
2053 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2057 <!-- JAL-2018-->Export features in Jalview format (again)
2058 includes graduated colourschemes
2061 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2062 working with big alignments and lots of hidden columns
2065 <!-- JAL-2053-->Hidden column markers not always rendered
2066 at right of alignment window
2069 <!-- JAL-2067 -->Tidied up links in help file table of
2073 <!-- JAL-2072 -->Feature based tree calculation not shown
2077 <!-- JAL-2075 -->Hidden columns ignored during feature
2078 based tree calculation
2081 <!-- JAL-2065 -->Alignment view stops updating when show
2082 unconserved enabled for group on alignment
2085 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2089 <!-- JAL-2146 -->Alignment column in status incorrectly
2090 shown as "Sequence position" when mousing over
2094 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2095 hidden columns present
2098 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2099 user created annotation added to alignment
2102 <!-- JAL-1841 -->RNA Structure consensus only computed for
2103 '()' base pair annotation
2106 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2107 in zero scores for all base pairs in RNA Structure
2111 <!-- JAL-2174-->Extend selection with columns containing
2115 <!-- JAL-2275 -->Pfam format writer puts extra space at
2116 beginning of sequence
2119 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2123 <!-- JAL-2238 -->Cannot create groups on an alignment from
2124 from a tree when t-coffee scores are shown
2127 <!-- JAL-1836,1967 -->Cannot import and view PDB
2128 structures with chains containing negative resnums (4q4h)
2131 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2135 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2136 to Clustal, PIR and PileUp output
2139 <!-- JAL-2008 -->Reordering sequence features that are
2140 not visible causes alignment window to repaint
2143 <!-- JAL-2006 -->Threshold sliders don't work in
2144 graduated colour and colour by annotation row for e-value
2145 scores associated with features and annotation rows
2148 <!-- JAL-1797 -->amino acid physicochemical conservation
2149 calculation should be case independent
2152 <!-- JAL-2173 -->Remove annotation also updates hidden
2156 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2157 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2158 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2161 <!-- JAL-2065 -->Null pointer exceptions and redraw
2162 problems when reference sequence defined and 'show
2163 non-conserved' enabled
2166 <!-- JAL-1306 -->Quality and Conservation are now shown on
2167 load even when Consensus calculation is disabled
2170 <!-- JAL-1932 -->Remove right on penultimate column of
2171 alignment does nothing
2174 <em>Application</em>
2177 <!-- JAL-1552-->URLs and links can't be imported by
2178 drag'n'drop on OSX when launched via webstart (note - not
2179 yet fixed for El Capitan)
2182 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2183 output when running on non-gb/us i18n platforms
2186 <!-- JAL-1944 -->Error thrown when exporting a view with
2187 hidden sequences as flat-file alignment
2190 <!-- JAL-2030-->InstallAnywhere distribution fails when
2194 <!-- JAL-2080-->Jalview very slow to launch via webstart
2195 (also hotfix for 2.9.0b2)
2198 <!-- JAL-2085 -->Cannot save project when view has a
2199 reference sequence defined
2202 <!-- JAL-1011 -->Columns are suddenly selected in other
2203 alignments and views when revealing hidden columns
2206 <!-- JAL-1989 -->Hide columns not mirrored in complement
2207 view in a cDNA/Protein splitframe
2210 <!-- JAL-1369 -->Cannot save/restore representative
2211 sequence from project when only one sequence is
2215 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2216 in Structure Chooser
2219 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2220 structure consensus didn't refresh annotation panel
2223 <!-- JAL-1962 -->View mapping in structure view shows
2224 mappings between sequence and all chains in a PDB file
2227 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2228 dialogs format columns correctly, don't display array
2229 data, sort columns according to type
2232 <!-- JAL-1975 -->Export complete shown after destination
2233 file chooser is cancelled during an image export
2236 <!-- JAL-2025 -->Error when querying PDB Service with
2237 sequence name containing special characters
2240 <!-- JAL-2024 -->Manual PDB structure querying should be
2244 <!-- JAL-2104 -->Large tooltips with broken HTML
2245 formatting don't wrap
2248 <!-- JAL-1128 -->Figures exported from wrapped view are
2249 truncated so L looks like I in consensus annotation
2252 <!-- JAL-2003 -->Export features should only export the
2253 currently displayed features for the current selection or
2257 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2258 after fetching cross-references, and restoring from
2262 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2263 followed in the structure viewer
2266 <!-- JAL-2163 -->Titles for individual alignments in
2267 splitframe not restored from project
2270 <!-- JAL-2145 -->missing autocalculated annotation at
2271 trailing end of protein alignment in transcript/product
2272 splitview when pad-gaps not enabled by default
2275 <!-- JAL-1797 -->amino acid physicochemical conservation
2279 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2280 article has been read (reopened issue due to
2281 internationalisation problems)
2284 <!-- JAL-1960 -->Only offer PDB structures in structure
2285 viewer based on sequence name, PDB and UniProt
2290 <!-- JAL-1976 -->No progress bar shown during export of
2294 <!-- JAL-2213 -->Structures not always superimposed after
2295 multiple structures are shown for one or more sequences.
2298 <!-- JAL-1370 -->Reference sequence characters should not
2299 be replaced with '.' when 'Show unconserved' format option
2303 <!-- JAL-1823 -->Cannot specify chain code when entering
2304 specific PDB id for sequence
2307 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2308 'Export hidden sequences' is enabled, but 'export hidden
2309 columns' is disabled.
2312 <!--JAL-2026-->Best Quality option in structure chooser
2313 selects lowest rather than highest resolution structures
2317 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2318 to sequence mapping in 'View Mappings' report
2321 <!-- JAL-2284 -->Unable to read old Jalview projects that
2322 contain non-XML data added after Jalvew wrote project.
2325 <!-- JAL-2118 -->Newly created annotation row reorders
2326 after clicking on it to create new annotation for a
2330 <!-- JAL-1980 -->Null Pointer Exception raised when
2331 pressing Add on an orphaned cut'n'paste window.
2333 <!-- may exclude, this is an external service stability issue JAL-1941
2334 -- > RNA 3D structure not added via DSSR service</li> -->
2339 <!-- JAL-2151 -->Incorrect columns are selected when
2340 hidden columns present before start of sequence
2343 <!-- JAL-1986 -->Missing dependencies on applet pages
2347 <!-- JAL-1947 -->Overview pixel size changes when
2348 sequences are hidden in applet
2351 <!-- JAL-1996 -->Updated instructions for applet
2352 deployment on examples pages.
