3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">2.11</a><br />
61 <em>20/06/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
68 <!-- JAL-2620 -->Alternative genetic code tables for
69 'Translate as cDNA'</li>
71 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
72 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
75 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
76 shaded according to any associated attributes (e.g. variant
77 attributes from VCF file, or key-value pairs imported from
81 <!-- JAL-2897 -->Show synonymous codon variants on peptide
85 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
89 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
90 algorithm (Z-sort/transparency and filter aware)
93 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
99 <!-- JAL-3141 -->Backup files created when saving Jalview project
102 <li><strong>Principal Components Analysis Viewer</strong>
105 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
106 and Viewer state saved in Jalview Project
108 <li>'Change parameters' option removed from viewer's
111 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
115 <!-- JAL-2965 -->PCA plot is depth cued
120 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
122 <li><strong>Speed and Efficiency</strong>
125 <!-- JAL-3198 -->More efficient creation of selections and
126 multiple groups when working with large alignments
129 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
133 <li><strong>User Interface</strong>
136 <!-- JAL-2933 -->Finder panel remembers last position in each
140 <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
141 what is shown)<br />Only visible region of alignment is shown by
142 default (can be changed in user preferences)
145 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
146 to the Overwrite Dialog
149 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
153 <!-- JAL-1244 -->Status bar shows bounds when dragging a
154 selection region, and gap count when inserting or deleting gaps
157 <!-- JAL-3132 -->Status bar updates over sequence and annotation
161 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
165 <!-- JAL-3073 -->Can select columns by dragging left/right in 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>
211 <em>Development and Release Processes</em>
214 <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
215 Installers built with Install4j (licensed to the Jalview open
216 source project) rather than InstallAnywhere
219 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
220 settings, receive over the air updates and launch specific
221 versions via (<a href="https://github.com/threerings/getdown">Three
225 <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
228 <!-- JAL-3225 -->Eclipse project configuration managed with
232 Atlassian Bamboo continuous integration for
233 unattended Test Suite execution</li>
235 <!-- JAL-2864 -->Memory test suite to detect leaks in common
238 <!-- JAL-3140 -->IntervalStoreJ (NCList
239 implementation that alows updates) used for Sequence Feature collections</li>
242 <td align="left" valign="top">
245 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
247 <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
249 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
251 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
252 Jalview project involving multiple views</li>
254 <!-- JAL-3164 -->Overview for complementary view in a linked
255 CDS/Protein alignment is not updated when Hide Columns by
256 Annotation dialog hides columns</li>
258 <!-- JAL-3158 -->Selection highlighting in the complement of
259 a CDS/Protein alignment stops working after making a
260 selection in one view, then making another selection in the
263 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
265 <!-- JAL-3154 -->Table Columns could be re-ordered in
266 Feature Settings and Jalview Preferences panels</li>
268 <!-- JAL-2865 -->Jalview hangs when closing windows
269 or the overview updates with large alignments</li>
271 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
272 region if columns were selected by dragging right-to-left
273 and the mouse moved to the left of the first column</li>
275 <!-- JAL-3218 -->Couldn't hide selected columns adjacent
276 to a hidden column marker via scale popup menu</li>
278 <!-- JAL-2846 -->Error message for trying to load in invalid
279 URLs doesn't tell users the invalid URL</li>
281 <!-- JAL-3178 -->Nonpositional features lose feature group
282 on export as Jalview features file</li>
284 <!-- JAL-2060 -->'Graduated colour' option not offered for
285 manually created features (where if feature score is Float.NaN)
288 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
289 printed when columns are hidden</li>
291 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
293 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
294 dragging out of Scale or Annotation Panel</li>
296 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
298 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
300 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
302 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
304 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
306 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
308 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
309 opening an alignment</li>
311 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
313 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
314 different groups in the alignment are selected</li>
316 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
318 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
320 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
322 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
324 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
326 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
328 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
330 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
332 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
334 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
336 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
338 <!-- JAL-914 -->Help page can be opened twice</li>
343 <!-- JAL-2822 -->Start and End should be updated when
344 sequence data at beginning or end of alignment added/removed
345 via 'Edit' sequence</li>
347 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
348 sequence features correctly when start of sequence is
349 removed (Known defect since 2.10)</li>
351 <em>New Known Defects</em>
354 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
356 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
358 <!-- JAL-3240 -->Display is incorrect after removing gapped
359 columns within hidden columns
362 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
363 window after dragging left to select columns to left of visible
370 <td width="60" nowrap>
372 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
375 <td><div align="left">
379 <!-- JAL-3101 -->Default memory for Jalview webstart and
380 InstallAnywhere increased to 1G.
383 <!-- JAL-247 -->Hidden sequence markers and representative
384 sequence bolding included when exporting alignment as EPS,
385 SVG, PNG or HTML. <em>Display is configured via the
386 Format menu, or for command-line use via a jalview
387 properties file.</em>
390 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
391 API and sequence data now imported as JSON.
394 <!-- JAL-3065 -->Change in recommended way of starting
395 Jalview via a Java command line: add jars in lib directory
396 to CLASSPATH, rather than via the deprecated java.ext.dirs
403 <!-- JAL-3047 -->Support added to execute test suite
404 instrumented with <a href="http://openclover.org/">Open
409 <td><div align="left">
413 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
414 row shown in Feredoxin Structure alignment view of example
418 <!-- JAL-2854 -->Annotation obscures sequences if lots of
419 annotation displayed.
422 <!-- JAL-3107 -->Group conservation/consensus not shown
423 for newly created group when 'Apply to all groups'
427 <!-- JAL-3087 -->Corrupted display when switching to
428 wrapped mode when sequence panel's vertical scrollbar is
432 <!-- JAL-3003 -->Alignment is black in exported EPS file
433 when sequences are selected in exported view.</em>
436 <!-- JAL-3059 -->Groups with different coloured borders
437 aren't rendered with correct colour.
440 <!-- JAL-3092 -->Jalview could hang when importing certain
441 types of knotted RNA secondary structure.
444 <!-- JAL-3095 -->Sequence highlight and selection in
445 trimmed VARNA 2D structure is incorrect for sequences that
449 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
450 annotation when columns are inserted into an alignment,
451 and when exporting as Stockholm flatfile.
454 <!-- JAL-3053 -->Jalview annotation rows containing upper
455 and lower-case 'E' and 'H' do not automatically get
456 treated as RNA secondary structure.
459 <!-- JAL-3106 -->.jvp should be used as default extension
460 (not .jar) when saving a jalview project file.
463 <!-- JAL-3105 -->Mac Users: closing a window correctly
464 transfers focus to previous window on OSX
467 <em>Java 10 Issues Resolved</em>
470 <!-- JAL-2988 -->OSX - Can't save new files via the File
471 or export menus by typing in a name into the Save dialog
475 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
476 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
477 'look and feel' which has improved compatibility with the
478 latest version of OSX.
485 <td width="60" nowrap>
487 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
488 <em>7/06/2018</em></strong>
491 <td><div align="left">
495 <!-- JAL-2920 -->Use HGVS nomenclature for variant
496 annotation retrieved from Uniprot
499 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
500 onto the Jalview Desktop
504 <td><div align="left">
508 <!-- JAL-3017 -->Cannot import features with multiple
509 variant elements (blocks import of some Uniprot records)
512 <!-- JAL-2997 -->Clustal files with sequence positions in
513 right-hand column parsed correctly
516 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
517 not alignment area in exported graphic
520 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
521 window has input focus
524 <!-- JAL-2992 -->Annotation panel set too high when
525 annotation added to view (Windows)
528 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
529 network connectivity is poor
532 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
533 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
534 the currently open URL and links from a page viewed in
535 Firefox or Chrome on Windows is now fully supported. If
536 you are using Edge, only links in the page can be
537 dragged, and with Internet Explorer, only the currently
538 open URL in the browser can be dropped onto Jalview.</em>
544 <td width="60" nowrap>
546 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
549 <td><div align="left">
553 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
554 for disabling automatic superposition of multiple
555 structures and open structures in existing views
558 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
559 ID and annotation area margins can be click-dragged to
563 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
567 <!-- JAL-2759 -->Improved performance for large alignments
568 and lots of hidden columns
571 <!-- JAL-2593 -->Improved performance when rendering lots
572 of features (particularly when transparency is disabled)
577 <td><div align="left">
580 <!-- JAL-2899 -->Structure and Overview aren't updated
581 when Colour By Annotation threshold slider is adjusted
584 <!-- JAL-2778 -->Slow redraw when Overview panel shown
585 overlapping alignment panel
588 <!-- JAL-2929 -->Overview doesn't show end of unpadded
592 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
593 improved: CDS not handled correctly if transcript has no
597 <!-- JAL-2321 -->Secondary structure and temperature
598 factor annotation not added to sequence when local PDB
599 file associated with it by drag'n'drop or structure
603 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
604 dialog doesn't import PDB files dropped on an alignment
607 <!-- JAL-2666 -->Linked scrolling via protein horizontal
608 scroll bar doesn't work for some CDS/Protein views
611 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
612 Java 1.8u153 onwards and Java 1.9u4+.
615 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
616 columns in annotation row
619 <!-- JAL-2913 -->Preferences panel's ID Width control is not
620 honored in batch mode
623 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
624 for structures added to existing Jmol view
627 <!-- JAL-2223 -->'View Mappings' includes duplicate
628 entries after importing project with multiple views
631 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
632 protein sequences via SIFTS from associated PDB entries
633 with negative residue numbers or missing residues fails
636 <!-- JAL-2952 -->Exception when shading sequence with negative
637 Temperature Factor values from annotated PDB files (e.g.
638 as generated by CONSURF)
641 <!-- JAL-2920 -->Uniprot 'sequence variant' features
642 tooltip doesn't include a text description of mutation
645 <!-- JAL-2922 -->Invert displayed features very slow when
646 structure and/or overview windows are also shown
649 <!-- JAL-2954 -->Selecting columns from highlighted regions
650 very slow for alignments with large numbers of sequences
653 <!-- JAL-2925 -->Copy Consensus fails for group consensus
654 with 'StringIndexOutOfBounds'
657 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
658 platforms running Java 10
661 <!-- JAL-2960 -->Adding a structure to existing structure
662 view appears to do nothing because the view is hidden behind the alignment view
668 <!-- JAL-2926 -->Copy consensus sequence option in applet
669 should copy the group consensus when popup is opened on it
675 <!-- JAL-2913 -->Fixed ID width preference is not respected
678 <em>New Known Defects</em>
681 <!-- JAL-2973 --> Exceptions occasionally raised when
682 editing a large alignment and overview is displayed
685 <!-- JAL-2974 -->'Overview updating' progress bar is shown
686 repeatedly after a series of edits even when the overview
687 is no longer reflecting updates
690 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
691 structures for protein subsequence (if 'Trim Retrieved
692 Sequences' enabled) or Ensembl isoforms (Workaround in
693 2.10.4 is to fail back to N&W mapping)
700 <td width="60" nowrap>
702 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
705 <td><div align="left">
706 <ul><li>Updated Certum Codesigning Certificate
707 (Valid till 30th November 2018)</li></ul></div></td>
708 <td><div align="left">
711 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
712 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
713 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
714 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
715 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
716 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
717 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
723 <td width="60" nowrap>
725 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
728 <td><div align="left">
732 <!-- JAL-2446 -->Faster and more efficient management and
733 rendering of sequence features
736 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
737 429 rate limit request hander
740 <!-- JAL-2773 -->Structure views don't get updated unless
741 their colours have changed
744 <!-- JAL-2495 -->All linked sequences are highlighted for
745 a structure mousover (Jmol) or selection (Chimera)
748 <!-- JAL-2790 -->'Cancel' button in progress bar for
749 JABAWS AACon, RNAAliFold and Disorder prediction jobs
752 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
753 view from Ensembl locus cross-references
756 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
760 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
761 feature can be disabled
764 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
765 PDB easier retrieval of sequences for lists of IDs
768 <!-- JAL-2758 -->Short names for sequences retrieved from
774 <li>Groovy interpreter updated to 2.4.12</li>
775 <li>Example groovy script for generating a matrix of
776 percent identity scores for current alignment.</li>
778 <em>Testing and Deployment</em>
781 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
785 <td><div align="left">
789 <!-- JAL-2643 -->Pressing tab after updating the colour
790 threshold text field doesn't trigger an update to the
794 <!-- JAL-2682 -->Race condition when parsing sequence ID
798 <!-- JAL-2608 -->Overview windows are also closed when
799 alignment window is closed
802 <!-- JAL-2548 -->Export of features doesn't always respect
806 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
807 takes a long time in Cursor mode
813 <!-- JAL-2777 -->Structures with whitespace chainCode
814 cannot be viewed in Chimera
817 <!-- JAL-2728 -->Protein annotation panel too high in
821 <!-- JAL-2757 -->Can't edit the query after the server
822 error warning icon is shown in Uniprot and PDB Free Text
826 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
829 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
832 <!-- JAL-2739 -->Hidden column marker in last column not
833 rendered when switching back from Wrapped to normal view
836 <!-- JAL-2768 -->Annotation display corrupted when
837 scrolling right in unwapped alignment view
840 <!-- JAL-2542 -->Existing features on subsequence
841 incorrectly relocated when full sequence retrieved from
845 <!-- JAL-2733 -->Last reported memory still shown when
846 Desktop->Show Memory is unticked (OSX only)
849 <!-- JAL-2658 -->Amend Features dialog doesn't allow
850 features of same type and group to be selected for
854 <!-- JAL-2524 -->Jalview becomes sluggish in wide
855 alignments when hidden columns are present
858 <!-- JAL-2392 -->Jalview freezes when loading and
859 displaying several structures
862 <!-- JAL-2732 -->Black outlines left after resizing or
866 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
867 within the Jalview desktop on OSX
870 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
871 when in wrapped alignment mode
874 <!-- JAL-2636 -->Scale mark not shown when close to right
875 hand end of alignment
878 <!-- JAL-2684 -->Pairwise alignment of selected regions of
879 each selected sequence do not have correct start/end
883 <!-- JAL-2793 -->Alignment ruler height set incorrectly
884 after canceling the Alignment Window's Font dialog
887 <!-- JAL-2036 -->Show cross-references not enabled after
888 restoring project until a new view is created
891 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
892 URL links appears when only default EMBL-EBI link is
893 configured (since 2.10.2b2)
896 <!-- JAL-2775 -->Overview redraws whole window when box
900 <!-- JAL-2225 -->Structure viewer doesn't map all chains
901 in a multi-chain structure when viewing alignment
902 involving more than one chain (since 2.10)
905 <!-- JAL-2811 -->Double residue highlights in cursor mode
906 if new selection moves alignment window
909 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
910 arrow key in cursor mode to pass hidden column marker
913 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
914 that produces correctly annotated transcripts and products
917 <!-- JAL-2776 -->Toggling a feature group after first time
918 doesn't update associated structure view
921 <em>Applet</em><br />
924 <!-- JAL-2687 -->Concurrent modification exception when
925 closing alignment panel
928 <em>BioJSON</em><br />
931 <!-- JAL-2546 -->BioJSON export does not preserve
932 non-positional features
935 <em>New Known Issues</em>
938 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
939 sequence features correctly (for many previous versions of
943 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
944 using cursor in wrapped panel other than top
947 <!-- JAL-2791 -->Select columns containing feature ignores
948 graduated colour threshold
951 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
952 always preserve numbering and sequence features
955 <em>Known Java 9 Issues</em>
958 <!-- JAL-2902 -->Groovy Console very slow to open and is
959 not responsive when entering characters (Webstart, Java
966 <td width="60" nowrap>
968 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
969 <em>2/10/2017</em></strong>
972 <td><div align="left">
973 <em>New features in Jalview Desktop</em>
976 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
978 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
982 <td><div align="left">
986 <td width="60" nowrap>
988 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
989 <em>7/9/2017</em></strong>
992 <td><div align="left">
996 <!-- JAL-2588 -->Show gaps in overview window by colouring
997 in grey (sequences used to be coloured grey, and gaps were
1001 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1005 <!-- JAL-2587 -->Overview updates immediately on increase
1006 in size and progress bar shown as higher resolution
1007 overview is recalculated
1012 <td><div align="left">
1016 <!-- JAL-2664 -->Overview window redraws every hidden
1017 column region row by row
1020 <!-- JAL-2681 -->duplicate protein sequences shown after
1021 retrieving Ensembl crossrefs for sequences from Uniprot
1024 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1025 format setting is unticked
1028 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1029 if group has show boxes format setting unticked
1032 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1033 autoscrolling whilst dragging current selection group to
1034 include sequences and columns not currently displayed
1037 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1038 assemblies are imported via CIF file
1041 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1042 displayed when threshold or conservation colouring is also
1046 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1050 <!-- JAL-2673 -->Jalview continues to scroll after
1051 dragging a selected region off the visible region of the
1055 <!-- JAL-2724 -->Cannot apply annotation based
1056 colourscheme to all groups in a view
1059 <!-- JAL-2511 -->IDs don't line up with sequences
1060 initially after font size change using the Font chooser or
1067 <td width="60" nowrap>
1068 <div align="center">
1069 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1072 <td><div align="left">
1073 <em>Calculations</em>
1077 <!-- JAL-1933 -->Occupancy annotation row shows number of
1078 ungapped positions in each column of the alignment.
