3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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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
244 <!-- JAL-3225 -->Eclipse project configuration managed with
247 <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
248 Atlassian Bamboo continuous integration for
249 unattended Test Suite execution</li>
251 <!-- JAL-2864 -->Memory test suite to detect leaks in common
253 <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
254 <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>
257 <td align="left" valign="top">
260 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
263 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
264 superposition in Jmol fail on Windows
267 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
268 structures for sequences with lots of PDB structures
271 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
275 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
276 project involving multiple views
279 <!-- JAL-3164 -->Overview for complementary view in a linked
280 CDS/Protein alignment is not updated when Hide Columns by
281 Annotation dialog hides columns
284 <!-- JAL-3158 -->Selection highlighting in the complement of a
285 CDS/Protein alignment stops working after making a selection in
286 one view, then making another selection in the other view
289 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
293 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
294 Settings and Jalview Preferences panels
297 <!-- JAL-2865 -->Jalview hangs when closing windows or the
298 overview updates with large alignments
301 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
302 region if columns were selected by dragging right-to-left and the
303 mouse moved to the left of the first column
306 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
307 hidden column marker via scale popup menu
310 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
311 doesn't tell users the invalid URL
314 <!-- JAL-3178 -->Nonpositional features lose feature group on
315 export as Jalview features file
318 <!-- JAL-2816 -->Tooltips displayed for features filtered by
322 <!-- JAL-2060 -->'Graduated colour' option not offered for
323 manually created features (where if feature score is Float.NaN)
326 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
327 when columns are hidden
330 <!-- JAL-3082 -->Regular expression error for '(' in Select
331 Columns by Annotation description
334 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
335 out of Scale or Annotation Panel
338 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
342 <!-- JAL-3074 -->Left/right drag in annotation can scroll
346 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
350 <!-- JAL-3002 -->Column display is out by one after Page Down,
351 Page Up in wrapped mode
354 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
357 <!-- JAL-2932 -->Finder searches in minimised alignments
360 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
361 on opening an alignment
364 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
368 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
369 different groups in the alignment are selected
372 <!-- JAL-2717 -->Internationalised colour scheme names not shown
376 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
380 <!-- JAL-3125 -->Value input for graduated feature colour
381 threshold gets 'unrounded'
384 <!-- JAL-2982 -->PCA image export doesn't respect background
388 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
391 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
394 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
398 <!-- JAL-2964 -->Associate Tree with All Views not restored from
402 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
403 shown in complementary view
406 <!-- JAL-2898 -->stop_gained variants not shown correctly on
410 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
411 without normalisation
414 <!-- JAL-3021 -->Sequence Details report opens positioned to top
418 <!-- JAL-914 -->Help page can be opened twice
420 </ul> <em>Editing</em>
423 <!-- JAL-2822 -->Start and End should be updated when sequence
424 data at beginning or end of alignment added/removed via 'Edit'
428 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
429 relocate sequence features correctly when start of sequence is
430 removed (Known defect since 2.10)
433 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
434 dialog corrupts dataset sequence
437 <!-- JAL-868 -->Structure colours not updated when associated tree
438 repartitions the alignment view (Regression in 2.10.5)
442 <em>New Known Defects</em>
445 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
446 regions of protein alignment.
449 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
450 is restored from a Jalview 2.11 project
453 <!-- JAL-3213 -->Alignment panel height can be too small after
457 <!-- JAL-3240 -->Display is incorrect after removing gapped
458 columns within hidden columns
461 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
462 window after dragging left to select columns to left of visible
466 <!-- JAL-2876 -->Features coloured according to their description
467 string and thresholded by score in earlier versions of Jalview are
468 not shown as thresholded features in 2.11. To workaround please
469 create a Score filter instead.
471 <li><strong>Java 11 Specific defects</strong>
474 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
482 <td width="60" nowrap>
484 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
487 <td><div align="left">
491 <!-- JAL-3101 -->Default memory for Jalview webstart and
492 InstallAnywhere increased to 1G.
495 <!-- JAL-247 -->Hidden sequence markers and representative
496 sequence bolding included when exporting alignment as EPS,
497 SVG, PNG or HTML. <em>Display is configured via the
498 Format menu, or for command-line use via a jalview
499 properties file.</em>
502 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
503 API and sequence data now imported as JSON.
506 <!-- JAL-3065 -->Change in recommended way of starting
507 Jalview via a Java command line: add jars in lib directory
508 to CLASSPATH, rather than via the deprecated java.ext.dirs
515 <!-- JAL-3047 -->Support added to execute test suite
516 instrumented with <a href="http://openclover.org/">Open
521 <td><div align="left">
525 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
526 row shown in Feredoxin Structure alignment view of example
530 <!-- JAL-2854 -->Annotation obscures sequences if lots of
531 annotation displayed.
534 <!-- JAL-3107 -->Group conservation/consensus not shown
535 for newly created group when 'Apply to all groups'
539 <!-- JAL-3087 -->Corrupted display when switching to
540 wrapped mode when sequence panel's vertical scrollbar is
544 <!-- JAL-3003 -->Alignment is black in exported EPS file
545 when sequences are selected in exported view.</em>
548 <!-- JAL-3059 -->Groups with different coloured borders
549 aren't rendered with correct colour.
552 <!-- JAL-3092 -->Jalview could hang when importing certain
553 types of knotted RNA secondary structure.
556 <!-- JAL-3095 -->Sequence highlight and selection in
557 trimmed VARNA 2D structure is incorrect for sequences that
561 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
562 annotation when columns are inserted into an alignment,
563 and when exporting as Stockholm flatfile.
566 <!-- JAL-3053 -->Jalview annotation rows containing upper
567 and lower-case 'E' and 'H' do not automatically get
568 treated as RNA secondary structure.
571 <!-- JAL-3106 -->.jvp should be used as default extension
572 (not .jar) when saving a jalview project file.
575 <!-- JAL-3105 -->Mac Users: closing a window correctly
576 transfers focus to previous window on OSX
579 <em>Java 10 Issues Resolved</em>
582 <!-- JAL-2988 -->OSX - Can't save new files via the File
583 or export menus by typing in a name into the Save dialog
587 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
588 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
589 'look and feel' which has improved compatibility with the
590 latest version of OSX.
597 <td width="60" nowrap>
599 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
600 <em>7/06/2018</em></strong>
603 <td><div align="left">
607 <!-- JAL-2920 -->Use HGVS nomenclature for variant
608 annotation retrieved from Uniprot
611 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
612 onto the Jalview Desktop
616 <td><div align="left">
620 <!-- JAL-3017 -->Cannot import features with multiple
621 variant elements (blocks import of some Uniprot records)
624 <!-- JAL-2997 -->Clustal files with sequence positions in
625 right-hand column parsed correctly
628 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
629 not alignment area in exported graphic
632 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
633 window has input focus
636 <!-- JAL-2992 -->Annotation panel set too high when
637 annotation added to view (Windows)
640 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
641 network connectivity is poor
644 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
645 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
646 the currently open URL and links from a page viewed in
647 Firefox or Chrome on Windows is now fully supported. If
648 you are using Edge, only links in the page can be
649 dragged, and with Internet Explorer, only the currently
650 open URL in the browser can be dropped onto Jalview.</em>
656 <td width="60" nowrap>
658 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
661 <td><div align="left">
665 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
666 for disabling automatic superposition of multiple
667 structures and open structures in existing views
670 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
671 ID and annotation area margins can be click-dragged to
675 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
679 <!-- JAL-2759 -->Improved performance for large alignments
680 and lots of hidden columns
683 <!-- JAL-2593 -->Improved performance when rendering lots
684 of features (particularly when transparency is disabled)