2359 <td width="60" nowrap>
2360 <div align="center">
2361 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2362 <em>16/10/2015</em></strong>
2365 <td><em>General</em>
2367 <li>Time stamps for signed Jalview application and applet
2372 <em>Application</em>
2374 <li>Duplicate group consensus and conservation rows
2375 shown when tree is partitioned</li>
2376 <li>Erratic behaviour when tree partitions made with
2377 multiple cDNA/Protein split views</li>
2383 <td width="60" nowrap>
2384 <div align="center">
2385 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2386 <em>8/10/2015</em></strong>
2389 <td><em>General</em>
2391 <li>Updated Spanish translations of localized text for
2393 </ul> <em>Application</em>
2395 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2396 <li>Signed OSX InstallAnywhere installer<br></li>
2397 <li>Support for per-sequence based annotations in BioJSON</li>
2398 </ul> <em>Applet</em>
2400 <li>Split frame example added to applet examples page</li>
2401 </ul> <em>Build and Deployment</em>
2404 <!-- JAL-1888 -->New ant target for running Jalview's test
2412 <li>Mapping of cDNA to protein in split frames
2413 incorrect when sequence start > 1</li>
2414 <li>Broken images in filter column by annotation dialog
2416 <li>Feature colours not parsed from features file</li>
2417 <li>Exceptions and incomplete link URLs recovered when
2418 loading a features file containing HTML tags in feature
2422 <em>Application</em>
2424 <li>Annotations corrupted after BioJS export and
2426 <li>Incorrect sequence limits after Fetch DB References
2427 with 'trim retrieved sequences'</li>
2428 <li>Incorrect warning about deleting all data when
2429 deleting selected columns</li>
2430 <li>Patch to build system for shipping properly signed
2431 JNLP templates for webstart launch</li>
2432 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2433 unreleased structures for download or viewing</li>
2434 <li>Tab/space/return keystroke operation of EMBL-PDBe
2435 fetcher/viewer dialogs works correctly</li>
2436 <li>Disabled 'minimise' button on Jalview windows
2437 running on OSX to workaround redraw hang bug</li>
2438 <li>Split cDNA/Protein view position and geometry not
2439 recovered from jalview project</li>
2440 <li>Initial enabled/disabled state of annotation menu
2441 sorter 'show autocalculated first/last' corresponds to
2443 <li>Restoring of Clustal, RNA Helices and T-Coffee
2444 color schemes from BioJSON</li>
2448 <li>Reorder sequences mirrored in cDNA/Protein split
2450 <li>Applet with Jmol examples not loading correctly</li>
2456 <td><div align="center">
2457 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2459 <td><em>General</em>
2461 <li>Linked visualisation and analysis of DNA and Protein
2464 <li>Translated cDNA alignments shown as split protein
2465 and DNA alignment views</li>
2466 <li>Codon consensus annotation for linked protein and
2467 cDNA alignment views</li>
2468 <li>Link cDNA or Protein product sequences by loading
2469 them onto Protein or cDNA alignments</li>
2470 <li>Reconstruct linked cDNA alignment from aligned
2471 protein sequences</li>
2474 <li>Jmol integration updated to Jmol v14.2.14</li>
2475 <li>Import and export of Jalview alignment views as <a
2476 href="features/bioJsonFormat.html">BioJSON</a></li>
2477 <li>New alignment annotation file statements for
2478 reference sequences and marking hidden columns</li>
2479 <li>Reference sequence based alignment shading to
2480 highlight variation</li>
2481 <li>Select or hide columns according to alignment
2483 <li>Find option for locating sequences by description</li>
2484 <li>Conserved physicochemical properties shown in amino
2485 acid conservation row</li>
2486 <li>Alignments can be sorted by number of RNA helices</li>
2487 </ul> <em>Application</em>
2489 <li>New cDNA/Protein analysis capabilities
2491 <li>Get Cross-References should open a Split Frame
2492 view with cDNA/Protein</li>
2493 <li>Detect when nucleotide sequences and protein
2494 sequences are placed in the same alignment</li>
2495 <li>Split cDNA/Protein views are saved in Jalview
2500 <li>Use REST API to talk to Chimera</li>
2501 <li>Selected regions in Chimera are highlighted in linked
2502 Jalview windows</li>
2504 <li>VARNA RNA viewer updated to v3.93</li>
2505 <li>VARNA views are saved in Jalview Projects</li>
2506 <li>Pseudoknots displayed as Jalview RNA annotation can
2507 be shown in VARNA</li>
2509 <li>Make groups for selection uses marked columns as well
2510 as the active selected region</li>
2512 <li>Calculate UPGMA and NJ trees using sequence feature
2514 <li>New Export options
2516 <li>New Export Settings dialog to control hidden
2517 region export in flat file generation</li>
2519 <li>Export alignment views for display with the <a
2520 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2522 <li>Export scrollable SVG in HTML page</li>
2523 <li>Optional embedding of BioJSON data when exporting
2524 alignment figures to HTML</li>
2526 <li>3D structure retrieval and display
2528 <li>Free text and structured queries with the PDBe
2530 <li>PDBe Search API based discovery and selection of
2531 PDB structures for a sequence set</li>
2535 <li>JPred4 employed for protein secondary structure
2537 <li>Hide Insertions menu option to hide unaligned columns
2538 for one or a group of sequences</li>
2539 <li>Automatically hide insertions in alignments imported
2540 from the JPred4 web server</li>
2541 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2542 system on OSX<br />LGPL libraries courtesy of <a
2543 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2545 <li>changed 'View nucleotide structure' submenu to 'View
2546 VARNA 2D Structure'</li>
2547 <li>change "View protein structure" menu option to "3D
2550 </ul> <em>Applet</em>
2552 <li>New layout for applet example pages</li>
2553 <li>New parameters to enable SplitFrame view
2554 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2555 <li>New example demonstrating linked viewing of cDNA and
2556 Protein alignments</li>
2557 </ul> <em>Development and deployment</em>
2559 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2560 <li>Include installation type and git revision in build
2561 properties and console log output</li>
2562 <li>Jalview Github organisation, and new github site for
2563 storing BioJsMSA Templates</li>
2564 <li>Jalview's unit tests now managed with TestNG</li>
2567 <!-- <em>General</em>
2569 </ul> --> <!-- issues resolved --> <em>Application</em>
2571 <li>Escape should close any open find dialogs</li>
2572 <li>Typo in select-by-features status report</li>
2573 <li>Consensus RNA secondary secondary structure
2574 predictions are not highlighted in amber</li>
2575 <li>Missing gap character in v2.7 example file means
2576 alignment appears unaligned when pad-gaps is not enabled</li>
2577 <li>First switch to RNA Helices colouring doesn't colour
2578 associated structure views</li>
2579 <li>ID width preference option is greyed out when auto
2580 width checkbox not enabled</li>
2581 <li>Stopped a warning dialog from being shown when
2582 creating user defined colours</li>
2583 <li>'View Mapping' in structure viewer shows sequence
2584 mappings for just that viewer's sequences</li>
2585 <li>Workaround for superposing PDB files containing
2586 multiple models in Chimera</li>
2587 <li>Report sequence position in status bar when hovering
2588 over Jmol structure</li>
2589 <li>Cannot output gaps as '.' symbols with Selection ->
2590 output to text box</li>
2591 <li>Flat file exports of alignments with hidden columns
2592 have incorrect sequence start/end</li>
2593 <li>'Aligning' a second chain to a Chimera structure from
2595 <li>Colour schemes applied to structure viewers don't
2596 work for nucleotide</li>
2597 <li>Loading/cut'n'pasting an empty or invalid file leads
2598 to a grey/invisible alignment window</li>
2599 <li>Exported Jpred annotation from a sequence region
2600 imports to different position</li>
2601 <li>Space at beginning of sequence feature tooltips shown
2602 on some platforms</li>
2603 <li>Chimera viewer 'View | Show Chain' menu is not
2605 <li>'New View' fails with a Null Pointer Exception in
2606 console if Chimera has been opened</li>
2607 <li>Mouseover to Chimera not working</li>
2608 <li>Miscellaneous ENA XML feature qualifiers not
2610 <li>NPE in annotation renderer after 'Extract Scores'</li>
2611 <li>If two structures in one Chimera window, mouseover of
2612 either sequence shows on first structure</li>
2613 <li>'Show annotations' options should not make
2614 non-positional annotations visible</li>
2615 <li>Subsequence secondary structure annotation not shown
2616 in right place after 'view flanking regions'</li>
2617 <li>File Save As type unset when current file format is
2619 <li>Save as '.jar' option removed for saving Jalview
2621 <li>Colour by Sequence colouring in Chimera more
2623 <li>Cannot 'add reference annotation' for a sequence in
2624 several views on same alignment</li>
2625 <li>Cannot show linked products for EMBL / ENA records</li>
2626 <li>Jalview's tooltip wraps long texts containing no
2628 </ul> <em>Applet</em>
2630 <li>Jmol to JalviewLite mouseover/link not working</li>
2631 <li>JalviewLite can't import sequences with ID
2632 descriptions containing angle brackets</li>
2633 </ul> <em>General</em>
2635 <li>Cannot export and reimport RNA secondary structure
2636 via jalview annotation file</li>
2637 <li>Random helix colour palette for colour by annotation
2638 with RNA secondary structure</li>
2639 <li>Mouseover to cDNA from STOP residue in protein
2640 translation doesn't work.</li>
2641 <li>hints when using the select by annotation dialog box</li>
2642 <li>Jmol alignment incorrect if PDB file has alternate CA
2644 <li>FontChooser message dialog appears to hang after
2645 choosing 1pt font</li>
2646 <li>Peptide secondary structure incorrectly imported from
2647 annotation file when annotation display text includes 'e' or
2649 <li>Cannot set colour of new feature type whilst creating
2651 <li>cDNA translation alignment should not be sequence
2652 order dependent</li>
2653 <li>'Show unconserved' doesn't work for lower case
2655 <li>Nucleotide ambiguity codes involving R not recognised</li>
2656 </ul> <em>Deployment and Documentation</em>
2658 <li>Applet example pages appear different to the rest of
2659 www.jalview.org</li>
2660 </ul> <em>Application Known issues</em>
2662 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2663 <li>Misleading message appears after trying to delete
2665 <li>Jalview icon not shown in dock after InstallAnywhere
2666 version launches</li>
2667 <li>Fetching EMBL reference for an RNA sequence results
2668 fails with a sequence mismatch</li>
2669 <li>Corrupted or unreadable alignment display when
2670 scrolling alignment to right</li>
2671 <li>ArrayIndexOutOfBoundsException thrown when remove
2672 empty columns called on alignment with ragged gapped ends</li>
2673 <li>auto calculated alignment annotation rows do not get
2674 placed above or below non-autocalculated rows</li>
2675 <li>Jalview dekstop becomes sluggish at full screen in