1081 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1082 a calculation dialog box
1085 <!-- JAL-2379 -->Revised implementation of PCA for speed
1086 and memory efficiency (~30x faster)
1089 <!-- JAL-2403 -->Revised implementation of sequence
1090 similarity scores as used by Tree, PCA, Shading Consensus
1091 and other calculations
1094 <!-- JAL-2416 -->Score matrices are stored as resource
1095 files within the Jalview codebase
1098 <!-- JAL-2500 -->Trees computed on Sequence Feature
1099 Similarity may have different topology due to increased
1106 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1107 model for alignments and groups
1110 <!-- JAL-384 -->Custom shading schemes created via groovy
1117 <!-- JAL-2526 -->Efficiency improvements for interacting
1118 with alignment and overview windows
1121 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1125 <!-- JAL-2388 -->Hidden columns and sequences can be
1129 <!-- JAL-2611 -->Click-drag in visible area allows fine
1130 adjustment of visible position
1134 <em>Data import/export</em>
1137 <!-- JAL-2535 -->Posterior probability annotation from
1138 Stockholm files imported as sequence associated annotation
1141 <!-- JAL-2507 -->More robust per-sequence positional
1142 annotation input/output via stockholm flatfile
1145 <!-- JAL-2533 -->Sequence names don't include file
1146 extension when importing structure files without embedded
1147 names or PDB accessions
1150 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1151 format sequence substitution matrices
1154 <em>User Interface</em>
1157 <!-- JAL-2447 --> Experimental Features Checkbox in
1158 Desktop's Tools menu to hide or show untested features in
1162 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1163 via Overview or sequence motif search operations
1166 <!-- JAL-2547 -->Amend sequence features dialog box can be
1167 opened by double clicking gaps within sequence feature
1171 <!-- JAL-1476 -->Status bar message shown when not enough
1172 aligned positions were available to create a 3D structure
1176 <em>3D Structure</em>
1179 <!-- JAL-2430 -->Hidden regions in alignment views are not
1180 coloured in linked structure views
1183 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1184 file-based command exchange
1187 <!-- JAL-2375 -->Structure chooser automatically shows
1188 Cached Structures rather than querying the PDBe if
1189 structures are already available for sequences
1192 <!-- JAL-2520 -->Structures imported via URL are cached in
1193 the Jalview project rather than downloaded again when the
1194 project is reopened.
1197 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1198 to transfer Chimera's structure attributes as Jalview
1199 features, and vice-versa (<strong>Experimental
1203 <em>Web Services</em>
1206 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1209 <!-- JAL-2335 -->Filter non-standard amino acids and
1210 nucleotides when submitting to AACon and other MSA
1214 <!-- JAL-2316, -->URLs for viewing database
1215 cross-references provided by identifiers.org and the
1216 EMBL-EBI's MIRIAM DB
1223 <!-- JAL-2344 -->FileFormatI interface for describing and
1224 identifying file formats (instead of String constants)
1227 <!-- JAL-2228 -->FeatureCounter script refactored for
1228 efficiency when counting all displayed features (not
1229 backwards compatible with 2.10.1)
1232 <em>Example files</em>
1235 <!-- JAL-2631 -->Graduated feature colour style example
1236 included in the example feature file
1239 <em>Documentation</em>
1242 <!-- JAL-2339 -->Release notes reformatted for readability
1243 with the built-in Java help viewer
1246 <!-- JAL-1644 -->Find documentation updated with 'search
1247 sequence description' option
1253 <!-- JAL-2485, -->External service integration tests for
1254 Uniprot REST Free Text Search Client
1257 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1260 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1265 <td><div align="left">
1266 <em>Calculations</em>
1269 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1270 matrix - C->R should be '-3'<br />Old matrix restored
1271 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1273 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1274 Jalview's treatment of gaps in PCA and substitution matrix
1275 based Tree calculations.<br /> <br />In earlier versions
1276 of Jalview, gaps matching gaps were penalised, and gaps
1277 matching non-gaps penalised even more. In the PCA
1278 calculation, gaps were actually treated as non-gaps - so
1279 different costs were applied, which meant Jalview's PCAs
1280 were different to those produced by SeqSpace.<br />Jalview
1281 now treats gaps in the same way as SeqSpace (ie it scores
1282 them as 0). <br /> <br />Enter the following in the
1283 Groovy console to restore pre-2.10.2 behaviour:<br />
1284 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1285 // for 2.10.1 mode <br />
1286 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1287 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1288 these settings will affect all subsequent tree and PCA
1289 calculations (not recommended)</em></li>
1291 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1292 scaling of branch lengths for trees computed using
1293 Sequence Feature Similarity.
1296 <!-- JAL-2377 -->PCA calculation could hang when
1297 generating output report when working with highly
1298 redundant alignments
1301 <!-- JAL-2544 --> Sort by features includes features to
1302 right of selected region when gaps present on right-hand
1306 <em>User Interface</em>
1309 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1310 doesn't reselect a specific sequence's associated
1311 annotation after it was used for colouring a view
1314 <!-- JAL-2419 -->Current selection lost if popup menu
1315 opened on a region of alignment without groups
1318 <!-- JAL-2374 -->Popup menu not always shown for regions
1319 of an alignment with overlapping groups
1322 <!-- JAL-2310 -->Finder double counts if both a sequence's
1323 name and description match
1326 <!-- JAL-2370 -->Hiding column selection containing two
1327 hidden regions results in incorrect hidden regions
1330 <!-- JAL-2386 -->'Apply to all groups' setting when
1331 changing colour does not apply Conservation slider value
1335 <!-- JAL-2373 -->Percentage identity and conservation menu
1336 items do not show a tick or allow shading to be disabled
1339 <!-- JAL-2385 -->Conservation shading or PID threshold
1340 lost when base colourscheme changed if slider not visible
1343 <!-- JAL-2547 -->Sequence features shown in tooltip for
1344 gaps before start of features
1347 <!-- JAL-2623 -->Graduated feature colour threshold not
1348 restored to UI when feature colour is edited
1351 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1352 a time when scrolling vertically in wrapped mode.
1355 <!-- JAL-2630 -->Structure and alignment overview update
1356 as graduate feature colour settings are modified via the
1360 <!-- JAL-2034 -->Overview window doesn't always update
1361 when a group defined on the alignment is resized
1364 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1365 wrapped view result in positional status updates
1369 <!-- JAL-2563 -->Status bar doesn't show position for
1370 ambiguous amino acid and nucleotide symbols
1373 <!-- JAL-2602 -->Copy consensus sequence failed if
1374 alignment included gapped columns
1377 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1378 widgets don't permanently disappear
1381 <!-- JAL-2503 -->Cannot select or filter quantitative
1382 annotation that are shown only as column labels (e.g.
1383 T-Coffee column reliability scores)
1386 <!-- JAL-2594 -->Exception thrown if trying to create a
1387 sequence feature on gaps only
1390 <!-- JAL-2504 -->Features created with 'New feature'
1391 button from a Find inherit previously defined feature type
1392 rather than the Find query string
1395 <!-- JAL-2423 -->incorrect title in output window when
1396 exporting tree calculated in Jalview
1399 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1400 and then revealing them reorders sequences on the
1404 <!-- JAL-964 -->Group panel in sequence feature settings
1405 doesn't update to reflect available set of groups after
1406 interactively adding or modifying features
1409 <!-- JAL-2225 -->Sequence Database chooser unusable on
1413 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1414 only excluded gaps in current sequence and ignored
1421 <!-- JAL-2421 -->Overview window visible region moves
1422 erratically when hidden rows or columns are present
1425 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1426 Structure Viewer's colour menu don't correspond to
1430 <!-- JAL-2405 -->Protein specific colours only offered in
1431 colour and group colour menu for protein alignments
1434 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1435 reflect currently selected view or group's shading
1439 <!-- JAL-2624 -->Feature colour thresholds not respected
1440 when rendered on overview and structures when opacity at
1444 <!-- JAL-2589 -->User defined gap colour not shown in
1445 overview when features overlaid on alignment
1448 <em>Data import/export</em>
1451 <!-- JAL-2576 -->Very large alignments take a long time to
1455 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1456 added after a sequence was imported are not written to
1460 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1461 when importing RNA secondary structure via Stockholm
1464 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1465 not shown in correct direction for simple pseudoknots
1468 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1469 with lightGray or darkGray via features file (but can
1473 <!-- JAL-2383 -->Above PID colour threshold not recovered
1474 when alignment view imported from project
1477 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1478 structure and sequences extracted from structure files
1479 imported via URL and viewed in Jmol
1482 <!-- JAL-2520 -->Structures loaded via URL are saved in
1483 Jalview Projects rather than fetched via URL again when
1484 the project is loaded and the structure viewed
1487 <em>Web Services</em>
1490 <!-- JAL-2519 -->EnsemblGenomes example failing after
1491 release of Ensembl v.88
1494 <!-- JAL-2366 -->Proxy server address and port always
1495 appear enabled in Preferences->Connections
1498 <!-- JAL-2461 -->DAS registry not found exceptions
1499 removed from console output
1502 <!-- JAL-2582 -->Cannot retrieve protein products from
1503 Ensembl by Peptide ID
1506 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1507 created from SIFTs, and spurious 'Couldn't open structure
1508 in Chimera' errors raised after April 2017 update (problem
1509 due to 'null' string rather than empty string used for
1510 residues with no corresponding PDB mapping).
