3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">2.11</a><br />
61 <em>20/06/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-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
127 <li><strong>Principal Components Analysis Viewer</strong>
130 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
131 and Viewer state saved in Jalview Project
133 <li>'Change parameters' option removed from viewer's
136 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
140 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
145 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
147 <li><strong>Speed and Efficiency</strong>
150 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
151 multiple groups when working with large alignments
154 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
158 <li><strong>User Interface</strong>
161 <!-- JAL-2933 -->Finder panel remembers last position in each
165 <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
166 what is shown)<br />Only visible region of alignment is shown by
167 default (can be changed in user preferences)
170 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
171 to the Overwrite Dialog
174 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
178 <!-- JAL-1244 -->Status bar shows bounds when dragging a
179 selection region, and gap count when inserting or deleting gaps
182 <!-- JAL-3132 -->Status bar updates over sequence and annotation
186 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
190 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
194 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
197 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
201 <!-- JAL-3181 -->Consistent ordering of links in sequence id
205 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
207 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
211 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
212 <li><strong>Java 11 Support (not yet on general release)</strong>
215 <!-- -->OSX GUI integrations for App menu's 'About' entry and
220 <em>Deprecations</em>
223 <!-- JAL-3035 -->DAS sequence retrieval and annotation
224 capabilities removed from the Jalview Desktop
227 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
228 unmarshalling has been replaced by JAXB for Jalview projects
229 and XML based data retrieval clients</li>
230 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
231 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
232 </ul> <em>Documentation</em>
235 <!-- JAL-3003 -->Added remarks about transparent rendering effects
236 not supported in EPS figure export
238 </ul> <em>Development and Release Processes</em>
241 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
243 <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
245 <!-- JAL-3225 -->Eclipse project configuration managed with
248 <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
249 Atlassian Bamboo continuous integration for
250 unattended Test Suite execution</li>
252 <!-- JAL-2864 -->Memory test suite to detect leaks in common
254 <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
255 <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>
258 <td align="left" valign="top">
261 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
264 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
265 superposition in Jmol fail on Windows
268 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
269 structures for sequences with lots of PDB structures
272 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
276 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
277 project involving multiple views
280 <!-- JAL-3164 -->Overview for complementary view in a linked
281 CDS/Protein alignment is not updated when Hide Columns by
282 Annotation dialog hides columns
285 <!-- JAL-3158 -->Selection highlighting in the complement of a
286 CDS/Protein alignment stops working after making a selection in
287 one view, then making another selection in the other view
290 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
294 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
295 Settings and Jalview Preferences panels
298 <!-- JAL-2865 -->Jalview hangs when closing windows or the
299 overview updates with large alignments
302 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
303 region if columns were selected by dragging right-to-left and the
304 mouse moved to the left of the first column
307 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
308 hidden column marker via scale popup menu
311 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
312 doesn't tell users the invalid URL
315 <!-- JAL-3178 -->Nonpositional features lose feature group on
316 export as Jalview features file
319 <!-- JAL-2816 -->Tooltips displayed for features filtered by
323 <!-- JAL-2060 -->'Graduated colour' option not offered for
324 manually created features (where if feature score is Float.NaN)
327 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
328 when columns are hidden
331 <!-- JAL-3082 -->Regular expression error for '(' in Select
332 Columns by Annotation description
335 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
336 out of Scale or Annotation Panel
339 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
343 <!-- JAL-3074 -->Left/right drag in annotation can scroll
347 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
351 <!-- JAL-3002 -->Column display is out by one after Page Down,
352 Page Up in wrapped mode
355 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
358 <!-- JAL-2932 -->Finder searches in minimised alignments
361 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
362 on opening an alignment
365 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
369 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
370 different groups in the alignment are selected
373 <!-- JAL-2717 -->Internationalised colour scheme names not shown
377 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
381 <!-- JAL-3125 -->Value input for graduated feature colour
382 threshold gets 'unrounded'
385 <!-- JAL-2982 -->PCA image export doesn't respect background
389 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
392 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
395 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
399 <!-- JAL-2964 -->Associate Tree with All Views not restored from
403 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
404 shown in complementary view
407 <!-- JAL-2898 -->stop_gained variants not shown correctly on
411 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
412 without normalisation
415 <!-- JAL-3021 -->Sequence Details report opens positioned to top
419 <!-- JAL-914 -->Help page can be opened twice
421 </ul> <em>Editing</em>
424 <!-- JAL-2822 -->Start and End should be updated when sequence
425 data at beginning or end of alignment added/removed via 'Edit'
429 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
430 relocate sequence features correctly when start of sequence is
431 removed (Known defect since 2.10)
434 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
435 dialog corrupts dataset sequence
438 <!-- JAL-868 -->Structure colours not updated when associated tree
439 repartitions the alignment view (Regression in 2.10.5)
443 <em>New Known Defects</em>
446 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
447 regions of protein alignment.
450 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
451 is restored from a Jalview 2.11 project
454 <!-- JAL-3213 -->Alignment panel height can be too small after
458 <!-- JAL-3240 -->Display is incorrect after removing gapped
459 columns within hidden columns
462 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
463 window after dragging left to select columns to left of visible
467 <!-- JAL-2876 -->Features coloured according to their description
468 string and thresholded by score in earlier versions of Jalview are
469 not shown as thresholded features in 2.11. To workaround please
470 create a Score filter instead.
472 <li><strong>Java 11 Specific defects</strong>
475 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
483 <td width="60" nowrap>
485 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
488 <td><div align="left">
492 <!-- JAL-3101 -->Default memory for Jalview webstart and
493 InstallAnywhere increased to 1G.
496 <!-- JAL-247 -->Hidden sequence markers and representative
497 sequence bolding included when exporting alignment as EPS,
498 SVG, PNG or HTML. <em>Display is configured via the
499 Format menu, or for command-line use via a jalview
500 properties file.</em>
503 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
504 API and sequence data now imported as JSON.
507 <!-- JAL-3065 -->Change in recommended way of starting
508 Jalview via a Java command line: add jars in lib directory
509 to CLASSPATH, rather than via the deprecated java.ext.dirs
516 <!-- JAL-3047 -->Support added to execute test suite
517 instrumented with <a href="http://openclover.org/">Open
522 <td><div align="left">
526 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
527 row shown in Feredoxin Structure alignment view of example
531 <!-- JAL-2854 -->Annotation obscures sequences if lots of
532 annotation displayed.
535 <!-- JAL-3107 -->Group conservation/consensus not shown
536 for newly created group when 'Apply to all groups'
540 <!-- JAL-3087 -->Corrupted display when switching to
541 wrapped mode when sequence panel's vertical scrollbar is
545 <!-- JAL-3003 -->Alignment is black in exported EPS file
546 when sequences are selected in exported view.</em>
549 <!-- JAL-3059 -->Groups with different coloured borders
550 aren't rendered with correct colour.
553 <!-- JAL-3092 -->Jalview could hang when importing certain
554 types of knotted RNA secondary structure.
557 <!-- JAL-3095 -->Sequence highlight and selection in
558 trimmed VARNA 2D structure is incorrect for sequences that
562 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
563 annotation when columns are inserted into an alignment,
564 and when exporting as Stockholm flatfile.
567 <!-- JAL-3053 -->Jalview annotation rows containing upper
568 and lower-case 'E' and 'H' do not automatically get
569 treated as RNA secondary structure.
572 <!-- JAL-3106 -->.jvp should be used as default extension
573 (not .jar) when saving a jalview project file.
576 <!-- JAL-3105 -->Mac Users: closing a window correctly
577 transfers focus to previous window on OSX
580 <em>Java 10 Issues Resolved</em>
583 <!-- JAL-2988 -->OSX - Can't save new files via the File
584 or export menus by typing in a name into the Save dialog
588 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
589 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
590 'look and feel' which has improved compatibility with the
591 latest version of OSX.
598 <td width="60" nowrap>
600 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
601 <em>7/06/2018</em></strong>
604 <td><div align="left">
608 <!-- JAL-2920 -->Use HGVS nomenclature for variant
609 annotation retrieved from Uniprot
612 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
613 onto the Jalview Desktop
617 <td><div align="left">
621 <!-- JAL-3017 -->Cannot import features with multiple
622 variant elements (blocks import of some Uniprot records)
625 <!-- JAL-2997 -->Clustal files with sequence positions in
626 right-hand column parsed correctly
629 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
630 not alignment area in exported graphic
633 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
634 window has input focus
637 <!-- JAL-2992 -->Annotation panel set too high when
638 annotation added to view (Windows)
641 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
642 network connectivity is poor
645 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
646 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
647 the currently open URL and links from a page viewed in
648 Firefox or Chrome on Windows is now fully supported. If
649 you are using Edge, only links in the page can be
650 dragged, and with Internet Explorer, only the currently
651 open URL in the browser can be dropped onto Jalview.</em>
657 <td width="60" nowrap>
659 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
662 <td><div align="left">
666 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
667 for disabling automatic superposition of multiple
668 structures and open structures in existing views
671 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
672 ID and annotation area margins can be click-dragged to
676 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
680 <!-- JAL-2759 -->Improved performance for large alignments
681 and lots of hidden columns
684 <!-- JAL-2593 -->Improved performance when rendering lots
685 of features (particularly when transparency is disabled)