2676 ultra-high resolution</li>
2677 <li>Cannot disable consensus calculation independently of
2678 quality and conservation</li>
2679 <li>Mouseover highlighting between cDNA and protein can
2680 become sluggish with more than one splitframe shown</li>
2681 </ul> <em>Applet Known Issues</em>
2683 <li>Core PDB parsing code requires Jmol</li>
2684 <li>Sequence canvas panel goes white when alignment
2685 window is being resized</li>
2691 <td><div align="center">
2692 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2694 <td><em>General</em>
2696 <li>Updated Java code signing certificate donated by
2698 <li>Features and annotation preserved when performing
2699 pairwise alignment</li>
2700 <li>RNA pseudoknot annotation can be
2701 imported/exported/displayed</li>
2702 <li>'colour by annotation' can colour by RNA and
2703 protein secondary structure</li>
2704 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2705 post-hoc with 2.9 release</em>)
2708 </ul> <em>Application</em>
2710 <li>Extract and display secondary structure for sequences
2711 with 3D structures</li>
2712 <li>Support for parsing RNAML</li>
2713 <li>Annotations menu for layout
2715 <li>sort sequence annotation rows by alignment</li>
2716 <li>place sequence annotation above/below alignment
2719 <li>Output in Stockholm format</li>
2720 <li>Internationalisation: improved Spanish (es)
2722 <li>Structure viewer preferences tab</li>
2723 <li>Disorder and Secondary Structure annotation tracks
2724 shared between alignments</li>
2725 <li>UCSF Chimera launch and linked highlighting from
2727 <li>Show/hide all sequence associated annotation rows for
2728 all or current selection</li>
2729 <li>disorder and secondary structure predictions
2730 available as dataset annotation</li>
2731 <li>Per-sequence rna helices colouring</li>
2734 <li>Sequence database accessions imported when fetching
2735 alignments from Rfam</li>
2736 <li>update VARNA version to 3.91</li>
2738 <li>New groovy scripts for exporting aligned positions,
2739 conservation values, and calculating sum of pairs scores.</li>
2740 <li>Command line argument to set default JABAWS server</li>
2741 <li>include installation type in build properties and
2742 console log output</li>
2743 <li>Updated Jalview project format to preserve dataset
2747 <!-- issues resolved --> <em>Application</em>
2749 <li>Distinguish alignment and sequence associated RNA
2750 structure in structure->view->VARNA</li>
2751 <li>Raise dialog box if user deletes all sequences in an
2753 <li>Pressing F1 results in documentation opening twice</li>
2754 <li>Sequence feature tooltip is wrapped</li>
2755 <li>Double click on sequence associated annotation
2756 selects only first column</li>
2757 <li>Redundancy removal doesn't result in unlinked
2758 leaves shown in tree</li>
2759 <li>Undos after several redundancy removals don't undo
2761 <li>Hide sequence doesn't hide associated annotation</li>
2762 <li>User defined colours dialog box too big to fit on
2763 screen and buttons not visible</li>
2764 <li>author list isn't updated if already written to
2765 Jalview properties</li>
2766 <li>Popup menu won't open after retrieving sequence
2768 <li>File open window for associate PDB doesn't open</li>
2769 <li>Left-then-right click on a sequence id opens a
2770 browser search window</li>
2771 <li>Cannot open sequence feature shading/sort popup menu
2772 in feature settings dialog</li>
2773 <li>better tooltip placement for some areas of Jalview
2775 <li>Allow addition of JABAWS Server which doesn't
2776 pass validation</li>
2777 <li>Web services parameters dialog box is too large to
2779 <li>Muscle nucleotide alignment preset obscured by
2781 <li>JABAWS preset submenus don't contain newly
2782 defined user preset</li>
2783 <li>MSA web services warns user if they were launched
2784 with invalid input</li>
2785 <li>Jalview cannot contact DAS Registy when running on
2788 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2789 'Superpose with' submenu not shown when new view
2793 </ul> <!-- <em>Applet</em>
2795 </ul> <em>General</em>
2797 </ul>--> <em>Deployment and Documentation</em>
2799 <li>2G and 1G options in launchApp have no effect on
2800 memory allocation</li>
2801 <li>launchApp service doesn't automatically open
2802 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2804 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2805 InstallAnywhere reports cannot find valid JVM when Java
2806 1.7_055 is available
2808 </ul> <em>Application Known issues</em>
2811 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2812 corrupted or unreadable alignment display when scrolling
2816 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2817 retrieval fails but progress bar continues for DAS retrieval
2818 with large number of ID
2821 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2822 flatfile output of visible region has incorrect sequence
2826 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2827 rna structure consensus doesn't update when secondary
2828 structure tracks are rearranged
2831 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2832 invalid rna structure positional highlighting does not
2833 highlight position of invalid base pairs
2836 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2837 out of memory errors are not raised when saving Jalview
2838 project from alignment window file menu
2841 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2842 Switching to RNA Helices colouring doesn't propagate to
2846 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2847 colour by RNA Helices not enabled when user created
2848 annotation added to alignment
2851 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2852 Jalview icon not shown on dock in Mountain Lion/Webstart
2854 </ul> <em>Applet Known Issues</em>
2857 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2858 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2861 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2862 Jalview and Jmol example not compatible with IE9
2865 <li>Sort by annotation score doesn't reverse order
2871 <td><div align="center">
2872 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2875 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2878 <li>Internationalisation of user interface (usually
2879 called i18n support) and translation for Spanish locale</li>
2880 <li>Define/Undefine group on current selection with
2881 Ctrl-G/Shift Ctrl-G</li>
2882 <li>Improved group creation/removal options in
2883 alignment/sequence Popup menu</li>
2884 <li>Sensible precision for symbol distribution
2885 percentages shown in logo tooltip.</li>
2886 <li>Annotation panel height set according to amount of
2887 annotation when alignment first opened</li>
2888 </ul> <em>Application</em>
2890 <li>Interactive consensus RNA secondary structure
2891 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2892 <li>Select columns containing particular features from
2893 Feature Settings dialog</li>
2894 <li>View all 'representative' PDB structures for selected
2896 <li>Update Jalview project format:
2898 <li>New file extension for Jalview projects '.jvp'</li>
2899 <li>Preserve sequence and annotation dataset (to
2900 store secondary structure annotation,etc)</li>
2901 <li>Per group and alignment annotation and RNA helix
2905 <li>New similarity measures for PCA and Tree calculation
2907 <li>Experimental support for retrieval and viewing of
2908 flanking regions for an alignment</li>
2912 <!-- issues resolved --> <em>Application</em>
2914 <li>logo keeps spinning and status remains at queued or
2915 running after job is cancelled</li>
2916 <li>cannot export features from alignments imported from
2917 Jalview/VAMSAS projects</li>
2918 <li>Buggy slider for web service parameters that take
2920 <li>Newly created RNA secondary structure line doesn't
2921 have 'display all symbols' flag set</li>
2922 <li>T-COFFEE alignment score shading scheme and other
2923 annotation shading not saved in Jalview project</li>
2924 <li>Local file cannot be loaded in freshly downloaded
2926 <li>Jalview icon not shown on dock in Mountain
2928 <li>Load file from desktop file browser fails</li>
2929 <li>Occasional NPE thrown when calculating large trees</li>
2930 <li>Cannot reorder or slide sequences after dragging an
2931 alignment onto desktop</li>
2932 <li>Colour by annotation dialog throws NPE after using
2933 'extract scores' function</li>
2934 <li>Loading/cut'n'pasting an empty file leads to a grey
2935 alignment window</li>
2936 <li>Disorder thresholds rendered incorrectly after
2937 performing IUPred disorder prediction</li>
2938 <li>Multiple group annotated consensus rows shown when
2939 changing 'normalise logo' display setting</li>
2940 <li>Find shows blank dialog after 'finished searching' if
2941 nothing matches query</li>
2942 <li>Null Pointer Exceptions raised when sorting by
2943 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2945 <li>Errors in Jmol console when structures in alignment
2946 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2948 <li>Not all working JABAWS services are shown in
2950 <li>JAVAWS version of Jalview fails to launch with
2951 'invalid literal/length code'</li>
2952 <li>Annotation/RNA Helix colourschemes cannot be applied
2953 to alignment with groups (actually fixed in 2.8.0b1)</li>
2954 <li>RNA Helices and T-Coffee Scores available as default
2957 </ul> <em>Applet</em>
2959 <li>Remove group option is shown even when selection is
2961 <li>Apply to all groups ticked but colourscheme changes
2962 don't affect groups</li>
2963 <li>Documented RNA Helices and T-Coffee Scores as valid
2964 colourscheme name</li>
2965 <li>Annotation labels drawn on sequence IDs when
2966 Annotation panel is not displayed</li>
2967 <li>Increased font size for dropdown menus on OSX and
2968 embedded windows</li>
2969 </ul> <em>Other</em>
2971 <li>Consensus sequence for alignments/groups with a
2972 single sequence were not calculated</li>
2973 <li>annotation files that contain only groups imported as
2974 annotation and junk sequences</li>
2975 <li>Fasta files with sequences containing '*' incorrectly
2976 recognised as PFAM or BLC</li>
2977 <li>conservation/PID slider apply all groups option
2978 doesn't affect background (2.8.0b1)
2980 <li>redundancy highlighting is erratic at 0% and 100%</li>
2981 <li>Remove gapped columns fails for sequences with ragged
2983 <li>AMSA annotation row with leading spaces is not
2984 registered correctly on import</li>
2985 <li>Jalview crashes when selecting PCA analysis for
2986 certain alignments</li>
2987 <li>Opening the colour by annotation dialog for an
2988 existing annotation based 'use original colours'
2989 colourscheme loses original colours setting</li>
2994 <td><div align="center">
2995 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2996 <em>30/1/2014</em></strong>
3000 <li>Trusted certificates for JalviewLite applet and
3001 Jalview Desktop application<br />Certificate was donated by
3002 <a href="https://www.certum.eu">Certum</a> to the Jalview
3003 open source project).