1513 <em>Application UI</em>
1516 <!-- JAL-2361 -->User Defined Colours not added to Colour
1520 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1521 case' residues (button in colourscheme editor debugged and
1522 new documentation and tooltips added)
1525 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1526 doesn't restore group-specific text colour thresholds
1529 <!-- JAL-2243 -->Feature settings panel does not update as
1530 new features are added to alignment
1533 <!-- JAL-2532 -->Cancel in feature settings reverts
1534 changes to feature colours via the Amend features dialog
1537 <!-- JAL-2506 -->Null pointer exception when attempting to
1538 edit graduated feature colour via amend features dialog
1542 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1543 selection menu changes colours of alignment views
1546 <!-- JAL-2426 -->Spurious exceptions in console raised
1547 from alignment calculation workers after alignment has
1551 <!-- JAL-1608 -->Typo in selection popup menu - Create
1552 groups now 'Create Group'
1555 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1556 Create/Undefine group doesn't always work
1559 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1560 shown again after pressing 'Cancel'
1563 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1564 adjusts start position in wrap mode
1567 <!-- JAL-2563 -->Status bar doesn't show positions for
1568 ambiguous amino acids
1571 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1572 CDS/Protein view after CDS sequences added for aligned
1576 <!-- JAL-2592 -->User defined colourschemes called 'User
1577 Defined' don't appear in Colours menu
1583 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1584 score models doesn't always result in an updated PCA plot
1587 <!-- JAL-2442 -->Features not rendered as transparent on
1588 overview or linked structure view
1591 <!-- JAL-2372 -->Colour group by conservation doesn't
1595 <!-- JAL-2517 -->Hitting Cancel after applying
1596 user-defined colourscheme doesn't restore original
1603 <!-- JAL-2314 -->Unit test failure:
1604 jalview.ws.jabaws.RNAStructExportImport setup fails
1607 <!-- JAL-2307 -->Unit test failure:
1608 jalview.ws.sifts.SiftsClientTest due to compatibility
1609 problems with deep array comparison equality asserts in
1610 successive versions of TestNG
1613 <!-- JAL-2479 -->Relocated StructureChooserTest and
1614 ParameterUtilsTest Unit tests to Network suite
1617 <em>New Known Issues</em>
1620 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1621 phase after a sequence motif find operation
1624 <!-- JAL-2550 -->Importing annotation file with rows
1625 containing just upper and lower case letters are
1626 interpreted as WUSS RNA secondary structure symbols
1629 <!-- JAL-2590 -->Cannot load and display Newick trees
1630 reliably from eggnog Ortholog database
1633 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1634 containing features of type Highlight' when 'B' is pressed
1635 to mark columns containing highlighted regions.
1638 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1639 doesn't always add secondary structure annotation.
1644 <td width="60" nowrap>
1645 <div align="center">
1646 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1649 <td><div align="left">
1653 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1654 for all consensus calculations
1657 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1660 <li>Updated Jalview's Certum code signing certificate
1663 <em>Application</em>
1666 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1667 set of database cross-references, sorted alphabetically
1670 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1671 from database cross references. Users with custom links
1672 will receive a <a href="webServices/urllinks.html#warning">warning
1673 dialog</a> asking them to update their preferences.
1676 <!-- JAL-2287-->Cancel button and escape listener on
1677 dialog warning user about disconnecting Jalview from a
1681 <!-- JAL-2320-->Jalview's Chimera control window closes if
1682 the Chimera it is connected to is shut down
1685 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1686 columns menu item to mark columns containing highlighted
1687 regions (e.g. from structure selections or results of a
1691 <!-- JAL-2284-->Command line option for batch-generation
1692 of HTML pages rendering alignment data with the BioJS
1702 <!-- JAL-2286 -->Columns with more than one modal residue
1703 are not coloured or thresholded according to percent
1704 identity (first observed in Jalview 2.8.2)
1707 <!-- JAL-2301 -->Threonine incorrectly reported as not
1711 <!-- JAL-2318 -->Updates to documentation pages (above PID
1712 threshold, amino acid properties)
1715 <!-- JAL-2292 -->Lower case residues in sequences are not
1716 reported as mapped to residues in a structure file in the
1720 <!--JAL-2324 -->Identical features with non-numeric scores
1721 could be added multiple times to a sequence
1724 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1725 bond features shown as two highlighted residues rather
1726 than a range in linked structure views, and treated
1727 correctly when selecting and computing trees from features
1730 <!-- JAL-2281-->Custom URL links for database
1731 cross-references are matched to database name regardless
1736 <em>Application</em>
1739 <!-- JAL-2282-->Custom URL links for specific database
1740 names without regular expressions also offer links from
1744 <!-- JAL-2315-->Removing a single configured link in the
1745 URL links pane in Connections preferences doesn't actually
1746 update Jalview configuration
1749 <!-- JAL-2272-->CTRL-Click on a selected region to open
1750 the alignment area popup menu doesn't work on El-Capitan
1753 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1754 files with similarly named sequences if dropped onto the
1758 <!-- JAL-2312 -->Additional mappings are shown for PDB
1759 entries where more chains exist in the PDB accession than
1760 are reported in the SIFTS file
1763 <!-- JAL-2317-->Certain structures do not get mapped to
1764 the structure view when displayed with Chimera
1767 <!-- JAL-2317-->No chains shown in the Chimera view
1768 panel's View->Show Chains submenu
1771 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1772 work for wrapped alignment views
1775 <!--JAL-2197 -->Rename UI components for running JPred
1776 predictions from 'JNet' to 'JPred'
1779 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1780 corrupted when annotation panel vertical scroll is not at
1781 first annotation row
1784 <!--JAL-2332 -->Attempting to view structure for Hen
1785 lysozyme results in a PDB Client error dialog box
1788 <!-- JAL-2319 -->Structure View's mapping report switched
1789 ranges for PDB and sequence for SIFTS
1792 SIFTS 'Not_Observed' residues mapped to non-existant
1796 <!-- <em>New Known Issues</em>
1803 <td width="60" nowrap>
1804 <div align="center">
1805 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1806 <em>25/10/2016</em></strong>
1809 <td><em>Application</em>
1811 <li>3D Structure chooser opens with 'Cached structures'
1812 view if structures already loaded</li>
1813 <li>Progress bar reports models as they are loaded to
1814 structure views</li>
1820 <li>Colour by conservation always enabled and no tick
1821 shown in menu when BLOSUM or PID shading applied</li>
1822 <li>FER1_ARATH and FER2_ARATH labels were switched in
1823 example sequences/projects/trees</li>
1825 <em>Application</em>
1827 <li>Jalview projects with views of local PDB structure
1828 files saved on Windows cannot be opened on OSX</li>
1829 <li>Multiple structure views can be opened and superposed
1830 without timeout for structures with multiple models or
1831 multiple sequences in alignment</li>
1832 <li>Cannot import or associated local PDB files without a
1833 PDB ID HEADER line</li>
1834 <li>RMSD is not output in Jmol console when superposition
1836 <li>Drag and drop of URL from Browser fails for Linux and
1837 OSX versions earlier than El Capitan</li>
1838 <li>ENA client ignores invalid content from ENA server</li>
1839 <li>Exceptions are not raised in console when ENA client
1840 attempts to fetch non-existent IDs via Fetch DB Refs UI
1842 <li>Exceptions are not raised in console when a new view
1843 is created on the alignment</li>
1844 <li>OSX right-click fixed for group selections: CMD-click
1845 to insert/remove gaps in groups and CTRL-click to open group
1848 <em>Build and deployment</em>
1850 <li>URL link checker now copes with multi-line anchor
1853 <em>New Known Issues</em>
1855 <li>Drag and drop from URL links in browsers do not work
1862 <td width="60" nowrap>
1863 <div align="center">
1864 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1867 <td><em>General</em>
1870 <!-- JAL-2124 -->Updated Spanish translations.
1873 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1874 for importing structure data to Jalview. Enables mmCIF and
1878 <!-- JAL-192 --->Alignment ruler shows positions relative to
1882 <!-- JAL-2202 -->Position/residue shown in status bar when
1883 mousing over sequence associated annotation
1886 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1890 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1891 '()', canonical '[]' and invalid '{}' base pair populations
1895 <!-- JAL-2092 -->Feature settings popup menu options for
1896 showing or hiding columns containing a feature
1899 <!-- JAL-1557 -->Edit selected group by double clicking on
1900 group and sequence associated annotation labels
1903 <!-- JAL-2236 -->Sequence name added to annotation label in
1904 select/hide columns by annotation and colour by annotation
1908 </ul> <em>Application</em>
1911 <!-- JAL-2050-->Automatically hide introns when opening a
1912 gene/transcript view
1915 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1919 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1920 structure mappings with the EMBL-EBI PDBe SIFTS database
1923 <!-- JAL-2079 -->Updated download sites used for Rfam and
1924 Pfam sources to xfam.org
1927 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1930 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1931 over sequences in Jalview
1934 <!-- JAL-2027-->Support for reverse-complement coding
1935 regions in ENA and EMBL
1938 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1939 for record retrieval via ENA rest API
1942 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1946 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1947 groovy script execution
1950 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1951 alignment window's Calculate menu
1954 <!-- JAL-1812 -->Allow groovy scripts that call
1955 Jalview.getAlignFrames() to run in headless mode
1958 <!-- JAL-2068 -->Support for creating new alignment
1959 calculation workers from groovy scripts
1962 <!-- JAL-1369 --->Store/restore reference sequence in
1966 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1967 associations are now saved/restored from project
1970 <!-- JAL-1993 -->Database selection dialog always shown
1971 before sequence fetcher is opened
1974 <!-- JAL-2183 -->Double click on an entry in Jalview's
1975 database chooser opens a sequence fetcher
1978 <!-- JAL-1563 -->Free-text search client for UniProt using
1979 the UniProt REST API
1982 <!-- JAL-2168 -->-nonews command line parameter to prevent
1983 the news reader opening
1986 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1987 querying stored in preferences
1990 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1994 <!-- JAL-1977-->Tooltips shown on database chooser
1997 <!-- JAL-391 -->Reverse complement function in calculate
1998 menu for nucleotide sequences
2001 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2002 and feature counts preserves alignment ordering (and
2003 debugged for complex feature sets).
2006 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2007 viewing structures with Jalview 2.10
2010 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2011 genome, transcript CCDS and gene ids via the Ensembl and
2012 Ensembl Genomes REST API
2015 <!-- JAL-2049 -->Protein sequence variant annotation
2016 computed for 'sequence_variant' annotation on CDS regions
2020 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2024 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2025 Ref Fetcher fails to match, or otherwise updates sequence
2026 data from external database records.
2029 <!-- JAL-2154 -->Revised Jalview Project format for
2030 efficient recovery of sequence coding and alignment
2031 annotation relationships.
2033 </ul> <!-- <em>Applet</em>
2044 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2048 <!-- JAL-2018-->Export features in Jalview format (again)
2049 includes graduated colourschemes
2052 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2053 working with big alignments and lots of hidden columns
2056 <!-- JAL-2053-->Hidden column markers not always rendered
2057 at right of alignment window
2060 <!-- JAL-2067 -->Tidied up links in help file table of
2064 <!-- JAL-2072 -->Feature based tree calculation not shown
2068 <!-- JAL-2075 -->Hidden columns ignored during feature
2069 based tree calculation
2072 <!-- JAL-2065 -->Alignment view stops updating when show
2073 unconserved enabled for group on alignment
2076 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2080 <!-- JAL-2146 -->Alignment column in status incorrectly
2081 shown as "Sequence position" when mousing over
2085 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2086 hidden columns present
2089 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2090 user created annotation added to alignment
2093 <!-- JAL-1841 -->RNA Structure consensus only computed for
2094 '()' base pair annotation
2097 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2098 in zero scores for all base pairs in RNA Structure
2102 <!-- JAL-2174-->Extend selection with columns containing
2106 <!-- JAL-2275 -->Pfam format writer puts extra space at
2107 beginning of sequence
2110 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2114 <!-- JAL-2238 -->Cannot create groups on an alignment from
2115 from a tree when t-coffee scores are shown
2118 <!-- JAL-1836,1967 -->Cannot import and view PDB
2119 structures with chains containing negative resnums (4q4h)
2122 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2126 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2127 to Clustal, PIR and PileUp output
2130 <!-- JAL-2008 -->Reordering sequence features that are
2131 not visible causes alignment window to repaint
2134 <!-- JAL-2006 -->Threshold sliders don't work in
2135 graduated colour and colour by annotation row for e-value
2136 scores associated with features and annotation rows
2139 <!-- JAL-1797 -->amino acid physicochemical conservation
2140 calculation should be case independent
2143 <!-- JAL-2173 -->Remove annotation also updates hidden
2147 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2148 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2149 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2152 <!-- JAL-2065 -->Null pointer exceptions and redraw
2153 problems when reference sequence defined and 'show
2154 non-conserved' enabled
2157 <!-- JAL-1306 -->Quality and Conservation are now shown on
2158 load even when Consensus calculation is disabled
2161 <!-- JAL-1932 -->Remove right on penultimate column of
2162 alignment does nothing
2165 <em>Application</em>
2168 <!-- JAL-1552-->URLs and links can't be imported by
2169 drag'n'drop on OSX when launched via webstart (note - not
2170 yet fixed for El Capitan)
2173 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2174 output when running on non-gb/us i18n platforms
2177 <!-- JAL-1944 -->Error thrown when exporting a view with
2178 hidden sequences as flat-file alignment
2181 <!-- JAL-2030-->InstallAnywhere distribution fails when
2185 <!-- JAL-2080-->Jalview very slow to launch via webstart
2186 (also hotfix for 2.9.0b2)
2189 <!-- JAL-2085 -->Cannot save project when view has a
2190 reference sequence defined
2193 <!-- JAL-1011 -->Columns are suddenly selected in other
2194 alignments and views when revealing hidden columns
2197 <!-- JAL-1989 -->Hide columns not mirrored in complement
2198 view in a cDNA/Protein splitframe
2201 <!-- JAL-1369 -->Cannot save/restore representative
2202 sequence from project when only one sequence is
2206 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2207 in Structure Chooser
2210 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2211 structure consensus didn't refresh annotation panel
2214 <!-- JAL-1962 -->View mapping in structure view shows
2215 mappings between sequence and all chains in a PDB file
2218 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2219 dialogs format columns correctly, don't display array
2220 data, sort columns according to type
2223 <!-- JAL-1975 -->Export complete shown after destination
2224 file chooser is cancelled during an image export
2227 <!-- JAL-2025 -->Error when querying PDB Service with
2228 sequence name containing special characters
2231 <!-- JAL-2024 -->Manual PDB structure querying should be
2235 <!-- JAL-2104 -->Large tooltips with broken HTML
2236 formatting don't wrap
2239 <!-- JAL-1128 -->Figures exported from wrapped view are
2240 truncated so L looks like I in consensus annotation
2243 <!-- JAL-2003 -->Export features should only export the
2244 currently displayed features for the current selection or
2248 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2249 after fetching cross-references, and restoring from
2253 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2254 followed in the structure viewer
2257 <!-- JAL-2163 -->Titles for individual alignments in
2258 splitframe not restored from project
2261 <!-- JAL-2145 -->missing autocalculated annotation at
2262 trailing end of protein alignment in transcript/product
2263 splitview when pad-gaps not enabled by default
2266 <!-- JAL-1797 -->amino acid physicochemical conservation
2270 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2271 article has been read (reopened issue due to
2272 internationalisation problems)
2275 <!-- JAL-1960 -->Only offer PDB structures in structure
2276 viewer based on sequence name, PDB and UniProt
2281 <!-- JAL-1976 -->No progress bar shown during export of
2285 <!-- JAL-2213 -->Structures not always superimposed after
2286 multiple structures are shown for one or more sequences.
