3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">2.11</a><br />
61 <em>14/05/2019 (final due date !)</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
68 <!-- JAL-3141 -->Optional automatic backups when saving
69 Jalview project or alignment files</li>
71 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
72 Viewer state is saved in Jalview Project<br />The 'Change
73 parameters' option has also been removed from the PCA viewer</li>
75 <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
77 <!-- JAL-2620 -->Alternative genetic code tables supported for
78 'Translate as cDNA'</li>
80 <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
82 <!-- JAL-3198 -->More efficient creation of selections and
83 multiple groups when working with large alignments</li>
85 <!-- JAL-3200 -->Speedier import of annotation rows when
86 parsing stockholm files</li>
88 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
90 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
91 shaded according to any associated attributes (e.g. variant
92 attributes from VCF file, or key-value pairs imported from
93 column 9 of GFF file)</li>
95 <!-- JAL-2897 -->Show synonymous codon variants on peptide sequences</li>
97 <!-- JAL-2792 -->Popup report of a selected sequence feature's details</li>
99 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
100 algorithm (Z-sort/transparency and filter aware)</li>
102 <!-- JAL-2527 -->Alignment Overview now by default shows
103 only visible region of alignment (this can be changed in
104 user preferences)</li>
106 <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
108 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
109 all sequences are hidden</li>
111 <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
112 region, and gap count when inserting or deleting gaps</li>
114 <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
116 <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
118 <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
120 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
122 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
124 <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
126 <!-- JAL-3203 -->Overview panel default changed to not show hidden regions</li>
128 <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
130 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
132 <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent
133 to a hidden column marker</li>
135 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
137 <!-- JAL-2965 -->PCA depth queuing with graduated colours</li>
139 <em>Deprecations</em>
142 <!-- JAL-3035 -->DAS sequence retrieval and annotation
143 capabilities removed from the Jalview Desktop
146 <em>Release Processes</em>
149 Atlassian Bamboo continuous integration server for
150 unattended Test Suite execution</li>
152 <!-- JAL-2864 -->Memory test suite to detect leaks in common
155 <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
156 implementation) used for Sequence Feature collections</li>
158 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
159 unmarshalling has been replaced by JAXB for Jalview projects
160 and XML based data retrieval clients</li>
163 <td align="left" valign="top">
166 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
168 <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
170 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
172 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
173 Jalview project involving multiple views</li>
175 <!-- JAL-3164 -->Overview for complementary view in a linked
176 CDS/Protein alignment is not updated when Hide Columns by
177 Annotation dialog hides columns</li>
179 <!-- JAL-3158 -->Selection highlighting in the complement of
180 a CDS/Protein alignment stops working after making a
181 selection in one view, then making another selection in the
184 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
186 <!-- JAL-3154 -->Table Columns could be re-ordered in
187 Feature Settings and Jalview Preferences panels</li>
189 <!-- JAL-2865 -->Jalview hangs when closing windows
190 or the overview updates with large alignments</li>
192 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
193 region if columns were selected by dragging right-to-left
194 and the mouse moved to the left of the first column</li>
196 <!-- JAL-2846 -->Error message for trying to load in invalid
197 URLs doesn't tell users the invalid URL</li>
199 <!-- JAL-3178 -->Nonpositional features lose feature group
200 on export as Jalview features file</li>
202 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
203 printed when columns are hidden</li>
205 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
207 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
208 dragging out of Scale or Annotation Panel</li>
210 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
212 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
214 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
216 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
218 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
220 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
222 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
223 opening an alignment</li>
225 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
227 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
228 different groups in the alignment are selected</li>
230 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
232 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
234 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
236 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
238 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
240 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
242 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
244 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
246 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
248 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
250 <!-- JAL-914 -->Help page can be opened twice</li>
255 <!-- JAL-2822 -->Start and End should be updated when
256 sequence data at beginning or end of alignment added/removed
257 via 'Edit' sequence</li>
259 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
260 sequence features correctly when start of sequence is
261 removed (Known defect since 2.10)</li>
263 <em>New Known Defects</em>
266 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
268 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
273 <td width="60" nowrap>
275 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
278 <td><div align="left">
282 <!-- JAL-3101 -->Default memory for Jalview webstart and
283 InstallAnywhere increased to 1G.
286 <!-- JAL-247 -->Hidden sequence markers and representative
287 sequence bolding included when exporting alignment as EPS,
288 SVG, PNG or HTML. <em>Display is configured via the
289 Format menu, or for command-line use via a jalview
290 properties file.</em>
293 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
294 API and sequence data now imported as JSON.
297 <!-- JAL-3065 -->Change in recommended way of starting
298 Jalview via a Java command line: add jars in lib directory
299 to CLASSPATH, rather than via the deprecated java.ext.dirs
306 <!-- JAL-3047 -->Support added to execute test suite
307 instrumented with <a href="http://openclover.org/">Open
312 <td><div align="left">
316 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
317 row shown in Feredoxin Structure alignment view of example
321 <!-- JAL-2854 -->Annotation obscures sequences if lots of
322 annotation displayed.
325 <!-- JAL-3107 -->Group conservation/consensus not shown
326 for newly created group when 'Apply to all groups'
330 <!-- JAL-3087 -->Corrupted display when switching to
331 wrapped mode when sequence panel's vertical scrollbar is
335 <!-- JAL-3003 -->Alignment is black in exported EPS file
336 when sequences are selected in exported view.</em>
339 <!-- JAL-3059 -->Groups with different coloured borders
340 aren't rendered with correct colour.
343 <!-- JAL-3092 -->Jalview could hang when importing certain
344 types of knotted RNA secondary structure.
347 <!-- JAL-3095 -->Sequence highlight and selection in
348 trimmed VARNA 2D structure is incorrect for sequences that
352 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
353 annotation when columns are inserted into an alignment,
354 and when exporting as Stockholm flatfile.
357 <!-- JAL-3053 -->Jalview annotation rows containing upper
358 and lower-case 'E' and 'H' do not automatically get
359 treated as RNA secondary structure.
362 <!-- JAL-3106 -->.jvp should be used as default extension
363 (not .jar) when saving a jalview project file.
366 <!-- JAL-3105 -->Mac Users: closing a window correctly
367 transfers focus to previous window on OSX
370 <em>Java 10 Issues Resolved</em>
373 <!-- JAL-2988 -->OSX - Can't save new files via the File
374 or export menus by typing in a name into the Save dialog
378 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
379 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
380 'look and feel' which has improved compatibility with the
381 latest version of OSX.
388 <td width="60" nowrap>
390 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
391 <em>7/06/2018</em></strong>
394 <td><div align="left">
398 <!-- JAL-2920 -->Use HGVS nomenclature for variant
399 annotation retrieved from Uniprot
402 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
403 onto the Jalview Desktop
407 <td><div align="left">
411 <!-- JAL-3017 -->Cannot import features with multiple
412 variant elements (blocks import of some Uniprot records)
415 <!-- JAL-2997 -->Clustal files with sequence positions in
416 right-hand column parsed correctly
419 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
420 not alignment area in exported graphic
423 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
424 window has input focus
427 <!-- JAL-2992 -->Annotation panel set too high when
428 annotation added to view (Windows)
431 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
432 network connectivity is poor
435 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
436 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
437 the currently open URL and links from a page viewed in
438 Firefox or Chrome on Windows is now fully supported. If
439 you are using Edge, only links in the page can be
440 dragged, and with Internet Explorer, only the currently
441 open URL in the browser can be dropped onto Jalview.</em>
447 <td width="60" nowrap>
449 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
452 <td><div align="left">
456 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
457 for disabling automatic superposition of multiple
458 structures and open structures in existing views
461 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
462 ID and annotation area margins can be click-dragged to
466 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
470 <!-- JAL-2759 -->Improved performance for large alignments
471 and lots of hidden columns
474 <!-- JAL-2593 -->Improved performance when rendering lots
475 of features (particularly when transparency is disabled)
480 <td><div align="left">
483 <!-- JAL-2899 -->Structure and Overview aren't updated
484 when Colour By Annotation threshold slider is adjusted
487 <!-- JAL-2778 -->Slow redraw when Overview panel shown
488 overlapping alignment panel
491 <!-- JAL-2929 -->Overview doesn't show end of unpadded
495 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
496 improved: CDS not handled correctly if transcript has no
500 <!-- JAL-2321 -->Secondary structure and temperature
501 factor annotation not added to sequence when local PDB
502 file associated with it by drag'n'drop or structure
506 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
507 dialog doesn't import PDB files dropped on an alignment
510 <!-- JAL-2666 -->Linked scrolling via protein horizontal
511 scroll bar doesn't work for some CDS/Protein views
514 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
515 Java 1.8u153 onwards and Java 1.9u4+.
518 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
519 columns in annotation row
522 <!-- JAL-2913 -->Preferences panel's ID Width control is not
523 honored in batch mode
526 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
527 for structures added to existing Jmol view
530 <!-- JAL-2223 -->'View Mappings' includes duplicate
531 entries after importing project with multiple views
534 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
535 protein sequences via SIFTS from associated PDB entries
536 with negative residue numbers or missing residues fails
539 <!-- JAL-2952 -->Exception when shading sequence with negative
540 Temperature Factor values from annotated PDB files (e.g.
541 as generated by CONSURF)
544 <!-- JAL-2920 -->Uniprot 'sequence variant' features
545 tooltip doesn't include a text description of mutation
548 <!-- JAL-2922 -->Invert displayed features very slow when
549 structure and/or overview windows are also shown
552 <!-- JAL-2954 -->Selecting columns from highlighted regions
553 very slow for alignments with large numbers of sequences
556 <!-- JAL-2925 -->Copy Consensus fails for group consensus
557 with 'StringIndexOutOfBounds'
560 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
561 platforms running Java 10
564 <!-- JAL-2960 -->Adding a structure to existing structure
565 view appears to do nothing because the view is hidden behind the alignment view
571 <!-- JAL-2926 -->Copy consensus sequence option in applet
572 should copy the group consensus when popup is opened on it
578 <!-- JAL-2913 -->Fixed ID width preference is not respected
581 <em>New Known Defects</em>
584 <!-- JAL-2973 --> Exceptions occasionally raised when
585 editing a large alignment and overview is displayed
588 <!-- JAL-2974 -->'Overview updating' progress bar is shown
589 repeatedly after a series of edits even when the overview
590 is no longer reflecting updates
593 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
594 structures for protein subsequence (if 'Trim Retrieved
595 Sequences' enabled) or Ensembl isoforms (Workaround in
596 2.10.4 is to fail back to N&W mapping)
603 <td width="60" nowrap>
605 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
608 <td><div align="left">
609 <ul><li>Updated Certum Codesigning Certificate
610 (Valid till 30th November 2018)</li></ul></div></td>
611 <td><div align="left">
614 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
615 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
616 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
617 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
618 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
619 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
620 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
626 <td width="60" nowrap>
628 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
631 <td><div align="left">
635 <!-- JAL-2446 -->Faster and more efficient management and
636 rendering of sequence features
639 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
640 429 rate limit request hander
643 <!-- JAL-2773 -->Structure views don't get updated unless
644 their colours have changed
647 <!-- JAL-2495 -->All linked sequences are highlighted for
648 a structure mousover (Jmol) or selection (Chimera)
651 <!-- JAL-2790 -->'Cancel' button in progress bar for
652 JABAWS AACon, RNAAliFold and Disorder prediction jobs
655 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
656 view from Ensembl locus cross-references
659 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
663 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
664 feature can be disabled
667 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
668 PDB easier retrieval of sequences for lists of IDs
671 <!-- JAL-2758 -->Short names for sequences retrieved from
677 <li>Groovy interpreter updated to 2.4.12</li>
678 <li>Example groovy script for generating a matrix of
679 percent identity scores for current alignment.</li>
681 <em>Testing and Deployment</em>
684 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
688 <td><div align="left">
692 <!-- JAL-2643 -->Pressing tab after updating the colour
693 threshold text field doesn't trigger an update to the
697 <!-- JAL-2682 -->Race condition when parsing sequence ID
701 <!-- JAL-2608 -->Overview windows are also closed when
702 alignment window is closed
705 <!-- JAL-2548 -->Export of features doesn't always respect
709 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
710 takes a long time in Cursor mode
716 <!-- JAL-2777 -->Structures with whitespace chainCode
717 cannot be viewed in Chimera
720 <!-- JAL-2728 -->Protein annotation panel too high in
724 <!-- JAL-2757 -->Can't edit the query after the server
725 error warning icon is shown in Uniprot and PDB Free Text
729 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
732 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
735 <!-- JAL-2739 -->Hidden column marker in last column not
736 rendered when switching back from Wrapped to normal view
739 <!-- JAL-2768 -->Annotation display corrupted when
740 scrolling right in unwapped alignment view
743 <!-- JAL-2542 -->Existing features on subsequence
744 incorrectly relocated when full sequence retrieved from
748 <!-- JAL-2733 -->Last reported memory still shown when
749 Desktop->Show Memory is unticked (OSX only)
752 <!-- JAL-2658 -->Amend Features dialog doesn't allow
753 features of same type and group to be selected for
757 <!-- JAL-2524 -->Jalview becomes sluggish in wide
758 alignments when hidden columns are present
761 <!-- JAL-2392 -->Jalview freezes when loading and
762 displaying several structures
765 <!-- JAL-2732 -->Black outlines left after resizing or
769 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
770 within the Jalview desktop on OSX
773 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
774 when in wrapped alignment mode
777 <!-- JAL-2636 -->Scale mark not shown when close to right
778 hand end of alignment
781 <!-- JAL-2684 -->Pairwise alignment of selected regions of
782 each selected sequence do not have correct start/end
786 <!-- JAL-2793 -->Alignment ruler height set incorrectly
787 after canceling the Alignment Window's Font dialog
790 <!-- JAL-2036 -->Show cross-references not enabled after
791 restoring project until a new view is created
794 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
795 URL links appears when only default EMBL-EBI link is
796 configured (since 2.10.2b2)
799 <!-- JAL-2775 -->Overview redraws whole window when box
803 <!-- JAL-2225 -->Structure viewer doesn't map all chains
804 in a multi-chain structure when viewing alignment
805 involving more than one chain (since 2.10)
808 <!-- JAL-2811 -->Double residue highlights in cursor mode
809 if new selection moves alignment window
812 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
813 arrow key in cursor mode to pass hidden column marker
816 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
817 that produces correctly annotated transcripts and products
820 <!-- JAL-2776 -->Toggling a feature group after first time
821 doesn't update associated structure view
824 <em>Applet</em><br />
827 <!-- JAL-2687 -->Concurrent modification exception when
828 closing alignment panel
831 <em>BioJSON</em><br />
834 <!-- JAL-2546 -->BioJSON export does not preserve
835 non-positional features
838 <em>New Known Issues</em>
841 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
842 sequence features correctly (for many previous versions of
846 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
847 using cursor in wrapped panel other than top
850 <!-- JAL-2791 -->Select columns containing feature ignores
851 graduated colour threshold
854 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
855 always preserve numbering and sequence features
858 <em>Known Java 9 Issues</em>
861 <!-- JAL-2902 -->Groovy Console very slow to open and is
862 not responsive when entering characters (Webstart, Java
869 <td width="60" nowrap>
871 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
872 <em>2/10/2017</em></strong>
875 <td><div align="left">
876 <em>New features in Jalview Desktop</em>
879 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
881 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
885 <td><div align="left">
889 <td width="60" nowrap>
891 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
892 <em>7/9/2017</em></strong>
895 <td><div align="left">
899 <!-- JAL-2588 -->Show gaps in overview window by colouring
900 in grey (sequences used to be coloured grey, and gaps were
904 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
908 <!-- JAL-2587 -->Overview updates immediately on increase
909 in size and progress bar shown as higher resolution
910 overview is recalculated
915 <td><div align="left">
919 <!-- JAL-2664 -->Overview window redraws every hidden
920 column region row by row
923 <!-- JAL-2681 -->duplicate protein sequences shown after
924 retrieving Ensembl crossrefs for sequences from Uniprot
927 <!-- JAL-2603 -->Overview window throws NPE if show boxes
928 format setting is unticked
931 <!-- JAL-2610 -->Groups are coloured wrongly in overview
932 if group has show boxes format setting unticked
935 <!-- JAL-2672,JAL-2665 -->Redraw problems when
936 autoscrolling whilst dragging current selection group to
937 include sequences and columns not currently displayed
940 <!-- JAL-2691 -->Not all chains are mapped when multimeric
941 assemblies are imported via CIF file
944 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
945 displayed when threshold or conservation colouring is also
949 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
953 <!-- JAL-2673 -->Jalview continues to scroll after
954 dragging a selected region off the visible region of the
958 <!-- JAL-2724 -->Cannot apply annotation based
959 colourscheme to all groups in a view
962 <!-- JAL-2511 -->IDs don't line up with sequences
963 initially after font size change using the Font chooser or
970 <td width="60" nowrap>
972 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
975 <td><div align="left">
976 <em>Calculations</em>
980 <!-- JAL-1933 -->Occupancy annotation row shows number of
981 ungapped positions in each column of the alignment.
