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-3141 -->Optional automatic backups when saving
67 Jalview project or alignment files</li>
69 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
70 Viewer state is saved in Jalview Project<br />The 'Change
71 parameters' option has also been removed from the PCA viewer</li>
73 <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
75 <!-- JAL-2620 -->Alternative genetic code tables supported for
76 'Translate as cDNA'</li>
78 <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
80 <!-- JAL-3198 -->More efficient creation of selections and
81 multiple groups when working with large alignments</li>
83 <!-- JAL-3200 -->Speedier import of annotation rows when
84 parsing stockholm files</li>
86 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
88 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
89 shaded according to any associated attributes (e.g. variant
90 attributes from VCF file, or key-value pairs imported from
91 column 9 of GFF file)</li>
93 <!-- JAL-2897 -->Show synonymous codon variants on peptide sequences</li>
95 <!-- JAL-2792 -->Popup report of a selected sequence feature's details</li>
97 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
98 algorithm (Z-sort/transparency and filter aware)</li>
100 <!-- JAL-2527 -->Alignment Overview now by default shows
101 only visible region of alignment (this can be changed in
102 user preferences)</li>
104 <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
106 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
107 all sequences are hidden</li>
109 <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
110 region, and gap count when inserting or deleting gaps</li>
112 <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
114 <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
116 <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
118 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
120 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
122 <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
124 <!-- JAL-3203 -->Overview panel default changed to not show hidden regions</li>
126 <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
128 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
130 <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent
131 to a hidden column marker</li>
133 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
135 <!-- JAL-2965 -->PCA depth queuing with graduated colours</li>
137 <em>Deprecations</em>
140 <!-- JAL-3035 -->DAS sequence retrieval and annotation
141 capabilities removed from the Jalview Desktop
144 <em>Release Processes</em>
147 Atlassian Bamboo continuous integration server for
148 unattended Test Suite execution</li>
150 <!-- JAL-2864 -->Memory test suite to detect leaks in common
153 <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
154 implementation) used for Sequence Feature collections</li>
156 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
157 unmarshalling has been replaced by JAXB for Jalview projects
158 and XML based data retrieval clients</li>
161 <td align="left" valign="top">
164 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
166 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
167 Jalview project involving multiple views</li>
169 <!-- JAL-3164 -->Overview for complementary view in a linked
170 CDS/Protein alignment is not updated when Hide Columns by
171 Annotation dialog hides columns</li>
173 <!-- JAL-3158 -->Selection highlighting in the complement of
174 a CDS/Protein alignment stops working after making a
175 selection in one view, then making another selection in the
178 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
180 <!-- JAL-3154 -->Table Columns could be re-ordered in
181 Feature Settings and Jalview Preferences panels</li>
183 <!-- JAL-2865 -->Jalview hangs when closing windows
184 or the overview updates with large alignments</li>
186 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
187 region if columns were selected by dragging right-to-left
188 and the mouse moved to the left of the first column</li>
190 <!-- JAL-2846 -->Error message for trying to load in invalid
191 URLs doesn't tell users the invalid URL</li>
193 <!-- JAL-3178 -->Nonpositional features lose feature group
194 on export as Jalview features file</li>
196 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
197 printed when columns are hidden</li>
199 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
201 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
202 dragging out of Scale or Annotation Panel</li>
204 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
206 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
208 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
210 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
212 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
214 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
216 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
217 opening an alignment</li>
219 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
221 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
222 different groups in the alignment are selected</li>
224 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
226 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
228 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
230 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
232 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
234 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
236 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
238 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
240 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
242 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
244 <!-- JAL-914 -->Help page can be opened twice</li>
249 <!-- JAL-2822 -->Start and End should be updated when
250 sequence data at beginning or end of alignment added/removed
251 via 'Edit' sequence</li>
253 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
254 sequence features correctly when start of sequence is
255 removed (Known defect since 2.10)</li>
257 <em>New Known Defects</em>
260 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
262 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
267 <td width="60" nowrap>
269 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
272 <td><div align="left">
276 <!-- JAL-3101 -->Default memory for Jalview webstart and
277 InstallAnywhere increased to 1G.
280 <!-- JAL-247 -->Hidden sequence markers and representative
281 sequence bolding included when exporting alignment as EPS,
282 SVG, PNG or HTML. <em>Display is configured via the
283 Format menu, or for command-line use via a jalview
284 properties file.</em>
287 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
288 API and sequence data now imported as JSON.
291 <!-- JAL-3065 -->Change in recommended way of starting
292 Jalview via a Java command line: add jars in lib directory
293 to CLASSPATH, rather than via the deprecated java.ext.dirs
300 <!-- JAL-3047 -->Support added to execute test suite
301 instrumented with <a href="http://openclover.org/">Open
306 <td><div align="left">
310 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
311 row shown in Feredoxin Structure alignment view of example
315 <!-- JAL-2854 -->Annotation obscures sequences if lots of
316 annotation displayed.
319 <!-- JAL-3107 -->Group conservation/consensus not shown
320 for newly created group when 'Apply to all groups'
324 <!-- JAL-3087 -->Corrupted display when switching to
325 wrapped mode when sequence panel's vertical scrollbar is
329 <!-- JAL-3003 -->Alignment is black in exported EPS file
330 when sequences are selected in exported view.</em>
333 <!-- JAL-3059 -->Groups with different coloured borders
334 aren't rendered with correct colour.
337 <!-- JAL-3092 -->Jalview could hang when importing certain
338 types of knotted RNA secondary structure.
341 <!-- JAL-3095 -->Sequence highlight and selection in
342 trimmed VARNA 2D structure is incorrect for sequences that
346 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
347 annotation when columns are inserted into an alignment,
348 and when exporting as Stockholm flatfile.
351 <!-- JAL-3053 -->Jalview annotation rows containing upper
352 and lower-case 'E' and 'H' do not automatically get
353 treated as RNA secondary structure.
356 <!-- JAL-3106 -->.jvp should be used as default extension
357 (not .jar) when saving a jalview project file.
360 <!-- JAL-3105 -->Mac Users: closing a window correctly
361 transfers focus to previous window on OSX
364 <em>Java 10 Issues Resolved</em>
367 <!-- JAL-2988 -->OSX - Can't save new files via the File
368 or export menus by typing in a name into the Save dialog
372 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
373 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
374 'look and feel' which has improved compatibility with the
375 latest version of OSX.
382 <td width="60" nowrap>
384 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
385 <em>7/06/2018</em></strong>
388 <td><div align="left">
392 <!-- JAL-2920 -->Use HGVS nomenclature for variant
393 annotation retrieved from Uniprot
396 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
397 onto the Jalview Desktop
401 <td><div align="left">
405 <!-- JAL-3017 -->Cannot import features with multiple
406 variant elements (blocks import of some Uniprot records)
409 <!-- JAL-2997 -->Clustal files with sequence positions in
410 right-hand column parsed correctly
413 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
414 not alignment area in exported graphic
417 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
418 window has input focus
421 <!-- JAL-2992 -->Annotation panel set too high when
422 annotation added to view (Windows)
425 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
426 network connectivity is poor
429 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
430 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
431 the currently open URL and links from a page viewed in
432 Firefox or Chrome on Windows is now fully supported. If
433 you are using Edge, only links in the page can be
434 dragged, and with Internet Explorer, only the currently
435 open URL in the browser can be dropped onto Jalview.</em>
441 <td width="60" nowrap>
443 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
446 <td><div align="left">
450 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
451 for disabling automatic superposition of multiple
452 structures and open structures in existing views
455 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
456 ID and annotation area margins can be click-dragged to
460 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
464 <!-- JAL-2759 -->Improved performance for large alignments
465 and lots of hidden columns
468 <!-- JAL-2593 -->Improved performance when rendering lots
469 of features (particularly when transparency is disabled)
474 <td><div align="left">
477 <!-- JAL-2899 -->Structure and Overview aren't updated
478 when Colour By Annotation threshold slider is adjusted
481 <!-- JAL-2778 -->Slow redraw when Overview panel shown
482 overlapping alignment panel
485 <!-- JAL-2929 -->Overview doesn't show end of unpadded
489 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
490 improved: CDS not handled correctly if transcript has no
494 <!-- JAL-2321 -->Secondary structure and temperature
495 factor annotation not added to sequence when local PDB
496 file associated with it by drag'n'drop or structure
500 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
501 dialog doesn't import PDB files dropped on an alignment
504 <!-- JAL-2666 -->Linked scrolling via protein horizontal
505 scroll bar doesn't work for some CDS/Protein views
508 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
509 Java 1.8u153 onwards and Java 1.9u4+.
512 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
513 columns in annotation row
516 <!-- JAL-2913 -->Preferences panel's ID Width control is not
517 honored in batch mode
520 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
521 for structures added to existing Jmol view
524 <!-- JAL-2223 -->'View Mappings' includes duplicate
525 entries after importing project with multiple views
528 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
529 protein sequences via SIFTS from associated PDB entries
530 with negative residue numbers or missing residues fails
533 <!-- JAL-2952 -->Exception when shading sequence with negative
534 Temperature Factor values from annotated PDB files (e.g.
535 as generated by CONSURF)
538 <!-- JAL-2920 -->Uniprot 'sequence variant' features
539 tooltip doesn't include a text description of mutation
542 <!-- JAL-2922 -->Invert displayed features very slow when
543 structure and/or overview windows are also shown
546 <!-- JAL-2954 -->Selecting columns from highlighted regions
547 very slow for alignments with large numbers of sequences
550 <!-- JAL-2925 -->Copy Consensus fails for group consensus
551 with 'StringIndexOutOfBounds'
554 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
555 platforms running Java 10
558 <!-- JAL-2960 -->Adding a structure to existing structure
559 view appears to do nothing because the view is hidden behind the alignment view
565 <!-- JAL-2926 -->Copy consensus sequence option in applet
566 should copy the group consensus when popup is opened on it
572 <!-- JAL-2913 -->Fixed ID width preference is not respected
575 <em>New Known Defects</em>
578 <!-- JAL-2973 --> Exceptions occasionally raised when
579 editing a large alignment and overview is displayed
582 <!-- JAL-2974 -->'Overview updating' progress bar is shown
583 repeatedly after a series of edits even when the overview
584 is no longer reflecting updates
587 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
588 structures for protein subsequence (if 'Trim Retrieved
589 Sequences' enabled) or Ensembl isoforms (Workaround in
590 2.10.4 is to fail back to N&W mapping)
597 <td width="60" nowrap>
599 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
602 <td><div align="left">
603 <ul><li>Updated Certum Codesigning Certificate
604 (Valid till 30th November 2018)</li></ul></div></td>
605 <td><div align="left">
608 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
609 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
610 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
611 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
612 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
613 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
614 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
620 <td width="60" nowrap>
622 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
625 <td><div align="left">
629 <!-- JAL-2446 -->Faster and more efficient management and
630 rendering of sequence features
633 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
634 429 rate limit request hander
637 <!-- JAL-2773 -->Structure views don't get updated unless
638 their colours have changed
641 <!-- JAL-2495 -->All linked sequences are highlighted for
642 a structure mousover (Jmol) or selection (Chimera)
645 <!-- JAL-2790 -->'Cancel' button in progress bar for
646 JABAWS AACon, RNAAliFold and Disorder prediction jobs
649 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
650 view from Ensembl locus cross-references
653 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
657 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
658 feature can be disabled
661 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
662 PDB easier retrieval of sequences for lists of IDs
665 <!-- JAL-2758 -->Short names for sequences retrieved from
671 <li>Groovy interpreter updated to 2.4.12</li>
672 <li>Example groovy script for generating a matrix of
673 percent identity scores for current alignment.</li>
675 <em>Testing and Deployment</em>
678 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
682 <td><div align="left">
686 <!-- JAL-2643 -->Pressing tab after updating the colour
687 threshold text field doesn't trigger an update to the
691 <!-- JAL-2682 -->Race condition when parsing sequence ID
695 <!-- JAL-2608 -->Overview windows are also closed when
696 alignment window is closed
699 <!-- JAL-2548 -->Export of features doesn't always respect
703 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
704 takes a long time in Cursor mode
710 <!-- JAL-2777 -->Structures with whitespace chainCode
711 cannot be viewed in Chimera
714 <!-- JAL-2728 -->Protein annotation panel too high in
718 <!-- JAL-2757 -->Can't edit the query after the server
719 error warning icon is shown in Uniprot and PDB Free Text
723 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
726 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
729 <!-- JAL-2739 -->Hidden column marker in last column not
730 rendered when switching back from Wrapped to normal view
733 <!-- JAL-2768 -->Annotation display corrupted when
734 scrolling right in unwapped alignment view
737 <!-- JAL-2542 -->Existing features on subsequence
738 incorrectly relocated when full sequence retrieved from
742 <!-- JAL-2733 -->Last reported memory still shown when
743 Desktop->Show Memory is unticked (OSX only)
746 <!-- JAL-2658 -->Amend Features dialog doesn't allow
747 features of same type and group to be selected for
751 <!-- JAL-2524 -->Jalview becomes sluggish in wide
752 alignments when hidden columns are present
755 <!-- JAL-2392 -->Jalview freezes when loading and
756 displaying several structures
759 <!-- JAL-2732 -->Black outlines left after resizing or
763 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
764 within the Jalview desktop on OSX
767 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
768 when in wrapped alignment mode
771 <!-- JAL-2636 -->Scale mark not shown when close to right
772 hand end of alignment
775 <!-- JAL-2684 -->Pairwise alignment of selected regions of
776 each selected sequence do not have correct start/end
780 <!-- JAL-2793 -->Alignment ruler height set incorrectly
781 after canceling the Alignment Window's Font dialog
784 <!-- JAL-2036 -->Show cross-references not enabled after
785 restoring project until a new view is created
788 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
789 URL links appears when only default EMBL-EBI link is
790 configured (since 2.10.2b2)
793 <!-- JAL-2775 -->Overview redraws whole window when box
797 <!-- JAL-2225 -->Structure viewer doesn't map all chains
798 in a multi-chain structure when viewing alignment
799 involving more than one chain (since 2.10)
802 <!-- JAL-2811 -->Double residue highlights in cursor mode
803 if new selection moves alignment window
806 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
807 arrow key in cursor mode to pass hidden column marker
810 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
811 that produces correctly annotated transcripts and products
814 <!-- JAL-2776 -->Toggling a feature group after first time
815 doesn't update associated structure view
818 <em>Applet</em><br />
821 <!-- JAL-2687 -->Concurrent modification exception when
822 closing alignment panel
825 <em>BioJSON</em><br />
828 <!-- JAL-2546 -->BioJSON export does not preserve
829 non-positional features
832 <em>New Known Issues</em>
835 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
836 sequence features correctly (for many previous versions of
840 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
841 using cursor in wrapped panel other than top
844 <!-- JAL-2791 -->Select columns containing feature ignores
845 graduated colour threshold
848 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
849 always preserve numbering and sequence features
852 <em>Known Java 9 Issues</em>
855 <!-- JAL-2902 -->Groovy Console very slow to open and is
856 not responsive when entering characters (Webstart, Java
863 <td width="60" nowrap>
865 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
866 <em>2/10/2017</em></strong>
869 <td><div align="left">
870 <em>New features in Jalview Desktop</em>
873 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
875 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
879 <td><div align="left">
883 <td width="60" nowrap>
885 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
886 <em>7/9/2017</em></strong>
889 <td><div align="left">
893 <!-- JAL-2588 -->Show gaps in overview window by colouring
894 in grey (sequences used to be coloured grey, and gaps were
898 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
902 <!-- JAL-2587 -->Overview updates immediately on increase
903 in size and progress bar shown as higher resolution
904 overview is recalculated
909 <td><div align="left">
913 <!-- JAL-2664 -->Overview window redraws every hidden
914 column region row by row
917 <!-- JAL-2681 -->duplicate protein sequences shown after
918 retrieving Ensembl crossrefs for sequences from Uniprot
921 <!-- JAL-2603 -->Overview window throws NPE if show boxes
922 format setting is unticked
925 <!-- JAL-2610 -->Groups are coloured wrongly in overview
926 if group has show boxes format setting unticked
929 <!-- JAL-2672,JAL-2665 -->Redraw problems when
930 autoscrolling whilst dragging current selection group to
931 include sequences and columns not currently displayed
934 <!-- JAL-2691 -->Not all chains are mapped when multimeric
935 assemblies are imported via CIF file
938 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
939 displayed when threshold or conservation colouring is also
943 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
947 <!-- JAL-2673 -->Jalview continues to scroll after
948 dragging a selected region off the visible region of the
952 <!-- JAL-2724 -->Cannot apply annotation based
953 colourscheme to all groups in a view
956 <!-- JAL-2511 -->IDs don't line up with sequences
957 initially after font size change using the Font chooser or
964 <td width="60" nowrap>
966 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
969 <td><div align="left">
970 <em>Calculations</em>
974 <!-- JAL-1933 -->Occupancy annotation row shows number of
975 ungapped positions in each column of the alignment.