3005 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3006 <li>Output in Stockholm format</li>
3007 <li>Allow import of data from gzipped files</li>
3008 <li>Export/import group and sequence associated line
3009 graph thresholds</li>
3010 <li>Nucleotide substitution matrix that supports RNA and
3011 ambiguity codes</li>
3012 <li>Allow disorder predictions to be made on the current
3013 selection (or visible selection) in the same way that JPred
3015 <li>Groovy scripting for headless Jalview operation</li>
3016 </ul> <em>Other improvements</em>
3018 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3019 <li>COMBINE statement uses current SEQUENCE_REF and
3020 GROUP_REF scope to group annotation rows</li>
3021 <li>Support '' style escaping of quotes in Newick
3023 <li>Group options for JABAWS service by command line name</li>
3024 <li>Empty tooltip shown for JABA service options with a
3025 link but no description</li>
3026 <li>Select primary source when selecting authority in
3027 database fetcher GUI</li>
3028 <li>Add .mfa to FASTA file extensions recognised by
3030 <li>Annotation label tooltip text wrap</li>
3035 <li>Slow scrolling when lots of annotation rows are
3037 <li>Lots of NPE (and slowness) after creating RNA
3038 secondary structure annotation line</li>
3039 <li>Sequence database accessions not imported when
3040 fetching alignments from Rfam</li>
3041 <li>Incorrect SHMR submission for sequences with
3043 <li>View all structures does not always superpose
3045 <li>Option widgets in service parameters not updated to
3046 reflect user or preset settings</li>
3047 <li>Null pointer exceptions for some services without
3048 presets or adjustable parameters</li>
3049 <li>Discover PDB IDs entry in structure menu doesn't
3050 discover PDB xRefs</li>
3051 <li>Exception encountered while trying to retrieve
3052 features with DAS</li>
3053 <li>Lowest value in annotation row isn't coloured
3054 when colour by annotation (per sequence) is coloured</li>
3055 <li>Keyboard mode P jumps to start of gapped region when
3056 residue follows a gap</li>
3057 <li>Jalview appears to hang importing an alignment with
3058 Wrap as default or after enabling Wrap</li>
3059 <li>'Right click to add annotations' message
3060 shown in wrap mode when no annotations present</li>
3061 <li>Disorder predictions fail with NPE if no automatic
3062 annotation already exists on alignment</li>
3063 <li>oninit javascript function should be called after
3064 initialisation completes</li>
3065 <li>Remove redundancy after disorder prediction corrupts
3066 alignment window display</li>
3067 <li>Example annotation file in documentation is invalid</li>
3068 <li>Grouped line graph annotation rows are not exported
3069 to annotation file</li>
3070 <li>Multi-harmony analysis cannot be run when only two
3072 <li>Cannot create multiple groups of line graphs with
3073 several 'combine' statements in annotation file</li>
3074 <li>Pressing return several times causes Number Format
3075 exceptions in keyboard mode</li>
3076 <li>Multi-harmony (SHMMR) method doesn't submit
3077 correct partitions for input data</li>
3078 <li>Translation from DNA to Amino Acids fails</li>
3079 <li>Jalview fail to load newick tree with quoted label</li>
3080 <li>--headless flag isn't understood</li>
3081 <li>ClassCastException when generating EPS in headless
3083 <li>Adjusting sequence-associated shading threshold only
3084 changes one row's threshold</li>
3085 <li>Preferences and Feature settings panel panel
3086 doesn't open</li>
3087 <li>hide consensus histogram also hides conservation and
3088 quality histograms</li>
3093 <td><div align="center">
3094 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3096 <td><em>Application</em>
3098 <li>Support for JABAWS 2.0 Services (AACon alignment
3099 conservation, protein disorder and Clustal Omega)</li>
3100 <li>JABAWS server status indicator in Web Services
3102 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3103 in Jalview alignment window</li>
3104 <li>Updated Jalview build and deploy framework for OSX
3105 mountain lion, windows 7, and 8</li>
3106 <li>Nucleotide substitution matrix for PCA that supports
3107 RNA and ambiguity codes</li>
3109 <li>Improved sequence database retrieval GUI</li>
3110 <li>Support fetching and database reference look up
3111 against multiple DAS sources (Fetch all from in 'fetch db
3113 <li>Jalview project improvements
3115 <li>Store and retrieve the 'belowAlignment'
3116 flag for annotation</li>
3117 <li>calcId attribute to group annotation rows on the
3119 <li>Store AACon calculation settings for a view in
3120 Jalview project</li>
3124 <li>horizontal scrolling gesture support</li>
3125 <li>Visual progress indicator when PCA calculation is
3127 <li>Simpler JABA web services menus</li>
3128 <li>visual indication that web service results are still
3129 being retrieved from server</li>
3130 <li>Serialise the dialogs that are shown when Jalview
3131 starts up for first time</li>
3132 <li>Jalview user agent string for interacting with HTTP
3134 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3136 <li>Examples directory and Groovy library included in
3137 InstallAnywhere distribution</li>
3138 </ul> <em>Applet</em>
3140 <li>RNA alignment and secondary structure annotation
3141 visualization applet example</li>
3142 </ul> <em>General</em>
3144 <li>Normalise option for consensus sequence logo</li>
3145 <li>Reset button in PCA window to return dimensions to
3147 <li>Allow seqspace or Jalview variant of alignment PCA
3149 <li>PCA with either nucleic acid and protein substitution
3151 <li>Allow windows containing HTML reports to be exported
3153 <li>Interactive display and editing of RNA secondary
3154 structure contacts</li>
3155 <li>RNA Helix Alignment Colouring</li>
3156 <li>RNA base pair logo consensus</li>
3157 <li>Parse sequence associated secondary structure
3158 information in Stockholm files</li>
3159 <li>HTML Export database accessions and annotation
3160 information presented in tooltip for sequences</li>
3161 <li>Import secondary structure from LOCARNA clustalw
3162 style RNA alignment files</li>
3163 <li>import and visualise T-COFFEE quality scores for an
3165 <li>'colour by annotation' per sequence option to
3166 shade each sequence according to its associated alignment
3168 <li>New Jalview Logo</li>
3169 </ul> <em>Documentation and Development</em>
3171 <li>documentation for score matrices used in Jalview</li>
3172 <li>New Website!</li>
3174 <td><em>Application</em>
3176 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3177 wsdbfetch REST service</li>
3178 <li>Stop windows being moved outside desktop on OSX</li>
3179 <li>Filetype associations not installed for webstart
3181 <li>Jalview does not always retrieve progress of a JABAWS
3182 job execution in full once it is complete</li>
3183 <li>revise SHMR RSBS definition to ensure alignment is
3184 uploaded via ali_file parameter</li>
3185 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3186 <li>View all structures superposed fails with exception</li>
3187 <li>Jnet job queues forever if a very short sequence is
3188 submitted for prediction</li>
3189 <li>Cut and paste menu not opened when mouse clicked on
3191 <li>Putting fractional value into integer text box in
3192 alignment parameter dialog causes Jalview to hang</li>
3193 <li>Structure view highlighting doesn't work on
3195 <li>View all structures fails with exception shown in
3197 <li>Characters in filename associated with PDBEntry not
3198 escaped in a platform independent way</li>
3199 <li>Jalview desktop fails to launch with exception when
3201 <li>Tree calculation reports 'you must have 2 or more
3202 sequences selected' when selection is empty</li>
3203 <li>Jalview desktop fails to launch with jar signature
3204 failure when java web start temporary file caching is
3206 <li>DAS Sequence retrieval with range qualification
3207 results in sequence xref which includes range qualification</li>
3208 <li>Errors during processing of command line arguments
3209 cause progress bar (JAL-898) to be removed</li>
3210 <li>Replace comma for semi-colon option not disabled for
3211 DAS sources in sequence fetcher</li>
3212 <li>Cannot close news reader when JABAWS server warning
3213 dialog is shown</li>
3214 <li>Option widgets not updated to reflect user settings</li>
3215 <li>Edited sequence not submitted to web service</li>
3216 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3217 <li>InstallAnywhere installer doesn't unpack and run
3218 on OSX Mountain Lion</li>
3219 <li>Annotation panel not given a scroll bar when
3220 sequences with alignment annotation are pasted into the
3222 <li>Sequence associated annotation rows not associated
3223 when loaded from Jalview project</li>
3224 <li>Browser launch fails with NPE on java 1.7</li>
3225 <li>JABAWS alignment marked as finished when job was
3226 cancelled or job failed due to invalid input</li>
3227 <li>NPE with v2.7 example when clicking on Tree
3228 associated with all views</li>
3229 <li>Exceptions when copy/paste sequences with grouped
3230 annotation rows to new window</li>
3231 </ul> <em>Applet</em>
3233 <li>Sequence features are momentarily displayed before
3234 they are hidden using hidefeaturegroups applet parameter</li>
3235 <li>loading features via javascript API automatically