688 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
689 exchange of Jalview features and Chimera attributes made
695 <td><div align="left">
698 <!-- JAL-2899 -->Structure and Overview aren't updated
699 when Colour By Annotation threshold slider is adjusted
702 <!-- JAL-2778 -->Slow redraw when Overview panel shown
703 overlapping alignment panel
706 <!-- JAL-2929 -->Overview doesn't show end of unpadded
710 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
711 improved: CDS not handled correctly if transcript has no
715 <!-- JAL-2321 -->Secondary structure and temperature
716 factor annotation not added to sequence when local PDB
717 file associated with it by drag'n'drop or structure
721 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
722 dialog doesn't import PDB files dropped on an alignment
725 <!-- JAL-2666 -->Linked scrolling via protein horizontal
726 scroll bar doesn't work for some CDS/Protein views
729 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
730 Java 1.8u153 onwards and Java 1.9u4+.
733 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
734 columns in annotation row
737 <!-- JAL-2913 -->Preferences panel's ID Width control is not
738 honored in batch mode
741 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
742 for structures added to existing Jmol view
745 <!-- JAL-2223 -->'View Mappings' includes duplicate
746 entries after importing project with multiple views
749 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
750 protein sequences via SIFTS from associated PDB entries
751 with negative residue numbers or missing residues fails
754 <!-- JAL-2952 -->Exception when shading sequence with negative
755 Temperature Factor values from annotated PDB files (e.g.
756 as generated by CONSURF)
759 <!-- JAL-2920 -->Uniprot 'sequence variant' features
760 tooltip doesn't include a text description of mutation
763 <!-- JAL-2922 -->Invert displayed features very slow when
764 structure and/or overview windows are also shown
767 <!-- JAL-2954 -->Selecting columns from highlighted regions
768 very slow for alignments with large numbers of sequences
771 <!-- JAL-2925 -->Copy Consensus fails for group consensus
772 with 'StringIndexOutOfBounds'
775 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
776 platforms running Java 10
779 <!-- JAL-2960 -->Adding a structure to existing structure
780 view appears to do nothing because the view is hidden behind the alignment view
786 <!-- JAL-2926 -->Copy consensus sequence option in applet
787 should copy the group consensus when popup is opened on it
793 <!-- JAL-2913 -->Fixed ID width preference is not respected
796 <em>New Known Defects</em>
799 <!-- JAL-2973 --> Exceptions occasionally raised when
800 editing a large alignment and overview is displayed
803 <!-- JAL-2974 -->'Overview updating' progress bar is shown
804 repeatedly after a series of edits even when the overview
805 is no longer reflecting updates
808 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
809 structures for protein subsequence (if 'Trim Retrieved
810 Sequences' enabled) or Ensembl isoforms (Workaround in
811 2.10.4 is to fail back to N&W mapping)
818 <td width="60" nowrap>
820 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
823 <td><div align="left">
824 <ul><li>Updated Certum Codesigning Certificate
825 (Valid till 30th November 2018)</li></ul></div></td>
826 <td><div align="left">
829 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
830 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
831 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
832 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
833 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
834 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
835 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
841 <td width="60" nowrap>
843 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
846 <td><div align="left">
850 <!-- JAL-2446 -->Faster and more efficient management and
851 rendering of sequence features
854 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
855 429 rate limit request hander
858 <!-- JAL-2773 -->Structure views don't get updated unless
859 their colours have changed
862 <!-- JAL-2495 -->All linked sequences are highlighted for
863 a structure mousover (Jmol) or selection (Chimera)
866 <!-- JAL-2790 -->'Cancel' button in progress bar for
867 JABAWS AACon, RNAAliFold and Disorder prediction jobs
870 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
871 view from Ensembl locus cross-references
874 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
878 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
879 feature can be disabled
882 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
883 PDB easier retrieval of sequences for lists of IDs
886 <!-- JAL-2758 -->Short names for sequences retrieved from
892 <li>Groovy interpreter updated to 2.4.12</li>
893 <li>Example groovy script for generating a matrix of
894 percent identity scores for current alignment.</li>
896 <em>Testing and Deployment</em>
899 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
903 <td><div align="left">
907 <!-- JAL-2643 -->Pressing tab after updating the colour
908 threshold text field doesn't trigger an update to the
912 <!-- JAL-2682 -->Race condition when parsing sequence ID
916 <!-- JAL-2608 -->Overview windows are also closed when
917 alignment window is closed
920 <!-- JAL-2548 -->Export of features doesn't always respect
924 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
925 takes a long time in Cursor mode
931 <!-- JAL-2777 -->Structures with whitespace chainCode
932 cannot be viewed in Chimera
935 <!-- JAL-2728 -->Protein annotation panel too high in
939 <!-- JAL-2757 -->Can't edit the query after the server
940 error warning icon is shown in Uniprot and PDB Free Text
944 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
947 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
950 <!-- JAL-2739 -->Hidden column marker in last column not
951 rendered when switching back from Wrapped to normal view
954 <!-- JAL-2768 -->Annotation display corrupted when
955 scrolling right in unwapped alignment view
958 <!-- JAL-2542 -->Existing features on subsequence
959 incorrectly relocated when full sequence retrieved from
963 <!-- JAL-2733 -->Last reported memory still shown when
964 Desktop->Show Memory is unticked (OSX only)
967 <!-- JAL-2658 -->Amend Features dialog doesn't allow
968 features of same type and group to be selected for
972 <!-- JAL-2524 -->Jalview becomes sluggish in wide
973 alignments when hidden columns are present
976 <!-- JAL-2392 -->Jalview freezes when loading and
977 displaying several structures
980 <!-- JAL-2732 -->Black outlines left after resizing or
984 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
985 within the Jalview desktop on OSX
988 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
989 when in wrapped alignment mode
992 <!-- JAL-2636 -->Scale mark not shown when close to right
993 hand end of alignment
996 <!-- JAL-2684 -->Pairwise alignment of selected regions of
997 each selected sequence do not have correct start/end
1001 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1002 after canceling the Alignment Window's Font dialog
1005 <!-- JAL-2036 -->Show cross-references not enabled after
1006 restoring project until a new view is created
1009 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1010 URL links appears when only default EMBL-EBI link is
1011 configured (since 2.10.2b2)
1014 <!-- JAL-2775 -->Overview redraws whole window when box
1015 position is adjusted
1018 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1019 in a multi-chain structure when viewing alignment
1020 involving more than one chain (since 2.10)
1023 <!-- JAL-2811 -->Double residue highlights in cursor mode
1024 if new selection moves alignment window
1027 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1028 arrow key in cursor mode to pass hidden column marker
1031 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1032 that produces correctly annotated transcripts and products
1035 <!-- JAL-2776 -->Toggling a feature group after first time
1036 doesn't update associated structure view
1039 <em>Applet</em><br />
1042 <!-- JAL-2687 -->Concurrent modification exception when
1043 closing alignment panel
1046 <em>BioJSON</em><br />
1049 <!-- JAL-2546 -->BioJSON export does not preserve
1050 non-positional features
1053 <em>New Known Issues</em>
1056 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1057 sequence features correctly (for many previous versions of
1061 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1062 using cursor in wrapped panel other than top
1065 <!-- JAL-2791 -->Select columns containing feature ignores
1066 graduated colour threshold
1069 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1070 always preserve numbering and sequence features
1073 <em>Known Java 9 Issues</em>
1076 <!-- JAL-2902 -->Groovy Console very slow to open and is
1077 not responsive when entering characters (Webstart, Java
1084 <td width="60" nowrap>
1085 <div align="center">
1086 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1087 <em>2/10/2017</em></strong>
1090 <td><div align="left">
1091 <em>New features in Jalview Desktop</em>
1094 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1096 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1100 <td><div align="left">
1104 <td width="60" nowrap>
1105 <div align="center">
1106 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1107 <em>7/9/2017</em></strong>
1110 <td><div align="left">
1114 <!-- JAL-2588 -->Show gaps in overview window by colouring
1115 in grey (sequences used to be coloured grey, and gaps were
1119 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1123 <!-- JAL-2587 -->Overview updates immediately on increase
1124 in size and progress bar shown as higher resolution
1125 overview is recalculated
1130 <td><div align="left">
1134 <!-- JAL-2664 -->Overview window redraws every hidden
1135 column region row by row
1138 <!-- JAL-2681 -->duplicate protein sequences shown after
1139 retrieving Ensembl crossrefs for sequences from Uniprot
1142 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1143 format setting is unticked
1146 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1147 if group has show boxes format setting unticked
1150 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1151 autoscrolling whilst dragging current selection group to
1152 include sequences and columns not currently displayed
1155 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1156 assemblies are imported via CIF file
1159 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1160 displayed when threshold or conservation colouring is also
1164 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1168 <!-- JAL-2673 -->Jalview continues to scroll after
1169 dragging a selected region off the visible region of the
1173 <!-- JAL-2724 -->Cannot apply annotation based
1174 colourscheme to all groups in a view
1177 <!-- JAL-2511 -->IDs don't line up with sequences
1178 initially after font size change using the Font chooser or
1185 <td width="60" nowrap>
1186 <div align="center">
1187 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1190 <td><div align="left">
1191 <em>Calculations</em>
1195 <!-- JAL-1933 -->Occupancy annotation row shows number of
1196 ungapped positions in each column of the alignment.
1199 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1200 a calculation dialog box
1203 <!-- JAL-2379 -->Revised implementation of PCA for speed
1204 and memory efficiency (~30x faster)
1207 <!-- JAL-2403 -->Revised implementation of sequence
1208 similarity scores as used by Tree, PCA, Shading Consensus
1209 and other calculations
1212 <!-- JAL-2416 -->Score matrices are stored as resource
1213 files within the Jalview codebase
1216 <!-- JAL-2500 -->Trees computed on Sequence Feature
1217 Similarity may have different topology due to increased
1224 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1225 model for alignments and groups
1228 <!-- JAL-384 -->Custom shading schemes created via groovy
1235 <!-- JAL-2526 -->Efficiency improvements for interacting
1236 with alignment and overview windows
1239 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1243 <!-- JAL-2388 -->Hidden columns and sequences can be
1247 <!-- JAL-2611 -->Click-drag in visible area allows fine
1248 adjustment of visible position
1252 <em>Data import/export</em>
1255 <!-- JAL-2535 -->Posterior probability annotation from
1256 Stockholm files imported as sequence associated annotation
1259 <!-- JAL-2507 -->More robust per-sequence positional
1260 annotation input/output via stockholm flatfile
1263 <!-- JAL-2533 -->Sequence names don't include file
1264 extension when importing structure files without embedded
1265 names or PDB accessions
1268 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1269 format sequence substitution matrices
1272 <em>User Interface</em>
1275 <!-- JAL-2447 --> Experimental Features Checkbox in
1276 Desktop's Tools menu to hide or show untested features in
1280 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1281 via Overview or sequence motif search operations
1284 <!-- JAL-2547 -->Amend sequence features dialog box can be
1285 opened by double clicking gaps within sequence feature
1289 <!-- JAL-1476 -->Status bar message shown when not enough
1290 aligned positions were available to create a 3D structure
1294 <em>3D Structure</em>
1297 <!-- JAL-2430 -->Hidden regions in alignment views are not
1298 coloured in linked structure views
1301 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1302 file-based command exchange
1305 <!-- JAL-2375 -->Structure chooser automatically shows
1306 Cached Structures rather than querying the PDBe if
1307 structures are already available for sequences
1310 <!-- JAL-2520 -->Structures imported via URL are cached in
1311 the Jalview project rather than downloaded again when the
1312 project is reopened.
1315 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1316 to transfer Chimera's structure attributes as Jalview
1317 features, and vice-versa (<strong>Experimental
1321 <em>Web Services</em>
1324 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1327 <!-- JAL-2335 -->Filter non-standard amino acids and
1328 nucleotides when submitting to AACon and other MSA
1332 <!-- JAL-2316, -->URLs for viewing database
1333 cross-references provided by identifiers.org and the
1334 EMBL-EBI's MIRIAM DB
1341 <!-- JAL-2344 -->FileFormatI interface for describing and
1342 identifying file formats (instead of String constants)
1345 <!-- JAL-2228 -->FeatureCounter script refactored for
1346 efficiency when counting all displayed features (not
1347 backwards compatible with 2.10.1)
1350 <em>Example files</em>
1353 <!-- JAL-2631 -->Graduated feature colour style example
1354 included in the example feature file
1357 <em>Documentation</em>
1360 <!-- JAL-2339 -->Release notes reformatted for readability
1361 with the built-in Java help viewer
1364 <!-- JAL-1644 -->Find documentation updated with 'search
1365 sequence description' option
1371 <!-- JAL-2485, -->External service integration tests for
1372 Uniprot REST Free Text Search Client
1375 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1378 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1383 <td><div align="left">
1384 <em>Calculations</em>
1387 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1388 matrix - C->R should be '-3'<br />Old matrix restored
1389 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1391 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1392 Jalview's treatment of gaps in PCA and substitution matrix
1393 based Tree calculations.<br /> <br />In earlier versions
1394 of Jalview, gaps matching gaps were penalised, and gaps
1395 matching non-gaps penalised even more. In the PCA
1396 calculation, gaps were actually treated as non-gaps - so
1397 different costs were applied, which meant Jalview's PCAs
1398 were different to those produced by SeqSpace.<br />Jalview
1399 now treats gaps in the same way as SeqSpace (ie it scores
1400 them as 0). <br /> <br />Enter the following in the
1401 Groovy console to restore pre-2.10.2 behaviour:<br />
1402 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1403 // for 2.10.1 mode <br />
1404 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1405 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1406 these settings will affect all subsequent tree and PCA
1407 calculations (not recommended)</em></li>
1409 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1410 scaling of branch lengths for trees computed using
1411 Sequence Feature Similarity.
1414 <!-- JAL-2377 -->PCA calculation could hang when
1415 generating output report when working with highly
1416 redundant alignments
1419 <!-- JAL-2544 --> Sort by features includes features to
1420 right of selected region when gaps present on right-hand
1424 <em>User Interface</em>
1427 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1428 doesn't reselect a specific sequence's associated
1429 annotation after it was used for colouring a view
1432 <!-- JAL-2419 -->Current selection lost if popup menu
1433 opened on a region of alignment without groups
1436 <!-- JAL-2374 -->Popup menu not always shown for regions
1437 of an alignment with overlapping groups
1440 <!-- JAL-2310 -->Finder double counts if both a sequence's
1441 name and description match
1444 <!-- JAL-2370 -->Hiding column selection containing two
1445 hidden regions results in incorrect hidden regions
1448 <!-- JAL-2386 -->'Apply to all groups' setting when
1449 changing colour does not apply Conservation slider value
1453 <!-- JAL-2373 -->Percentage identity and conservation menu
1454 items do not show a tick or allow shading to be disabled
1457 <!-- JAL-2385 -->Conservation shading or PID threshold
1458 lost when base colourscheme changed if slider not visible
1461 <!-- JAL-2547 -->Sequence features shown in tooltip for
1462 gaps before start of features
1465 <!-- JAL-2623 -->Graduated feature colour threshold not
1466 restored to UI when feature colour is edited
1469 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1470 a time when scrolling vertically in wrapped mode.
1473 <!-- JAL-2630 -->Structure and alignment overview update
1474 as graduate feature colour settings are modified via the
1478 <!-- JAL-2034 -->Overview window doesn't always update
1479 when a group defined on the alignment is resized
1482 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1483 wrapped view result in positional status updates
1487 <!-- JAL-2563 -->Status bar doesn't show position for
1488 ambiguous amino acid and nucleotide symbols
1491 <!-- JAL-2602 -->Copy consensus sequence failed if
1492 alignment included gapped columns
1495 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1496 widgets don't permanently disappear
1499 <!-- JAL-2503 -->Cannot select or filter quantitative
1500 annotation that are shown only as column labels (e.g.
1501 T-Coffee column reliability scores)
1504 <!-- JAL-2594 -->Exception thrown if trying to create a
1505 sequence feature on gaps only
1508 <!-- JAL-2504 -->Features created with 'New feature'
1509 button from a Find inherit previously defined feature type
1510 rather than the Find query string
1513 <!-- JAL-2423 -->incorrect title in output window when
1514 exporting tree calculated in Jalview
1517 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1518 and then revealing them reorders sequences on the
1522 <!-- JAL-964 -->Group panel in sequence feature settings
1523 doesn't update to reflect available set of groups after
1524 interactively adding or modifying features
1527 <!-- JAL-2225 -->Sequence Database chooser unusable on
1531 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1532 only excluded gaps in current sequence and ignored
1539 <!-- JAL-2421 -->Overview window visible region moves
1540 erratically when hidden rows or columns are present
1543 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1544 Structure Viewer's colour menu don't correspond to
1548 <!-- JAL-2405 -->Protein specific colours only offered in
1549 colour and group colour menu for protein alignments
1552 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1553 reflect currently selected view or group's shading
1557 <!-- JAL-2624 -->Feature colour thresholds not respected
1558 when rendered on overview and structures when opacity at
1562 <!-- JAL-2589 -->User defined gap colour not shown in
1563 overview when features overlaid on alignment
1566 <!-- JAL-2567 -->Feature settings for different views not
1567 recovered correctly from Jalview project file
1570 <!-- JAL-2256 -->Feature colours in overview when first opened
1571 (automatically via preferences) are different to the main
1575 <em>Data import/export</em>
1578 <!-- JAL-2576 -->Very large alignments take a long time to
1582 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1583 added after a sequence was imported are not written to
1587 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1588 when importing RNA secondary structure via Stockholm
1591 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1592 not shown in correct direction for simple pseudoknots
1595 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1596 with lightGray or darkGray via features file (but can
1600 <!-- JAL-2383 -->Above PID colour threshold not recovered
1601 when alignment view imported from project
1604 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1605 structure and sequences extracted from structure files
1606 imported via URL and viewed in Jmol
1609 <!-- JAL-2520 -->Structures loaded via URL are saved in
1610 Jalview Projects rather than fetched via URL again when
1611 the project is loaded and the structure viewed
1614 <em>Web Services</em>
1617 <!-- JAL-2519 -->EnsemblGenomes example failing after
1618 release of Ensembl v.88
1621 <!-- JAL-2366 -->Proxy server address and port always
1622 appear enabled in Preferences->Connections
1625 <!-- JAL-2461 -->DAS registry not found exceptions
1626 removed from console output
1629 <!-- JAL-2582 -->Cannot retrieve protein products from
1630 Ensembl by Peptide ID
1633 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1634 created from SIFTs, and spurious 'Couldn't open structure
1635 in Chimera' errors raised after April 2017 update (problem
1636 due to 'null' string rather than empty string used for
1637 residues with no corresponding PDB mapping).