978 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
979 a calculation dialog box
982 <!-- JAL-2379 -->Revised implementation of PCA for speed
983 and memory efficiency (~30x faster)
986 <!-- JAL-2403 -->Revised implementation of sequence
987 similarity scores as used by Tree, PCA, Shading Consensus
988 and other calculations
991 <!-- JAL-2416 -->Score matrices are stored as resource
992 files within the Jalview codebase
995 <!-- JAL-2500 -->Trees computed on Sequence Feature
996 Similarity may have different topology due to increased
1003 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1004 model for alignments and groups
1007 <!-- JAL-384 -->Custom shading schemes created via groovy
1014 <!-- JAL-2526 -->Efficiency improvements for interacting
1015 with alignment and overview windows
1018 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1022 <!-- JAL-2388 -->Hidden columns and sequences can be
1026 <!-- JAL-2611 -->Click-drag in visible area allows fine
1027 adjustment of visible position
1031 <em>Data import/export</em>
1034 <!-- JAL-2535 -->Posterior probability annotation from
1035 Stockholm files imported as sequence associated annotation
1038 <!-- JAL-2507 -->More robust per-sequence positional
1039 annotation input/output via stockholm flatfile
1042 <!-- JAL-2533 -->Sequence names don't include file
1043 extension when importing structure files without embedded
1044 names or PDB accessions
1047 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1048 format sequence substitution matrices
1051 <em>User Interface</em>
1054 <!-- JAL-2447 --> Experimental Features Checkbox in
1055 Desktop's Tools menu to hide or show untested features in
1059 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1060 via Overview or sequence motif search operations
1063 <!-- JAL-2547 -->Amend sequence features dialog box can be
1064 opened by double clicking gaps within sequence feature
1068 <!-- JAL-1476 -->Status bar message shown when not enough
1069 aligned positions were available to create a 3D structure
1073 <em>3D Structure</em>
1076 <!-- JAL-2430 -->Hidden regions in alignment views are not
1077 coloured in linked structure views
1080 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1081 file-based command exchange
1084 <!-- JAL-2375 -->Structure chooser automatically shows
1085 Cached Structures rather than querying the PDBe if
1086 structures are already available for sequences
1089 <!-- JAL-2520 -->Structures imported via URL are cached in
1090 the Jalview project rather than downloaded again when the
1091 project is reopened.
1094 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1095 to transfer Chimera's structure attributes as Jalview
1096 features, and vice-versa (<strong>Experimental
1100 <em>Web Services</em>
1103 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1106 <!-- JAL-2335 -->Filter non-standard amino acids and
1107 nucleotides when submitting to AACon and other MSA
1111 <!-- JAL-2316, -->URLs for viewing database
1112 cross-references provided by identifiers.org and the
1113 EMBL-EBI's MIRIAM DB
1120 <!-- JAL-2344 -->FileFormatI interface for describing and
1121 identifying file formats (instead of String constants)
1124 <!-- JAL-2228 -->FeatureCounter script refactored for
1125 efficiency when counting all displayed features (not
1126 backwards compatible with 2.10.1)
1129 <em>Example files</em>
1132 <!-- JAL-2631 -->Graduated feature colour style example
1133 included in the example feature file
1136 <em>Documentation</em>
1139 <!-- JAL-2339 -->Release notes reformatted for readability
1140 with the built-in Java help viewer
1143 <!-- JAL-1644 -->Find documentation updated with 'search
1144 sequence description' option
1150 <!-- JAL-2485, -->External service integration tests for
1151 Uniprot REST Free Text Search Client
1154 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1157 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1162 <td><div align="left">
1163 <em>Calculations</em>
1166 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1167 matrix - C->R should be '-3'<br />Old matrix restored
1168 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1170 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1171 Jalview's treatment of gaps in PCA and substitution matrix
1172 based Tree calculations.<br /> <br />In earlier versions
1173 of Jalview, gaps matching gaps were penalised, and gaps
1174 matching non-gaps penalised even more. In the PCA
1175 calculation, gaps were actually treated as non-gaps - so
1176 different costs were applied, which meant Jalview's PCAs
1177 were different to those produced by SeqSpace.<br />Jalview
1178 now treats gaps in the same way as SeqSpace (ie it scores
1179 them as 0). <br /> <br />Enter the following in the
1180 Groovy console to restore pre-2.10.2 behaviour:<br />
1181 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1182 // for 2.10.1 mode <br />
1183 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1184 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1185 these settings will affect all subsequent tree and PCA
1186 calculations (not recommended)</em></li>
1188 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1189 scaling of branch lengths for trees computed using
1190 Sequence Feature Similarity.
1193 <!-- JAL-2377 -->PCA calculation could hang when
1194 generating output report when working with highly
1195 redundant alignments
1198 <!-- JAL-2544 --> Sort by features includes features to
1199 right of selected region when gaps present on right-hand
1203 <em>User Interface</em>
1206 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1207 doesn't reselect a specific sequence's associated
1208 annotation after it was used for colouring a view
1211 <!-- JAL-2419 -->Current selection lost if popup menu
1212 opened on a region of alignment without groups
1215 <!-- JAL-2374 -->Popup menu not always shown for regions
1216 of an alignment with overlapping groups
1219 <!-- JAL-2310 -->Finder double counts if both a sequence's
1220 name and description match
1223 <!-- JAL-2370 -->Hiding column selection containing two
1224 hidden regions results in incorrect hidden regions
1227 <!-- JAL-2386 -->'Apply to all groups' setting when
1228 changing colour does not apply Conservation slider value
1232 <!-- JAL-2373 -->Percentage identity and conservation menu
1233 items do not show a tick or allow shading to be disabled
1236 <!-- JAL-2385 -->Conservation shading or PID threshold
1237 lost when base colourscheme changed if slider not visible
1240 <!-- JAL-2547 -->Sequence features shown in tooltip for
1241 gaps before start of features
1244 <!-- JAL-2623 -->Graduated feature colour threshold not
1245 restored to UI when feature colour is edited
1248 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1249 a time when scrolling vertically in wrapped mode.
1252 <!-- JAL-2630 -->Structure and alignment overview update
1253 as graduate feature colour settings are modified via the
1257 <!-- JAL-2034 -->Overview window doesn't always update
1258 when a group defined on the alignment is resized
1261 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1262 wrapped view result in positional status updates
1266 <!-- JAL-2563 -->Status bar doesn't show position for
1267 ambiguous amino acid and nucleotide symbols
1270 <!-- JAL-2602 -->Copy consensus sequence failed if
1271 alignment included gapped columns
1274 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1275 widgets don't permanently disappear
1278 <!-- JAL-2503 -->Cannot select or filter quantitative
1279 annotation that are shown only as column labels (e.g.
1280 T-Coffee column reliability scores)
1283 <!-- JAL-2594 -->Exception thrown if trying to create a
1284 sequence feature on gaps only
1287 <!-- JAL-2504 -->Features created with 'New feature'
1288 button from a Find inherit previously defined feature type
1289 rather than the Find query string
1292 <!-- JAL-2423 -->incorrect title in output window when
1293 exporting tree calculated in Jalview
1296 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1297 and then revealing them reorders sequences on the
1301 <!-- JAL-964 -->Group panel in sequence feature settings
1302 doesn't update to reflect available set of groups after
1303 interactively adding or modifying features
1306 <!-- JAL-2225 -->Sequence Database chooser unusable on
1310 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1311 only excluded gaps in current sequence and ignored
1318 <!-- JAL-2421 -->Overview window visible region moves
1319 erratically when hidden rows or columns are present
1322 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1323 Structure Viewer's colour menu don't correspond to
1327 <!-- JAL-2405 -->Protein specific colours only offered in
1328 colour and group colour menu for protein alignments
1331 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1332 reflect currently selected view or group's shading
1336 <!-- JAL-2624 -->Feature colour thresholds not respected
1337 when rendered on overview and structures when opacity at
1341 <!-- JAL-2589 -->User defined gap colour not shown in
1342 overview when features overlaid on alignment
1345 <em>Data import/export</em>
1348 <!-- JAL-2576 -->Very large alignments take a long time to
1352 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1353 added after a sequence was imported are not written to
1357 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1358 when importing RNA secondary structure via Stockholm
1361 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1362 not shown in correct direction for simple pseudoknots
1365 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1366 with lightGray or darkGray via features file (but can
1370 <!-- JAL-2383 -->Above PID colour threshold not recovered
1371 when alignment view imported from project
1374 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1375 structure and sequences extracted from structure files
1376 imported via URL and viewed in Jmol
1379 <!-- JAL-2520 -->Structures loaded via URL are saved in
1380 Jalview Projects rather than fetched via URL again when
1381 the project is loaded and the structure viewed
1384 <em>Web Services</em>
1387 <!-- JAL-2519 -->EnsemblGenomes example failing after
1388 release of Ensembl v.88
1391 <!-- JAL-2366 -->Proxy server address and port always
1392 appear enabled in Preferences->Connections
1395 <!-- JAL-2461 -->DAS registry not found exceptions
1396 removed from console output
1399 <!-- JAL-2582 -->Cannot retrieve protein products from
1400 Ensembl by Peptide ID
1403 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1404 created from SIFTs, and spurious 'Couldn't open structure
1405 in Chimera' errors raised after April 2017 update (problem
1406 due to 'null' string rather than empty string used for
1407 residues with no corresponding PDB mapping).