687 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
688 exchange of Jalview features and Chimera attributes made
694 <td><div align="left">
697 <!-- JAL-2899 -->Structure and Overview aren't updated
698 when Colour By Annotation threshold slider is adjusted
701 <!-- JAL-2778 -->Slow redraw when Overview panel shown
702 overlapping alignment panel
705 <!-- JAL-2929 -->Overview doesn't show end of unpadded
709 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
710 improved: CDS not handled correctly if transcript has no
714 <!-- JAL-2321 -->Secondary structure and temperature
715 factor annotation not added to sequence when local PDB
716 file associated with it by drag'n'drop or structure
720 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
721 dialog doesn't import PDB files dropped on an alignment
724 <!-- JAL-2666 -->Linked scrolling via protein horizontal
725 scroll bar doesn't work for some CDS/Protein views
728 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
729 Java 1.8u153 onwards and Java 1.9u4+.
732 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
733 columns in annotation row
736 <!-- JAL-2913 -->Preferences panel's ID Width control is not
737 honored in batch mode
740 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
741 for structures added to existing Jmol view
744 <!-- JAL-2223 -->'View Mappings' includes duplicate
745 entries after importing project with multiple views
748 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
749 protein sequences via SIFTS from associated PDB entries
750 with negative residue numbers or missing residues fails
753 <!-- JAL-2952 -->Exception when shading sequence with negative
754 Temperature Factor values from annotated PDB files (e.g.
755 as generated by CONSURF)
758 <!-- JAL-2920 -->Uniprot 'sequence variant' features
759 tooltip doesn't include a text description of mutation
762 <!-- JAL-2922 -->Invert displayed features very slow when
763 structure and/or overview windows are also shown
766 <!-- JAL-2954 -->Selecting columns from highlighted regions
767 very slow for alignments with large numbers of sequences
770 <!-- JAL-2925 -->Copy Consensus fails for group consensus
771 with 'StringIndexOutOfBounds'
774 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
775 platforms running Java 10
778 <!-- JAL-2960 -->Adding a structure to existing structure
779 view appears to do nothing because the view is hidden behind the alignment view
785 <!-- JAL-2926 -->Copy consensus sequence option in applet
786 should copy the group consensus when popup is opened on it
792 <!-- JAL-2913 -->Fixed ID width preference is not respected
795 <em>New Known Defects</em>
798 <!-- JAL-2973 --> Exceptions occasionally raised when
799 editing a large alignment and overview is displayed
802 <!-- JAL-2974 -->'Overview updating' progress bar is shown
803 repeatedly after a series of edits even when the overview
804 is no longer reflecting updates
807 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
808 structures for protein subsequence (if 'Trim Retrieved
809 Sequences' enabled) or Ensembl isoforms (Workaround in
810 2.10.4 is to fail back to N&W mapping)
817 <td width="60" nowrap>
819 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
822 <td><div align="left">
823 <ul><li>Updated Certum Codesigning Certificate
824 (Valid till 30th November 2018)</li></ul></div></td>
825 <td><div align="left">
828 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
829 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
830 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
831 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
832 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
833 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
834 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
840 <td width="60" nowrap>
842 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
845 <td><div align="left">
849 <!-- JAL-2446 -->Faster and more efficient management and
850 rendering of sequence features
853 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
854 429 rate limit request hander
857 <!-- JAL-2773 -->Structure views don't get updated unless
858 their colours have changed
861 <!-- JAL-2495 -->All linked sequences are highlighted for
862 a structure mousover (Jmol) or selection (Chimera)
865 <!-- JAL-2790 -->'Cancel' button in progress bar for
866 JABAWS AACon, RNAAliFold and Disorder prediction jobs
869 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
870 view from Ensembl locus cross-references
873 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
877 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
878 feature can be disabled
881 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
882 PDB easier retrieval of sequences for lists of IDs
885 <!-- JAL-2758 -->Short names for sequences retrieved from
891 <li>Groovy interpreter updated to 2.4.12</li>
892 <li>Example groovy script for generating a matrix of
893 percent identity scores for current alignment.</li>
895 <em>Testing and Deployment</em>
898 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
902 <td><div align="left">
906 <!-- JAL-2643 -->Pressing tab after updating the colour
907 threshold text field doesn't trigger an update to the
911 <!-- JAL-2682 -->Race condition when parsing sequence ID
915 <!-- JAL-2608 -->Overview windows are also closed when
916 alignment window is closed
919 <!-- JAL-2548 -->Export of features doesn't always respect
923 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
924 takes a long time in Cursor mode
930 <!-- JAL-2777 -->Structures with whitespace chainCode
931 cannot be viewed in Chimera
934 <!-- JAL-2728 -->Protein annotation panel too high in
938 <!-- JAL-2757 -->Can't edit the query after the server
939 error warning icon is shown in Uniprot and PDB Free Text
943 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
946 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
949 <!-- JAL-2739 -->Hidden column marker in last column not
950 rendered when switching back from Wrapped to normal view
953 <!-- JAL-2768 -->Annotation display corrupted when
954 scrolling right in unwapped alignment view
957 <!-- JAL-2542 -->Existing features on subsequence
958 incorrectly relocated when full sequence retrieved from
962 <!-- JAL-2733 -->Last reported memory still shown when
963 Desktop->Show Memory is unticked (OSX only)
966 <!-- JAL-2658 -->Amend Features dialog doesn't allow
967 features of same type and group to be selected for
971 <!-- JAL-2524 -->Jalview becomes sluggish in wide
972 alignments when hidden columns are present
975 <!-- JAL-2392 -->Jalview freezes when loading and
976 displaying several structures
979 <!-- JAL-2732 -->Black outlines left after resizing or
983 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
984 within the Jalview desktop on OSX
987 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
988 when in wrapped alignment mode
991 <!-- JAL-2636 -->Scale mark not shown when close to right
992 hand end of alignment
995 <!-- JAL-2684 -->Pairwise alignment of selected regions of
996 each selected sequence do not have correct start/end
1000 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1001 after canceling the Alignment Window's Font dialog
1004 <!-- JAL-2036 -->Show cross-references not enabled after
1005 restoring project until a new view is created
1008 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1009 URL links appears when only default EMBL-EBI link is
1010 configured (since 2.10.2b2)
1013 <!-- JAL-2775 -->Overview redraws whole window when box
1014 position is adjusted
1017 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1018 in a multi-chain structure when viewing alignment
1019 involving more than one chain (since 2.10)
1022 <!-- JAL-2811 -->Double residue highlights in cursor mode
1023 if new selection moves alignment window
1026 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1027 arrow key in cursor mode to pass hidden column marker
1030 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1031 that produces correctly annotated transcripts and products
1034 <!-- JAL-2776 -->Toggling a feature group after first time
1035 doesn't update associated structure view
1038 <em>Applet</em><br />
1041 <!-- JAL-2687 -->Concurrent modification exception when
1042 closing alignment panel
1045 <em>BioJSON</em><br />
1048 <!-- JAL-2546 -->BioJSON export does not preserve
1049 non-positional features
1052 <em>New Known Issues</em>
1055 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1056 sequence features correctly (for many previous versions of
1060 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1061 using cursor in wrapped panel other than top
1064 <!-- JAL-2791 -->Select columns containing feature ignores
1065 graduated colour threshold
1068 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1069 always preserve numbering and sequence features
1072 <em>Known Java 9 Issues</em>
1075 <!-- JAL-2902 -->Groovy Console very slow to open and is
1076 not responsive when entering characters (Webstart, Java
1083 <td width="60" nowrap>
1084 <div align="center">
1085 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1086 <em>2/10/2017</em></strong>
1089 <td><div align="left">
1090 <em>New features in Jalview Desktop</em>
1093 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1095 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1099 <td><div align="left">
1103 <td width="60" nowrap>
1104 <div align="center">
1105 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1106 <em>7/9/2017</em></strong>
1109 <td><div align="left">
1113 <!-- JAL-2588 -->Show gaps in overview window by colouring
1114 in grey (sequences used to be coloured grey, and gaps were
1118 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1122 <!-- JAL-2587 -->Overview updates immediately on increase
1123 in size and progress bar shown as higher resolution
1124 overview is recalculated
1129 <td><div align="left">
1133 <!-- JAL-2664 -->Overview window redraws every hidden
1134 column region row by row
1137 <!-- JAL-2681 -->duplicate protein sequences shown after
1138 retrieving Ensembl crossrefs for sequences from Uniprot
1141 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1142 format setting is unticked
1145 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1146 if group has show boxes format setting unticked
1149 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1150 autoscrolling whilst dragging current selection group to
1151 include sequences and columns not currently displayed
1154 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1155 assemblies are imported via CIF file
1158 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1159 displayed when threshold or conservation colouring is also
1163 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1167 <!-- JAL-2673 -->Jalview continues to scroll after
1168 dragging a selected region off the visible region of the
1172 <!-- JAL-2724 -->Cannot apply annotation based
1173 colourscheme to all groups in a view
1176 <!-- JAL-2511 -->IDs don't line up with sequences
1177 initially after font size change using the Font chooser or
1184 <td width="60" nowrap>
1185 <div align="center">
1186 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1189 <td><div align="left">
1190 <em>Calculations</em>
1194 <!-- JAL-1933 -->Occupancy annotation row shows number of
1195 ungapped positions in each column of the alignment.
1198 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1199 a calculation dialog box
1202 <!-- JAL-2379 -->Revised implementation of PCA for speed
1203 and memory efficiency (~30x faster)
1206 <!-- JAL-2403 -->Revised implementation of sequence
1207 similarity scores as used by Tree, PCA, Shading Consensus
1208 and other calculations
1211 <!-- JAL-2416 -->Score matrices are stored as resource
1212 files within the Jalview codebase
1215 <!-- JAL-2500 -->Trees computed on Sequence Feature
1216 Similarity may have different topology due to increased
1223 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1224 model for alignments and groups
1227 <!-- JAL-384 -->Custom shading schemes created via groovy
1234 <!-- JAL-2526 -->Efficiency improvements for interacting
1235 with alignment and overview windows
1238 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1242 <!-- JAL-2388 -->Hidden columns and sequences can be
1246 <!-- JAL-2611 -->Click-drag in visible area allows fine
1247 adjustment of visible position
1251 <em>Data import/export</em>
1254 <!-- JAL-2535 -->Posterior probability annotation from
1255 Stockholm files imported as sequence associated annotation
1258 <!-- JAL-2507 -->More robust per-sequence positional
1259 annotation input/output via stockholm flatfile
1262 <!-- JAL-2533 -->Sequence names don't include file
1263 extension when importing structure files without embedded
1264 names or PDB accessions
1267 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1268 format sequence substitution matrices
1271 <em>User Interface</em>
1274 <!-- JAL-2447 --> Experimental Features Checkbox in
1275 Desktop's Tools menu to hide or show untested features in
1279 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1280 via Overview or sequence motif search operations
1283 <!-- JAL-2547 -->Amend sequence features dialog box can be
1284 opened by double clicking gaps within sequence feature
1288 <!-- JAL-1476 -->Status bar message shown when not enough
1289 aligned positions were available to create a 3D structure
1293 <em>3D Structure</em>
1296 <!-- JAL-2430 -->Hidden regions in alignment views are not
1297 coloured in linked structure views
1300 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1301 file-based command exchange
1304 <!-- JAL-2375 -->Structure chooser automatically shows
1305 Cached Structures rather than querying the PDBe if
1306 structures are already available for sequences
1309 <!-- JAL-2520 -->Structures imported via URL are cached in
1310 the Jalview project rather than downloaded again when the
1311 project is reopened.
1314 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1315 to transfer Chimera's structure attributes as Jalview
1316 features, and vice-versa (<strong>Experimental
1320 <em>Web Services</em>
1323 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1326 <!-- JAL-2335 -->Filter non-standard amino acids and
1327 nucleotides when submitting to AACon and other MSA
1331 <!-- JAL-2316, -->URLs for viewing database
1332 cross-references provided by identifiers.org and the
1333 EMBL-EBI's MIRIAM DB
1340 <!-- JAL-2344 -->FileFormatI interface for describing and
1341 identifying file formats (instead of String constants)
1344 <!-- JAL-2228 -->FeatureCounter script refactored for
1345 efficiency when counting all displayed features (not
1346 backwards compatible with 2.10.1)
1349 <em>Example files</em>
1352 <!-- JAL-2631 -->Graduated feature colour style example
1353 included in the example feature file
1356 <em>Documentation</em>
1359 <!-- JAL-2339 -->Release notes reformatted for readability
1360 with the built-in Java help viewer
1363 <!-- JAL-1644 -->Find documentation updated with 'search
1364 sequence description' option
1370 <!-- JAL-2485, -->External service integration tests for
1371 Uniprot REST Free Text Search Client
1374 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1377 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1382 <td><div align="left">
1383 <em>Calculations</em>
1386 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1387 matrix - C->R should be '-3'<br />Old matrix restored
1388 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1390 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1391 Jalview's treatment of gaps in PCA and substitution matrix
1392 based Tree calculations.<br /> <br />In earlier versions
1393 of Jalview, gaps matching gaps were penalised, and gaps
1394 matching non-gaps penalised even more. In the PCA
1395 calculation, gaps were actually treated as non-gaps - so
1396 different costs were applied, which meant Jalview's PCAs
1397 were different to those produced by SeqSpace.<br />Jalview
1398 now treats gaps in the same way as SeqSpace (ie it scores
1399 them as 0). <br /> <br />Enter the following in the
1400 Groovy console to restore pre-2.10.2 behaviour:<br />
1401 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1402 // for 2.10.1 mode <br />
1403 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1404 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1405 these settings will affect all subsequent tree and PCA
1406 calculations (not recommended)</em></li>
1408 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1409 scaling of branch lengths for trees computed using
1410 Sequence Feature Similarity.
1413 <!-- JAL-2377 -->PCA calculation could hang when
1414 generating output report when working with highly
1415 redundant alignments
1418 <!-- JAL-2544 --> Sort by features includes features to
1419 right of selected region when gaps present on right-hand
1423 <em>User Interface</em>
1426 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1427 doesn't reselect a specific sequence's associated
1428 annotation after it was used for colouring a view
1431 <!-- JAL-2419 -->Current selection lost if popup menu
1432 opened on a region of alignment without groups
1435 <!-- JAL-2374 -->Popup menu not always shown for regions
1436 of an alignment with overlapping groups
1439 <!-- JAL-2310 -->Finder double counts if both a sequence's
1440 name and description match
1443 <!-- JAL-2370 -->Hiding column selection containing two
1444 hidden regions results in incorrect hidden regions
1447 <!-- JAL-2386 -->'Apply to all groups' setting when
1448 changing colour does not apply Conservation slider value
1452 <!-- JAL-2373 -->Percentage identity and conservation menu
1453 items do not show a tick or allow shading to be disabled
1456 <!-- JAL-2385 -->Conservation shading or PID threshold
1457 lost when base colourscheme changed if slider not visible
1460 <!-- JAL-2547 -->Sequence features shown in tooltip for
1461 gaps before start of features
1464 <!-- JAL-2623 -->Graduated feature colour threshold not
1465 restored to UI when feature colour is edited
1468 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1469 a time when scrolling vertically in wrapped mode.
1472 <!-- JAL-2630 -->Structure and alignment overview update
1473 as graduate feature colour settings are modified via the
1477 <!-- JAL-2034 -->Overview window doesn't always update
1478 when a group defined on the alignment is resized
1481 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1482 wrapped view result in positional status updates
1486 <!-- JAL-2563 -->Status bar doesn't show position for
1487 ambiguous amino acid and nucleotide symbols
1490 <!-- JAL-2602 -->Copy consensus sequence failed if
1491 alignment included gapped columns
1494 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1495 widgets don't permanently disappear
1498 <!-- JAL-2503 -->Cannot select or filter quantitative
1499 annotation that are shown only as column labels (e.g.