1640 <em>Application UI</em>
1643 <!-- JAL-2361 -->User Defined Colours not added to Colour
1647 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1648 case' residues (button in colourscheme editor debugged and
1649 new documentation and tooltips added)
1652 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1653 doesn't restore group-specific text colour thresholds
1656 <!-- JAL-2243 -->Feature settings panel does not update as
1657 new features are added to alignment
1660 <!-- JAL-2532 -->Cancel in feature settings reverts
1661 changes to feature colours via the Amend features dialog
1664 <!-- JAL-2506 -->Null pointer exception when attempting to
1665 edit graduated feature colour via amend features dialog
1669 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1670 selection menu changes colours of alignment views
1673 <!-- JAL-2426 -->Spurious exceptions in console raised
1674 from alignment calculation workers after alignment has
1678 <!-- JAL-1608 -->Typo in selection popup menu - Create
1679 groups now 'Create Group'
1682 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1683 Create/Undefine group doesn't always work
1686 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1687 shown again after pressing 'Cancel'
1690 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1691 adjusts start position in wrap mode
1694 <!-- JAL-2563 -->Status bar doesn't show positions for
1695 ambiguous amino acids
1698 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1699 CDS/Protein view after CDS sequences added for aligned
1703 <!-- JAL-2592 -->User defined colourschemes called 'User
1704 Defined' don't appear in Colours menu
1710 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1711 score models doesn't always result in an updated PCA plot
1714 <!-- JAL-2442 -->Features not rendered as transparent on
1715 overview or linked structure view
1718 <!-- JAL-2372 -->Colour group by conservation doesn't
1722 <!-- JAL-2517 -->Hitting Cancel after applying
1723 user-defined colourscheme doesn't restore original
1730 <!-- JAL-2314 -->Unit test failure:
1731 jalview.ws.jabaws.RNAStructExportImport setup fails
1734 <!-- JAL-2307 -->Unit test failure:
1735 jalview.ws.sifts.SiftsClientTest due to compatibility
1736 problems with deep array comparison equality asserts in
1737 successive versions of TestNG
1740 <!-- JAL-2479 -->Relocated StructureChooserTest and
1741 ParameterUtilsTest Unit tests to Network suite
1744 <em>New Known Issues</em>
1747 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1748 phase after a sequence motif find operation
1751 <!-- JAL-2550 -->Importing annotation file with rows
1752 containing just upper and lower case letters are
1753 interpreted as WUSS RNA secondary structure symbols
1756 <!-- JAL-2590 -->Cannot load and display Newick trees
1757 reliably from eggnog Ortholog database
1760 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1761 containing features of type Highlight' when 'B' is pressed
1762 to mark columns containing highlighted regions.
1765 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1766 doesn't always add secondary structure annotation.
1771 <td width="60" nowrap>
1772 <div align="center">
1773 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1776 <td><div align="left">
1780 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1781 for all consensus calculations
1784 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1787 <li>Updated Jalview's Certum code signing certificate
1790 <em>Application</em>
1793 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1794 set of database cross-references, sorted alphabetically
1797 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1798 from database cross references. Users with custom links
1799 will receive a <a href="webServices/urllinks.html#warning">warning
1800 dialog</a> asking them to update their preferences.
1803 <!-- JAL-2287-->Cancel button and escape listener on
1804 dialog warning user about disconnecting Jalview from a
1808 <!-- JAL-2320-->Jalview's Chimera control window closes if
1809 the Chimera it is connected to is shut down
1812 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1813 columns menu item to mark columns containing highlighted
1814 regions (e.g. from structure selections or results of a
1818 <!-- JAL-2284-->Command line option for batch-generation
1819 of HTML pages rendering alignment data with the BioJS
1829 <!-- JAL-2286 -->Columns with more than one modal residue
1830 are not coloured or thresholded according to percent
1831 identity (first observed in Jalview 2.8.2)
1834 <!-- JAL-2301 -->Threonine incorrectly reported as not
1838 <!-- JAL-2318 -->Updates to documentation pages (above PID
1839 threshold, amino acid properties)
1842 <!-- JAL-2292 -->Lower case residues in sequences are not
1843 reported as mapped to residues in a structure file in the
1847 <!--JAL-2324 -->Identical features with non-numeric scores
1848 could be added multiple times to a sequence
1851 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1852 bond features shown as two highlighted residues rather
1853 than a range in linked structure views, and treated
1854 correctly when selecting and computing trees from features
1857 <!-- JAL-2281-->Custom URL links for database
1858 cross-references are matched to database name regardless
1863 <em>Application</em>
1866 <!-- JAL-2282-->Custom URL links for specific database
1867 names without regular expressions also offer links from
1871 <!-- JAL-2315-->Removing a single configured link in the
1872 URL links pane in Connections preferences doesn't actually
1873 update Jalview configuration
1876 <!-- JAL-2272-->CTRL-Click on a selected region to open
1877 the alignment area popup menu doesn't work on El-Capitan
1880 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1881 files with similarly named sequences if dropped onto the
1885 <!-- JAL-2312 -->Additional mappings are shown for PDB
1886 entries where more chains exist in the PDB accession than
1887 are reported in the SIFTS file
1890 <!-- JAL-2317-->Certain structures do not get mapped to
1891 the structure view when displayed with Chimera
1894 <!-- JAL-2317-->No chains shown in the Chimera view
1895 panel's View->Show Chains submenu
1898 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1899 work for wrapped alignment views
1902 <!--JAL-2197 -->Rename UI components for running JPred
1903 predictions from 'JNet' to 'JPred'
1906 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1907 corrupted when annotation panel vertical scroll is not at
1908 first annotation row
1911 <!--JAL-2332 -->Attempting to view structure for Hen
1912 lysozyme results in a PDB Client error dialog box
1915 <!-- JAL-2319 -->Structure View's mapping report switched
1916 ranges for PDB and sequence for SIFTS
1919 SIFTS 'Not_Observed' residues mapped to non-existant
1923 <!-- <em>New Known Issues</em>
1930 <td width="60" nowrap>
1931 <div align="center">
1932 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1933 <em>25/10/2016</em></strong>
1936 <td><em>Application</em>
1938 <li>3D Structure chooser opens with 'Cached structures'
1939 view if structures already loaded</li>
1940 <li>Progress bar reports models as they are loaded to
1941 structure views</li>
1947 <li>Colour by conservation always enabled and no tick
1948 shown in menu when BLOSUM or PID shading applied</li>
1949 <li>FER1_ARATH and FER2_ARATH labels were switched in
1950 example sequences/projects/trees</li>
1952 <em>Application</em>
1954 <li>Jalview projects with views of local PDB structure
1955 files saved on Windows cannot be opened on OSX</li>
1956 <li>Multiple structure views can be opened and superposed
1957 without timeout for structures with multiple models or
1958 multiple sequences in alignment</li>
1959 <li>Cannot import or associated local PDB files without a
1960 PDB ID HEADER line</li>
1961 <li>RMSD is not output in Jmol console when superposition
1963 <li>Drag and drop of URL from Browser fails for Linux and
1964 OSX versions earlier than El Capitan</li>
1965 <li>ENA client ignores invalid content from ENA server</li>
1966 <li>Exceptions are not raised in console when ENA client
1967 attempts to fetch non-existent IDs via Fetch DB Refs UI
1969 <li>Exceptions are not raised in console when a new view
1970 is created on the alignment</li>
1971 <li>OSX right-click fixed for group selections: CMD-click
1972 to insert/remove gaps in groups and CTRL-click to open group
1975 <em>Build and deployment</em>
1977 <li>URL link checker now copes with multi-line anchor
1980 <em>New Known Issues</em>
1982 <li>Drag and drop from URL links in browsers do not work
1989 <td width="60" nowrap>
1990 <div align="center">
1991 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1994 <td><em>General</em>
1997 <!-- JAL-2124 -->Updated Spanish translations.
2000 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2001 for importing structure data to Jalview. Enables mmCIF and
2005 <!-- JAL-192 --->Alignment ruler shows positions relative to
2009 <!-- JAL-2202 -->Position/residue shown in status bar when
2010 mousing over sequence associated annotation
2013 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2017 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2018 '()', canonical '[]' and invalid '{}' base pair populations
2022 <!-- JAL-2092 -->Feature settings popup menu options for
2023 showing or hiding columns containing a feature
2026 <!-- JAL-1557 -->Edit selected group by double clicking on
2027 group and sequence associated annotation labels
2030 <!-- JAL-2236 -->Sequence name added to annotation label in
2031 select/hide columns by annotation and colour by annotation
2035 </ul> <em>Application</em>
2038 <!-- JAL-2050-->Automatically hide introns when opening a
2039 gene/transcript view
2042 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2046 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2047 structure mappings with the EMBL-EBI PDBe SIFTS database
2050 <!-- JAL-2079 -->Updated download sites used for Rfam and
2051 Pfam sources to xfam.org
2054 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2057 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2058 over sequences in Jalview
2061 <!-- JAL-2027-->Support for reverse-complement coding
2062 regions in ENA and EMBL
2065 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2066 for record retrieval via ENA rest API
2069 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2073 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2074 groovy script execution
2077 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2078 alignment window's Calculate menu
2081 <!-- JAL-1812 -->Allow groovy scripts that call
2082 Jalview.getAlignFrames() to run in headless mode
2085 <!-- JAL-2068 -->Support for creating new alignment
2086 calculation workers from groovy scripts
2089 <!-- JAL-1369 --->Store/restore reference sequence in
2093 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2094 associations are now saved/restored from project
2097 <!-- JAL-1993 -->Database selection dialog always shown
2098 before sequence fetcher is opened
2101 <!-- JAL-2183 -->Double click on an entry in Jalview's
2102 database chooser opens a sequence fetcher
2105 <!-- JAL-1563 -->Free-text search client for UniProt using
2106 the UniProt REST API
2109 <!-- JAL-2168 -->-nonews command line parameter to prevent
2110 the news reader opening
2113 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2114 querying stored in preferences
2117 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2121 <!-- JAL-1977-->Tooltips shown on database chooser
2124 <!-- JAL-391 -->Reverse complement function in calculate
2125 menu for nucleotide sequences
2128 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2129 and feature counts preserves alignment ordering (and
2130 debugged for complex feature sets).
2133 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2134 viewing structures with Jalview 2.10
2137 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2138 genome, transcript CCDS and gene ids via the Ensembl and
2139 Ensembl Genomes REST API
2142 <!-- JAL-2049 -->Protein sequence variant annotation
2143 computed for 'sequence_variant' annotation on CDS regions
2147 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2151 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2152 Ref Fetcher fails to match, or otherwise updates sequence
2153 data from external database records.
2156 <!-- JAL-2154 -->Revised Jalview Project format for
2157 efficient recovery of sequence coding and alignment
2158 annotation relationships.
2160 </ul> <!-- <em>Applet</em>
2171 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2175 <!-- JAL-2018-->Export features in Jalview format (again)
2176 includes graduated colourschemes
2179 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2180 working with big alignments and lots of hidden columns
2183 <!-- JAL-2053-->Hidden column markers not always rendered
2184 at right of alignment window
2187 <!-- JAL-2067 -->Tidied up links in help file table of
2191 <!-- JAL-2072 -->Feature based tree calculation not shown
2195 <!-- JAL-2075 -->Hidden columns ignored during feature
2196 based tree calculation
2199 <!-- JAL-2065 -->Alignment view stops updating when show
2200 unconserved enabled for group on alignment
2203 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2207 <!-- JAL-2146 -->Alignment column in status incorrectly
2208 shown as "Sequence position" when mousing over
2212 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2213 hidden columns present
2216 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2217 user created annotation added to alignment
2220 <!-- JAL-1841 -->RNA Structure consensus only computed for
2221 '()' base pair annotation
2224 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2225 in zero scores for all base pairs in RNA Structure
2229 <!-- JAL-2174-->Extend selection with columns containing
2233 <!-- JAL-2275 -->Pfam format writer puts extra space at
2234 beginning of sequence
2237 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2241 <!-- JAL-2238 -->Cannot create groups on an alignment from
2242 from a tree when t-coffee scores are shown
2245 <!-- JAL-1836,1967 -->Cannot import and view PDB
2246 structures with chains containing negative resnums (4q4h)
2249 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2253 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2254 to Clustal, PIR and PileUp output
2257 <!-- JAL-2008 -->Reordering sequence features that are
2258 not visible causes alignment window to repaint
2261 <!-- JAL-2006 -->Threshold sliders don't work in
2262 graduated colour and colour by annotation row for e-value
2263 scores associated with features and annotation rows
2266 <!-- JAL-1797 -->amino acid physicochemical conservation
2267 calculation should be case independent
2270 <!-- JAL-2173 -->Remove annotation also updates hidden
2274 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2275 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2276 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2279 <!-- JAL-2065 -->Null pointer exceptions and redraw
2280 problems when reference sequence defined and 'show
2281 non-conserved' enabled
2284 <!-- JAL-1306 -->Quality and Conservation are now shown on
2285 load even when Consensus calculation is disabled
2288 <!-- JAL-1932 -->Remove right on penultimate column of
2289 alignment does nothing
2292 <em>Application</em>
2295 <!-- JAL-1552-->URLs and links can't be imported by
2296 drag'n'drop on OSX when launched via webstart (note - not
2297 yet fixed for El Capitan)
2300 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2301 output when running on non-gb/us i18n platforms
2304 <!-- JAL-1944 -->Error thrown when exporting a view with
2305 hidden sequences as flat-file alignment
2308 <!-- JAL-2030-->InstallAnywhere distribution fails when
2312 <!-- JAL-2080-->Jalview very slow to launch via webstart
2313 (also hotfix for 2.9.0b2)
2316 <!-- JAL-2085 -->Cannot save project when view has a
2317 reference sequence defined
2320 <!-- JAL-1011 -->Columns are suddenly selected in other
2321 alignments and views when revealing hidden columns
2324 <!-- JAL-1989 -->Hide columns not mirrored in complement
2325 view in a cDNA/Protein splitframe
2328 <!-- JAL-1369 -->Cannot save/restore representative
2329 sequence from project when only one sequence is
2333 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2334 in Structure Chooser
2337 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2338 structure consensus didn't refresh annotation panel
2341 <!-- JAL-1962 -->View mapping in structure view shows
2342 mappings between sequence and all chains in a PDB file
2345 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2346 dialogs format columns correctly, don't display array
2347 data, sort columns according to type
2350 <!-- JAL-1975 -->Export complete shown after destination
2351 file chooser is cancelled during an image export
2354 <!-- JAL-2025 -->Error when querying PDB Service with
2355 sequence name containing special characters
2358 <!-- JAL-2024 -->Manual PDB structure querying should be
2362 <!-- JAL-2104 -->Large tooltips with broken HTML
2363 formatting don't wrap
2366 <!-- JAL-1128 -->Figures exported from wrapped view are
2367 truncated so L looks like I in consensus annotation
2370 <!-- JAL-2003 -->Export features should only export the
2371 currently displayed features for the current selection or
2375 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2376 after fetching cross-references, and restoring from
2380 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2381 followed in the structure viewer
2384 <!-- JAL-2163 -->Titles for individual alignments in
2385 splitframe not restored from project
2388 <!-- JAL-2145 -->missing autocalculated annotation at
2389 trailing end of protein alignment in transcript/product
2390 splitview when pad-gaps not enabled by default
2393 <!-- JAL-1797 -->amino acid physicochemical conservation
2397 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2398 article has been read (reopened issue due to
2399 internationalisation problems)
2402 <!-- JAL-1960 -->Only offer PDB structures in structure
2403 viewer based on sequence name, PDB and UniProt
2408 <!-- JAL-1976 -->No progress bar shown during export of
2412 <!-- JAL-2213 -->Structures not always superimposed after
2413 multiple structures are shown for one or more sequences.