984 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
985 a calculation dialog box
988 <!-- JAL-2379 -->Revised implementation of PCA for speed
989 and memory efficiency (~30x faster)
992 <!-- JAL-2403 -->Revised implementation of sequence
993 similarity scores as used by Tree, PCA, Shading Consensus
994 and other calculations
997 <!-- JAL-2416 -->Score matrices are stored as resource
998 files within the Jalview codebase
1001 <!-- JAL-2500 -->Trees computed on Sequence Feature
1002 Similarity may have different topology due to increased
1009 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1010 model for alignments and groups
1013 <!-- JAL-384 -->Custom shading schemes created via groovy
1020 <!-- JAL-2526 -->Efficiency improvements for interacting
1021 with alignment and overview windows
1024 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1028 <!-- JAL-2388 -->Hidden columns and sequences can be
1032 <!-- JAL-2611 -->Click-drag in visible area allows fine
1033 adjustment of visible position
1037 <em>Data import/export</em>
1040 <!-- JAL-2535 -->Posterior probability annotation from
1041 Stockholm files imported as sequence associated annotation
1044 <!-- JAL-2507 -->More robust per-sequence positional
1045 annotation input/output via stockholm flatfile
1048 <!-- JAL-2533 -->Sequence names don't include file
1049 extension when importing structure files without embedded
1050 names or PDB accessions
1053 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1054 format sequence substitution matrices
1057 <em>User Interface</em>
1060 <!-- JAL-2447 --> Experimental Features Checkbox in
1061 Desktop's Tools menu to hide or show untested features in
1065 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1066 via Overview or sequence motif search operations
1069 <!-- JAL-2547 -->Amend sequence features dialog box can be
1070 opened by double clicking gaps within sequence feature
1074 <!-- JAL-1476 -->Status bar message shown when not enough
1075 aligned positions were available to create a 3D structure
1079 <em>3D Structure</em>
1082 <!-- JAL-2430 -->Hidden regions in alignment views are not
1083 coloured in linked structure views
1086 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1087 file-based command exchange
1090 <!-- JAL-2375 -->Structure chooser automatically shows
1091 Cached Structures rather than querying the PDBe if
1092 structures are already available for sequences
1095 <!-- JAL-2520 -->Structures imported via URL are cached in
1096 the Jalview project rather than downloaded again when the
1097 project is reopened.
1100 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1101 to transfer Chimera's structure attributes as Jalview
1102 features, and vice-versa (<strong>Experimental
1106 <em>Web Services</em>
1109 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1112 <!-- JAL-2335 -->Filter non-standard amino acids and
1113 nucleotides when submitting to AACon and other MSA
1117 <!-- JAL-2316, -->URLs for viewing database
1118 cross-references provided by identifiers.org and the
1119 EMBL-EBI's MIRIAM DB
1126 <!-- JAL-2344 -->FileFormatI interface for describing and
1127 identifying file formats (instead of String constants)
1130 <!-- JAL-2228 -->FeatureCounter script refactored for
1131 efficiency when counting all displayed features (not
1132 backwards compatible with 2.10.1)
1135 <em>Example files</em>
1138 <!-- JAL-2631 -->Graduated feature colour style example
1139 included in the example feature file
1142 <em>Documentation</em>
1145 <!-- JAL-2339 -->Release notes reformatted for readability
1146 with the built-in Java help viewer
1149 <!-- JAL-1644 -->Find documentation updated with 'search
1150 sequence description' option
1156 <!-- JAL-2485, -->External service integration tests for
1157 Uniprot REST Free Text Search Client
1160 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1163 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1168 <td><div align="left">
1169 <em>Calculations</em>
1172 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1173 matrix - C->R should be '-3'<br />Old matrix restored
1174 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1176 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1177 Jalview's treatment of gaps in PCA and substitution matrix
1178 based Tree calculations.<br /> <br />In earlier versions
1179 of Jalview, gaps matching gaps were penalised, and gaps
1180 matching non-gaps penalised even more. In the PCA
1181 calculation, gaps were actually treated as non-gaps - so
1182 different costs were applied, which meant Jalview's PCAs
1183 were different to those produced by SeqSpace.<br />Jalview
1184 now treats gaps in the same way as SeqSpace (ie it scores
1185 them as 0). <br /> <br />Enter the following in the
1186 Groovy console to restore pre-2.10.2 behaviour:<br />
1187 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1188 // for 2.10.1 mode <br />
1189 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1190 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1191 these settings will affect all subsequent tree and PCA
1192 calculations (not recommended)</em></li>
1194 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1195 scaling of branch lengths for trees computed using
1196 Sequence Feature Similarity.
1199 <!-- JAL-2377 -->PCA calculation could hang when
1200 generating output report when working with highly
1201 redundant alignments
1204 <!-- JAL-2544 --> Sort by features includes features to
1205 right of selected region when gaps present on right-hand
1209 <em>User Interface</em>
1212 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1213 doesn't reselect a specific sequence's associated
1214 annotation after it was used for colouring a view
1217 <!-- JAL-2419 -->Current selection lost if popup menu
1218 opened on a region of alignment without groups
1221 <!-- JAL-2374 -->Popup menu not always shown for regions
1222 of an alignment with overlapping groups
1225 <!-- JAL-2310 -->Finder double counts if both a sequence's
1226 name and description match
1229 <!-- JAL-2370 -->Hiding column selection containing two
1230 hidden regions results in incorrect hidden regions
1233 <!-- JAL-2386 -->'Apply to all groups' setting when
1234 changing colour does not apply Conservation slider value
1238 <!-- JAL-2373 -->Percentage identity and conservation menu
1239 items do not show a tick or allow shading to be disabled
1242 <!-- JAL-2385 -->Conservation shading or PID threshold
1243 lost when base colourscheme changed if slider not visible
1246 <!-- JAL-2547 -->Sequence features shown in tooltip for
1247 gaps before start of features
1250 <!-- JAL-2623 -->Graduated feature colour threshold not
1251 restored to UI when feature colour is edited
1254 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1255 a time when scrolling vertically in wrapped mode.
1258 <!-- JAL-2630 -->Structure and alignment overview update
1259 as graduate feature colour settings are modified via the
1263 <!-- JAL-2034 -->Overview window doesn't always update
1264 when a group defined on the alignment is resized
1267 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1268 wrapped view result in positional status updates
1272 <!-- JAL-2563 -->Status bar doesn't show position for
1273 ambiguous amino acid and nucleotide symbols
1276 <!-- JAL-2602 -->Copy consensus sequence failed if
1277 alignment included gapped columns
1280 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1281 widgets don't permanently disappear
1284 <!-- JAL-2503 -->Cannot select or filter quantitative
1285 annotation that are shown only as column labels (e.g.
1286 T-Coffee column reliability scores)
1289 <!-- JAL-2594 -->Exception thrown if trying to create a
1290 sequence feature on gaps only
1293 <!-- JAL-2504 -->Features created with 'New feature'
1294 button from a Find inherit previously defined feature type
1295 rather than the Find query string
1298 <!-- JAL-2423 -->incorrect title in output window when
1299 exporting tree calculated in Jalview
1302 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1303 and then revealing them reorders sequences on the
1307 <!-- JAL-964 -->Group panel in sequence feature settings
1308 doesn't update to reflect available set of groups after
1309 interactively adding or modifying features
1312 <!-- JAL-2225 -->Sequence Database chooser unusable on
1316 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1317 only excluded gaps in current sequence and ignored
1324 <!-- JAL-2421 -->Overview window visible region moves
1325 erratically when hidden rows or columns are present
1328 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1329 Structure Viewer's colour menu don't correspond to
1333 <!-- JAL-2405 -->Protein specific colours only offered in
1334 colour and group colour menu for protein alignments
1337 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1338 reflect currently selected view or group's shading
1342 <!-- JAL-2624 -->Feature colour thresholds not respected
1343 when rendered on overview and structures when opacity at
1347 <!-- JAL-2589 -->User defined gap colour not shown in
1348 overview when features overlaid on alignment
1351 <em>Data import/export</em>
1354 <!-- JAL-2576 -->Very large alignments take a long time to
1358 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1359 added after a sequence was imported are not written to
1363 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1364 when importing RNA secondary structure via Stockholm
1367 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1368 not shown in correct direction for simple pseudoknots
1371 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1372 with lightGray or darkGray via features file (but can
1376 <!-- JAL-2383 -->Above PID colour threshold not recovered
1377 when alignment view imported from project
1380 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1381 structure and sequences extracted from structure files
1382 imported via URL and viewed in Jmol
1385 <!-- JAL-2520 -->Structures loaded via URL are saved in
1386 Jalview Projects rather than fetched via URL again when
1387 the project is loaded and the structure viewed
1390 <em>Web Services</em>
1393 <!-- JAL-2519 -->EnsemblGenomes example failing after
1394 release of Ensembl v.88
1397 <!-- JAL-2366 -->Proxy server address and port always
1398 appear enabled in Preferences->Connections
1401 <!-- JAL-2461 -->DAS registry not found exceptions
1402 removed from console output
1405 <!-- JAL-2582 -->Cannot retrieve protein products from
1406 Ensembl by Peptide ID
1409 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1410 created from SIFTs, and spurious 'Couldn't open structure
1411 in Chimera' errors raised after April 2017 update (problem
1412 due to 'null' string rather than empty string used for
1413 residues with no corresponding PDB mapping).