1500 T-Coffee column reliability scores)
1503 <!-- JAL-2594 -->Exception thrown if trying to create a
1504 sequence feature on gaps only
1507 <!-- JAL-2504 -->Features created with 'New feature'
1508 button from a Find inherit previously defined feature type
1509 rather than the Find query string
1512 <!-- JAL-2423 -->incorrect title in output window when
1513 exporting tree calculated in Jalview
1516 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1517 and then revealing them reorders sequences on the
1521 <!-- JAL-964 -->Group panel in sequence feature settings
1522 doesn't update to reflect available set of groups after
1523 interactively adding or modifying features
1526 <!-- JAL-2225 -->Sequence Database chooser unusable on
1530 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1531 only excluded gaps in current sequence and ignored
1538 <!-- JAL-2421 -->Overview window visible region moves
1539 erratically when hidden rows or columns are present
1542 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1543 Structure Viewer's colour menu don't correspond to
1547 <!-- JAL-2405 -->Protein specific colours only offered in
1548 colour and group colour menu for protein alignments
1551 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1552 reflect currently selected view or group's shading
1556 <!-- JAL-2624 -->Feature colour thresholds not respected
1557 when rendered on overview and structures when opacity at
1561 <!-- JAL-2589 -->User defined gap colour not shown in
1562 overview when features overlaid on alignment
1565 <!-- JAL-2567 -->Feature settings for different views not
1566 recovered correctly from Jalview project file
1569 <!-- JAL-2256 -->Feature colours in overview when first opened
1570 (automatically via preferences) are different to the main
1574 <em>Data import/export</em>
1577 <!-- JAL-2576 -->Very large alignments take a long time to
1581 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1582 added after a sequence was imported are not written to
1586 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1587 when importing RNA secondary structure via Stockholm
1590 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1591 not shown in correct direction for simple pseudoknots
1594 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1595 with lightGray or darkGray via features file (but can
1599 <!-- JAL-2383 -->Above PID colour threshold not recovered
1600 when alignment view imported from project
1603 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1604 structure and sequences extracted from structure files
1605 imported via URL and viewed in Jmol
1608 <!-- JAL-2520 -->Structures loaded via URL are saved in
1609 Jalview Projects rather than fetched via URL again when
1610 the project is loaded and the structure viewed
1613 <em>Web Services</em>
1616 <!-- JAL-2519 -->EnsemblGenomes example failing after
1617 release of Ensembl v.88
1620 <!-- JAL-2366 -->Proxy server address and port always
1621 appear enabled in Preferences->Connections
1624 <!-- JAL-2461 -->DAS registry not found exceptions
1625 removed from console output
1628 <!-- JAL-2582 -->Cannot retrieve protein products from
1629 Ensembl by Peptide ID
1632 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1633 created from SIFTs, and spurious 'Couldn't open structure
1634 in Chimera' errors raised after April 2017 update (problem
1635 due to 'null' string rather than empty string used for
1636 residues with no corresponding PDB mapping).
1639 <em>Application UI</em>
1642 <!-- JAL-2361 -->User Defined Colours not added to Colour
1646 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1647 case' residues (button in colourscheme editor debugged and
1648 new documentation and tooltips added)
1651 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1652 doesn't restore group-specific text colour thresholds
1655 <!-- JAL-2243 -->Feature settings panel does not update as
1656 new features are added to alignment
1659 <!-- JAL-2532 -->Cancel in feature settings reverts
1660 changes to feature colours via the Amend features dialog
1663 <!-- JAL-2506 -->Null pointer exception when attempting to
1664 edit graduated feature colour via amend features dialog
1668 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1669 selection menu changes colours of alignment views
1672 <!-- JAL-2426 -->Spurious exceptions in console raised
1673 from alignment calculation workers after alignment has
1677 <!-- JAL-1608 -->Typo in selection popup menu - Create
1678 groups now 'Create Group'
1681 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1682 Create/Undefine group doesn't always work
1685 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1686 shown again after pressing 'Cancel'
1689 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1690 adjusts start position in wrap mode
1693 <!-- JAL-2563 -->Status bar doesn't show positions for
1694 ambiguous amino acids
1697 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1698 CDS/Protein view after CDS sequences added for aligned
1702 <!-- JAL-2592 -->User defined colourschemes called 'User
1703 Defined' don't appear in Colours menu
1709 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1710 score models doesn't always result in an updated PCA plot
1713 <!-- JAL-2442 -->Features not rendered as transparent on
1714 overview or linked structure view
1717 <!-- JAL-2372 -->Colour group by conservation doesn't
1721 <!-- JAL-2517 -->Hitting Cancel after applying
1722 user-defined colourscheme doesn't restore original
1729 <!-- JAL-2314 -->Unit test failure:
1730 jalview.ws.jabaws.RNAStructExportImport setup fails
1733 <!-- JAL-2307 -->Unit test failure:
1734 jalview.ws.sifts.SiftsClientTest due to compatibility
1735 problems with deep array comparison equality asserts in
1736 successive versions of TestNG
1739 <!-- JAL-2479 -->Relocated StructureChooserTest and
1740 ParameterUtilsTest Unit tests to Network suite
1743 <em>New Known Issues</em>
1746 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1747 phase after a sequence motif find operation
1750 <!-- JAL-2550 -->Importing annotation file with rows
1751 containing just upper and lower case letters are
1752 interpreted as WUSS RNA secondary structure symbols
1755 <!-- JAL-2590 -->Cannot load and display Newick trees
1756 reliably from eggnog Ortholog database
1759 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1760 containing features of type Highlight' when 'B' is pressed
1761 to mark columns containing highlighted regions.
1764 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1765 doesn't always add secondary structure annotation.
1770 <td width="60" nowrap>
1771 <div align="center">
1772 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1775 <td><div align="left">
1779 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1780 for all consensus calculations
1783 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1786 <li>Updated Jalview's Certum code signing certificate
1789 <em>Application</em>
1792 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1793 set of database cross-references, sorted alphabetically
1796 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1797 from database cross references. Users with custom links
1798 will receive a <a href="webServices/urllinks.html#warning">warning
1799 dialog</a> asking them to update their preferences.
1802 <!-- JAL-2287-->Cancel button and escape listener on
1803 dialog warning user about disconnecting Jalview from a
1807 <!-- JAL-2320-->Jalview's Chimera control window closes if
1808 the Chimera it is connected to is shut down
1811 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1812 columns menu item to mark columns containing highlighted
1813 regions (e.g. from structure selections or results of a
1817 <!-- JAL-2284-->Command line option for batch-generation
1818 of HTML pages rendering alignment data with the BioJS
1828 <!-- JAL-2286 -->Columns with more than one modal residue
1829 are not coloured or thresholded according to percent
1830 identity (first observed in Jalview 2.8.2)
1833 <!-- JAL-2301 -->Threonine incorrectly reported as not
1837 <!-- JAL-2318 -->Updates to documentation pages (above PID
1838 threshold, amino acid properties)
1841 <!-- JAL-2292 -->Lower case residues in sequences are not
1842 reported as mapped to residues in a structure file in the
1846 <!--JAL-2324 -->Identical features with non-numeric scores
1847 could be added multiple times to a sequence
1850 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1851 bond features shown as two highlighted residues rather
1852 than a range in linked structure views, and treated
1853 correctly when selecting and computing trees from features
1856 <!-- JAL-2281-->Custom URL links for database
1857 cross-references are matched to database name regardless
1862 <em>Application</em>
1865 <!-- JAL-2282-->Custom URL links for specific database
1866 names without regular expressions also offer links from
1870 <!-- JAL-2315-->Removing a single configured link in the
1871 URL links pane in Connections preferences doesn't actually
1872 update Jalview configuration
1875 <!-- JAL-2272-->CTRL-Click on a selected region to open
1876 the alignment area popup menu doesn't work on El-Capitan
1879 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1880 files with similarly named sequences if dropped onto the
1884 <!-- JAL-2312 -->Additional mappings are shown for PDB
1885 entries where more chains exist in the PDB accession than
1886 are reported in the SIFTS file
1889 <!-- JAL-2317-->Certain structures do not get mapped to
1890 the structure view when displayed with Chimera
1893 <!-- JAL-2317-->No chains shown in the Chimera view
1894 panel's View->Show Chains submenu
1897 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1898 work for wrapped alignment views
1901 <!--JAL-2197 -->Rename UI components for running JPred
1902 predictions from 'JNet' to 'JPred'
1905 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1906 corrupted when annotation panel vertical scroll is not at
1907 first annotation row
1910 <!--JAL-2332 -->Attempting to view structure for Hen
1911 lysozyme results in a PDB Client error dialog box
1914 <!-- JAL-2319 -->Structure View's mapping report switched
1915 ranges for PDB and sequence for SIFTS
1918 SIFTS 'Not_Observed' residues mapped to non-existant
1922 <!-- <em>New Known Issues</em>
1929 <td width="60" nowrap>
1930 <div align="center">
1931 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1932 <em>25/10/2016</em></strong>
1935 <td><em>Application</em>
1937 <li>3D Structure chooser opens with 'Cached structures'
1938 view if structures already loaded</li>
1939 <li>Progress bar reports models as they are loaded to
1940 structure views</li>
1946 <li>Colour by conservation always enabled and no tick
1947 shown in menu when BLOSUM or PID shading applied</li>
1948 <li>FER1_ARATH and FER2_ARATH labels were switched in
1949 example sequences/projects/trees</li>
1951 <em>Application</em>
1953 <li>Jalview projects with views of local PDB structure
1954 files saved on Windows cannot be opened on OSX</li>
1955 <li>Multiple structure views can be opened and superposed
1956 without timeout for structures with multiple models or
1957 multiple sequences in alignment</li>
1958 <li>Cannot import or associated local PDB files without a
1959 PDB ID HEADER line</li>
1960 <li>RMSD is not output in Jmol console when superposition
1962 <li>Drag and drop of URL from Browser fails for Linux and
1963 OSX versions earlier than El Capitan</li>
1964 <li>ENA client ignores invalid content from ENA server</li>
1965 <li>Exceptions are not raised in console when ENA client
1966 attempts to fetch non-existent IDs via Fetch DB Refs UI
1968 <li>Exceptions are not raised in console when a new view
1969 is created on the alignment</li>
1970 <li>OSX right-click fixed for group selections: CMD-click
1971 to insert/remove gaps in groups and CTRL-click to open group
1974 <em>Build and deployment</em>
1976 <li>URL link checker now copes with multi-line anchor
1979 <em>New Known Issues</em>
1981 <li>Drag and drop from URL links in browsers do not work
1988 <td width="60" nowrap>
1989 <div align="center">
1990 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1993 <td><em>General</em>
1996 <!-- JAL-2124 -->Updated Spanish translations.