1410 <em>Application UI</em>
1413 <!-- JAL-2361 -->User Defined Colours not added to Colour
1417 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1418 case' residues (button in colourscheme editor debugged and
1419 new documentation and tooltips added)
1422 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1423 doesn't restore group-specific text colour thresholds
1426 <!-- JAL-2243 -->Feature settings panel does not update as
1427 new features are added to alignment
1430 <!-- JAL-2532 -->Cancel in feature settings reverts
1431 changes to feature colours via the Amend features dialog
1434 <!-- JAL-2506 -->Null pointer exception when attempting to
1435 edit graduated feature colour via amend features dialog
1439 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1440 selection menu changes colours of alignment views
1443 <!-- JAL-2426 -->Spurious exceptions in console raised
1444 from alignment calculation workers after alignment has
1448 <!-- JAL-1608 -->Typo in selection popup menu - Create
1449 groups now 'Create Group'
1452 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1453 Create/Undefine group doesn't always work
1456 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1457 shown again after pressing 'Cancel'
1460 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1461 adjusts start position in wrap mode
1464 <!-- JAL-2563 -->Status bar doesn't show positions for
1465 ambiguous amino acids
1468 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1469 CDS/Protein view after CDS sequences added for aligned
1473 <!-- JAL-2592 -->User defined colourschemes called 'User
1474 Defined' don't appear in Colours menu
1480 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1481 score models doesn't always result in an updated PCA plot
1484 <!-- JAL-2442 -->Features not rendered as transparent on
1485 overview or linked structure view
1488 <!-- JAL-2372 -->Colour group by conservation doesn't
1492 <!-- JAL-2517 -->Hitting Cancel after applying
1493 user-defined colourscheme doesn't restore original
1500 <!-- JAL-2314 -->Unit test failure:
1501 jalview.ws.jabaws.RNAStructExportImport setup fails
1504 <!-- JAL-2307 -->Unit test failure:
1505 jalview.ws.sifts.SiftsClientTest due to compatibility
1506 problems with deep array comparison equality asserts in
1507 successive versions of TestNG
1510 <!-- JAL-2479 -->Relocated StructureChooserTest and
1511 ParameterUtilsTest Unit tests to Network suite
1514 <em>New Known Issues</em>
1517 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1518 phase after a sequence motif find operation
1521 <!-- JAL-2550 -->Importing annotation file with rows
1522 containing just upper and lower case letters are
1523 interpreted as WUSS RNA secondary structure symbols
1526 <!-- JAL-2590 -->Cannot load and display Newick trees
1527 reliably from eggnog Ortholog database
1530 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1531 containing features of type Highlight' when 'B' is pressed
1532 to mark columns containing highlighted regions.
1535 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1536 doesn't always add secondary structure annotation.
1541 <td width="60" nowrap>
1542 <div align="center">
1543 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1546 <td><div align="left">
1550 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1551 for all consensus calculations
1554 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1557 <li>Updated Jalview's Certum code signing certificate
1560 <em>Application</em>
1563 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1564 set of database cross-references, sorted alphabetically
1567 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1568 from database cross references. Users with custom links
1569 will receive a <a href="webServices/urllinks.html#warning">warning
1570 dialog</a> asking them to update their preferences.
1573 <!-- JAL-2287-->Cancel button and escape listener on
1574 dialog warning user about disconnecting Jalview from a
1578 <!-- JAL-2320-->Jalview's Chimera control window closes if
1579 the Chimera it is connected to is shut down
1582 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1583 columns menu item to mark columns containing highlighted
1584 regions (e.g. from structure selections or results of a
1588 <!-- JAL-2284-->Command line option for batch-generation
1589 of HTML pages rendering alignment data with the BioJS
1599 <!-- JAL-2286 -->Columns with more than one modal residue
1600 are not coloured or thresholded according to percent
1601 identity (first observed in Jalview 2.8.2)
1604 <!-- JAL-2301 -->Threonine incorrectly reported as not
1608 <!-- JAL-2318 -->Updates to documentation pages (above PID
1609 threshold, amino acid properties)
1612 <!-- JAL-2292 -->Lower case residues in sequences are not
1613 reported as mapped to residues in a structure file in the
1617 <!--JAL-2324 -->Identical features with non-numeric scores
1618 could be added multiple times to a sequence
1621 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1622 bond features shown as two highlighted residues rather
1623 than a range in linked structure views, and treated
1624 correctly when selecting and computing trees from features
1627 <!-- JAL-2281-->Custom URL links for database
1628 cross-references are matched to database name regardless
1633 <em>Application</em>
1636 <!-- JAL-2282-->Custom URL links for specific database
1637 names without regular expressions also offer links from
1641 <!-- JAL-2315-->Removing a single configured link in the
1642 URL links pane in Connections preferences doesn't actually
1643 update Jalview configuration
1646 <!-- JAL-2272-->CTRL-Click on a selected region to open
1647 the alignment area popup menu doesn't work on El-Capitan
1650 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1651 files with similarly named sequences if dropped onto the
1655 <!-- JAL-2312 -->Additional mappings are shown for PDB
1656 entries where more chains exist in the PDB accession than
1657 are reported in the SIFTS file
1660 <!-- JAL-2317-->Certain structures do not get mapped to
1661 the structure view when displayed with Chimera
1664 <!-- JAL-2317-->No chains shown in the Chimera view
1665 panel's View->Show Chains submenu
1668 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1669 work for wrapped alignment views
1672 <!--JAL-2197 -->Rename UI components for running JPred
1673 predictions from 'JNet' to 'JPred'
1676 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1677 corrupted when annotation panel vertical scroll is not at
1678 first annotation row
1681 <!--JAL-2332 -->Attempting to view structure for Hen
1682 lysozyme results in a PDB Client error dialog box
1685 <!-- JAL-2319 -->Structure View's mapping report switched
1686 ranges for PDB and sequence for SIFTS
1689 SIFTS 'Not_Observed' residues mapped to non-existant
1693 <!-- <em>New Known Issues</em>
1700 <td width="60" nowrap>
1701 <div align="center">
1702 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1703 <em>25/10/2016</em></strong>
1706 <td><em>Application</em>
1708 <li>3D Structure chooser opens with 'Cached structures'
1709 view if structures already loaded</li>
1710 <li>Progress bar reports models as they are loaded to
1711 structure views</li>
1717 <li>Colour by conservation always enabled and no tick
1718 shown in menu when BLOSUM or PID shading applied</li>
1719 <li>FER1_ARATH and FER2_ARATH labels were switched in
1720 example sequences/projects/trees</li>
1722 <em>Application</em>
1724 <li>Jalview projects with views of local PDB structure
1725 files saved on Windows cannot be opened on OSX</li>
1726 <li>Multiple structure views can be opened and superposed
1727 without timeout for structures with multiple models or
1728 multiple sequences in alignment</li>
1729 <li>Cannot import or associated local PDB files without a
1730 PDB ID HEADER line</li>
1731 <li>RMSD is not output in Jmol console when superposition
1733 <li>Drag and drop of URL from Browser fails for Linux and
1734 OSX versions earlier than El Capitan</li>
1735 <li>ENA client ignores invalid content from ENA server</li>
1736 <li>Exceptions are not raised in console when ENA client
1737 attempts to fetch non-existent IDs via Fetch DB Refs UI
1739 <li>Exceptions are not raised in console when a new view
1740 is created on the alignment</li>
1741 <li>OSX right-click fixed for group selections: CMD-click
1742 to insert/remove gaps in groups and CTRL-click to open group
1745 <em>Build and deployment</em>
1747 <li>URL link checker now copes with multi-line anchor
1750 <em>New Known Issues</em>
1752 <li>Drag and drop from URL links in browsers do not work
1759 <td width="60" nowrap>
1760 <div align="center">
1761 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1764 <td><em>General</em>
1767 <!-- JAL-2124 -->Updated Spanish translations.
1770 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1771 for importing structure data to Jalview. Enables mmCIF and
1775 <!-- JAL-192 --->Alignment ruler shows positions relative to
1779 <!-- JAL-2202 -->Position/residue shown in status bar when
1780 mousing over sequence associated annotation
1783 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1787 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1788 '()', canonical '[]' and invalid '{}' base pair populations
1792 <!-- JAL-2092 -->Feature settings popup menu options for
1793 showing or hiding columns containing a feature
1796 <!-- JAL-1557 -->Edit selected group by double clicking on
1797 group and sequence associated annotation labels
1800 <!-- JAL-2236 -->Sequence name added to annotation label in
1801 select/hide columns by annotation and colour by annotation
1805 </ul> <em>Application</em>
1808 <!-- JAL-2050-->Automatically hide introns when opening a
1809 gene/transcript view
1812 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1816 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1817 structure mappings with the EMBL-EBI PDBe SIFTS database
1820 <!-- JAL-2079 -->Updated download sites used for Rfam and
1821 Pfam sources to xfam.org
1824 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1827 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1828 over sequences in Jalview
1831 <!-- JAL-2027-->Support for reverse-complement coding
1832 regions in ENA and EMBL
1835 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1836 for record retrieval via ENA rest API
1839 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1843 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1844 groovy script execution
1847 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1848 alignment window's Calculate menu
1851 <!-- JAL-1812 -->Allow groovy scripts that call
1852 Jalview.getAlignFrames() to run in headless mode
1855 <!-- JAL-2068 -->Support for creating new alignment
1856 calculation workers from groovy scripts
1859 <!-- JAL-1369 --->Store/restore reference sequence in
1863 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1864 associations are now saved/restored from project
1867 <!-- JAL-1993 -->Database selection dialog always shown
1868 before sequence fetcher is opened
1871 <!-- JAL-2183 -->Double click on an entry in Jalview's
1872 database chooser opens a sequence fetcher
1875 <!-- JAL-1563 -->Free-text search client for UniProt using
1876 the UniProt REST API
1879 <!-- JAL-2168 -->-nonews command line parameter to prevent
1880 the news reader opening
1883 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1884 querying stored in preferences
1887 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1891 <!-- JAL-1977-->Tooltips shown on database chooser
1894 <!-- JAL-391 -->Reverse complement function in calculate
1895 menu for nucleotide sequences
1898 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1899 and feature counts preserves alignment ordering (and
1900 debugged for complex feature sets).
1903 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1904 viewing structures with Jalview 2.10
1907 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1908 genome, transcript CCDS and gene ids via the Ensembl and
1909 Ensembl Genomes REST API
1912 <!-- JAL-2049 -->Protein sequence variant annotation
1913 computed for 'sequence_variant' annotation on CDS regions
1917 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1921 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1922 Ref Fetcher fails to match, or otherwise updates sequence
1923 data from external database records.
1926 <!-- JAL-2154 -->Revised Jalview Project format for
1927 efficient recovery of sequence coding and alignment
1928 annotation relationships.
1930 </ul> <!-- <em>Applet</em>
1941 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1945 <!-- JAL-2018-->Export features in Jalview format (again)
1946 includes graduated colourschemes
1949 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1950 working with big alignments and lots of hidden columns
1953 <!-- JAL-2053-->Hidden column markers not always rendered
1954 at right of alignment window
1957 <!-- JAL-2067 -->Tidied up links in help file table of
1961 <!-- JAL-2072 -->Feature based tree calculation not shown
1965 <!-- JAL-2075 -->Hidden columns ignored during feature
1966 based tree calculation
1969 <!-- JAL-2065 -->Alignment view stops updating when show
1970 unconserved enabled for group on alignment
1973 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1977 <!-- JAL-2146 -->Alignment column in status incorrectly
1978 shown as "Sequence position" when mousing over
1982 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1983 hidden columns present
1986 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1987 user created annotation added to alignment
1990 <!-- JAL-1841 -->RNA Structure consensus only computed for
1991 '()' base pair annotation
1994 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1995 in zero scores for all base pairs in RNA Structure
1999 <!-- JAL-2174-->Extend selection with columns containing
2003 <!-- JAL-2275 -->Pfam format writer puts extra space at
2004 beginning of sequence
2007 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2011 <!-- JAL-2238 -->Cannot create groups on an alignment from
2012 from a tree when t-coffee scores are shown
2015 <!-- JAL-1836,1967 -->Cannot import and view PDB
2016 structures with chains containing negative resnums (4q4h)
2019 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2023 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2024 to Clustal, PIR and PileUp output
2027 <!-- JAL-2008 -->Reordering sequence features that are
2028 not visible causes alignment window to repaint
2031 <!-- JAL-2006 -->Threshold sliders don't work in
2032 graduated colour and colour by annotation row for e-value
2033 scores associated with features and annotation rows
2036 <!-- JAL-1797 -->amino acid physicochemical conservation
2037 calculation should be case independent
2040 <!-- JAL-2173 -->Remove annotation also updates hidden
2044 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2045 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2046 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2049 <!-- JAL-2065 -->Null pointer exceptions and redraw
2050 problems when reference sequence defined and 'show
2051 non-conserved' enabled
2054 <!-- JAL-1306 -->Quality and Conservation are now shown on
2055 load even when Consensus calculation is disabled
2058 <!-- JAL-1932 -->Remove right on penultimate column of
2059 alignment does nothing
2062 <em>Application</em>
2065 <!-- JAL-1552-->URLs and links can't be imported by
2066 drag'n'drop on OSX when launched via webstart (note - not
2067 yet fixed for El Capitan)
2070 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2071 output when running on non-gb/us i18n platforms
2074 <!-- JAL-1944 -->Error thrown when exporting a view with
2075 hidden sequences as flat-file alignment
2078 <!-- JAL-2030-->InstallAnywhere distribution fails when
2082 <!-- JAL-2080-->Jalview very slow to launch via webstart
2083 (also hotfix for 2.9.0b2)
2086 <!-- JAL-2085 -->Cannot save project when view has a
2087 reference sequence defined
2090 <!-- JAL-1011 -->Columns are suddenly selected in other
2091 alignments and views when revealing hidden columns
2094 <!-- JAL-1989 -->Hide columns not mirrored in complement
2095 view in a cDNA/Protein splitframe
2098 <!-- JAL-1369 -->Cannot save/restore representative
2099 sequence from project when only one sequence is
2103 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2104 in Structure Chooser
2107 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2108 structure consensus didn't refresh annotation panel
2111 <!-- JAL-1962 -->View mapping in structure view shows
2112 mappings between sequence and all chains in a PDB file
2115 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2116 dialogs format columns correctly, don't display array
2117 data, sort columns according to type
2120 <!-- JAL-1975 -->Export complete shown after destination
2121 file chooser is cancelled during an image export
2124 <!-- JAL-2025 -->Error when querying PDB Service with
2125 sequence name containing special characters
2128 <!-- JAL-2024 -->Manual PDB structure querying should be
2132 <!-- JAL-2104 -->Large tooltips with broken HTML
2133 formatting don't wrap
2136 <!-- JAL-1128 -->Figures exported from wrapped view are
2137 truncated so L looks like I in consensus annotation
2140 <!-- JAL-2003 -->Export features should only export the
2141 currently displayed features for the current selection or
2145 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2146 after fetching cross-references, and restoring from
2150 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2151 followed in the structure viewer
2154 <!-- JAL-2163 -->Titles for individual alignments in
2155 splitframe not restored from project
2158 <!-- JAL-2145 -->missing autocalculated annotation at
2159 trailing end of protein alignment in transcript/product
2160 splitview when pad-gaps not enabled by default
2163 <!-- JAL-1797 -->amino acid physicochemical conservation
2167 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2168 article has been read (reopened issue due to
2169 internationalisation problems)
2172 <!-- JAL-1960 -->Only offer PDB structures in structure
2173 viewer based on sequence name, PDB and UniProt
2178 <!-- JAL-1976 -->No progress bar shown during export of
2182 <!-- JAL-2213 -->Structures not always superimposed after
2183 multiple structures are shown for one or more sequences.