2416 <!-- JAL-1370 -->Reference sequence characters should not
2417 be replaced with '.' when 'Show unconserved' format option
2421 <!-- JAL-1823 -->Cannot specify chain code when entering
2422 specific PDB id for sequence
2425 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2426 'Export hidden sequences' is enabled, but 'export hidden
2427 columns' is disabled.
2430 <!--JAL-2026-->Best Quality option in structure chooser
2431 selects lowest rather than highest resolution structures
2435 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2436 to sequence mapping in 'View Mappings' report
2439 <!-- JAL-2284 -->Unable to read old Jalview projects that
2440 contain non-XML data added after Jalvew wrote project.
2443 <!-- JAL-2118 -->Newly created annotation row reorders
2444 after clicking on it to create new annotation for a
2448 <!-- JAL-1980 -->Null Pointer Exception raised when
2449 pressing Add on an orphaned cut'n'paste window.
2451 <!-- may exclude, this is an external service stability issue JAL-1941
2452 -- > RNA 3D structure not added via DSSR service</li> -->
2457 <!-- JAL-2151 -->Incorrect columns are selected when
2458 hidden columns present before start of sequence
2461 <!-- JAL-1986 -->Missing dependencies on applet pages
2465 <!-- JAL-1947 -->Overview pixel size changes when
2466 sequences are hidden in applet
2469 <!-- JAL-1996 -->Updated instructions for applet
2470 deployment on examples pages.
2477 <td width="60" nowrap>
2478 <div align="center">
2479 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2480 <em>16/10/2015</em></strong>
2483 <td><em>General</em>
2485 <li>Time stamps for signed Jalview application and applet
2490 <em>Application</em>
2492 <li>Duplicate group consensus and conservation rows
2493 shown when tree is partitioned</li>
2494 <li>Erratic behaviour when tree partitions made with
2495 multiple cDNA/Protein split views</li>
2501 <td width="60" nowrap>
2502 <div align="center">
2503 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2504 <em>8/10/2015</em></strong>
2507 <td><em>General</em>
2509 <li>Updated Spanish translations of localized text for
2511 </ul> <em>Application</em>
2513 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2514 <li>Signed OSX InstallAnywhere installer<br></li>
2515 <li>Support for per-sequence based annotations in BioJSON</li>
2516 </ul> <em>Applet</em>
2518 <li>Split frame example added to applet examples page</li>
2519 </ul> <em>Build and Deployment</em>
2522 <!-- JAL-1888 -->New ant target for running Jalview's test
2530 <li>Mapping of cDNA to protein in split frames
2531 incorrect when sequence start > 1</li>
2532 <li>Broken images in filter column by annotation dialog
2534 <li>Feature colours not parsed from features file</li>
2535 <li>Exceptions and incomplete link URLs recovered when
2536 loading a features file containing HTML tags in feature
2540 <em>Application</em>
2542 <li>Annotations corrupted after BioJS export and
2544 <li>Incorrect sequence limits after Fetch DB References
2545 with 'trim retrieved sequences'</li>
2546 <li>Incorrect warning about deleting all data when
2547 deleting selected columns</li>
2548 <li>Patch to build system for shipping properly signed
2549 JNLP templates for webstart launch</li>
2550 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2551 unreleased structures for download or viewing</li>
2552 <li>Tab/space/return keystroke operation of EMBL-PDBe
2553 fetcher/viewer dialogs works correctly</li>
2554 <li>Disabled 'minimise' button on Jalview windows
2555 running on OSX to workaround redraw hang bug</li>
2556 <li>Split cDNA/Protein view position and geometry not
2557 recovered from jalview project</li>
2558 <li>Initial enabled/disabled state of annotation menu
2559 sorter 'show autocalculated first/last' corresponds to
2561 <li>Restoring of Clustal, RNA Helices and T-Coffee
2562 color schemes from BioJSON</li>
2566 <li>Reorder sequences mirrored in cDNA/Protein split
2568 <li>Applet with Jmol examples not loading correctly</li>
2574 <td><div align="center">
2575 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2577 <td><em>General</em>
2579 <li>Linked visualisation and analysis of DNA and Protein
2582 <li>Translated cDNA alignments shown as split protein
2583 and DNA alignment views</li>
2584 <li>Codon consensus annotation for linked protein and
2585 cDNA alignment views</li>
2586 <li>Link cDNA or Protein product sequences by loading
2587 them onto Protein or cDNA alignments</li>
2588 <li>Reconstruct linked cDNA alignment from aligned
2589 protein sequences</li>
2592 <li>Jmol integration updated to Jmol v14.2.14</li>
2593 <li>Import and export of Jalview alignment views as <a
2594 href="features/bioJsonFormat.html">BioJSON</a></li>
2595 <li>New alignment annotation file statements for
2596 reference sequences and marking hidden columns</li>
2597 <li>Reference sequence based alignment shading to
2598 highlight variation</li>
2599 <li>Select or hide columns according to alignment
2601 <li>Find option for locating sequences by description</li>
2602 <li>Conserved physicochemical properties shown in amino
2603 acid conservation row</li>
2604 <li>Alignments can be sorted by number of RNA helices</li>
2605 </ul> <em>Application</em>
2607 <li>New cDNA/Protein analysis capabilities
2609 <li>Get Cross-References should open a Split Frame
2610 view with cDNA/Protein</li>
2611 <li>Detect when nucleotide sequences and protein
2612 sequences are placed in the same alignment</li>
2613 <li>Split cDNA/Protein views are saved in Jalview
2618 <li>Use REST API to talk to Chimera</li>
2619 <li>Selected regions in Chimera are highlighted in linked
2620 Jalview windows</li>
2622 <li>VARNA RNA viewer updated to v3.93</li>
2623 <li>VARNA views are saved in Jalview Projects</li>
2624 <li>Pseudoknots displayed as Jalview RNA annotation can
2625 be shown in VARNA</li>
2627 <li>Make groups for selection uses marked columns as well
2628 as the active selected region</li>
2630 <li>Calculate UPGMA and NJ trees using sequence feature
2632 <li>New Export options
2634 <li>New Export Settings dialog to control hidden
2635 region export in flat file generation</li>
2637 <li>Export alignment views for display with the <a
2638 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2640 <li>Export scrollable SVG in HTML page</li>
2641 <li>Optional embedding of BioJSON data when exporting
2642 alignment figures to HTML</li>
2644 <li>3D structure retrieval and display
2646 <li>Free text and structured queries with the PDBe
2648 <li>PDBe Search API based discovery and selection of
2649 PDB structures for a sequence set</li>
2653 <li>JPred4 employed for protein secondary structure
2655 <li>Hide Insertions menu option to hide unaligned columns
2656 for one or a group of sequences</li>
2657 <li>Automatically hide insertions in alignments imported
2658 from the JPred4 web server</li>
2659 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2660 system on OSX<br />LGPL libraries courtesy of <a
2661 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2663 <li>changed 'View nucleotide structure' submenu to 'View
2664 VARNA 2D Structure'</li>
2665 <li>change "View protein structure" menu option to "3D
2668 </ul> <em>Applet</em>
2670 <li>New layout for applet example pages</li>
2671 <li>New parameters to enable SplitFrame view
2672 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2673 <li>New example demonstrating linked viewing of cDNA and
2674 Protein alignments</li>
2675 </ul> <em>Development and deployment</em>
2677 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2678 <li>Include installation type and git revision in build
2679 properties and console log output</li>
2680 <li>Jalview Github organisation, and new github site for
2681 storing BioJsMSA Templates</li>
2682 <li>Jalview's unit tests now managed with TestNG</li>
2685 <!-- <em>General</em>
2687 </ul> --> <!-- issues resolved --> <em>Application</em>
2689 <li>Escape should close any open find dialogs</li>
2690 <li>Typo in select-by-features status report</li>
2691 <li>Consensus RNA secondary secondary structure
2692 predictions are not highlighted in amber</li>
2693 <li>Missing gap character in v2.7 example file means
2694 alignment appears unaligned when pad-gaps is not enabled</li>
2695 <li>First switch to RNA Helices colouring doesn't colour
2696 associated structure views</li>
2697 <li>ID width preference option is greyed out when auto
2698 width checkbox not enabled</li>
2699 <li>Stopped a warning dialog from being shown when
2700 creating user defined colours</li>
2701 <li>'View Mapping' in structure viewer shows sequence
2702 mappings for just that viewer's sequences</li>
2703 <li>Workaround for superposing PDB files containing
2704 multiple models in Chimera</li>
2705 <li>Report sequence position in status bar when hovering
2706 over Jmol structure</li>
2707 <li>Cannot output gaps as '.' symbols with Selection ->
2708 output to text box</li>
2709 <li>Flat file exports of alignments with hidden columns
2710 have incorrect sequence start/end</li>
2711 <li>'Aligning' a second chain to a Chimera structure from
2713 <li>Colour schemes applied to structure viewers don't
2714 work for nucleotide</li>
2715 <li>Loading/cut'n'pasting an empty or invalid file leads
2716 to a grey/invisible alignment window</li>
2717 <li>Exported Jpred annotation from a sequence region
2718 imports to different position</li>
2719 <li>Space at beginning of sequence feature tooltips shown
2720 on some platforms</li>
2721 <li>Chimera viewer 'View | Show Chain' menu is not
2723 <li>'New View' fails with a Null Pointer Exception in
2724 console if Chimera has been opened</li>
2725 <li>Mouseover to Chimera not working</li>
2726 <li>Miscellaneous ENA XML feature qualifiers not
2728 <li>NPE in annotation renderer after 'Extract Scores'</li>
2729 <li>If two structures in one Chimera window, mouseover of
2730 either sequence shows on first structure</li>
2731 <li>'Show annotations' options should not make
2732 non-positional annotations visible</li>
2733 <li>Subsequence secondary structure annotation not shown
2734 in right place after 'view flanking regions'</li>
2735 <li>File Save As type unset when current file format is
2737 <li>Save as '.jar' option removed for saving Jalview
2739 <li>Colour by Sequence colouring in Chimera more
2741 <li>Cannot 'add reference annotation' for a sequence in
2742 several views on same alignment</li>
2743 <li>Cannot show linked products for EMBL / ENA records</li>
2744 <li>Jalview's tooltip wraps long texts containing no
2746 </ul> <em>Applet</em>
2748 <li>Jmol to JalviewLite mouseover/link not working</li>
2749 <li>JalviewLite can't import sequences with ID
2750 descriptions containing angle brackets</li>
2751 </ul> <em>General</em>
2753 <li>Cannot export and reimport RNA secondary structure
2754 via jalview annotation file</li>
2755 <li>Random helix colour palette for colour by annotation
2756 with RNA secondary structure</li>
2757 <li>Mouseover to cDNA from STOP residue in protein
2758 translation doesn't work.</li>
2759 <li>hints when using the select by annotation dialog box</li>
2760 <li>Jmol alignment incorrect if PDB file has alternate CA
2762 <li>FontChooser message dialog appears to hang after
2763 choosing 1pt font</li>
2764 <li>Peptide secondary structure incorrectly imported from
2765 annotation file when annotation display text includes 'e' or
2767 <li>Cannot set colour of new feature type whilst creating
2769 <li>cDNA translation alignment should not be sequence
2770 order dependent</li>
2771 <li>'Show unconserved' doesn't work for lower case
2773 <li>Nucleotide ambiguity codes involving R not recognised</li>
2774 </ul> <em>Deployment and Documentation</em>
2776 <li>Applet example pages appear different to the rest of
2777 www.jalview.org</li>