3236 enables feature display</li>
3237 <li>scrollToColumnIn javascript API method doesn't
3239 </ul> <em>General</em>
3241 <li>Redundancy removal fails for rna alignment</li>
3242 <li>PCA calculation fails when sequence has been selected
3243 and then deselected</li>
3244 <li>PCA window shows grey box when first opened on OSX</li>
3245 <li>Letters coloured pink in sequence logo when alignment
3246 coloured with clustalx</li>
3247 <li>Choosing fonts without letter symbols defined causes
3248 exceptions and redraw errors</li>
3249 <li>Initial PCA plot view is not same as manually
3250 reconfigured view</li>
3251 <li>Grouped annotation graph label has incorrect line
3253 <li>Grouped annotation graph label display is corrupted
3254 for lots of labels</li>
3259 <div align="center">
3260 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3263 <td><em>Application</em>
3265 <li>Jalview Desktop News Reader</li>
3266 <li>Tweaked default layout of web services menu</li>
3267 <li>View/alignment association menu to enable user to
3268 easily specify which alignment a multi-structure view takes
3269 its colours/correspondences from</li>
3270 <li>Allow properties file location to be specified as URL</li>
3271 <li>Extend Jalview project to preserve associations
3272 between many alignment views and a single Jmol display</li>
3273 <li>Store annotation row height in Jalview project file</li>
3274 <li>Annotation row column label formatting attributes
3275 stored in project file</li>
3276 <li>Annotation row order for auto-calculated annotation
3277 rows preserved in Jalview project file</li>
3278 <li>Visual progress indication when Jalview state is
3279 saved using Desktop window menu</li>
3280 <li>Visual indication that command line arguments are
3281 still being processed</li>
3282 <li>Groovy script execution from URL</li>
3283 <li>Colour by annotation default min and max colours in
3285 <li>Automatically associate PDB files dragged onto an
3286 alignment with sequences that have high similarity and
3288 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3289 <li>'view structures' option to open many
3290 structures in same window</li>
3291 <li>Sort associated views menu option for tree panel</li>
3292 <li>Group all JABA and non-JABA services for a particular
3293 analysis function in its own submenu</li>
3294 </ul> <em>Applet</em>
3296 <li>Userdefined and autogenerated annotation rows for
3298 <li>Adjustment of alignment annotation pane height</li>
3299 <li>Annotation scrollbar for annotation panel</li>
3300 <li>Drag to reorder annotation rows in annotation panel</li>
3301 <li>'automaticScrolling' parameter</li>
3302 <li>Allow sequences with partial ID string matches to be
3303 annotated from GFF/Jalview features files</li>
3304 <li>Sequence logo annotation row in applet</li>
3305 <li>Absolute paths relative to host server in applet
3306 parameters are treated as such</li>
3307 <li>New in the JalviewLite javascript API:
3309 <li>JalviewLite.js javascript library</li>
3310 <li>Javascript callbacks for
3312 <li>Applet initialisation</li>
3313 <li>Sequence/alignment mouse-overs and selections</li>
3316 <li>scrollTo row and column alignment scrolling
3318 <li>Select sequence/alignment regions from javascript</li>
3319 <li>javascript structure viewer harness to pass
3320 messages between Jmol and Jalview when running as
3321 distinct applets</li>
3322 <li>sortBy method</li>
3323 <li>Set of applet and application examples shipped
3324 with documentation</li>
3325 <li>New example to demonstrate JalviewLite and Jmol
3326 javascript message exchange</li>
3328 </ul> <em>General</em>
3330 <li>Enable Jmol displays to be associated with multiple
3331 multiple alignments</li>
3332 <li>Option to automatically sort alignment with new tree</li>
3333 <li>User configurable link to enable redirects to a
3334 www.Jalview.org mirror</li>
3335 <li>Jmol colours option for Jmol displays</li>
3336 <li>Configurable newline string when writing alignment
3337 and other flat files</li>
3338 <li>Allow alignment annotation description lines to
3339 contain html tags</li>
3340 </ul> <em>Documentation and Development</em>
3342 <li>Add groovy test harness for bulk load testing to
3344 <li>Groovy script to load and align a set of sequences
3345 using a web service before displaying the result in the
3346 Jalview desktop</li>
3347 <li>Restructured javascript and applet api documentation</li>
3348 <li>Ant target to publish example html files with applet
3350 <li>Netbeans project for building Jalview from source</li>
3351 <li>ant task to create online javadoc for Jalview source</li>
3353 <td><em>Application</em>
3355 <li>User defined colourscheme throws exception when
3356 current built in colourscheme is saved as new scheme</li>
3357 <li>AlignFrame->Save in application pops up save
3358 dialog for valid filename/format</li>
3359 <li>Cannot view associated structure for UniProt sequence</li>
3360 <li>PDB file association breaks for UniProt sequence
3362 <li>Associate PDB from file dialog does not tell you
3363 which sequence is to be associated with the file</li>
3364 <li>Find All raises null pointer exception when query
3365 only matches sequence IDs</li>
3366 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3367 <li>Jalview project with Jmol views created with Jalview
3368 2.4 cannot be loaded</li>
3369 <li>Filetype associations not installed for webstart
3371 <li>Two or more chains in a single PDB file associated
3372 with sequences in different alignments do not get coloured
3373 by their associated sequence</li>
3374 <li>Visibility status of autocalculated annotation row
3375 not preserved when project is loaded</li>
3376 <li>Annotation row height and visibility attributes not
3377 stored in Jalview project</li>
3378 <li>Tree bootstraps are not preserved when saved as a
3379 Jalview project</li>
3380 <li>Envision2 workflow tooltips are corrupted</li>
3381 <li>Enabling show group conservation also enables colour
3382 by conservation</li>
3383 <li>Duplicate group associated conservation or consensus
3384 created on new view</li>
3385 <li>Annotation scrollbar not displayed after 'show
3386 all hidden annotation rows' option selected</li>
3387 <li>Alignment quality not updated after alignment
3388 annotation row is hidden then shown</li>
3389 <li>Preserve colouring of structures coloured by
3390 sequences in pre Jalview 2.7 projects</li>
3391 <li>Web service job parameter dialog is not laid out
3393 <li>Web services menu not refreshed after 'reset
3394 services' button is pressed in preferences</li>
3395 <li>Annotation off by one in Jalview v2_3 example project</li>
3396 <li>Structures imported from file and saved in project
3397 get name like jalview_pdb1234.txt when reloaded</li>
3398 <li>Jalview does not always retrieve progress of a JABAWS
3399 job execution in full once it is complete</li>
3400 </ul> <em>Applet</em>
3402 <li>Alignment height set incorrectly when lots of
3403 annotation rows are displayed</li>
3404 <li>Relative URLs in feature HTML text not resolved to
3406 <li>View follows highlighting does not work for positions
3408 <li><= shown as = in tooltip</li>
3409 <li>Export features raises exception when no features
3411 <li>Separator string used for serialising lists of IDs
3412 for javascript api is modified when separator string
3413 provided as parameter</li>
3414 <li>Null pointer exception when selecting tree leaves for
3415 alignment with no existing selection</li>
3416 <li>Relative URLs for datasources assumed to be relative
3417 to applet's codebase</li>
3418 <li>Status bar not updated after finished searching and
3419 search wraps around to first result</li>
3420 <li>StructureSelectionManager instance shared between
3421 several Jalview applets causes race conditions and memory
3423 <li>Hover tooltip and mouseover of position on structure
3424 not sent from Jmol in applet</li>
3425 <li>Certain sequences of javascript method calls to
3426 applet API fatally hang browser</li>
3427 </ul> <em>General</em>
3429 <li>View follows structure mouseover scrolls beyond
3430 position with wrapped view and hidden regions</li>
3431 <li>Find sequence position moves to wrong residue
3432 with/without hidden columns</li>
3433 <li>Sequence length given in alignment properties window
3435 <li>InvalidNumberFormat exceptions thrown when trying to
3436 import PDB like structure files</li>
3437 <li>Positional search results are only highlighted
3438 between user-supplied sequence start/end bounds</li>
3439 <li>End attribute of sequence is not validated</li>
3440 <li>Find dialog only finds first sequence containing a
3441 given sequence position</li>
3442 <li>Sequence numbering not preserved in MSF alignment
3444 <li>Jalview PDB file reader does not extract sequence
3445 from nucleotide chains correctly</li>
3446 <li>Structure colours not updated when tree partition
3447 changed in alignment</li>
3448 <li>Sequence associated secondary structure not correctly
3449 parsed in interleaved stockholm</li>
3450 <li>Colour by annotation dialog does not restore current
3452 <li>Hiding (nearly) all sequences doesn't work
3454 <li>Sequences containing lowercase letters are not
3455 properly associated with their pdb files</li>
3456 </ul> <em>Documentation and Development</em>
3458 <li>schemas/JalviewWsParamSet.xsd corrupted by
