3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">2.11</a><br />
61 <em>27/06/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
67 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
68 source project) rather than InstallAnywhere
71 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
72 settings, receive over the air updates and launch specific
73 versions via (<a href="https://github.com/threerings/getdown">Three
77 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
78 formats supported by jalview (including .jvp project files)
81 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
82 arguments and switch between different getdown channels
85 <!-- JAL-3141 -->Backup files created when saving Jalview project
90 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
91 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
93 <!-- JAL-2620 -->Alternative genetic code tables for
94 'Translate as cDNA'</li>
96 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
97 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
100 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
101 implementation that alows updates) used for Sequence Feature collections</li>
104 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
105 shaded according to any associated attributes (e.g. variant
106 attributes from VCF file, or key-value pairs imported from
107 column 9 of GFF file)
110 <!-- JAL-2897 -->Show synonymous codon variants on peptide
114 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
118 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
119 algorithm (Z-sort/transparency and filter aware)
122 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
128 <!-- JAL-3205 -->Symmetric score matrices for faster
129 tree and PCA calculations
131 <li><strong>Principal Components Analysis Viewer</strong>
134 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
135 and Viewer state saved in Jalview Project
137 <li>'Change parameters' option removed from viewer's
140 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
144 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
149 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
151 <li><strong>Speed and Efficiency</strong>
154 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
155 multiple groups when working with large alignments
158 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
162 <li><strong>User Interface</strong>
165 <!-- JAL-2933 -->Finder panel remembers last position in each
169 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
170 what is shown)<br />Only visible region of alignment is shown by
171 default (can be changed in user preferences)
174 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
175 to the Overwrite Dialog
178 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
182 <!-- JAL-1244 -->Status bar shows bounds when dragging a
183 selection region, and gap count when inserting or deleting gaps
186 <!-- JAL-3132 -->Status bar updates over sequence and annotation
190 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
194 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
198 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
201 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
205 <!-- JAL-3181 -->Consistent ordering of links in sequence id
209 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
211 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
215 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
216 <li><strong>Java 11 Support (not yet on general release)</strong>
219 <!-- -->OSX GUI integrations for App menu's 'About' entry and
224 <em>Deprecations</em>
227 <!-- JAL-3035 -->DAS sequence retrieval and annotation
228 capabilities removed from the Jalview Desktop
231 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
232 unmarshalling has been replaced by JAXB for Jalview projects
233 and XML based data retrieval clients</li>
234 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
235 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
236 </ul> <em>Documentation</em>
239 <!-- JAL-3003 -->Added remarks about transparent rendering effects
240 not supported in EPS figure export
242 </ul> <em>Development and Release Processes</em>
245 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
247 <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
249 <!-- JAL-3225 -->Eclipse project configuration managed with
252 <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
253 Atlassian Bamboo continuous integration for
254 unattended Test Suite execution</li>
256 <!-- JAL-2864 -->Memory test suite to detect leaks in common
258 <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
259 <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>
262 <td align="left" valign="top">
265 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
268 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
269 superposition in Jmol fail on Windows
272 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
273 structures for sequences with lots of PDB structures
276 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
280 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
281 project involving multiple views
284 <!-- JAL-3164 -->Overview for complementary view in a linked
285 CDS/Protein alignment is not updated when Hide Columns by
286 Annotation dialog hides columns
289 <!-- JAL-3158 -->Selection highlighting in the complement of a
290 CDS/Protein alignment stops working after making a selection in
291 one view, then making another selection in the other view
294 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
298 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
299 Settings and Jalview Preferences panels
302 <!-- JAL-2865 -->Jalview hangs when closing windows or the
303 overview updates with large alignments
306 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
307 region if columns were selected by dragging right-to-left and the
308 mouse moved to the left of the first column
311 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
312 hidden column marker via scale popup menu
315 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
316 doesn't tell users the invalid URL
319 <!-- JAL-3178 -->Nonpositional features lose feature group on
320 export as Jalview features file
323 <!-- JAL-2816 -->Tooltips displayed for features filtered by
327 <!-- JAL-2060 -->'Graduated colour' option not offered for
328 manually created features (where if feature score is Float.NaN)
331 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
332 when columns are hidden
335 <!-- JAL-3082 -->Regular expression error for '(' in Select
336 Columns by Annotation description
339 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
340 out of Scale or Annotation Panel
343 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
347 <!-- JAL-3074 -->Left/right drag in annotation can scroll
351 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
355 <!-- JAL-3002 -->Column display is out by one after Page Down,
356 Page Up in wrapped mode
359 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
362 <!-- JAL-2932 -->Finder searches in minimised alignments
365 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
366 on opening an alignment
369 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
373 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
374 different groups in the alignment are selected
377 <!-- JAL-2717 -->Internationalised colour scheme names not shown
381 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
385 <!-- JAL-3125 -->Value input for graduated feature colour
386 threshold gets 'unrounded'
389 <!-- JAL-2982 -->PCA image export doesn't respect background
393 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
396 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
399 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
403 <!-- JAL-2964 -->Associate Tree with All Views not restored from
407 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
408 shown in complementary view
411 <!-- JAL-2898 -->stop_gained variants not shown correctly on
415 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
416 without normalisation
419 <!-- JAL-3021 -->Sequence Details report opens positioned to top
423 <!-- JAL-914 -->Help page can be opened twice
425 </ul> <em>Editing</em>
428 <!-- JAL-2822 -->Start and End should be updated when sequence
429 data at beginning or end of alignment added/removed via 'Edit'
433 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
434 relocate sequence features correctly when start of sequence is
435 removed (Known defect since 2.10)
438 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
439 dialog corrupts dataset sequence
442 <!-- JAL-868 -->Structure colours not updated when associated tree
443 repartitions the alignment view (Regression in 2.10.5)
447 <em>New Known Defects</em>
450 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
451 regions of protein alignment.
454 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
455 is restored from a Jalview 2.11 project
458 <!-- JAL-3213 -->Alignment panel height can be too small after
462 <!-- JAL-3240 -->Display is incorrect after removing gapped
463 columns within hidden columns
466 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
467 window after dragging left to select columns to left of visible
471 <!-- JAL-2876 -->Features coloured according to their description
472 string and thresholded by score in earlier versions of Jalview are
473 not shown as thresholded features in 2.11. To workaround please
474 create a Score filter instead.
476 <li><strong>Java 11 Specific defects</strong>
479 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
487 <td width="60" nowrap>
489 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
492 <td><div align="left">
496 <!-- JAL-3101 -->Default memory for Jalview webstart and
497 InstallAnywhere increased to 1G.
500 <!-- JAL-247 -->Hidden sequence markers and representative
501 sequence bolding included when exporting alignment as EPS,
502 SVG, PNG or HTML. <em>Display is configured via the
503 Format menu, or for command-line use via a jalview
504 properties file.</em>
507 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
508 API and sequence data now imported as JSON.
511 <!-- JAL-3065 -->Change in recommended way of starting
512 Jalview via a Java command line: add jars in lib directory
513 to CLASSPATH, rather than via the deprecated java.ext.dirs
520 <!-- JAL-3047 -->Support added to execute test suite
521 instrumented with <a href="http://openclover.org/">Open
526 <td><div align="left">
530 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
531 row shown in Feredoxin Structure alignment view of example
535 <!-- JAL-2854 -->Annotation obscures sequences if lots of
536 annotation displayed.
539 <!-- JAL-3107 -->Group conservation/consensus not shown
540 for newly created group when 'Apply to all groups'
544 <!-- JAL-3087 -->Corrupted display when switching to
545 wrapped mode when sequence panel's vertical scrollbar is
549 <!-- JAL-3003 -->Alignment is black in exported EPS file
550 when sequences are selected in exported view.</em>
553 <!-- JAL-3059 -->Groups with different coloured borders
554 aren't rendered with correct colour.
557 <!-- JAL-3092 -->Jalview could hang when importing certain
558 types of knotted RNA secondary structure.
561 <!-- JAL-3095 -->Sequence highlight and selection in
562 trimmed VARNA 2D structure is incorrect for sequences that
566 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
567 annotation when columns are inserted into an alignment,
568 and when exporting as Stockholm flatfile.
571 <!-- JAL-3053 -->Jalview annotation rows containing upper
572 and lower-case 'E' and 'H' do not automatically get
573 treated as RNA secondary structure.
576 <!-- JAL-3106 -->.jvp should be used as default extension
577 (not .jar) when saving a jalview project file.
580 <!-- JAL-3105 -->Mac Users: closing a window correctly
581 transfers focus to previous window on OSX
584 <em>Java 10 Issues Resolved</em>
587 <!-- JAL-2988 -->OSX - Can't save new files via the File
588 or export menus by typing in a name into the Save dialog
592 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
593 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
594 'look and feel' which has improved compatibility with the
595 latest version of OSX.
602 <td width="60" nowrap>
604 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
605 <em>7/06/2018</em></strong>
608 <td><div align="left">
612 <!-- JAL-2920 -->Use HGVS nomenclature for variant
613 annotation retrieved from Uniprot
616 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
617 onto the Jalview Desktop
621 <td><div align="left">
625 <!-- JAL-3017 -->Cannot import features with multiple
626 variant elements (blocks import of some Uniprot records)
629 <!-- JAL-2997 -->Clustal files with sequence positions in
630 right-hand column parsed correctly
633 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
634 not alignment area in exported graphic
637 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
638 window has input focus
641 <!-- JAL-2992 -->Annotation panel set too high when
642 annotation added to view (Windows)
645 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
646 network connectivity is poor
649 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
650 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
651 the currently open URL and links from a page viewed in
652 Firefox or Chrome on Windows is now fully supported. If
653 you are using Edge, only links in the page can be
654 dragged, and with Internet Explorer, only the currently
655 open URL in the browser can be dropped onto Jalview.</em>
658 <em>New Known Defects</em>
660 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
665 <td width="60" nowrap>
667 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
670 <td><div align="left">
674 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
675 for disabling automatic superposition of multiple
676 structures and open structures in existing views
679 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
680 ID and annotation area margins can be click-dragged to
684 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
688 <!-- JAL-2759 -->Improved performance for large alignments
689 and lots of hidden columns
692 <!-- JAL-2593 -->Improved performance when rendering lots
693 of features (particularly when transparency is disabled)