2778 </ul> <em>Application Known issues</em>
2780 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2781 <li>Misleading message appears after trying to delete
2783 <li>Jalview icon not shown in dock after InstallAnywhere
2784 version launches</li>
2785 <li>Fetching EMBL reference for an RNA sequence results
2786 fails with a sequence mismatch</li>
2787 <li>Corrupted or unreadable alignment display when
2788 scrolling alignment to right</li>
2789 <li>ArrayIndexOutOfBoundsException thrown when remove
2790 empty columns called on alignment with ragged gapped ends</li>
2791 <li>auto calculated alignment annotation rows do not get
2792 placed above or below non-autocalculated rows</li>
2793 <li>Jalview dekstop becomes sluggish at full screen in
2794 ultra-high resolution</li>
2795 <li>Cannot disable consensus calculation independently of
2796 quality and conservation</li>
2797 <li>Mouseover highlighting between cDNA and protein can
2798 become sluggish with more than one splitframe shown</li>
2799 </ul> <em>Applet Known Issues</em>
2801 <li>Core PDB parsing code requires Jmol</li>
2802 <li>Sequence canvas panel goes white when alignment
2803 window is being resized</li>
2809 <td><div align="center">
2810 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2812 <td><em>General</em>
2814 <li>Updated Java code signing certificate donated by
2816 <li>Features and annotation preserved when performing
2817 pairwise alignment</li>
2818 <li>RNA pseudoknot annotation can be
2819 imported/exported/displayed</li>
2820 <li>'colour by annotation' can colour by RNA and
2821 protein secondary structure</li>
2822 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2823 post-hoc with 2.9 release</em>)
2826 </ul> <em>Application</em>
2828 <li>Extract and display secondary structure for sequences
2829 with 3D structures</li>
2830 <li>Support for parsing RNAML</li>
2831 <li>Annotations menu for layout
2833 <li>sort sequence annotation rows by alignment</li>
2834 <li>place sequence annotation above/below alignment
2837 <li>Output in Stockholm format</li>
2838 <li>Internationalisation: improved Spanish (es)
2840 <li>Structure viewer preferences tab</li>
2841 <li>Disorder and Secondary Structure annotation tracks
2842 shared between alignments</li>
2843 <li>UCSF Chimera launch and linked highlighting from
2845 <li>Show/hide all sequence associated annotation rows for
2846 all or current selection</li>
2847 <li>disorder and secondary structure predictions
2848 available as dataset annotation</li>
2849 <li>Per-sequence rna helices colouring</li>
2852 <li>Sequence database accessions imported when fetching
2853 alignments from Rfam</li>
2854 <li>update VARNA version to 3.91</li>
2856 <li>New groovy scripts for exporting aligned positions,
2857 conservation values, and calculating sum of pairs scores.</li>
2858 <li>Command line argument to set default JABAWS server</li>
2859 <li>include installation type in build properties and
2860 console log output</li>
2861 <li>Updated Jalview project format to preserve dataset
2865 <!-- issues resolved --> <em>Application</em>
2867 <li>Distinguish alignment and sequence associated RNA
2868 structure in structure->view->VARNA</li>
2869 <li>Raise dialog box if user deletes all sequences in an
2871 <li>Pressing F1 results in documentation opening twice</li>
2872 <li>Sequence feature tooltip is wrapped</li>
2873 <li>Double click on sequence associated annotation
2874 selects only first column</li>
2875 <li>Redundancy removal doesn't result in unlinked
2876 leaves shown in tree</li>
2877 <li>Undos after several redundancy removals don't undo
2879 <li>Hide sequence doesn't hide associated annotation</li>
2880 <li>User defined colours dialog box too big to fit on
2881 screen and buttons not visible</li>
2882 <li>author list isn't updated if already written to
2883 Jalview properties</li>
2884 <li>Popup menu won't open after retrieving sequence
2886 <li>File open window for associate PDB doesn't open</li>
2887 <li>Left-then-right click on a sequence id opens a
2888 browser search window</li>
2889 <li>Cannot open sequence feature shading/sort popup menu
2890 in feature settings dialog</li>
2891 <li>better tooltip placement for some areas of Jalview
2893 <li>Allow addition of JABAWS Server which doesn't
2894 pass validation</li>
2895 <li>Web services parameters dialog box is too large to
2897 <li>Muscle nucleotide alignment preset obscured by
2899 <li>JABAWS preset submenus don't contain newly
2900 defined user preset</li>
2901 <li>MSA web services warns user if they were launched
2902 with invalid input</li>
2903 <li>Jalview cannot contact DAS Registy when running on
2906 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2907 'Superpose with' submenu not shown when new view
2911 </ul> <!-- <em>Applet</em>
2913 </ul> <em>General</em>
2915 </ul>--> <em>Deployment and Documentation</em>
2917 <li>2G and 1G options in launchApp have no effect on
2918 memory allocation</li>
2919 <li>launchApp service doesn't automatically open
2920 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2922 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2923 InstallAnywhere reports cannot find valid JVM when Java
2924 1.7_055 is available
2926 </ul> <em>Application Known issues</em>
2929 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2930 corrupted or unreadable alignment display when scrolling
2934 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2935 retrieval fails but progress bar continues for DAS retrieval
2936 with large number of ID
2939 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2940 flatfile output of visible region has incorrect sequence
2944 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2945 rna structure consensus doesn't update when secondary
2946 structure tracks are rearranged
2949 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2950 invalid rna structure positional highlighting does not
2951 highlight position of invalid base pairs
2954 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2955 out of memory errors are not raised when saving Jalview
2956 project from alignment window file menu
2959 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2960 Switching to RNA Helices colouring doesn't propagate to
2964 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2965 colour by RNA Helices not enabled when user created
2966 annotation added to alignment
2969 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2970 Jalview icon not shown on dock in Mountain Lion/Webstart
2972 </ul> <em>Applet Known Issues</em>
2975 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2976 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2979 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2980 Jalview and Jmol example not compatible with IE9
2983 <li>Sort by annotation score doesn't reverse order
2989 <td><div align="center">
2990 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2993 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2996 <li>Internationalisation of user interface (usually
2997 called i18n support) and translation for Spanish locale</li>
2998 <li>Define/Undefine group on current selection with
2999 Ctrl-G/Shift Ctrl-G</li>
3000 <li>Improved group creation/removal options in
3001 alignment/sequence Popup menu</li>
3002 <li>Sensible precision for symbol distribution
3003 percentages shown in logo tooltip.</li>
3004 <li>Annotation panel height set according to amount of
3005 annotation when alignment first opened</li>
3006 </ul> <em>Application</em>
3008 <li>Interactive consensus RNA secondary structure
3009 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3010 <li>Select columns containing particular features from
3011 Feature Settings dialog</li>
3012 <li>View all 'representative' PDB structures for selected
3014 <li>Update Jalview project format:
3016 <li>New file extension for Jalview projects '.jvp'</li>
3017 <li>Preserve sequence and annotation dataset (to
3018 store secondary structure annotation,etc)</li>
3019 <li>Per group and alignment annotation and RNA helix
3023 <li>New similarity measures for PCA and Tree calculation
3025 <li>Experimental support for retrieval and viewing of
3026 flanking regions for an alignment</li>
3030 <!-- issues resolved --> <em>Application</em>
3032 <li>logo keeps spinning and status remains at queued or
3033 running after job is cancelled</li>
3034 <li>cannot export features from alignments imported from
3035 Jalview/VAMSAS projects</li>
3036 <li>Buggy slider for web service parameters that take
3038 <li>Newly created RNA secondary structure line doesn't
3039 have 'display all symbols' flag set</li>
3040 <li>T-COFFEE alignment score shading scheme and other
3041 annotation shading not saved in Jalview project</li>
3042 <li>Local file cannot be loaded in freshly downloaded
3044 <li>Jalview icon not shown on dock in Mountain
3046 <li>Load file from desktop file browser fails</li>
3047 <li>Occasional NPE thrown when calculating large trees</li>
3048 <li>Cannot reorder or slide sequences after dragging an
3049 alignment onto desktop</li>
3050 <li>Colour by annotation dialog throws NPE after using
3051 'extract scores' function</li>
3052 <li>Loading/cut'n'pasting an empty file leads to a grey
3053 alignment window</li>
3054 <li>Disorder thresholds rendered incorrectly after
3055 performing IUPred disorder prediction</li>
3056 <li>Multiple group annotated consensus rows shown when
3057 changing 'normalise logo' display setting</li>
3058 <li>Find shows blank dialog after 'finished searching' if
3059 nothing matches query</li>
3060 <li>Null Pointer Exceptions raised when sorting by
3061 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3063 <li>Errors in Jmol console when structures in alignment
3064 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3066 <li>Not all working JABAWS services are shown in
3068 <li>JAVAWS version of Jalview fails to launch with
3069 'invalid literal/length code'</li>
3070 <li>Annotation/RNA Helix colourschemes cannot be applied
3071 to alignment with groups (actually fixed in 2.8.0b1)</li>
3072 <li>RNA Helices and T-Coffee Scores available as default
3075 </ul> <em>Applet</em>
3077 <li>Remove group option is shown even when selection is
3079 <li>Apply to all groups ticked but colourscheme changes
3080 don't affect groups</li>
3081 <li>Documented RNA Helices and T-Coffee Scores as valid
3082 colourscheme name</li>
3083 <li>Annotation labels drawn on sequence IDs when
3084 Annotation panel is not displayed</li>
3085 <li>Increased font size for dropdown menus on OSX and
3086 embedded windows</li>
3087 </ul> <em>Other</em>
3089 <li>Consensus sequence for alignments/groups with a
3090 single sequence were not calculated</li>
3091 <li>annotation files that contain only groups imported as
3092 annotation and junk sequences</li>
3093 <li>Fasta files with sequences containing '*' incorrectly
3094 recognised as PFAM or BLC</li>
3095 <li>conservation/PID slider apply all groups option
3096 doesn't affect background (2.8.0b1)
3098 <li>redundancy highlighting is erratic at 0% and 100%</li>
3099 <li>Remove gapped columns fails for sequences with ragged
3101 <li>AMSA annotation row with leading spaces is not
3102 registered correctly on import</li>
3103 <li>Jalview crashes when selecting PCA analysis for
3104 certain alignments</li>
3105 <li>Opening the colour by annotation dialog for an
3106 existing annotation based 'use original colours'
3107 colourscheme loses original colours setting</li>
3112 <td><div align="center">
3113 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3114 <em>30/1/2014</em></strong>
3118 <li>Trusted certificates for JalviewLite applet and
3119 Jalview Desktop application<br />Certificate was donated by
3120 <a href="https://www.certum.eu">Certum</a> to the Jalview
3121 open source project).