3459 ApplyCopyright tool</li>
3464 <div align="center">
3465 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3468 <td><em>Application</em>
3470 <li>New warning dialog when the Jalview Desktop cannot
3471 contact web services</li>
3472 <li>JABA service parameters for a preset are shown in
3473 service job window</li>
3474 <li>JABA Service menu entries reworded</li>
3478 <li>Modeller PIR IO broken - cannot correctly import a
3479 pir file emitted by Jalview</li>
3480 <li>Existing feature settings transferred to new
3481 alignment view created from cut'n'paste</li>
3482 <li>Improved test for mixed amino/nucleotide chains when
3483 parsing PDB files</li>
3484 <li>Consensus and conservation annotation rows
3485 occasionally become blank for all new windows</li>
3486 <li>Exception raised when right clicking above sequences
3487 in wrapped view mode</li>
3488 </ul> <em>Application</em>
3490 <li>multiple multiply aligned structure views cause cpu
3491 usage to hit 100% and computer to hang</li>
3492 <li>Web Service parameter layout breaks for long user
3493 parameter names</li>
3494 <li>Jaba service discovery hangs desktop if Jaba server
3501 <div align="center">
3502 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3505 <td><em>Application</em>
3507 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3508 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3511 <li>Web Services preference tab</li>
3512 <li>Analysis parameters dialog box and user defined
3514 <li>Improved speed and layout of Envision2 service menu</li>
3515 <li>Superpose structures using associated sequence
3517 <li>Export coordinates and projection as CSV from PCA
3519 </ul> <em>Applet</em>
3521 <li>enable javascript: execution by the applet via the
3522 link out mechanism</li>
3523 </ul> <em>Other</em>
3525 <li>Updated the Jmol Jalview interface to work with Jmol
3527 <li>The Jalview Desktop and JalviewLite applet now
3528 require Java 1.5</li>
3529 <li>Allow Jalview feature colour specification for GFF
3530 sequence annotation files</li>
3531 <li>New 'colour by label' keword in Jalview feature file
3532 type colour specification</li>
3533 <li>New Jalview Desktop Groovy API method that allows a
3534 script to check if it being run in an interactive session or
3535 in a batch operation from the Jalview command line</li>
3539 <li>clustalx colourscheme colours Ds preferentially when
3540 both D+E are present in over 50% of the column</li>
3541 </ul> <em>Application</em>
3543 <li>typo in AlignmentFrame->View->Hide->all but
3544 selected Regions menu item</li>
3545 <li>sequence fetcher replaces ',' for ';' when the ',' is
3546 part of a valid accession ID</li>
3547 <li>fatal OOM if object retrieved by sequence fetcher
3548 runs out of memory</li>
3549 <li>unhandled Out of Memory Error when viewing pca
3550 analysis results</li>
3551 <li>InstallAnywhere builds fail to launch on OS X java
3552 10.5 update 4 (due to apple Java 1.6 update)</li>
3553 <li>Installanywhere Jalview silently fails to launch</li>
3554 </ul> <em>Applet</em>
3556 <li>Jalview.getFeatureGroups() raises an
3557 ArrayIndexOutOfBoundsException if no feature groups are
3564 <div align="center">
3565 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3571 <li>Alignment prettyprinter doesn't cope with long
3573 <li>clustalx colourscheme colours Ds preferentially when
3574 both D+E are present in over 50% of the column</li>
3575 <li>nucleic acid structures retrieved from PDB do not
3576 import correctly</li>
3577 <li>More columns get selected than were clicked on when a
3578 number of columns are hidden</li>
3579 <li>annotation label popup menu not providing correct
3580 add/hide/show options when rows are hidden or none are
3582 <li>Stockholm format shown in list of readable formats,
3583 and parser copes better with alignments from RFAM.</li>
3584 <li>CSV output of consensus only includes the percentage
3585 of all symbols if sequence logo display is enabled</li>
3587 </ul> <em>Applet</em>
3589 <li>annotation panel disappears when annotation is
3591 </ul> <em>Application</em>
3593 <li>Alignment view not redrawn properly when new
3594 alignment opened where annotation panel is visible but no
3595 annotations are present on alignment</li>
3596 <li>pasted region containing hidden columns is
3597 incorrectly displayed in new alignment window</li>
3598 <li>Jalview slow to complete operations when stdout is
3599 flooded (fix is to close the Jalview console)</li>
3600 <li>typo in AlignmentFrame->View->Hide->all but
3601 selected Rregions menu item.</li>
3602 <li>inconsistent group submenu and Format submenu entry
3603 'Un' or 'Non'conserved</li>
3604 <li>Sequence feature settings are being shared by
3605 multiple distinct alignments</li>
3606 <li>group annotation not recreated when tree partition is
3608 <li>double click on group annotation to select sequences
3609 does not propagate to associated trees</li>
3610 <li>Mac OSX specific issues:
3612 <li>exception raised when mouse clicked on desktop
3613 window background</li>
3614 <li>Desktop menu placed on menu bar and application
3615 name set correctly</li>
3616 <li>sequence feature settings not wide enough for the
3617 save feature colourscheme button</li>
3626 <div align="center">
3627 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3630 <td><em>New Capabilities</em>
3632 <li>URL links generated from description line for
3633 regular-expression based URL links (applet and application)
3635 <li>Non-positional feature URL links are shown in link
3637 <li>Linked viewing of nucleic acid sequences and
3639 <li>Automatic Scrolling option in View menu to display
3640 the currently highlighted region of an alignment.</li>
3641 <li>Order an alignment by sequence length, or using the
3642 average score or total feature count for each sequence.</li>
3643 <li>Shading features by score or associated description</li>
3644 <li>Subdivide alignment and groups based on identity of
3645 selected subsequence (Make Groups from Selection).</li>
3646 <li>New hide/show options including Shift+Control+H to
3647 hide everything but the currently selected region.</li>
3648 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3649 </ul> <em>Application</em>
3651 <li>Fetch DB References capabilities and UI expanded to
3652 support retrieval from DAS sequence sources</li>
3653 <li>Local DAS Sequence sources can be added via the
3654 command line or via the Add local source dialog box.</li>
3655 <li>DAS Dbref and DbxRef feature types are parsed as
3656 database references and protein_name is parsed as
3657 description line (BioSapiens terms).</li>
3658 <li>Enable or disable non-positional feature and database
3659 references in sequence ID tooltip from View menu in
3661 <!-- <li>New hidden columns and rows and representatives capabilities
3662 in annotations file (in progress - not yet fully implemented)</li> -->
3663 <li>Group-associated consensus, sequence logos and
3664 conservation plots</li>
3665 <li>Symbol distributions for each column can be exported
3666 and visualized as sequence logos</li>
3667 <li>Optionally scale multi-character column labels to fit
3668 within each column of annotation row<!-- todo for applet -->
3670 <li>Optional automatic sort of associated alignment view
3671 when a new tree is opened.</li>
3672 <li>Jalview Java Console</li>
3673 <li>Better placement of desktop window when moving
3674 between different screens.</li>
3675 <li>New preference items for sequence ID tooltip and
3676 consensus annotation</li>
3677 <li>Client to submit sequences and IDs to Envision2
3679 <li><em>Vamsas Capabilities</em>
3681 <li>Improved VAMSAS synchronization (Jalview archive
3682 used to preserve views, structures, and tree display
3684 <li>Import of vamsas documents from disk or URL via
3686 <li>Sharing of selected regions between views and
3687 with other VAMSAS applications (Experimental feature!)</li>
3688 <li>Updated API to VAMSAS version 0.2</li>
3690 </ul> <em>Applet</em>
3692 <li>Middle button resizes annotation row height</li>
3695 <li>sortByTree (true/false) - automatically sort the
3696 associated alignment view by the tree when a new tree is
3698 <li>showTreeBootstraps (true/false) - show or hide
3699 branch bootstraps (default is to show them if available)</li>
3700 <li>showTreeDistances (true/false) - show or hide
3701 branch lengths (default is to show them if available)</li>
3702 <li>showUnlinkedTreeNodes (true/false) - indicate if
3703 unassociated nodes should be highlighted in the tree
3705 <li>heightScale and widthScale (1.0 or more) -
3706 increase the height or width of a cell in the alignment
3707 grid relative to the current font size.</li>
3710 <li>Non-positional features displayed in sequence ID
3712 </ul> <em>Other</em>
3714 <li>Features format: graduated colour definitions and
3715 specification of feature scores</li>
3716 <li>Alignment Annotations format: new keywords for group
3717 associated annotation (GROUP_REF) and annotation row display
3718 properties (ROW_PROPERTIES)</li>
3719 <li>XML formats extended to support graduated feature
3720 colourschemes, group associated annotation, and profile
3721 visualization settings.</li></td>
3724 <li>Source field in GFF files parsed as feature source
3725 rather than description</li>
3726 <li>Non-positional features are now included in sequence