1416 <em>Application UI</em>
1419 <!-- JAL-2361 -->User Defined Colours not added to Colour
1423 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1424 case' residues (button in colourscheme editor debugged and
1425 new documentation and tooltips added)
1428 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1429 doesn't restore group-specific text colour thresholds
1432 <!-- JAL-2243 -->Feature settings panel does not update as
1433 new features are added to alignment
1436 <!-- JAL-2532 -->Cancel in feature settings reverts
1437 changes to feature colours via the Amend features dialog
1440 <!-- JAL-2506 -->Null pointer exception when attempting to
1441 edit graduated feature colour via amend features dialog
1445 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1446 selection menu changes colours of alignment views
1449 <!-- JAL-2426 -->Spurious exceptions in console raised
1450 from alignment calculation workers after alignment has
1454 <!-- JAL-1608 -->Typo in selection popup menu - Create
1455 groups now 'Create Group'
1458 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1459 Create/Undefine group doesn't always work
1462 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1463 shown again after pressing 'Cancel'
1466 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1467 adjusts start position in wrap mode
1470 <!-- JAL-2563 -->Status bar doesn't show positions for
1471 ambiguous amino acids
1474 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1475 CDS/Protein view after CDS sequences added for aligned
1479 <!-- JAL-2592 -->User defined colourschemes called 'User
1480 Defined' don't appear in Colours menu
1486 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1487 score models doesn't always result in an updated PCA plot
1490 <!-- JAL-2442 -->Features not rendered as transparent on
1491 overview or linked structure view
1494 <!-- JAL-2372 -->Colour group by conservation doesn't
1498 <!-- JAL-2517 -->Hitting Cancel after applying
1499 user-defined colourscheme doesn't restore original
1506 <!-- JAL-2314 -->Unit test failure:
1507 jalview.ws.jabaws.RNAStructExportImport setup fails
1510 <!-- JAL-2307 -->Unit test failure:
1511 jalview.ws.sifts.SiftsClientTest due to compatibility
1512 problems with deep array comparison equality asserts in
1513 successive versions of TestNG
1516 <!-- JAL-2479 -->Relocated StructureChooserTest and
1517 ParameterUtilsTest Unit tests to Network suite
1520 <em>New Known Issues</em>
1523 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1524 phase after a sequence motif find operation
1527 <!-- JAL-2550 -->Importing annotation file with rows
1528 containing just upper and lower case letters are
1529 interpreted as WUSS RNA secondary structure symbols
1532 <!-- JAL-2590 -->Cannot load and display Newick trees
1533 reliably from eggnog Ortholog database
1536 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1537 containing features of type Highlight' when 'B' is pressed
1538 to mark columns containing highlighted regions.
1541 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1542 doesn't always add secondary structure annotation.
1547 <td width="60" nowrap>
1548 <div align="center">
1549 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1552 <td><div align="left">
1556 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1557 for all consensus calculations
1560 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1563 <li>Updated Jalview's Certum code signing certificate
1566 <em>Application</em>
1569 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1570 set of database cross-references, sorted alphabetically
1573 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1574 from database cross references. Users with custom links
1575 will receive a <a href="webServices/urllinks.html#warning">warning
1576 dialog</a> asking them to update their preferences.
1579 <!-- JAL-2287-->Cancel button and escape listener on
1580 dialog warning user about disconnecting Jalview from a
1584 <!-- JAL-2320-->Jalview's Chimera control window closes if
1585 the Chimera it is connected to is shut down
1588 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1589 columns menu item to mark columns containing highlighted
1590 regions (e.g. from structure selections or results of a
1594 <!-- JAL-2284-->Command line option for batch-generation
1595 of HTML pages rendering alignment data with the BioJS
1605 <!-- JAL-2286 -->Columns with more than one modal residue
1606 are not coloured or thresholded according to percent
1607 identity (first observed in Jalview 2.8.2)
1610 <!-- JAL-2301 -->Threonine incorrectly reported as not
1614 <!-- JAL-2318 -->Updates to documentation pages (above PID
1615 threshold, amino acid properties)
1618 <!-- JAL-2292 -->Lower case residues in sequences are not
1619 reported as mapped to residues in a structure file in the
1623 <!--JAL-2324 -->Identical features with non-numeric scores
1624 could be added multiple times to a sequence
1627 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1628 bond features shown as two highlighted residues rather
1629 than a range in linked structure views, and treated
1630 correctly when selecting and computing trees from features
1633 <!-- JAL-2281-->Custom URL links for database
1634 cross-references are matched to database name regardless
1639 <em>Application</em>
1642 <!-- JAL-2282-->Custom URL links for specific database
1643 names without regular expressions also offer links from
1647 <!-- JAL-2315-->Removing a single configured link in the
1648 URL links pane in Connections preferences doesn't actually
1649 update Jalview configuration
1652 <!-- JAL-2272-->CTRL-Click on a selected region to open
1653 the alignment area popup menu doesn't work on El-Capitan
1656 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1657 files with similarly named sequences if dropped onto the
1661 <!-- JAL-2312 -->Additional mappings are shown for PDB
1662 entries where more chains exist in the PDB accession than
1663 are reported in the SIFTS file
1666 <!-- JAL-2317-->Certain structures do not get mapped to
1667 the structure view when displayed with Chimera
1670 <!-- JAL-2317-->No chains shown in the Chimera view
1671 panel's View->Show Chains submenu
1674 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1675 work for wrapped alignment views
1678 <!--JAL-2197 -->Rename UI components for running JPred
1679 predictions from 'JNet' to 'JPred'
1682 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1683 corrupted when annotation panel vertical scroll is not at
1684 first annotation row
1687 <!--JAL-2332 -->Attempting to view structure for Hen
1688 lysozyme results in a PDB Client error dialog box
1691 <!-- JAL-2319 -->Structure View's mapping report switched
1692 ranges for PDB and sequence for SIFTS
1695 SIFTS 'Not_Observed' residues mapped to non-existant
1699 <!-- <em>New Known Issues</em>
1706 <td width="60" nowrap>
1707 <div align="center">
1708 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1709 <em>25/10/2016</em></strong>
1712 <td><em>Application</em>
1714 <li>3D Structure chooser opens with 'Cached structures'
1715 view if structures already loaded</li>
1716 <li>Progress bar reports models as they are loaded to
1717 structure views</li>
1723 <li>Colour by conservation always enabled and no tick
1724 shown in menu when BLOSUM or PID shading applied</li>
1725 <li>FER1_ARATH and FER2_ARATH labels were switched in
1726 example sequences/projects/trees</li>
1728 <em>Application</em>
1730 <li>Jalview projects with views of local PDB structure
1731 files saved on Windows cannot be opened on OSX</li>
1732 <li>Multiple structure views can be opened and superposed
1733 without timeout for structures with multiple models or
1734 multiple sequences in alignment</li>
1735 <li>Cannot import or associated local PDB files without a
1736 PDB ID HEADER line</li>
1737 <li>RMSD is not output in Jmol console when superposition
1739 <li>Drag and drop of URL from Browser fails for Linux and
1740 OSX versions earlier than El Capitan</li>
1741 <li>ENA client ignores invalid content from ENA server</li>
1742 <li>Exceptions are not raised in console when ENA client
1743 attempts to fetch non-existent IDs via Fetch DB Refs UI
1745 <li>Exceptions are not raised in console when a new view
1746 is created on the alignment</li>
1747 <li>OSX right-click fixed for group selections: CMD-click
1748 to insert/remove gaps in groups and CTRL-click to open group
1751 <em>Build and deployment</em>
1753 <li>URL link checker now copes with multi-line anchor
1756 <em>New Known Issues</em>
1758 <li>Drag and drop from URL links in browsers do not work
1765 <td width="60" nowrap>
1766 <div align="center">
1767 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1770 <td><em>General</em>
1773 <!-- JAL-2124 -->Updated Spanish translations.
1776 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1777 for importing structure data to Jalview. Enables mmCIF and
1781 <!-- JAL-192 --->Alignment ruler shows positions relative to
1785 <!-- JAL-2202 -->Position/residue shown in status bar when
1786 mousing over sequence associated annotation
1789 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1793 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1794 '()', canonical '[]' and invalid '{}' base pair populations
1798 <!-- JAL-2092 -->Feature settings popup menu options for
1799 showing or hiding columns containing a feature
1802 <!-- JAL-1557 -->Edit selected group by double clicking on
1803 group and sequence associated annotation labels
1806 <!-- JAL-2236 -->Sequence name added to annotation label in
1807 select/hide columns by annotation and colour by annotation
1811 </ul> <em>Application</em>
1814 <!-- JAL-2050-->Automatically hide introns when opening a
1815 gene/transcript view
1818 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1822 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1823 structure mappings with the EMBL-EBI PDBe SIFTS database
1826 <!-- JAL-2079 -->Updated download sites used for Rfam and
1827 Pfam sources to xfam.org
1830 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1833 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1834 over sequences in Jalview
1837 <!-- JAL-2027-->Support for reverse-complement coding
1838 regions in ENA and EMBL
1841 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1842 for record retrieval via ENA rest API
1845 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1849 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1850 groovy script execution
1853 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1854 alignment window's Calculate menu
1857 <!-- JAL-1812 -->Allow groovy scripts that call
1858 Jalview.getAlignFrames() to run in headless mode
1861 <!-- JAL-2068 -->Support for creating new alignment
1862 calculation workers from groovy scripts
1865 <!-- JAL-1369 --->Store/restore reference sequence in
1869 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1870 associations are now saved/restored from project
1873 <!-- JAL-1993 -->Database selection dialog always shown
1874 before sequence fetcher is opened
1877 <!-- JAL-2183 -->Double click on an entry in Jalview's
1878 database chooser opens a sequence fetcher
1881 <!-- JAL-1563 -->Free-text search client for UniProt using
1882 the UniProt REST API
1885 <!-- JAL-2168 -->-nonews command line parameter to prevent
1886 the news reader opening
1889 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1890 querying stored in preferences
1893 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1897 <!-- JAL-1977-->Tooltips shown on database chooser
1900 <!-- JAL-391 -->Reverse complement function in calculate
1901 menu for nucleotide sequences
1904 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1905 and feature counts preserves alignment ordering (and
1906 debugged for complex feature sets).
1909 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1910 viewing structures with Jalview 2.10
1913 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1914 genome, transcript CCDS and gene ids via the Ensembl and
1915 Ensembl Genomes REST API
1918 <!-- JAL-2049 -->Protein sequence variant annotation
1919 computed for 'sequence_variant' annotation on CDS regions
1923 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1927 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1928 Ref Fetcher fails to match, or otherwise updates sequence
1929 data from external database records.
1932 <!-- JAL-2154 -->Revised Jalview Project format for
1933 efficient recovery of sequence coding and alignment
1934 annotation relationships.
1936 </ul> <!-- <em>Applet</em>
1947 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1951 <!-- JAL-2018-->Export features in Jalview format (again)
1952 includes graduated colourschemes
1955 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1956 working with big alignments and lots of hidden columns
1959 <!-- JAL-2053-->Hidden column markers not always rendered
1960 at right of alignment window
1963 <!-- JAL-2067 -->Tidied up links in help file table of
1967 <!-- JAL-2072 -->Feature based tree calculation not shown
1971 <!-- JAL-2075 -->Hidden columns ignored during feature
1972 based tree calculation
1975 <!-- JAL-2065 -->Alignment view stops updating when show
1976 unconserved enabled for group on alignment
1979 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1983 <!-- JAL-2146 -->Alignment column in status incorrectly
1984 shown as "Sequence position" when mousing over
1988 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1989 hidden columns present
1992 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1993 user created annotation added to alignment
1996 <!-- JAL-1841 -->RNA Structure consensus only computed for
1997 '()' base pair annotation
2000 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2001 in zero scores for all base pairs in RNA Structure
2005 <!-- JAL-2174-->Extend selection with columns containing
2009 <!-- JAL-2275 -->Pfam format writer puts extra space at
2010 beginning of sequence
2013 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2017 <!-- JAL-2238 -->Cannot create groups on an alignment from
2018 from a tree when t-coffee scores are shown
2021 <!-- JAL-1836,1967 -->Cannot import and view PDB
2022 structures with chains containing negative resnums (4q4h)
2025 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2029 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2030 to Clustal, PIR and PileUp output
2033 <!-- JAL-2008 -->Reordering sequence features that are
2034 not visible causes alignment window to repaint
2037 <!-- JAL-2006 -->Threshold sliders don't work in
2038 graduated colour and colour by annotation row for e-value
2039 scores associated with features and annotation rows
2042 <!-- JAL-1797 -->amino acid physicochemical conservation
2043 calculation should be case independent
2046 <!-- JAL-2173 -->Remove annotation also updates hidden
2050 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2051 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2052 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2055 <!-- JAL-2065 -->Null pointer exceptions and redraw
2056 problems when reference sequence defined and 'show
2057 non-conserved' enabled
2060 <!-- JAL-1306 -->Quality and Conservation are now shown on
2061 load even when Consensus calculation is disabled
2064 <!-- JAL-1932 -->Remove right on penultimate column of
2065 alignment does nothing
2068 <em>Application</em>
2071 <!-- JAL-1552-->URLs and links can't be imported by
2072 drag'n'drop on OSX when launched via webstart (note - not
2073 yet fixed for El Capitan)
2076 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2077 output when running on non-gb/us i18n platforms
2080 <!-- JAL-1944 -->Error thrown when exporting a view with
2081 hidden sequences as flat-file alignment
2084 <!-- JAL-2030-->InstallAnywhere distribution fails when
2088 <!-- JAL-2080-->Jalview very slow to launch via webstart
2089 (also hotfix for 2.9.0b2)
2092 <!-- JAL-2085 -->Cannot save project when view has a
2093 reference sequence defined
2096 <!-- JAL-1011 -->Columns are suddenly selected in other
2097 alignments and views when revealing hidden columns
2100 <!-- JAL-1989 -->Hide columns not mirrored in complement
2101 view in a cDNA/Protein splitframe
2104 <!-- JAL-1369 -->Cannot save/restore representative
2105 sequence from project when only one sequence is
2109 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2110 in Structure Chooser
2113 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2114 structure consensus didn't refresh annotation panel
2117 <!-- JAL-1962 -->View mapping in structure view shows
2118 mappings between sequence and all chains in a PDB file
2121 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2122 dialogs format columns correctly, don't display array
2123 data, sort columns according to type
2126 <!-- JAL-1975 -->Export complete shown after destination
2127 file chooser is cancelled during an image export
2130 <!-- JAL-2025 -->Error when querying PDB Service with
2131 sequence name containing special characters
2134 <!-- JAL-2024 -->Manual PDB structure querying should be
2138 <!-- JAL-2104 -->Large tooltips with broken HTML
2139 formatting don't wrap
2142 <!-- JAL-1128 -->Figures exported from wrapped view are
2143 truncated so L looks like I in consensus annotation
2146 <!-- JAL-2003 -->Export features should only export the
2147 currently displayed features for the current selection or
2151 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2152 after fetching cross-references, and restoring from
2156 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2157 followed in the structure viewer
2160 <!-- JAL-2163 -->Titles for individual alignments in
2161 splitframe not restored from project
2164 <!-- JAL-2145 -->missing autocalculated annotation at
2165 trailing end of protein alignment in transcript/product
2166 splitview when pad-gaps not enabled by default
2169 <!-- JAL-1797 -->amino acid physicochemical conservation
2173 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2174 article has been read (reopened issue due to
2175 internationalisation problems)
2178 <!-- JAL-1960 -->Only offer PDB structures in structure
2179 viewer based on sequence name, PDB and UniProt
2184 <!-- JAL-1976 -->No progress bar shown during export of
2188 <!-- JAL-2213 -->Structures not always superimposed after
2189 multiple structures are shown for one or more sequences.