2186 <!-- JAL-1370 -->Reference sequence characters should not
2187 be replaced with '.' when 'Show unconserved' format option
2191 <!-- JAL-1823 -->Cannot specify chain code when entering
2192 specific PDB id for sequence
2195 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2196 'Export hidden sequences' is enabled, but 'export hidden
2197 columns' is disabled.
2200 <!--JAL-2026-->Best Quality option in structure chooser
2201 selects lowest rather than highest resolution structures
2205 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2206 to sequence mapping in 'View Mappings' report
2209 <!-- JAL-2284 -->Unable to read old Jalview projects that
2210 contain non-XML data added after Jalvew wrote project.
2213 <!-- JAL-2118 -->Newly created annotation row reorders
2214 after clicking on it to create new annotation for a
2218 <!-- JAL-1980 -->Null Pointer Exception raised when
2219 pressing Add on an orphaned cut'n'paste window.
2221 <!-- may exclude, this is an external service stability issue JAL-1941
2222 -- > RNA 3D structure not added via DSSR service</li> -->
2227 <!-- JAL-2151 -->Incorrect columns are selected when
2228 hidden columns present before start of sequence
2231 <!-- JAL-1986 -->Missing dependencies on applet pages
2235 <!-- JAL-1947 -->Overview pixel size changes when
2236 sequences are hidden in applet
2239 <!-- JAL-1996 -->Updated instructions for applet
2240 deployment on examples pages.
2247 <td width="60" nowrap>
2248 <div align="center">
2249 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2250 <em>16/10/2015</em></strong>
2253 <td><em>General</em>
2255 <li>Time stamps for signed Jalview application and applet
2260 <em>Application</em>
2262 <li>Duplicate group consensus and conservation rows
2263 shown when tree is partitioned</li>
2264 <li>Erratic behaviour when tree partitions made with
2265 multiple cDNA/Protein split views</li>
2271 <td width="60" nowrap>
2272 <div align="center">
2273 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2274 <em>8/10/2015</em></strong>
2277 <td><em>General</em>
2279 <li>Updated Spanish translations of localized text for
2281 </ul> <em>Application</em>
2283 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2284 <li>Signed OSX InstallAnywhere installer<br></li>
2285 <li>Support for per-sequence based annotations in BioJSON</li>
2286 </ul> <em>Applet</em>
2288 <li>Split frame example added to applet examples page</li>
2289 </ul> <em>Build and Deployment</em>
2292 <!-- JAL-1888 -->New ant target for running Jalview's test
2300 <li>Mapping of cDNA to protein in split frames
2301 incorrect when sequence start > 1</li>
2302 <li>Broken images in filter column by annotation dialog
2304 <li>Feature colours not parsed from features file</li>
2305 <li>Exceptions and incomplete link URLs recovered when
2306 loading a features file containing HTML tags in feature
2310 <em>Application</em>
2312 <li>Annotations corrupted after BioJS export and
2314 <li>Incorrect sequence limits after Fetch DB References
2315 with 'trim retrieved sequences'</li>
2316 <li>Incorrect warning about deleting all data when
2317 deleting selected columns</li>
2318 <li>Patch to build system for shipping properly signed
2319 JNLP templates for webstart launch</li>
2320 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2321 unreleased structures for download or viewing</li>
2322 <li>Tab/space/return keystroke operation of EMBL-PDBe
2323 fetcher/viewer dialogs works correctly</li>
2324 <li>Disabled 'minimise' button on Jalview windows
2325 running on OSX to workaround redraw hang bug</li>
2326 <li>Split cDNA/Protein view position and geometry not
2327 recovered from jalview project</li>
2328 <li>Initial enabled/disabled state of annotation menu
2329 sorter 'show autocalculated first/last' corresponds to
2331 <li>Restoring of Clustal, RNA Helices and T-Coffee
2332 color schemes from BioJSON</li>
2336 <li>Reorder sequences mirrored in cDNA/Protein split
2338 <li>Applet with Jmol examples not loading correctly</li>
2344 <td><div align="center">
2345 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2347 <td><em>General</em>
2349 <li>Linked visualisation and analysis of DNA and Protein
2352 <li>Translated cDNA alignments shown as split protein
2353 and DNA alignment views</li>
2354 <li>Codon consensus annotation for linked protein and
2355 cDNA alignment views</li>
2356 <li>Link cDNA or Protein product sequences by loading
2357 them onto Protein or cDNA alignments</li>
2358 <li>Reconstruct linked cDNA alignment from aligned
2359 protein sequences</li>
2362 <li>Jmol integration updated to Jmol v14.2.14</li>
2363 <li>Import and export of Jalview alignment views as <a
2364 href="features/bioJsonFormat.html">BioJSON</a></li>
2365 <li>New alignment annotation file statements for
2366 reference sequences and marking hidden columns</li>
2367 <li>Reference sequence based alignment shading to
2368 highlight variation</li>
2369 <li>Select or hide columns according to alignment
2371 <li>Find option for locating sequences by description</li>
2372 <li>Conserved physicochemical properties shown in amino
2373 acid conservation row</li>
2374 <li>Alignments can be sorted by number of RNA helices</li>
2375 </ul> <em>Application</em>
2377 <li>New cDNA/Protein analysis capabilities
2379 <li>Get Cross-References should open a Split Frame
2380 view with cDNA/Protein</li>
2381 <li>Detect when nucleotide sequences and protein
2382 sequences are placed in the same alignment</li>
2383 <li>Split cDNA/Protein views are saved in Jalview
2388 <li>Use REST API to talk to Chimera</li>
2389 <li>Selected regions in Chimera are highlighted in linked
2390 Jalview windows</li>
2392 <li>VARNA RNA viewer updated to v3.93</li>
2393 <li>VARNA views are saved in Jalview Projects</li>
2394 <li>Pseudoknots displayed as Jalview RNA annotation can
2395 be shown in VARNA</li>
2397 <li>Make groups for selection uses marked columns as well
2398 as the active selected region</li>
2400 <li>Calculate UPGMA and NJ trees using sequence feature
2402 <li>New Export options
2404 <li>New Export Settings dialog to control hidden
2405 region export in flat file generation</li>
2407 <li>Export alignment views for display with the <a
2408 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2410 <li>Export scrollable SVG in HTML page</li>
2411 <li>Optional embedding of BioJSON data when exporting
2412 alignment figures to HTML</li>
2414 <li>3D structure retrieval and display
2416 <li>Free text and structured queries with the PDBe
2418 <li>PDBe Search API based discovery and selection of
2419 PDB structures for a sequence set</li>
2423 <li>JPred4 employed for protein secondary structure
2425 <li>Hide Insertions menu option to hide unaligned columns
2426 for one or a group of sequences</li>
2427 <li>Automatically hide insertions in alignments imported
2428 from the JPred4 web server</li>
2429 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2430 system on OSX<br />LGPL libraries courtesy of <a
2431 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2433 <li>changed 'View nucleotide structure' submenu to 'View
2434 VARNA 2D Structure'</li>
2435 <li>change "View protein structure" menu option to "3D
2438 </ul> <em>Applet</em>
2440 <li>New layout for applet example pages</li>
2441 <li>New parameters to enable SplitFrame view
2442 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2443 <li>New example demonstrating linked viewing of cDNA and
2444 Protein alignments</li>
2445 </ul> <em>Development and deployment</em>
2447 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2448 <li>Include installation type and git revision in build
2449 properties and console log output</li>
2450 <li>Jalview Github organisation, and new github site for
2451 storing BioJsMSA Templates</li>
2452 <li>Jalview's unit tests now managed with TestNG</li>
2455 <!-- <em>General</em>
2457 </ul> --> <!-- issues resolved --> <em>Application</em>
2459 <li>Escape should close any open find dialogs</li>
2460 <li>Typo in select-by-features status report</li>
2461 <li>Consensus RNA secondary secondary structure
2462 predictions are not highlighted in amber</li>
2463 <li>Missing gap character in v2.7 example file means
2464 alignment appears unaligned when pad-gaps is not enabled</li>
2465 <li>First switch to RNA Helices colouring doesn't colour
2466 associated structure views</li>
2467 <li>ID width preference option is greyed out when auto
2468 width checkbox not enabled</li>
2469 <li>Stopped a warning dialog from being shown when
2470 creating user defined colours</li>
2471 <li>'View Mapping' in structure viewer shows sequence
2472 mappings for just that viewer's sequences</li>
2473 <li>Workaround for superposing PDB files containing
2474 multiple models in Chimera</li>
2475 <li>Report sequence position in status bar when hovering
2476 over Jmol structure</li>
2477 <li>Cannot output gaps as '.' symbols with Selection ->
2478 output to text box</li>
2479 <li>Flat file exports of alignments with hidden columns
2480 have incorrect sequence start/end</li>
2481 <li>'Aligning' a second chain to a Chimera structure from
2483 <li>Colour schemes applied to structure viewers don't
2484 work for nucleotide</li>
2485 <li>Loading/cut'n'pasting an empty or invalid file leads
2486 to a grey/invisible alignment window</li>
2487 <li>Exported Jpred annotation from a sequence region
2488 imports to different position</li>
2489 <li>Space at beginning of sequence feature tooltips shown
2490 on some platforms</li>
2491 <li>Chimera viewer 'View | Show Chain' menu is not
2493 <li>'New View' fails with a Null Pointer Exception in
2494 console if Chimera has been opened</li>
2495 <li>Mouseover to Chimera not working</li>
2496 <li>Miscellaneous ENA XML feature qualifiers not
2498 <li>NPE in annotation renderer after 'Extract Scores'</li>
2499 <li>If two structures in one Chimera window, mouseover of
2500 either sequence shows on first structure</li>
2501 <li>'Show annotations' options should not make
2502 non-positional annotations visible</li>
2503 <li>Subsequence secondary structure annotation not shown
2504 in right place after 'view flanking regions'</li>
2505 <li>File Save As type unset when current file format is
2507 <li>Save as '.jar' option removed for saving Jalview
2509 <li>Colour by Sequence colouring in Chimera more
2511 <li>Cannot 'add reference annotation' for a sequence in
2512 several views on same alignment</li>
2513 <li>Cannot show linked products for EMBL / ENA records</li>
2514 <li>Jalview's tooltip wraps long texts containing no
2516 </ul> <em>Applet</em>
2518 <li>Jmol to JalviewLite mouseover/link not working</li>
2519 <li>JalviewLite can't import sequences with ID
2520 descriptions containing angle brackets</li>
2521 </ul> <em>General</em>
2523 <li>Cannot export and reimport RNA secondary structure
2524 via jalview annotation file</li>
2525 <li>Random helix colour palette for colour by annotation
2526 with RNA secondary structure</li>
2527 <li>Mouseover to cDNA from STOP residue in protein
2528 translation doesn't work.</li>
2529 <li>hints when using the select by annotation dialog box</li>
2530 <li>Jmol alignment incorrect if PDB file has alternate CA
2532 <li>FontChooser message dialog appears to hang after
2533 choosing 1pt font</li>
2534 <li>Peptide secondary structure incorrectly imported from
2535 annotation file when annotation display text includes 'e' or
2537 <li>Cannot set colour of new feature type whilst creating
2539 <li>cDNA translation alignment should not be sequence
2540 order dependent</li>
2541 <li>'Show unconserved' doesn't work for lower case
2543 <li>Nucleotide ambiguity codes involving R not recognised</li>
2544 </ul> <em>Deployment and Documentation</em>
2546 <li>Applet example pages appear different to the rest of
2547 www.jalview.org</li>