696 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
697 exchange of Jalview features and Chimera attributes made
703 <td><div align="left">
706 <!-- JAL-2899 -->Structure and Overview aren't updated
707 when Colour By Annotation threshold slider is adjusted
710 <!-- JAL-2778 -->Slow redraw when Overview panel shown
711 overlapping alignment panel
714 <!-- JAL-2929 -->Overview doesn't show end of unpadded
718 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
719 improved: CDS not handled correctly if transcript has no
723 <!-- JAL-2321 -->Secondary structure and temperature
724 factor annotation not added to sequence when local PDB
725 file associated with it by drag'n'drop or structure
729 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
730 dialog doesn't import PDB files dropped on an alignment
733 <!-- JAL-2666 -->Linked scrolling via protein horizontal
734 scroll bar doesn't work for some CDS/Protein views
737 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
738 Java 1.8u153 onwards and Java 1.9u4+.
741 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
742 columns in annotation row
745 <!-- JAL-2913 -->Preferences panel's ID Width control is not
746 honored in batch mode
749 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
750 for structures added to existing Jmol view
753 <!-- JAL-2223 -->'View Mappings' includes duplicate
754 entries after importing project with multiple views
757 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
758 protein sequences via SIFTS from associated PDB entries
759 with negative residue numbers or missing residues fails
762 <!-- JAL-2952 -->Exception when shading sequence with negative
763 Temperature Factor values from annotated PDB files (e.g.
764 as generated by CONSURF)
767 <!-- JAL-2920 -->Uniprot 'sequence variant' features
768 tooltip doesn't include a text description of mutation
771 <!-- JAL-2922 -->Invert displayed features very slow when
772 structure and/or overview windows are also shown
775 <!-- JAL-2954 -->Selecting columns from highlighted regions
776 very slow for alignments with large numbers of sequences
779 <!-- JAL-2925 -->Copy Consensus fails for group consensus
780 with 'StringIndexOutOfBounds'
783 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
784 platforms running Java 10
787 <!-- JAL-2960 -->Adding a structure to existing structure
788 view appears to do nothing because the view is hidden behind the alignment view
794 <!-- JAL-2926 -->Copy consensus sequence option in applet
795 should copy the group consensus when popup is opened on it
801 <!-- JAL-2913 -->Fixed ID width preference is not respected
804 <em>New Known Defects</em>
807 <!-- JAL-2973 --> Exceptions occasionally raised when
808 editing a large alignment and overview is displayed
811 <!-- JAL-2974 -->'Overview updating' progress bar is shown
812 repeatedly after a series of edits even when the overview
813 is no longer reflecting updates
816 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
817 structures for protein subsequence (if 'Trim Retrieved
818 Sequences' enabled) or Ensembl isoforms (Workaround in
819 2.10.4 is to fail back to N&W mapping)
822 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
823 option gives blank output
830 <td width="60" nowrap>
832 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
835 <td><div align="left">
836 <ul><li>Updated Certum Codesigning Certificate
837 (Valid till 30th November 2018)</li></ul></div></td>
838 <td><div align="left">
841 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
842 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
843 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
844 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
845 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
846 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
847 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
853 <td width="60" nowrap>
855 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
858 <td><div align="left">
862 <!-- JAL-2446 -->Faster and more efficient management and
863 rendering of sequence features
866 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
867 429 rate limit request hander
870 <!-- JAL-2773 -->Structure views don't get updated unless
871 their colours have changed
874 <!-- JAL-2495 -->All linked sequences are highlighted for
875 a structure mousover (Jmol) or selection (Chimera)
878 <!-- JAL-2790 -->'Cancel' button in progress bar for
879 JABAWS AACon, RNAAliFold and Disorder prediction jobs
882 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
883 view from Ensembl locus cross-references
886 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
890 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
891 feature can be disabled
894 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
895 PDB easier retrieval of sequences for lists of IDs
898 <!-- JAL-2758 -->Short names for sequences retrieved from
904 <li>Groovy interpreter updated to 2.4.12</li>
905 <li>Example groovy script for generating a matrix of
906 percent identity scores for current alignment.</li>
908 <em>Testing and Deployment</em>
911 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
915 <td><div align="left">
919 <!-- JAL-2643 -->Pressing tab after updating the colour
920 threshold text field doesn't trigger an update to the
924 <!-- JAL-2682 -->Race condition when parsing sequence ID
928 <!-- JAL-2608 -->Overview windows are also closed when
929 alignment window is closed
932 <!-- JAL-2548 -->Export of features doesn't always respect
936 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
937 takes a long time in Cursor mode
943 <!-- JAL-2777 -->Structures with whitespace chainCode
944 cannot be viewed in Chimera
947 <!-- JAL-2728 -->Protein annotation panel too high in
951 <!-- JAL-2757 -->Can't edit the query after the server
952 error warning icon is shown in Uniprot and PDB Free Text
956 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
959 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
962 <!-- JAL-2739 -->Hidden column marker in last column not
963 rendered when switching back from Wrapped to normal view
966 <!-- JAL-2768 -->Annotation display corrupted when
967 scrolling right in unwapped alignment view
970 <!-- JAL-2542 -->Existing features on subsequence
971 incorrectly relocated when full sequence retrieved from
975 <!-- JAL-2733 -->Last reported memory still shown when
976 Desktop->Show Memory is unticked (OSX only)
979 <!-- JAL-2658 -->Amend Features dialog doesn't allow
980 features of same type and group to be selected for
984 <!-- JAL-2524 -->Jalview becomes sluggish in wide
985 alignments when hidden columns are present
988 <!-- JAL-2392 -->Jalview freezes when loading and
989 displaying several structures
992 <!-- JAL-2732 -->Black outlines left after resizing or
996 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
997 within the Jalview desktop on OSX
1000 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1001 when in wrapped alignment mode
1004 <!-- JAL-2636 -->Scale mark not shown when close to right
1005 hand end of alignment
1008 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1009 each selected sequence do not have correct start/end
1013 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1014 after canceling the Alignment Window's Font dialog
1017 <!-- JAL-2036 -->Show cross-references not enabled after
1018 restoring project until a new view is created
1021 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1022 URL links appears when only default EMBL-EBI link is
1023 configured (since 2.10.2b2)
1026 <!-- JAL-2775 -->Overview redraws whole window when box
1027 position is adjusted
1030 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1031 in a multi-chain structure when viewing alignment
1032 involving more than one chain (since 2.10)
1035 <!-- JAL-2811 -->Double residue highlights in cursor mode
1036 if new selection moves alignment window
1039 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1040 arrow key in cursor mode to pass hidden column marker
1043 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1044 that produces correctly annotated transcripts and products
1047 <!-- JAL-2776 -->Toggling a feature group after first time
1048 doesn't update associated structure view
1051 <em>Applet</em><br />
1054 <!-- JAL-2687 -->Concurrent modification exception when
1055 closing alignment panel
1058 <em>BioJSON</em><br />
1061 <!-- JAL-2546 -->BioJSON export does not preserve
1062 non-positional features
1065 <em>New Known Issues</em>
1068 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1069 sequence features correctly (for many previous versions of
1073 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1074 using cursor in wrapped panel other than top
1077 <!-- JAL-2791 -->Select columns containing feature ignores
1078 graduated colour threshold
1081 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1082 always preserve numbering and sequence features
1085 <em>Known Java 9 Issues</em>
1088 <!-- JAL-2902 -->Groovy Console very slow to open and is
1089 not responsive when entering characters (Webstart, Java
1096 <td width="60" nowrap>
1097 <div align="center">
1098 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1099 <em>2/10/2017</em></strong>
1102 <td><div align="left">
1103 <em>New features in Jalview Desktop</em>
1106 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1108 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1112 <td><div align="left">
1116 <td width="60" nowrap>
1117 <div align="center">
1118 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1119 <em>7/9/2017</em></strong>
1122 <td><div align="left">
1126 <!-- JAL-2588 -->Show gaps in overview window by colouring
1127 in grey (sequences used to be coloured grey, and gaps were
1131 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1135 <!-- JAL-2587 -->Overview updates immediately on increase
1136 in size and progress bar shown as higher resolution
1137 overview is recalculated
1142 <td><div align="left">
1146 <!-- JAL-2664 -->Overview window redraws every hidden
1147 column region row by row
1150 <!-- JAL-2681 -->duplicate protein sequences shown after
1151 retrieving Ensembl crossrefs for sequences from Uniprot
1154 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1155 format setting is unticked
1158 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1159 if group has show boxes format setting unticked
1162 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1163 autoscrolling whilst dragging current selection group to
1164 include sequences and columns not currently displayed
1167 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1168 assemblies are imported via CIF file
1171 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1172 displayed when threshold or conservation colouring is also
1176 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1180 <!-- JAL-2673 -->Jalview continues to scroll after
1181 dragging a selected region off the visible region of the
1185 <!-- JAL-2724 -->Cannot apply annotation based
1186 colourscheme to all groups in a view
1189 <!-- JAL-2511 -->IDs don't line up with sequences
1190 initially after font size change using the Font chooser or
1197 <td width="60" nowrap>
1198 <div align="center">
1199 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1202 <td><div align="left">
1203 <em>Calculations</em>
1207 <!-- JAL-1933 -->Occupancy annotation row shows number of
1208 ungapped positions in each column of the alignment.
1211 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1212 a calculation dialog box
1215 <!-- JAL-2379 -->Revised implementation of PCA for speed
1216 and memory efficiency (~30x faster)
1219 <!-- JAL-2403 -->Revised implementation of sequence
1220 similarity scores as used by Tree, PCA, Shading Consensus
1221 and other calculations
1224 <!-- JAL-2416 -->Score matrices are stored as resource
1225 files within the Jalview codebase
1228 <!-- JAL-2500 -->Trees computed on Sequence Feature
1229 Similarity may have different topology due to increased
1236 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1237 model for alignments and groups
1240 <!-- JAL-384 -->Custom shading schemes created via groovy
1247 <!-- JAL-2526 -->Efficiency improvements for interacting
1248 with alignment and overview windows
1251 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1255 <!-- JAL-2388 -->Hidden columns and sequences can be
1259 <!-- JAL-2611 -->Click-drag in visible area allows fine
1260 adjustment of visible position
1264 <em>Data import/export</em>
1267 <!-- JAL-2535 -->Posterior probability annotation from
1268 Stockholm files imported as sequence associated annotation
1271 <!-- JAL-2507 -->More robust per-sequence positional
1272 annotation input/output via stockholm flatfile
1275 <!-- JAL-2533 -->Sequence names don't include file
1276 extension when importing structure files without embedded
1277 names or PDB accessions
1280 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1281 format sequence substitution matrices
1284 <em>User Interface</em>
1287 <!-- JAL-2447 --> Experimental Features Checkbox in
1288 Desktop's Tools menu to hide or show untested features in
1292 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1293 via Overview or sequence motif search operations
1296 <!-- JAL-2547 -->Amend sequence features dialog box can be
1297 opened by double clicking gaps within sequence feature
1301 <!-- JAL-1476 -->Status bar message shown when not enough
1302 aligned positions were available to create a 3D structure
1306 <em>3D Structure</em>
1309 <!-- JAL-2430 -->Hidden regions in alignment views are not
1310 coloured in linked structure views
1313 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1314 file-based command exchange
1317 <!-- JAL-2375 -->Structure chooser automatically shows
1318 Cached Structures rather than querying the PDBe if
1319 structures are already available for sequences
1322 <!-- JAL-2520 -->Structures imported via URL are cached in
1323 the Jalview project rather than downloaded again when the
1324 project is reopened.
1327 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1328 to transfer Chimera's structure attributes as Jalview
1329 features, and vice-versa (<strong>Experimental
1333 <em>Web Services</em>
1336 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1339 <!-- JAL-2335 -->Filter non-standard amino acids and
1340 nucleotides when submitting to AACon and other MSA
1344 <!-- JAL-2316, -->URLs for viewing database
1345 cross-references provided by identifiers.org and the
1346 EMBL-EBI's MIRIAM DB
1353 <!-- JAL-2344 -->FileFormatI interface for describing and
1354 identifying file formats (instead of String constants)
1357 <!-- JAL-2228 -->FeatureCounter script refactored for
1358 efficiency when counting all displayed features (not
1359 backwards compatible with 2.10.1)
1362 <em>Example files</em>
1365 <!-- JAL-2631 -->Graduated feature colour style example
1366 included in the example feature file
1369 <em>Documentation</em>
1372 <!-- JAL-2339 -->Release notes reformatted for readability
1373 with the built-in Java help viewer
1376 <!-- JAL-1644 -->Find documentation updated with 'search
1377 sequence description' option
1383 <!-- JAL-2485, -->External service integration tests for
1384 Uniprot REST Free Text Search Client
1387 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1390 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1395 <td><div align="left">
1396 <em>Calculations</em>
1399 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1400 matrix - C->R should be '-3'<br />Old matrix restored
1401 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1403 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1404 Jalview's treatment of gaps in PCA and substitution matrix
1405 based Tree calculations.<br /> <br />In earlier versions
1406 of Jalview, gaps matching gaps were penalised, and gaps
1407 matching non-gaps penalised even more. In the PCA
1408 calculation, gaps were actually treated as non-gaps - so
1409 different costs were applied, which meant Jalview's PCAs
1410 were different to those produced by SeqSpace.<br />Jalview
1411 now treats gaps in the same way as SeqSpace (ie it scores
1412 them as 0). <br /> <br />Enter the following in the
1413 Groovy console to restore pre-2.10.2 behaviour:<br />
1414 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1415 // for 2.10.1 mode <br />
1416 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1417 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1418 these settings will affect all subsequent tree and PCA
1419 calculations (not recommended)</em></li>
1421 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1422 scaling of branch lengths for trees computed using
1423 Sequence Feature Similarity.
1426 <!-- JAL-2377 -->PCA calculation could hang when
1427 generating output report when working with highly
1428 redundant alignments
1431 <!-- JAL-2544 --> Sort by features includes features to
1432 right of selected region when gaps present on right-hand
1436 <em>User Interface</em>
1439 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1440 doesn't reselect a specific sequence's associated
1441 annotation after it was used for colouring a view
1444 <!-- JAL-2419 -->Current selection lost if popup menu
1445 opened on a region of alignment without groups
1448 <!-- JAL-2374 -->Popup menu not always shown for regions
1449 of an alignment with overlapping groups
1452 <!-- JAL-2310 -->Finder double counts if both a sequence's
1453 name and description match
1456 <!-- JAL-2370 -->Hiding column selection containing two
1457 hidden regions results in incorrect hidden regions
1460 <!-- JAL-2386 -->'Apply to all groups' setting when
1461 changing colour does not apply Conservation slider value
1465 <!-- JAL-2373 -->Percentage identity and conservation menu
1466 items do not show a tick or allow shading to be disabled
1469 <!-- JAL-2385 -->Conservation shading or PID threshold
1470 lost when base colourscheme changed if slider not visible
1473 <!-- JAL-2547 -->Sequence features shown in tooltip for
1474 gaps before start of features
1477 <!-- JAL-2623 -->Graduated feature colour threshold not
1478 restored to UI when feature colour is edited
1481 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1482 a time when scrolling vertically in wrapped mode.
1485 <!-- JAL-2630 -->Structure and alignment overview update
1486 as graduate feature colour settings are modified via the
1490 <!-- JAL-2034 -->Overview window doesn't always update
1491 when a group defined on the alignment is resized
1494 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1495 wrapped view result in positional status updates
1499 <!-- JAL-2563 -->Status bar doesn't show position for
1500 ambiguous amino acid and nucleotide symbols
1503 <!-- JAL-2602 -->Copy consensus sequence failed if
1504 alignment included gapped columns
1507 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1508 widgets don't permanently disappear
1511 <!-- JAL-2503 -->Cannot select or filter quantitative
1512 annotation that are shown only as column labels (e.g.
1513 T-Coffee column reliability scores)
1516 <!-- JAL-2594 -->Exception thrown if trying to create a
1517 sequence feature on gaps only
1520 <!-- JAL-2504 -->Features created with 'New feature'
1521 button from a Find inherit previously defined feature type
1522 rather than the Find query string
1525 <!-- JAL-2423 -->incorrect title in output window when
1526 exporting tree calculated in Jalview
1529 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1530 and then revealing them reorders sequences on the
1534 <!-- JAL-964 -->Group panel in sequence feature settings
1535 doesn't update to reflect available set of groups after
1536 interactively adding or modifying features
1539 <!-- JAL-2225 -->Sequence Database chooser unusable on
1543 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1544 only excluded gaps in current sequence and ignored
1551 <!-- JAL-2421 -->Overview window visible region moves
1552 erratically when hidden rows or columns are present
1555 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1556 Structure Viewer's colour menu don't correspond to
1560 <!-- JAL-2405 -->Protein specific colours only offered in
1561 colour and group colour menu for protein alignments
1564 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1565 reflect currently selected view or group's shading
1569 <!-- JAL-2624 -->Feature colour thresholds not respected
1570 when rendered on overview and structures when opacity at
1574 <!-- JAL-2589 -->User defined gap colour not shown in
1575 overview when features overlaid on alignment
1578 <!-- JAL-2567 -->Feature settings for different views not
1579 recovered correctly from Jalview project file
1582 <!-- JAL-2256 -->Feature colours in overview when first opened
1583 (automatically via preferences) are different to the main
1587 <em>Data import/export</em>
1590 <!-- JAL-2576 -->Very large alignments take a long time to
1594 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1595 added after a sequence was imported are not written to
1599 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1600 when importing RNA secondary structure via Stockholm
1603 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1604 not shown in correct direction for simple pseudoknots
1607 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1608 with lightGray or darkGray via features file (but can
1612 <!-- JAL-2383 -->Above PID colour threshold not recovered
1613 when alignment view imported from project
1616 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1617 structure and sequences extracted from structure files
1618 imported via URL and viewed in Jmol
1621 <!-- JAL-2520 -->Structures loaded via URL are saved in
1622 Jalview Projects rather than fetched via URL again when
1623 the project is loaded and the structure viewed
1626 <em>Web Services</em>
1629 <!-- JAL-2519 -->EnsemblGenomes example failing after
1630 release of Ensembl v.88
1633 <!-- JAL-2366 -->Proxy server address and port always
1634 appear enabled in Preferences->Connections
1637 <!-- JAL-2461 -->DAS registry not found exceptions
1638 removed from console output
1641 <!-- JAL-2582 -->Cannot retrieve protein products from
1642 Ensembl by Peptide ID
1645 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1646 created from SIFTs, and spurious 'Couldn't open structure
1647 in Chimera' errors raised after April 2017 update (problem
1648 due to 'null' string rather than empty string used for
1649 residues with no corresponding PDB mapping).