2289 <!-- JAL-1370 -->Reference sequence characters should not
2290 be replaced with '.' when 'Show unconserved' format option
2294 <!-- JAL-1823 -->Cannot specify chain code when entering
2295 specific PDB id for sequence
2298 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2299 'Export hidden sequences' is enabled, but 'export hidden
2300 columns' is disabled.
2303 <!--JAL-2026-->Best Quality option in structure chooser
2304 selects lowest rather than highest resolution structures
2308 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2309 to sequence mapping in 'View Mappings' report
2312 <!-- JAL-2284 -->Unable to read old Jalview projects that
2313 contain non-XML data added after Jalvew wrote project.
2316 <!-- JAL-2118 -->Newly created annotation row reorders
2317 after clicking on it to create new annotation for a
2321 <!-- JAL-1980 -->Null Pointer Exception raised when
2322 pressing Add on an orphaned cut'n'paste window.
2324 <!-- may exclude, this is an external service stability issue JAL-1941
2325 -- > RNA 3D structure not added via DSSR service</li> -->
2330 <!-- JAL-2151 -->Incorrect columns are selected when
2331 hidden columns present before start of sequence
2334 <!-- JAL-1986 -->Missing dependencies on applet pages
2338 <!-- JAL-1947 -->Overview pixel size changes when
2339 sequences are hidden in applet
2342 <!-- JAL-1996 -->Updated instructions for applet
2343 deployment on examples pages.
2350 <td width="60" nowrap>
2351 <div align="center">
2352 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2353 <em>16/10/2015</em></strong>
2356 <td><em>General</em>
2358 <li>Time stamps for signed Jalview application and applet
2363 <em>Application</em>
2365 <li>Duplicate group consensus and conservation rows
2366 shown when tree is partitioned</li>
2367 <li>Erratic behaviour when tree partitions made with
2368 multiple cDNA/Protein split views</li>
2374 <td width="60" nowrap>
2375 <div align="center">
2376 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2377 <em>8/10/2015</em></strong>
2380 <td><em>General</em>
2382 <li>Updated Spanish translations of localized text for
2384 </ul> <em>Application</em>
2386 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2387 <li>Signed OSX InstallAnywhere installer<br></li>
2388 <li>Support for per-sequence based annotations in BioJSON</li>
2389 </ul> <em>Applet</em>
2391 <li>Split frame example added to applet examples page</li>
2392 </ul> <em>Build and Deployment</em>
2395 <!-- JAL-1888 -->New ant target for running Jalview's test
2403 <li>Mapping of cDNA to protein in split frames
2404 incorrect when sequence start > 1</li>
2405 <li>Broken images in filter column by annotation dialog
2407 <li>Feature colours not parsed from features file</li>
2408 <li>Exceptions and incomplete link URLs recovered when
2409 loading a features file containing HTML tags in feature
2413 <em>Application</em>
2415 <li>Annotations corrupted after BioJS export and
2417 <li>Incorrect sequence limits after Fetch DB References
2418 with 'trim retrieved sequences'</li>
2419 <li>Incorrect warning about deleting all data when
2420 deleting selected columns</li>
2421 <li>Patch to build system for shipping properly signed
2422 JNLP templates for webstart launch</li>
2423 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2424 unreleased structures for download or viewing</li>
2425 <li>Tab/space/return keystroke operation of EMBL-PDBe
2426 fetcher/viewer dialogs works correctly</li>
2427 <li>Disabled 'minimise' button on Jalview windows
2428 running on OSX to workaround redraw hang bug</li>
2429 <li>Split cDNA/Protein view position and geometry not
2430 recovered from jalview project</li>
2431 <li>Initial enabled/disabled state of annotation menu
2432 sorter 'show autocalculated first/last' corresponds to
2434 <li>Restoring of Clustal, RNA Helices and T-Coffee
2435 color schemes from BioJSON</li>
2439 <li>Reorder sequences mirrored in cDNA/Protein split
2441 <li>Applet with Jmol examples not loading correctly</li>
2447 <td><div align="center">
2448 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2450 <td><em>General</em>
2452 <li>Linked visualisation and analysis of DNA and Protein
2455 <li>Translated cDNA alignments shown as split protein
2456 and DNA alignment views</li>
2457 <li>Codon consensus annotation for linked protein and
2458 cDNA alignment views</li>
2459 <li>Link cDNA or Protein product sequences by loading
2460 them onto Protein or cDNA alignments</li>
2461 <li>Reconstruct linked cDNA alignment from aligned
2462 protein sequences</li>
2465 <li>Jmol integration updated to Jmol v14.2.14</li>
2466 <li>Import and export of Jalview alignment views as <a
2467 href="features/bioJsonFormat.html">BioJSON</a></li>
2468 <li>New alignment annotation file statements for
2469 reference sequences and marking hidden columns</li>
2470 <li>Reference sequence based alignment shading to
2471 highlight variation</li>
2472 <li>Select or hide columns according to alignment
2474 <li>Find option for locating sequences by description</li>
2475 <li>Conserved physicochemical properties shown in amino
2476 acid conservation row</li>
2477 <li>Alignments can be sorted by number of RNA helices</li>
2478 </ul> <em>Application</em>
2480 <li>New cDNA/Protein analysis capabilities
2482 <li>Get Cross-References should open a Split Frame
2483 view with cDNA/Protein</li>
2484 <li>Detect when nucleotide sequences and protein
2485 sequences are placed in the same alignment</li>
2486 <li>Split cDNA/Protein views are saved in Jalview
2491 <li>Use REST API to talk to Chimera</li>
2492 <li>Selected regions in Chimera are highlighted in linked
2493 Jalview windows</li>
2495 <li>VARNA RNA viewer updated to v3.93</li>
2496 <li>VARNA views are saved in Jalview Projects</li>
2497 <li>Pseudoknots displayed as Jalview RNA annotation can
2498 be shown in VARNA</li>
2500 <li>Make groups for selection uses marked columns as well
2501 as the active selected region</li>
2503 <li>Calculate UPGMA and NJ trees using sequence feature
2505 <li>New Export options
2507 <li>New Export Settings dialog to control hidden
2508 region export in flat file generation</li>
2510 <li>Export alignment views for display with the <a
2511 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2513 <li>Export scrollable SVG in HTML page</li>
2514 <li>Optional embedding of BioJSON data when exporting
2515 alignment figures to HTML</li>
2517 <li>3D structure retrieval and display
2519 <li>Free text and structured queries with the PDBe
2521 <li>PDBe Search API based discovery and selection of
2522 PDB structures for a sequence set</li>
2526 <li>JPred4 employed for protein secondary structure
2528 <li>Hide Insertions menu option to hide unaligned columns
2529 for one or a group of sequences</li>
2530 <li>Automatically hide insertions in alignments imported
2531 from the JPred4 web server</li>
2532 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2533 system on OSX<br />LGPL libraries courtesy of <a
2534 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2536 <li>changed 'View nucleotide structure' submenu to 'View
2537 VARNA 2D Structure'</li>
2538 <li>change "View protein structure" menu option to "3D
2541 </ul> <em>Applet</em>
2543 <li>New layout for applet example pages</li>
2544 <li>New parameters to enable SplitFrame view
2545 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2546 <li>New example demonstrating linked viewing of cDNA and
2547 Protein alignments</li>
2548 </ul> <em>Development and deployment</em>
2550 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2551 <li>Include installation type and git revision in build
2552 properties and console log output</li>
2553 <li>Jalview Github organisation, and new github site for
2554 storing BioJsMSA Templates</li>
2555 <li>Jalview's unit tests now managed with TestNG</li>
2558 <!-- <em>General</em>
2560 </ul> --> <!-- issues resolved --> <em>Application</em>
2562 <li>Escape should close any open find dialogs</li>
2563 <li>Typo in select-by-features status report</li>
2564 <li>Consensus RNA secondary secondary structure
2565 predictions are not highlighted in amber</li>
2566 <li>Missing gap character in v2.7 example file means
2567 alignment appears unaligned when pad-gaps is not enabled</li>
2568 <li>First switch to RNA Helices colouring doesn't colour
2569 associated structure views</li>
2570 <li>ID width preference option is greyed out when auto
2571 width checkbox not enabled</li>
2572 <li>Stopped a warning dialog from being shown when
2573 creating user defined colours</li>
2574 <li>'View Mapping' in structure viewer shows sequence
2575 mappings for just that viewer's sequences</li>
2576 <li>Workaround for superposing PDB files containing
2577 multiple models in Chimera</li>
2578 <li>Report sequence position in status bar when hovering
2579 over Jmol structure</li>
2580 <li>Cannot output gaps as '.' symbols with Selection ->
2581 output to text box</li>
2582 <li>Flat file exports of alignments with hidden columns
2583 have incorrect sequence start/end</li>
2584 <li>'Aligning' a second chain to a Chimera structure from
2586 <li>Colour schemes applied to structure viewers don't
2587 work for nucleotide</li>
2588 <li>Loading/cut'n'pasting an empty or invalid file leads
2589 to a grey/invisible alignment window</li>
2590 <li>Exported Jpred annotation from a sequence region
2591 imports to different position</li>
2592 <li>Space at beginning of sequence feature tooltips shown
2593 on some platforms</li>
2594 <li>Chimera viewer 'View | Show Chain' menu is not
2596 <li>'New View' fails with a Null Pointer Exception in
2597 console if Chimera has been opened</li>
2598 <li>Mouseover to Chimera not working</li>
2599 <li>Miscellaneous ENA XML feature qualifiers not
2601 <li>NPE in annotation renderer after 'Extract Scores'</li>
2602 <li>If two structures in one Chimera window, mouseover of
2603 either sequence shows on first structure</li>
2604 <li>'Show annotations' options should not make
2605 non-positional annotations visible</li>
2606 <li>Subsequence secondary structure annotation not shown
2607 in right place after 'view flanking regions'</li>
2608 <li>File Save As type unset when current file format is
2610 <li>Save as '.jar' option removed for saving Jalview
2612 <li>Colour by Sequence colouring in Chimera more
2614 <li>Cannot 'add reference annotation' for a sequence in
2615 several views on same alignment</li>
2616 <li>Cannot show linked products for EMBL / ENA records</li>
2617 <li>Jalview's tooltip wraps long texts containing no
2619 </ul> <em>Applet</em>
2621 <li>Jmol to JalviewLite mouseover/link not working</li>
2622 <li>JalviewLite can't import sequences with ID
2623 descriptions containing angle brackets</li>
2624 </ul> <em>General</em>
2626 <li>Cannot export and reimport RNA secondary structure
2627 via jalview annotation file</li>
2628 <li>Random helix colour palette for colour by annotation
2629 with RNA secondary structure</li>
2630 <li>Mouseover to cDNA from STOP residue in protein
2631 translation doesn't work.</li>
2632 <li>hints when using the select by annotation dialog box</li>
2633 <li>Jmol alignment incorrect if PDB file has alternate CA
2635 <li>FontChooser message dialog appears to hang after
2636 choosing 1pt font</li>
2637 <li>Peptide secondary structure incorrectly imported from
2638 annotation file when annotation display text includes 'e' or
2640 <li>Cannot set colour of new feature type whilst creating
2642 <li>cDNA translation alignment should not be sequence
2643 order dependent</li>
2644 <li>'Show unconserved' doesn't work for lower case
2646 <li>Nucleotide ambiguity codes involving R not recognised</li>
2647 </ul> <em>Deployment and Documentation</em>
2649 <li>Applet example pages appear different to the rest of
2650 www.jalview.org</li>