1999 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2000 for importing structure data to Jalview. Enables mmCIF and
2004 <!-- JAL-192 --->Alignment ruler shows positions relative to
2008 <!-- JAL-2202 -->Position/residue shown in status bar when
2009 mousing over sequence associated annotation
2012 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2016 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2017 '()', canonical '[]' and invalid '{}' base pair populations
2021 <!-- JAL-2092 -->Feature settings popup menu options for
2022 showing or hiding columns containing a feature
2025 <!-- JAL-1557 -->Edit selected group by double clicking on
2026 group and sequence associated annotation labels
2029 <!-- JAL-2236 -->Sequence name added to annotation label in
2030 select/hide columns by annotation and colour by annotation
2034 </ul> <em>Application</em>
2037 <!-- JAL-2050-->Automatically hide introns when opening a
2038 gene/transcript view
2041 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2045 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2046 structure mappings with the EMBL-EBI PDBe SIFTS database
2049 <!-- JAL-2079 -->Updated download sites used for Rfam and
2050 Pfam sources to xfam.org
2053 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2056 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2057 over sequences in Jalview
2060 <!-- JAL-2027-->Support for reverse-complement coding
2061 regions in ENA and EMBL
2064 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2065 for record retrieval via ENA rest API
2068 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2072 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2073 groovy script execution
2076 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2077 alignment window's Calculate menu
2080 <!-- JAL-1812 -->Allow groovy scripts that call
2081 Jalview.getAlignFrames() to run in headless mode
2084 <!-- JAL-2068 -->Support for creating new alignment
2085 calculation workers from groovy scripts
2088 <!-- JAL-1369 --->Store/restore reference sequence in
2092 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2093 associations are now saved/restored from project
2096 <!-- JAL-1993 -->Database selection dialog always shown
2097 before sequence fetcher is opened
2100 <!-- JAL-2183 -->Double click on an entry in Jalview's
2101 database chooser opens a sequence fetcher
2104 <!-- JAL-1563 -->Free-text search client for UniProt using
2105 the UniProt REST API
2108 <!-- JAL-2168 -->-nonews command line parameter to prevent
2109 the news reader opening
2112 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2113 querying stored in preferences
2116 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2120 <!-- JAL-1977-->Tooltips shown on database chooser
2123 <!-- JAL-391 -->Reverse complement function in calculate
2124 menu for nucleotide sequences
2127 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2128 and feature counts preserves alignment ordering (and
2129 debugged for complex feature sets).
2132 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2133 viewing structures with Jalview 2.10
2136 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2137 genome, transcript CCDS and gene ids via the Ensembl and
2138 Ensembl Genomes REST API
2141 <!-- JAL-2049 -->Protein sequence variant annotation
2142 computed for 'sequence_variant' annotation on CDS regions
2146 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2150 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2151 Ref Fetcher fails to match, or otherwise updates sequence
2152 data from external database records.
2155 <!-- JAL-2154 -->Revised Jalview Project format for
2156 efficient recovery of sequence coding and alignment
2157 annotation relationships.
2159 </ul> <!-- <em>Applet</em>
2170 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2174 <!-- JAL-2018-->Export features in Jalview format (again)
2175 includes graduated colourschemes
2178 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2179 working with big alignments and lots of hidden columns
2182 <!-- JAL-2053-->Hidden column markers not always rendered
2183 at right of alignment window
2186 <!-- JAL-2067 -->Tidied up links in help file table of
2190 <!-- JAL-2072 -->Feature based tree calculation not shown
2194 <!-- JAL-2075 -->Hidden columns ignored during feature
2195 based tree calculation
2198 <!-- JAL-2065 -->Alignment view stops updating when show
2199 unconserved enabled for group on alignment
2202 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2206 <!-- JAL-2146 -->Alignment column in status incorrectly
2207 shown as "Sequence position" when mousing over
2211 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2212 hidden columns present
2215 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2216 user created annotation added to alignment
2219 <!-- JAL-1841 -->RNA Structure consensus only computed for
2220 '()' base pair annotation
2223 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2224 in zero scores for all base pairs in RNA Structure
2228 <!-- JAL-2174-->Extend selection with columns containing
2232 <!-- JAL-2275 -->Pfam format writer puts extra space at
2233 beginning of sequence
2236 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2240 <!-- JAL-2238 -->Cannot create groups on an alignment from
2241 from a tree when t-coffee scores are shown
2244 <!-- JAL-1836,1967 -->Cannot import and view PDB
2245 structures with chains containing negative resnums (4q4h)
2248 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2252 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2253 to Clustal, PIR and PileUp output
2256 <!-- JAL-2008 -->Reordering sequence features that are
2257 not visible causes alignment window to repaint
2260 <!-- JAL-2006 -->Threshold sliders don't work in
2261 graduated colour and colour by annotation row for e-value
2262 scores associated with features and annotation rows
2265 <!-- JAL-1797 -->amino acid physicochemical conservation
2266 calculation should be case independent
2269 <!-- JAL-2173 -->Remove annotation also updates hidden
2273 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2274 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2275 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2278 <!-- JAL-2065 -->Null pointer exceptions and redraw
2279 problems when reference sequence defined and 'show
2280 non-conserved' enabled
2283 <!-- JAL-1306 -->Quality and Conservation are now shown on
2284 load even when Consensus calculation is disabled
2287 <!-- JAL-1932 -->Remove right on penultimate column of
2288 alignment does nothing
2291 <em>Application</em>
2294 <!-- JAL-1552-->URLs and links can't be imported by
2295 drag'n'drop on OSX when launched via webstart (note - not
2296 yet fixed for El Capitan)
2299 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2300 output when running on non-gb/us i18n platforms
2303 <!-- JAL-1944 -->Error thrown when exporting a view with
2304 hidden sequences as flat-file alignment
2307 <!-- JAL-2030-->InstallAnywhere distribution fails when
2311 <!-- JAL-2080-->Jalview very slow to launch via webstart
2312 (also hotfix for 2.9.0b2)
2315 <!-- JAL-2085 -->Cannot save project when view has a
2316 reference sequence defined
2319 <!-- JAL-1011 -->Columns are suddenly selected in other
2320 alignments and views when revealing hidden columns
2323 <!-- JAL-1989 -->Hide columns not mirrored in complement
2324 view in a cDNA/Protein splitframe
2327 <!-- JAL-1369 -->Cannot save/restore representative
2328 sequence from project when only one sequence is
2332 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2333 in Structure Chooser
2336 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2337 structure consensus didn't refresh annotation panel
2340 <!-- JAL-1962 -->View mapping in structure view shows
2341 mappings between sequence and all chains in a PDB file
2344 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2345 dialogs format columns correctly, don't display array
2346 data, sort columns according to type
2349 <!-- JAL-1975 -->Export complete shown after destination
2350 file chooser is cancelled during an image export
2353 <!-- JAL-2025 -->Error when querying PDB Service with
2354 sequence name containing special characters
2357 <!-- JAL-2024 -->Manual PDB structure querying should be
2361 <!-- JAL-2104 -->Large tooltips with broken HTML
2362 formatting don't wrap
2365 <!-- JAL-1128 -->Figures exported from wrapped view are
2366 truncated so L looks like I in consensus annotation
2369 <!-- JAL-2003 -->Export features should only export the
2370 currently displayed features for the current selection or
2374 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2375 after fetching cross-references, and restoring from
2379 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2380 followed in the structure viewer
2383 <!-- JAL-2163 -->Titles for individual alignments in
2384 splitframe not restored from project
2387 <!-- JAL-2145 -->missing autocalculated annotation at
2388 trailing end of protein alignment in transcript/product
2389 splitview when pad-gaps not enabled by default
2392 <!-- JAL-1797 -->amino acid physicochemical conservation
2396 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2397 article has been read (reopened issue due to
2398 internationalisation problems)
2401 <!-- JAL-1960 -->Only offer PDB structures in structure
2402 viewer based on sequence name, PDB and UniProt
2407 <!-- JAL-1976 -->No progress bar shown during export of
2411 <!-- JAL-2213 -->Structures not always superimposed after
2412 multiple structures are shown for one or more sequences.
2415 <!-- JAL-1370 -->Reference sequence characters should not
2416 be replaced with '.' when 'Show unconserved' format option
2420 <!-- JAL-1823 -->Cannot specify chain code when entering
2421 specific PDB id for sequence
2424 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2425 'Export hidden sequences' is enabled, but 'export hidden
2426 columns' is disabled.
2429 <!--JAL-2026-->Best Quality option in structure chooser
2430 selects lowest rather than highest resolution structures
2434 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2435 to sequence mapping in 'View Mappings' report
2438 <!-- JAL-2284 -->Unable to read old Jalview projects that
2439 contain non-XML data added after Jalvew wrote project.
2442 <!-- JAL-2118 -->Newly created annotation row reorders
2443 after clicking on it to create new annotation for a
2447 <!-- JAL-1980 -->Null Pointer Exception raised when
2448 pressing Add on an orphaned cut'n'paste window.
2450 <!-- may exclude, this is an external service stability issue JAL-1941
2451 -- > RNA 3D structure not added via DSSR service</li> -->
2456 <!-- JAL-2151 -->Incorrect columns are selected when
2457 hidden columns present before start of sequence
2460 <!-- JAL-1986 -->Missing dependencies on applet pages
2464 <!-- JAL-1947 -->Overview pixel size changes when
2465 sequences are hidden in applet
2468 <!-- JAL-1996 -->Updated instructions for applet
2469 deployment on examples pages.