1652 <em>Application UI</em>
1655 <!-- JAL-2361 -->User Defined Colours not added to Colour
1659 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1660 case' residues (button in colourscheme editor debugged and
1661 new documentation and tooltips added)
1664 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1665 doesn't restore group-specific text colour thresholds
1668 <!-- JAL-2243 -->Feature settings panel does not update as
1669 new features are added to alignment
1672 <!-- JAL-2532 -->Cancel in feature settings reverts
1673 changes to feature colours via the Amend features dialog
1676 <!-- JAL-2506 -->Null pointer exception when attempting to
1677 edit graduated feature colour via amend features dialog
1681 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1682 selection menu changes colours of alignment views
1685 <!-- JAL-2426 -->Spurious exceptions in console raised
1686 from alignment calculation workers after alignment has
1690 <!-- JAL-1608 -->Typo in selection popup menu - Create
1691 groups now 'Create Group'
1694 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1695 Create/Undefine group doesn't always work
1698 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1699 shown again after pressing 'Cancel'
1702 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1703 adjusts start position in wrap mode
1706 <!-- JAL-2563 -->Status bar doesn't show positions for
1707 ambiguous amino acids
1710 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1711 CDS/Protein view after CDS sequences added for aligned
1715 <!-- JAL-2592 -->User defined colourschemes called 'User
1716 Defined' don't appear in Colours menu
1722 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1723 score models doesn't always result in an updated PCA plot
1726 <!-- JAL-2442 -->Features not rendered as transparent on
1727 overview or linked structure view
1730 <!-- JAL-2372 -->Colour group by conservation doesn't
1734 <!-- JAL-2517 -->Hitting Cancel after applying
1735 user-defined colourscheme doesn't restore original
1742 <!-- JAL-2314 -->Unit test failure:
1743 jalview.ws.jabaws.RNAStructExportImport setup fails
1746 <!-- JAL-2307 -->Unit test failure:
1747 jalview.ws.sifts.SiftsClientTest due to compatibility
1748 problems with deep array comparison equality asserts in
1749 successive versions of TestNG
1752 <!-- JAL-2479 -->Relocated StructureChooserTest and
1753 ParameterUtilsTest Unit tests to Network suite
1756 <em>New Known Issues</em>
1759 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1760 phase after a sequence motif find operation
1763 <!-- JAL-2550 -->Importing annotation file with rows
1764 containing just upper and lower case letters are
1765 interpreted as WUSS RNA secondary structure symbols
1768 <!-- JAL-2590 -->Cannot load and display Newick trees
1769 reliably from eggnog Ortholog database
1772 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1773 containing features of type Highlight' when 'B' is pressed
1774 to mark columns containing highlighted regions.
1777 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1778 doesn't always add secondary structure annotation.
1783 <td width="60" nowrap>
1784 <div align="center">
1785 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1788 <td><div align="left">
1792 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1793 for all consensus calculations
1796 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1799 <li>Updated Jalview's Certum code signing certificate
1802 <em>Application</em>
1805 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1806 set of database cross-references, sorted alphabetically
1809 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1810 from database cross references. Users with custom links
1811 will receive a <a href="webServices/urllinks.html#warning">warning
1812 dialog</a> asking them to update their preferences.
1815 <!-- JAL-2287-->Cancel button and escape listener on
1816 dialog warning user about disconnecting Jalview from a
1820 <!-- JAL-2320-->Jalview's Chimera control window closes if
1821 the Chimera it is connected to is shut down
1824 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1825 columns menu item to mark columns containing highlighted
1826 regions (e.g. from structure selections or results of a
1830 <!-- JAL-2284-->Command line option for batch-generation
1831 of HTML pages rendering alignment data with the BioJS
1841 <!-- JAL-2286 -->Columns with more than one modal residue
1842 are not coloured or thresholded according to percent
1843 identity (first observed in Jalview 2.8.2)
1846 <!-- JAL-2301 -->Threonine incorrectly reported as not
1850 <!-- JAL-2318 -->Updates to documentation pages (above PID
1851 threshold, amino acid properties)
1854 <!-- JAL-2292 -->Lower case residues in sequences are not
1855 reported as mapped to residues in a structure file in the
1859 <!--JAL-2324 -->Identical features with non-numeric scores
1860 could be added multiple times to a sequence
1863 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1864 bond features shown as two highlighted residues rather
1865 than a range in linked structure views, and treated
1866 correctly when selecting and computing trees from features
1869 <!-- JAL-2281-->Custom URL links for database
1870 cross-references are matched to database name regardless
1875 <em>Application</em>
1878 <!-- JAL-2282-->Custom URL links for specific database
1879 names without regular expressions also offer links from
1883 <!-- JAL-2315-->Removing a single configured link in the
1884 URL links pane in Connections preferences doesn't actually
1885 update Jalview configuration
1888 <!-- JAL-2272-->CTRL-Click on a selected region to open
1889 the alignment area popup menu doesn't work on El-Capitan
1892 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1893 files with similarly named sequences if dropped onto the
1897 <!-- JAL-2312 -->Additional mappings are shown for PDB
1898 entries where more chains exist in the PDB accession than
1899 are reported in the SIFTS file
1902 <!-- JAL-2317-->Certain structures do not get mapped to
1903 the structure view when displayed with Chimera
1906 <!-- JAL-2317-->No chains shown in the Chimera view
1907 panel's View->Show Chains submenu
1910 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1911 work for wrapped alignment views
1914 <!--JAL-2197 -->Rename UI components for running JPred
1915 predictions from 'JNet' to 'JPred'
1918 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1919 corrupted when annotation panel vertical scroll is not at
1920 first annotation row
1923 <!--JAL-2332 -->Attempting to view structure for Hen
1924 lysozyme results in a PDB Client error dialog box
1927 <!-- JAL-2319 -->Structure View's mapping report switched
1928 ranges for PDB and sequence for SIFTS
1931 SIFTS 'Not_Observed' residues mapped to non-existant
1935 <!-- <em>New Known Issues</em>
1942 <td width="60" nowrap>
1943 <div align="center">
1944 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1945 <em>25/10/2016</em></strong>
1948 <td><em>Application</em>
1950 <li>3D Structure chooser opens with 'Cached structures'
1951 view if structures already loaded</li>
1952 <li>Progress bar reports models as they are loaded to
1953 structure views</li>
1959 <li>Colour by conservation always enabled and no tick
1960 shown in menu when BLOSUM or PID shading applied</li>
1961 <li>FER1_ARATH and FER2_ARATH labels were switched in
1962 example sequences/projects/trees</li>
1964 <em>Application</em>
1966 <li>Jalview projects with views of local PDB structure
1967 files saved on Windows cannot be opened on OSX</li>
1968 <li>Multiple structure views can be opened and superposed
1969 without timeout for structures with multiple models or
1970 multiple sequences in alignment</li>
1971 <li>Cannot import or associated local PDB files without a
1972 PDB ID HEADER line</li>
1973 <li>RMSD is not output in Jmol console when superposition
1975 <li>Drag and drop of URL from Browser fails for Linux and
1976 OSX versions earlier than El Capitan</li>
1977 <li>ENA client ignores invalid content from ENA server</li>
1978 <li>Exceptions are not raised in console when ENA client
1979 attempts to fetch non-existent IDs via Fetch DB Refs UI
1981 <li>Exceptions are not raised in console when a new view
1982 is created on the alignment</li>
1983 <li>OSX right-click fixed for group selections: CMD-click
1984 to insert/remove gaps in groups and CTRL-click to open group
1987 <em>Build and deployment</em>
1989 <li>URL link checker now copes with multi-line anchor
1992 <em>New Known Issues</em>
1994 <li>Drag and drop from URL links in browsers do not work
2001 <td width="60" nowrap>
2002 <div align="center">
2003 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2006 <td><em>General</em>
2009 <!-- JAL-2124 -->Updated Spanish translations.
2012 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2013 for importing structure data to Jalview. Enables mmCIF and
2017 <!-- JAL-192 --->Alignment ruler shows positions relative to
2021 <!-- JAL-2202 -->Position/residue shown in status bar when
2022 mousing over sequence associated annotation
2025 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2029 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2030 '()', canonical '[]' and invalid '{}' base pair populations
2034 <!-- JAL-2092 -->Feature settings popup menu options for
2035 showing or hiding columns containing a feature
2038 <!-- JAL-1557 -->Edit selected group by double clicking on
2039 group and sequence associated annotation labels
2042 <!-- JAL-2236 -->Sequence name added to annotation label in
2043 select/hide columns by annotation and colour by annotation
2047 </ul> <em>Application</em>
2050 <!-- JAL-2050-->Automatically hide introns when opening a
2051 gene/transcript view
2054 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2058 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2059 structure mappings with the EMBL-EBI PDBe SIFTS database
2062 <!-- JAL-2079 -->Updated download sites used for Rfam and
2063 Pfam sources to xfam.org
2066 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2069 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2070 over sequences in Jalview
2073 <!-- JAL-2027-->Support for reverse-complement coding
2074 regions in ENA and EMBL
2077 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2078 for record retrieval via ENA rest API
2081 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2085 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2086 groovy script execution
2089 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2090 alignment window's Calculate menu
2093 <!-- JAL-1812 -->Allow groovy scripts that call
2094 Jalview.getAlignFrames() to run in headless mode
2097 <!-- JAL-2068 -->Support for creating new alignment
2098 calculation workers from groovy scripts
2101 <!-- JAL-1369 --->Store/restore reference sequence in
2105 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2106 associations are now saved/restored from project
2109 <!-- JAL-1993 -->Database selection dialog always shown
2110 before sequence fetcher is opened
2113 <!-- JAL-2183 -->Double click on an entry in Jalview's
2114 database chooser opens a sequence fetcher
2117 <!-- JAL-1563 -->Free-text search client for UniProt using
2118 the UniProt REST API
2121 <!-- JAL-2168 -->-nonews command line parameter to prevent
2122 the news reader opening
2125 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2126 querying stored in preferences
2129 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2133 <!-- JAL-1977-->Tooltips shown on database chooser
2136 <!-- JAL-391 -->Reverse complement function in calculate
2137 menu for nucleotide sequences
2140 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2141 and feature counts preserves alignment ordering (and
2142 debugged for complex feature sets).
2145 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2146 viewing structures with Jalview 2.10
2149 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2150 genome, transcript CCDS and gene ids via the Ensembl and
2151 Ensembl Genomes REST API
2154 <!-- JAL-2049 -->Protein sequence variant annotation
2155 computed for 'sequence_variant' annotation on CDS regions
2159 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2163 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2164 Ref Fetcher fails to match, or otherwise updates sequence
2165 data from external database records.
2168 <!-- JAL-2154 -->Revised Jalview Project format for
2169 efficient recovery of sequence coding and alignment
2170 annotation relationships.