2192 <!-- JAL-1370 -->Reference sequence characters should not
2193 be replaced with '.' when 'Show unconserved' format option
2197 <!-- JAL-1823 -->Cannot specify chain code when entering
2198 specific PDB id for sequence
2201 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2202 'Export hidden sequences' is enabled, but 'export hidden
2203 columns' is disabled.
2206 <!--JAL-2026-->Best Quality option in structure chooser
2207 selects lowest rather than highest resolution structures
2211 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2212 to sequence mapping in 'View Mappings' report
2215 <!-- JAL-2284 -->Unable to read old Jalview projects that
2216 contain non-XML data added after Jalvew wrote project.
2219 <!-- JAL-2118 -->Newly created annotation row reorders
2220 after clicking on it to create new annotation for a
2224 <!-- JAL-1980 -->Null Pointer Exception raised when
2225 pressing Add on an orphaned cut'n'paste window.
2227 <!-- may exclude, this is an external service stability issue JAL-1941
2228 -- > RNA 3D structure not added via DSSR service</li> -->
2233 <!-- JAL-2151 -->Incorrect columns are selected when
2234 hidden columns present before start of sequence
2237 <!-- JAL-1986 -->Missing dependencies on applet pages
2241 <!-- JAL-1947 -->Overview pixel size changes when
2242 sequences are hidden in applet
2245 <!-- JAL-1996 -->Updated instructions for applet
2246 deployment on examples pages.
2253 <td width="60" nowrap>
2254 <div align="center">
2255 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2256 <em>16/10/2015</em></strong>
2259 <td><em>General</em>
2261 <li>Time stamps for signed Jalview application and applet
2266 <em>Application</em>
2268 <li>Duplicate group consensus and conservation rows
2269 shown when tree is partitioned</li>
2270 <li>Erratic behaviour when tree partitions made with
2271 multiple cDNA/Protein split views</li>
2277 <td width="60" nowrap>
2278 <div align="center">
2279 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2280 <em>8/10/2015</em></strong>
2283 <td><em>General</em>
2285 <li>Updated Spanish translations of localized text for
2287 </ul> <em>Application</em>
2289 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2290 <li>Signed OSX InstallAnywhere installer<br></li>
2291 <li>Support for per-sequence based annotations in BioJSON</li>
2292 </ul> <em>Applet</em>
2294 <li>Split frame example added to applet examples page</li>
2295 </ul> <em>Build and Deployment</em>
2298 <!-- JAL-1888 -->New ant target for running Jalview's test
2306 <li>Mapping of cDNA to protein in split frames
2307 incorrect when sequence start > 1</li>
2308 <li>Broken images in filter column by annotation dialog
2310 <li>Feature colours not parsed from features file</li>
2311 <li>Exceptions and incomplete link URLs recovered when
2312 loading a features file containing HTML tags in feature
2316 <em>Application</em>
2318 <li>Annotations corrupted after BioJS export and
2320 <li>Incorrect sequence limits after Fetch DB References
2321 with 'trim retrieved sequences'</li>
2322 <li>Incorrect warning about deleting all data when
2323 deleting selected columns</li>
2324 <li>Patch to build system for shipping properly signed
2325 JNLP templates for webstart launch</li>
2326 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2327 unreleased structures for download or viewing</li>
2328 <li>Tab/space/return keystroke operation of EMBL-PDBe
2329 fetcher/viewer dialogs works correctly</li>
2330 <li>Disabled 'minimise' button on Jalview windows
2331 running on OSX to workaround redraw hang bug</li>
2332 <li>Split cDNA/Protein view position and geometry not
2333 recovered from jalview project</li>
2334 <li>Initial enabled/disabled state of annotation menu
2335 sorter 'show autocalculated first/last' corresponds to
2337 <li>Restoring of Clustal, RNA Helices and T-Coffee
2338 color schemes from BioJSON</li>
2342 <li>Reorder sequences mirrored in cDNA/Protein split
2344 <li>Applet with Jmol examples not loading correctly</li>
2350 <td><div align="center">
2351 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2353 <td><em>General</em>
2355 <li>Linked visualisation and analysis of DNA and Protein
2358 <li>Translated cDNA alignments shown as split protein
2359 and DNA alignment views</li>
2360 <li>Codon consensus annotation for linked protein and
2361 cDNA alignment views</li>
2362 <li>Link cDNA or Protein product sequences by loading
2363 them onto Protein or cDNA alignments</li>
2364 <li>Reconstruct linked cDNA alignment from aligned
2365 protein sequences</li>
2368 <li>Jmol integration updated to Jmol v14.2.14</li>
2369 <li>Import and export of Jalview alignment views as <a
2370 href="features/bioJsonFormat.html">BioJSON</a></li>
2371 <li>New alignment annotation file statements for
2372 reference sequences and marking hidden columns</li>
2373 <li>Reference sequence based alignment shading to
2374 highlight variation</li>
2375 <li>Select or hide columns according to alignment
2377 <li>Find option for locating sequences by description</li>
2378 <li>Conserved physicochemical properties shown in amino
2379 acid conservation row</li>
2380 <li>Alignments can be sorted by number of RNA helices</li>
2381 </ul> <em>Application</em>
2383 <li>New cDNA/Protein analysis capabilities
2385 <li>Get Cross-References should open a Split Frame
2386 view with cDNA/Protein</li>
2387 <li>Detect when nucleotide sequences and protein
2388 sequences are placed in the same alignment</li>
2389 <li>Split cDNA/Protein views are saved in Jalview
2394 <li>Use REST API to talk to Chimera</li>
2395 <li>Selected regions in Chimera are highlighted in linked
2396 Jalview windows</li>
2398 <li>VARNA RNA viewer updated to v3.93</li>
2399 <li>VARNA views are saved in Jalview Projects</li>
2400 <li>Pseudoknots displayed as Jalview RNA annotation can
2401 be shown in VARNA</li>
2403 <li>Make groups for selection uses marked columns as well
2404 as the active selected region</li>
2406 <li>Calculate UPGMA and NJ trees using sequence feature
2408 <li>New Export options
2410 <li>New Export Settings dialog to control hidden
2411 region export in flat file generation</li>
2413 <li>Export alignment views for display with the <a
2414 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2416 <li>Export scrollable SVG in HTML page</li>
2417 <li>Optional embedding of BioJSON data when exporting
2418 alignment figures to HTML</li>
2420 <li>3D structure retrieval and display
2422 <li>Free text and structured queries with the PDBe
2424 <li>PDBe Search API based discovery and selection of
2425 PDB structures for a sequence set</li>
2429 <li>JPred4 employed for protein secondary structure
2431 <li>Hide Insertions menu option to hide unaligned columns
2432 for one or a group of sequences</li>
2433 <li>Automatically hide insertions in alignments imported
2434 from the JPred4 web server</li>
2435 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2436 system on OSX<br />LGPL libraries courtesy of <a
2437 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2439 <li>changed 'View nucleotide structure' submenu to 'View
2440 VARNA 2D Structure'</li>
2441 <li>change "View protein structure" menu option to "3D
2444 </ul> <em>Applet</em>
2446 <li>New layout for applet example pages</li>
2447 <li>New parameters to enable SplitFrame view
2448 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2449 <li>New example demonstrating linked viewing of cDNA and
2450 Protein alignments</li>
2451 </ul> <em>Development and deployment</em>
2453 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2454 <li>Include installation type and git revision in build
2455 properties and console log output</li>
2456 <li>Jalview Github organisation, and new github site for
2457 storing BioJsMSA Templates</li>
2458 <li>Jalview's unit tests now managed with TestNG</li>
2461 <!-- <em>General</em>
2463 </ul> --> <!-- issues resolved --> <em>Application</em>
2465 <li>Escape should close any open find dialogs</li>
2466 <li>Typo in select-by-features status report</li>
2467 <li>Consensus RNA secondary secondary structure
2468 predictions are not highlighted in amber</li>
2469 <li>Missing gap character in v2.7 example file means
2470 alignment appears unaligned when pad-gaps is not enabled</li>
2471 <li>First switch to RNA Helices colouring doesn't colour
2472 associated structure views</li>
2473 <li>ID width preference option is greyed out when auto
2474 width checkbox not enabled</li>
2475 <li>Stopped a warning dialog from being shown when
2476 creating user defined colours</li>
2477 <li>'View Mapping' in structure viewer shows sequence
2478 mappings for just that viewer's sequences</li>
2479 <li>Workaround for superposing PDB files containing
2480 multiple models in Chimera</li>
2481 <li>Report sequence position in status bar when hovering
2482 over Jmol structure</li>
2483 <li>Cannot output gaps as '.' symbols with Selection ->
2484 output to text box</li>
2485 <li>Flat file exports of alignments with hidden columns
2486 have incorrect sequence start/end</li>
2487 <li>'Aligning' a second chain to a Chimera structure from
2489 <li>Colour schemes applied to structure viewers don't
2490 work for nucleotide</li>
2491 <li>Loading/cut'n'pasting an empty or invalid file leads
2492 to a grey/invisible alignment window</li>
2493 <li>Exported Jpred annotation from a sequence region
2494 imports to different position</li>
2495 <li>Space at beginning of sequence feature tooltips shown
2496 on some platforms</li>
2497 <li>Chimera viewer 'View | Show Chain' menu is not
2499 <li>'New View' fails with a Null Pointer Exception in
2500 console if Chimera has been opened</li>
2501 <li>Mouseover to Chimera not working</li>
2502 <li>Miscellaneous ENA XML feature qualifiers not
2504 <li>NPE in annotation renderer after 'Extract Scores'</li>
2505 <li>If two structures in one Chimera window, mouseover of
2506 either sequence shows on first structure</li>
2507 <li>'Show annotations' options should not make
2508 non-positional annotations visible</li>
2509 <li>Subsequence secondary structure annotation not shown
2510 in right place after 'view flanking regions'</li>
2511 <li>File Save As type unset when current file format is
2513 <li>Save as '.jar' option removed for saving Jalview
2515 <li>Colour by Sequence colouring in Chimera more
2517 <li>Cannot 'add reference annotation' for a sequence in
2518 several views on same alignment</li>
2519 <li>Cannot show linked products for EMBL / ENA records</li>
2520 <li>Jalview's tooltip wraps long texts containing no
2522 </ul> <em>Applet</em>
2524 <li>Jmol to JalviewLite mouseover/link not working</li>
2525 <li>JalviewLite can't import sequences with ID
2526 descriptions containing angle brackets</li>
2527 </ul> <em>General</em>
2529 <li>Cannot export and reimport RNA secondary structure
2530 via jalview annotation file</li>
2531 <li>Random helix colour palette for colour by annotation
2532 with RNA secondary structure</li>
2533 <li>Mouseover to cDNA from STOP residue in protein
2534 translation doesn't work.</li>
2535 <li>hints when using the select by annotation dialog box</li>
2536 <li>Jmol alignment incorrect if PDB file has alternate CA
2538 <li>FontChooser message dialog appears to hang after
2539 choosing 1pt font</li>
2540 <li>Peptide secondary structure incorrectly imported from
2541 annotation file when annotation display text includes 'e' or
2543 <li>Cannot set colour of new feature type whilst creating
2545 <li>cDNA translation alignment should not be sequence
2546 order dependent</li>
2547 <li>'Show unconserved' doesn't work for lower case
2549 <li>Nucleotide ambiguity codes involving R not recognised</li>
2550 </ul> <em>Deployment and Documentation</em>
2552 <li>Applet example pages appear different to the rest of
2553 www.jalview.org</li>