3123 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3124 <li>Output in Stockholm format</li>
3125 <li>Allow import of data from gzipped files</li>
3126 <li>Export/import group and sequence associated line
3127 graph thresholds</li>
3128 <li>Nucleotide substitution matrix that supports RNA and
3129 ambiguity codes</li>
3130 <li>Allow disorder predictions to be made on the current
3131 selection (or visible selection) in the same way that JPred
3133 <li>Groovy scripting for headless Jalview operation</li>
3134 </ul> <em>Other improvements</em>
3136 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3137 <li>COMBINE statement uses current SEQUENCE_REF and
3138 GROUP_REF scope to group annotation rows</li>
3139 <li>Support '' style escaping of quotes in Newick
3141 <li>Group options for JABAWS service by command line name</li>
3142 <li>Empty tooltip shown for JABA service options with a
3143 link but no description</li>
3144 <li>Select primary source when selecting authority in
3145 database fetcher GUI</li>
3146 <li>Add .mfa to FASTA file extensions recognised by
3148 <li>Annotation label tooltip text wrap</li>
3153 <li>Slow scrolling when lots of annotation rows are
3155 <li>Lots of NPE (and slowness) after creating RNA
3156 secondary structure annotation line</li>
3157 <li>Sequence database accessions not imported when
3158 fetching alignments from Rfam</li>
3159 <li>Incorrect SHMR submission for sequences with
3161 <li>View all structures does not always superpose
3163 <li>Option widgets in service parameters not updated to
3164 reflect user or preset settings</li>
3165 <li>Null pointer exceptions for some services without
3166 presets or adjustable parameters</li>
3167 <li>Discover PDB IDs entry in structure menu doesn't
3168 discover PDB xRefs</li>
3169 <li>Exception encountered while trying to retrieve
3170 features with DAS</li>
3171 <li>Lowest value in annotation row isn't coloured
3172 when colour by annotation (per sequence) is coloured</li>
3173 <li>Keyboard mode P jumps to start of gapped region when
3174 residue follows a gap</li>
3175 <li>Jalview appears to hang importing an alignment with
3176 Wrap as default or after enabling Wrap</li>
3177 <li>'Right click to add annotations' message
3178 shown in wrap mode when no annotations present</li>
3179 <li>Disorder predictions fail with NPE if no automatic
3180 annotation already exists on alignment</li>
3181 <li>oninit javascript function should be called after
3182 initialisation completes</li>
3183 <li>Remove redundancy after disorder prediction corrupts
3184 alignment window display</li>
3185 <li>Example annotation file in documentation is invalid</li>
3186 <li>Grouped line graph annotation rows are not exported
3187 to annotation file</li>
3188 <li>Multi-harmony analysis cannot be run when only two
3190 <li>Cannot create multiple groups of line graphs with
3191 several 'combine' statements in annotation file</li>
3192 <li>Pressing return several times causes Number Format
3193 exceptions in keyboard mode</li>
3194 <li>Multi-harmony (SHMMR) method doesn't submit
3195 correct partitions for input data</li>
3196 <li>Translation from DNA to Amino Acids fails</li>
3197 <li>Jalview fail to load newick tree with quoted label</li>
3198 <li>--headless flag isn't understood</li>
3199 <li>ClassCastException when generating EPS in headless
3201 <li>Adjusting sequence-associated shading threshold only
3202 changes one row's threshold</li>
3203 <li>Preferences and Feature settings panel panel
3204 doesn't open</li>
3205 <li>hide consensus histogram also hides conservation and
3206 quality histograms</li>
3211 <td><div align="center">
3212 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3214 <td><em>Application</em>
3216 <li>Support for JABAWS 2.0 Services (AACon alignment
3217 conservation, protein disorder and Clustal Omega)</li>
3218 <li>JABAWS server status indicator in Web Services
3220 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3221 in Jalview alignment window</li>
3222 <li>Updated Jalview build and deploy framework for OSX
3223 mountain lion, windows 7, and 8</li>
3224 <li>Nucleotide substitution matrix for PCA that supports
3225 RNA and ambiguity codes</li>
3227 <li>Improved sequence database retrieval GUI</li>
3228 <li>Support fetching and database reference look up
3229 against multiple DAS sources (Fetch all from in 'fetch db
3231 <li>Jalview project improvements
3233 <li>Store and retrieve the 'belowAlignment'
3234 flag for annotation</li>
3235 <li>calcId attribute to group annotation rows on the
3237 <li>Store AACon calculation settings for a view in
3238 Jalview project</li>
3242 <li>horizontal scrolling gesture support</li>
3243 <li>Visual progress indicator when PCA calculation is
3245 <li>Simpler JABA web services menus</li>
3246 <li>visual indication that web service results are still
3247 being retrieved from server</li>
3248 <li>Serialise the dialogs that are shown when Jalview
3249 starts up for first time</li>
3250 <li>Jalview user agent string for interacting with HTTP
3252 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3254 <li>Examples directory and Groovy library included in
3255 InstallAnywhere distribution</li>
3256 </ul> <em>Applet</em>
3258 <li>RNA alignment and secondary structure annotation
3259 visualization applet example</li>
3260 </ul> <em>General</em>
3262 <li>Normalise option for consensus sequence logo</li>
3263 <li>Reset button in PCA window to return dimensions to
3265 <li>Allow seqspace or Jalview variant of alignment PCA
3267 <li>PCA with either nucleic acid and protein substitution
3269 <li>Allow windows containing HTML reports to be exported
3271 <li>Interactive display and editing of RNA secondary
3272 structure contacts</li>
3273 <li>RNA Helix Alignment Colouring</li>
3274 <li>RNA base pair logo consensus</li>
3275 <li>Parse sequence associated secondary structure
3276 information in Stockholm files</li>
3277 <li>HTML Export database accessions and annotation
3278 information presented in tooltip for sequences</li>
3279 <li>Import secondary structure from LOCARNA clustalw
3280 style RNA alignment files</li>
3281 <li>import and visualise T-COFFEE quality scores for an
3283 <li>'colour by annotation' per sequence option to
3284 shade each sequence according to its associated alignment
3286 <li>New Jalview Logo</li>
3287 </ul> <em>Documentation and Development</em>
3289 <li>documentation for score matrices used in Jalview</li>
3290 <li>New Website!</li>
3292 <td><em>Application</em>
3294 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3295 wsdbfetch REST service</li>
3296 <li>Stop windows being moved outside desktop on OSX</li>
3297 <li>Filetype associations not installed for webstart
3299 <li>Jalview does not always retrieve progress of a JABAWS
3300 job execution in full once it is complete</li>
3301 <li>revise SHMR RSBS definition to ensure alignment is
3302 uploaded via ali_file parameter</li>
3303 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3304 <li>View all structures superposed fails with exception</li>
3305 <li>Jnet job queues forever if a very short sequence is
3306 submitted for prediction</li>
3307 <li>Cut and paste menu not opened when mouse clicked on
3309 <li>Putting fractional value into integer text box in
3310 alignment parameter dialog causes Jalview to hang</li>
3311 <li>Structure view highlighting doesn't work on
3313 <li>View all structures fails with exception shown in
3315 <li>Characters in filename associated with PDBEntry not
3316 escaped in a platform independent way</li>
3317 <li>Jalview desktop fails to launch with exception when
3319 <li>Tree calculation reports 'you must have 2 or more
3320 sequences selected' when selection is empty</li>
3321 <li>Jalview desktop fails to launch with jar signature
3322 failure when java web start temporary file caching is
3324 <li>DAS Sequence retrieval with range qualification
3325 results in sequence xref which includes range qualification</li>
3326 <li>Errors during processing of command line arguments
3327 cause progress bar (JAL-898) to be removed</li>
3328 <li>Replace comma for semi-colon option not disabled for
3329 DAS sources in sequence fetcher</li>
3330 <li>Cannot close news reader when JABAWS server warning
3331 dialog is shown</li>
3332 <li>Option widgets not updated to reflect user settings</li>
3333 <li>Edited sequence not submitted to web service</li>
3334 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3335 <li>InstallAnywhere installer doesn't unpack and run
3336 on OSX Mountain Lion</li>
3337 <li>Annotation panel not given a scroll bar when
3338 sequences with alignment annotation are pasted into the
3340 <li>Sequence associated annotation rows not associated
3341 when loaded from Jalview project</li>
3342 <li>Browser launch fails with NPE on java 1.7</li>
3343 <li>JABAWS alignment marked as finished when job was
3344 cancelled or job failed due to invalid input</li>
3345 <li>NPE with v2.7 example when clicking on Tree
3346 associated with all views</li>
3347 <li>Exceptions when copy/paste sequences with grouped
3348 annotation rows to new window</li>
3349 </ul> <em>Applet</em>
3351 <li>Sequence features are momentarily displayed before
3352 they are hidden using hidefeaturegroups applet parameter</li>
3353 <li>loading features via javascript API automatically
3354 enables feature display</li>
3355 <li>scrollToColumnIn javascript API method doesn't
3357 </ul> <em>General</em>
3359 <li>Redundancy removal fails for rna alignment</li>
3360 <li>PCA calculation fails when sequence has been selected
3361 and then deselected</li>
3362 <li>PCA window shows grey box when first opened on OSX</li>
3363 <li>Letters coloured pink in sequence logo when alignment
3364 coloured with clustalx</li>
3365 <li>Choosing fonts without letter symbols defined causes
3366 exceptions and redraw errors</li>
3367 <li>Initial PCA plot view is not same as manually
3368 reconfigured view</li>
3369 <li>Grouped annotation graph label has incorrect line
3371 <li>Grouped annotation graph label display is corrupted
3372 for lots of labels</li>
3377 <div align="center">
3378 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3381 <td><em>Application</em>
3383 <li>Jalview Desktop News Reader</li>
3384 <li>Tweaked default layout of web services menu</li>
3385 <li>View/alignment association menu to enable user to
3386 easily specify which alignment a multi-structure view takes
3387 its colours/correspondences from</li>
3388 <li>Allow properties file location to be specified as URL</li>
3389 <li>Extend Jalview project to preserve associations
3390 between many alignment views and a single Jmol display</li>
3391 <li>Store annotation row height in Jalview project file</li>
3392 <li>Annotation row column label formatting attributes
3393 stored in project file</li>
3394 <li>Annotation row order for auto-calculated annotation
3395 rows preserved in Jalview project file</li>
3396 <li>Visual progress indication when Jalview state is
3397 saved using Desktop window menu</li>
3398 <li>Visual indication that command line arguments are
3399 still being processed</li>
3400 <li>Groovy script execution from URL</li>
3401 <li>Colour by annotation default min and max colours in
3403 <li>Automatically associate PDB files dragged onto an
3404 alignment with sequences that have high similarity and
3406 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3407 <li>'view structures' option to open many
3408 structures in same window</li>
3409 <li>Sort associated views menu option for tree panel</li>
3410 <li>Group all JABA and non-JABA services for a particular
3411 analysis function in its own submenu</li>
3412 </ul> <em>Applet</em>
3414 <li>Userdefined and autogenerated annotation rows for
3416 <li>Adjustment of alignment annotation pane height</li>
3417 <li>Annotation scrollbar for annotation panel</li>
3418 <li>Drag to reorder annotation rows in annotation panel</li>
3419 <li>'automaticScrolling' parameter</li>
3420 <li>Allow sequences with partial ID string matches to be
3421 annotated from GFF/Jalview features files</li>
3422 <li>Sequence logo annotation row in applet</li>
3423 <li>Absolute paths relative to host server in applet
3424 parameters are treated as such</li>
3425 <li>New in the JalviewLite javascript API:
3427 <li>JalviewLite.js javascript library</li>
3428 <li>Javascript callbacks for
3430 <li>Applet initialisation</li>
3431 <li>Sequence/alignment mouse-overs and selections</li>
3434 <li>scrollTo row and column alignment scrolling
3436 <li>Select sequence/alignment regions from javascript</li>
3437 <li>javascript structure viewer harness to pass
3438 messages between Jmol and Jalview when running as
3439 distinct applets</li>
3440 <li>sortBy method</li>
3441 <li>Set of applet and application examples shipped
3442 with documentation</li>
3443 <li>New example to demonstrate JalviewLite and Jmol
3444 javascript message exchange</li>
3446 </ul> <em>General</em>
3448 <li>Enable Jmol displays to be associated with multiple
3449 multiple alignments</li>
3450 <li>Option to automatically sort alignment with new tree</li>
3451 <li>User configurable link to enable redirects to a
3452 www.Jalview.org mirror</li>
3453 <li>Jmol colours option for Jmol displays</li>
3454 <li>Configurable newline string when writing alignment
3455 and other flat files</li>
3456 <li>Allow alignment annotation description lines to
3457 contain html tags</li>
3458 </ul> <em>Documentation and Development</em>
3460 <li>Add groovy test harness for bulk load testing to
3462 <li>Groovy script to load and align a set of sequences
3463 using a web service before displaying the result in the
3464 Jalview desktop</li>
3465 <li>Restructured javascript and applet api documentation</li>
3466 <li>Ant target to publish example html files with applet
3468 <li>Netbeans project for building Jalview from source</li>
3469 <li>ant task to create online javadoc for Jalview source</li>
3471 <td><em>Application</em>
3473 <li>User defined colourscheme throws exception when
3474 current built in colourscheme is saved as new scheme</li>
3475 <li>AlignFrame->Save in application pops up save
3476 dialog for valid filename/format</li>
3477 <li>Cannot view associated structure for UniProt sequence</li>
3478 <li>PDB file association breaks for UniProt sequence
3480 <li>Associate PDB from file dialog does not tell you
3481 which sequence is to be associated with the file</li>
3482 <li>Find All raises null pointer exception when query
3483 only matches sequence IDs</li>
3484 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3485 <li>Jalview project with Jmol views created with Jalview
3486 2.4 cannot be loaded</li>
3487 <li>Filetype associations not installed for webstart
3489 <li>Two or more chains in a single PDB file associated
3490 with sequences in different alignments do not get coloured
3491 by their associated sequence</li>
3492 <li>Visibility status of autocalculated annotation row
3493 not preserved when project is loaded</li>
3494 <li>Annotation row height and visibility attributes not
3495 stored in Jalview project</li>
3496 <li>Tree bootstraps are not preserved when saved as a
3497 Jalview project</li>
3498 <li>Envision2 workflow tooltips are corrupted</li>
3499 <li>Enabling show group conservation also enables colour
3500 by conservation</li>
3501 <li>Duplicate group associated conservation or consensus
3502 created on new view</li>
3503 <li>Annotation scrollbar not displayed after 'show
3504 all hidden annotation rows' option selected</li>