2172 </ul> <!-- <em>Applet</em>
2183 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2187 <!-- JAL-2018-->Export features in Jalview format (again)
2188 includes graduated colourschemes
2191 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2192 working with big alignments and lots of hidden columns
2195 <!-- JAL-2053-->Hidden column markers not always rendered
2196 at right of alignment window
2199 <!-- JAL-2067 -->Tidied up links in help file table of
2203 <!-- JAL-2072 -->Feature based tree calculation not shown
2207 <!-- JAL-2075 -->Hidden columns ignored during feature
2208 based tree calculation
2211 <!-- JAL-2065 -->Alignment view stops updating when show
2212 unconserved enabled for group on alignment
2215 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2219 <!-- JAL-2146 -->Alignment column in status incorrectly
2220 shown as "Sequence position" when mousing over
2224 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2225 hidden columns present
2228 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2229 user created annotation added to alignment
2232 <!-- JAL-1841 -->RNA Structure consensus only computed for
2233 '()' base pair annotation
2236 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2237 in zero scores for all base pairs in RNA Structure
2241 <!-- JAL-2174-->Extend selection with columns containing
2245 <!-- JAL-2275 -->Pfam format writer puts extra space at
2246 beginning of sequence
2249 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2253 <!-- JAL-2238 -->Cannot create groups on an alignment from
2254 from a tree when t-coffee scores are shown
2257 <!-- JAL-1836,1967 -->Cannot import and view PDB
2258 structures with chains containing negative resnums (4q4h)
2261 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2265 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2266 to Clustal, PIR and PileUp output
2269 <!-- JAL-2008 -->Reordering sequence features that are
2270 not visible causes alignment window to repaint
2273 <!-- JAL-2006 -->Threshold sliders don't work in
2274 graduated colour and colour by annotation row for e-value
2275 scores associated with features and annotation rows
2278 <!-- JAL-1797 -->amino acid physicochemical conservation
2279 calculation should be case independent
2282 <!-- JAL-2173 -->Remove annotation also updates hidden
2286 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2287 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2288 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2291 <!-- JAL-2065 -->Null pointer exceptions and redraw
2292 problems when reference sequence defined and 'show
2293 non-conserved' enabled
2296 <!-- JAL-1306 -->Quality and Conservation are now shown on
2297 load even when Consensus calculation is disabled
2300 <!-- JAL-1932 -->Remove right on penultimate column of
2301 alignment does nothing
2304 <em>Application</em>
2307 <!-- JAL-1552-->URLs and links can't be imported by
2308 drag'n'drop on OSX when launched via webstart (note - not
2309 yet fixed for El Capitan)
2312 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2313 output when running on non-gb/us i18n platforms
2316 <!-- JAL-1944 -->Error thrown when exporting a view with
2317 hidden sequences as flat-file alignment
2320 <!-- JAL-2030-->InstallAnywhere distribution fails when
2324 <!-- JAL-2080-->Jalview very slow to launch via webstart
2325 (also hotfix for 2.9.0b2)
2328 <!-- JAL-2085 -->Cannot save project when view has a
2329 reference sequence defined
2332 <!-- JAL-1011 -->Columns are suddenly selected in other
2333 alignments and views when revealing hidden columns
2336 <!-- JAL-1989 -->Hide columns not mirrored in complement
2337 view in a cDNA/Protein splitframe
2340 <!-- JAL-1369 -->Cannot save/restore representative
2341 sequence from project when only one sequence is
2345 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2346 in Structure Chooser
2349 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2350 structure consensus didn't refresh annotation panel
2353 <!-- JAL-1962 -->View mapping in structure view shows
2354 mappings between sequence and all chains in a PDB file
2357 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2358 dialogs format columns correctly, don't display array
2359 data, sort columns according to type
2362 <!-- JAL-1975 -->Export complete shown after destination
2363 file chooser is cancelled during an image export
2366 <!-- JAL-2025 -->Error when querying PDB Service with
2367 sequence name containing special characters
2370 <!-- JAL-2024 -->Manual PDB structure querying should be
2374 <!-- JAL-2104 -->Large tooltips with broken HTML
2375 formatting don't wrap
2378 <!-- JAL-1128 -->Figures exported from wrapped view are
2379 truncated so L looks like I in consensus annotation
2382 <!-- JAL-2003 -->Export features should only export the
2383 currently displayed features for the current selection or
2387 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2388 after fetching cross-references, and restoring from
2392 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2393 followed in the structure viewer
2396 <!-- JAL-2163 -->Titles for individual alignments in
2397 splitframe not restored from project
2400 <!-- JAL-2145 -->missing autocalculated annotation at
2401 trailing end of protein alignment in transcript/product
2402 splitview when pad-gaps not enabled by default
2405 <!-- JAL-1797 -->amino acid physicochemical conservation
2409 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2410 article has been read (reopened issue due to
2411 internationalisation problems)
2414 <!-- JAL-1960 -->Only offer PDB structures in structure
2415 viewer based on sequence name, PDB and UniProt
2420 <!-- JAL-1976 -->No progress bar shown during export of
2424 <!-- JAL-2213 -->Structures not always superimposed after
2425 multiple structures are shown for one or more sequences.
2428 <!-- JAL-1370 -->Reference sequence characters should not
2429 be replaced with '.' when 'Show unconserved' format option
2433 <!-- JAL-1823 -->Cannot specify chain code when entering
2434 specific PDB id for sequence
2437 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2438 'Export hidden sequences' is enabled, but 'export hidden
2439 columns' is disabled.
2442 <!--JAL-2026-->Best Quality option in structure chooser
2443 selects lowest rather than highest resolution structures
2447 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2448 to sequence mapping in 'View Mappings' report
2451 <!-- JAL-2284 -->Unable to read old Jalview projects that
2452 contain non-XML data added after Jalvew wrote project.
2455 <!-- JAL-2118 -->Newly created annotation row reorders
2456 after clicking on it to create new annotation for a
2460 <!-- JAL-1980 -->Null Pointer Exception raised when
2461 pressing Add on an orphaned cut'n'paste window.
2463 <!-- may exclude, this is an external service stability issue JAL-1941
2464 -- > RNA 3D structure not added via DSSR service</li> -->
2469 <!-- JAL-2151 -->Incorrect columns are selected when
2470 hidden columns present before start of sequence
2473 <!-- JAL-1986 -->Missing dependencies on applet pages
2477 <!-- JAL-1947 -->Overview pixel size changes when
2478 sequences are hidden in applet
2481 <!-- JAL-1996 -->Updated instructions for applet
2482 deployment on examples pages.
2489 <td width="60" nowrap>
2490 <div align="center">
2491 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2492 <em>16/10/2015</em></strong>
2495 <td><em>General</em>
2497 <li>Time stamps for signed Jalview application and applet
2502 <em>Application</em>
2504 <li>Duplicate group consensus and conservation rows
2505 shown when tree is partitioned</li>
2506 <li>Erratic behaviour when tree partitions made with
2507 multiple cDNA/Protein split views</li>
2513 <td width="60" nowrap>
2514 <div align="center">
2515 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2516 <em>8/10/2015</em></strong>
2519 <td><em>General</em>
2521 <li>Updated Spanish translations of localized text for
2523 </ul> <em>Application</em>
2525 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2526 <li>Signed OSX InstallAnywhere installer<br></li>
2527 <li>Support for per-sequence based annotations in BioJSON</li>
2528 </ul> <em>Applet</em>
2530 <li>Split frame example added to applet examples page</li>
2531 </ul> <em>Build and Deployment</em>
2534 <!-- JAL-1888 -->New ant target for running Jalview's test
2542 <li>Mapping of cDNA to protein in split frames
2543 incorrect when sequence start > 1</li>
2544 <li>Broken images in filter column by annotation dialog
2546 <li>Feature colours not parsed from features file</li>
2547 <li>Exceptions and incomplete link URLs recovered when
2548 loading a features file containing HTML tags in feature
2552 <em>Application</em>
2554 <li>Annotations corrupted after BioJS export and
2556 <li>Incorrect sequence limits after Fetch DB References
2557 with 'trim retrieved sequences'</li>
2558 <li>Incorrect warning about deleting all data when
2559 deleting selected columns</li>
2560 <li>Patch to build system for shipping properly signed
2561 JNLP templates for webstart launch</li>
2562 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2563 unreleased structures for download or viewing</li>
2564 <li>Tab/space/return keystroke operation of EMBL-PDBe
2565 fetcher/viewer dialogs works correctly</li>
2566 <li>Disabled 'minimise' button on Jalview windows
2567 running on OSX to workaround redraw hang bug</li>
2568 <li>Split cDNA/Protein view position and geometry not
2569 recovered from jalview project</li>
2570 <li>Initial enabled/disabled state of annotation menu
2571 sorter 'show autocalculated first/last' corresponds to
2573 <li>Restoring of Clustal, RNA Helices and T-Coffee
2574 color schemes from BioJSON</li>
2578 <li>Reorder sequences mirrored in cDNA/Protein split
2580 <li>Applet with Jmol examples not loading correctly</li>
2586 <td><div align="center">
2587 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2589 <td><em>General</em>
2591 <li>Linked visualisation and analysis of DNA and Protein
2594 <li>Translated cDNA alignments shown as split protein
2595 and DNA alignment views</li>
2596 <li>Codon consensus annotation for linked protein and
2597 cDNA alignment views</li>
2598 <li>Link cDNA or Protein product sequences by loading
2599 them onto Protein or cDNA alignments</li>
2600 <li>Reconstruct linked cDNA alignment from aligned
2601 protein sequences</li>
2604 <li>Jmol integration updated to Jmol v14.2.14</li>
2605 <li>Import and export of Jalview alignment views as <a
2606 href="features/bioJsonFormat.html">BioJSON</a></li>
2607 <li>New alignment annotation file statements for
2608 reference sequences and marking hidden columns</li>
2609 <li>Reference sequence based alignment shading to
2610 highlight variation</li>
2611 <li>Select or hide columns according to alignment
2613 <li>Find option for locating sequences by description</li>
2614 <li>Conserved physicochemical properties shown in amino
2615 acid conservation row</li>
2616 <li>Alignments can be sorted by number of RNA helices</li>
2617 </ul> <em>Application</em>
2619 <li>New cDNA/Protein analysis capabilities
2621 <li>Get Cross-References should open a Split Frame
2622 view with cDNA/Protein</li>
2623 <li>Detect when nucleotide sequences and protein
2624 sequences are placed in the same alignment</li>
2625 <li>Split cDNA/Protein views are saved in Jalview
2630 <li>Use REST API to talk to Chimera</li>
2631 <li>Selected regions in Chimera are highlighted in linked
2632 Jalview windows</li>
2634 <li>VARNA RNA viewer updated to v3.93</li>
2635 <li>VARNA views are saved in Jalview Projects</li>
2636 <li>Pseudoknots displayed as Jalview RNA annotation can
2637 be shown in VARNA</li>
2639 <li>Make groups for selection uses marked columns as well
2640 as the active selected region</li>
2642 <li>Calculate UPGMA and NJ trees using sequence feature
2644 <li>New Export options
2646 <li>New Export Settings dialog to control hidden
2647 region export in flat file generation</li>
2649 <li>Export alignment views for display with the <a
2650 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2652 <li>Export scrollable SVG in HTML page</li>
2653 <li>Optional embedding of BioJSON data when exporting
2654 alignment figures to HTML</li>
2656 <li>3D structure retrieval and display
2658 <li>Free text and structured queries with the PDBe
2660 <li>PDBe Search API based discovery and selection of
2661 PDB structures for a sequence set</li>
2665 <li>JPred4 employed for protein secondary structure
2667 <li>Hide Insertions menu option to hide unaligned columns
2668 for one or a group of sequences</li>
2669 <li>Automatically hide insertions in alignments imported
2670 from the JPred4 web server</li>
2671 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2672 system on OSX<br />LGPL libraries courtesy of <a
2673 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2675 <li>changed 'View nucleotide structure' submenu to 'View
2676 VARNA 2D Structure'</li>
2677 <li>change "View protein structure" menu option to "3D
2680 </ul> <em>Applet</em>
2682 <li>New layout for applet example pages</li>
2683 <li>New parameters to enable SplitFrame view
2684 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2685 <li>New example demonstrating linked viewing of cDNA and
2686 Protein alignments</li>
2687 </ul> <em>Development and deployment</em>
2689 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2690 <li>Include installation type and git revision in build
2691 properties and console log output</li>
2692 <li>Jalview Github organisation, and new github site for
2693 storing BioJsMSA Templates</li>
2694 <li>Jalview's unit tests now managed with TestNG</li>
2697 <!-- <em>General</em>
2699 </ul> --> <!-- issues resolved --> <em>Application</em>
2701 <li>Escape should close any open find dialogs</li>
2702 <li>Typo in select-by-features status report</li>
2703 <li>Consensus RNA secondary secondary structure
2704 predictions are not highlighted in amber</li>
2705 <li>Missing gap character in v2.7 example file means
2706 alignment appears unaligned when pad-gaps is not enabled</li>
2707 <li>First switch to RNA Helices colouring doesn't colour
2708 associated structure views</li>
2709 <li>ID width preference option is greyed out when auto
2710 width checkbox not enabled</li>
2711 <li>Stopped a warning dialog from being shown when
2712 creating user defined colours</li>
2713 <li>'View Mapping' in structure viewer shows sequence
2714 mappings for just that viewer's sequences</li>
2715 <li>Workaround for superposing PDB files containing
2716 multiple models in Chimera</li>
2717 <li>Report sequence position in status bar when hovering
2718 over Jmol structure</li>