2476 <td width="60" nowrap>
2477 <div align="center">
2478 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2479 <em>16/10/2015</em></strong>
2482 <td><em>General</em>
2484 <li>Time stamps for signed Jalview application and applet
2489 <em>Application</em>
2491 <li>Duplicate group consensus and conservation rows
2492 shown when tree is partitioned</li>
2493 <li>Erratic behaviour when tree partitions made with
2494 multiple cDNA/Protein split views</li>
2500 <td width="60" nowrap>
2501 <div align="center">
2502 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2503 <em>8/10/2015</em></strong>
2506 <td><em>General</em>
2508 <li>Updated Spanish translations of localized text for
2510 </ul> <em>Application</em>
2512 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2513 <li>Signed OSX InstallAnywhere installer<br></li>
2514 <li>Support for per-sequence based annotations in BioJSON</li>
2515 </ul> <em>Applet</em>
2517 <li>Split frame example added to applet examples page</li>
2518 </ul> <em>Build and Deployment</em>
2521 <!-- JAL-1888 -->New ant target for running Jalview's test
2529 <li>Mapping of cDNA to protein in split frames
2530 incorrect when sequence start > 1</li>
2531 <li>Broken images in filter column by annotation dialog
2533 <li>Feature colours not parsed from features file</li>
2534 <li>Exceptions and incomplete link URLs recovered when
2535 loading a features file containing HTML tags in feature
2539 <em>Application</em>
2541 <li>Annotations corrupted after BioJS export and
2543 <li>Incorrect sequence limits after Fetch DB References
2544 with 'trim retrieved sequences'</li>
2545 <li>Incorrect warning about deleting all data when
2546 deleting selected columns</li>
2547 <li>Patch to build system for shipping properly signed
2548 JNLP templates for webstart launch</li>
2549 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2550 unreleased structures for download or viewing</li>
2551 <li>Tab/space/return keystroke operation of EMBL-PDBe
2552 fetcher/viewer dialogs works correctly</li>
2553 <li>Disabled 'minimise' button on Jalview windows
2554 running on OSX to workaround redraw hang bug</li>
2555 <li>Split cDNA/Protein view position and geometry not
2556 recovered from jalview project</li>
2557 <li>Initial enabled/disabled state of annotation menu
2558 sorter 'show autocalculated first/last' corresponds to
2560 <li>Restoring of Clustal, RNA Helices and T-Coffee
2561 color schemes from BioJSON</li>
2565 <li>Reorder sequences mirrored in cDNA/Protein split
2567 <li>Applet with Jmol examples not loading correctly</li>
2573 <td><div align="center">
2574 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2576 <td><em>General</em>
2578 <li>Linked visualisation and analysis of DNA and Protein
2581 <li>Translated cDNA alignments shown as split protein
2582 and DNA alignment views</li>
2583 <li>Codon consensus annotation for linked protein and
2584 cDNA alignment views</li>
2585 <li>Link cDNA or Protein product sequences by loading
2586 them onto Protein or cDNA alignments</li>
2587 <li>Reconstruct linked cDNA alignment from aligned
2588 protein sequences</li>
2591 <li>Jmol integration updated to Jmol v14.2.14</li>
2592 <li>Import and export of Jalview alignment views as <a
2593 href="features/bioJsonFormat.html">BioJSON</a></li>
2594 <li>New alignment annotation file statements for
2595 reference sequences and marking hidden columns</li>
2596 <li>Reference sequence based alignment shading to
2597 highlight variation</li>
2598 <li>Select or hide columns according to alignment
2600 <li>Find option for locating sequences by description</li>
2601 <li>Conserved physicochemical properties shown in amino
2602 acid conservation row</li>
2603 <li>Alignments can be sorted by number of RNA helices</li>
2604 </ul> <em>Application</em>
2606 <li>New cDNA/Protein analysis capabilities
2608 <li>Get Cross-References should open a Split Frame
2609 view with cDNA/Protein</li>
2610 <li>Detect when nucleotide sequences and protein
2611 sequences are placed in the same alignment</li>
2612 <li>Split cDNA/Protein views are saved in Jalview
2617 <li>Use REST API to talk to Chimera</li>
2618 <li>Selected regions in Chimera are highlighted in linked
2619 Jalview windows</li>
2621 <li>VARNA RNA viewer updated to v3.93</li>
2622 <li>VARNA views are saved in Jalview Projects</li>
2623 <li>Pseudoknots displayed as Jalview RNA annotation can
2624 be shown in VARNA</li>
2626 <li>Make groups for selection uses marked columns as well
2627 as the active selected region</li>
2629 <li>Calculate UPGMA and NJ trees using sequence feature
2631 <li>New Export options
2633 <li>New Export Settings dialog to control hidden
2634 region export in flat file generation</li>
2636 <li>Export alignment views for display with the <a
2637 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2639 <li>Export scrollable SVG in HTML page</li>
2640 <li>Optional embedding of BioJSON data when exporting
2641 alignment figures to HTML</li>
2643 <li>3D structure retrieval and display
2645 <li>Free text and structured queries with the PDBe
2647 <li>PDBe Search API based discovery and selection of
2648 PDB structures for a sequence set</li>
2652 <li>JPred4 employed for protein secondary structure
2654 <li>Hide Insertions menu option to hide unaligned columns
2655 for one or a group of sequences</li>
2656 <li>Automatically hide insertions in alignments imported
2657 from the JPred4 web server</li>
2658 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2659 system on OSX<br />LGPL libraries courtesy of <a
2660 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2662 <li>changed 'View nucleotide structure' submenu to 'View
2663 VARNA 2D Structure'</li>
2664 <li>change "View protein structure" menu option to "3D
2667 </ul> <em>Applet</em>
2669 <li>New layout for applet example pages</li>
2670 <li>New parameters to enable SplitFrame view
2671 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2672 <li>New example demonstrating linked viewing of cDNA and
2673 Protein alignments</li>
2674 </ul> <em>Development and deployment</em>
2676 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2677 <li>Include installation type and git revision in build
2678 properties and console log output</li>
2679 <li>Jalview Github organisation, and new github site for
2680 storing BioJsMSA Templates</li>
2681 <li>Jalview's unit tests now managed with TestNG</li>
2684 <!-- <em>General</em>
2686 </ul> --> <!-- issues resolved --> <em>Application</em>
2688 <li>Escape should close any open find dialogs</li>
2689 <li>Typo in select-by-features status report</li>
2690 <li>Consensus RNA secondary secondary structure
2691 predictions are not highlighted in amber</li>
2692 <li>Missing gap character in v2.7 example file means
2693 alignment appears unaligned when pad-gaps is not enabled</li>
2694 <li>First switch to RNA Helices colouring doesn't colour
2695 associated structure views</li>
2696 <li>ID width preference option is greyed out when auto
2697 width checkbox not enabled</li>
2698 <li>Stopped a warning dialog from being shown when
2699 creating user defined colours</li>
2700 <li>'View Mapping' in structure viewer shows sequence
2701 mappings for just that viewer's sequences</li>
2702 <li>Workaround for superposing PDB files containing
2703 multiple models in Chimera</li>
2704 <li>Report sequence position in status bar when hovering
2705 over Jmol structure</li>
2706 <li>Cannot output gaps as '.' symbols with Selection ->
2707 output to text box</li>
2708 <li>Flat file exports of alignments with hidden columns
2709 have incorrect sequence start/end</li>
2710 <li>'Aligning' a second chain to a Chimera structure from
2712 <li>Colour schemes applied to structure viewers don't
2713 work for nucleotide</li>
2714 <li>Loading/cut'n'pasting an empty or invalid file leads
2715 to a grey/invisible alignment window</li>
2716 <li>Exported Jpred annotation from a sequence region
2717 imports to different position</li>
2718 <li>Space at beginning of sequence feature tooltips shown
2719 on some platforms</li>
2720 <li>Chimera viewer 'View | Show Chain' menu is not
2722 <li>'New View' fails with a Null Pointer Exception in
2723 console if Chimera has been opened</li>
2724 <li>Mouseover to Chimera not working</li>
2725 <li>Miscellaneous ENA XML feature qualifiers not
2727 <li>NPE in annotation renderer after 'Extract Scores'</li>
2728 <li>If two structures in one Chimera window, mouseover of
2729 either sequence shows on first structure</li>
2730 <li>'Show annotations' options should not make
2731 non-positional annotations visible</li>
2732 <li>Subsequence secondary structure annotation not shown
2733 in right place after 'view flanking regions'</li>
2734 <li>File Save As type unset when current file format is
2736 <li>Save as '.jar' option removed for saving Jalview
2738 <li>Colour by Sequence colouring in Chimera more
2740 <li>Cannot 'add reference annotation' for a sequence in
2741 several views on same alignment</li>
2742 <li>Cannot show linked products for EMBL / ENA records</li>
2743 <li>Jalview's tooltip wraps long texts containing no
2745 </ul> <em>Applet</em>
2747 <li>Jmol to JalviewLite mouseover/link not working</li>
2748 <li>JalviewLite can't import sequences with ID
2749 descriptions containing angle brackets</li>
2750 </ul> <em>General</em>
2752 <li>Cannot export and reimport RNA secondary structure
2753 via jalview annotation file</li>
2754 <li>Random helix colour palette for colour by annotation
2755 with RNA secondary structure</li>
2756 <li>Mouseover to cDNA from STOP residue in protein
2757 translation doesn't work.</li>
2758 <li>hints when using the select by annotation dialog box</li>
2759 <li>Jmol alignment incorrect if PDB file has alternate CA
2761 <li>FontChooser message dialog appears to hang after
2762 choosing 1pt font</li>
2763 <li>Peptide secondary structure incorrectly imported from
2764 annotation file when annotation display text includes 'e' or
2766 <li>Cannot set colour of new feature type whilst creating
2768 <li>cDNA translation alignment should not be sequence
2769 order dependent</li>
2770 <li>'Show unconserved' doesn't work for lower case
2772 <li>Nucleotide ambiguity codes involving R not recognised</li>
2773 </ul> <em>Deployment and Documentation</em>
2775 <li>Applet example pages appear different to the rest of
2776 www.jalview.org</li>
2777 </ul> <em>Application Known issues</em>
2779 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2780 <li>Misleading message appears after trying to delete
2782 <li>Jalview icon not shown in dock after InstallAnywhere
2783 version launches</li>
2784 <li>Fetching EMBL reference for an RNA sequence results
2785 fails with a sequence mismatch</li>
2786 <li>Corrupted or unreadable alignment display when
2787 scrolling alignment to right</li>
2788 <li>ArrayIndexOutOfBoundsException thrown when remove
2789 empty columns called on alignment with ragged gapped ends</li>
2790 <li>auto calculated alignment annotation rows do not get
2791 placed above or below non-autocalculated rows</li>
2792 <li>Jalview dekstop becomes sluggish at full screen in
2793 ultra-high resolution</li>
2794 <li>Cannot disable consensus calculation independently of
2795 quality and conservation</li>
2796 <li>Mouseover highlighting between cDNA and protein can
2797 become sluggish with more than one splitframe shown</li>
2798 </ul> <em>Applet Known Issues</em>
2800 <li>Core PDB parsing code requires Jmol</li>
2801 <li>Sequence canvas panel goes white when alignment
2802 window is being resized</li>
2808 <td><div align="center">
2809 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2811 <td><em>General</em>
2813 <li>Updated Java code signing certificate donated by
2815 <li>Features and annotation preserved when performing
2816 pairwise alignment</li>
2817 <li>RNA pseudoknot annotation can be
2818 imported/exported/displayed</li>
2819 <li>'colour by annotation' can colour by RNA and
2820 protein secondary structure</li>
2821 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2822 post-hoc with 2.9 release</em>)
2825 </ul> <em>Application</em>
2827 <li>Extract and display secondary structure for sequences
2828 with 3D structures</li>
2829 <li>Support for parsing RNAML</li>
2830 <li>Annotations menu for layout
2832 <li>sort sequence annotation rows by alignment</li>
2833 <li>place sequence annotation above/below alignment
2836 <li>Output in Stockholm format</li>
2837 <li>Internationalisation: improved Spanish (es)
2839 <li>Structure viewer preferences tab</li>
2840 <li>Disorder and Secondary Structure annotation tracks
2841 shared between alignments</li>
2842 <li>UCSF Chimera launch and linked highlighting from
2844 <li>Show/hide all sequence associated annotation rows for
2845 all or current selection</li>
2846 <li>disorder and secondary structure predictions
2847 available as dataset annotation</li>
2848 <li>Per-sequence rna helices colouring</li>
2851 <li>Sequence database accessions imported when fetching
2852 alignments from Rfam</li>