2554 </ul> <em>Application Known issues</em>
2556 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2557 <li>Misleading message appears after trying to delete
2559 <li>Jalview icon not shown in dock after InstallAnywhere
2560 version launches</li>
2561 <li>Fetching EMBL reference for an RNA sequence results
2562 fails with a sequence mismatch</li>
2563 <li>Corrupted or unreadable alignment display when
2564 scrolling alignment to right</li>
2565 <li>ArrayIndexOutOfBoundsException thrown when remove
2566 empty columns called on alignment with ragged gapped ends</li>
2567 <li>auto calculated alignment annotation rows do not get
2568 placed above or below non-autocalculated rows</li>
2569 <li>Jalview dekstop becomes sluggish at full screen in
2570 ultra-high resolution</li>
2571 <li>Cannot disable consensus calculation independently of
2572 quality and conservation</li>
2573 <li>Mouseover highlighting between cDNA and protein can
2574 become sluggish with more than one splitframe shown</li>
2575 </ul> <em>Applet Known Issues</em>
2577 <li>Core PDB parsing code requires Jmol</li>
2578 <li>Sequence canvas panel goes white when alignment
2579 window is being resized</li>
2585 <td><div align="center">
2586 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2588 <td><em>General</em>
2590 <li>Updated Java code signing certificate donated by
2592 <li>Features and annotation preserved when performing
2593 pairwise alignment</li>
2594 <li>RNA pseudoknot annotation can be
2595 imported/exported/displayed</li>
2596 <li>'colour by annotation' can colour by RNA and
2597 protein secondary structure</li>
2598 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2599 post-hoc with 2.9 release</em>)
2602 </ul> <em>Application</em>
2604 <li>Extract and display secondary structure for sequences
2605 with 3D structures</li>
2606 <li>Support for parsing RNAML</li>
2607 <li>Annotations menu for layout
2609 <li>sort sequence annotation rows by alignment</li>
2610 <li>place sequence annotation above/below alignment
2613 <li>Output in Stockholm format</li>
2614 <li>Internationalisation: improved Spanish (es)
2616 <li>Structure viewer preferences tab</li>
2617 <li>Disorder and Secondary Structure annotation tracks
2618 shared between alignments</li>
2619 <li>UCSF Chimera launch and linked highlighting from
2621 <li>Show/hide all sequence associated annotation rows for
2622 all or current selection</li>
2623 <li>disorder and secondary structure predictions
2624 available as dataset annotation</li>
2625 <li>Per-sequence rna helices colouring</li>
2628 <li>Sequence database accessions imported when fetching
2629 alignments from Rfam</li>
2630 <li>update VARNA version to 3.91</li>
2632 <li>New groovy scripts for exporting aligned positions,
2633 conservation values, and calculating sum of pairs scores.</li>
2634 <li>Command line argument to set default JABAWS server</li>
2635 <li>include installation type in build properties and
2636 console log output</li>
2637 <li>Updated Jalview project format to preserve dataset
2641 <!-- issues resolved --> <em>Application</em>
2643 <li>Distinguish alignment and sequence associated RNA
2644 structure in structure->view->VARNA</li>
2645 <li>Raise dialog box if user deletes all sequences in an
2647 <li>Pressing F1 results in documentation opening twice</li>
2648 <li>Sequence feature tooltip is wrapped</li>
2649 <li>Double click on sequence associated annotation
2650 selects only first column</li>
2651 <li>Redundancy removal doesn't result in unlinked
2652 leaves shown in tree</li>
2653 <li>Undos after several redundancy removals don't undo
2655 <li>Hide sequence doesn't hide associated annotation</li>
2656 <li>User defined colours dialog box too big to fit on
2657 screen and buttons not visible</li>
2658 <li>author list isn't updated if already written to
2659 Jalview properties</li>
2660 <li>Popup menu won't open after retrieving sequence
2662 <li>File open window for associate PDB doesn't open</li>
2663 <li>Left-then-right click on a sequence id opens a
2664 browser search window</li>
2665 <li>Cannot open sequence feature shading/sort popup menu
2666 in feature settings dialog</li>
2667 <li>better tooltip placement for some areas of Jalview
2669 <li>Allow addition of JABAWS Server which doesn't
2670 pass validation</li>
2671 <li>Web services parameters dialog box is too large to
2673 <li>Muscle nucleotide alignment preset obscured by
2675 <li>JABAWS preset submenus don't contain newly
2676 defined user preset</li>
2677 <li>MSA web services warns user if they were launched
2678 with invalid input</li>
2679 <li>Jalview cannot contact DAS Registy when running on
2682 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2683 'Superpose with' submenu not shown when new view
2687 </ul> <!-- <em>Applet</em>
2689 </ul> <em>General</em>
2691 </ul>--> <em>Deployment and Documentation</em>
2693 <li>2G and 1G options in launchApp have no effect on
2694 memory allocation</li>
2695 <li>launchApp service doesn't automatically open
2696 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2698 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2699 InstallAnywhere reports cannot find valid JVM when Java
2700 1.7_055 is available
2702 </ul> <em>Application Known issues</em>
2705 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2706 corrupted or unreadable alignment display when scrolling
2710 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2711 retrieval fails but progress bar continues for DAS retrieval
2712 with large number of ID
2715 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2716 flatfile output of visible region has incorrect sequence
2720 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2721 rna structure consensus doesn't update when secondary
2722 structure tracks are rearranged
2725 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2726 invalid rna structure positional highlighting does not
2727 highlight position of invalid base pairs
2730 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2731 out of memory errors are not raised when saving Jalview
2732 project from alignment window file menu
2735 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2736 Switching to RNA Helices colouring doesn't propagate to
2740 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2741 colour by RNA Helices not enabled when user created
2742 annotation added to alignment
2745 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2746 Jalview icon not shown on dock in Mountain Lion/Webstart
2748 </ul> <em>Applet Known Issues</em>
2751 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2752 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2755 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2756 Jalview and Jmol example not compatible with IE9
2759 <li>Sort by annotation score doesn't reverse order
2765 <td><div align="center">
2766 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2769 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2772 <li>Internationalisation of user interface (usually
2773 called i18n support) and translation for Spanish locale</li>
2774 <li>Define/Undefine group on current selection with
2775 Ctrl-G/Shift Ctrl-G</li>
2776 <li>Improved group creation/removal options in
2777 alignment/sequence Popup menu</li>
2778 <li>Sensible precision for symbol distribution
2779 percentages shown in logo tooltip.</li>
2780 <li>Annotation panel height set according to amount of
2781 annotation when alignment first opened</li>
2782 </ul> <em>Application</em>
2784 <li>Interactive consensus RNA secondary structure
2785 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2786 <li>Select columns containing particular features from
2787 Feature Settings dialog</li>
2788 <li>View all 'representative' PDB structures for selected
2790 <li>Update Jalview project format:
2792 <li>New file extension for Jalview projects '.jvp'</li>
2793 <li>Preserve sequence and annotation dataset (to
2794 store secondary structure annotation,etc)</li>
2795 <li>Per group and alignment annotation and RNA helix
2799 <li>New similarity measures for PCA and Tree calculation
2801 <li>Experimental support for retrieval and viewing of
2802 flanking regions for an alignment</li>
2806 <!-- issues resolved --> <em>Application</em>
2808 <li>logo keeps spinning and status remains at queued or
2809 running after job is cancelled</li>
2810 <li>cannot export features from alignments imported from
2811 Jalview/VAMSAS projects</li>
2812 <li>Buggy slider for web service parameters that take
2814 <li>Newly created RNA secondary structure line doesn't
2815 have 'display all symbols' flag set</li>
2816 <li>T-COFFEE alignment score shading scheme and other
2817 annotation shading not saved in Jalview project</li>
2818 <li>Local file cannot be loaded in freshly downloaded
2820 <li>Jalview icon not shown on dock in Mountain
2822 <li>Load file from desktop file browser fails</li>
2823 <li>Occasional NPE thrown when calculating large trees</li>
2824 <li>Cannot reorder or slide sequences after dragging an
2825 alignment onto desktop</li>
2826 <li>Colour by annotation dialog throws NPE after using
2827 'extract scores' function</li>
2828 <li>Loading/cut'n'pasting an empty file leads to a grey
2829 alignment window</li>
2830 <li>Disorder thresholds rendered incorrectly after
2831 performing IUPred disorder prediction</li>
2832 <li>Multiple group annotated consensus rows shown when
2833 changing 'normalise logo' display setting</li>
2834 <li>Find shows blank dialog after 'finished searching' if
2835 nothing matches query</li>
2836 <li>Null Pointer Exceptions raised when sorting by
2837 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2839 <li>Errors in Jmol console when structures in alignment
2840 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2842 <li>Not all working JABAWS services are shown in
2844 <li>JAVAWS version of Jalview fails to launch with
2845 'invalid literal/length code'</li>
2846 <li>Annotation/RNA Helix colourschemes cannot be applied
2847 to alignment with groups (actually fixed in 2.8.0b1)</li>
2848 <li>RNA Helices and T-Coffee Scores available as default
2851 </ul> <em>Applet</em>
2853 <li>Remove group option is shown even when selection is
2855 <li>Apply to all groups ticked but colourscheme changes
2856 don't affect groups</li>
2857 <li>Documented RNA Helices and T-Coffee Scores as valid
2858 colourscheme name</li>
2859 <li>Annotation labels drawn on sequence IDs when
2860 Annotation panel is not displayed</li>
2861 <li>Increased font size for dropdown menus on OSX and
2862 embedded windows</li>
2863 </ul> <em>Other</em>
2865 <li>Consensus sequence for alignments/groups with a
2866 single sequence were not calculated</li>
2867 <li>annotation files that contain only groups imported as
2868 annotation and junk sequences</li>
2869 <li>Fasta files with sequences containing '*' incorrectly
2870 recognised as PFAM or BLC</li>
2871 <li>conservation/PID slider apply all groups option
2872 doesn't affect background (2.8.0b1)
2874 <li>redundancy highlighting is erratic at 0% and 100%</li>
2875 <li>Remove gapped columns fails for sequences with ragged
2877 <li>AMSA annotation row with leading spaces is not
2878 registered correctly on import</li>
2879 <li>Jalview crashes when selecting PCA analysis for
2880 certain alignments</li>
2881 <li>Opening the colour by annotation dialog for an
2882 existing annotation based 'use original colours'
2883 colourscheme loses original colours setting</li>
2888 <td><div align="center">
2889 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2890 <em>30/1/2014</em></strong>
2894 <li>Trusted certificates for JalviewLite applet and
2895 Jalview Desktop application<br />Certificate was donated by
2896 <a href="https://www.certum.eu">Certum</a> to the Jalview
2897 open source project).