2719 <li>Cannot output gaps as '.' symbols with Selection ->
2720 output to text box</li>
2721 <li>Flat file exports of alignments with hidden columns
2722 have incorrect sequence start/end</li>
2723 <li>'Aligning' a second chain to a Chimera structure from
2725 <li>Colour schemes applied to structure viewers don't
2726 work for nucleotide</li>
2727 <li>Loading/cut'n'pasting an empty or invalid file leads
2728 to a grey/invisible alignment window</li>
2729 <li>Exported Jpred annotation from a sequence region
2730 imports to different position</li>
2731 <li>Space at beginning of sequence feature tooltips shown
2732 on some platforms</li>
2733 <li>Chimera viewer 'View | Show Chain' menu is not
2735 <li>'New View' fails with a Null Pointer Exception in
2736 console if Chimera has been opened</li>
2737 <li>Mouseover to Chimera not working</li>
2738 <li>Miscellaneous ENA XML feature qualifiers not
2740 <li>NPE in annotation renderer after 'Extract Scores'</li>
2741 <li>If two structures in one Chimera window, mouseover of
2742 either sequence shows on first structure</li>
2743 <li>'Show annotations' options should not make
2744 non-positional annotations visible</li>
2745 <li>Subsequence secondary structure annotation not shown
2746 in right place after 'view flanking regions'</li>
2747 <li>File Save As type unset when current file format is
2749 <li>Save as '.jar' option removed for saving Jalview
2751 <li>Colour by Sequence colouring in Chimera more
2753 <li>Cannot 'add reference annotation' for a sequence in
2754 several views on same alignment</li>
2755 <li>Cannot show linked products for EMBL / ENA records</li>
2756 <li>Jalview's tooltip wraps long texts containing no
2758 </ul> <em>Applet</em>
2760 <li>Jmol to JalviewLite mouseover/link not working</li>
2761 <li>JalviewLite can't import sequences with ID
2762 descriptions containing angle brackets</li>
2763 </ul> <em>General</em>
2765 <li>Cannot export and reimport RNA secondary structure
2766 via jalview annotation file</li>
2767 <li>Random helix colour palette for colour by annotation
2768 with RNA secondary structure</li>
2769 <li>Mouseover to cDNA from STOP residue in protein
2770 translation doesn't work.</li>
2771 <li>hints when using the select by annotation dialog box</li>
2772 <li>Jmol alignment incorrect if PDB file has alternate CA
2774 <li>FontChooser message dialog appears to hang after
2775 choosing 1pt font</li>
2776 <li>Peptide secondary structure incorrectly imported from
2777 annotation file when annotation display text includes 'e' or
2779 <li>Cannot set colour of new feature type whilst creating
2781 <li>cDNA translation alignment should not be sequence
2782 order dependent</li>
2783 <li>'Show unconserved' doesn't work for lower case
2785 <li>Nucleotide ambiguity codes involving R not recognised</li>
2786 </ul> <em>Deployment and Documentation</em>
2788 <li>Applet example pages appear different to the rest of
2789 www.jalview.org</li>
2790 </ul> <em>Application Known issues</em>
2792 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2793 <li>Misleading message appears after trying to delete
2795 <li>Jalview icon not shown in dock after InstallAnywhere
2796 version launches</li>
2797 <li>Fetching EMBL reference for an RNA sequence results
2798 fails with a sequence mismatch</li>
2799 <li>Corrupted or unreadable alignment display when
2800 scrolling alignment to right</li>
2801 <li>ArrayIndexOutOfBoundsException thrown when remove
2802 empty columns called on alignment with ragged gapped ends</li>
2803 <li>auto calculated alignment annotation rows do not get
2804 placed above or below non-autocalculated rows</li>
2805 <li>Jalview dekstop becomes sluggish at full screen in
2806 ultra-high resolution</li>
2807 <li>Cannot disable consensus calculation independently of
2808 quality and conservation</li>
2809 <li>Mouseover highlighting between cDNA and protein can
2810 become sluggish with more than one splitframe shown</li>
2811 </ul> <em>Applet Known Issues</em>
2813 <li>Core PDB parsing code requires Jmol</li>
2814 <li>Sequence canvas panel goes white when alignment
2815 window is being resized</li>
2821 <td><div align="center">
2822 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2824 <td><em>General</em>
2826 <li>Updated Java code signing certificate donated by
2828 <li>Features and annotation preserved when performing
2829 pairwise alignment</li>
2830 <li>RNA pseudoknot annotation can be
2831 imported/exported/displayed</li>
2832 <li>'colour by annotation' can colour by RNA and
2833 protein secondary structure</li>
2834 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2835 post-hoc with 2.9 release</em>)
2838 </ul> <em>Application</em>
2840 <li>Extract and display secondary structure for sequences
2841 with 3D structures</li>
2842 <li>Support for parsing RNAML</li>
2843 <li>Annotations menu for layout
2845 <li>sort sequence annotation rows by alignment</li>
2846 <li>place sequence annotation above/below alignment
2849 <li>Output in Stockholm format</li>
2850 <li>Internationalisation: improved Spanish (es)
2852 <li>Structure viewer preferences tab</li>
2853 <li>Disorder and Secondary Structure annotation tracks
2854 shared between alignments</li>
2855 <li>UCSF Chimera launch and linked highlighting from
2857 <li>Show/hide all sequence associated annotation rows for
2858 all or current selection</li>
2859 <li>disorder and secondary structure predictions
2860 available as dataset annotation</li>
2861 <li>Per-sequence rna helices colouring</li>
2864 <li>Sequence database accessions imported when fetching
2865 alignments from Rfam</li>
2866 <li>update VARNA version to 3.91</li>
2868 <li>New groovy scripts for exporting aligned positions,
2869 conservation values, and calculating sum of pairs scores.</li>
2870 <li>Command line argument to set default JABAWS server</li>
2871 <li>include installation type in build properties and
2872 console log output</li>
2873 <li>Updated Jalview project format to preserve dataset
2877 <!-- issues resolved --> <em>Application</em>
2879 <li>Distinguish alignment and sequence associated RNA
2880 structure in structure->view->VARNA</li>
2881 <li>Raise dialog box if user deletes all sequences in an
2883 <li>Pressing F1 results in documentation opening twice</li>
2884 <li>Sequence feature tooltip is wrapped</li>
2885 <li>Double click on sequence associated annotation
2886 selects only first column</li>
2887 <li>Redundancy removal doesn't result in unlinked
2888 leaves shown in tree</li>
2889 <li>Undos after several redundancy removals don't undo
2891 <li>Hide sequence doesn't hide associated annotation</li>
2892 <li>User defined colours dialog box too big to fit on
2893 screen and buttons not visible</li>
2894 <li>author list isn't updated if already written to
2895 Jalview properties</li>
2896 <li>Popup menu won't open after retrieving sequence
2898 <li>File open window for associate PDB doesn't open</li>
2899 <li>Left-then-right click on a sequence id opens a
2900 browser search window</li>
2901 <li>Cannot open sequence feature shading/sort popup menu
2902 in feature settings dialog</li>
2903 <li>better tooltip placement for some areas of Jalview
2905 <li>Allow addition of JABAWS Server which doesn't
2906 pass validation</li>
2907 <li>Web services parameters dialog box is too large to
2909 <li>Muscle nucleotide alignment preset obscured by
2911 <li>JABAWS preset submenus don't contain newly
2912 defined user preset</li>
2913 <li>MSA web services warns user if they were launched
2914 with invalid input</li>
2915 <li>Jalview cannot contact DAS Registy when running on
2918 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2919 'Superpose with' submenu not shown when new view
2923 </ul> <!-- <em>Applet</em>
2925 </ul> <em>General</em>
2927 </ul>--> <em>Deployment and Documentation</em>
2929 <li>2G and 1G options in launchApp have no effect on
2930 memory allocation</li>
2931 <li>launchApp service doesn't automatically open
2932 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2934 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2935 InstallAnywhere reports cannot find valid JVM when Java
2936 1.7_055 is available
2938 </ul> <em>Application Known issues</em>
2941 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2942 corrupted or unreadable alignment display when scrolling
2946 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2947 retrieval fails but progress bar continues for DAS retrieval
2948 with large number of ID
2951 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2952 flatfile output of visible region has incorrect sequence
2956 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2957 rna structure consensus doesn't update when secondary
2958 structure tracks are rearranged
2961 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2962 invalid rna structure positional highlighting does not
2963 highlight position of invalid base pairs
2966 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2967 out of memory errors are not raised when saving Jalview
2968 project from alignment window file menu
2971 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2972 Switching to RNA Helices colouring doesn't propagate to
2976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2977 colour by RNA Helices not enabled when user created
2978 annotation added to alignment
2981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2982 Jalview icon not shown on dock in Mountain Lion/Webstart
2984 </ul> <em>Applet Known Issues</em>
2987 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2988 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2992 Jalview and Jmol example not compatible with IE9
2995 <li>Sort by annotation score doesn't reverse order
3001 <td><div align="center">
3002 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3005 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3008 <li>Internationalisation of user interface (usually
3009 called i18n support) and translation for Spanish locale</li>
3010 <li>Define/Undefine group on current selection with
3011 Ctrl-G/Shift Ctrl-G</li>
3012 <li>Improved group creation/removal options in
3013 alignment/sequence Popup menu</li>
3014 <li>Sensible precision for symbol distribution
3015 percentages shown in logo tooltip.</li>
3016 <li>Annotation panel height set according to amount of
3017 annotation when alignment first opened</li>
3018 </ul> <em>Application</em>
3020 <li>Interactive consensus RNA secondary structure
3021 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3022 <li>Select columns containing particular features from
3023 Feature Settings dialog</li>
3024 <li>View all 'representative' PDB structures for selected
3026 <li>Update Jalview project format:
3028 <li>New file extension for Jalview projects '.jvp'</li>
3029 <li>Preserve sequence and annotation dataset (to
3030 store secondary structure annotation,etc)</li>
3031 <li>Per group and alignment annotation and RNA helix
3035 <li>New similarity measures for PCA and Tree calculation
3037 <li>Experimental support for retrieval and viewing of
3038 flanking regions for an alignment</li>
3042 <!-- issues resolved --> <em>Application</em>
3044 <li>logo keeps spinning and status remains at queued or
3045 running after job is cancelled</li>
3046 <li>cannot export features from alignments imported from
3047 Jalview/VAMSAS projects</li>
3048 <li>Buggy slider for web service parameters that take
3050 <li>Newly created RNA secondary structure line doesn't
3051 have 'display all symbols' flag set</li>
3052 <li>T-COFFEE alignment score shading scheme and other
3053 annotation shading not saved in Jalview project</li>
3054 <li>Local file cannot be loaded in freshly downloaded
3056 <li>Jalview icon not shown on dock in Mountain
3058 <li>Load file from desktop file browser fails</li>
3059 <li>Occasional NPE thrown when calculating large trees</li>
3060 <li>Cannot reorder or slide sequences after dragging an
3061 alignment onto desktop</li>
3062 <li>Colour by annotation dialog throws NPE after using
3063 'extract scores' function</li>
3064 <li>Loading/cut'n'pasting an empty file leads to a grey
3065 alignment window</li>
3066 <li>Disorder thresholds rendered incorrectly after
3067 performing IUPred disorder prediction</li>
3068 <li>Multiple group annotated consensus rows shown when
3069 changing 'normalise logo' display setting</li>
3070 <li>Find shows blank dialog after 'finished searching' if
3071 nothing matches query</li>
3072 <li>Null Pointer Exceptions raised when sorting by
3073 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3075 <li>Errors in Jmol console when structures in alignment
3076 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3078 <li>Not all working JABAWS services are shown in
3080 <li>JAVAWS version of Jalview fails to launch with
3081 'invalid literal/length code'</li>
3082 <li>Annotation/RNA Helix colourschemes cannot be applied
3083 to alignment with groups (actually fixed in 2.8.0b1)</li>
3084 <li>RNA Helices and T-Coffee Scores available as default
3087 </ul> <em>Applet</em>
3089 <li>Remove group option is shown even when selection is
3091 <li>Apply to all groups ticked but colourscheme changes
3092 don't affect groups</li>
3093 <li>Documented RNA Helices and T-Coffee Scores as valid
3094 colourscheme name</li>
3095 <li>Annotation labels drawn on sequence IDs when
3096 Annotation panel is not displayed</li>
3097 <li>Increased font size for dropdown menus on OSX and
3098 embedded windows</li>
3099 </ul> <em>Other</em>
3101 <li>Consensus sequence for alignments/groups with a
3102 single sequence were not calculated</li>
3103 <li>annotation files that contain only groups imported as
3104 annotation and junk sequences</li>
3105 <li>Fasta files with sequences containing '*' incorrectly
3106 recognised as PFAM or BLC</li>
3107 <li>conservation/PID slider apply all groups option
3108 doesn't affect background (2.8.0b1)
3110 <li>redundancy highlighting is erratic at 0% and 100%</li>
3111 <li>Remove gapped columns fails for sequences with ragged
3113 <li>AMSA annotation row with leading spaces is not
3114 registered correctly on import</li>
3115 <li>Jalview crashes when selecting PCA analysis for
3116 certain alignments</li>
3117 <li>Opening the colour by annotation dialog for an
3118 existing annotation based 'use original colours'
3119 colourscheme loses original colours setting</li>
3124 <td><div align="center">
3125 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3126 <em>30/1/2014</em></strong>
3130 <li>Trusted certificates for JalviewLite applet and
3131 Jalview Desktop application<br />Certificate was donated by
3132 <a href="https://www.certum.eu">Certum</a> to the Jalview
3133 open source project).