2853 <li>update VARNA version to 3.91</li>
2855 <li>New groovy scripts for exporting aligned positions,
2856 conservation values, and calculating sum of pairs scores.</li>
2857 <li>Command line argument to set default JABAWS server</li>
2858 <li>include installation type in build properties and
2859 console log output</li>
2860 <li>Updated Jalview project format to preserve dataset
2864 <!-- issues resolved --> <em>Application</em>
2866 <li>Distinguish alignment and sequence associated RNA
2867 structure in structure->view->VARNA</li>
2868 <li>Raise dialog box if user deletes all sequences in an
2870 <li>Pressing F1 results in documentation opening twice</li>
2871 <li>Sequence feature tooltip is wrapped</li>
2872 <li>Double click on sequence associated annotation
2873 selects only first column</li>
2874 <li>Redundancy removal doesn't result in unlinked
2875 leaves shown in tree</li>
2876 <li>Undos after several redundancy removals don't undo
2878 <li>Hide sequence doesn't hide associated annotation</li>
2879 <li>User defined colours dialog box too big to fit on
2880 screen and buttons not visible</li>
2881 <li>author list isn't updated if already written to
2882 Jalview properties</li>
2883 <li>Popup menu won't open after retrieving sequence
2885 <li>File open window for associate PDB doesn't open</li>
2886 <li>Left-then-right click on a sequence id opens a
2887 browser search window</li>
2888 <li>Cannot open sequence feature shading/sort popup menu
2889 in feature settings dialog</li>
2890 <li>better tooltip placement for some areas of Jalview
2892 <li>Allow addition of JABAWS Server which doesn't
2893 pass validation</li>
2894 <li>Web services parameters dialog box is too large to
2896 <li>Muscle nucleotide alignment preset obscured by
2898 <li>JABAWS preset submenus don't contain newly
2899 defined user preset</li>
2900 <li>MSA web services warns user if they were launched
2901 with invalid input</li>
2902 <li>Jalview cannot contact DAS Registy when running on
2905 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2906 'Superpose with' submenu not shown when new view
2910 </ul> <!-- <em>Applet</em>
2912 </ul> <em>General</em>
2914 </ul>--> <em>Deployment and Documentation</em>
2916 <li>2G and 1G options in launchApp have no effect on
2917 memory allocation</li>
2918 <li>launchApp service doesn't automatically open
2919 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2921 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2922 InstallAnywhere reports cannot find valid JVM when Java
2923 1.7_055 is available
2925 </ul> <em>Application Known issues</em>
2928 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2929 corrupted or unreadable alignment display when scrolling
2933 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2934 retrieval fails but progress bar continues for DAS retrieval
2935 with large number of ID
2938 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2939 flatfile output of visible region has incorrect sequence
2943 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2944 rna structure consensus doesn't update when secondary
2945 structure tracks are rearranged
2948 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2949 invalid rna structure positional highlighting does not
2950 highlight position of invalid base pairs
2953 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2954 out of memory errors are not raised when saving Jalview
2955 project from alignment window file menu
2958 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2959 Switching to RNA Helices colouring doesn't propagate to
2963 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2964 colour by RNA Helices not enabled when user created
2965 annotation added to alignment
2968 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2969 Jalview icon not shown on dock in Mountain Lion/Webstart
2971 </ul> <em>Applet Known Issues</em>
2974 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2975 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2978 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2979 Jalview and Jmol example not compatible with IE9
2982 <li>Sort by annotation score doesn't reverse order
2988 <td><div align="center">
2989 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2992 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2995 <li>Internationalisation of user interface (usually
2996 called i18n support) and translation for Spanish locale</li>
2997 <li>Define/Undefine group on current selection with
2998 Ctrl-G/Shift Ctrl-G</li>
2999 <li>Improved group creation/removal options in
3000 alignment/sequence Popup menu</li>
3001 <li>Sensible precision for symbol distribution
3002 percentages shown in logo tooltip.</li>
3003 <li>Annotation panel height set according to amount of
3004 annotation when alignment first opened</li>
3005 </ul> <em>Application</em>
3007 <li>Interactive consensus RNA secondary structure
3008 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3009 <li>Select columns containing particular features from
3010 Feature Settings dialog</li>
3011 <li>View all 'representative' PDB structures for selected
3013 <li>Update Jalview project format:
3015 <li>New file extension for Jalview projects '.jvp'</li>
3016 <li>Preserve sequence and annotation dataset (to
3017 store secondary structure annotation,etc)</li>
3018 <li>Per group and alignment annotation and RNA helix
3022 <li>New similarity measures for PCA and Tree calculation
3024 <li>Experimental support for retrieval and viewing of
3025 flanking regions for an alignment</li>
3029 <!-- issues resolved --> <em>Application</em>
3031 <li>logo keeps spinning and status remains at queued or
3032 running after job is cancelled</li>
3033 <li>cannot export features from alignments imported from
3034 Jalview/VAMSAS projects</li>
3035 <li>Buggy slider for web service parameters that take
3037 <li>Newly created RNA secondary structure line doesn't
3038 have 'display all symbols' flag set</li>
3039 <li>T-COFFEE alignment score shading scheme and other
3040 annotation shading not saved in Jalview project</li>
3041 <li>Local file cannot be loaded in freshly downloaded
3043 <li>Jalview icon not shown on dock in Mountain
3045 <li>Load file from desktop file browser fails</li>
3046 <li>Occasional NPE thrown when calculating large trees</li>
3047 <li>Cannot reorder or slide sequences after dragging an
3048 alignment onto desktop</li>
3049 <li>Colour by annotation dialog throws NPE after using
3050 'extract scores' function</li>
3051 <li>Loading/cut'n'pasting an empty file leads to a grey
3052 alignment window</li>
3053 <li>Disorder thresholds rendered incorrectly after
3054 performing IUPred disorder prediction</li>
3055 <li>Multiple group annotated consensus rows shown when
3056 changing 'normalise logo' display setting</li>
3057 <li>Find shows blank dialog after 'finished searching' if
3058 nothing matches query</li>
3059 <li>Null Pointer Exceptions raised when sorting by
3060 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3062 <li>Errors in Jmol console when structures in alignment
3063 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3065 <li>Not all working JABAWS services are shown in
3067 <li>JAVAWS version of Jalview fails to launch with
3068 'invalid literal/length code'</li>
3069 <li>Annotation/RNA Helix colourschemes cannot be applied
3070 to alignment with groups (actually fixed in 2.8.0b1)</li>
3071 <li>RNA Helices and T-Coffee Scores available as default
3074 </ul> <em>Applet</em>
3076 <li>Remove group option is shown even when selection is
3078 <li>Apply to all groups ticked but colourscheme changes
3079 don't affect groups</li>
3080 <li>Documented RNA Helices and T-Coffee Scores as valid
3081 colourscheme name</li>
3082 <li>Annotation labels drawn on sequence IDs when
3083 Annotation panel is not displayed</li>
3084 <li>Increased font size for dropdown menus on OSX and
3085 embedded windows</li>
3086 </ul> <em>Other</em>
3088 <li>Consensus sequence for alignments/groups with a
3089 single sequence were not calculated</li>
3090 <li>annotation files that contain only groups imported as
3091 annotation and junk sequences</li>
3092 <li>Fasta files with sequences containing '*' incorrectly
3093 recognised as PFAM or BLC</li>
3094 <li>conservation/PID slider apply all groups option
3095 doesn't affect background (2.8.0b1)
3097 <li>redundancy highlighting is erratic at 0% and 100%</li>
3098 <li>Remove gapped columns fails for sequences with ragged
3100 <li>AMSA annotation row with leading spaces is not
3101 registered correctly on import</li>
3102 <li>Jalview crashes when selecting PCA analysis for
3103 certain alignments</li>
3104 <li>Opening the colour by annotation dialog for an
3105 existing annotation based 'use original colours'
3106 colourscheme loses original colours setting</li>
3111 <td><div align="center">
3112 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3113 <em>30/1/2014</em></strong>
3117 <li>Trusted certificates for JalviewLite applet and
3118 Jalview Desktop application<br />Certificate was donated by
3119 <a href="https://www.certum.eu">Certum</a> to the Jalview
3120 open source project).
3122 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3123 <li>Output in Stockholm format</li>
3124 <li>Allow import of data from gzipped files</li>
3125 <li>Export/import group and sequence associated line
3126 graph thresholds</li>
3127 <li>Nucleotide substitution matrix that supports RNA and
3128 ambiguity codes</li>
3129 <li>Allow disorder predictions to be made on the current
3130 selection (or visible selection) in the same way that JPred
3132 <li>Groovy scripting for headless Jalview operation</li>
3133 </ul> <em>Other improvements</em>
3135 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3136 <li>COMBINE statement uses current SEQUENCE_REF and
3137 GROUP_REF scope to group annotation rows</li>
3138 <li>Support '' style escaping of quotes in Newick
3140 <li>Group options for JABAWS service by command line name</li>
3141 <li>Empty tooltip shown for JABA service options with a
3142 link but no description</li>
3143 <li>Select primary source when selecting authority in
3144 database fetcher GUI</li>
3145 <li>Add .mfa to FASTA file extensions recognised by
3147 <li>Annotation label tooltip text wrap</li>
3152 <li>Slow scrolling when lots of annotation rows are
3154 <li>Lots of NPE (and slowness) after creating RNA
3155 secondary structure annotation line</li>
3156 <li>Sequence database accessions not imported when
3157 fetching alignments from Rfam</li>
3158 <li>Incorrect SHMR submission for sequences with
3160 <li>View all structures does not always superpose
3162 <li>Option widgets in service parameters not updated to
3163 reflect user or preset settings</li>
3164 <li>Null pointer exceptions for some services without
3165 presets or adjustable parameters</li>
3166 <li>Discover PDB IDs entry in structure menu doesn't
3167 discover PDB xRefs</li>
3168 <li>Exception encountered while trying to retrieve
3169 features with DAS</li>
3170 <li>Lowest value in annotation row isn't coloured
3171 when colour by annotation (per sequence) is coloured</li>
3172 <li>Keyboard mode P jumps to start of gapped region when
3173 residue follows a gap</li>
3174 <li>Jalview appears to hang importing an alignment with
3175 Wrap as default or after enabling Wrap</li>
3176 <li>'Right click to add annotations' message
3177 shown in wrap mode when no annotations present</li>
3178 <li>Disorder predictions fail with NPE if no automatic
3179 annotation already exists on alignment</li>
3180 <li>oninit javascript function should be called after
3181 initialisation completes</li>
3182 <li>Remove redundancy after disorder prediction corrupts
3183 alignment window display</li>
3184 <li>Example annotation file in documentation is invalid</li>
3185 <li>Grouped line graph annotation rows are not exported
3186 to annotation file</li>
3187 <li>Multi-harmony analysis cannot be run when only two
3189 <li>Cannot create multiple groups of line graphs with
3190 several 'combine' statements in annotation file</li>
3191 <li>Pressing return several times causes Number Format
3192 exceptions in keyboard mode</li>
3193 <li>Multi-harmony (SHMMR) method doesn't submit
3194 correct partitions for input data</li>
3195 <li>Translation from DNA to Amino Acids fails</li>
3196 <li>Jalview fail to load newick tree with quoted label</li>
3197 <li>--headless flag isn't understood</li>
3198 <li>ClassCastException when generating EPS in headless
3200 <li>Adjusting sequence-associated shading threshold only
3201 changes one row's threshold</li>
3202 <li>Preferences and Feature settings panel panel
3203 doesn't open</li>
3204 <li>hide consensus histogram also hides conservation and
3205 quality histograms</li>
3210 <td><div align="center">
3211 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3213 <td><em>Application</em>
3215 <li>Support for JABAWS 2.0 Services (AACon alignment
3216 conservation, protein disorder and Clustal Omega)</li>