2899 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2900 <li>Output in Stockholm format</li>
2901 <li>Allow import of data from gzipped files</li>
2902 <li>Export/import group and sequence associated line
2903 graph thresholds</li>
2904 <li>Nucleotide substitution matrix that supports RNA and
2905 ambiguity codes</li>
2906 <li>Allow disorder predictions to be made on the current
2907 selection (or visible selection) in the same way that JPred
2909 <li>Groovy scripting for headless Jalview operation</li>
2910 </ul> <em>Other improvements</em>
2912 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2913 <li>COMBINE statement uses current SEQUENCE_REF and
2914 GROUP_REF scope to group annotation rows</li>
2915 <li>Support '' style escaping of quotes in Newick
2917 <li>Group options for JABAWS service by command line name</li>
2918 <li>Empty tooltip shown for JABA service options with a
2919 link but no description</li>
2920 <li>Select primary source when selecting authority in
2921 database fetcher GUI</li>
2922 <li>Add .mfa to FASTA file extensions recognised by
2924 <li>Annotation label tooltip text wrap</li>
2929 <li>Slow scrolling when lots of annotation rows are
2931 <li>Lots of NPE (and slowness) after creating RNA
2932 secondary structure annotation line</li>
2933 <li>Sequence database accessions not imported when
2934 fetching alignments from Rfam</li>
2935 <li>Incorrect SHMR submission for sequences with
2937 <li>View all structures does not always superpose
2939 <li>Option widgets in service parameters not updated to
2940 reflect user or preset settings</li>
2941 <li>Null pointer exceptions for some services without
2942 presets or adjustable parameters</li>
2943 <li>Discover PDB IDs entry in structure menu doesn't
2944 discover PDB xRefs</li>
2945 <li>Exception encountered while trying to retrieve
2946 features with DAS</li>
2947 <li>Lowest value in annotation row isn't coloured
2948 when colour by annotation (per sequence) is coloured</li>
2949 <li>Keyboard mode P jumps to start of gapped region when
2950 residue follows a gap</li>
2951 <li>Jalview appears to hang importing an alignment with
2952 Wrap as default or after enabling Wrap</li>
2953 <li>'Right click to add annotations' message
2954 shown in wrap mode when no annotations present</li>
2955 <li>Disorder predictions fail with NPE if no automatic
2956 annotation already exists on alignment</li>
2957 <li>oninit javascript function should be called after
2958 initialisation completes</li>
2959 <li>Remove redundancy after disorder prediction corrupts
2960 alignment window display</li>
2961 <li>Example annotation file in documentation is invalid</li>
2962 <li>Grouped line graph annotation rows are not exported
2963 to annotation file</li>
2964 <li>Multi-harmony analysis cannot be run when only two
2966 <li>Cannot create multiple groups of line graphs with
2967 several 'combine' statements in annotation file</li>
2968 <li>Pressing return several times causes Number Format
2969 exceptions in keyboard mode</li>
2970 <li>Multi-harmony (SHMMR) method doesn't submit
2971 correct partitions for input data</li>
2972 <li>Translation from DNA to Amino Acids fails</li>
2973 <li>Jalview fail to load newick tree with quoted label</li>
2974 <li>--headless flag isn't understood</li>
2975 <li>ClassCastException when generating EPS in headless
2977 <li>Adjusting sequence-associated shading threshold only
2978 changes one row's threshold</li>
2979 <li>Preferences and Feature settings panel panel
2980 doesn't open</li>
2981 <li>hide consensus histogram also hides conservation and
2982 quality histograms</li>
2987 <td><div align="center">
2988 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2990 <td><em>Application</em>
2992 <li>Support for JABAWS 2.0 Services (AACon alignment
2993 conservation, protein disorder and Clustal Omega)</li>
2994 <li>JABAWS server status indicator in Web Services
2996 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2997 in Jalview alignment window</li>
2998 <li>Updated Jalview build and deploy framework for OSX
2999 mountain lion, windows 7, and 8</li>
3000 <li>Nucleotide substitution matrix for PCA that supports
3001 RNA and ambiguity codes</li>
3003 <li>Improved sequence database retrieval GUI</li>
3004 <li>Support fetching and database reference look up
3005 against multiple DAS sources (Fetch all from in 'fetch db
3007 <li>Jalview project improvements
3009 <li>Store and retrieve the 'belowAlignment'
3010 flag for annotation</li>
3011 <li>calcId attribute to group annotation rows on the
3013 <li>Store AACon calculation settings for a view in
3014 Jalview project</li>
3018 <li>horizontal scrolling gesture support</li>
3019 <li>Visual progress indicator when PCA calculation is
3021 <li>Simpler JABA web services menus</li>
3022 <li>visual indication that web service results are still
3023 being retrieved from server</li>
3024 <li>Serialise the dialogs that are shown when Jalview
3025 starts up for first time</li>
3026 <li>Jalview user agent string for interacting with HTTP
3028 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3030 <li>Examples directory and Groovy library included in
3031 InstallAnywhere distribution</li>
3032 </ul> <em>Applet</em>
3034 <li>RNA alignment and secondary structure annotation
3035 visualization applet example</li>
3036 </ul> <em>General</em>
3038 <li>Normalise option for consensus sequence logo</li>
3039 <li>Reset button in PCA window to return dimensions to
3041 <li>Allow seqspace or Jalview variant of alignment PCA
3043 <li>PCA with either nucleic acid and protein substitution
3045 <li>Allow windows containing HTML reports to be exported
3047 <li>Interactive display and editing of RNA secondary
3048 structure contacts</li>
3049 <li>RNA Helix Alignment Colouring</li>
3050 <li>RNA base pair logo consensus</li>
3051 <li>Parse sequence associated secondary structure
3052 information in Stockholm files</li>
3053 <li>HTML Export database accessions and annotation
3054 information presented in tooltip for sequences</li>
3055 <li>Import secondary structure from LOCARNA clustalw
3056 style RNA alignment files</li>
3057 <li>import and visualise T-COFFEE quality scores for an
3059 <li>'colour by annotation' per sequence option to
3060 shade each sequence according to its associated alignment
3062 <li>New Jalview Logo</li>
3063 </ul> <em>Documentation and Development</em>
3065 <li>documentation for score matrices used in Jalview</li>
3066 <li>New Website!</li>
3068 <td><em>Application</em>
3070 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3071 wsdbfetch REST service</li>
3072 <li>Stop windows being moved outside desktop on OSX</li>
3073 <li>Filetype associations not installed for webstart
3075 <li>Jalview does not always retrieve progress of a JABAWS
3076 job execution in full once it is complete</li>
3077 <li>revise SHMR RSBS definition to ensure alignment is
3078 uploaded via ali_file parameter</li>
3079 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3080 <li>View all structures superposed fails with exception</li>
3081 <li>Jnet job queues forever if a very short sequence is
3082 submitted for prediction</li>
3083 <li>Cut and paste menu not opened when mouse clicked on
3085 <li>Putting fractional value into integer text box in
3086 alignment parameter dialog causes Jalview to hang</li>
3087 <li>Structure view highlighting doesn't work on
3089 <li>View all structures fails with exception shown in
3091 <li>Characters in filename associated with PDBEntry not
3092 escaped in a platform independent way</li>
3093 <li>Jalview desktop fails to launch with exception when
3095 <li>Tree calculation reports 'you must have 2 or more
3096 sequences selected' when selection is empty</li>
3097 <li>Jalview desktop fails to launch with jar signature
3098 failure when java web start temporary file caching is
3100 <li>DAS Sequence retrieval with range qualification
3101 results in sequence xref which includes range qualification</li>
3102 <li>Errors during processing of command line arguments
3103 cause progress bar (JAL-898) to be removed</li>
3104 <li>Replace comma for semi-colon option not disabled for
3105 DAS sources in sequence fetcher</li>
3106 <li>Cannot close news reader when JABAWS server warning
3107 dialog is shown</li>
3108 <li>Option widgets not updated to reflect user settings</li>
3109 <li>Edited sequence not submitted to web service</li>
3110 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3111 <li>InstallAnywhere installer doesn't unpack and run
3112 on OSX Mountain Lion</li>
3113 <li>Annotation panel not given a scroll bar when
3114 sequences with alignment annotation are pasted into the
3116 <li>Sequence associated annotation rows not associated
3117 when loaded from Jalview project</li>
3118 <li>Browser launch fails with NPE on java 1.7</li>
3119 <li>JABAWS alignment marked as finished when job was
3120 cancelled or job failed due to invalid input</li>
3121 <li>NPE with v2.7 example when clicking on Tree
3122 associated with all views</li>
3123 <li>Exceptions when copy/paste sequences with grouped
3124 annotation rows to new window</li>
3125 </ul> <em>Applet</em>
3127 <li>Sequence features are momentarily displayed before
3128 they are hidden using hidefeaturegroups applet parameter</li>
3129 <li>loading features via javascript API automatically
3130 enables feature display</li>
3131 <li>scrollToColumnIn javascript API method doesn't
3133 </ul> <em>General</em>
3135 <li>Redundancy removal fails for rna alignment</li>
3136 <li>PCA calculation fails when sequence has been selected
3137 and then deselected</li>
3138 <li>PCA window shows grey box when first opened on OSX</li>
3139 <li>Letters coloured pink in sequence logo when alignment
3140 coloured with clustalx</li>
3141 <li>Choosing fonts without letter symbols defined causes
3142 exceptions and redraw errors</li>
3143 <li>Initial PCA plot view is not same as manually
3144 reconfigured view</li>
3145 <li>Grouped annotation graph label has incorrect line
3147 <li>Grouped annotation graph label display is corrupted
3148 for lots of labels</li>
3153 <div align="center">
3154 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3157 <td><em>Application</em>
3159 <li>Jalview Desktop News Reader</li>
3160 <li>Tweaked default layout of web services menu</li>
3161 <li>View/alignment association menu to enable user to
3162 easily specify which alignment a multi-structure view takes
3163 its colours/correspondences from</li>
3164 <li>Allow properties file location to be specified as URL</li>
3165 <li>Extend Jalview project to preserve associations
3166 between many alignment views and a single Jmol display</li>
3167 <li>Store annotation row height in Jalview project file</li>
3168 <li>Annotation row column label formatting attributes
3169 stored in project file</li>
3170 <li>Annotation row order for auto-calculated annotation
3171 rows preserved in Jalview project file</li>
3172 <li>Visual progress indication when Jalview state is
3173 saved using Desktop window menu</li>
3174 <li>Visual indication that command line arguments are
3175 still being processed</li>
3176 <li>Groovy script execution from URL</li>
3177 <li>Colour by annotation default min and max colours in
3179 <li>Automatically associate PDB files dragged onto an
3180 alignment with sequences that have high similarity and
3182 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3183 <li>'view structures' option to open many
3184 structures in same window</li>
3185 <li>Sort associated views menu option for tree panel</li>
3186 <li>Group all JABA and non-JABA services for a particular
3187 analysis function in its own submenu</li>
3188 </ul> <em>Applet</em>
3190 <li>Userdefined and autogenerated annotation rows for
3192 <li>Adjustment of alignment annotation pane height</li>
3193 <li>Annotation scrollbar for annotation panel</li>
3194 <li>Drag to reorder annotation rows in annotation panel</li>
3195 <li>'automaticScrolling' parameter</li>
3196 <li>Allow sequences with partial ID string matches to be
3197 annotated from GFF/Jalview features files</li>
3198 <li>Sequence logo annotation row in applet</li>
3199 <li>Absolute paths relative to host server in applet
3200 parameters are treated as such</li>
3201 <li>New in the JalviewLite javascript API:
3203 <li>JalviewLite.js javascript library</li>
3204 <li>Javascript callbacks for
3206 <li>Applet initialisation</li>
3207 <li>Sequence/alignment mouse-overs and selections</li>
3210 <li>scrollTo row and column alignment scrolling
3212 <li>Select sequence/alignment regions from javascript</li>
3213 <li>javascript structure viewer harness to pass
3214 messages between Jmol and Jalview when running as
3215 distinct applets</li>
3216 <li>sortBy method</li>
3217 <li>Set of applet and application examples shipped
3218 with documentation</li>
3219 <li>New example to demonstrate JalviewLite and Jmol
3220 javascript message exchange</li>
3222 </ul> <em>General</em>
3224 <li>Enable Jmol displays to be associated with multiple
3225 multiple alignments</li>
3226 <li>Option to automatically sort alignment with new tree</li>
3227 <li>User configurable link to enable redirects to a
3228 www.Jalview.org mirror</li>
3229 <li>Jmol colours option for Jmol displays</li>
3230 <li>Configurable newline string when writing alignment
3231 and other flat files</li>
3232 <li>Allow alignment annotation description lines to
3233 contain html tags</li>
3234 </ul> <em>Documentation and Development</em>
3236 <li>Add groovy test harness for bulk load testing to
3238 <li>Groovy script to load and align a set of sequences
3239 using a web service before displaying the result in the
3240 Jalview desktop</li>
3241 <li>Restructured javascript and applet api documentation</li>
3242 <li>Ant target to publish example html files with applet
3244 <li>Netbeans project for building Jalview from source</li>
3245 <li>ant task to create online javadoc for Jalview source</li>
3247 <td><em>Application</em>
3249 <li>User defined colourscheme throws exception when
3250 current built in colourscheme is saved as new scheme</li>
3251 <li>AlignFrame->Save in application pops up save
3252 dialog for valid filename/format</li>
3253 <li>Cannot view associated structure for UniProt sequence</li>
3254 <li>PDB file association breaks for UniProt sequence
3256 <li>Associate PDB from file dialog does not tell you
3257 which sequence is to be associated with the file</li>
3258 <li>Find All raises null pointer exception when query
3259 only matches sequence IDs</li>
3260 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3261 <li>Jalview project with Jmol views created with Jalview
3262 2.4 cannot be loaded</li>
3263 <li>Filetype associations not installed for webstart
3265 <li>Two or more chains in a single PDB file associated
3266 with sequences in different alignments do not get coloured
3267 by their associated sequence</li>
3268 <li>Visibility status of autocalculated annotation row
3269 not preserved when project is loaded</li>
3270 <li>Annotation row height and visibility attributes not
3271 stored in Jalview project</li>
3272 <li>Tree bootstraps are not preserved when saved as a
3273 Jalview project</li>
3274 <li>Envision2 workflow tooltips are corrupted</li>
3275 <li>Enabling show group conservation also enables colour
3276 by conservation</li>
3277 <li>Duplicate group associated conservation or consensus
3278 created on new view</li>
3279 <li>Annotation scrollbar not displayed after 'show
3280 all hidden annotation rows' option selected</li>