3135 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3136 <li>Output in Stockholm format</li>
3137 <li>Allow import of data from gzipped files</li>
3138 <li>Export/import group and sequence associated line
3139 graph thresholds</li>
3140 <li>Nucleotide substitution matrix that supports RNA and
3141 ambiguity codes</li>
3142 <li>Allow disorder predictions to be made on the current
3143 selection (or visible selection) in the same way that JPred
3145 <li>Groovy scripting for headless Jalview operation</li>
3146 </ul> <em>Other improvements</em>
3148 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3149 <li>COMBINE statement uses current SEQUENCE_REF and
3150 GROUP_REF scope to group annotation rows</li>
3151 <li>Support '' style escaping of quotes in Newick
3153 <li>Group options for JABAWS service by command line name</li>
3154 <li>Empty tooltip shown for JABA service options with a
3155 link but no description</li>
3156 <li>Select primary source when selecting authority in
3157 database fetcher GUI</li>
3158 <li>Add .mfa to FASTA file extensions recognised by
3160 <li>Annotation label tooltip text wrap</li>
3165 <li>Slow scrolling when lots of annotation rows are
3167 <li>Lots of NPE (and slowness) after creating RNA
3168 secondary structure annotation line</li>
3169 <li>Sequence database accessions not imported when
3170 fetching alignments from Rfam</li>
3171 <li>Incorrect SHMR submission for sequences with
3173 <li>View all structures does not always superpose
3175 <li>Option widgets in service parameters not updated to
3176 reflect user or preset settings</li>
3177 <li>Null pointer exceptions for some services without
3178 presets or adjustable parameters</li>
3179 <li>Discover PDB IDs entry in structure menu doesn't
3180 discover PDB xRefs</li>
3181 <li>Exception encountered while trying to retrieve
3182 features with DAS</li>
3183 <li>Lowest value in annotation row isn't coloured
3184 when colour by annotation (per sequence) is coloured</li>
3185 <li>Keyboard mode P jumps to start of gapped region when
3186 residue follows a gap</li>
3187 <li>Jalview appears to hang importing an alignment with
3188 Wrap as default or after enabling Wrap</li>
3189 <li>'Right click to add annotations' message
3190 shown in wrap mode when no annotations present</li>
3191 <li>Disorder predictions fail with NPE if no automatic
3192 annotation already exists on alignment</li>
3193 <li>oninit javascript function should be called after
3194 initialisation completes</li>
3195 <li>Remove redundancy after disorder prediction corrupts
3196 alignment window display</li>
3197 <li>Example annotation file in documentation is invalid</li>
3198 <li>Grouped line graph annotation rows are not exported
3199 to annotation file</li>
3200 <li>Multi-harmony analysis cannot be run when only two
3202 <li>Cannot create multiple groups of line graphs with
3203 several 'combine' statements in annotation file</li>
3204 <li>Pressing return several times causes Number Format
3205 exceptions in keyboard mode</li>
3206 <li>Multi-harmony (SHMMR) method doesn't submit
3207 correct partitions for input data</li>
3208 <li>Translation from DNA to Amino Acids fails</li>
3209 <li>Jalview fail to load newick tree with quoted label</li>
3210 <li>--headless flag isn't understood</li>
3211 <li>ClassCastException when generating EPS in headless
3213 <li>Adjusting sequence-associated shading threshold only
3214 changes one row's threshold</li>
3215 <li>Preferences and Feature settings panel panel
3216 doesn't open</li>
3217 <li>hide consensus histogram also hides conservation and
3218 quality histograms</li>
3223 <td><div align="center">
3224 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3226 <td><em>Application</em>
3228 <li>Support for JABAWS 2.0 Services (AACon alignment
3229 conservation, protein disorder and Clustal Omega)</li>
3230 <li>JABAWS server status indicator in Web Services
3232 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3233 in Jalview alignment window</li>
3234 <li>Updated Jalview build and deploy framework for OSX
3235 mountain lion, windows 7, and 8</li>
3236 <li>Nucleotide substitution matrix for PCA that supports
3237 RNA and ambiguity codes</li>
3239 <li>Improved sequence database retrieval GUI</li>
3240 <li>Support fetching and database reference look up
3241 against multiple DAS sources (Fetch all from in 'fetch db
3243 <li>Jalview project improvements
3245 <li>Store and retrieve the 'belowAlignment'
3246 flag for annotation</li>
3247 <li>calcId attribute to group annotation rows on the
3249 <li>Store AACon calculation settings for a view in
3250 Jalview project</li>
3254 <li>horizontal scrolling gesture support</li>
3255 <li>Visual progress indicator when PCA calculation is
3257 <li>Simpler JABA web services menus</li>
3258 <li>visual indication that web service results are still
3259 being retrieved from server</li>
3260 <li>Serialise the dialogs that are shown when Jalview
3261 starts up for first time</li>
3262 <li>Jalview user agent string for interacting with HTTP
3264 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3266 <li>Examples directory and Groovy library included in
3267 InstallAnywhere distribution</li>
3268 </ul> <em>Applet</em>
3270 <li>RNA alignment and secondary structure annotation
3271 visualization applet example</li>
3272 </ul> <em>General</em>
3274 <li>Normalise option for consensus sequence logo</li>
3275 <li>Reset button in PCA window to return dimensions to
3277 <li>Allow seqspace or Jalview variant of alignment PCA
3279 <li>PCA with either nucleic acid and protein substitution
3281 <li>Allow windows containing HTML reports to be exported
3283 <li>Interactive display and editing of RNA secondary
3284 structure contacts</li>
3285 <li>RNA Helix Alignment Colouring</li>
3286 <li>RNA base pair logo consensus</li>
3287 <li>Parse sequence associated secondary structure
3288 information in Stockholm files</li>
3289 <li>HTML Export database accessions and annotation
3290 information presented in tooltip for sequences</li>
3291 <li>Import secondary structure from LOCARNA clustalw
3292 style RNA alignment files</li>
3293 <li>import and visualise T-COFFEE quality scores for an
3295 <li>'colour by annotation' per sequence option to
3296 shade each sequence according to its associated alignment
3298 <li>New Jalview Logo</li>
3299 </ul> <em>Documentation and Development</em>
3301 <li>documentation for score matrices used in Jalview</li>
3302 <li>New Website!</li>
3304 <td><em>Application</em>
3306 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3307 wsdbfetch REST service</li>
3308 <li>Stop windows being moved outside desktop on OSX</li>
3309 <li>Filetype associations not installed for webstart
3311 <li>Jalview does not always retrieve progress of a JABAWS
3312 job execution in full once it is complete</li>
3313 <li>revise SHMR RSBS definition to ensure alignment is
3314 uploaded via ali_file parameter</li>
3315 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3316 <li>View all structures superposed fails with exception</li>
3317 <li>Jnet job queues forever if a very short sequence is
3318 submitted for prediction</li>
3319 <li>Cut and paste menu not opened when mouse clicked on
3321 <li>Putting fractional value into integer text box in
3322 alignment parameter dialog causes Jalview to hang</li>
3323 <li>Structure view highlighting doesn't work on
3325 <li>View all structures fails with exception shown in
3327 <li>Characters in filename associated with PDBEntry not
3328 escaped in a platform independent way</li>
3329 <li>Jalview desktop fails to launch with exception when
3331 <li>Tree calculation reports 'you must have 2 or more
3332 sequences selected' when selection is empty</li>
3333 <li>Jalview desktop fails to launch with jar signature
3334 failure when java web start temporary file caching is
3336 <li>DAS Sequence retrieval with range qualification
3337 results in sequence xref which includes range qualification</li>
3338 <li>Errors during processing of command line arguments
3339 cause progress bar (JAL-898) to be removed</li>
3340 <li>Replace comma for semi-colon option not disabled for
3341 DAS sources in sequence fetcher</li>
3342 <li>Cannot close news reader when JABAWS server warning
3343 dialog is shown</li>
3344 <li>Option widgets not updated to reflect user settings</li>
3345 <li>Edited sequence not submitted to web service</li>
3346 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3347 <li>InstallAnywhere installer doesn't unpack and run
3348 on OSX Mountain Lion</li>
3349 <li>Annotation panel not given a scroll bar when
3350 sequences with alignment annotation are pasted into the
3352 <li>Sequence associated annotation rows not associated
3353 when loaded from Jalview project</li>
3354 <li>Browser launch fails with NPE on java 1.7</li>
3355 <li>JABAWS alignment marked as finished when job was
3356 cancelled or job failed due to invalid input</li>
3357 <li>NPE with v2.7 example when clicking on Tree
3358 associated with all views</li>
3359 <li>Exceptions when copy/paste sequences with grouped
3360 annotation rows to new window</li>
3361 </ul> <em>Applet</em>
3363 <li>Sequence features are momentarily displayed before
3364 they are hidden using hidefeaturegroups applet parameter</li>
3365 <li>loading features via javascript API automatically
3366 enables feature display</li>
3367 <li>scrollToColumnIn javascript API method doesn't
3369 </ul> <em>General</em>
3371 <li>Redundancy removal fails for rna alignment</li>
3372 <li>PCA calculation fails when sequence has been selected
3373 and then deselected</li>
3374 <li>PCA window shows grey box when first opened on OSX</li>
3375 <li>Letters coloured pink in sequence logo when alignment
3376 coloured with clustalx</li>
3377 <li>Choosing fonts without letter symbols defined causes
3378 exceptions and redraw errors</li>
3379 <li>Initial PCA plot view is not same as manually
3380 reconfigured view</li>
3381 <li>Grouped annotation graph label has incorrect line
3383 <li>Grouped annotation graph label display is corrupted
3384 for lots of labels</li>
3389 <div align="center">
3390 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3393 <td><em>Application</em>
3395 <li>Jalview Desktop News Reader</li>
3396 <li>Tweaked default layout of web services menu</li>
3397 <li>View/alignment association menu to enable user to
3398 easily specify which alignment a multi-structure view takes
3399 its colours/correspondences from</li>
3400 <li>Allow properties file location to be specified as URL</li>
3401 <li>Extend Jalview project to preserve associations
3402 between many alignment views and a single Jmol display</li>
3403 <li>Store annotation row height in Jalview project file</li>
3404 <li>Annotation row column label formatting attributes
3405 stored in project file</li>
3406 <li>Annotation row order for auto-calculated annotation
3407 rows preserved in Jalview project file</li>
3408 <li>Visual progress indication when Jalview state is
3409 saved using Desktop window menu</li>
3410 <li>Visual indication that command line arguments are
3411 still being processed</li>
3412 <li>Groovy script execution from URL</li>
3413 <li>Colour by annotation default min and max colours in
3415 <li>Automatically associate PDB files dragged onto an
3416 alignment with sequences that have high similarity and
3418 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3419 <li>'view structures' option to open many
3420 structures in same window</li>
3421 <li>Sort associated views menu option for tree panel</li>
3422 <li>Group all JABA and non-JABA services for a particular
3423 analysis function in its own submenu</li>
3424 </ul> <em>Applet</em>
3426 <li>Userdefined and autogenerated annotation rows for
3428 <li>Adjustment of alignment annotation pane height</li>
3429 <li>Annotation scrollbar for annotation panel</li>
3430 <li>Drag to reorder annotation rows in annotation panel</li>
3431 <li>'automaticScrolling' parameter</li>
3432 <li>Allow sequences with partial ID string matches to be
3433 annotated from GFF/Jalview features files</li>
3434 <li>Sequence logo annotation row in applet</li>
3435 <li>Absolute paths relative to host server in applet
3436 parameters are treated as such</li>
3437 <li>New in the JalviewLite javascript API:
3439 <li>JalviewLite.js javascript library</li>
3440 <li>Javascript callbacks for
3442 <li>Applet initialisation</li>
3443 <li>Sequence/alignment mouse-overs and selections</li>
3446 <li>scrollTo row and column alignment scrolling
3448 <li>Select sequence/alignment regions from javascript</li>
3449 <li>javascript structure viewer harness to pass
3450 messages between Jmol and Jalview when running as
3451 distinct applets</li>
3452 <li>sortBy method</li>
3453 <li>Set of applet and application examples shipped
3454 with documentation</li>
3455 <li>New example to demonstrate JalviewLite and Jmol
3456 javascript message exchange</li>
3458 </ul> <em>General</em>
3460 <li>Enable Jmol displays to be associated with multiple
3461 multiple alignments</li>
3462 <li>Option to automatically sort alignment with new tree</li>
3463 <li>User configurable link to enable redirects to a
3464 www.Jalview.org mirror</li>
3465 <li>Jmol colours option for Jmol displays</li>
3466 <li>Configurable newline string when writing alignment
3467 and other flat files</li>
3468 <li>Allow alignment annotation description lines to
3469 contain html tags</li>
3470 </ul> <em>Documentation and Development</em>
3472 <li>Add groovy test harness for bulk load testing to
3474 <li>Groovy script to load and align a set of sequences
3475 using a web service before displaying the result in the
3476 Jalview desktop</li>
3477 <li>Restructured javascript and applet api documentation</li>
3478 <li>Ant target to publish example html files with applet
3480 <li>Netbeans project for building Jalview from source</li>
3481 <li>ant task to create online javadoc for Jalview source</li>
3483 <td><em>Application</em>
3485 <li>User defined colourscheme throws exception when
3486 current built in colourscheme is saved as new scheme</li>
3487 <li>AlignFrame->Save in application pops up save
3488 dialog for valid filename/format</li>
3489 <li>Cannot view associated structure for UniProt sequence</li>
3490 <li>PDB file association breaks for UniProt sequence
3492 <li>Associate PDB from file dialog does not tell you
3493 which sequence is to be associated with the file</li>
3494 <li>Find All raises null pointer exception when query
3495 only matches sequence IDs</li>
3496 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3497 <li>Jalview project with Jmol views created with Jalview
3498 2.4 cannot be loaded</li>
3499 <li>Filetype associations not installed for webstart
3501 <li>Two or more chains in a single PDB file associated
3502 with sequences in different alignments do not get coloured
3503 by their associated sequence</li>
3504 <li>Visibility status of autocalculated annotation row
3505 not preserved when project is loaded</li>
3506 <li>Annotation row height and visibility attributes not
3507 stored in Jalview project</li>
3508 <li>Tree bootstraps are not preserved when saved as a
3509 Jalview project</li>
3510 <li>Envision2 workflow tooltips are corrupted</li>
3511 <li>Enabling show group conservation also enables colour
3512 by conservation</li>
3513 <li>Duplicate group associated conservation or consensus
3514 created on new view</li>
3515 <li>Annotation scrollbar not displayed after 'show
3516 all hidden annotation rows' option selected</li>