3505 <li>Alignment quality not updated after alignment
3506 annotation row is hidden then shown</li>
3507 <li>Preserve colouring of structures coloured by
3508 sequences in pre Jalview 2.7 projects</li>
3509 <li>Web service job parameter dialog is not laid out
3511 <li>Web services menu not refreshed after 'reset
3512 services' button is pressed in preferences</li>
3513 <li>Annotation off by one in Jalview v2_3 example project</li>
3514 <li>Structures imported from file and saved in project
3515 get name like jalview_pdb1234.txt when reloaded</li>
3516 <li>Jalview does not always retrieve progress of a JABAWS
3517 job execution in full once it is complete</li>
3518 </ul> <em>Applet</em>
3520 <li>Alignment height set incorrectly when lots of
3521 annotation rows are displayed</li>
3522 <li>Relative URLs in feature HTML text not resolved to
3524 <li>View follows highlighting does not work for positions
3526 <li><= shown as = in tooltip</li>
3527 <li>Export features raises exception when no features
3529 <li>Separator string used for serialising lists of IDs
3530 for javascript api is modified when separator string
3531 provided as parameter</li>
3532 <li>Null pointer exception when selecting tree leaves for
3533 alignment with no existing selection</li>
3534 <li>Relative URLs for datasources assumed to be relative
3535 to applet's codebase</li>
3536 <li>Status bar not updated after finished searching and
3537 search wraps around to first result</li>
3538 <li>StructureSelectionManager instance shared between
3539 several Jalview applets causes race conditions and memory
3541 <li>Hover tooltip and mouseover of position on structure
3542 not sent from Jmol in applet</li>
3543 <li>Certain sequences of javascript method calls to
3544 applet API fatally hang browser</li>
3545 </ul> <em>General</em>
3547 <li>View follows structure mouseover scrolls beyond
3548 position with wrapped view and hidden regions</li>
3549 <li>Find sequence position moves to wrong residue
3550 with/without hidden columns</li>
3551 <li>Sequence length given in alignment properties window
3553 <li>InvalidNumberFormat exceptions thrown when trying to
3554 import PDB like structure files</li>
3555 <li>Positional search results are only highlighted
3556 between user-supplied sequence start/end bounds</li>
3557 <li>End attribute of sequence is not validated</li>
3558 <li>Find dialog only finds first sequence containing a
3559 given sequence position</li>
3560 <li>Sequence numbering not preserved in MSF alignment
3562 <li>Jalview PDB file reader does not extract sequence
3563 from nucleotide chains correctly</li>
3564 <li>Structure colours not updated when tree partition
3565 changed in alignment</li>
3566 <li>Sequence associated secondary structure not correctly
3567 parsed in interleaved stockholm</li>
3568 <li>Colour by annotation dialog does not restore current
3570 <li>Hiding (nearly) all sequences doesn't work
3572 <li>Sequences containing lowercase letters are not
3573 properly associated with their pdb files</li>
3574 </ul> <em>Documentation and Development</em>
3576 <li>schemas/JalviewWsParamSet.xsd corrupted by
3577 ApplyCopyright tool</li>
3582 <div align="center">
3583 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3586 <td><em>Application</em>
3588 <li>New warning dialog when the Jalview Desktop cannot
3589 contact web services</li>
3590 <li>JABA service parameters for a preset are shown in
3591 service job window</li>
3592 <li>JABA Service menu entries reworded</li>
3596 <li>Modeller PIR IO broken - cannot correctly import a
3597 pir file emitted by Jalview</li>
3598 <li>Existing feature settings transferred to new
3599 alignment view created from cut'n'paste</li>
3600 <li>Improved test for mixed amino/nucleotide chains when
3601 parsing PDB files</li>
3602 <li>Consensus and conservation annotation rows
3603 occasionally become blank for all new windows</li>
3604 <li>Exception raised when right clicking above sequences
3605 in wrapped view mode</li>
3606 </ul> <em>Application</em>
3608 <li>multiple multiply aligned structure views cause cpu
3609 usage to hit 100% and computer to hang</li>
3610 <li>Web Service parameter layout breaks for long user
3611 parameter names</li>
3612 <li>Jaba service discovery hangs desktop if Jaba server
3619 <div align="center">
3620 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3623 <td><em>Application</em>
3625 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3626 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3629 <li>Web Services preference tab</li>
3630 <li>Analysis parameters dialog box and user defined
3632 <li>Improved speed and layout of Envision2 service menu</li>
3633 <li>Superpose structures using associated sequence
3635 <li>Export coordinates and projection as CSV from PCA
3637 </ul> <em>Applet</em>
3639 <li>enable javascript: execution by the applet via the
3640 link out mechanism</li>
3641 </ul> <em>Other</em>
3643 <li>Updated the Jmol Jalview interface to work with Jmol
3645 <li>The Jalview Desktop and JalviewLite applet now
3646 require Java 1.5</li>
3647 <li>Allow Jalview feature colour specification for GFF
3648 sequence annotation files</li>
3649 <li>New 'colour by label' keword in Jalview feature file
3650 type colour specification</li>
3651 <li>New Jalview Desktop Groovy API method that allows a
3652 script to check if it being run in an interactive session or
3653 in a batch operation from the Jalview command line</li>
3657 <li>clustalx colourscheme colours Ds preferentially when
3658 both D+E are present in over 50% of the column</li>
3659 </ul> <em>Application</em>
3661 <li>typo in AlignmentFrame->View->Hide->all but
3662 selected Regions menu item</li>
3663 <li>sequence fetcher replaces ',' for ';' when the ',' is
3664 part of a valid accession ID</li>
3665 <li>fatal OOM if object retrieved by sequence fetcher
3666 runs out of memory</li>
3667 <li>unhandled Out of Memory Error when viewing pca
3668 analysis results</li>
3669 <li>InstallAnywhere builds fail to launch on OS X java
3670 10.5 update 4 (due to apple Java 1.6 update)</li>
3671 <li>Installanywhere Jalview silently fails to launch</li>
3672 </ul> <em>Applet</em>
3674 <li>Jalview.getFeatureGroups() raises an
3675 ArrayIndexOutOfBoundsException if no feature groups are
3682 <div align="center">
3683 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3689 <li>Alignment prettyprinter doesn't cope with long
3691 <li>clustalx colourscheme colours Ds preferentially when
3692 both D+E are present in over 50% of the column</li>
3693 <li>nucleic acid structures retrieved from PDB do not
3694 import correctly</li>
3695 <li>More columns get selected than were clicked on when a
3696 number of columns are hidden</li>
3697 <li>annotation label popup menu not providing correct
3698 add/hide/show options when rows are hidden or none are
3700 <li>Stockholm format shown in list of readable formats,
3701 and parser copes better with alignments from RFAM.</li>
3702 <li>CSV output of consensus only includes the percentage
3703 of all symbols if sequence logo display is enabled</li>
3705 </ul> <em>Applet</em>
3707 <li>annotation panel disappears when annotation is
3709 </ul> <em>Application</em>
3711 <li>Alignment view not redrawn properly when new
3712 alignment opened where annotation panel is visible but no
3713 annotations are present on alignment</li>
3714 <li>pasted region containing hidden columns is
3715 incorrectly displayed in new alignment window</li>
3716 <li>Jalview slow to complete operations when stdout is
3717 flooded (fix is to close the Jalview console)</li>
3718 <li>typo in AlignmentFrame->View->Hide->all but
3719 selected Rregions menu item.</li>
3720 <li>inconsistent group submenu and Format submenu entry
3721 'Un' or 'Non'conserved</li>
3722 <li>Sequence feature settings are being shared by
3723 multiple distinct alignments</li>
3724 <li>group annotation not recreated when tree partition is
3726 <li>double click on group annotation to select sequences
3727 does not propagate to associated trees</li>
3728 <li>Mac OSX specific issues:
3730 <li>exception raised when mouse clicked on desktop
3731 window background</li>
3732 <li>Desktop menu placed on menu bar and application
3733 name set correctly</li>
3734 <li>sequence feature settings not wide enough for the
3735 save feature colourscheme button</li>
3744 <div align="center">
3745 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3748 <td><em>New Capabilities</em>
3750 <li>URL links generated from description line for
3751 regular-expression based URL links (applet and application)
3753 <li>Non-positional feature URL links are shown in link
3755 <li>Linked viewing of nucleic acid sequences and
3757 <li>Automatic Scrolling option in View menu to display
3758 the currently highlighted region of an alignment.</li>
3759 <li>Order an alignment by sequence length, or using the
3760 average score or total feature count for each sequence.</li>
3761 <li>Shading features by score or associated description</li>
3762 <li>Subdivide alignment and groups based on identity of
3763 selected subsequence (Make Groups from Selection).</li>
3764 <li>New hide/show options including Shift+Control+H to
3765 hide everything but the currently selected region.</li>
3766 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3767 </ul> <em>Application</em>
3769 <li>Fetch DB References capabilities and UI expanded to
3770 support retrieval from DAS sequence sources</li>
3771 <li>Local DAS Sequence sources can be added via the
3772 command line or via the Add local source dialog box.</li>
3773 <li>DAS Dbref and DbxRef feature types are parsed as
3774 database references and protein_name is parsed as
3775 description line (BioSapiens terms).</li>
3776 <li>Enable or disable non-positional feature and database
3777 references in sequence ID tooltip from View menu in
3779 <!-- <li>New hidden columns and rows and representatives capabilities
3780 in annotations file (in progress - not yet fully implemented)</li> -->
3781 <li>Group-associated consensus, sequence logos and
3782 conservation plots</li>
3783 <li>Symbol distributions for each column can be exported
3784 and visualized as sequence logos</li>
3785 <li>Optionally scale multi-character column labels to fit
3786 within each column of annotation row<!-- todo for applet -->
3788 <li>Optional automatic sort of associated alignment view
3789 when a new tree is opened.</li>
3790 <li>Jalview Java Console</li>
3791 <li>Better placement of desktop window when moving
3792 between different screens.</li>
3793 <li>New preference items for sequence ID tooltip and
3794 consensus annotation</li>
3795 <li>Client to submit sequences and IDs to Envision2
3797 <li><em>Vamsas Capabilities</em>
3799 <li>Improved VAMSAS synchronization (Jalview archive
3800 used to preserve views, structures, and tree display
3802 <li>Import of vamsas documents from disk or URL via
3804 <li>Sharing of selected regions between views and
3805 with other VAMSAS applications (Experimental feature!)</li>
3806 <li>Updated API to VAMSAS version 0.2</li>
3808 </ul> <em>Applet</em>
3810 <li>Middle button resizes annotation row height</li>
3813 <li>sortByTree (true/false) - automatically sort the
3814 associated alignment view by the tree when a new tree is
3816 <li>showTreeBootstraps (true/false) - show or hide
3817 branch bootstraps (default is to show them if available)</li>
3818 <li>showTreeDistances (true/false) - show or hide
3819 branch lengths (default is to show them if available)</li>
3820 <li>showUnlinkedTreeNodes (true/false) - indicate if
3821 unassociated nodes should be highlighted in the tree
3823 <li>heightScale and widthScale (1.0 or more) -
3824 increase the height or width of a cell in the alignment
3825 grid relative to the current font size.</li>
3828 <li>Non-positional features displayed in sequence ID
3830 </ul> <em>Other</em>
3832 <li>Features format: graduated colour definitions and
3833 specification of feature scores</li>
3834 <li>Alignment Annotations format: new keywords for group
3835 associated annotation (GROUP_REF) and annotation row display
3836 properties (ROW_PROPERTIES)</li>
3837 <li>XML formats extended to support graduated feature
3838 colourschemes, group associated annotation, and profile
3839 visualization settings.</li></td>
3842 <li>Source field in GFF files parsed as feature source
3843 rather than description</li>
3844 <li>Non-positional features are now included in sequence
3845 feature and gff files (controlled via non-positional feature
3846 visibility in tooltip).</li>
3847 <li>URL links generated for all feature links (bugfix)</li>
3848 <li>Added URL embedding instructions to features file
3850 <li>Codons containing ambiguous nucleotides translated as
3851 'X' in peptide product</li>
3852 <li>Match case switch in find dialog box works for both
3853 sequence ID and sequence string and query strings do not
3854 have to be in upper case to match case-insensitively.</li>
3855 <li>AMSA files only contain first column of
3856 multi-character column annotation labels</li>
3857 <li>Jalview Annotation File generation/parsing consistent
3858 with documentation (e.g. Stockholm annotation can be
3859 exported and re-imported)</li>
3860 <li>PDB files without embedded PDB IDs given a friendly
3862 <li>Find incrementally searches ID string matches as well
3863 as subsequence matches, and correctly reports total number
3867 <li>Better handling of exceptions during sequence
3869 <li>Dasobert generated non-positional feature URL
3870 link text excludes the start_end suffix</li>
3871 <li>DAS feature and source retrieval buttons disabled
3872 when fetch or registry operations in progress.</li>
3873 <li>PDB files retrieved from URLs are cached properly</li>
3874 <li>Sequence description lines properly shared via
3876 <li>Sequence fetcher fetches multiple records for all
3878 <li>Ensured that command line das feature retrieval
3879 completes before alignment figures are generated.</li>
3880 <li>Reduced time taken when opening file browser for
3882 <li>isAligned check prior to calculating tree, PCA or
3883 submitting an MSA to JNet now excludes hidden sequences.</li>
3884 <li>User defined group colours properly recovered
3885 from Jalview projects.</li>
3894 <div align="center">
3895 <strong>2.4.0.b2</strong><br> 28/10/2009
3900 <li>Experimental support for google analytics usage
3902 <li>Jalview privacy settings (user preferences and docs).</li>
3907 <li>Race condition in applet preventing startup in
3909 <li>Exception when feature created from selection beyond
3910 length of sequence.</li>
3911 <li>Allow synthetic PDB files to be imported gracefully</li>
3912 <li>Sequence associated annotation rows associate with
3913 all sequences with a given id</li>
3914 <li>Find function matches case-insensitively for sequence
3915 ID string searches</li>
3916 <li>Non-standard characters do not cause pairwise
3917 alignment to fail with exception</li>
3918 </ul> <em>Application Issues</em>
3920 <li>Sequences are now validated against EMBL database</li>
3921 <li>Sequence fetcher fetches multiple records for all
3923 </ul> <em>InstallAnywhere Issues</em>
3925 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3926 issue with installAnywhere mechanism)</li>
3927 <li>Command line launching of JARs from InstallAnywhere
3928 version (java class versioning error fixed)</li>
3935 <div align="center">
3936 <strong>2.4</strong><br> 27/8/2008
3939 <td><em>User Interface</em>
3941 <li>Linked highlighting of codon and amino acid from
3942 translation and protein products</li>