3217 <li>JABAWS server status indicator in Web Services
3219 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3220 in Jalview alignment window</li>
3221 <li>Updated Jalview build and deploy framework for OSX
3222 mountain lion, windows 7, and 8</li>
3223 <li>Nucleotide substitution matrix for PCA that supports
3224 RNA and ambiguity codes</li>
3226 <li>Improved sequence database retrieval GUI</li>
3227 <li>Support fetching and database reference look up
3228 against multiple DAS sources (Fetch all from in 'fetch db
3230 <li>Jalview project improvements
3232 <li>Store and retrieve the 'belowAlignment'
3233 flag for annotation</li>
3234 <li>calcId attribute to group annotation rows on the
3236 <li>Store AACon calculation settings for a view in
3237 Jalview project</li>
3241 <li>horizontal scrolling gesture support</li>
3242 <li>Visual progress indicator when PCA calculation is
3244 <li>Simpler JABA web services menus</li>
3245 <li>visual indication that web service results are still
3246 being retrieved from server</li>
3247 <li>Serialise the dialogs that are shown when Jalview
3248 starts up for first time</li>
3249 <li>Jalview user agent string for interacting with HTTP
3251 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3253 <li>Examples directory and Groovy library included in
3254 InstallAnywhere distribution</li>
3255 </ul> <em>Applet</em>
3257 <li>RNA alignment and secondary structure annotation
3258 visualization applet example</li>
3259 </ul> <em>General</em>
3261 <li>Normalise option for consensus sequence logo</li>
3262 <li>Reset button in PCA window to return dimensions to
3264 <li>Allow seqspace or Jalview variant of alignment PCA
3266 <li>PCA with either nucleic acid and protein substitution
3268 <li>Allow windows containing HTML reports to be exported
3270 <li>Interactive display and editing of RNA secondary
3271 structure contacts</li>
3272 <li>RNA Helix Alignment Colouring</li>
3273 <li>RNA base pair logo consensus</li>
3274 <li>Parse sequence associated secondary structure
3275 information in Stockholm files</li>
3276 <li>HTML Export database accessions and annotation
3277 information presented in tooltip for sequences</li>
3278 <li>Import secondary structure from LOCARNA clustalw
3279 style RNA alignment files</li>
3280 <li>import and visualise T-COFFEE quality scores for an
3282 <li>'colour by annotation' per sequence option to
3283 shade each sequence according to its associated alignment
3285 <li>New Jalview Logo</li>
3286 </ul> <em>Documentation and Development</em>
3288 <li>documentation for score matrices used in Jalview</li>
3289 <li>New Website!</li>
3291 <td><em>Application</em>
3293 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3294 wsdbfetch REST service</li>
3295 <li>Stop windows being moved outside desktop on OSX</li>
3296 <li>Filetype associations not installed for webstart
3298 <li>Jalview does not always retrieve progress of a JABAWS
3299 job execution in full once it is complete</li>
3300 <li>revise SHMR RSBS definition to ensure alignment is
3301 uploaded via ali_file parameter</li>
3302 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3303 <li>View all structures superposed fails with exception</li>
3304 <li>Jnet job queues forever if a very short sequence is
3305 submitted for prediction</li>
3306 <li>Cut and paste menu not opened when mouse clicked on
3308 <li>Putting fractional value into integer text box in
3309 alignment parameter dialog causes Jalview to hang</li>
3310 <li>Structure view highlighting doesn't work on
3312 <li>View all structures fails with exception shown in
3314 <li>Characters in filename associated with PDBEntry not
3315 escaped in a platform independent way</li>
3316 <li>Jalview desktop fails to launch with exception when
3318 <li>Tree calculation reports 'you must have 2 or more
3319 sequences selected' when selection is empty</li>
3320 <li>Jalview desktop fails to launch with jar signature
3321 failure when java web start temporary file caching is
3323 <li>DAS Sequence retrieval with range qualification
3324 results in sequence xref which includes range qualification</li>
3325 <li>Errors during processing of command line arguments
3326 cause progress bar (JAL-898) to be removed</li>
3327 <li>Replace comma for semi-colon option not disabled for
3328 DAS sources in sequence fetcher</li>
3329 <li>Cannot close news reader when JABAWS server warning
3330 dialog is shown</li>
3331 <li>Option widgets not updated to reflect user settings</li>
3332 <li>Edited sequence not submitted to web service</li>
3333 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3334 <li>InstallAnywhere installer doesn't unpack and run
3335 on OSX Mountain Lion</li>
3336 <li>Annotation panel not given a scroll bar when
3337 sequences with alignment annotation are pasted into the
3339 <li>Sequence associated annotation rows not associated
3340 when loaded from Jalview project</li>
3341 <li>Browser launch fails with NPE on java 1.7</li>
3342 <li>JABAWS alignment marked as finished when job was
3343 cancelled or job failed due to invalid input</li>
3344 <li>NPE with v2.7 example when clicking on Tree
3345 associated with all views</li>
3346 <li>Exceptions when copy/paste sequences with grouped
3347 annotation rows to new window</li>
3348 </ul> <em>Applet</em>
3350 <li>Sequence features are momentarily displayed before
3351 they are hidden using hidefeaturegroups applet parameter</li>
3352 <li>loading features via javascript API automatically
3353 enables feature display</li>
3354 <li>scrollToColumnIn javascript API method doesn't
3356 </ul> <em>General</em>
3358 <li>Redundancy removal fails for rna alignment</li>
3359 <li>PCA calculation fails when sequence has been selected
3360 and then deselected</li>
3361 <li>PCA window shows grey box when first opened on OSX</li>
3362 <li>Letters coloured pink in sequence logo when alignment
3363 coloured with clustalx</li>
3364 <li>Choosing fonts without letter symbols defined causes
3365 exceptions and redraw errors</li>
3366 <li>Initial PCA plot view is not same as manually
3367 reconfigured view</li>
3368 <li>Grouped annotation graph label has incorrect line
3370 <li>Grouped annotation graph label display is corrupted
3371 for lots of labels</li>
3376 <div align="center">
3377 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3380 <td><em>Application</em>
3382 <li>Jalview Desktop News Reader</li>
3383 <li>Tweaked default layout of web services menu</li>
3384 <li>View/alignment association menu to enable user to
3385 easily specify which alignment a multi-structure view takes
3386 its colours/correspondences from</li>
3387 <li>Allow properties file location to be specified as URL</li>
3388 <li>Extend Jalview project to preserve associations
3389 between many alignment views and a single Jmol display</li>
3390 <li>Store annotation row height in Jalview project file</li>
3391 <li>Annotation row column label formatting attributes
3392 stored in project file</li>
3393 <li>Annotation row order for auto-calculated annotation
3394 rows preserved in Jalview project file</li>
3395 <li>Visual progress indication when Jalview state is
3396 saved using Desktop window menu</li>
3397 <li>Visual indication that command line arguments are
3398 still being processed</li>
3399 <li>Groovy script execution from URL</li>
3400 <li>Colour by annotation default min and max colours in
3402 <li>Automatically associate PDB files dragged onto an
3403 alignment with sequences that have high similarity and
3405 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3406 <li>'view structures' option to open many
3407 structures in same window</li>
3408 <li>Sort associated views menu option for tree panel</li>
3409 <li>Group all JABA and non-JABA services for a particular
3410 analysis function in its own submenu</li>
3411 </ul> <em>Applet</em>
3413 <li>Userdefined and autogenerated annotation rows for
3415 <li>Adjustment of alignment annotation pane height</li>
3416 <li>Annotation scrollbar for annotation panel</li>
3417 <li>Drag to reorder annotation rows in annotation panel</li>
3418 <li>'automaticScrolling' parameter</li>
3419 <li>Allow sequences with partial ID string matches to be
3420 annotated from GFF/Jalview features files</li>
3421 <li>Sequence logo annotation row in applet</li>
3422 <li>Absolute paths relative to host server in applet
3423 parameters are treated as such</li>
3424 <li>New in the JalviewLite javascript API:
3426 <li>JalviewLite.js javascript library</li>
3427 <li>Javascript callbacks for
3429 <li>Applet initialisation</li>
3430 <li>Sequence/alignment mouse-overs and selections</li>
3433 <li>scrollTo row and column alignment scrolling
3435 <li>Select sequence/alignment regions from javascript</li>
3436 <li>javascript structure viewer harness to pass
3437 messages between Jmol and Jalview when running as
3438 distinct applets</li>
3439 <li>sortBy method</li>
3440 <li>Set of applet and application examples shipped
3441 with documentation</li>
3442 <li>New example to demonstrate JalviewLite and Jmol
3443 javascript message exchange</li>
3445 </ul> <em>General</em>
3447 <li>Enable Jmol displays to be associated with multiple
3448 multiple alignments</li>
3449 <li>Option to automatically sort alignment with new tree</li>
3450 <li>User configurable link to enable redirects to a
3451 www.Jalview.org mirror</li>
3452 <li>Jmol colours option for Jmol displays</li>
3453 <li>Configurable newline string when writing alignment
3454 and other flat files</li>
3455 <li>Allow alignment annotation description lines to
3456 contain html tags</li>
3457 </ul> <em>Documentation and Development</em>
3459 <li>Add groovy test harness for bulk load testing to
3461 <li>Groovy script to load and align a set of sequences
3462 using a web service before displaying the result in the
3463 Jalview desktop</li>
3464 <li>Restructured javascript and applet api documentation</li>
3465 <li>Ant target to publish example html files with applet
3467 <li>Netbeans project for building Jalview from source</li>
3468 <li>ant task to create online javadoc for Jalview source</li>
3470 <td><em>Application</em>
3472 <li>User defined colourscheme throws exception when
3473 current built in colourscheme is saved as new scheme</li>
3474 <li>AlignFrame->Save in application pops up save
3475 dialog for valid filename/format</li>
3476 <li>Cannot view associated structure for UniProt sequence</li>
3477 <li>PDB file association breaks for UniProt sequence
3479 <li>Associate PDB from file dialog does not tell you
3480 which sequence is to be associated with the file</li>
3481 <li>Find All raises null pointer exception when query
3482 only matches sequence IDs</li>
3483 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3484 <li>Jalview project with Jmol views created with Jalview
3485 2.4 cannot be loaded</li>
3486 <li>Filetype associations not installed for webstart
3488 <li>Two or more chains in a single PDB file associated
3489 with sequences in different alignments do not get coloured
3490 by their associated sequence</li>
3491 <li>Visibility status of autocalculated annotation row
3492 not preserved when project is loaded</li>
3493 <li>Annotation row height and visibility attributes not
3494 stored in Jalview project</li>
3495 <li>Tree bootstraps are not preserved when saved as a
3496 Jalview project</li>
3497 <li>Envision2 workflow tooltips are corrupted</li>
3498 <li>Enabling show group conservation also enables colour
3499 by conservation</li>
3500 <li>Duplicate group associated conservation or consensus
3501 created on new view</li>
3502 <li>Annotation scrollbar not displayed after 'show
3503 all hidden annotation rows' option selected</li>
3504 <li>Alignment quality not updated after alignment
3505 annotation row is hidden then shown</li>
3506 <li>Preserve colouring of structures coloured by
3507 sequences in pre Jalview 2.7 projects</li>
3508 <li>Web service job parameter dialog is not laid out
3510 <li>Web services menu not refreshed after 'reset
3511 services' button is pressed in preferences</li>
3512 <li>Annotation off by one in Jalview v2_3 example project</li>
3513 <li>Structures imported from file and saved in project
3514 get name like jalview_pdb1234.txt when reloaded</li>
3515 <li>Jalview does not always retrieve progress of a JABAWS
3516 job execution in full once it is complete</li>
3517 </ul> <em>Applet</em>
3519 <li>Alignment height set incorrectly when lots of
3520 annotation rows are displayed</li>
3521 <li>Relative URLs in feature HTML text not resolved to
3523 <li>View follows highlighting does not work for positions
3525 <li><= shown as = in tooltip</li>
3526 <li>Export features raises exception when no features
3528 <li>Separator string used for serialising lists of IDs
3529 for javascript api is modified when separator string
3530 provided as parameter</li>
3531 <li>Null pointer exception when selecting tree leaves for
3532 alignment with no existing selection</li>
3533 <li>Relative URLs for datasources assumed to be relative
3534 to applet's codebase</li>