2548 </ul> <em>Application Known issues</em>
2550 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2551 <li>Misleading message appears after trying to delete
2553 <li>Jalview icon not shown in dock after InstallAnywhere
2554 version launches</li>
2555 <li>Fetching EMBL reference for an RNA sequence results
2556 fails with a sequence mismatch</li>
2557 <li>Corrupted or unreadable alignment display when
2558 scrolling alignment to right</li>
2559 <li>ArrayIndexOutOfBoundsException thrown when remove
2560 empty columns called on alignment with ragged gapped ends</li>
2561 <li>auto calculated alignment annotation rows do not get
2562 placed above or below non-autocalculated rows</li>
2563 <li>Jalview dekstop becomes sluggish at full screen in
2564 ultra-high resolution</li>
2565 <li>Cannot disable consensus calculation independently of
2566 quality and conservation</li>
2567 <li>Mouseover highlighting between cDNA and protein can
2568 become sluggish with more than one splitframe shown</li>
2569 </ul> <em>Applet Known Issues</em>
2571 <li>Core PDB parsing code requires Jmol</li>
2572 <li>Sequence canvas panel goes white when alignment
2573 window is being resized</li>
2579 <td><div align="center">
2580 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2582 <td><em>General</em>
2584 <li>Updated Java code signing certificate donated by
2586 <li>Features and annotation preserved when performing
2587 pairwise alignment</li>
2588 <li>RNA pseudoknot annotation can be
2589 imported/exported/displayed</li>
2590 <li>'colour by annotation' can colour by RNA and
2591 protein secondary structure</li>
2592 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2593 post-hoc with 2.9 release</em>)
2596 </ul> <em>Application</em>
2598 <li>Extract and display secondary structure for sequences
2599 with 3D structures</li>
2600 <li>Support for parsing RNAML</li>
2601 <li>Annotations menu for layout
2603 <li>sort sequence annotation rows by alignment</li>
2604 <li>place sequence annotation above/below alignment
2607 <li>Output in Stockholm format</li>
2608 <li>Internationalisation: improved Spanish (es)
2610 <li>Structure viewer preferences tab</li>
2611 <li>Disorder and Secondary Structure annotation tracks
2612 shared between alignments</li>
2613 <li>UCSF Chimera launch and linked highlighting from
2615 <li>Show/hide all sequence associated annotation rows for
2616 all or current selection</li>
2617 <li>disorder and secondary structure predictions
2618 available as dataset annotation</li>
2619 <li>Per-sequence rna helices colouring</li>
2622 <li>Sequence database accessions imported when fetching
2623 alignments from Rfam</li>
2624 <li>update VARNA version to 3.91</li>
2626 <li>New groovy scripts for exporting aligned positions,
2627 conservation values, and calculating sum of pairs scores.</li>
2628 <li>Command line argument to set default JABAWS server</li>
2629 <li>include installation type in build properties and
2630 console log output</li>
2631 <li>Updated Jalview project format to preserve dataset
2635 <!-- issues resolved --> <em>Application</em>
2637 <li>Distinguish alignment and sequence associated RNA
2638 structure in structure->view->VARNA</li>
2639 <li>Raise dialog box if user deletes all sequences in an
2641 <li>Pressing F1 results in documentation opening twice</li>
2642 <li>Sequence feature tooltip is wrapped</li>
2643 <li>Double click on sequence associated annotation
2644 selects only first column</li>
2645 <li>Redundancy removal doesn't result in unlinked
2646 leaves shown in tree</li>
2647 <li>Undos after several redundancy removals don't undo
2649 <li>Hide sequence doesn't hide associated annotation</li>
2650 <li>User defined colours dialog box too big to fit on
2651 screen and buttons not visible</li>
2652 <li>author list isn't updated if already written to
2653 Jalview properties</li>
2654 <li>Popup menu won't open after retrieving sequence
2656 <li>File open window for associate PDB doesn't open</li>
2657 <li>Left-then-right click on a sequence id opens a
2658 browser search window</li>
2659 <li>Cannot open sequence feature shading/sort popup menu
2660 in feature settings dialog</li>
2661 <li>better tooltip placement for some areas of Jalview
2663 <li>Allow addition of JABAWS Server which doesn't
2664 pass validation</li>
2665 <li>Web services parameters dialog box is too large to
2667 <li>Muscle nucleotide alignment preset obscured by
2669 <li>JABAWS preset submenus don't contain newly
2670 defined user preset</li>
2671 <li>MSA web services warns user if they were launched
2672 with invalid input</li>
2673 <li>Jalview cannot contact DAS Registy when running on
2676 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2677 'Superpose with' submenu not shown when new view
2681 </ul> <!-- <em>Applet</em>
2683 </ul> <em>General</em>
2685 </ul>--> <em>Deployment and Documentation</em>
2687 <li>2G and 1G options in launchApp have no effect on
2688 memory allocation</li>
2689 <li>launchApp service doesn't automatically open
2690 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2692 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2693 InstallAnywhere reports cannot find valid JVM when Java
2694 1.7_055 is available
2696 </ul> <em>Application Known issues</em>
2699 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2700 corrupted or unreadable alignment display when scrolling
2704 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2705 retrieval fails but progress bar continues for DAS retrieval
2706 with large number of ID
2709 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2710 flatfile output of visible region has incorrect sequence
2714 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2715 rna structure consensus doesn't update when secondary
2716 structure tracks are rearranged
2719 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2720 invalid rna structure positional highlighting does not
2721 highlight position of invalid base pairs
2724 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2725 out of memory errors are not raised when saving Jalview
2726 project from alignment window file menu
2729 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2730 Switching to RNA Helices colouring doesn't propagate to
2734 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2735 colour by RNA Helices not enabled when user created
2736 annotation added to alignment
2739 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2740 Jalview icon not shown on dock in Mountain Lion/Webstart
2742 </ul> <em>Applet Known Issues</em>
2745 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2746 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2749 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2750 Jalview and Jmol example not compatible with IE9
2753 <li>Sort by annotation score doesn't reverse order
2759 <td><div align="center">
2760 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2763 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2766 <li>Internationalisation of user interface (usually
2767 called i18n support) and translation for Spanish locale</li>
2768 <li>Define/Undefine group on current selection with
2769 Ctrl-G/Shift Ctrl-G</li>
2770 <li>Improved group creation/removal options in
2771 alignment/sequence Popup menu</li>
2772 <li>Sensible precision for symbol distribution
2773 percentages shown in logo tooltip.</li>
2774 <li>Annotation panel height set according to amount of
2775 annotation when alignment first opened</li>
2776 </ul> <em>Application</em>
2778 <li>Interactive consensus RNA secondary structure
2779 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2780 <li>Select columns containing particular features from
2781 Feature Settings dialog</li>
2782 <li>View all 'representative' PDB structures for selected
2784 <li>Update Jalview project format:
2786 <li>New file extension for Jalview projects '.jvp'</li>
2787 <li>Preserve sequence and annotation dataset (to
2788 store secondary structure annotation,etc)</li>
2789 <li>Per group and alignment annotation and RNA helix
2793 <li>New similarity measures for PCA and Tree calculation
2795 <li>Experimental support for retrieval and viewing of
2796 flanking regions for an alignment</li>
2800 <!-- issues resolved --> <em>Application</em>
2802 <li>logo keeps spinning and status remains at queued or
2803 running after job is cancelled</li>
2804 <li>cannot export features from alignments imported from
2805 Jalview/VAMSAS projects</li>
2806 <li>Buggy slider for web service parameters that take
2808 <li>Newly created RNA secondary structure line doesn't
2809 have 'display all symbols' flag set</li>
2810 <li>T-COFFEE alignment score shading scheme and other
2811 annotation shading not saved in Jalview project</li>
2812 <li>Local file cannot be loaded in freshly downloaded
2814 <li>Jalview icon not shown on dock in Mountain
2816 <li>Load file from desktop file browser fails</li>
2817 <li>Occasional NPE thrown when calculating large trees</li>
2818 <li>Cannot reorder or slide sequences after dragging an
2819 alignment onto desktop</li>
2820 <li>Colour by annotation dialog throws NPE after using
2821 'extract scores' function</li>
2822 <li>Loading/cut'n'pasting an empty file leads to a grey
2823 alignment window</li>
2824 <li>Disorder thresholds rendered incorrectly after
2825 performing IUPred disorder prediction</li>
2826 <li>Multiple group annotated consensus rows shown when
2827 changing 'normalise logo' display setting</li>
2828 <li>Find shows blank dialog after 'finished searching' if
2829 nothing matches query</li>
2830 <li>Null Pointer Exceptions raised when sorting by
2831 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2833 <li>Errors in Jmol console when structures in alignment
2834 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2836 <li>Not all working JABAWS services are shown in
2838 <li>JAVAWS version of Jalview fails to launch with
2839 'invalid literal/length code'</li>
2840 <li>Annotation/RNA Helix colourschemes cannot be applied
2841 to alignment with groups (actually fixed in 2.8.0b1)</li>
2842 <li>RNA Helices and T-Coffee Scores available as default
2845 </ul> <em>Applet</em>
2847 <li>Remove group option is shown even when selection is
2849 <li>Apply to all groups ticked but colourscheme changes
2850 don't affect groups</li>
2851 <li>Documented RNA Helices and T-Coffee Scores as valid
2852 colourscheme name</li>
2853 <li>Annotation labels drawn on sequence IDs when
2854 Annotation panel is not displayed</li>
2855 <li>Increased font size for dropdown menus on OSX and
2856 embedded windows</li>
2857 </ul> <em>Other</em>
2859 <li>Consensus sequence for alignments/groups with a
2860 single sequence were not calculated</li>
2861 <li>annotation files that contain only groups imported as
2862 annotation and junk sequences</li>
2863 <li>Fasta files with sequences containing '*' incorrectly
2864 recognised as PFAM or BLC</li>
2865 <li>conservation/PID slider apply all groups option
2866 doesn't affect background (2.8.0b1)
2868 <li>redundancy highlighting is erratic at 0% and 100%</li>
2869 <li>Remove gapped columns fails for sequences with ragged
2871 <li>AMSA annotation row with leading spaces is not
2872 registered correctly on import</li>
2873 <li>Jalview crashes when selecting PCA analysis for
2874 certain alignments</li>
2875 <li>Opening the colour by annotation dialog for an
2876 existing annotation based 'use original colours'
2877 colourscheme loses original colours setting</li>
2882 <td><div align="center">
2883 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2884 <em>30/1/2014</em></strong>
2888 <li>Trusted certificates for JalviewLite applet and
2889 Jalview Desktop application<br />Certificate was donated by
2890 <a href="https://www.certum.eu">Certum</a> to the Jalview
2891 open source project).