2651 </ul> <em>Application Known issues</em>
2653 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2654 <li>Misleading message appears after trying to delete
2656 <li>Jalview icon not shown in dock after InstallAnywhere
2657 version launches</li>
2658 <li>Fetching EMBL reference for an RNA sequence results
2659 fails with a sequence mismatch</li>
2660 <li>Corrupted or unreadable alignment display when
2661 scrolling alignment to right</li>
2662 <li>ArrayIndexOutOfBoundsException thrown when remove
2663 empty columns called on alignment with ragged gapped ends</li>
2664 <li>auto calculated alignment annotation rows do not get
2665 placed above or below non-autocalculated rows</li>
2666 <li>Jalview dekstop becomes sluggish at full screen in
2667 ultra-high resolution</li>
2668 <li>Cannot disable consensus calculation independently of
2669 quality and conservation</li>
2670 <li>Mouseover highlighting between cDNA and protein can
2671 become sluggish with more than one splitframe shown</li>
2672 </ul> <em>Applet Known Issues</em>
2674 <li>Core PDB parsing code requires Jmol</li>
2675 <li>Sequence canvas panel goes white when alignment
2676 window is being resized</li>
2682 <td><div align="center">
2683 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2685 <td><em>General</em>
2687 <li>Updated Java code signing certificate donated by
2689 <li>Features and annotation preserved when performing
2690 pairwise alignment</li>
2691 <li>RNA pseudoknot annotation can be
2692 imported/exported/displayed</li>
2693 <li>'colour by annotation' can colour by RNA and
2694 protein secondary structure</li>
2695 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2696 post-hoc with 2.9 release</em>)
2699 </ul> <em>Application</em>
2701 <li>Extract and display secondary structure for sequences
2702 with 3D structures</li>
2703 <li>Support for parsing RNAML</li>
2704 <li>Annotations menu for layout
2706 <li>sort sequence annotation rows by alignment</li>
2707 <li>place sequence annotation above/below alignment
2710 <li>Output in Stockholm format</li>
2711 <li>Internationalisation: improved Spanish (es)
2713 <li>Structure viewer preferences tab</li>
2714 <li>Disorder and Secondary Structure annotation tracks
2715 shared between alignments</li>
2716 <li>UCSF Chimera launch and linked highlighting from
2718 <li>Show/hide all sequence associated annotation rows for
2719 all or current selection</li>
2720 <li>disorder and secondary structure predictions
2721 available as dataset annotation</li>
2722 <li>Per-sequence rna helices colouring</li>
2725 <li>Sequence database accessions imported when fetching
2726 alignments from Rfam</li>
2727 <li>update VARNA version to 3.91</li>
2729 <li>New groovy scripts for exporting aligned positions,
2730 conservation values, and calculating sum of pairs scores.</li>
2731 <li>Command line argument to set default JABAWS server</li>
2732 <li>include installation type in build properties and
2733 console log output</li>
2734 <li>Updated Jalview project format to preserve dataset
2738 <!-- issues resolved --> <em>Application</em>
2740 <li>Distinguish alignment and sequence associated RNA
2741 structure in structure->view->VARNA</li>
2742 <li>Raise dialog box if user deletes all sequences in an
2744 <li>Pressing F1 results in documentation opening twice</li>
2745 <li>Sequence feature tooltip is wrapped</li>
2746 <li>Double click on sequence associated annotation
2747 selects only first column</li>
2748 <li>Redundancy removal doesn't result in unlinked
2749 leaves shown in tree</li>
2750 <li>Undos after several redundancy removals don't undo
2752 <li>Hide sequence doesn't hide associated annotation</li>
2753 <li>User defined colours dialog box too big to fit on
2754 screen and buttons not visible</li>
2755 <li>author list isn't updated if already written to
2756 Jalview properties</li>
2757 <li>Popup menu won't open after retrieving sequence
2759 <li>File open window for associate PDB doesn't open</li>
2760 <li>Left-then-right click on a sequence id opens a
2761 browser search window</li>
2762 <li>Cannot open sequence feature shading/sort popup menu
2763 in feature settings dialog</li>
2764 <li>better tooltip placement for some areas of Jalview
2766 <li>Allow addition of JABAWS Server which doesn't
2767 pass validation</li>
2768 <li>Web services parameters dialog box is too large to
2770 <li>Muscle nucleotide alignment preset obscured by
2772 <li>JABAWS preset submenus don't contain newly
2773 defined user preset</li>
2774 <li>MSA web services warns user if they were launched
2775 with invalid input</li>
2776 <li>Jalview cannot contact DAS Registy when running on
2779 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2780 'Superpose with' submenu not shown when new view
2784 </ul> <!-- <em>Applet</em>
2786 </ul> <em>General</em>
2788 </ul>--> <em>Deployment and Documentation</em>
2790 <li>2G and 1G options in launchApp have no effect on
2791 memory allocation</li>
2792 <li>launchApp service doesn't automatically open
2793 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2795 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2796 InstallAnywhere reports cannot find valid JVM when Java
2797 1.7_055 is available
2799 </ul> <em>Application Known issues</em>
2802 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2803 corrupted or unreadable alignment display when scrolling
2807 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2808 retrieval fails but progress bar continues for DAS retrieval
2809 with large number of ID
2812 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2813 flatfile output of visible region has incorrect sequence
2817 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2818 rna structure consensus doesn't update when secondary
2819 structure tracks are rearranged
2822 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2823 invalid rna structure positional highlighting does not
2824 highlight position of invalid base pairs
2827 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2828 out of memory errors are not raised when saving Jalview
2829 project from alignment window file menu
2832 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2833 Switching to RNA Helices colouring doesn't propagate to
2837 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2838 colour by RNA Helices not enabled when user created
2839 annotation added to alignment
2842 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2843 Jalview icon not shown on dock in Mountain Lion/Webstart
2845 </ul> <em>Applet Known Issues</em>
2848 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2849 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2852 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2853 Jalview and Jmol example not compatible with IE9
2856 <li>Sort by annotation score doesn't reverse order
2862 <td><div align="center">
2863 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2866 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2869 <li>Internationalisation of user interface (usually
2870 called i18n support) and translation for Spanish locale</li>
2871 <li>Define/Undefine group on current selection with
2872 Ctrl-G/Shift Ctrl-G</li>
2873 <li>Improved group creation/removal options in
2874 alignment/sequence Popup menu</li>
2875 <li>Sensible precision for symbol distribution
2876 percentages shown in logo tooltip.</li>
2877 <li>Annotation panel height set according to amount of
2878 annotation when alignment first opened</li>
2879 </ul> <em>Application</em>
2881 <li>Interactive consensus RNA secondary structure
2882 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2883 <li>Select columns containing particular features from
2884 Feature Settings dialog</li>
2885 <li>View all 'representative' PDB structures for selected
2887 <li>Update Jalview project format:
2889 <li>New file extension for Jalview projects '.jvp'</li>
2890 <li>Preserve sequence and annotation dataset (to
2891 store secondary structure annotation,etc)</li>
2892 <li>Per group and alignment annotation and RNA helix
2896 <li>New similarity measures for PCA and Tree calculation
2898 <li>Experimental support for retrieval and viewing of
2899 flanking regions for an alignment</li>
2903 <!-- issues resolved --> <em>Application</em>
2905 <li>logo keeps spinning and status remains at queued or
2906 running after job is cancelled</li>
2907 <li>cannot export features from alignments imported from
2908 Jalview/VAMSAS projects</li>
2909 <li>Buggy slider for web service parameters that take
2911 <li>Newly created RNA secondary structure line doesn't
2912 have 'display all symbols' flag set</li>
2913 <li>T-COFFEE alignment score shading scheme and other
2914 annotation shading not saved in Jalview project</li>
2915 <li>Local file cannot be loaded in freshly downloaded
2917 <li>Jalview icon not shown on dock in Mountain
2919 <li>Load file from desktop file browser fails</li>
2920 <li>Occasional NPE thrown when calculating large trees</li>
2921 <li>Cannot reorder or slide sequences after dragging an
2922 alignment onto desktop</li>
2923 <li>Colour by annotation dialog throws NPE after using
2924 'extract scores' function</li>
2925 <li>Loading/cut'n'pasting an empty file leads to a grey
2926 alignment window</li>
2927 <li>Disorder thresholds rendered incorrectly after
2928 performing IUPred disorder prediction</li>
2929 <li>Multiple group annotated consensus rows shown when
2930 changing 'normalise logo' display setting</li>
2931 <li>Find shows blank dialog after 'finished searching' if
2932 nothing matches query</li>
2933 <li>Null Pointer Exceptions raised when sorting by
2934 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2936 <li>Errors in Jmol console when structures in alignment
2937 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2939 <li>Not all working JABAWS services are shown in
2941 <li>JAVAWS version of Jalview fails to launch with
2942 'invalid literal/length code'</li>
2943 <li>Annotation/RNA Helix colourschemes cannot be applied
2944 to alignment with groups (actually fixed in 2.8.0b1)</li>
2945 <li>RNA Helices and T-Coffee Scores available as default
2948 </ul> <em>Applet</em>
2950 <li>Remove group option is shown even when selection is
2952 <li>Apply to all groups ticked but colourscheme changes
2953 don't affect groups</li>
2954 <li>Documented RNA Helices and T-Coffee Scores as valid
2955 colourscheme name</li>
2956 <li>Annotation labels drawn on sequence IDs when
2957 Annotation panel is not displayed</li>
2958 <li>Increased font size for dropdown menus on OSX and
2959 embedded windows</li>
2960 </ul> <em>Other</em>
2962 <li>Consensus sequence for alignments/groups with a
2963 single sequence were not calculated</li>
2964 <li>annotation files that contain only groups imported as
2965 annotation and junk sequences</li>
2966 <li>Fasta files with sequences containing '*' incorrectly
2967 recognised as PFAM or BLC</li>
2968 <li>conservation/PID slider apply all groups option
2969 doesn't affect background (2.8.0b1)
2971 <li>redundancy highlighting is erratic at 0% and 100%</li>
2972 <li>Remove gapped columns fails for sequences with ragged
2974 <li>AMSA annotation row with leading spaces is not
2975 registered correctly on import</li>
2976 <li>Jalview crashes when selecting PCA analysis for
2977 certain alignments</li>
2978 <li>Opening the colour by annotation dialog for an
2979 existing annotation based 'use original colours'
2980 colourscheme loses original colours setting</li>
2985 <td><div align="center">
2986 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2987 <em>30/1/2014</em></strong>
2991 <li>Trusted certificates for JalviewLite applet and
2992 Jalview Desktop application<br />Certificate was donated by
2993 <a href="https://www.certum.eu">Certum</a> to the Jalview
2994 open source project).