3727 feature and gff files (controlled via non-positional feature
3728 visibility in tooltip).</li>
3729 <li>URL links generated for all feature links (bugfix)</li>
3730 <li>Added URL embedding instructions to features file
3732 <li>Codons containing ambiguous nucleotides translated as
3733 'X' in peptide product</li>
3734 <li>Match case switch in find dialog box works for both
3735 sequence ID and sequence string and query strings do not
3736 have to be in upper case to match case-insensitively.</li>
3737 <li>AMSA files only contain first column of
3738 multi-character column annotation labels</li>
3739 <li>Jalview Annotation File generation/parsing consistent
3740 with documentation (e.g. Stockholm annotation can be
3741 exported and re-imported)</li>
3742 <li>PDB files without embedded PDB IDs given a friendly
3744 <li>Find incrementally searches ID string matches as well
3745 as subsequence matches, and correctly reports total number
3749 <li>Better handling of exceptions during sequence
3751 <li>Dasobert generated non-positional feature URL
3752 link text excludes the start_end suffix</li>
3753 <li>DAS feature and source retrieval buttons disabled
3754 when fetch or registry operations in progress.</li>
3755 <li>PDB files retrieved from URLs are cached properly</li>
3756 <li>Sequence description lines properly shared via
3758 <li>Sequence fetcher fetches multiple records for all
3760 <li>Ensured that command line das feature retrieval
3761 completes before alignment figures are generated.</li>
3762 <li>Reduced time taken when opening file browser for
3764 <li>isAligned check prior to calculating tree, PCA or
3765 submitting an MSA to JNet now excludes hidden sequences.</li>
3766 <li>User defined group colours properly recovered
3767 from Jalview projects.</li>
3776 <div align="center">
3777 <strong>2.4.0.b2</strong><br> 28/10/2009
3782 <li>Experimental support for google analytics usage
3784 <li>Jalview privacy settings (user preferences and docs).</li>
3789 <li>Race condition in applet preventing startup in
3791 <li>Exception when feature created from selection beyond
3792 length of sequence.</li>
3793 <li>Allow synthetic PDB files to be imported gracefully</li>
3794 <li>Sequence associated annotation rows associate with
3795 all sequences with a given id</li>
3796 <li>Find function matches case-insensitively for sequence
3797 ID string searches</li>
3798 <li>Non-standard characters do not cause pairwise
3799 alignment to fail with exception</li>
3800 </ul> <em>Application Issues</em>
3802 <li>Sequences are now validated against EMBL database</li>
3803 <li>Sequence fetcher fetches multiple records for all
3805 </ul> <em>InstallAnywhere Issues</em>
3807 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3808 issue with installAnywhere mechanism)</li>
3809 <li>Command line launching of JARs from InstallAnywhere
3810 version (java class versioning error fixed)</li>
3817 <div align="center">
3818 <strong>2.4</strong><br> 27/8/2008
3821 <td><em>User Interface</em>
3823 <li>Linked highlighting of codon and amino acid from
3824 translation and protein products</li>
3825 <li>Linked highlighting of structure associated with
3826 residue mapping to codon position</li>
3827 <li>Sequence Fetcher provides example accession numbers
3828 and 'clear' button</li>
3829 <li>MemoryMonitor added as an option under Desktop's
3831 <li>Extract score function to parse whitespace separated
3832 numeric data in description line</li>
3833 <li>Column labels in alignment annotation can be centred.</li>
3834 <li>Tooltip for sequence associated annotation give name
3836 </ul> <em>Web Services and URL fetching</em>
3838 <li>JPred3 web service</li>
3839 <li>Prototype sequence search client (no public services
3841 <li>Fetch either seed alignment or full alignment from
3843 <li>URL Links created for matching database cross
3844 references as well as sequence ID</li>
3845 <li>URL Links can be created using regular-expressions</li>
3846 </ul> <em>Sequence Database Connectivity</em>
3848 <li>Retrieval of cross-referenced sequences from other
3850 <li>Generalised database reference retrieval and
3851 validation to all fetchable databases</li>
3852 <li>Fetch sequences from DAS sources supporting the
3853 sequence command</li>
3854 </ul> <em>Import and Export</em>
3855 <li>export annotation rows as CSV for spreadsheet import</li>
3856 <li>Jalview projects record alignment dataset associations,
3857 EMBL products, and cDNA sequence mappings</li>
3858 <li>Sequence Group colour can be specified in Annotation
3860 <li>Ad-hoc colouring of group in Annotation File using RGB
3861 triplet as name of colourscheme</li>
3862 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3864 <li>treenode binding for VAMSAS tree exchange</li>
3865 <li>local editing and update of sequences in VAMSAS
3866 alignments (experimental)</li>
3867 <li>Create new or select existing session to join</li>
3868 <li>load and save of vamsas documents</li>
3869 </ul> <em>Application command line</em>
3871 <li>-tree parameter to open trees (introduced for passing
3873 <li>-fetchfrom command line argument to specify nicknames
3874 of DAS servers to query for alignment features</li>
3875 <li>-dasserver command line argument to add new servers
3876 that are also automatically queried for features</li>
3877 <li>-groovy command line argument executes a given groovy
3878 script after all input data has been loaded and parsed</li>
3879 </ul> <em>Applet-Application data exchange</em>
3881 <li>Trees passed as applet parameters can be passed to
3882 application (when using "View in full
3883 application")</li>
3884 </ul> <em>Applet Parameters</em>
3886 <li>feature group display control parameter</li>
3887 <li>debug parameter</li>
3888 <li>showbutton parameter</li>
3889 </ul> <em>Applet API methods</em>
3891 <li>newView public method</li>
3892 <li>Window (current view) specific get/set public methods</li>
3893 <li>Feature display control methods</li>
3894 <li>get list of currently selected sequences</li>
3895 </ul> <em>New Jalview distribution features</em>
3897 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3898 <li>RELEASE file gives build properties for the latest
3899 Jalview release.</li>
3900 <li>Java 1.1 Applet build made easier and donotobfuscate
3901 property controls execution of obfuscator</li>
3902 <li>Build target for generating source distribution</li>
3903 <li>Debug flag for javacc</li>
3904 <li>.jalview_properties file is documented (slightly) in
3905 jalview.bin.Cache</li>
3906 <li>Continuous Build Integration for stable and
3907 development version of Application, Applet and source
3912 <li>selected region output includes visible annotations
3913 (for certain formats)</li>
3914 <li>edit label/displaychar contains existing label/char
3916 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3917 <li>shorter peptide product names from EMBL records</li>
3918 <li>Newick string generator makes compact representations</li>
3919 <li>bootstrap values parsed correctly for tree files with
3921 <li>pathological filechooser bug avoided by not allowing
3922 filenames containing a ':'</li>
3923 <li>Fixed exception when parsing GFF files containing
3924 global sequence features</li>
3925 <li>Alignment datasets are finalized only when number of
3926 references from alignment sequences goes to zero</li>
3927 <li>Close of tree branch colour box without colour
3928 selection causes cascading exceptions</li>
3929 <li>occasional negative imgwidth exceptions</li>
3930 <li>better reporting of non-fatal warnings to user when
3931 file parsing fails.</li>
3932 <li>Save works when Jalview project is default format</li>
3933 <li>Save as dialog opened if current alignment format is
3934 not a valid output format</li>
3935 <li>UniProt canonical names introduced for both das and
3937 <li>Histidine should be midblue (not pink!) in Zappo</li>
3938 <li>error messages passed up and output when data read
3940 <li>edit undo recovers previous dataset sequence when
3941 sequence is edited</li>
3942 <li>allow PDB files without pdb ID HEADER lines (like
3943 those generated by MODELLER) to be read in properly</li>
3944 <li>allow reading of JPred concise files as a normal
3946 <li>Stockholm annotation parsing and alignment properties
3947 import fixed for PFAM records</li>
3948 <li>Structure view windows have correct name in Desktop
3950 <li>annotation consisting of sequence associated scores
3951 can be read and written correctly to annotation file</li>
3952 <li>Aligned cDNA translation to aligned peptide works
3954 <li>Fixed display of hidden sequence markers and
3955 non-italic font for representatives in Applet</li>
3956 <li>Applet Menus are always embedded in applet window on
3958 <li>Newly shown features appear at top of stack (in
3960 <li>Annotations added via parameter not drawn properly
3961 due to null pointer exceptions</li>
3962 <li>Secondary structure lines are drawn starting from
3963 first column of alignment</li>
3964 <li>UniProt XML import updated for new schema release in
3966 <li>Sequence feature to sequence ID match for Features
3967 file is case-insensitive</li>
3968 <li>Sequence features read from Features file appended to
3969 all sequences with matching IDs</li>
3970 <li>PDB structure coloured correctly for associated views
3971 containing a sub-sequence</li>