2893 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2894 <li>Output in Stockholm format</li>
2895 <li>Allow import of data from gzipped files</li>
2896 <li>Export/import group and sequence associated line
2897 graph thresholds</li>
2898 <li>Nucleotide substitution matrix that supports RNA and
2899 ambiguity codes</li>
2900 <li>Allow disorder predictions to be made on the current
2901 selection (or visible selection) in the same way that JPred
2903 <li>Groovy scripting for headless Jalview operation</li>
2904 </ul> <em>Other improvements</em>
2906 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2907 <li>COMBINE statement uses current SEQUENCE_REF and
2908 GROUP_REF scope to group annotation rows</li>
2909 <li>Support '' style escaping of quotes in Newick
2911 <li>Group options for JABAWS service by command line name</li>
2912 <li>Empty tooltip shown for JABA service options with a
2913 link but no description</li>
2914 <li>Select primary source when selecting authority in
2915 database fetcher GUI</li>
2916 <li>Add .mfa to FASTA file extensions recognised by
2918 <li>Annotation label tooltip text wrap</li>
2923 <li>Slow scrolling when lots of annotation rows are
2925 <li>Lots of NPE (and slowness) after creating RNA
2926 secondary structure annotation line</li>
2927 <li>Sequence database accessions not imported when
2928 fetching alignments from Rfam</li>
2929 <li>Incorrect SHMR submission for sequences with
2931 <li>View all structures does not always superpose
2933 <li>Option widgets in service parameters not updated to
2934 reflect user or preset settings</li>
2935 <li>Null pointer exceptions for some services without
2936 presets or adjustable parameters</li>
2937 <li>Discover PDB IDs entry in structure menu doesn't
2938 discover PDB xRefs</li>
2939 <li>Exception encountered while trying to retrieve
2940 features with DAS</li>
2941 <li>Lowest value in annotation row isn't coloured
2942 when colour by annotation (per sequence) is coloured</li>
2943 <li>Keyboard mode P jumps to start of gapped region when
2944 residue follows a gap</li>
2945 <li>Jalview appears to hang importing an alignment with
2946 Wrap as default or after enabling Wrap</li>
2947 <li>'Right click to add annotations' message
2948 shown in wrap mode when no annotations present</li>
2949 <li>Disorder predictions fail with NPE if no automatic
2950 annotation already exists on alignment</li>
2951 <li>oninit javascript function should be called after
2952 initialisation completes</li>
2953 <li>Remove redundancy after disorder prediction corrupts
2954 alignment window display</li>
2955 <li>Example annotation file in documentation is invalid</li>
2956 <li>Grouped line graph annotation rows are not exported
2957 to annotation file</li>
2958 <li>Multi-harmony analysis cannot be run when only two
2960 <li>Cannot create multiple groups of line graphs with
2961 several 'combine' statements in annotation file</li>
2962 <li>Pressing return several times causes Number Format
2963 exceptions in keyboard mode</li>
2964 <li>Multi-harmony (SHMMR) method doesn't submit
2965 correct partitions for input data</li>
2966 <li>Translation from DNA to Amino Acids fails</li>
2967 <li>Jalview fail to load newick tree with quoted label</li>
2968 <li>--headless flag isn't understood</li>
2969 <li>ClassCastException when generating EPS in headless
2971 <li>Adjusting sequence-associated shading threshold only
2972 changes one row's threshold</li>
2973 <li>Preferences and Feature settings panel panel
2974 doesn't open</li>
2975 <li>hide consensus histogram also hides conservation and
2976 quality histograms</li>
2981 <td><div align="center">
2982 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2984 <td><em>Application</em>
2986 <li>Support for JABAWS 2.0 Services (AACon alignment
2987 conservation, protein disorder and Clustal Omega)</li>
2988 <li>JABAWS server status indicator in Web Services
2990 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2991 in Jalview alignment window</li>
2992 <li>Updated Jalview build and deploy framework for OSX
2993 mountain lion, windows 7, and 8</li>
2994 <li>Nucleotide substitution matrix for PCA that supports
2995 RNA and ambiguity codes</li>
2997 <li>Improved sequence database retrieval GUI</li>
2998 <li>Support fetching and database reference look up
2999 against multiple DAS sources (Fetch all from in 'fetch db
3001 <li>Jalview project improvements
3003 <li>Store and retrieve the 'belowAlignment'
3004 flag for annotation</li>
3005 <li>calcId attribute to group annotation rows on the
3007 <li>Store AACon calculation settings for a view in
3008 Jalview project</li>
3012 <li>horizontal scrolling gesture support</li>
3013 <li>Visual progress indicator when PCA calculation is
3015 <li>Simpler JABA web services menus</li>
3016 <li>visual indication that web service results are still
3017 being retrieved from server</li>
3018 <li>Serialise the dialogs that are shown when Jalview
3019 starts up for first time</li>
3020 <li>Jalview user agent string for interacting with HTTP
3022 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3024 <li>Examples directory and Groovy library included in
3025 InstallAnywhere distribution</li>
3026 </ul> <em>Applet</em>
3028 <li>RNA alignment and secondary structure annotation
3029 visualization applet example</li>
3030 </ul> <em>General</em>
3032 <li>Normalise option for consensus sequence logo</li>
3033 <li>Reset button in PCA window to return dimensions to
3035 <li>Allow seqspace or Jalview variant of alignment PCA
3037 <li>PCA with either nucleic acid and protein substitution
3039 <li>Allow windows containing HTML reports to be exported
3041 <li>Interactive display and editing of RNA secondary
3042 structure contacts</li>
3043 <li>RNA Helix Alignment Colouring</li>
3044 <li>RNA base pair logo consensus</li>
3045 <li>Parse sequence associated secondary structure
3046 information in Stockholm files</li>
3047 <li>HTML Export database accessions and annotation
3048 information presented in tooltip for sequences</li>
3049 <li>Import secondary structure from LOCARNA clustalw
3050 style RNA alignment files</li>
3051 <li>import and visualise T-COFFEE quality scores for an
3053 <li>'colour by annotation' per sequence option to
3054 shade each sequence according to its associated alignment
3056 <li>New Jalview Logo</li>
3057 </ul> <em>Documentation and Development</em>
3059 <li>documentation for score matrices used in Jalview</li>
3060 <li>New Website!</li>
3062 <td><em>Application</em>
3064 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3065 wsdbfetch REST service</li>
3066 <li>Stop windows being moved outside desktop on OSX</li>
3067 <li>Filetype associations not installed for webstart
3069 <li>Jalview does not always retrieve progress of a JABAWS
3070 job execution in full once it is complete</li>
3071 <li>revise SHMR RSBS definition to ensure alignment is
3072 uploaded via ali_file parameter</li>
3073 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3074 <li>View all structures superposed fails with exception</li>
3075 <li>Jnet job queues forever if a very short sequence is
3076 submitted for prediction</li>
3077 <li>Cut and paste menu not opened when mouse clicked on
3079 <li>Putting fractional value into integer text box in
3080 alignment parameter dialog causes Jalview to hang</li>
3081 <li>Structure view highlighting doesn't work on
3083 <li>View all structures fails with exception shown in
3085 <li>Characters in filename associated with PDBEntry not
3086 escaped in a platform independent way</li>
3087 <li>Jalview desktop fails to launch with exception when
3089 <li>Tree calculation reports 'you must have 2 or more
3090 sequences selected' when selection is empty</li>
3091 <li>Jalview desktop fails to launch with jar signature
3092 failure when java web start temporary file caching is
3094 <li>DAS Sequence retrieval with range qualification
3095 results in sequence xref which includes range qualification</li>
3096 <li>Errors during processing of command line arguments
3097 cause progress bar (JAL-898) to be removed</li>
3098 <li>Replace comma for semi-colon option not disabled for
3099 DAS sources in sequence fetcher</li>
3100 <li>Cannot close news reader when JABAWS server warning
3101 dialog is shown</li>
3102 <li>Option widgets not updated to reflect user settings</li>
3103 <li>Edited sequence not submitted to web service</li>
3104 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3105 <li>InstallAnywhere installer doesn't unpack and run
3106 on OSX Mountain Lion</li>
3107 <li>Annotation panel not given a scroll bar when
3108 sequences with alignment annotation are pasted into the
3110 <li>Sequence associated annotation rows not associated
3111 when loaded from Jalview project</li>
3112 <li>Browser launch fails with NPE on java 1.7</li>
3113 <li>JABAWS alignment marked as finished when job was
3114 cancelled or job failed due to invalid input</li>
3115 <li>NPE with v2.7 example when clicking on Tree
3116 associated with all views</li>
3117 <li>Exceptions when copy/paste sequences with grouped
3118 annotation rows to new window</li>
3119 </ul> <em>Applet</em>
3121 <li>Sequence features are momentarily displayed before
3122 they are hidden using hidefeaturegroups applet parameter</li>
3123 <li>loading features via javascript API automatically
3124 enables feature display</li>
3125 <li>scrollToColumnIn javascript API method doesn't
3127 </ul> <em>General</em>
3129 <li>Redundancy removal fails for rna alignment</li>
3130 <li>PCA calculation fails when sequence has been selected
3131 and then deselected</li>
3132 <li>PCA window shows grey box when first opened on OSX</li>
3133 <li>Letters coloured pink in sequence logo when alignment
3134 coloured with clustalx</li>
3135 <li>Choosing fonts without letter symbols defined causes
3136 exceptions and redraw errors</li>
3137 <li>Initial PCA plot view is not same as manually
3138 reconfigured view</li>
3139 <li>Grouped annotation graph label has incorrect line
3141 <li>Grouped annotation graph label display is corrupted
3142 for lots of labels</li>
3147 <div align="center">
3148 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3151 <td><em>Application</em>
3153 <li>Jalview Desktop News Reader</li>
3154 <li>Tweaked default layout of web services menu</li>
3155 <li>View/alignment association menu to enable user to
3156 easily specify which alignment a multi-structure view takes
3157 its colours/correspondences from</li>
3158 <li>Allow properties file location to be specified as URL</li>
3159 <li>Extend Jalview project to preserve associations
3160 between many alignment views and a single Jmol display</li>
3161 <li>Store annotation row height in Jalview project file</li>
3162 <li>Annotation row column label formatting attributes
3163 stored in project file</li>
3164 <li>Annotation row order for auto-calculated annotation
3165 rows preserved in Jalview project file</li>
3166 <li>Visual progress indication when Jalview state is
3167 saved using Desktop window menu</li>
3168 <li>Visual indication that command line arguments are
3169 still being processed</li>
3170 <li>Groovy script execution from URL</li>
3171 <li>Colour by annotation default min and max colours in
3173 <li>Automatically associate PDB files dragged onto an
3174 alignment with sequences that have high similarity and
3176 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3177 <li>'view structures' option to open many
3178 structures in same window</li>
3179 <li>Sort associated views menu option for tree panel</li>
3180 <li>Group all JABA and non-JABA services for a particular
3181 analysis function in its own submenu</li>
3182 </ul> <em>Applet</em>
3184 <li>Userdefined and autogenerated annotation rows for
3186 <li>Adjustment of alignment annotation pane height</li>
3187 <li>Annotation scrollbar for annotation panel</li>
3188 <li>Drag to reorder annotation rows in annotation panel</li>
3189 <li>'automaticScrolling' parameter</li>
3190 <li>Allow sequences with partial ID string matches to be
3191 annotated from GFF/Jalview features files</li>
3192 <li>Sequence logo annotation row in applet</li>
3193 <li>Absolute paths relative to host server in applet
3194 parameters are treated as such</li>
3195 <li>New in the JalviewLite javascript API:
3197 <li>JalviewLite.js javascript library</li>
3198 <li>Javascript callbacks for
3200 <li>Applet initialisation</li>
3201 <li>Sequence/alignment mouse-overs and selections</li>
3204 <li>scrollTo row and column alignment scrolling
3206 <li>Select sequence/alignment regions from javascript</li>
3207 <li>javascript structure viewer harness to pass
3208 messages between Jmol and Jalview when running as
3209 distinct applets</li>
3210 <li>sortBy method</li>
3211 <li>Set of applet and application examples shipped
3212 with documentation</li>
3213 <li>New example to demonstrate JalviewLite and Jmol
3214 javascript message exchange</li>
3216 </ul> <em>General</em>
3218 <li>Enable Jmol displays to be associated with multiple
3219 multiple alignments</li>
3220 <li>Option to automatically sort alignment with new tree</li>
3221 <li>User configurable link to enable redirects to a
3222 www.Jalview.org mirror</li>
3223 <li>Jmol colours option for Jmol displays</li>
3224 <li>Configurable newline string when writing alignment
3225 and other flat files</li>
3226 <li>Allow alignment annotation description lines to
3227 contain html tags</li>
3228 </ul> <em>Documentation and Development</em>
3230 <li>Add groovy test harness for bulk load testing to
3232 <li>Groovy script to load and align a set of sequences
3233 using a web service before displaying the result in the
3234 Jalview desktop</li>
3235 <li>Restructured javascript and applet api documentation</li>
3236 <li>Ant target to publish example html files with applet
3238 <li>Netbeans project for building Jalview from source</li>
3239 <li>ant task to create online javadoc for Jalview source</li>
3241 <td><em>Application</em>
3243 <li>User defined colourscheme throws exception when
3244 current built in colourscheme is saved as new scheme</li>
3245 <li>AlignFrame->Save in application pops up save
3246 dialog for valid filename/format</li>
3247 <li>Cannot view associated structure for UniProt sequence</li>
3248 <li>PDB file association breaks for UniProt sequence
3250 <li>Associate PDB from file dialog does not tell you
3251 which sequence is to be associated with the file</li>
3252 <li>Find All raises null pointer exception when query
3253 only matches sequence IDs</li>
3254 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3255 <li>Jalview project with Jmol views created with Jalview
3256 2.4 cannot be loaded</li>
3257 <li>Filetype associations not installed for webstart
3259 <li>Two or more chains in a single PDB file associated
3260 with sequences in different alignments do not get coloured
3261 by their associated sequence</li>
3262 <li>Visibility status of autocalculated annotation row
3263 not preserved when project is loaded</li>
3264 <li>Annotation row height and visibility attributes not
3265 stored in Jalview project</li>
3266 <li>Tree bootstraps are not preserved when saved as a
3267 Jalview project</li>
3268 <li>Envision2 workflow tooltips are corrupted</li>
3269 <li>Enabling show group conservation also enables colour
3270 by conservation</li>
3271 <li>Duplicate group associated conservation or consensus
3272 created on new view</li>
3273 <li>Annotation scrollbar not displayed after 'show
3274 all hidden annotation rows' option selected</li>