3281 <li>Alignment quality not updated after alignment
3282 annotation row is hidden then shown</li>
3283 <li>Preserve colouring of structures coloured by
3284 sequences in pre Jalview 2.7 projects</li>
3285 <li>Web service job parameter dialog is not laid out
3287 <li>Web services menu not refreshed after 'reset
3288 services' button is pressed in preferences</li>
3289 <li>Annotation off by one in Jalview v2_3 example project</li>
3290 <li>Structures imported from file and saved in project
3291 get name like jalview_pdb1234.txt when reloaded</li>
3292 <li>Jalview does not always retrieve progress of a JABAWS
3293 job execution in full once it is complete</li>
3294 </ul> <em>Applet</em>
3296 <li>Alignment height set incorrectly when lots of
3297 annotation rows are displayed</li>
3298 <li>Relative URLs in feature HTML text not resolved to
3300 <li>View follows highlighting does not work for positions
3302 <li><= shown as = in tooltip</li>
3303 <li>Export features raises exception when no features
3305 <li>Separator string used for serialising lists of IDs
3306 for javascript api is modified when separator string
3307 provided as parameter</li>
3308 <li>Null pointer exception when selecting tree leaves for
3309 alignment with no existing selection</li>
3310 <li>Relative URLs for datasources assumed to be relative
3311 to applet's codebase</li>
3312 <li>Status bar not updated after finished searching and
3313 search wraps around to first result</li>
3314 <li>StructureSelectionManager instance shared between
3315 several Jalview applets causes race conditions and memory
3317 <li>Hover tooltip and mouseover of position on structure
3318 not sent from Jmol in applet</li>
3319 <li>Certain sequences of javascript method calls to
3320 applet API fatally hang browser</li>
3321 </ul> <em>General</em>
3323 <li>View follows structure mouseover scrolls beyond
3324 position with wrapped view and hidden regions</li>
3325 <li>Find sequence position moves to wrong residue
3326 with/without hidden columns</li>
3327 <li>Sequence length given in alignment properties window
3329 <li>InvalidNumberFormat exceptions thrown when trying to
3330 import PDB like structure files</li>
3331 <li>Positional search results are only highlighted
3332 between user-supplied sequence start/end bounds</li>
3333 <li>End attribute of sequence is not validated</li>
3334 <li>Find dialog only finds first sequence containing a
3335 given sequence position</li>
3336 <li>Sequence numbering not preserved in MSF alignment
3338 <li>Jalview PDB file reader does not extract sequence
3339 from nucleotide chains correctly</li>
3340 <li>Structure colours not updated when tree partition
3341 changed in alignment</li>
3342 <li>Sequence associated secondary structure not correctly
3343 parsed in interleaved stockholm</li>
3344 <li>Colour by annotation dialog does not restore current
3346 <li>Hiding (nearly) all sequences doesn't work
3348 <li>Sequences containing lowercase letters are not
3349 properly associated with their pdb files</li>
3350 </ul> <em>Documentation and Development</em>
3352 <li>schemas/JalviewWsParamSet.xsd corrupted by
3353 ApplyCopyright tool</li>
3358 <div align="center">
3359 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3362 <td><em>Application</em>
3364 <li>New warning dialog when the Jalview Desktop cannot
3365 contact web services</li>
3366 <li>JABA service parameters for a preset are shown in
3367 service job window</li>
3368 <li>JABA Service menu entries reworded</li>
3372 <li>Modeller PIR IO broken - cannot correctly import a
3373 pir file emitted by Jalview</li>
3374 <li>Existing feature settings transferred to new
3375 alignment view created from cut'n'paste</li>
3376 <li>Improved test for mixed amino/nucleotide chains when
3377 parsing PDB files</li>
3378 <li>Consensus and conservation annotation rows
3379 occasionally become blank for all new windows</li>
3380 <li>Exception raised when right clicking above sequences
3381 in wrapped view mode</li>
3382 </ul> <em>Application</em>
3384 <li>multiple multiply aligned structure views cause cpu
3385 usage to hit 100% and computer to hang</li>
3386 <li>Web Service parameter layout breaks for long user
3387 parameter names</li>
3388 <li>Jaba service discovery hangs desktop if Jaba server
3395 <div align="center">
3396 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3399 <td><em>Application</em>
3401 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3402 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3405 <li>Web Services preference tab</li>
3406 <li>Analysis parameters dialog box and user defined
3408 <li>Improved speed and layout of Envision2 service menu</li>
3409 <li>Superpose structures using associated sequence
3411 <li>Export coordinates and projection as CSV from PCA
3413 </ul> <em>Applet</em>
3415 <li>enable javascript: execution by the applet via the
3416 link out mechanism</li>
3417 </ul> <em>Other</em>
3419 <li>Updated the Jmol Jalview interface to work with Jmol
3421 <li>The Jalview Desktop and JalviewLite applet now
3422 require Java 1.5</li>
3423 <li>Allow Jalview feature colour specification for GFF
3424 sequence annotation files</li>
3425 <li>New 'colour by label' keword in Jalview feature file
3426 type colour specification</li>
3427 <li>New Jalview Desktop Groovy API method that allows a
3428 script to check if it being run in an interactive session or
3429 in a batch operation from the Jalview command line</li>
3433 <li>clustalx colourscheme colours Ds preferentially when
3434 both D+E are present in over 50% of the column</li>
3435 </ul> <em>Application</em>
3437 <li>typo in AlignmentFrame->View->Hide->all but
3438 selected Regions menu item</li>
3439 <li>sequence fetcher replaces ',' for ';' when the ',' is
3440 part of a valid accession ID</li>
3441 <li>fatal OOM if object retrieved by sequence fetcher
3442 runs out of memory</li>
3443 <li>unhandled Out of Memory Error when viewing pca
3444 analysis results</li>
3445 <li>InstallAnywhere builds fail to launch on OS X java
3446 10.5 update 4 (due to apple Java 1.6 update)</li>
3447 <li>Installanywhere Jalview silently fails to launch</li>
3448 </ul> <em>Applet</em>
3450 <li>Jalview.getFeatureGroups() raises an
3451 ArrayIndexOutOfBoundsException if no feature groups are
3458 <div align="center">
3459 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3465 <li>Alignment prettyprinter doesn't cope with long
3467 <li>clustalx colourscheme colours Ds preferentially when
3468 both D+E are present in over 50% of the column</li>
3469 <li>nucleic acid structures retrieved from PDB do not
3470 import correctly</li>
3471 <li>More columns get selected than were clicked on when a
3472 number of columns are hidden</li>
3473 <li>annotation label popup menu not providing correct
3474 add/hide/show options when rows are hidden or none are
3476 <li>Stockholm format shown in list of readable formats,
3477 and parser copes better with alignments from RFAM.</li>
3478 <li>CSV output of consensus only includes the percentage
3479 of all symbols if sequence logo display is enabled</li>
3481 </ul> <em>Applet</em>
3483 <li>annotation panel disappears when annotation is
3485 </ul> <em>Application</em>
3487 <li>Alignment view not redrawn properly when new
3488 alignment opened where annotation panel is visible but no
3489 annotations are present on alignment</li>
3490 <li>pasted region containing hidden columns is
3491 incorrectly displayed in new alignment window</li>
3492 <li>Jalview slow to complete operations when stdout is
3493 flooded (fix is to close the Jalview console)</li>
3494 <li>typo in AlignmentFrame->View->Hide->all but
3495 selected Rregions menu item.</li>
3496 <li>inconsistent group submenu and Format submenu entry
3497 'Un' or 'Non'conserved</li>
3498 <li>Sequence feature settings are being shared by
3499 multiple distinct alignments</li>
3500 <li>group annotation not recreated when tree partition is
3502 <li>double click on group annotation to select sequences
3503 does not propagate to associated trees</li>
3504 <li>Mac OSX specific issues:
3506 <li>exception raised when mouse clicked on desktop
3507 window background</li>
3508 <li>Desktop menu placed on menu bar and application
3509 name set correctly</li>
3510 <li>sequence feature settings not wide enough for the
3511 save feature colourscheme button</li>
3520 <div align="center">
3521 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3524 <td><em>New Capabilities</em>
3526 <li>URL links generated from description line for
3527 regular-expression based URL links (applet and application)
3529 <li>Non-positional feature URL links are shown in link
3531 <li>Linked viewing of nucleic acid sequences and
3533 <li>Automatic Scrolling option in View menu to display
3534 the currently highlighted region of an alignment.</li>
3535 <li>Order an alignment by sequence length, or using the
3536 average score or total feature count for each sequence.</li>
3537 <li>Shading features by score or associated description</li>
3538 <li>Subdivide alignment and groups based on identity of
3539 selected subsequence (Make Groups from Selection).</li>
3540 <li>New hide/show options including Shift+Control+H to
3541 hide everything but the currently selected region.</li>
3542 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3543 </ul> <em>Application</em>
3545 <li>Fetch DB References capabilities and UI expanded to
3546 support retrieval from DAS sequence sources</li>
3547 <li>Local DAS Sequence sources can be added via the
3548 command line or via the Add local source dialog box.</li>
3549 <li>DAS Dbref and DbxRef feature types are parsed as
3550 database references and protein_name is parsed as
3551 description line (BioSapiens terms).</li>
3552 <li>Enable or disable non-positional feature and database
3553 references in sequence ID tooltip from View menu in
3555 <!-- <li>New hidden columns and rows and representatives capabilities
3556 in annotations file (in progress - not yet fully implemented)</li> -->
3557 <li>Group-associated consensus, sequence logos and
3558 conservation plots</li>
3559 <li>Symbol distributions for each column can be exported
3560 and visualized as sequence logos</li>
3561 <li>Optionally scale multi-character column labels to fit
3562 within each column of annotation row<!-- todo for applet -->
3564 <li>Optional automatic sort of associated alignment view
3565 when a new tree is opened.</li>
3566 <li>Jalview Java Console</li>
3567 <li>Better placement of desktop window when moving
3568 between different screens.</li>
3569 <li>New preference items for sequence ID tooltip and
3570 consensus annotation</li>
3571 <li>Client to submit sequences and IDs to Envision2
3573 <li><em>Vamsas Capabilities</em>
3575 <li>Improved VAMSAS synchronization (Jalview archive
3576 used to preserve views, structures, and tree display
3578 <li>Import of vamsas documents from disk or URL via
3580 <li>Sharing of selected regions between views and
3581 with other VAMSAS applications (Experimental feature!)</li>
3582 <li>Updated API to VAMSAS version 0.2</li>
3584 </ul> <em>Applet</em>
3586 <li>Middle button resizes annotation row height</li>
3589 <li>sortByTree (true/false) - automatically sort the
3590 associated alignment view by the tree when a new tree is
3592 <li>showTreeBootstraps (true/false) - show or hide
3593 branch bootstraps (default is to show them if available)</li>
3594 <li>showTreeDistances (true/false) - show or hide
3595 branch lengths (default is to show them if available)</li>
3596 <li>showUnlinkedTreeNodes (true/false) - indicate if
3597 unassociated nodes should be highlighted in the tree
3599 <li>heightScale and widthScale (1.0 or more) -
3600 increase the height or width of a cell in the alignment
3601 grid relative to the current font size.</li>
3604 <li>Non-positional features displayed in sequence ID
3606 </ul> <em>Other</em>
3608 <li>Features format: graduated colour definitions and
3609 specification of feature scores</li>
3610 <li>Alignment Annotations format: new keywords for group
3611 associated annotation (GROUP_REF) and annotation row display
3612 properties (ROW_PROPERTIES)</li>
3613 <li>XML formats extended to support graduated feature
3614 colourschemes, group associated annotation, and profile
3615 visualization settings.</li></td>
3618 <li>Source field in GFF files parsed as feature source
3619 rather than description</li>
3620 <li>Non-positional features are now included in sequence
3621 feature and gff files (controlled via non-positional feature
3622 visibility in tooltip).</li>
3623 <li>URL links generated for all feature links (bugfix)</li>
3624 <li>Added URL embedding instructions to features file
3626 <li>Codons containing ambiguous nucleotides translated as
3627 'X' in peptide product</li>
3628 <li>Match case switch in find dialog box works for both
3629 sequence ID and sequence string and query strings do not
3630 have to be in upper case to match case-insensitively.</li>
3631 <li>AMSA files only contain first column of
3632 multi-character column annotation labels</li>
3633 <li>Jalview Annotation File generation/parsing consistent
3634 with documentation (e.g. Stockholm annotation can be
3635 exported and re-imported)</li>
3636 <li>PDB files without embedded PDB IDs given a friendly
3638 <li>Find incrementally searches ID string matches as well
3639 as subsequence matches, and correctly reports total number
3643 <li>Better handling of exceptions during sequence
3645 <li>Dasobert generated non-positional feature URL
3646 link text excludes the start_end suffix</li>
3647 <li>DAS feature and source retrieval buttons disabled
3648 when fetch or registry operations in progress.</li>
3649 <li>PDB files retrieved from URLs are cached properly</li>
3650 <li>Sequence description lines properly shared via
3652 <li>Sequence fetcher fetches multiple records for all
3654 <li>Ensured that command line das feature retrieval
3655 completes before alignment figures are generated.</li>
3656 <li>Reduced time taken when opening file browser for
3658 <li>isAligned check prior to calculating tree, PCA or
3659 submitting an MSA to JNet now excludes hidden sequences.</li>
3660 <li>User defined group colours properly recovered
3661 from Jalview projects.</li>
3670 <div align="center">
3671 <strong>2.4.0.b2</strong><br> 28/10/2009
3676 <li>Experimental support for google analytics usage
3678 <li>Jalview privacy settings (user preferences and docs).</li>
3683 <li>Race condition in applet preventing startup in
3685 <li>Exception when feature created from selection beyond
3686 length of sequence.</li>
3687 <li>Allow synthetic PDB files to be imported gracefully</li>
3688 <li>Sequence associated annotation rows associate with
3689 all sequences with a given id</li>
3690 <li>Find function matches case-insensitively for sequence
3691 ID string searches</li>
3692 <li>Non-standard characters do not cause pairwise
3693 alignment to fail with exception</li>
3694 </ul> <em>Application Issues</em>
3696 <li>Sequences are now validated against EMBL database</li>
3697 <li>Sequence fetcher fetches multiple records for all
3699 </ul> <em>InstallAnywhere Issues</em>
3701 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3702 issue with installAnywhere mechanism)</li>
3703 <li>Command line launching of JARs from InstallAnywhere
3704 version (java class versioning error fixed)</li>
3711 <div align="center">
3712 <strong>2.4</strong><br> 27/8/2008
3715 <td><em>User Interface</em>
3717 <li>Linked highlighting of codon and amino acid from
3718 translation and protein products</li>