3517 <li>Alignment quality not updated after alignment
3518 annotation row is hidden then shown</li>
3519 <li>Preserve colouring of structures coloured by
3520 sequences in pre Jalview 2.7 projects</li>
3521 <li>Web service job parameter dialog is not laid out
3523 <li>Web services menu not refreshed after 'reset
3524 services' button is pressed in preferences</li>
3525 <li>Annotation off by one in Jalview v2_3 example project</li>
3526 <li>Structures imported from file and saved in project
3527 get name like jalview_pdb1234.txt when reloaded</li>
3528 <li>Jalview does not always retrieve progress of a JABAWS
3529 job execution in full once it is complete</li>
3530 </ul> <em>Applet</em>
3532 <li>Alignment height set incorrectly when lots of
3533 annotation rows are displayed</li>
3534 <li>Relative URLs in feature HTML text not resolved to
3536 <li>View follows highlighting does not work for positions
3538 <li><= shown as = in tooltip</li>
3539 <li>Export features raises exception when no features
3541 <li>Separator string used for serialising lists of IDs
3542 for javascript api is modified when separator string
3543 provided as parameter</li>
3544 <li>Null pointer exception when selecting tree leaves for
3545 alignment with no existing selection</li>
3546 <li>Relative URLs for datasources assumed to be relative
3547 to applet's codebase</li>
3548 <li>Status bar not updated after finished searching and
3549 search wraps around to first result</li>
3550 <li>StructureSelectionManager instance shared between
3551 several Jalview applets causes race conditions and memory
3553 <li>Hover tooltip and mouseover of position on structure
3554 not sent from Jmol in applet</li>
3555 <li>Certain sequences of javascript method calls to
3556 applet API fatally hang browser</li>
3557 </ul> <em>General</em>
3559 <li>View follows structure mouseover scrolls beyond
3560 position with wrapped view and hidden regions</li>
3561 <li>Find sequence position moves to wrong residue
3562 with/without hidden columns</li>
3563 <li>Sequence length given in alignment properties window
3565 <li>InvalidNumberFormat exceptions thrown when trying to
3566 import PDB like structure files</li>
3567 <li>Positional search results are only highlighted
3568 between user-supplied sequence start/end bounds</li>
3569 <li>End attribute of sequence is not validated</li>
3570 <li>Find dialog only finds first sequence containing a
3571 given sequence position</li>
3572 <li>Sequence numbering not preserved in MSF alignment
3574 <li>Jalview PDB file reader does not extract sequence
3575 from nucleotide chains correctly</li>
3576 <li>Structure colours not updated when tree partition
3577 changed in alignment</li>
3578 <li>Sequence associated secondary structure not correctly
3579 parsed in interleaved stockholm</li>
3580 <li>Colour by annotation dialog does not restore current
3582 <li>Hiding (nearly) all sequences doesn't work
3584 <li>Sequences containing lowercase letters are not
3585 properly associated with their pdb files</li>
3586 </ul> <em>Documentation and Development</em>
3588 <li>schemas/JalviewWsParamSet.xsd corrupted by
3589 ApplyCopyright tool</li>
3594 <div align="center">
3595 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3598 <td><em>Application</em>
3600 <li>New warning dialog when the Jalview Desktop cannot
3601 contact web services</li>
3602 <li>JABA service parameters for a preset are shown in
3603 service job window</li>
3604 <li>JABA Service menu entries reworded</li>
3608 <li>Modeller PIR IO broken - cannot correctly import a
3609 pir file emitted by Jalview</li>
3610 <li>Existing feature settings transferred to new
3611 alignment view created from cut'n'paste</li>
3612 <li>Improved test for mixed amino/nucleotide chains when
3613 parsing PDB files</li>
3614 <li>Consensus and conservation annotation rows
3615 occasionally become blank for all new windows</li>
3616 <li>Exception raised when right clicking above sequences
3617 in wrapped view mode</li>
3618 </ul> <em>Application</em>
3620 <li>multiple multiply aligned structure views cause cpu
3621 usage to hit 100% and computer to hang</li>
3622 <li>Web Service parameter layout breaks for long user
3623 parameter names</li>
3624 <li>Jaba service discovery hangs desktop if Jaba server
3631 <div align="center">
3632 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3635 <td><em>Application</em>
3637 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3638 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3641 <li>Web Services preference tab</li>
3642 <li>Analysis parameters dialog box and user defined
3644 <li>Improved speed and layout of Envision2 service menu</li>
3645 <li>Superpose structures using associated sequence
3647 <li>Export coordinates and projection as CSV from PCA
3649 </ul> <em>Applet</em>
3651 <li>enable javascript: execution by the applet via the
3652 link out mechanism</li>
3653 </ul> <em>Other</em>
3655 <li>Updated the Jmol Jalview interface to work with Jmol
3657 <li>The Jalview Desktop and JalviewLite applet now
3658 require Java 1.5</li>
3659 <li>Allow Jalview feature colour specification for GFF
3660 sequence annotation files</li>
3661 <li>New 'colour by label' keword in Jalview feature file
3662 type colour specification</li>
3663 <li>New Jalview Desktop Groovy API method that allows a
3664 script to check if it being run in an interactive session or
3665 in a batch operation from the Jalview command line</li>
3669 <li>clustalx colourscheme colours Ds preferentially when
3670 both D+E are present in over 50% of the column</li>
3671 </ul> <em>Application</em>
3673 <li>typo in AlignmentFrame->View->Hide->all but
3674 selected Regions menu item</li>
3675 <li>sequence fetcher replaces ',' for ';' when the ',' is
3676 part of a valid accession ID</li>
3677 <li>fatal OOM if object retrieved by sequence fetcher
3678 runs out of memory</li>
3679 <li>unhandled Out of Memory Error when viewing pca
3680 analysis results</li>
3681 <li>InstallAnywhere builds fail to launch on OS X java
3682 10.5 update 4 (due to apple Java 1.6 update)</li>
3683 <li>Installanywhere Jalview silently fails to launch</li>
3684 </ul> <em>Applet</em>
3686 <li>Jalview.getFeatureGroups() raises an
3687 ArrayIndexOutOfBoundsException if no feature groups are
3694 <div align="center">
3695 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3701 <li>Alignment prettyprinter doesn't cope with long
3703 <li>clustalx colourscheme colours Ds preferentially when
3704 both D+E are present in over 50% of the column</li>
3705 <li>nucleic acid structures retrieved from PDB do not
3706 import correctly</li>
3707 <li>More columns get selected than were clicked on when a
3708 number of columns are hidden</li>
3709 <li>annotation label popup menu not providing correct
3710 add/hide/show options when rows are hidden or none are
3712 <li>Stockholm format shown in list of readable formats,
3713 and parser copes better with alignments from RFAM.</li>
3714 <li>CSV output of consensus only includes the percentage
3715 of all symbols if sequence logo display is enabled</li>
3717 </ul> <em>Applet</em>
3719 <li>annotation panel disappears when annotation is
3721 </ul> <em>Application</em>
3723 <li>Alignment view not redrawn properly when new
3724 alignment opened where annotation panel is visible but no
3725 annotations are present on alignment</li>
3726 <li>pasted region containing hidden columns is
3727 incorrectly displayed in new alignment window</li>
3728 <li>Jalview slow to complete operations when stdout is
3729 flooded (fix is to close the Jalview console)</li>
3730 <li>typo in AlignmentFrame->View->Hide->all but
3731 selected Rregions menu item.</li>
3732 <li>inconsistent group submenu and Format submenu entry
3733 'Un' or 'Non'conserved</li>
3734 <li>Sequence feature settings are being shared by
3735 multiple distinct alignments</li>
3736 <li>group annotation not recreated when tree partition is
3738 <li>double click on group annotation to select sequences
3739 does not propagate to associated trees</li>
3740 <li>Mac OSX specific issues:
3742 <li>exception raised when mouse clicked on desktop
3743 window background</li>
3744 <li>Desktop menu placed on menu bar and application
3745 name set correctly</li>
3746 <li>sequence feature settings not wide enough for the
3747 save feature colourscheme button</li>
3756 <div align="center">
3757 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3760 <td><em>New Capabilities</em>
3762 <li>URL links generated from description line for
3763 regular-expression based URL links (applet and application)
3765 <li>Non-positional feature URL links are shown in link
3767 <li>Linked viewing of nucleic acid sequences and
3769 <li>Automatic Scrolling option in View menu to display
3770 the currently highlighted region of an alignment.</li>
3771 <li>Order an alignment by sequence length, or using the
3772 average score or total feature count for each sequence.</li>
3773 <li>Shading features by score or associated description</li>
3774 <li>Subdivide alignment and groups based on identity of
3775 selected subsequence (Make Groups from Selection).</li>
3776 <li>New hide/show options including Shift+Control+H to
3777 hide everything but the currently selected region.</li>
3778 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3779 </ul> <em>Application</em>
3781 <li>Fetch DB References capabilities and UI expanded to
3782 support retrieval from DAS sequence sources</li>
3783 <li>Local DAS Sequence sources can be added via the
3784 command line or via the Add local source dialog box.</li>
3785 <li>DAS Dbref and DbxRef feature types are parsed as
3786 database references and protein_name is parsed as
3787 description line (BioSapiens terms).</li>
3788 <li>Enable or disable non-positional feature and database
3789 references in sequence ID tooltip from View menu in
3791 <!-- <li>New hidden columns and rows and representatives capabilities
3792 in annotations file (in progress - not yet fully implemented)</li> -->
3793 <li>Group-associated consensus, sequence logos and
3794 conservation plots</li>
3795 <li>Symbol distributions for each column can be exported
3796 and visualized as sequence logos</li>
3797 <li>Optionally scale multi-character column labels to fit
3798 within each column of annotation row<!-- todo for applet -->
3800 <li>Optional automatic sort of associated alignment view
3801 when a new tree is opened.</li>
3802 <li>Jalview Java Console</li>
3803 <li>Better placement of desktop window when moving
3804 between different screens.</li>
3805 <li>New preference items for sequence ID tooltip and
3806 consensus annotation</li>
3807 <li>Client to submit sequences and IDs to Envision2
3809 <li><em>Vamsas Capabilities</em>
3811 <li>Improved VAMSAS synchronization (Jalview archive
3812 used to preserve views, structures, and tree display
3814 <li>Import of vamsas documents from disk or URL via
3816 <li>Sharing of selected regions between views and
3817 with other VAMSAS applications (Experimental feature!)</li>
3818 <li>Updated API to VAMSAS version 0.2</li>
3820 </ul> <em>Applet</em>
3822 <li>Middle button resizes annotation row height</li>
3825 <li>sortByTree (true/false) - automatically sort the
3826 associated alignment view by the tree when a new tree is
3828 <li>showTreeBootstraps (true/false) - show or hide
3829 branch bootstraps (default is to show them if available)</li>
3830 <li>showTreeDistances (true/false) - show or hide
3831 branch lengths (default is to show them if available)</li>
3832 <li>showUnlinkedTreeNodes (true/false) - indicate if
3833 unassociated nodes should be highlighted in the tree
3835 <li>heightScale and widthScale (1.0 or more) -
3836 increase the height or width of a cell in the alignment
3837 grid relative to the current font size.</li>
3840 <li>Non-positional features displayed in sequence ID
3842 </ul> <em>Other</em>
3844 <li>Features format: graduated colour definitions and
3845 specification of feature scores</li>
3846 <li>Alignment Annotations format: new keywords for group
3847 associated annotation (GROUP_REF) and annotation row display
3848 properties (ROW_PROPERTIES)</li>
3849 <li>XML formats extended to support graduated feature
3850 colourschemes, group associated annotation, and profile
3851 visualization settings.</li></td>
3854 <li>Source field in GFF files parsed as feature source
3855 rather than description</li>
3856 <li>Non-positional features are now included in sequence
3857 feature and gff files (controlled via non-positional feature
3858 visibility in tooltip).</li>
3859 <li>URL links generated for all feature links (bugfix)</li>
3860 <li>Added URL embedding instructions to features file
3862 <li>Codons containing ambiguous nucleotides translated as
3863 'X' in peptide product</li>
3864 <li>Match case switch in find dialog box works for both
3865 sequence ID and sequence string and query strings do not
3866 have to be in upper case to match case-insensitively.</li>
3867 <li>AMSA files only contain first column of
3868 multi-character column annotation labels</li>
3869 <li>Jalview Annotation File generation/parsing consistent
3870 with documentation (e.g. Stockholm annotation can be
3871 exported and re-imported)</li>
3872 <li>PDB files without embedded PDB IDs given a friendly
3874 <li>Find incrementally searches ID string matches as well
3875 as subsequence matches, and correctly reports total number
3879 <li>Better handling of exceptions during sequence
3881 <li>Dasobert generated non-positional feature URL
3882 link text excludes the start_end suffix</li>
3883 <li>DAS feature and source retrieval buttons disabled
3884 when fetch or registry operations in progress.</li>
3885 <li>PDB files retrieved from URLs are cached properly</li>
3886 <li>Sequence description lines properly shared via
3888 <li>Sequence fetcher fetches multiple records for all
3890 <li>Ensured that command line das feature retrieval
3891 completes before alignment figures are generated.</li>
3892 <li>Reduced time taken when opening file browser for
3894 <li>isAligned check prior to calculating tree, PCA or
3895 submitting an MSA to JNet now excludes hidden sequences.</li>
3896 <li>User defined group colours properly recovered
3897 from Jalview projects.</li>
3906 <div align="center">
3907 <strong>2.4.0.b2</strong><br> 28/10/2009
3912 <li>Experimental support for google analytics usage
3914 <li>Jalview privacy settings (user preferences and docs).</li>
3919 <li>Race condition in applet preventing startup in
3921 <li>Exception when feature created from selection beyond
3922 length of sequence.</li>
3923 <li>Allow synthetic PDB files to be imported gracefully</li>
3924 <li>Sequence associated annotation rows associate with
3925 all sequences with a given id</li>
3926 <li>Find function matches case-insensitively for sequence
3927 ID string searches</li>
3928 <li>Non-standard characters do not cause pairwise
3929 alignment to fail with exception</li>
3930 </ul> <em>Application Issues</em>
3932 <li>Sequences are now validated against EMBL database</li>
3933 <li>Sequence fetcher fetches multiple records for all
3935 </ul> <em>InstallAnywhere Issues</em>
3937 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3938 issue with installAnywhere mechanism)</li>
3939 <li>Command line launching of JARs from InstallAnywhere
3940 version (java class versioning error fixed)</li>
3947 <div align="center">
3948 <strong>2.4</strong><br> 27/8/2008
3951 <td><em>User Interface</em>
3953 <li>Linked highlighting of codon and amino acid from
3954 translation and protein products</li>