3275 <li>Alignment quality not updated after alignment
3276 annotation row is hidden then shown</li>
3277 <li>Preserve colouring of structures coloured by
3278 sequences in pre Jalview 2.7 projects</li>
3279 <li>Web service job parameter dialog is not laid out
3281 <li>Web services menu not refreshed after 'reset
3282 services' button is pressed in preferences</li>
3283 <li>Annotation off by one in Jalview v2_3 example project</li>
3284 <li>Structures imported from file and saved in project
3285 get name like jalview_pdb1234.txt when reloaded</li>
3286 <li>Jalview does not always retrieve progress of a JABAWS
3287 job execution in full once it is complete</li>
3288 </ul> <em>Applet</em>
3290 <li>Alignment height set incorrectly when lots of
3291 annotation rows are displayed</li>
3292 <li>Relative URLs in feature HTML text not resolved to
3294 <li>View follows highlighting does not work for positions
3296 <li><= shown as = in tooltip</li>
3297 <li>Export features raises exception when no features
3299 <li>Separator string used for serialising lists of IDs
3300 for javascript api is modified when separator string
3301 provided as parameter</li>
3302 <li>Null pointer exception when selecting tree leaves for
3303 alignment with no existing selection</li>
3304 <li>Relative URLs for datasources assumed to be relative
3305 to applet's codebase</li>
3306 <li>Status bar not updated after finished searching and
3307 search wraps around to first result</li>
3308 <li>StructureSelectionManager instance shared between
3309 several Jalview applets causes race conditions and memory
3311 <li>Hover tooltip and mouseover of position on structure
3312 not sent from Jmol in applet</li>
3313 <li>Certain sequences of javascript method calls to
3314 applet API fatally hang browser</li>
3315 </ul> <em>General</em>
3317 <li>View follows structure mouseover scrolls beyond
3318 position with wrapped view and hidden regions</li>
3319 <li>Find sequence position moves to wrong residue
3320 with/without hidden columns</li>
3321 <li>Sequence length given in alignment properties window
3323 <li>InvalidNumberFormat exceptions thrown when trying to
3324 import PDB like structure files</li>
3325 <li>Positional search results are only highlighted
3326 between user-supplied sequence start/end bounds</li>
3327 <li>End attribute of sequence is not validated</li>
3328 <li>Find dialog only finds first sequence containing a
3329 given sequence position</li>
3330 <li>Sequence numbering not preserved in MSF alignment
3332 <li>Jalview PDB file reader does not extract sequence
3333 from nucleotide chains correctly</li>
3334 <li>Structure colours not updated when tree partition
3335 changed in alignment</li>
3336 <li>Sequence associated secondary structure not correctly
3337 parsed in interleaved stockholm</li>
3338 <li>Colour by annotation dialog does not restore current
3340 <li>Hiding (nearly) all sequences doesn't work
3342 <li>Sequences containing lowercase letters are not
3343 properly associated with their pdb files</li>
3344 </ul> <em>Documentation and Development</em>
3346 <li>schemas/JalviewWsParamSet.xsd corrupted by
3347 ApplyCopyright tool</li>
3352 <div align="center">
3353 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3356 <td><em>Application</em>
3358 <li>New warning dialog when the Jalview Desktop cannot
3359 contact web services</li>
3360 <li>JABA service parameters for a preset are shown in
3361 service job window</li>
3362 <li>JABA Service menu entries reworded</li>
3366 <li>Modeller PIR IO broken - cannot correctly import a
3367 pir file emitted by Jalview</li>
3368 <li>Existing feature settings transferred to new
3369 alignment view created from cut'n'paste</li>
3370 <li>Improved test for mixed amino/nucleotide chains when
3371 parsing PDB files</li>
3372 <li>Consensus and conservation annotation rows
3373 occasionally become blank for all new windows</li>
3374 <li>Exception raised when right clicking above sequences
3375 in wrapped view mode</li>
3376 </ul> <em>Application</em>
3378 <li>multiple multiply aligned structure views cause cpu
3379 usage to hit 100% and computer to hang</li>
3380 <li>Web Service parameter layout breaks for long user
3381 parameter names</li>
3382 <li>Jaba service discovery hangs desktop if Jaba server
3389 <div align="center">
3390 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3393 <td><em>Application</em>
3395 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3396 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3399 <li>Web Services preference tab</li>
3400 <li>Analysis parameters dialog box and user defined
3402 <li>Improved speed and layout of Envision2 service menu</li>
3403 <li>Superpose structures using associated sequence
3405 <li>Export coordinates and projection as CSV from PCA
3407 </ul> <em>Applet</em>
3409 <li>enable javascript: execution by the applet via the
3410 link out mechanism</li>
3411 </ul> <em>Other</em>
3413 <li>Updated the Jmol Jalview interface to work with Jmol
3415 <li>The Jalview Desktop and JalviewLite applet now
3416 require Java 1.5</li>
3417 <li>Allow Jalview feature colour specification for GFF
3418 sequence annotation files</li>
3419 <li>New 'colour by label' keword in Jalview feature file
3420 type colour specification</li>
3421 <li>New Jalview Desktop Groovy API method that allows a
3422 script to check if it being run in an interactive session or
3423 in a batch operation from the Jalview command line</li>
3427 <li>clustalx colourscheme colours Ds preferentially when
3428 both D+E are present in over 50% of the column</li>
3429 </ul> <em>Application</em>
3431 <li>typo in AlignmentFrame->View->Hide->all but
3432 selected Regions menu item</li>
3433 <li>sequence fetcher replaces ',' for ';' when the ',' is
3434 part of a valid accession ID</li>
3435 <li>fatal OOM if object retrieved by sequence fetcher
3436 runs out of memory</li>
3437 <li>unhandled Out of Memory Error when viewing pca
3438 analysis results</li>
3439 <li>InstallAnywhere builds fail to launch on OS X java
3440 10.5 update 4 (due to apple Java 1.6 update)</li>
3441 <li>Installanywhere Jalview silently fails to launch</li>
3442 </ul> <em>Applet</em>
3444 <li>Jalview.getFeatureGroups() raises an
3445 ArrayIndexOutOfBoundsException if no feature groups are
3452 <div align="center">
3453 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3459 <li>Alignment prettyprinter doesn't cope with long
3461 <li>clustalx colourscheme colours Ds preferentially when
3462 both D+E are present in over 50% of the column</li>
3463 <li>nucleic acid structures retrieved from PDB do not
3464 import correctly</li>
3465 <li>More columns get selected than were clicked on when a
3466 number of columns are hidden</li>
3467 <li>annotation label popup menu not providing correct
3468 add/hide/show options when rows are hidden or none are
3470 <li>Stockholm format shown in list of readable formats,
3471 and parser copes better with alignments from RFAM.</li>
3472 <li>CSV output of consensus only includes the percentage
3473 of all symbols if sequence logo display is enabled</li>
3475 </ul> <em>Applet</em>
3477 <li>annotation panel disappears when annotation is
3479 </ul> <em>Application</em>
3481 <li>Alignment view not redrawn properly when new
3482 alignment opened where annotation panel is visible but no
3483 annotations are present on alignment</li>
3484 <li>pasted region containing hidden columns is
3485 incorrectly displayed in new alignment window</li>
3486 <li>Jalview slow to complete operations when stdout is
3487 flooded (fix is to close the Jalview console)</li>
3488 <li>typo in AlignmentFrame->View->Hide->all but
3489 selected Rregions menu item.</li>
3490 <li>inconsistent group submenu and Format submenu entry
3491 'Un' or 'Non'conserved</li>
3492 <li>Sequence feature settings are being shared by
3493 multiple distinct alignments</li>
3494 <li>group annotation not recreated when tree partition is
3496 <li>double click on group annotation to select sequences
3497 does not propagate to associated trees</li>
3498 <li>Mac OSX specific issues:
3500 <li>exception raised when mouse clicked on desktop
3501 window background</li>
3502 <li>Desktop menu placed on menu bar and application
3503 name set correctly</li>
3504 <li>sequence feature settings not wide enough for the
3505 save feature colourscheme button</li>
3514 <div align="center">
3515 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3518 <td><em>New Capabilities</em>
3520 <li>URL links generated from description line for
3521 regular-expression based URL links (applet and application)
3523 <li>Non-positional feature URL links are shown in link
3525 <li>Linked viewing of nucleic acid sequences and
3527 <li>Automatic Scrolling option in View menu to display
3528 the currently highlighted region of an alignment.</li>
3529 <li>Order an alignment by sequence length, or using the
3530 average score or total feature count for each sequence.</li>
3531 <li>Shading features by score or associated description</li>
3532 <li>Subdivide alignment and groups based on identity of
3533 selected subsequence (Make Groups from Selection).</li>
3534 <li>New hide/show options including Shift+Control+H to
3535 hide everything but the currently selected region.</li>
3536 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3537 </ul> <em>Application</em>
3539 <li>Fetch DB References capabilities and UI expanded to
3540 support retrieval from DAS sequence sources</li>
3541 <li>Local DAS Sequence sources can be added via the
3542 command line or via the Add local source dialog box.</li>
3543 <li>DAS Dbref and DbxRef feature types are parsed as
3544 database references and protein_name is parsed as
3545 description line (BioSapiens terms).</li>
3546 <li>Enable or disable non-positional feature and database
3547 references in sequence ID tooltip from View menu in
3549 <!-- <li>New hidden columns and rows and representatives capabilities
3550 in annotations file (in progress - not yet fully implemented)</li> -->
3551 <li>Group-associated consensus, sequence logos and
3552 conservation plots</li>
3553 <li>Symbol distributions for each column can be exported
3554 and visualized as sequence logos</li>
3555 <li>Optionally scale multi-character column labels to fit
3556 within each column of annotation row<!-- todo for applet -->
3558 <li>Optional automatic sort of associated alignment view
3559 when a new tree is opened.</li>
3560 <li>Jalview Java Console</li>
3561 <li>Better placement of desktop window when moving
3562 between different screens.</li>
3563 <li>New preference items for sequence ID tooltip and
3564 consensus annotation</li>
3565 <li>Client to submit sequences and IDs to Envision2
3567 <li><em>Vamsas Capabilities</em>
3569 <li>Improved VAMSAS synchronization (Jalview archive
3570 used to preserve views, structures, and tree display
3572 <li>Import of vamsas documents from disk or URL via
3574 <li>Sharing of selected regions between views and
3575 with other VAMSAS applications (Experimental feature!)</li>
3576 <li>Updated API to VAMSAS version 0.2</li>
3578 </ul> <em>Applet</em>
3580 <li>Middle button resizes annotation row height</li>
3583 <li>sortByTree (true/false) - automatically sort the
3584 associated alignment view by the tree when a new tree is
3586 <li>showTreeBootstraps (true/false) - show or hide
3587 branch bootstraps (default is to show them if available)</li>
3588 <li>showTreeDistances (true/false) - show or hide
3589 branch lengths (default is to show them if available)</li>
3590 <li>showUnlinkedTreeNodes (true/false) - indicate if
3591 unassociated nodes should be highlighted in the tree
3593 <li>heightScale and widthScale (1.0 or more) -
3594 increase the height or width of a cell in the alignment
3595 grid relative to the current font size.</li>
3598 <li>Non-positional features displayed in sequence ID
3600 </ul> <em>Other</em>
3602 <li>Features format: graduated colour definitions and
3603 specification of feature scores</li>
3604 <li>Alignment Annotations format: new keywords for group
3605 associated annotation (GROUP_REF) and annotation row display
3606 properties (ROW_PROPERTIES)</li>
3607 <li>XML formats extended to support graduated feature
3608 colourschemes, group associated annotation, and profile
3609 visualization settings.</li></td>
3612 <li>Source field in GFF files parsed as feature source
3613 rather than description</li>
3614 <li>Non-positional features are now included in sequence
3615 feature and gff files (controlled via non-positional feature
3616 visibility in tooltip).</li>
3617 <li>URL links generated for all feature links (bugfix)</li>
3618 <li>Added URL embedding instructions to features file
3620 <li>Codons containing ambiguous nucleotides translated as
3621 'X' in peptide product</li>
3622 <li>Match case switch in find dialog box works for both
3623 sequence ID and sequence string and query strings do not
3624 have to be in upper case to match case-insensitively.</li>
3625 <li>AMSA files only contain first column of
3626 multi-character column annotation labels</li>
3627 <li>Jalview Annotation File generation/parsing consistent
3628 with documentation (e.g. Stockholm annotation can be
3629 exported and re-imported)</li>
3630 <li>PDB files without embedded PDB IDs given a friendly
3632 <li>Find incrementally searches ID string matches as well
3633 as subsequence matches, and correctly reports total number
3637 <li>Better handling of exceptions during sequence
3639 <li>Dasobert generated non-positional feature URL
3640 link text excludes the start_end suffix</li>
3641 <li>DAS feature and source retrieval buttons disabled
3642 when fetch or registry operations in progress.</li>
3643 <li>PDB files retrieved from URLs are cached properly</li>
3644 <li>Sequence description lines properly shared via
3646 <li>Sequence fetcher fetches multiple records for all
3648 <li>Ensured that command line das feature retrieval
3649 completes before alignment figures are generated.</li>
3650 <li>Reduced time taken when opening file browser for
3652 <li>isAligned check prior to calculating tree, PCA or
3653 submitting an MSA to JNet now excludes hidden sequences.</li>
3654 <li>User defined group colours properly recovered
3655 from Jalview projects.</li>
3664 <div align="center">
3665 <strong>2.4.0.b2</strong><br> 28/10/2009
3670 <li>Experimental support for google analytics usage
3672 <li>Jalview privacy settings (user preferences and docs).</li>
3677 <li>Race condition in applet preventing startup in
3679 <li>Exception when feature created from selection beyond
3680 length of sequence.</li>
3681 <li>Allow synthetic PDB files to be imported gracefully</li>
3682 <li>Sequence associated annotation rows associate with
3683 all sequences with a given id</li>
3684 <li>Find function matches case-insensitively for sequence
3685 ID string searches</li>
3686 <li>Non-standard characters do not cause pairwise
3687 alignment to fail with exception</li>
3688 </ul> <em>Application Issues</em>
3690 <li>Sequences are now validated against EMBL database</li>
3691 <li>Sequence fetcher fetches multiple records for all
3693 </ul> <em>InstallAnywhere Issues</em>
3695 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3696 issue with installAnywhere mechanism)</li>
3697 <li>Command line launching of JARs from InstallAnywhere
3698 version (java class versioning error fixed)</li>
3705 <div align="center">
3706 <strong>2.4</strong><br> 27/8/2008
3709 <td><em>User Interface</em>
3711 <li>Linked highlighting of codon and amino acid from
3712 translation and protein products</li>