3972 <li>PDB files can be retrieved by applet from Jar files</li>
3973 <li>feature and annotation file applet parameters
3974 referring to different directories are retrieved correctly</li>
3975 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3976 <li>Fixed application hang whilst waiting for
3977 splash-screen version check to complete</li>
3978 <li>Applet properly URLencodes input parameter values
3979 when passing them to the launchApp service</li>
3980 <li>display name and local features preserved in results
3981 retrieved from web service</li>
3982 <li>Visual delay indication for sequence retrieval and
3983 sequence fetcher initialisation</li>
3984 <li>updated Application to use DAS 1.53e version of
3985 dasobert DAS client</li>
3986 <li>Re-instated Full AMSA support and .amsa file
3988 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3996 <div align="center">
3997 <strong>2.3</strong><br> 9/5/07
4002 <li>Jmol 11.0.2 integration</li>
4003 <li>PDB views stored in Jalview XML files</li>
4004 <li>Slide sequences</li>
4005 <li>Edit sequence in place</li>
4006 <li>EMBL CDS features</li>
4007 <li>DAS Feature mapping</li>
4008 <li>Feature ordering</li>
4009 <li>Alignment Properties</li>
4010 <li>Annotation Scores</li>
4011 <li>Sort by scores</li>
4012 <li>Feature/annotation editing in applet</li>
4017 <li>Headless state operation in 2.2.1</li>
4018 <li>Incorrect and unstable DNA pairwise alignment</li>
4019 <li>Cut and paste of sequences with annotation</li>
4020 <li>Feature group display state in XML</li>
4021 <li>Feature ordering in XML</li>
4022 <li>blc file iteration selection using filename # suffix</li>
4023 <li>Stockholm alignment properties</li>
4024 <li>Stockhom alignment secondary structure annotation</li>
4025 <li>2.2.1 applet had no feature transparency</li>
4026 <li>Number pad keys can be used in cursor mode</li>
4027 <li>Structure Viewer mirror image resolved</li>
4034 <div align="center">
4035 <strong>2.2.1</strong><br> 12/2/07
4040 <li>Non standard characters can be read and displayed
4041 <li>Annotations/Features can be imported/exported to the
4043 <li>Applet allows editing of sequence/annotation/group
4044 name & description
4045 <li>Preference setting to display sequence name in
4047 <li>Annotation file format extended to allow
4048 Sequence_groups to be defined
4049 <li>Default opening of alignment overview panel can be
4050 specified in preferences
4051 <li>PDB residue numbering annotation added to associated
4057 <li>Applet crash under certain Linux OS with Java 1.6
4059 <li>Annotation file export / import bugs fixed
4060 <li>PNG / EPS image output bugs fixed
4066 <div align="center">
4067 <strong>2.2</strong><br> 27/11/06
4072 <li>Multiple views on alignment
4073 <li>Sequence feature editing
4074 <li>"Reload" alignment
4075 <li>"Save" to current filename
4076 <li>Background dependent text colour
4077 <li>Right align sequence ids
4078 <li>User-defined lower case residue colours
4081 <li>Menu item accelerator keys
4082 <li>Control-V pastes to current alignment
4083 <li>Cancel button for DAS Feature Fetching
4084 <li>PCA and PDB Viewers zoom via mouse roller
4085 <li>User-defined sub-tree colours and sub-tree selection
4087 <li>'New Window' button on the 'Output to Text box'
4092 <li>New memory efficient Undo/Redo System
4093 <li>Optimised symbol lookups and conservation/consensus
4095 <li>Region Conservation/Consensus recalculated after
4097 <li>Fixed Remove Empty Columns Bug (empty columns at end
4099 <li>Slowed DAS Feature Fetching for increased robustness.
4101 <li>Made angle brackets in ASCII feature descriptions
4103 <li>Re-instated Zoom function for PCA
4104 <li>Sequence descriptions conserved in web service
4106 <li>UniProt ID discoverer uses any word separated by
4108 <li>WsDbFetch query/result association resolved
4109 <li>Tree leaf to sequence mapping improved
4110 <li>Smooth fonts switch moved to FontChooser dialog box.
4117 <div align="center">
4118 <strong>2.1.1</strong><br> 12/9/06
4123 <li>Copy consensus sequence to clipboard</li>
4128 <li>Image output - rightmost residues are rendered if
4129 sequence id panel has been resized</li>
4130 <li>Image output - all offscreen group boundaries are
4132 <li>Annotation files with sequence references - all
4133 elements in file are relative to sequence position</li>
4134 <li>Mac Applet users can use Alt key for group editing</li>
4140 <div align="center">
4141 <strong>2.1</strong><br> 22/8/06
4146 <li>MAFFT Multiple Alignment in default Web Service list</li>
4147 <li>DAS Feature fetching</li>
4148 <li>Hide sequences and columns</li>
4149 <li>Export Annotations and Features</li>
4150 <li>GFF file reading / writing</li>
4151 <li>Associate structures with sequences from local PDB
4153 <li>Add sequences to exisiting alignment</li>
4154 <li>Recently opened files / URL lists</li>
4155 <li>Applet can launch the full application</li>
4156 <li>Applet has transparency for features (Java 1.2
4158 <li>Applet has user defined colours parameter</li>
4159 <li>Applet can load sequences from parameter
4160 "sequence<em>x</em>"
4166 <li>Redundancy Panel reinstalled in the Applet</li>
4167 <li>Monospaced font - EPS / rescaling bug fixed</li>
4168 <li>Annotation files with sequence references bug fixed</li>
4174 <div align="center">
4175 <strong>2.08.1</strong><br> 2/5/06
4180 <li>Change case of selected region from Popup menu</li>
4181 <li>Choose to match case when searching</li>
4182 <li>Middle mouse button and mouse movement can compress /
4183 expand the visible width and height of the alignment</li>
4188 <li>Annotation Panel displays complete JNet results</li>
4194 <div align="center">
4195 <strong>2.08b</strong><br> 18/4/06
4201 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4202 <li>Righthand label on wrapped alignments shows correct
4209 <div align="center">
4210 <strong>2.08</strong><br> 10/4/06
4215 <li>Editing can be locked to the selection area</li>
4216 <li>Keyboard editing</li>
4217 <li>Create sequence features from searches</li>
4218 <li>Precalculated annotations can be loaded onto
4220 <li>Features file allows grouping of features</li>
4221 <li>Annotation Colouring scheme added</li>
4222 <li>Smooth fonts off by default - Faster rendering</li>
4223 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4228 <li>Drag & Drop fixed on Linux</li>
4229 <li>Jalview Archive file faster to load/save, sequence
4230 descriptions saved.</li>
4236 <div align="center">
4237 <strong>2.07</strong><br> 12/12/05
4242 <li>PDB Structure Viewer enhanced</li>
4243 <li>Sequence Feature retrieval and display enhanced</li>
4244 <li>Choose to output sequence start-end after sequence
4245 name for file output</li>
4246 <li>Sequence Fetcher WSDBFetch@EBI</li>
4247 <li>Applet can read feature files, PDB files and can be
4248 used for HTML form input</li>
4253 <li>HTML output writes groups and features</li>
4254 <li>Group editing is Control and mouse click</li>
4255 <li>File IO bugs</li>
4261 <div align="center">
4262 <strong>2.06</strong><br> 28/9/05
4267 <li>View annotations in wrapped mode</li>
4268 <li>More options for PCA viewer</li>
4273 <li>GUI bugs resolved</li>
4274 <li>Runs with -nodisplay from command line</li>
4280 <div align="center">
4281 <strong>2.05b</strong><br> 15/9/05
4286 <li>Choose EPS export as lineart or text</li>
4287 <li>Jar files are executable</li>
4288 <li>Can read in Uracil - maps to unknown residue</li>
4293 <li>Known OutOfMemory errors give warning message</li>
4294 <li>Overview window calculated more efficiently</li>
4295 <li>Several GUI bugs resolved</li>
4301 <div align="center">
4302 <strong>2.05</strong><br> 30/8/05
4307 <li>Edit and annotate in "Wrapped" view</li>
4312 <li>Several GUI bugs resolved</li>
4318 <div align="center">
4319 <strong>2.04</strong><br> 24/8/05
4324 <li>Hold down mouse wheel & scroll to change font
4330 <li>Improved JPred client reliability</li>
4331 <li>Improved loading of Jalview files</li>
4337 <div align="center">
4338 <strong>2.03</strong><br> 18/8/05
4343 <li>Set Proxy server name and port in preferences</li>
4344 <li>Multiple URL links from sequence ids</li>
4345 <li>User Defined Colours can have a scheme name and added
4347 <li>Choose to ignore gaps in consensus calculation</li>
4348 <li>Unix users can set default web browser</li>
4349 <li>Runs without GUI for batch processing</li>
4350 <li>Dynamically generated Web Service Menus</li>
4355 <li>InstallAnywhere download for Sparc Solaris</li>
4361 <div align="center">
4362 <strong>2.02</strong><br> 18/7/05
4368 <li>Copy & Paste order of sequences maintains
4369 alignment order.</li>
4375 <div align="center">
4376 <strong>2.01</strong><br> 12/7/05
4381 <li>Use delete key for deleting selection.</li>
4382 <li>Use Mouse wheel to scroll sequences.</li>
4383 <li>Help file updated to describe how to add alignment
4385 <li>Version and build date written to build properties
4387 <li>InstallAnywhere installation will check for updates
4388 at launch of Jalview.</li>
4393 <li>Delete gaps bug fixed.</li>
4394 <li>FileChooser sorts columns.</li>
4395 <li>Can remove groups one by one.</li>
4396 <li>Filechooser icons installed.</li>
4397 <li>Finder ignores return character when searching.
4398 Return key will initiate a search.<br>
4405 <div align="center">
4406 <strong>2.0</strong><br> 20/6/05
4411 <li>New codebase</li>