3955 <li>Linked highlighting of structure associated with
3956 residue mapping to codon position</li>
3957 <li>Sequence Fetcher provides example accession numbers
3958 and 'clear' button</li>
3959 <li>MemoryMonitor added as an option under Desktop's
3961 <li>Extract score function to parse whitespace separated
3962 numeric data in description line</li>
3963 <li>Column labels in alignment annotation can be centred.</li>
3964 <li>Tooltip for sequence associated annotation give name
3966 </ul> <em>Web Services and URL fetching</em>
3968 <li>JPred3 web service</li>
3969 <li>Prototype sequence search client (no public services
3971 <li>Fetch either seed alignment or full alignment from
3973 <li>URL Links created for matching database cross
3974 references as well as sequence ID</li>
3975 <li>URL Links can be created using regular-expressions</li>
3976 </ul> <em>Sequence Database Connectivity</em>
3978 <li>Retrieval of cross-referenced sequences from other
3980 <li>Generalised database reference retrieval and
3981 validation to all fetchable databases</li>
3982 <li>Fetch sequences from DAS sources supporting the
3983 sequence command</li>
3984 </ul> <em>Import and Export</em>
3985 <li>export annotation rows as CSV for spreadsheet import</li>
3986 <li>Jalview projects record alignment dataset associations,
3987 EMBL products, and cDNA sequence mappings</li>
3988 <li>Sequence Group colour can be specified in Annotation
3990 <li>Ad-hoc colouring of group in Annotation File using RGB
3991 triplet as name of colourscheme</li>
3992 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3994 <li>treenode binding for VAMSAS tree exchange</li>
3995 <li>local editing and update of sequences in VAMSAS
3996 alignments (experimental)</li>
3997 <li>Create new or select existing session to join</li>
3998 <li>load and save of vamsas documents</li>
3999 </ul> <em>Application command line</em>
4001 <li>-tree parameter to open trees (introduced for passing
4003 <li>-fetchfrom command line argument to specify nicknames
4004 of DAS servers to query for alignment features</li>
4005 <li>-dasserver command line argument to add new servers
4006 that are also automatically queried for features</li>
4007 <li>-groovy command line argument executes a given groovy
4008 script after all input data has been loaded and parsed</li>
4009 </ul> <em>Applet-Application data exchange</em>
4011 <li>Trees passed as applet parameters can be passed to
4012 application (when using "View in full
4013 application")</li>
4014 </ul> <em>Applet Parameters</em>
4016 <li>feature group display control parameter</li>
4017 <li>debug parameter</li>
4018 <li>showbutton parameter</li>
4019 </ul> <em>Applet API methods</em>
4021 <li>newView public method</li>
4022 <li>Window (current view) specific get/set public methods</li>
4023 <li>Feature display control methods</li>
4024 <li>get list of currently selected sequences</li>
4025 </ul> <em>New Jalview distribution features</em>
4027 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4028 <li>RELEASE file gives build properties for the latest
4029 Jalview release.</li>
4030 <li>Java 1.1 Applet build made easier and donotobfuscate
4031 property controls execution of obfuscator</li>
4032 <li>Build target for generating source distribution</li>
4033 <li>Debug flag for javacc</li>
4034 <li>.jalview_properties file is documented (slightly) in
4035 jalview.bin.Cache</li>
4036 <li>Continuous Build Integration for stable and
4037 development version of Application, Applet and source
4042 <li>selected region output includes visible annotations
4043 (for certain formats)</li>
4044 <li>edit label/displaychar contains existing label/char
4046 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4047 <li>shorter peptide product names from EMBL records</li>
4048 <li>Newick string generator makes compact representations</li>
4049 <li>bootstrap values parsed correctly for tree files with
4051 <li>pathological filechooser bug avoided by not allowing
4052 filenames containing a ':'</li>
4053 <li>Fixed exception when parsing GFF files containing
4054 global sequence features</li>
4055 <li>Alignment datasets are finalized only when number of
4056 references from alignment sequences goes to zero</li>
4057 <li>Close of tree branch colour box without colour
4058 selection causes cascading exceptions</li>
4059 <li>occasional negative imgwidth exceptions</li>
4060 <li>better reporting of non-fatal warnings to user when
4061 file parsing fails.</li>
4062 <li>Save works when Jalview project is default format</li>
4063 <li>Save as dialog opened if current alignment format is
4064 not a valid output format</li>
4065 <li>UniProt canonical names introduced for both das and
4067 <li>Histidine should be midblue (not pink!) in Zappo</li>
4068 <li>error messages passed up and output when data read
4070 <li>edit undo recovers previous dataset sequence when
4071 sequence is edited</li>
4072 <li>allow PDB files without pdb ID HEADER lines (like
4073 those generated by MODELLER) to be read in properly</li>
4074 <li>allow reading of JPred concise files as a normal
4076 <li>Stockholm annotation parsing and alignment properties
4077 import fixed for PFAM records</li>
4078 <li>Structure view windows have correct name in Desktop
4080 <li>annotation consisting of sequence associated scores
4081 can be read and written correctly to annotation file</li>
4082 <li>Aligned cDNA translation to aligned peptide works
4084 <li>Fixed display of hidden sequence markers and
4085 non-italic font for representatives in Applet</li>
4086 <li>Applet Menus are always embedded in applet window on
4088 <li>Newly shown features appear at top of stack (in
4090 <li>Annotations added via parameter not drawn properly
4091 due to null pointer exceptions</li>
4092 <li>Secondary structure lines are drawn starting from
4093 first column of alignment</li>
4094 <li>UniProt XML import updated for new schema release in
4096 <li>Sequence feature to sequence ID match for Features
4097 file is case-insensitive</li>
4098 <li>Sequence features read from Features file appended to
4099 all sequences with matching IDs</li>
4100 <li>PDB structure coloured correctly for associated views
4101 containing a sub-sequence</li>
4102 <li>PDB files can be retrieved by applet from Jar files</li>
4103 <li>feature and annotation file applet parameters
4104 referring to different directories are retrieved correctly</li>
4105 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4106 <li>Fixed application hang whilst waiting for
4107 splash-screen version check to complete</li>
4108 <li>Applet properly URLencodes input parameter values
4109 when passing them to the launchApp service</li>
4110 <li>display name and local features preserved in results
4111 retrieved from web service</li>
4112 <li>Visual delay indication for sequence retrieval and
4113 sequence fetcher initialisation</li>
4114 <li>updated Application to use DAS 1.53e version of
4115 dasobert DAS client</li>
4116 <li>Re-instated Full AMSA support and .amsa file
4118 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4126 <div align="center">
4127 <strong>2.3</strong><br> 9/5/07
4132 <li>Jmol 11.0.2 integration</li>
4133 <li>PDB views stored in Jalview XML files</li>
4134 <li>Slide sequences</li>
4135 <li>Edit sequence in place</li>
4136 <li>EMBL CDS features</li>
4137 <li>DAS Feature mapping</li>
4138 <li>Feature ordering</li>
4139 <li>Alignment Properties</li>
4140 <li>Annotation Scores</li>
4141 <li>Sort by scores</li>
4142 <li>Feature/annotation editing in applet</li>
4147 <li>Headless state operation in 2.2.1</li>
4148 <li>Incorrect and unstable DNA pairwise alignment</li>
4149 <li>Cut and paste of sequences with annotation</li>
4150 <li>Feature group display state in XML</li>
4151 <li>Feature ordering in XML</li>
4152 <li>blc file iteration selection using filename # suffix</li>
4153 <li>Stockholm alignment properties</li>
4154 <li>Stockhom alignment secondary structure annotation</li>
4155 <li>2.2.1 applet had no feature transparency</li>
4156 <li>Number pad keys can be used in cursor mode</li>
4157 <li>Structure Viewer mirror image resolved</li>
4164 <div align="center">
4165 <strong>2.2.1</strong><br> 12/2/07
4170 <li>Non standard characters can be read and displayed
4171 <li>Annotations/Features can be imported/exported to the
4173 <li>Applet allows editing of sequence/annotation/group
4174 name & description
4175 <li>Preference setting to display sequence name in
4177 <li>Annotation file format extended to allow
4178 Sequence_groups to be defined
4179 <li>Default opening of alignment overview panel can be
4180 specified in preferences
4181 <li>PDB residue numbering annotation added to associated
4187 <li>Applet crash under certain Linux OS with Java 1.6
4189 <li>Annotation file export / import bugs fixed
4190 <li>PNG / EPS image output bugs fixed
4196 <div align="center">
4197 <strong>2.2</strong><br> 27/11/06
4202 <li>Multiple views on alignment
4203 <li>Sequence feature editing
4204 <li>"Reload" alignment
4205 <li>"Save" to current filename
4206 <li>Background dependent text colour
4207 <li>Right align sequence ids
4208 <li>User-defined lower case residue colours
4211 <li>Menu item accelerator keys
4212 <li>Control-V pastes to current alignment
4213 <li>Cancel button for DAS Feature Fetching
4214 <li>PCA and PDB Viewers zoom via mouse roller
4215 <li>User-defined sub-tree colours and sub-tree selection
4217 <li>'New Window' button on the 'Output to Text box'
4222 <li>New memory efficient Undo/Redo System
4223 <li>Optimised symbol lookups and conservation/consensus
4225 <li>Region Conservation/Consensus recalculated after
4227 <li>Fixed Remove Empty Columns Bug (empty columns at end
4229 <li>Slowed DAS Feature Fetching for increased robustness.
4231 <li>Made angle brackets in ASCII feature descriptions
4233 <li>Re-instated Zoom function for PCA
4234 <li>Sequence descriptions conserved in web service
4236 <li>UniProt ID discoverer uses any word separated by
4238 <li>WsDbFetch query/result association resolved
4239 <li>Tree leaf to sequence mapping improved
4240 <li>Smooth fonts switch moved to FontChooser dialog box.
4247 <div align="center">
4248 <strong>2.1.1</strong><br> 12/9/06
4253 <li>Copy consensus sequence to clipboard</li>
4258 <li>Image output - rightmost residues are rendered if
4259 sequence id panel has been resized</li>
4260 <li>Image output - all offscreen group boundaries are
4262 <li>Annotation files with sequence references - all
4263 elements in file are relative to sequence position</li>
4264 <li>Mac Applet users can use Alt key for group editing</li>
4270 <div align="center">
4271 <strong>2.1</strong><br> 22/8/06
4276 <li>MAFFT Multiple Alignment in default Web Service list</li>
4277 <li>DAS Feature fetching</li>
4278 <li>Hide sequences and columns</li>
4279 <li>Export Annotations and Features</li>
4280 <li>GFF file reading / writing</li>
4281 <li>Associate structures with sequences from local PDB
4283 <li>Add sequences to exisiting alignment</li>
4284 <li>Recently opened files / URL lists</li>
4285 <li>Applet can launch the full application</li>
4286 <li>Applet has transparency for features (Java 1.2
4288 <li>Applet has user defined colours parameter</li>
4289 <li>Applet can load sequences from parameter
4290 "sequence<em>x</em>"
4296 <li>Redundancy Panel reinstalled in the Applet</li>
4297 <li>Monospaced font - EPS / rescaling bug fixed</li>
4298 <li>Annotation files with sequence references bug fixed</li>
4304 <div align="center">
4305 <strong>2.08.1</strong><br> 2/5/06
4310 <li>Change case of selected region from Popup menu</li>
4311 <li>Choose to match case when searching</li>
4312 <li>Middle mouse button and mouse movement can compress /
4313 expand the visible width and height of the alignment</li>
4318 <li>Annotation Panel displays complete JNet results</li>
4324 <div align="center">
4325 <strong>2.08b</strong><br> 18/4/06
4331 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4332 <li>Righthand label on wrapped alignments shows correct
4339 <div align="center">
4340 <strong>2.08</strong><br> 10/4/06
4345 <li>Editing can be locked to the selection area</li>
4346 <li>Keyboard editing</li>
4347 <li>Create sequence features from searches</li>
4348 <li>Precalculated annotations can be loaded onto
4350 <li>Features file allows grouping of features</li>
4351 <li>Annotation Colouring scheme added</li>
4352 <li>Smooth fonts off by default - Faster rendering</li>
4353 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4358 <li>Drag & Drop fixed on Linux</li>
4359 <li>Jalview Archive file faster to load/save, sequence
4360 descriptions saved.</li>
4366 <div align="center">
4367 <strong>2.07</strong><br> 12/12/05
4372 <li>PDB Structure Viewer enhanced</li>
4373 <li>Sequence Feature retrieval and display enhanced</li>
4374 <li>Choose to output sequence start-end after sequence
4375 name for file output</li>
4376 <li>Sequence Fetcher WSDBFetch@EBI</li>
4377 <li>Applet can read feature files, PDB files and can be
4378 used for HTML form input</li>
4383 <li>HTML output writes groups and features</li>
4384 <li>Group editing is Control and mouse click</li>
4385 <li>File IO bugs</li>
4391 <div align="center">
4392 <strong>2.06</strong><br> 28/9/05
4397 <li>View annotations in wrapped mode</li>
4398 <li>More options for PCA viewer</li>
4403 <li>GUI bugs resolved</li>
4404 <li>Runs with -nodisplay from command line</li>
4410 <div align="center">
4411 <strong>2.05b</strong><br> 15/9/05
4416 <li>Choose EPS export as lineart or text</li>
4417 <li>Jar files are executable</li>
4418 <li>Can read in Uracil - maps to unknown residue</li>
4423 <li>Known OutOfMemory errors give warning message</li>
4424 <li>Overview window calculated more efficiently</li>
4425 <li>Several GUI bugs resolved</li>
4431 <div align="center">
4432 <strong>2.05</strong><br> 30/8/05
4437 <li>Edit and annotate in "Wrapped" view</li>
4442 <li>Several GUI bugs resolved</li>
4448 <div align="center">
4449 <strong>2.04</strong><br> 24/8/05
4454 <li>Hold down mouse wheel & scroll to change font
4460 <li>Improved JPred client reliability</li>
4461 <li>Improved loading of Jalview files</li>
4467 <div align="center">
4468 <strong>2.03</strong><br> 18/8/05
4473 <li>Set Proxy server name and port in preferences</li>
4474 <li>Multiple URL links from sequence ids</li>
4475 <li>User Defined Colours can have a scheme name and added
4477 <li>Choose to ignore gaps in consensus calculation</li>
4478 <li>Unix users can set default web browser</li>
4479 <li>Runs without GUI for batch processing</li>
4480 <li>Dynamically generated Web Service Menus</li>
4485 <li>InstallAnywhere download for Sparc Solaris</li>
4491 <div align="center">
4492 <strong>2.02</strong><br> 18/7/05
4498 <li>Copy & Paste order of sequences maintains
4499 alignment order.</li>
4505 <div align="center">
4506 <strong>2.01</strong><br> 12/7/05
4511 <li>Use delete key for deleting selection.</li>
4512 <li>Use Mouse wheel to scroll sequences.</li>
4513 <li>Help file updated to describe how to add alignment
4515 <li>Version and build date written to build properties
4517 <li>InstallAnywhere installation will check for updates
4518 at launch of Jalview.</li>
4523 <li>Delete gaps bug fixed.</li>
4524 <li>FileChooser sorts columns.</li>
4525 <li>Can remove groups one by one.</li>
4526 <li>Filechooser icons installed.</li>
4527 <li>Finder ignores return character when searching.
4528 Return key will initiate a search.<br>
4535 <div align="center">
4536 <strong>2.0</strong><br> 20/6/05
4541 <li>New codebase</li>