3719 <li>Linked highlighting of structure associated with
3720 residue mapping to codon position</li>
3721 <li>Sequence Fetcher provides example accession numbers
3722 and 'clear' button</li>
3723 <li>MemoryMonitor added as an option under Desktop's
3725 <li>Extract score function to parse whitespace separated
3726 numeric data in description line</li>
3727 <li>Column labels in alignment annotation can be centred.</li>
3728 <li>Tooltip for sequence associated annotation give name
3730 </ul> <em>Web Services and URL fetching</em>
3732 <li>JPred3 web service</li>
3733 <li>Prototype sequence search client (no public services
3735 <li>Fetch either seed alignment or full alignment from
3737 <li>URL Links created for matching database cross
3738 references as well as sequence ID</li>
3739 <li>URL Links can be created using regular-expressions</li>
3740 </ul> <em>Sequence Database Connectivity</em>
3742 <li>Retrieval of cross-referenced sequences from other
3744 <li>Generalised database reference retrieval and
3745 validation to all fetchable databases</li>
3746 <li>Fetch sequences from DAS sources supporting the
3747 sequence command</li>
3748 </ul> <em>Import and Export</em>
3749 <li>export annotation rows as CSV for spreadsheet import</li>
3750 <li>Jalview projects record alignment dataset associations,
3751 EMBL products, and cDNA sequence mappings</li>
3752 <li>Sequence Group colour can be specified in Annotation
3754 <li>Ad-hoc colouring of group in Annotation File using RGB
3755 triplet as name of colourscheme</li>
3756 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3758 <li>treenode binding for VAMSAS tree exchange</li>
3759 <li>local editing and update of sequences in VAMSAS
3760 alignments (experimental)</li>
3761 <li>Create new or select existing session to join</li>
3762 <li>load and save of vamsas documents</li>
3763 </ul> <em>Application command line</em>
3765 <li>-tree parameter to open trees (introduced for passing
3767 <li>-fetchfrom command line argument to specify nicknames
3768 of DAS servers to query for alignment features</li>
3769 <li>-dasserver command line argument to add new servers
3770 that are also automatically queried for features</li>
3771 <li>-groovy command line argument executes a given groovy
3772 script after all input data has been loaded and parsed</li>
3773 </ul> <em>Applet-Application data exchange</em>
3775 <li>Trees passed as applet parameters can be passed to
3776 application (when using "View in full
3777 application")</li>
3778 </ul> <em>Applet Parameters</em>
3780 <li>feature group display control parameter</li>
3781 <li>debug parameter</li>
3782 <li>showbutton parameter</li>
3783 </ul> <em>Applet API methods</em>
3785 <li>newView public method</li>
3786 <li>Window (current view) specific get/set public methods</li>
3787 <li>Feature display control methods</li>
3788 <li>get list of currently selected sequences</li>
3789 </ul> <em>New Jalview distribution features</em>
3791 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3792 <li>RELEASE file gives build properties for the latest
3793 Jalview release.</li>
3794 <li>Java 1.1 Applet build made easier and donotobfuscate
3795 property controls execution of obfuscator</li>
3796 <li>Build target for generating source distribution</li>
3797 <li>Debug flag for javacc</li>
3798 <li>.jalview_properties file is documented (slightly) in
3799 jalview.bin.Cache</li>
3800 <li>Continuous Build Integration for stable and
3801 development version of Application, Applet and source
3806 <li>selected region output includes visible annotations
3807 (for certain formats)</li>
3808 <li>edit label/displaychar contains existing label/char
3810 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3811 <li>shorter peptide product names from EMBL records</li>
3812 <li>Newick string generator makes compact representations</li>
3813 <li>bootstrap values parsed correctly for tree files with
3815 <li>pathological filechooser bug avoided by not allowing
3816 filenames containing a ':'</li>
3817 <li>Fixed exception when parsing GFF files containing
3818 global sequence features</li>
3819 <li>Alignment datasets are finalized only when number of
3820 references from alignment sequences goes to zero</li>
3821 <li>Close of tree branch colour box without colour
3822 selection causes cascading exceptions</li>
3823 <li>occasional negative imgwidth exceptions</li>
3824 <li>better reporting of non-fatal warnings to user when
3825 file parsing fails.</li>
3826 <li>Save works when Jalview project is default format</li>
3827 <li>Save as dialog opened if current alignment format is
3828 not a valid output format</li>
3829 <li>UniProt canonical names introduced for both das and
3831 <li>Histidine should be midblue (not pink!) in Zappo</li>
3832 <li>error messages passed up and output when data read
3834 <li>edit undo recovers previous dataset sequence when
3835 sequence is edited</li>
3836 <li>allow PDB files without pdb ID HEADER lines (like
3837 those generated by MODELLER) to be read in properly</li>
3838 <li>allow reading of JPred concise files as a normal
3840 <li>Stockholm annotation parsing and alignment properties
3841 import fixed for PFAM records</li>
3842 <li>Structure view windows have correct name in Desktop
3844 <li>annotation consisting of sequence associated scores
3845 can be read and written correctly to annotation file</li>
3846 <li>Aligned cDNA translation to aligned peptide works
3848 <li>Fixed display of hidden sequence markers and
3849 non-italic font for representatives in Applet</li>
3850 <li>Applet Menus are always embedded in applet window on
3852 <li>Newly shown features appear at top of stack (in
3854 <li>Annotations added via parameter not drawn properly
3855 due to null pointer exceptions</li>
3856 <li>Secondary structure lines are drawn starting from
3857 first column of alignment</li>
3858 <li>UniProt XML import updated for new schema release in
3860 <li>Sequence feature to sequence ID match for Features
3861 file is case-insensitive</li>
3862 <li>Sequence features read from Features file appended to
3863 all sequences with matching IDs</li>
3864 <li>PDB structure coloured correctly for associated views
3865 containing a sub-sequence</li>
3866 <li>PDB files can be retrieved by applet from Jar files</li>
3867 <li>feature and annotation file applet parameters
3868 referring to different directories are retrieved correctly</li>
3869 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3870 <li>Fixed application hang whilst waiting for
3871 splash-screen version check to complete</li>
3872 <li>Applet properly URLencodes input parameter values
3873 when passing them to the launchApp service</li>
3874 <li>display name and local features preserved in results
3875 retrieved from web service</li>
3876 <li>Visual delay indication for sequence retrieval and
3877 sequence fetcher initialisation</li>
3878 <li>updated Application to use DAS 1.53e version of
3879 dasobert DAS client</li>
3880 <li>Re-instated Full AMSA support and .amsa file
3882 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3890 <div align="center">
3891 <strong>2.3</strong><br> 9/5/07
3896 <li>Jmol 11.0.2 integration</li>
3897 <li>PDB views stored in Jalview XML files</li>
3898 <li>Slide sequences</li>
3899 <li>Edit sequence in place</li>
3900 <li>EMBL CDS features</li>
3901 <li>DAS Feature mapping</li>
3902 <li>Feature ordering</li>
3903 <li>Alignment Properties</li>
3904 <li>Annotation Scores</li>
3905 <li>Sort by scores</li>
3906 <li>Feature/annotation editing in applet</li>
3911 <li>Headless state operation in 2.2.1</li>
3912 <li>Incorrect and unstable DNA pairwise alignment</li>
3913 <li>Cut and paste of sequences with annotation</li>
3914 <li>Feature group display state in XML</li>
3915 <li>Feature ordering in XML</li>
3916 <li>blc file iteration selection using filename # suffix</li>
3917 <li>Stockholm alignment properties</li>
3918 <li>Stockhom alignment secondary structure annotation</li>
3919 <li>2.2.1 applet had no feature transparency</li>
3920 <li>Number pad keys can be used in cursor mode</li>
3921 <li>Structure Viewer mirror image resolved</li>
3928 <div align="center">
3929 <strong>2.2.1</strong><br> 12/2/07
3934 <li>Non standard characters can be read and displayed
3935 <li>Annotations/Features can be imported/exported to the
3937 <li>Applet allows editing of sequence/annotation/group
3938 name & description
3939 <li>Preference setting to display sequence name in
3941 <li>Annotation file format extended to allow
3942 Sequence_groups to be defined
3943 <li>Default opening of alignment overview panel can be
3944 specified in preferences
3945 <li>PDB residue numbering annotation added to associated
3951 <li>Applet crash under certain Linux OS with Java 1.6
3953 <li>Annotation file export / import bugs fixed
3954 <li>PNG / EPS image output bugs fixed
3960 <div align="center">
3961 <strong>2.2</strong><br> 27/11/06
3966 <li>Multiple views on alignment
3967 <li>Sequence feature editing
3968 <li>"Reload" alignment
3969 <li>"Save" to current filename
3970 <li>Background dependent text colour
3971 <li>Right align sequence ids
3972 <li>User-defined lower case residue colours
3975 <li>Menu item accelerator keys
3976 <li>Control-V pastes to current alignment
3977 <li>Cancel button for DAS Feature Fetching
3978 <li>PCA and PDB Viewers zoom via mouse roller
3979 <li>User-defined sub-tree colours and sub-tree selection
3981 <li>'New Window' button on the 'Output to Text box'
3986 <li>New memory efficient Undo/Redo System
3987 <li>Optimised symbol lookups and conservation/consensus
3989 <li>Region Conservation/Consensus recalculated after
3991 <li>Fixed Remove Empty Columns Bug (empty columns at end
3993 <li>Slowed DAS Feature Fetching for increased robustness.
3995 <li>Made angle brackets in ASCII feature descriptions
3997 <li>Re-instated Zoom function for PCA
3998 <li>Sequence descriptions conserved in web service
4000 <li>UniProt ID discoverer uses any word separated by
4002 <li>WsDbFetch query/result association resolved
4003 <li>Tree leaf to sequence mapping improved
4004 <li>Smooth fonts switch moved to FontChooser dialog box.
4011 <div align="center">
4012 <strong>2.1.1</strong><br> 12/9/06
4017 <li>Copy consensus sequence to clipboard</li>
4022 <li>Image output - rightmost residues are rendered if
4023 sequence id panel has been resized</li>
4024 <li>Image output - all offscreen group boundaries are
4026 <li>Annotation files with sequence references - all
4027 elements in file are relative to sequence position</li>
4028 <li>Mac Applet users can use Alt key for group editing</li>
4034 <div align="center">
4035 <strong>2.1</strong><br> 22/8/06
4040 <li>MAFFT Multiple Alignment in default Web Service list</li>
4041 <li>DAS Feature fetching</li>
4042 <li>Hide sequences and columns</li>
4043 <li>Export Annotations and Features</li>
4044 <li>GFF file reading / writing</li>
4045 <li>Associate structures with sequences from local PDB
4047 <li>Add sequences to exisiting alignment</li>
4048 <li>Recently opened files / URL lists</li>
4049 <li>Applet can launch the full application</li>
4050 <li>Applet has transparency for features (Java 1.2
4052 <li>Applet has user defined colours parameter</li>
4053 <li>Applet can load sequences from parameter
4054 "sequence<em>x</em>"
4060 <li>Redundancy Panel reinstalled in the Applet</li>
4061 <li>Monospaced font - EPS / rescaling bug fixed</li>
4062 <li>Annotation files with sequence references bug fixed</li>
4068 <div align="center">
4069 <strong>2.08.1</strong><br> 2/5/06
4074 <li>Change case of selected region from Popup menu</li>
4075 <li>Choose to match case when searching</li>
4076 <li>Middle mouse button and mouse movement can compress /
4077 expand the visible width and height of the alignment</li>
4082 <li>Annotation Panel displays complete JNet results</li>
4088 <div align="center">
4089 <strong>2.08b</strong><br> 18/4/06
4095 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4096 <li>Righthand label on wrapped alignments shows correct
4103 <div align="center">
4104 <strong>2.08</strong><br> 10/4/06
4109 <li>Editing can be locked to the selection area</li>
4110 <li>Keyboard editing</li>
4111 <li>Create sequence features from searches</li>
4112 <li>Precalculated annotations can be loaded onto
4114 <li>Features file allows grouping of features</li>
4115 <li>Annotation Colouring scheme added</li>
4116 <li>Smooth fonts off by default - Faster rendering</li>
4117 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4122 <li>Drag & Drop fixed on Linux</li>
4123 <li>Jalview Archive file faster to load/save, sequence
4124 descriptions saved.</li>
4130 <div align="center">
4131 <strong>2.07</strong><br> 12/12/05
4136 <li>PDB Structure Viewer enhanced</li>
4137 <li>Sequence Feature retrieval and display enhanced</li>
4138 <li>Choose to output sequence start-end after sequence
4139 name for file output</li>
4140 <li>Sequence Fetcher WSDBFetch@EBI</li>
4141 <li>Applet can read feature files, PDB files and can be
4142 used for HTML form input</li>
4147 <li>HTML output writes groups and features</li>
4148 <li>Group editing is Control and mouse click</li>
4149 <li>File IO bugs</li>
4155 <div align="center">
4156 <strong>2.06</strong><br> 28/9/05
4161 <li>View annotations in wrapped mode</li>
4162 <li>More options for PCA viewer</li>
4167 <li>GUI bugs resolved</li>
4168 <li>Runs with -nodisplay from command line</li>
4174 <div align="center">
4175 <strong>2.05b</strong><br> 15/9/05
4180 <li>Choose EPS export as lineart or text</li>
4181 <li>Jar files are executable</li>
4182 <li>Can read in Uracil - maps to unknown residue</li>
4187 <li>Known OutOfMemory errors give warning message</li>
4188 <li>Overview window calculated more efficiently</li>
4189 <li>Several GUI bugs resolved</li>
4195 <div align="center">
4196 <strong>2.05</strong><br> 30/8/05
4201 <li>Edit and annotate in "Wrapped" view</li>
4206 <li>Several GUI bugs resolved</li>
4212 <div align="center">
4213 <strong>2.04</strong><br> 24/8/05
4218 <li>Hold down mouse wheel & scroll to change font
4224 <li>Improved JPred client reliability</li>
4225 <li>Improved loading of Jalview files</li>
4231 <div align="center">
4232 <strong>2.03</strong><br> 18/8/05
4237 <li>Set Proxy server name and port in preferences</li>
4238 <li>Multiple URL links from sequence ids</li>
4239 <li>User Defined Colours can have a scheme name and added
4241 <li>Choose to ignore gaps in consensus calculation</li>
4242 <li>Unix users can set default web browser</li>
4243 <li>Runs without GUI for batch processing</li>
4244 <li>Dynamically generated Web Service Menus</li>
4249 <li>InstallAnywhere download for Sparc Solaris</li>
4255 <div align="center">
4256 <strong>2.02</strong><br> 18/7/05
4262 <li>Copy & Paste order of sequences maintains
4263 alignment order.</li>
4269 <div align="center">
4270 <strong>2.01</strong><br> 12/7/05
4275 <li>Use delete key for deleting selection.</li>
4276 <li>Use Mouse wheel to scroll sequences.</li>
4277 <li>Help file updated to describe how to add alignment
4279 <li>Version and build date written to build properties
4281 <li>InstallAnywhere installation will check for updates
4282 at launch of Jalview.</li>
4287 <li>Delete gaps bug fixed.</li>
4288 <li>FileChooser sorts columns.</li>
4289 <li>Can remove groups one by one.</li>
4290 <li>Filechooser icons installed.</li>
4291 <li>Finder ignores return character when searching.
4292 Return key will initiate a search.<br>
4299 <div align="center">
4300 <strong>2.0</strong><br> 20/6/05
4305 <li>New codebase</li>