2996 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2997 <li>Output in Stockholm format</li>
2998 <li>Allow import of data from gzipped files</li>
2999 <li>Export/import group and sequence associated line
3000 graph thresholds</li>
3001 <li>Nucleotide substitution matrix that supports RNA and
3002 ambiguity codes</li>
3003 <li>Allow disorder predictions to be made on the current
3004 selection (or visible selection) in the same way that JPred
3006 <li>Groovy scripting for headless Jalview operation</li>
3007 </ul> <em>Other improvements</em>
3009 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3010 <li>COMBINE statement uses current SEQUENCE_REF and
3011 GROUP_REF scope to group annotation rows</li>
3012 <li>Support '' style escaping of quotes in Newick
3014 <li>Group options for JABAWS service by command line name</li>
3015 <li>Empty tooltip shown for JABA service options with a
3016 link but no description</li>
3017 <li>Select primary source when selecting authority in
3018 database fetcher GUI</li>
3019 <li>Add .mfa to FASTA file extensions recognised by
3021 <li>Annotation label tooltip text wrap</li>
3026 <li>Slow scrolling when lots of annotation rows are
3028 <li>Lots of NPE (and slowness) after creating RNA
3029 secondary structure annotation line</li>
3030 <li>Sequence database accessions not imported when
3031 fetching alignments from Rfam</li>
3032 <li>Incorrect SHMR submission for sequences with
3034 <li>View all structures does not always superpose
3036 <li>Option widgets in service parameters not updated to
3037 reflect user or preset settings</li>
3038 <li>Null pointer exceptions for some services without
3039 presets or adjustable parameters</li>
3040 <li>Discover PDB IDs entry in structure menu doesn't
3041 discover PDB xRefs</li>
3042 <li>Exception encountered while trying to retrieve
3043 features with DAS</li>
3044 <li>Lowest value in annotation row isn't coloured
3045 when colour by annotation (per sequence) is coloured</li>
3046 <li>Keyboard mode P jumps to start of gapped region when
3047 residue follows a gap</li>
3048 <li>Jalview appears to hang importing an alignment with
3049 Wrap as default or after enabling Wrap</li>
3050 <li>'Right click to add annotations' message
3051 shown in wrap mode when no annotations present</li>
3052 <li>Disorder predictions fail with NPE if no automatic
3053 annotation already exists on alignment</li>
3054 <li>oninit javascript function should be called after
3055 initialisation completes</li>
3056 <li>Remove redundancy after disorder prediction corrupts
3057 alignment window display</li>
3058 <li>Example annotation file in documentation is invalid</li>
3059 <li>Grouped line graph annotation rows are not exported
3060 to annotation file</li>
3061 <li>Multi-harmony analysis cannot be run when only two
3063 <li>Cannot create multiple groups of line graphs with
3064 several 'combine' statements in annotation file</li>
3065 <li>Pressing return several times causes Number Format
3066 exceptions in keyboard mode</li>
3067 <li>Multi-harmony (SHMMR) method doesn't submit
3068 correct partitions for input data</li>
3069 <li>Translation from DNA to Amino Acids fails</li>
3070 <li>Jalview fail to load newick tree with quoted label</li>
3071 <li>--headless flag isn't understood</li>
3072 <li>ClassCastException when generating EPS in headless
3074 <li>Adjusting sequence-associated shading threshold only
3075 changes one row's threshold</li>
3076 <li>Preferences and Feature settings panel panel
3077 doesn't open</li>
3078 <li>hide consensus histogram also hides conservation and
3079 quality histograms</li>
3084 <td><div align="center">
3085 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3087 <td><em>Application</em>
3089 <li>Support for JABAWS 2.0 Services (AACon alignment
3090 conservation, protein disorder and Clustal Omega)</li>
3091 <li>JABAWS server status indicator in Web Services
3093 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3094 in Jalview alignment window</li>
3095 <li>Updated Jalview build and deploy framework for OSX
3096 mountain lion, windows 7, and 8</li>
3097 <li>Nucleotide substitution matrix for PCA that supports
3098 RNA and ambiguity codes</li>
3100 <li>Improved sequence database retrieval GUI</li>
3101 <li>Support fetching and database reference look up
3102 against multiple DAS sources (Fetch all from in 'fetch db
3104 <li>Jalview project improvements
3106 <li>Store and retrieve the 'belowAlignment'
3107 flag for annotation</li>
3108 <li>calcId attribute to group annotation rows on the
3110 <li>Store AACon calculation settings for a view in
3111 Jalview project</li>
3115 <li>horizontal scrolling gesture support</li>
3116 <li>Visual progress indicator when PCA calculation is
3118 <li>Simpler JABA web services menus</li>
3119 <li>visual indication that web service results are still
3120 being retrieved from server</li>
3121 <li>Serialise the dialogs that are shown when Jalview
3122 starts up for first time</li>
3123 <li>Jalview user agent string for interacting with HTTP
3125 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3127 <li>Examples directory and Groovy library included in
3128 InstallAnywhere distribution</li>
3129 </ul> <em>Applet</em>
3131 <li>RNA alignment and secondary structure annotation
3132 visualization applet example</li>
3133 </ul> <em>General</em>
3135 <li>Normalise option for consensus sequence logo</li>
3136 <li>Reset button in PCA window to return dimensions to
3138 <li>Allow seqspace or Jalview variant of alignment PCA
3140 <li>PCA with either nucleic acid and protein substitution
3142 <li>Allow windows containing HTML reports to be exported
3144 <li>Interactive display and editing of RNA secondary
3145 structure contacts</li>
3146 <li>RNA Helix Alignment Colouring</li>
3147 <li>RNA base pair logo consensus</li>
3148 <li>Parse sequence associated secondary structure
3149 information in Stockholm files</li>
3150 <li>HTML Export database accessions and annotation
3151 information presented in tooltip for sequences</li>
3152 <li>Import secondary structure from LOCARNA clustalw
3153 style RNA alignment files</li>
3154 <li>import and visualise T-COFFEE quality scores for an
3156 <li>'colour by annotation' per sequence option to
3157 shade each sequence according to its associated alignment
3159 <li>New Jalview Logo</li>
3160 </ul> <em>Documentation and Development</em>
3162 <li>documentation for score matrices used in Jalview</li>
3163 <li>New Website!</li>
3165 <td><em>Application</em>
3167 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3168 wsdbfetch REST service</li>
3169 <li>Stop windows being moved outside desktop on OSX</li>
3170 <li>Filetype associations not installed for webstart
3172 <li>Jalview does not always retrieve progress of a JABAWS
3173 job execution in full once it is complete</li>
3174 <li>revise SHMR RSBS definition to ensure alignment is
3175 uploaded via ali_file parameter</li>
3176 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3177 <li>View all structures superposed fails with exception</li>
3178 <li>Jnet job queues forever if a very short sequence is
3179 submitted for prediction</li>
3180 <li>Cut and paste menu not opened when mouse clicked on
3182 <li>Putting fractional value into integer text box in
3183 alignment parameter dialog causes Jalview to hang</li>
3184 <li>Structure view highlighting doesn't work on
3186 <li>View all structures fails with exception shown in
3188 <li>Characters in filename associated with PDBEntry not
3189 escaped in a platform independent way</li>
3190 <li>Jalview desktop fails to launch with exception when
3192 <li>Tree calculation reports 'you must have 2 or more
3193 sequences selected' when selection is empty</li>
3194 <li>Jalview desktop fails to launch with jar signature
3195 failure when java web start temporary file caching is
3197 <li>DAS Sequence retrieval with range qualification
3198 results in sequence xref which includes range qualification</li>
3199 <li>Errors during processing of command line arguments
3200 cause progress bar (JAL-898) to be removed</li>
3201 <li>Replace comma for semi-colon option not disabled for
3202 DAS sources in sequence fetcher</li>
3203 <li>Cannot close news reader when JABAWS server warning
3204 dialog is shown</li>
3205 <li>Option widgets not updated to reflect user settings</li>
3206 <li>Edited sequence not submitted to web service</li>
3207 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3208 <li>InstallAnywhere installer doesn't unpack and run
3209 on OSX Mountain Lion</li>
3210 <li>Annotation panel not given a scroll bar when
3211 sequences with alignment annotation are pasted into the
3213 <li>Sequence associated annotation rows not associated
3214 when loaded from Jalview project</li>
3215 <li>Browser launch fails with NPE on java 1.7</li>
3216 <li>JABAWS alignment marked as finished when job was
3217 cancelled or job failed due to invalid input</li>
3218 <li>NPE with v2.7 example when clicking on Tree
3219 associated with all views</li>
3220 <li>Exceptions when copy/paste sequences with grouped
3221 annotation rows to new window</li>
3222 </ul> <em>Applet</em>
3224 <li>Sequence features are momentarily displayed before
3225 they are hidden using hidefeaturegroups applet parameter</li>
3226 <li>loading features via javascript API automatically
3227 enables feature display</li>
3228 <li>scrollToColumnIn javascript API method doesn't
3230 </ul> <em>General</em>
3232 <li>Redundancy removal fails for rna alignment</li>
3233 <li>PCA calculation fails when sequence has been selected
3234 and then deselected</li>
3235 <li>PCA window shows grey box when first opened on OSX</li>
3236 <li>Letters coloured pink in sequence logo when alignment
3237 coloured with clustalx</li>
3238 <li>Choosing fonts without letter symbols defined causes
3239 exceptions and redraw errors</li>
3240 <li>Initial PCA plot view is not same as manually
3241 reconfigured view</li>
3242 <li>Grouped annotation graph label has incorrect line
3244 <li>Grouped annotation graph label display is corrupted
3245 for lots of labels</li>
3250 <div align="center">
3251 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3254 <td><em>Application</em>
3256 <li>Jalview Desktop News Reader</li>
3257 <li>Tweaked default layout of web services menu</li>
3258 <li>View/alignment association menu to enable user to
3259 easily specify which alignment a multi-structure view takes
3260 its colours/correspondences from</li>
3261 <li>Allow properties file location to be specified as URL</li>
3262 <li>Extend Jalview project to preserve associations
3263 between many alignment views and a single Jmol display</li>
3264 <li>Store annotation row height in Jalview project file</li>
3265 <li>Annotation row column label formatting attributes
3266 stored in project file</li>
3267 <li>Annotation row order for auto-calculated annotation
3268 rows preserved in Jalview project file</li>
3269 <li>Visual progress indication when Jalview state is
3270 saved using Desktop window menu</li>
3271 <li>Visual indication that command line arguments are
3272 still being processed</li>
3273 <li>Groovy script execution from URL</li>
3274 <li>Colour by annotation default min and max colours in
3276 <li>Automatically associate PDB files dragged onto an
3277 alignment with sequences that have high similarity and
3279 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3280 <li>'view structures' option to open many
3281 structures in same window</li>
3282 <li>Sort associated views menu option for tree panel</li>
3283 <li>Group all JABA and non-JABA services for a particular
3284 analysis function in its own submenu</li>
3285 </ul> <em>Applet</em>
3287 <li>Userdefined and autogenerated annotation rows for
3289 <li>Adjustment of alignment annotation pane height</li>
3290 <li>Annotation scrollbar for annotation panel</li>
3291 <li>Drag to reorder annotation rows in annotation panel</li>
3292 <li>'automaticScrolling' parameter</li>
3293 <li>Allow sequences with partial ID string matches to be
3294 annotated from GFF/Jalview features files</li>
3295 <li>Sequence logo annotation row in applet</li>
3296 <li>Absolute paths relative to host server in applet
3297 parameters are treated as such</li>
3298 <li>New in the JalviewLite javascript API:
3300 <li>JalviewLite.js javascript library</li>
3301 <li>Javascript callbacks for
3303 <li>Applet initialisation</li>
3304 <li>Sequence/alignment mouse-overs and selections</li>
3307 <li>scrollTo row and column alignment scrolling
3309 <li>Select sequence/alignment regions from javascript</li>
3310 <li>javascript structure viewer harness to pass
3311 messages between Jmol and Jalview when running as
3312 distinct applets</li>
3313 <li>sortBy method</li>
3314 <li>Set of applet and application examples shipped
3315 with documentation</li>
3316 <li>New example to demonstrate JalviewLite and Jmol
3317 javascript message exchange</li>
3319 </ul> <em>General</em>
3321 <li>Enable Jmol displays to be associated with multiple
3322 multiple alignments</li>
3323 <li>Option to automatically sort alignment with new tree</li>
3324 <li>User configurable link to enable redirects to a
3325 www.Jalview.org mirror</li>
3326 <li>Jmol colours option for Jmol displays</li>
3327 <li>Configurable newline string when writing alignment
3328 and other flat files</li>
3329 <li>Allow alignment annotation description lines to
3330 contain html tags</li>
3331 </ul> <em>Documentation and Development</em>
3333 <li>Add groovy test harness for bulk load testing to
3335 <li>Groovy script to load and align a set of sequences
3336 using a web service before displaying the result in the
3337 Jalview desktop</li>
3338 <li>Restructured javascript and applet api documentation</li>
3339 <li>Ant target to publish example html files with applet
3341 <li>Netbeans project for building Jalview from source</li>
3342 <li>ant task to create online javadoc for Jalview source</li>
3344 <td><em>Application</em>
3346 <li>User defined colourscheme throws exception when
3347 current built in colourscheme is saved as new scheme</li>
3348 <li>AlignFrame->Save in application pops up save
3349 dialog for valid filename/format</li>
3350 <li>Cannot view associated structure for UniProt sequence</li>
3351 <li>PDB file association breaks for UniProt sequence
3353 <li>Associate PDB from file dialog does not tell you
3354 which sequence is to be associated with the file</li>
3355 <li>Find All raises null pointer exception when query
3356 only matches sequence IDs</li>
3357 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3358 <li>Jalview project with Jmol views created with Jalview
3359 2.4 cannot be loaded</li>
3360 <li>Filetype associations not installed for webstart
3362 <li>Two or more chains in a single PDB file associated
3363 with sequences in different alignments do not get coloured
3364 by their associated sequence</li>
3365 <li>Visibility status of autocalculated annotation row
3366 not preserved when project is loaded</li>
3367 <li>Annotation row height and visibility attributes not
3368 stored in Jalview project</li>
3369 <li>Tree bootstraps are not preserved when saved as a
3370 Jalview project</li>
3371 <li>Envision2 workflow tooltips are corrupted</li>
3372 <li>Enabling show group conservation also enables colour
3373 by conservation</li>
3374 <li>Duplicate group associated conservation or consensus
3375 created on new view</li>
3376 <li>Annotation scrollbar not displayed after 'show
3377 all hidden annotation rows' option selected</li>