3943 <li>Linked highlighting of structure associated with
3944 residue mapping to codon position</li>
3945 <li>Sequence Fetcher provides example accession numbers
3946 and 'clear' button</li>
3947 <li>MemoryMonitor added as an option under Desktop's
3949 <li>Extract score function to parse whitespace separated
3950 numeric data in description line</li>
3951 <li>Column labels in alignment annotation can be centred.</li>
3952 <li>Tooltip for sequence associated annotation give name
3954 </ul> <em>Web Services and URL fetching</em>
3956 <li>JPred3 web service</li>
3957 <li>Prototype sequence search client (no public services
3959 <li>Fetch either seed alignment or full alignment from
3961 <li>URL Links created for matching database cross
3962 references as well as sequence ID</li>
3963 <li>URL Links can be created using regular-expressions</li>
3964 </ul> <em>Sequence Database Connectivity</em>
3966 <li>Retrieval of cross-referenced sequences from other
3968 <li>Generalised database reference retrieval and
3969 validation to all fetchable databases</li>
3970 <li>Fetch sequences from DAS sources supporting the
3971 sequence command</li>
3972 </ul> <em>Import and Export</em>
3973 <li>export annotation rows as CSV for spreadsheet import</li>
3974 <li>Jalview projects record alignment dataset associations,
3975 EMBL products, and cDNA sequence mappings</li>
3976 <li>Sequence Group colour can be specified in Annotation
3978 <li>Ad-hoc colouring of group in Annotation File using RGB
3979 triplet as name of colourscheme</li>
3980 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3982 <li>treenode binding for VAMSAS tree exchange</li>
3983 <li>local editing and update of sequences in VAMSAS
3984 alignments (experimental)</li>
3985 <li>Create new or select existing session to join</li>
3986 <li>load and save of vamsas documents</li>
3987 </ul> <em>Application command line</em>
3989 <li>-tree parameter to open trees (introduced for passing
3991 <li>-fetchfrom command line argument to specify nicknames
3992 of DAS servers to query for alignment features</li>
3993 <li>-dasserver command line argument to add new servers
3994 that are also automatically queried for features</li>
3995 <li>-groovy command line argument executes a given groovy
3996 script after all input data has been loaded and parsed</li>
3997 </ul> <em>Applet-Application data exchange</em>
3999 <li>Trees passed as applet parameters can be passed to
4000 application (when using "View in full
4001 application")</li>
4002 </ul> <em>Applet Parameters</em>
4004 <li>feature group display control parameter</li>
4005 <li>debug parameter</li>
4006 <li>showbutton parameter</li>
4007 </ul> <em>Applet API methods</em>
4009 <li>newView public method</li>
4010 <li>Window (current view) specific get/set public methods</li>
4011 <li>Feature display control methods</li>
4012 <li>get list of currently selected sequences</li>
4013 </ul> <em>New Jalview distribution features</em>
4015 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4016 <li>RELEASE file gives build properties for the latest
4017 Jalview release.</li>
4018 <li>Java 1.1 Applet build made easier and donotobfuscate
4019 property controls execution of obfuscator</li>
4020 <li>Build target for generating source distribution</li>
4021 <li>Debug flag for javacc</li>
4022 <li>.jalview_properties file is documented (slightly) in
4023 jalview.bin.Cache</li>
4024 <li>Continuous Build Integration for stable and
4025 development version of Application, Applet and source
4030 <li>selected region output includes visible annotations
4031 (for certain formats)</li>
4032 <li>edit label/displaychar contains existing label/char
4034 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4035 <li>shorter peptide product names from EMBL records</li>
4036 <li>Newick string generator makes compact representations</li>
4037 <li>bootstrap values parsed correctly for tree files with
4039 <li>pathological filechooser bug avoided by not allowing
4040 filenames containing a ':'</li>
4041 <li>Fixed exception when parsing GFF files containing
4042 global sequence features</li>
4043 <li>Alignment datasets are finalized only when number of
4044 references from alignment sequences goes to zero</li>
4045 <li>Close of tree branch colour box without colour
4046 selection causes cascading exceptions</li>
4047 <li>occasional negative imgwidth exceptions</li>
4048 <li>better reporting of non-fatal warnings to user when
4049 file parsing fails.</li>
4050 <li>Save works when Jalview project is default format</li>
4051 <li>Save as dialog opened if current alignment format is
4052 not a valid output format</li>
4053 <li>UniProt canonical names introduced for both das and
4055 <li>Histidine should be midblue (not pink!) in Zappo</li>
4056 <li>error messages passed up and output when data read
4058 <li>edit undo recovers previous dataset sequence when
4059 sequence is edited</li>
4060 <li>allow PDB files without pdb ID HEADER lines (like
4061 those generated by MODELLER) to be read in properly</li>
4062 <li>allow reading of JPred concise files as a normal
4064 <li>Stockholm annotation parsing and alignment properties
4065 import fixed for PFAM records</li>
4066 <li>Structure view windows have correct name in Desktop
4068 <li>annotation consisting of sequence associated scores
4069 can be read and written correctly to annotation file</li>
4070 <li>Aligned cDNA translation to aligned peptide works
4072 <li>Fixed display of hidden sequence markers and
4073 non-italic font for representatives in Applet</li>
4074 <li>Applet Menus are always embedded in applet window on
4076 <li>Newly shown features appear at top of stack (in
4078 <li>Annotations added via parameter not drawn properly
4079 due to null pointer exceptions</li>
4080 <li>Secondary structure lines are drawn starting from
4081 first column of alignment</li>
4082 <li>UniProt XML import updated for new schema release in
4084 <li>Sequence feature to sequence ID match for Features
4085 file is case-insensitive</li>
4086 <li>Sequence features read from Features file appended to
4087 all sequences with matching IDs</li>
4088 <li>PDB structure coloured correctly for associated views
4089 containing a sub-sequence</li>
4090 <li>PDB files can be retrieved by applet from Jar files</li>
4091 <li>feature and annotation file applet parameters
4092 referring to different directories are retrieved correctly</li>
4093 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4094 <li>Fixed application hang whilst waiting for
4095 splash-screen version check to complete</li>
4096 <li>Applet properly URLencodes input parameter values
4097 when passing them to the launchApp service</li>
4098 <li>display name and local features preserved in results
4099 retrieved from web service</li>
4100 <li>Visual delay indication for sequence retrieval and
4101 sequence fetcher initialisation</li>
4102 <li>updated Application to use DAS 1.53e version of
4103 dasobert DAS client</li>
4104 <li>Re-instated Full AMSA support and .amsa file
4106 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4114 <div align="center">
4115 <strong>2.3</strong><br> 9/5/07
4120 <li>Jmol 11.0.2 integration</li>
4121 <li>PDB views stored in Jalview XML files</li>
4122 <li>Slide sequences</li>
4123 <li>Edit sequence in place</li>
4124 <li>EMBL CDS features</li>
4125 <li>DAS Feature mapping</li>
4126 <li>Feature ordering</li>
4127 <li>Alignment Properties</li>
4128 <li>Annotation Scores</li>
4129 <li>Sort by scores</li>
4130 <li>Feature/annotation editing in applet</li>
4135 <li>Headless state operation in 2.2.1</li>
4136 <li>Incorrect and unstable DNA pairwise alignment</li>
4137 <li>Cut and paste of sequences with annotation</li>
4138 <li>Feature group display state in XML</li>
4139 <li>Feature ordering in XML</li>
4140 <li>blc file iteration selection using filename # suffix</li>
4141 <li>Stockholm alignment properties</li>
4142 <li>Stockhom alignment secondary structure annotation</li>
4143 <li>2.2.1 applet had no feature transparency</li>
4144 <li>Number pad keys can be used in cursor mode</li>
4145 <li>Structure Viewer mirror image resolved</li>
4152 <div align="center">
4153 <strong>2.2.1</strong><br> 12/2/07
4158 <li>Non standard characters can be read and displayed
4159 <li>Annotations/Features can be imported/exported to the
4161 <li>Applet allows editing of sequence/annotation/group
4162 name & description
4163 <li>Preference setting to display sequence name in
4165 <li>Annotation file format extended to allow
4166 Sequence_groups to be defined
4167 <li>Default opening of alignment overview panel can be
4168 specified in preferences
4169 <li>PDB residue numbering annotation added to associated
4175 <li>Applet crash under certain Linux OS with Java 1.6
4177 <li>Annotation file export / import bugs fixed
4178 <li>PNG / EPS image output bugs fixed
4184 <div align="center">
4185 <strong>2.2</strong><br> 27/11/06
4190 <li>Multiple views on alignment
4191 <li>Sequence feature editing
4192 <li>"Reload" alignment
4193 <li>"Save" to current filename
4194 <li>Background dependent text colour
4195 <li>Right align sequence ids
4196 <li>User-defined lower case residue colours
4199 <li>Menu item accelerator keys
4200 <li>Control-V pastes to current alignment
4201 <li>Cancel button for DAS Feature Fetching
4202 <li>PCA and PDB Viewers zoom via mouse roller
4203 <li>User-defined sub-tree colours and sub-tree selection
4205 <li>'New Window' button on the 'Output to Text box'
4210 <li>New memory efficient Undo/Redo System
4211 <li>Optimised symbol lookups and conservation/consensus
4213 <li>Region Conservation/Consensus recalculated after
4215 <li>Fixed Remove Empty Columns Bug (empty columns at end
4217 <li>Slowed DAS Feature Fetching for increased robustness.
4219 <li>Made angle brackets in ASCII feature descriptions
4221 <li>Re-instated Zoom function for PCA
4222 <li>Sequence descriptions conserved in web service
4224 <li>UniProt ID discoverer uses any word separated by
4226 <li>WsDbFetch query/result association resolved
4227 <li>Tree leaf to sequence mapping improved
4228 <li>Smooth fonts switch moved to FontChooser dialog box.
4235 <div align="center">
4236 <strong>2.1.1</strong><br> 12/9/06
4241 <li>Copy consensus sequence to clipboard</li>
4246 <li>Image output - rightmost residues are rendered if
4247 sequence id panel has been resized</li>
4248 <li>Image output - all offscreen group boundaries are
4250 <li>Annotation files with sequence references - all
4251 elements in file are relative to sequence position</li>
4252 <li>Mac Applet users can use Alt key for group editing</li>
4258 <div align="center">
4259 <strong>2.1</strong><br> 22/8/06
4264 <li>MAFFT Multiple Alignment in default Web Service list</li>
4265 <li>DAS Feature fetching</li>
4266 <li>Hide sequences and columns</li>
4267 <li>Export Annotations and Features</li>
4268 <li>GFF file reading / writing</li>
4269 <li>Associate structures with sequences from local PDB
4271 <li>Add sequences to exisiting alignment</li>
4272 <li>Recently opened files / URL lists</li>
4273 <li>Applet can launch the full application</li>
4274 <li>Applet has transparency for features (Java 1.2
4276 <li>Applet has user defined colours parameter</li>
4277 <li>Applet can load sequences from parameter
4278 "sequence<em>x</em>"
4284 <li>Redundancy Panel reinstalled in the Applet</li>
4285 <li>Monospaced font - EPS / rescaling bug fixed</li>
4286 <li>Annotation files with sequence references bug fixed</li>
4292 <div align="center">
4293 <strong>2.08.1</strong><br> 2/5/06
4298 <li>Change case of selected region from Popup menu</li>
4299 <li>Choose to match case when searching</li>
4300 <li>Middle mouse button and mouse movement can compress /
4301 expand the visible width and height of the alignment</li>
4306 <li>Annotation Panel displays complete JNet results</li>
4312 <div align="center">
4313 <strong>2.08b</strong><br> 18/4/06
4319 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4320 <li>Righthand label on wrapped alignments shows correct
4327 <div align="center">
4328 <strong>2.08</strong><br> 10/4/06
4333 <li>Editing can be locked to the selection area</li>
4334 <li>Keyboard editing</li>
4335 <li>Create sequence features from searches</li>
4336 <li>Precalculated annotations can be loaded onto
4338 <li>Features file allows grouping of features</li>
4339 <li>Annotation Colouring scheme added</li>
4340 <li>Smooth fonts off by default - Faster rendering</li>
4341 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4346 <li>Drag & Drop fixed on Linux</li>
4347 <li>Jalview Archive file faster to load/save, sequence
4348 descriptions saved.</li>
4354 <div align="center">
4355 <strong>2.07</strong><br> 12/12/05
4360 <li>PDB Structure Viewer enhanced</li>
4361 <li>Sequence Feature retrieval and display enhanced</li>
4362 <li>Choose to output sequence start-end after sequence
4363 name for file output</li>
4364 <li>Sequence Fetcher WSDBFetch@EBI</li>
4365 <li>Applet can read feature files, PDB files and can be
4366 used for HTML form input</li>
4371 <li>HTML output writes groups and features</li>
4372 <li>Group editing is Control and mouse click</li>
4373 <li>File IO bugs</li>
4379 <div align="center">
4380 <strong>2.06</strong><br> 28/9/05
4385 <li>View annotations in wrapped mode</li>
4386 <li>More options for PCA viewer</li>
4391 <li>GUI bugs resolved</li>
4392 <li>Runs with -nodisplay from command line</li>
4398 <div align="center">
4399 <strong>2.05b</strong><br> 15/9/05
4404 <li>Choose EPS export as lineart or text</li>
4405 <li>Jar files are executable</li>
4406 <li>Can read in Uracil - maps to unknown residue</li>
4411 <li>Known OutOfMemory errors give warning message</li>
4412 <li>Overview window calculated more efficiently</li>
4413 <li>Several GUI bugs resolved</li>
4419 <div align="center">
4420 <strong>2.05</strong><br> 30/8/05
4425 <li>Edit and annotate in "Wrapped" view</li>
4430 <li>Several GUI bugs resolved</li>
4436 <div align="center">
4437 <strong>2.04</strong><br> 24/8/05
4442 <li>Hold down mouse wheel & scroll to change font
4448 <li>Improved JPred client reliability</li>
4449 <li>Improved loading of Jalview files</li>
4455 <div align="center">
4456 <strong>2.03</strong><br> 18/8/05
4461 <li>Set Proxy server name and port in preferences</li>
4462 <li>Multiple URL links from sequence ids</li>
4463 <li>User Defined Colours can have a scheme name and added
4465 <li>Choose to ignore gaps in consensus calculation</li>
4466 <li>Unix users can set default web browser</li>
4467 <li>Runs without GUI for batch processing</li>
4468 <li>Dynamically generated Web Service Menus</li>
4473 <li>InstallAnywhere download for Sparc Solaris</li>
4479 <div align="center">
4480 <strong>2.02</strong><br> 18/7/05
4486 <li>Copy & Paste order of sequences maintains
4487 alignment order.</li>
4493 <div align="center">
4494 <strong>2.01</strong><br> 12/7/05
4499 <li>Use delete key for deleting selection.</li>
4500 <li>Use Mouse wheel to scroll sequences.</li>
4501 <li>Help file updated to describe how to add alignment
4503 <li>Version and build date written to build properties
4505 <li>InstallAnywhere installation will check for updates
4506 at launch of Jalview.</li>
4511 <li>Delete gaps bug fixed.</li>
4512 <li>FileChooser sorts columns.</li>
4513 <li>Can remove groups one by one.</li>
4514 <li>Filechooser icons installed.</li>
4515 <li>Finder ignores return character when searching.
4516 Return key will initiate a search.<br>
4523 <div align="center">
4524 <strong>2.0</strong><br> 20/6/05
4529 <li>New codebase</li>