3713 <li>Linked highlighting of structure associated with
3714 residue mapping to codon position</li>
3715 <li>Sequence Fetcher provides example accession numbers
3716 and 'clear' button</li>
3717 <li>MemoryMonitor added as an option under Desktop's
3719 <li>Extract score function to parse whitespace separated
3720 numeric data in description line</li>
3721 <li>Column labels in alignment annotation can be centred.</li>
3722 <li>Tooltip for sequence associated annotation give name
3724 </ul> <em>Web Services and URL fetching</em>
3726 <li>JPred3 web service</li>
3727 <li>Prototype sequence search client (no public services
3729 <li>Fetch either seed alignment or full alignment from
3731 <li>URL Links created for matching database cross
3732 references as well as sequence ID</li>
3733 <li>URL Links can be created using regular-expressions</li>
3734 </ul> <em>Sequence Database Connectivity</em>
3736 <li>Retrieval of cross-referenced sequences from other
3738 <li>Generalised database reference retrieval and
3739 validation to all fetchable databases</li>
3740 <li>Fetch sequences from DAS sources supporting the
3741 sequence command</li>
3742 </ul> <em>Import and Export</em>
3743 <li>export annotation rows as CSV for spreadsheet import</li>
3744 <li>Jalview projects record alignment dataset associations,
3745 EMBL products, and cDNA sequence mappings</li>
3746 <li>Sequence Group colour can be specified in Annotation
3748 <li>Ad-hoc colouring of group in Annotation File using RGB
3749 triplet as name of colourscheme</li>
3750 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3752 <li>treenode binding for VAMSAS tree exchange</li>
3753 <li>local editing and update of sequences in VAMSAS
3754 alignments (experimental)</li>
3755 <li>Create new or select existing session to join</li>
3756 <li>load and save of vamsas documents</li>
3757 </ul> <em>Application command line</em>
3759 <li>-tree parameter to open trees (introduced for passing
3761 <li>-fetchfrom command line argument to specify nicknames
3762 of DAS servers to query for alignment features</li>
3763 <li>-dasserver command line argument to add new servers
3764 that are also automatically queried for features</li>
3765 <li>-groovy command line argument executes a given groovy
3766 script after all input data has been loaded and parsed</li>
3767 </ul> <em>Applet-Application data exchange</em>
3769 <li>Trees passed as applet parameters can be passed to
3770 application (when using "View in full
3771 application")</li>
3772 </ul> <em>Applet Parameters</em>
3774 <li>feature group display control parameter</li>
3775 <li>debug parameter</li>
3776 <li>showbutton parameter</li>
3777 </ul> <em>Applet API methods</em>
3779 <li>newView public method</li>
3780 <li>Window (current view) specific get/set public methods</li>
3781 <li>Feature display control methods</li>
3782 <li>get list of currently selected sequences</li>
3783 </ul> <em>New Jalview distribution features</em>
3785 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3786 <li>RELEASE file gives build properties for the latest
3787 Jalview release.</li>
3788 <li>Java 1.1 Applet build made easier and donotobfuscate
3789 property controls execution of obfuscator</li>
3790 <li>Build target for generating source distribution</li>
3791 <li>Debug flag for javacc</li>
3792 <li>.jalview_properties file is documented (slightly) in
3793 jalview.bin.Cache</li>
3794 <li>Continuous Build Integration for stable and
3795 development version of Application, Applet and source
3800 <li>selected region output includes visible annotations
3801 (for certain formats)</li>
3802 <li>edit label/displaychar contains existing label/char
3804 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3805 <li>shorter peptide product names from EMBL records</li>
3806 <li>Newick string generator makes compact representations</li>
3807 <li>bootstrap values parsed correctly for tree files with
3809 <li>pathological filechooser bug avoided by not allowing
3810 filenames containing a ':'</li>
3811 <li>Fixed exception when parsing GFF files containing
3812 global sequence features</li>
3813 <li>Alignment datasets are finalized only when number of
3814 references from alignment sequences goes to zero</li>
3815 <li>Close of tree branch colour box without colour
3816 selection causes cascading exceptions</li>
3817 <li>occasional negative imgwidth exceptions</li>
3818 <li>better reporting of non-fatal warnings to user when
3819 file parsing fails.</li>
3820 <li>Save works when Jalview project is default format</li>
3821 <li>Save as dialog opened if current alignment format is
3822 not a valid output format</li>
3823 <li>UniProt canonical names introduced for both das and
3825 <li>Histidine should be midblue (not pink!) in Zappo</li>
3826 <li>error messages passed up and output when data read
3828 <li>edit undo recovers previous dataset sequence when
3829 sequence is edited</li>
3830 <li>allow PDB files without pdb ID HEADER lines (like
3831 those generated by MODELLER) to be read in properly</li>
3832 <li>allow reading of JPred concise files as a normal
3834 <li>Stockholm annotation parsing and alignment properties
3835 import fixed for PFAM records</li>
3836 <li>Structure view windows have correct name in Desktop
3838 <li>annotation consisting of sequence associated scores
3839 can be read and written correctly to annotation file</li>
3840 <li>Aligned cDNA translation to aligned peptide works
3842 <li>Fixed display of hidden sequence markers and
3843 non-italic font for representatives in Applet</li>
3844 <li>Applet Menus are always embedded in applet window on
3846 <li>Newly shown features appear at top of stack (in
3848 <li>Annotations added via parameter not drawn properly
3849 due to null pointer exceptions</li>
3850 <li>Secondary structure lines are drawn starting from
3851 first column of alignment</li>
3852 <li>UniProt XML import updated for new schema release in
3854 <li>Sequence feature to sequence ID match for Features
3855 file is case-insensitive</li>
3856 <li>Sequence features read from Features file appended to
3857 all sequences with matching IDs</li>
3858 <li>PDB structure coloured correctly for associated views
3859 containing a sub-sequence</li>
3860 <li>PDB files can be retrieved by applet from Jar files</li>
3861 <li>feature and annotation file applet parameters
3862 referring to different directories are retrieved correctly</li>
3863 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3864 <li>Fixed application hang whilst waiting for
3865 splash-screen version check to complete</li>
3866 <li>Applet properly URLencodes input parameter values
3867 when passing them to the launchApp service</li>
3868 <li>display name and local features preserved in results
3869 retrieved from web service</li>
3870 <li>Visual delay indication for sequence retrieval and
3871 sequence fetcher initialisation</li>
3872 <li>updated Application to use DAS 1.53e version of
3873 dasobert DAS client</li>
3874 <li>Re-instated Full AMSA support and .amsa file
3876 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3884 <div align="center">
3885 <strong>2.3</strong><br> 9/5/07
3890 <li>Jmol 11.0.2 integration</li>
3891 <li>PDB views stored in Jalview XML files</li>
3892 <li>Slide sequences</li>
3893 <li>Edit sequence in place</li>
3894 <li>EMBL CDS features</li>
3895 <li>DAS Feature mapping</li>
3896 <li>Feature ordering</li>
3897 <li>Alignment Properties</li>
3898 <li>Annotation Scores</li>
3899 <li>Sort by scores</li>
3900 <li>Feature/annotation editing in applet</li>
3905 <li>Headless state operation in 2.2.1</li>
3906 <li>Incorrect and unstable DNA pairwise alignment</li>
3907 <li>Cut and paste of sequences with annotation</li>
3908 <li>Feature group display state in XML</li>
3909 <li>Feature ordering in XML</li>
3910 <li>blc file iteration selection using filename # suffix</li>
3911 <li>Stockholm alignment properties</li>
3912 <li>Stockhom alignment secondary structure annotation</li>
3913 <li>2.2.1 applet had no feature transparency</li>
3914 <li>Number pad keys can be used in cursor mode</li>
3915 <li>Structure Viewer mirror image resolved</li>
3922 <div align="center">
3923 <strong>2.2.1</strong><br> 12/2/07
3928 <li>Non standard characters can be read and displayed
3929 <li>Annotations/Features can be imported/exported to the
3931 <li>Applet allows editing of sequence/annotation/group
3932 name & description
3933 <li>Preference setting to display sequence name in
3935 <li>Annotation file format extended to allow
3936 Sequence_groups to be defined
3937 <li>Default opening of alignment overview panel can be
3938 specified in preferences
3939 <li>PDB residue numbering annotation added to associated
3945 <li>Applet crash under certain Linux OS with Java 1.6
3947 <li>Annotation file export / import bugs fixed
3948 <li>PNG / EPS image output bugs fixed
3954 <div align="center">
3955 <strong>2.2</strong><br> 27/11/06
3960 <li>Multiple views on alignment
3961 <li>Sequence feature editing
3962 <li>"Reload" alignment
3963 <li>"Save" to current filename
3964 <li>Background dependent text colour
3965 <li>Right align sequence ids
3966 <li>User-defined lower case residue colours
3969 <li>Menu item accelerator keys
3970 <li>Control-V pastes to current alignment
3971 <li>Cancel button for DAS Feature Fetching
3972 <li>PCA and PDB Viewers zoom via mouse roller
3973 <li>User-defined sub-tree colours and sub-tree selection
3975 <li>'New Window' button on the 'Output to Text box'
3980 <li>New memory efficient Undo/Redo System
3981 <li>Optimised symbol lookups and conservation/consensus
3983 <li>Region Conservation/Consensus recalculated after
3985 <li>Fixed Remove Empty Columns Bug (empty columns at end
3987 <li>Slowed DAS Feature Fetching for increased robustness.
3989 <li>Made angle brackets in ASCII feature descriptions
3991 <li>Re-instated Zoom function for PCA
3992 <li>Sequence descriptions conserved in web service
3994 <li>UniProt ID discoverer uses any word separated by
3996 <li>WsDbFetch query/result association resolved
3997 <li>Tree leaf to sequence mapping improved
3998 <li>Smooth fonts switch moved to FontChooser dialog box.
4005 <div align="center">
4006 <strong>2.1.1</strong><br> 12/9/06
4011 <li>Copy consensus sequence to clipboard</li>
4016 <li>Image output - rightmost residues are rendered if
4017 sequence id panel has been resized</li>
4018 <li>Image output - all offscreen group boundaries are
4020 <li>Annotation files with sequence references - all
4021 elements in file are relative to sequence position</li>
4022 <li>Mac Applet users can use Alt key for group editing</li>
4028 <div align="center">
4029 <strong>2.1</strong><br> 22/8/06
4034 <li>MAFFT Multiple Alignment in default Web Service list</li>
4035 <li>DAS Feature fetching</li>
4036 <li>Hide sequences and columns</li>
4037 <li>Export Annotations and Features</li>
4038 <li>GFF file reading / writing</li>
4039 <li>Associate structures with sequences from local PDB
4041 <li>Add sequences to exisiting alignment</li>
4042 <li>Recently opened files / URL lists</li>
4043 <li>Applet can launch the full application</li>
4044 <li>Applet has transparency for features (Java 1.2
4046 <li>Applet has user defined colours parameter</li>
4047 <li>Applet can load sequences from parameter
4048 "sequence<em>x</em>"
4054 <li>Redundancy Panel reinstalled in the Applet</li>
4055 <li>Monospaced font - EPS / rescaling bug fixed</li>
4056 <li>Annotation files with sequence references bug fixed</li>
4062 <div align="center">
4063 <strong>2.08.1</strong><br> 2/5/06
4068 <li>Change case of selected region from Popup menu</li>
4069 <li>Choose to match case when searching</li>
4070 <li>Middle mouse button and mouse movement can compress /
4071 expand the visible width and height of the alignment</li>
4076 <li>Annotation Panel displays complete JNet results</li>
4082 <div align="center">
4083 <strong>2.08b</strong><br> 18/4/06
4089 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4090 <li>Righthand label on wrapped alignments shows correct
4097 <div align="center">
4098 <strong>2.08</strong><br> 10/4/06
4103 <li>Editing can be locked to the selection area</li>
4104 <li>Keyboard editing</li>
4105 <li>Create sequence features from searches</li>
4106 <li>Precalculated annotations can be loaded onto
4108 <li>Features file allows grouping of features</li>
4109 <li>Annotation Colouring scheme added</li>
4110 <li>Smooth fonts off by default - Faster rendering</li>
4111 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4116 <li>Drag & Drop fixed on Linux</li>
4117 <li>Jalview Archive file faster to load/save, sequence
4118 descriptions saved.</li>
4124 <div align="center">
4125 <strong>2.07</strong><br> 12/12/05
4130 <li>PDB Structure Viewer enhanced</li>
4131 <li>Sequence Feature retrieval and display enhanced</li>
4132 <li>Choose to output sequence start-end after sequence
4133 name for file output</li>
4134 <li>Sequence Fetcher WSDBFetch@EBI</li>
4135 <li>Applet can read feature files, PDB files and can be
4136 used for HTML form input</li>
4141 <li>HTML output writes groups and features</li>
4142 <li>Group editing is Control and mouse click</li>
4143 <li>File IO bugs</li>
4149 <div align="center">
4150 <strong>2.06</strong><br> 28/9/05
4155 <li>View annotations in wrapped mode</li>
4156 <li>More options for PCA viewer</li>
4161 <li>GUI bugs resolved</li>
4162 <li>Runs with -nodisplay from command line</li>
4168 <div align="center">
4169 <strong>2.05b</strong><br> 15/9/05
4174 <li>Choose EPS export as lineart or text</li>
4175 <li>Jar files are executable</li>
4176 <li>Can read in Uracil - maps to unknown residue</li>
4181 <li>Known OutOfMemory errors give warning message</li>
4182 <li>Overview window calculated more efficiently</li>
4183 <li>Several GUI bugs resolved</li>
4189 <div align="center">
4190 <strong>2.05</strong><br> 30/8/05
4195 <li>Edit and annotate in "Wrapped" view</li>
4200 <li>Several GUI bugs resolved</li>
4206 <div align="center">
4207 <strong>2.04</strong><br> 24/8/05
4212 <li>Hold down mouse wheel & scroll to change font
4218 <li>Improved JPred client reliability</li>
4219 <li>Improved loading of Jalview files</li>
4225 <div align="center">
4226 <strong>2.03</strong><br> 18/8/05
4231 <li>Set Proxy server name and port in preferences</li>
4232 <li>Multiple URL links from sequence ids</li>
4233 <li>User Defined Colours can have a scheme name and added
4235 <li>Choose to ignore gaps in consensus calculation</li>
4236 <li>Unix users can set default web browser</li>
4237 <li>Runs without GUI for batch processing</li>
4238 <li>Dynamically generated Web Service Menus</li>
4243 <li>InstallAnywhere download for Sparc Solaris</li>
4249 <div align="center">
4250 <strong>2.02</strong><br> 18/7/05
4256 <li>Copy & Paste order of sequences maintains
4257 alignment order.</li>
4263 <div align="center">
4264 <strong>2.01</strong><br> 12/7/05
4269 <li>Use delete key for deleting selection.</li>
4270 <li>Use Mouse wheel to scroll sequences.</li>
4271 <li>Help file updated to describe how to add alignment
4273 <li>Version and build date written to build properties
4275 <li>InstallAnywhere installation will check for updates
4276 at launch of Jalview.</li>
4281 <li>Delete gaps bug fixed.</li>
4282 <li>FileChooser sorts columns.</li>
4283 <li>Can remove groups one by one.</li>
4284 <li>Filechooser icons installed.</li>
4285 <li>Finder ignores return character when searching.
4286 Return key will initiate a search.<br>
4293 <div align="center">
4294 <strong>2.0</strong><br> 20/6/05
4299 <li>New codebase</li>