3378 <li>Alignment quality not updated after alignment
3379 annotation row is hidden then shown</li>
3380 <li>Preserve colouring of structures coloured by
3381 sequences in pre Jalview 2.7 projects</li>
3382 <li>Web service job parameter dialog is not laid out
3384 <li>Web services menu not refreshed after 'reset
3385 services' button is pressed in preferences</li>
3386 <li>Annotation off by one in Jalview v2_3 example project</li>
3387 <li>Structures imported from file and saved in project
3388 get name like jalview_pdb1234.txt when reloaded</li>
3389 <li>Jalview does not always retrieve progress of a JABAWS
3390 job execution in full once it is complete</li>
3391 </ul> <em>Applet</em>
3393 <li>Alignment height set incorrectly when lots of
3394 annotation rows are displayed</li>
3395 <li>Relative URLs in feature HTML text not resolved to
3397 <li>View follows highlighting does not work for positions
3399 <li><= shown as = in tooltip</li>
3400 <li>Export features raises exception when no features
3402 <li>Separator string used for serialising lists of IDs
3403 for javascript api is modified when separator string
3404 provided as parameter</li>
3405 <li>Null pointer exception when selecting tree leaves for
3406 alignment with no existing selection</li>
3407 <li>Relative URLs for datasources assumed to be relative
3408 to applet's codebase</li>
3409 <li>Status bar not updated after finished searching and
3410 search wraps around to first result</li>
3411 <li>StructureSelectionManager instance shared between
3412 several Jalview applets causes race conditions and memory
3414 <li>Hover tooltip and mouseover of position on structure
3415 not sent from Jmol in applet</li>
3416 <li>Certain sequences of javascript method calls to
3417 applet API fatally hang browser</li>
3418 </ul> <em>General</em>
3420 <li>View follows structure mouseover scrolls beyond
3421 position with wrapped view and hidden regions</li>
3422 <li>Find sequence position moves to wrong residue
3423 with/without hidden columns</li>
3424 <li>Sequence length given in alignment properties window
3426 <li>InvalidNumberFormat exceptions thrown when trying to
3427 import PDB like structure files</li>
3428 <li>Positional search results are only highlighted
3429 between user-supplied sequence start/end bounds</li>
3430 <li>End attribute of sequence is not validated</li>
3431 <li>Find dialog only finds first sequence containing a
3432 given sequence position</li>
3433 <li>Sequence numbering not preserved in MSF alignment
3435 <li>Jalview PDB file reader does not extract sequence
3436 from nucleotide chains correctly</li>
3437 <li>Structure colours not updated when tree partition
3438 changed in alignment</li>
3439 <li>Sequence associated secondary structure not correctly
3440 parsed in interleaved stockholm</li>
3441 <li>Colour by annotation dialog does not restore current
3443 <li>Hiding (nearly) all sequences doesn't work
3445 <li>Sequences containing lowercase letters are not
3446 properly associated with their pdb files</li>
3447 </ul> <em>Documentation and Development</em>
3449 <li>schemas/JalviewWsParamSet.xsd corrupted by
3450 ApplyCopyright tool</li>
3455 <div align="center">
3456 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3459 <td><em>Application</em>
3461 <li>New warning dialog when the Jalview Desktop cannot
3462 contact web services</li>
3463 <li>JABA service parameters for a preset are shown in
3464 service job window</li>
3465 <li>JABA Service menu entries reworded</li>
3469 <li>Modeller PIR IO broken - cannot correctly import a
3470 pir file emitted by Jalview</li>
3471 <li>Existing feature settings transferred to new
3472 alignment view created from cut'n'paste</li>
3473 <li>Improved test for mixed amino/nucleotide chains when
3474 parsing PDB files</li>
3475 <li>Consensus and conservation annotation rows
3476 occasionally become blank for all new windows</li>
3477 <li>Exception raised when right clicking above sequences
3478 in wrapped view mode</li>
3479 </ul> <em>Application</em>
3481 <li>multiple multiply aligned structure views cause cpu
3482 usage to hit 100% and computer to hang</li>
3483 <li>Web Service parameter layout breaks for long user
3484 parameter names</li>
3485 <li>Jaba service discovery hangs desktop if Jaba server
3492 <div align="center">
3493 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3496 <td><em>Application</em>
3498 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3499 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3502 <li>Web Services preference tab</li>
3503 <li>Analysis parameters dialog box and user defined
3505 <li>Improved speed and layout of Envision2 service menu</li>
3506 <li>Superpose structures using associated sequence
3508 <li>Export coordinates and projection as CSV from PCA
3510 </ul> <em>Applet</em>
3512 <li>enable javascript: execution by the applet via the
3513 link out mechanism</li>
3514 </ul> <em>Other</em>
3516 <li>Updated the Jmol Jalview interface to work with Jmol
3518 <li>The Jalview Desktop and JalviewLite applet now
3519 require Java 1.5</li>
3520 <li>Allow Jalview feature colour specification for GFF
3521 sequence annotation files</li>
3522 <li>New 'colour by label' keword in Jalview feature file
3523 type colour specification</li>
3524 <li>New Jalview Desktop Groovy API method that allows a
3525 script to check if it being run in an interactive session or
3526 in a batch operation from the Jalview command line</li>
3530 <li>clustalx colourscheme colours Ds preferentially when
3531 both D+E are present in over 50% of the column</li>
3532 </ul> <em>Application</em>
3534 <li>typo in AlignmentFrame->View->Hide->all but
3535 selected Regions menu item</li>
3536 <li>sequence fetcher replaces ',' for ';' when the ',' is
3537 part of a valid accession ID</li>
3538 <li>fatal OOM if object retrieved by sequence fetcher
3539 runs out of memory</li>
3540 <li>unhandled Out of Memory Error when viewing pca
3541 analysis results</li>
3542 <li>InstallAnywhere builds fail to launch on OS X java
3543 10.5 update 4 (due to apple Java 1.6 update)</li>
3544 <li>Installanywhere Jalview silently fails to launch</li>
3545 </ul> <em>Applet</em>
3547 <li>Jalview.getFeatureGroups() raises an
3548 ArrayIndexOutOfBoundsException if no feature groups are
3555 <div align="center">
3556 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3562 <li>Alignment prettyprinter doesn't cope with long
3564 <li>clustalx colourscheme colours Ds preferentially when
3565 both D+E are present in over 50% of the column</li>
3566 <li>nucleic acid structures retrieved from PDB do not
3567 import correctly</li>
3568 <li>More columns get selected than were clicked on when a
3569 number of columns are hidden</li>
3570 <li>annotation label popup menu not providing correct
3571 add/hide/show options when rows are hidden or none are
3573 <li>Stockholm format shown in list of readable formats,
3574 and parser copes better with alignments from RFAM.</li>
3575 <li>CSV output of consensus only includes the percentage
3576 of all symbols if sequence logo display is enabled</li>
3578 </ul> <em>Applet</em>
3580 <li>annotation panel disappears when annotation is
3582 </ul> <em>Application</em>
3584 <li>Alignment view not redrawn properly when new
3585 alignment opened where annotation panel is visible but no
3586 annotations are present on alignment</li>
3587 <li>pasted region containing hidden columns is
3588 incorrectly displayed in new alignment window</li>
3589 <li>Jalview slow to complete operations when stdout is
3590 flooded (fix is to close the Jalview console)</li>
3591 <li>typo in AlignmentFrame->View->Hide->all but
3592 selected Rregions menu item.</li>
3593 <li>inconsistent group submenu and Format submenu entry
3594 'Un' or 'Non'conserved</li>
3595 <li>Sequence feature settings are being shared by
3596 multiple distinct alignments</li>
3597 <li>group annotation not recreated when tree partition is
3599 <li>double click on group annotation to select sequences
3600 does not propagate to associated trees</li>
3601 <li>Mac OSX specific issues:
3603 <li>exception raised when mouse clicked on desktop
3604 window background</li>
3605 <li>Desktop menu placed on menu bar and application
3606 name set correctly</li>
3607 <li>sequence feature settings not wide enough for the
3608 save feature colourscheme button</li>
3617 <div align="center">
3618 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3621 <td><em>New Capabilities</em>
3623 <li>URL links generated from description line for
3624 regular-expression based URL links (applet and application)
3626 <li>Non-positional feature URL links are shown in link
3628 <li>Linked viewing of nucleic acid sequences and
3630 <li>Automatic Scrolling option in View menu to display
3631 the currently highlighted region of an alignment.</li>
3632 <li>Order an alignment by sequence length, or using the
3633 average score or total feature count for each sequence.</li>
3634 <li>Shading features by score or associated description</li>
3635 <li>Subdivide alignment and groups based on identity of
3636 selected subsequence (Make Groups from Selection).</li>
3637 <li>New hide/show options including Shift+Control+H to
3638 hide everything but the currently selected region.</li>
3639 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3640 </ul> <em>Application</em>
3642 <li>Fetch DB References capabilities and UI expanded to
3643 support retrieval from DAS sequence sources</li>
3644 <li>Local DAS Sequence sources can be added via the
3645 command line or via the Add local source dialog box.</li>
3646 <li>DAS Dbref and DbxRef feature types are parsed as
3647 database references and protein_name is parsed as
3648 description line (BioSapiens terms).</li>
3649 <li>Enable or disable non-positional feature and database
3650 references in sequence ID tooltip from View menu in
3652 <!-- <li>New hidden columns and rows and representatives capabilities
3653 in annotations file (in progress - not yet fully implemented)</li> -->
3654 <li>Group-associated consensus, sequence logos and
3655 conservation plots</li>
3656 <li>Symbol distributions for each column can be exported
3657 and visualized as sequence logos</li>
3658 <li>Optionally scale multi-character column labels to fit
3659 within each column of annotation row<!-- todo for applet -->
3661 <li>Optional automatic sort of associated alignment view
3662 when a new tree is opened.</li>
3663 <li>Jalview Java Console</li>
3664 <li>Better placement of desktop window when moving
3665 between different screens.</li>
3666 <li>New preference items for sequence ID tooltip and
3667 consensus annotation</li>
3668 <li>Client to submit sequences and IDs to Envision2
3670 <li><em>Vamsas Capabilities</em>
3672 <li>Improved VAMSAS synchronization (Jalview archive
3673 used to preserve views, structures, and tree display
3675 <li>Import of vamsas documents from disk or URL via
3677 <li>Sharing of selected regions between views and
3678 with other VAMSAS applications (Experimental feature!)</li>
3679 <li>Updated API to VAMSAS version 0.2</li>
3681 </ul> <em>Applet</em>
3683 <li>Middle button resizes annotation row height</li>
3686 <li>sortByTree (true/false) - automatically sort the
3687 associated alignment view by the tree when a new tree is
3689 <li>showTreeBootstraps (true/false) - show or hide
3690 branch bootstraps (default is to show them if available)</li>
3691 <li>showTreeDistances (true/false) - show or hide
3692 branch lengths (default is to show them if available)</li>
3693 <li>showUnlinkedTreeNodes (true/false) - indicate if
3694 unassociated nodes should be highlighted in the tree
3696 <li>heightScale and widthScale (1.0 or more) -
3697 increase the height or width of a cell in the alignment
3698 grid relative to the current font size.</li>
3701 <li>Non-positional features displayed in sequence ID
3703 </ul> <em>Other</em>
3705 <li>Features format: graduated colour definitions and
3706 specification of feature scores</li>
3707 <li>Alignment Annotations format: new keywords for group
3708 associated annotation (GROUP_REF) and annotation row display
3709 properties (ROW_PROPERTIES)</li>
3710 <li>XML formats extended to support graduated feature
3711 colourschemes, group associated annotation, and profile
3712 visualization settings.</li></td>
3715 <li>Source field in GFF files parsed as feature source
3716 rather than description</li>
3717 <li>Non-positional features are now included in sequence
3718 feature and gff files (controlled via non-positional feature
3719 visibility in tooltip).</li>
3720 <li>URL links generated for all feature links (bugfix)</li>
3721 <li>Added URL embedding instructions to features file
3723 <li>Codons containing ambiguous nucleotides translated as
3724 'X' in peptide product</li>
3725 <li>Match case switch in find dialog box works for both
3726 sequence ID and sequence string and query strings do not
3727 have to be in upper case to match case-insensitively.</li>
3728 <li>AMSA files only contain first column of
3729 multi-character column annotation labels</li>
3730 <li>Jalview Annotation File generation/parsing consistent
3731 with documentation (e.g. Stockholm annotation can be
3732 exported and re-imported)</li>
3733 <li>PDB files without embedded PDB IDs given a friendly
3735 <li>Find incrementally searches ID string matches as well
3736 as subsequence matches, and correctly reports total number
3740 <li>Better handling of exceptions during sequence
3742 <li>Dasobert generated non-positional feature URL
3743 link text excludes the start_end suffix</li>
3744 <li>DAS feature and source retrieval buttons disabled
3745 when fetch or registry operations in progress.</li>
3746 <li>PDB files retrieved from URLs are cached properly</li>
3747 <li>Sequence description lines properly shared via
3749 <li>Sequence fetcher fetches multiple records for all
3751 <li>Ensured that command line das feature retrieval
3752 completes before alignment figures are generated.</li>
3753 <li>Reduced time taken when opening file browser for
3755 <li>isAligned check prior to calculating tree, PCA or
3756 submitting an MSA to JNet now excludes hidden sequences.</li>
3757 <li>User defined group colours properly recovered
3758 from Jalview projects.</li>
3767 <div align="center">
3768 <strong>2.4.0.b2</strong><br> 28/10/2009
3773 <li>Experimental support for google analytics usage
3775 <li>Jalview privacy settings (user preferences and docs).</li>
3780 <li>Race condition in applet preventing startup in
3782 <li>Exception when feature created from selection beyond
3783 length of sequence.</li>
3784 <li>Allow synthetic PDB files to be imported gracefully</li>
3785 <li>Sequence associated annotation rows associate with
3786 all sequences with a given id</li>
3787 <li>Find function matches case-insensitively for sequence
3788 ID string searches</li>
3789 <li>Non-standard characters do not cause pairwise
3790 alignment to fail with exception</li>
3791 </ul> <em>Application Issues</em>
3793 <li>Sequences are now validated against EMBL database</li>
3794 <li>Sequence fetcher fetches multiple records for all
3796 </ul> <em>InstallAnywhere Issues</em>
3798 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3799 issue with installAnywhere mechanism)</li>
3800 <li>Command line launching of JARs from InstallAnywhere
3801 version (java class versioning error fixed)</li>
3808 <div align="center">
3809 <strong>2.4</strong><br> 27/8/2008
3812 <td><em>User Interface</em>
3814 <li>Linked highlighting of codon and amino acid from
3815 translation and protein products</li>
3816 <li>Linked highlighting of structure associated with
3817 residue mapping to codon position</li>
3818 <li>Sequence Fetcher provides example accession numbers
3819 and 'clear' button</li>
3820 <li>MemoryMonitor added as an option under Desktop's
3822 <li>Extract score function to parse whitespace separated
3823 numeric data in description line</li>
3824 <li>Column labels in alignment annotation can be centred.</li>
3825 <li>Tooltip for sequence associated annotation give name
3827 </ul> <em>Web Services and URL fetching</em>
3829 <li>JPred3 web service</li>
3830 <li>Prototype sequence search client (no public services
3832 <li>Fetch either seed alignment or full alignment from
3834 <li>URL Links created for matching database cross
3835 references as well as sequence ID</li>
3836 <li>URL Links can be created using regular-expressions</li>
3837 </ul> <em>Sequence Database Connectivity</em>
3839 <li>Retrieval of cross-referenced sequences from other
3841 <li>Generalised database reference retrieval and
3842 validation to all fetchable databases</li>
3843 <li>Fetch sequences from DAS sources supporting the
3844 sequence command</li>
3845 </ul> <em>Import and Export</em>
3846 <li>export annotation rows as CSV for spreadsheet import</li>
3847 <li>Jalview projects record alignment dataset associations,
3848 EMBL products, and cDNA sequence mappings</li>
3849 <li>Sequence Group colour can be specified in Annotation
3851 <li>Ad-hoc colouring of group in Annotation File using RGB
3852 triplet as name of colourscheme</li>
3853 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3855 <li>treenode binding for VAMSAS tree exchange</li>
3856 <li>local editing and update of sequences in VAMSAS
3857 alignments (experimental)</li>
3858 <li>Create new or select existing session to join</li>
3859 <li>load and save of vamsas documents</li>
3860 </ul> <em>Application command line</em>
3862 <li>-tree parameter to open trees (introduced for passing
3864 <li>-fetchfrom command line argument to specify nicknames
3865 of DAS servers to query for alignment features</li>
3866 <li>-dasserver command line argument to add new servers
3867 that are also automatically queried for features</li>
3868 <li>-groovy command line argument executes a given groovy
3869 script after all input data has been loaded and parsed</li>
3870 </ul> <em>Applet-Application data exchange</em>
3872 <li>Trees passed as applet parameters can be passed to
3873 application (when using "View in full
3874 application")</li>
3875 </ul> <em>Applet Parameters</em>
3877 <li>feature group display control parameter</li>
3878 <li>debug parameter</li>
3879 <li>showbutton parameter</li>
3880 </ul> <em>Applet API methods</em>
3882 <li>newView public method</li>
3883 <li>Window (current view) specific get/set public methods</li>
3884 <li>Feature display control methods</li>
3885 <li>get list of currently selected sequences</li>
3886 </ul> <em>New Jalview distribution features</em>
3888 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3889 <li>RELEASE file gives build properties for the latest
3890 Jalview release.</li>
3891 <li>Java 1.1 Applet build made easier and donotobfuscate
3892 property controls execution of obfuscator</li>
3893 <li>Build target for generating source distribution</li>
3894 <li>Debug flag for javacc</li>
3895 <li>.jalview_properties file is documented (slightly) in
3896 jalview.bin.Cache</li>
3897 <li>Continuous Build Integration for stable and
3898 development version of Application, Applet and source
3903 <li>selected region output includes visible annotations
3904 (for certain formats)</li>
3905 <li>edit label/displaychar contains existing label/char
3907 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3908 <li>shorter peptide product names from EMBL records</li>
3909 <li>Newick string generator makes compact representations</li>
3910 <li>bootstrap values parsed correctly for tree files with
3912 <li>pathological filechooser bug avoided by not allowing
3913 filenames containing a ':'</li>
3914 <li>Fixed exception when parsing GFF files containing
3915 global sequence features</li>
3916 <li>Alignment datasets are finalized only when number of
3917 references from alignment sequences goes to zero</li>
3918 <li>Close of tree branch colour box without colour
3919 selection causes cascading exceptions</li>
3920 <li>occasional negative imgwidth exceptions</li>
3921 <li>better reporting of non-fatal warnings to user when
3922 file parsing fails.</li>
3923 <li>Save works when Jalview project is default format</li>
3924 <li>Save as dialog opened if current alignment format is
3925 not a valid output format</li>
3926 <li>UniProt canonical names introduced for both das and
3928 <li>Histidine should be midblue (not pink!) in Zappo</li>
3929 <li>error messages passed up and output when data read
3931 <li>edit undo recovers previous dataset sequence when
3932 sequence is edited</li>
3933 <li>allow PDB files without pdb ID HEADER lines (like
3934 those generated by MODELLER) to be read in properly</li>
3935 <li>allow reading of JPred concise files as a normal
3937 <li>Stockholm annotation parsing and alignment properties
3938 import fixed for PFAM records</li>
3939 <li>Structure view windows have correct name in Desktop
3941 <li>annotation consisting of sequence associated scores
3942 can be read and written correctly to annotation file</li>
3943 <li>Aligned cDNA translation to aligned peptide works
3945 <li>Fixed display of hidden sequence markers and
3946 non-italic font for representatives in Applet</li>
3947 <li>Applet Menus are always embedded in applet window on
3949 <li>Newly shown features appear at top of stack (in
3951 <li>Annotations added via parameter not drawn properly
3952 due to null pointer exceptions</li>
3953 <li>Secondary structure lines are drawn starting from
3954 first column of alignment</li>
3955 <li>UniProt XML import updated for new schema release in
3957 <li>Sequence feature to sequence ID match for Features
3958 file is case-insensitive</li>
3959 <li>Sequence features read from Features file appended to
3960 all sequences with matching IDs</li>
3961 <li>PDB structure coloured correctly for associated views
3962 containing a sub-sequence</li>
3963 <li>PDB files can be retrieved by applet from Jar files</li>
3964 <li>feature and annotation file applet parameters
3965 referring to different directories are retrieved correctly</li>
3966 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3967 <li>Fixed application hang whilst waiting for
3968 splash-screen version check to complete</li>
3969 <li>Applet properly URLencodes input parameter values
3970 when passing them to the launchApp service</li>
3971 <li>display name and local features preserved in results
3972 retrieved from web service</li>
3973 <li>Visual delay indication for sequence retrieval and
3974 sequence fetcher initialisation</li>
3975 <li>updated Application to use DAS 1.53e version of
3976 dasobert DAS client</li>
3977 <li>Re-instated Full AMSA support and .amsa file
3979 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3987 <div align="center">
3988 <strong>2.3</strong><br> 9/5/07
3993 <li>Jmol 11.0.2 integration</li>
3994 <li>PDB views stored in Jalview XML files</li>
3995 <li>Slide sequences</li>
3996 <li>Edit sequence in place</li>
3997 <li>EMBL CDS features</li>
3998 <li>DAS Feature mapping</li>
3999 <li>Feature ordering</li>
4000 <li>Alignment Properties</li>
4001 <li>Annotation Scores</li>
4002 <li>Sort by scores</li>
4003 <li>Feature/annotation editing in applet</li>
4008 <li>Headless state operation in 2.2.1</li>
4009 <li>Incorrect and unstable DNA pairwise alignment</li>
4010 <li>Cut and paste of sequences with annotation</li>
4011 <li>Feature group display state in XML</li>
4012 <li>Feature ordering in XML</li>
4013 <li>blc file iteration selection using filename # suffix</li>
4014 <li>Stockholm alignment properties</li>
4015 <li>Stockhom alignment secondary structure annotation</li>
4016 <li>2.2.1 applet had no feature transparency</li>
4017 <li>Number pad keys can be used in cursor mode</li>
4018 <li>Structure Viewer mirror image resolved</li>
4025 <div align="center">
4026 <strong>2.2.1</strong><br> 12/2/07
4031 <li>Non standard characters can be read and displayed
4032 <li>Annotations/Features can be imported/exported to the
4034 <li>Applet allows editing of sequence/annotation/group
4035 name & description
4036 <li>Preference setting to display sequence name in
4038 <li>Annotation file format extended to allow
4039 Sequence_groups to be defined
4040 <li>Default opening of alignment overview panel can be
4041 specified in preferences
4042 <li>PDB residue numbering annotation added to associated
4048 <li>Applet crash under certain Linux OS with Java 1.6
4050 <li>Annotation file export / import bugs fixed
4051 <li>PNG / EPS image output bugs fixed
4057 <div align="center">
4058 <strong>2.2</strong><br> 27/11/06
4063 <li>Multiple views on alignment
4064 <li>Sequence feature editing
4065 <li>"Reload" alignment
4066 <li>"Save" to current filename
4067 <li>Background dependent text colour
4068 <li>Right align sequence ids
4069 <li>User-defined lower case residue colours
4072 <li>Menu item accelerator keys
4073 <li>Control-V pastes to current alignment
4074 <li>Cancel button for DAS Feature Fetching
4075 <li>PCA and PDB Viewers zoom via mouse roller
4076 <li>User-defined sub-tree colours and sub-tree selection
4078 <li>'New Window' button on the 'Output to Text box'
4083 <li>New memory efficient Undo/Redo System
4084 <li>Optimised symbol lookups and conservation/consensus
4086 <li>Region Conservation/Consensus recalculated after
4088 <li>Fixed Remove Empty Columns Bug (empty columns at end
4090 <li>Slowed DAS Feature Fetching for increased robustness.
4092 <li>Made angle brackets in ASCII feature descriptions
4094 <li>Re-instated Zoom function for PCA
4095 <li>Sequence descriptions conserved in web service
4097 <li>UniProt ID discoverer uses any word separated by
4099 <li>WsDbFetch query/result association resolved
4100 <li>Tree leaf to sequence mapping improved
4101 <li>Smooth fonts switch moved to FontChooser dialog box.
4108 <div align="center">
4109 <strong>2.1.1</strong><br> 12/9/06
4114 <li>Copy consensus sequence to clipboard</li>
4119 <li>Image output - rightmost residues are rendered if
4120 sequence id panel has been resized</li>
4121 <li>Image output - all offscreen group boundaries are
4123 <li>Annotation files with sequence references - all
4124 elements in file are relative to sequence position</li>
4125 <li>Mac Applet users can use Alt key for group editing</li>
4131 <div align="center">
4132 <strong>2.1</strong><br> 22/8/06
4137 <li>MAFFT Multiple Alignment in default Web Service list</li>
4138 <li>DAS Feature fetching</li>
4139 <li>Hide sequences and columns</li>
4140 <li>Export Annotations and Features</li>
4141 <li>GFF file reading / writing</li>
4142 <li>Associate structures with sequences from local PDB
4144 <li>Add sequences to exisiting alignment</li>
4145 <li>Recently opened files / URL lists</li>
4146 <li>Applet can launch the full application</li>
4147 <li>Applet has transparency for features (Java 1.2
4149 <li>Applet has user defined colours parameter</li>
4150 <li>Applet can load sequences from parameter
4151 "sequence<em>x</em>"
4157 <li>Redundancy Panel reinstalled in the Applet</li>
4158 <li>Monospaced font - EPS / rescaling bug fixed</li>
4159 <li>Annotation files with sequence references bug fixed</li>
4165 <div align="center">
4166 <strong>2.08.1</strong><br> 2/5/06
4171 <li>Change case of selected region from Popup menu</li>
4172 <li>Choose to match case when searching</li>
4173 <li>Middle mouse button and mouse movement can compress /
4174 expand the visible width and height of the alignment</li>
4179 <li>Annotation Panel displays complete JNet results</li>
4185 <div align="center">
4186 <strong>2.08b</strong><br> 18/4/06
4192 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4193 <li>Righthand label on wrapped alignments shows correct
4200 <div align="center">
4201 <strong>2.08</strong><br> 10/4/06
4206 <li>Editing can be locked to the selection area</li>
4207 <li>Keyboard editing</li>
4208 <li>Create sequence features from searches</li>
4209 <li>Precalculated annotations can be loaded onto
4211 <li>Features file allows grouping of features</li>
4212 <li>Annotation Colouring scheme added</li>
4213 <li>Smooth fonts off by default - Faster rendering</li>
4214 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4219 <li>Drag & Drop fixed on Linux</li>
4220 <li>Jalview Archive file faster to load/save, sequence
4221 descriptions saved.</li>
4227 <div align="center">
4228 <strong>2.07</strong><br> 12/12/05
4233 <li>PDB Structure Viewer enhanced</li>
4234 <li>Sequence Feature retrieval and display enhanced</li>
4235 <li>Choose to output sequence start-end after sequence
4236 name for file output</li>
4237 <li>Sequence Fetcher WSDBFetch@EBI</li>
4238 <li>Applet can read feature files, PDB files and can be
4239 used for HTML form input</li>
4244 <li>HTML output writes groups and features</li>
4245 <li>Group editing is Control and mouse click</li>
4246 <li>File IO bugs</li>
4252 <div align="center">
4253 <strong>2.06</strong><br> 28/9/05
4258 <li>View annotations in wrapped mode</li>
4259 <li>More options for PCA viewer</li>
4264 <li>GUI bugs resolved</li>
4265 <li>Runs with -nodisplay from command line</li>
4271 <div align="center">
4272 <strong>2.05b</strong><br> 15/9/05
4277 <li>Choose EPS export as lineart or text</li>
4278 <li>Jar files are executable</li>
4279 <li>Can read in Uracil - maps to unknown residue</li>
4284 <li>Known OutOfMemory errors give warning message</li>
4285 <li>Overview window calculated more efficiently</li>
4286 <li>Several GUI bugs resolved</li>
4292 <div align="center">
4293 <strong>2.05</strong><br> 30/8/05
4298 <li>Edit and annotate in "Wrapped" view</li>
4303 <li>Several GUI bugs resolved</li>
4309 <div align="center">
4310 <strong>2.04</strong><br> 24/8/05
4315 <li>Hold down mouse wheel & scroll to change font
4321 <li>Improved JPred client reliability</li>
4322 <li>Improved loading of Jalview files</li>
4328 <div align="center">
4329 <strong>2.03</strong><br> 18/8/05
4334 <li>Set Proxy server name and port in preferences</li>
4335 <li>Multiple URL links from sequence ids</li>
4336 <li>User Defined Colours can have a scheme name and added
4338 <li>Choose to ignore gaps in consensus calculation</li>
4339 <li>Unix users can set default web browser</li>
4340 <li>Runs without GUI for batch processing</li>
4341 <li>Dynamically generated Web Service Menus</li>
4346 <li>InstallAnywhere download for Sparc Solaris</li>
4352 <div align="center">
4353 <strong>2.02</strong><br> 18/7/05
4359 <li>Copy & Paste order of sequences maintains
4360 alignment order.</li>
4366 <div align="center">
4367 <strong>2.01</strong><br> 12/7/05
4372 <li>Use delete key for deleting selection.</li>
4373 <li>Use Mouse wheel to scroll sequences.</li>
4374 <li>Help file updated to describe how to add alignment
4376 <li>Version and build date written to build properties
4378 <li>InstallAnywhere installation will check for updates
4379 at launch of Jalview.</li>
4384 <li>Delete gaps bug fixed.</li>
4385 <li>FileChooser sorts columns.</li>
4386 <li>Can remove groups one by one.</li>
4387 <li>Filechooser icons installed.</li>
4388 <li>Finder ignores return character when searching.
4389 Return key will initiate a search.<br>
4396 <div align="center">
4397 <strong>2.0</strong><br> 20/6/05
4402 <li>New codebase</li>