3535 <li>Status bar not updated after finished searching and
3536 search wraps around to first result</li>
3537 <li>StructureSelectionManager instance shared between
3538 several Jalview applets causes race conditions and memory
3540 <li>Hover tooltip and mouseover of position on structure
3541 not sent from Jmol in applet</li>
3542 <li>Certain sequences of javascript method calls to
3543 applet API fatally hang browser</li>
3544 </ul> <em>General</em>
3546 <li>View follows structure mouseover scrolls beyond
3547 position with wrapped view and hidden regions</li>
3548 <li>Find sequence position moves to wrong residue
3549 with/without hidden columns</li>
3550 <li>Sequence length given in alignment properties window
3552 <li>InvalidNumberFormat exceptions thrown when trying to
3553 import PDB like structure files</li>
3554 <li>Positional search results are only highlighted
3555 between user-supplied sequence start/end bounds</li>
3556 <li>End attribute of sequence is not validated</li>
3557 <li>Find dialog only finds first sequence containing a
3558 given sequence position</li>
3559 <li>Sequence numbering not preserved in MSF alignment
3561 <li>Jalview PDB file reader does not extract sequence
3562 from nucleotide chains correctly</li>
3563 <li>Structure colours not updated when tree partition
3564 changed in alignment</li>
3565 <li>Sequence associated secondary structure not correctly
3566 parsed in interleaved stockholm</li>
3567 <li>Colour by annotation dialog does not restore current
3569 <li>Hiding (nearly) all sequences doesn't work
3571 <li>Sequences containing lowercase letters are not
3572 properly associated with their pdb files</li>
3573 </ul> <em>Documentation and Development</em>
3575 <li>schemas/JalviewWsParamSet.xsd corrupted by
3576 ApplyCopyright tool</li>
3581 <div align="center">
3582 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3585 <td><em>Application</em>
3587 <li>New warning dialog when the Jalview Desktop cannot
3588 contact web services</li>
3589 <li>JABA service parameters for a preset are shown in
3590 service job window</li>
3591 <li>JABA Service menu entries reworded</li>
3595 <li>Modeller PIR IO broken - cannot correctly import a
3596 pir file emitted by Jalview</li>
3597 <li>Existing feature settings transferred to new
3598 alignment view created from cut'n'paste</li>
3599 <li>Improved test for mixed amino/nucleotide chains when
3600 parsing PDB files</li>
3601 <li>Consensus and conservation annotation rows
3602 occasionally become blank for all new windows</li>
3603 <li>Exception raised when right clicking above sequences
3604 in wrapped view mode</li>
3605 </ul> <em>Application</em>
3607 <li>multiple multiply aligned structure views cause cpu
3608 usage to hit 100% and computer to hang</li>
3609 <li>Web Service parameter layout breaks for long user
3610 parameter names</li>
3611 <li>Jaba service discovery hangs desktop if Jaba server
3618 <div align="center">
3619 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3622 <td><em>Application</em>
3624 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3625 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3628 <li>Web Services preference tab</li>
3629 <li>Analysis parameters dialog box and user defined
3631 <li>Improved speed and layout of Envision2 service menu</li>
3632 <li>Superpose structures using associated sequence
3634 <li>Export coordinates and projection as CSV from PCA
3636 </ul> <em>Applet</em>
3638 <li>enable javascript: execution by the applet via the
3639 link out mechanism</li>
3640 </ul> <em>Other</em>
3642 <li>Updated the Jmol Jalview interface to work with Jmol
3644 <li>The Jalview Desktop and JalviewLite applet now
3645 require Java 1.5</li>
3646 <li>Allow Jalview feature colour specification for GFF
3647 sequence annotation files</li>
3648 <li>New 'colour by label' keword in Jalview feature file
3649 type colour specification</li>
3650 <li>New Jalview Desktop Groovy API method that allows a
3651 script to check if it being run in an interactive session or
3652 in a batch operation from the Jalview command line</li>
3656 <li>clustalx colourscheme colours Ds preferentially when
3657 both D+E are present in over 50% of the column</li>
3658 </ul> <em>Application</em>
3660 <li>typo in AlignmentFrame->View->Hide->all but
3661 selected Regions menu item</li>
3662 <li>sequence fetcher replaces ',' for ';' when the ',' is
3663 part of a valid accession ID</li>
3664 <li>fatal OOM if object retrieved by sequence fetcher
3665 runs out of memory</li>
3666 <li>unhandled Out of Memory Error when viewing pca
3667 analysis results</li>
3668 <li>InstallAnywhere builds fail to launch on OS X java
3669 10.5 update 4 (due to apple Java 1.6 update)</li>
3670 <li>Installanywhere Jalview silently fails to launch</li>
3671 </ul> <em>Applet</em>
3673 <li>Jalview.getFeatureGroups() raises an
3674 ArrayIndexOutOfBoundsException if no feature groups are
3681 <div align="center">
3682 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3688 <li>Alignment prettyprinter doesn't cope with long
3690 <li>clustalx colourscheme colours Ds preferentially when
3691 both D+E are present in over 50% of the column</li>
3692 <li>nucleic acid structures retrieved from PDB do not
3693 import correctly</li>
3694 <li>More columns get selected than were clicked on when a
3695 number of columns are hidden</li>
3696 <li>annotation label popup menu not providing correct
3697 add/hide/show options when rows are hidden or none are
3699 <li>Stockholm format shown in list of readable formats,
3700 and parser copes better with alignments from RFAM.</li>
3701 <li>CSV output of consensus only includes the percentage
3702 of all symbols if sequence logo display is enabled</li>
3704 </ul> <em>Applet</em>
3706 <li>annotation panel disappears when annotation is
3708 </ul> <em>Application</em>
3710 <li>Alignment view not redrawn properly when new
3711 alignment opened where annotation panel is visible but no
3712 annotations are present on alignment</li>
3713 <li>pasted region containing hidden columns is
3714 incorrectly displayed in new alignment window</li>
3715 <li>Jalview slow to complete operations when stdout is
3716 flooded (fix is to close the Jalview console)</li>
3717 <li>typo in AlignmentFrame->View->Hide->all but
3718 selected Rregions menu item.</li>
3719 <li>inconsistent group submenu and Format submenu entry
3720 'Un' or 'Non'conserved</li>
3721 <li>Sequence feature settings are being shared by
3722 multiple distinct alignments</li>
3723 <li>group annotation not recreated when tree partition is
3725 <li>double click on group annotation to select sequences
3726 does not propagate to associated trees</li>
3727 <li>Mac OSX specific issues:
3729 <li>exception raised when mouse clicked on desktop
3730 window background</li>
3731 <li>Desktop menu placed on menu bar and application
3732 name set correctly</li>
3733 <li>sequence feature settings not wide enough for the
3734 save feature colourscheme button</li>
3743 <div align="center">
3744 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3747 <td><em>New Capabilities</em>
3749 <li>URL links generated from description line for
3750 regular-expression based URL links (applet and application)
3752 <li>Non-positional feature URL links are shown in link
3754 <li>Linked viewing of nucleic acid sequences and
3756 <li>Automatic Scrolling option in View menu to display
3757 the currently highlighted region of an alignment.</li>
3758 <li>Order an alignment by sequence length, or using the
3759 average score or total feature count for each sequence.</li>
3760 <li>Shading features by score or associated description</li>
3761 <li>Subdivide alignment and groups based on identity of
3762 selected subsequence (Make Groups from Selection).</li>
3763 <li>New hide/show options including Shift+Control+H to
3764 hide everything but the currently selected region.</li>
3765 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3766 </ul> <em>Application</em>
3768 <li>Fetch DB References capabilities and UI expanded to
3769 support retrieval from DAS sequence sources</li>
3770 <li>Local DAS Sequence sources can be added via the
3771 command line or via the Add local source dialog box.</li>
3772 <li>DAS Dbref and DbxRef feature types are parsed as
3773 database references and protein_name is parsed as
3774 description line (BioSapiens terms).</li>
3775 <li>Enable or disable non-positional feature and database
3776 references in sequence ID tooltip from View menu in
3778 <!-- <li>New hidden columns and rows and representatives capabilities
3779 in annotations file (in progress - not yet fully implemented)</li> -->
3780 <li>Group-associated consensus, sequence logos and
3781 conservation plots</li>
3782 <li>Symbol distributions for each column can be exported
3783 and visualized as sequence logos</li>
3784 <li>Optionally scale multi-character column labels to fit
3785 within each column of annotation row<!-- todo for applet -->
3787 <li>Optional automatic sort of associated alignment view
3788 when a new tree is opened.</li>
3789 <li>Jalview Java Console</li>
3790 <li>Better placement of desktop window when moving
3791 between different screens.</li>
3792 <li>New preference items for sequence ID tooltip and
3793 consensus annotation</li>
3794 <li>Client to submit sequences and IDs to Envision2
3796 <li><em>Vamsas Capabilities</em>
3798 <li>Improved VAMSAS synchronization (Jalview archive
3799 used to preserve views, structures, and tree display
3801 <li>Import of vamsas documents from disk or URL via
3803 <li>Sharing of selected regions between views and
3804 with other VAMSAS applications (Experimental feature!)</li>
3805 <li>Updated API to VAMSAS version 0.2</li>
3807 </ul> <em>Applet</em>
3809 <li>Middle button resizes annotation row height</li>
3812 <li>sortByTree (true/false) - automatically sort the
3813 associated alignment view by the tree when a new tree is
3815 <li>showTreeBootstraps (true/false) - show or hide
3816 branch bootstraps (default is to show them if available)</li>
3817 <li>showTreeDistances (true/false) - show or hide
3818 branch lengths (default is to show them if available)</li>
3819 <li>showUnlinkedTreeNodes (true/false) - indicate if
3820 unassociated nodes should be highlighted in the tree
3822 <li>heightScale and widthScale (1.0 or more) -
3823 increase the height or width of a cell in the alignment
3824 grid relative to the current font size.</li>
3827 <li>Non-positional features displayed in sequence ID
3829 </ul> <em>Other</em>
3831 <li>Features format: graduated colour definitions and
3832 specification of feature scores</li>
3833 <li>Alignment Annotations format: new keywords for group
3834 associated annotation (GROUP_REF) and annotation row display
3835 properties (ROW_PROPERTIES)</li>
3836 <li>XML formats extended to support graduated feature
3837 colourschemes, group associated annotation, and profile
3838 visualization settings.</li></td>
3841 <li>Source field in GFF files parsed as feature source
3842 rather than description</li>
3843 <li>Non-positional features are now included in sequence
3844 feature and gff files (controlled via non-positional feature
3845 visibility in tooltip).</li>
3846 <li>URL links generated for all feature links (bugfix)</li>
3847 <li>Added URL embedding instructions to features file
3849 <li>Codons containing ambiguous nucleotides translated as
3850 'X' in peptide product</li>
3851 <li>Match case switch in find dialog box works for both
3852 sequence ID and sequence string and query strings do not
3853 have to be in upper case to match case-insensitively.</li>
3854 <li>AMSA files only contain first column of
3855 multi-character column annotation labels</li>
3856 <li>Jalview Annotation File generation/parsing consistent
3857 with documentation (e.g. Stockholm annotation can be
3858 exported and re-imported)</li>
3859 <li>PDB files without embedded PDB IDs given a friendly
3861 <li>Find incrementally searches ID string matches as well
3862 as subsequence matches, and correctly reports total number
3866 <li>Better handling of exceptions during sequence
3868 <li>Dasobert generated non-positional feature URL
3869 link text excludes the start_end suffix</li>
3870 <li>DAS feature and source retrieval buttons disabled
3871 when fetch or registry operations in progress.</li>
3872 <li>PDB files retrieved from URLs are cached properly</li>
3873 <li>Sequence description lines properly shared via
3875 <li>Sequence fetcher fetches multiple records for all
3877 <li>Ensured that command line das feature retrieval
3878 completes before alignment figures are generated.</li>
3879 <li>Reduced time taken when opening file browser for
3881 <li>isAligned check prior to calculating tree, PCA or
3882 submitting an MSA to JNet now excludes hidden sequences.</li>
3883 <li>User defined group colours properly recovered
3884 from Jalview projects.</li>
3893 <div align="center">
3894 <strong>2.4.0.b2</strong><br> 28/10/2009
3899 <li>Experimental support for google analytics usage
3901 <li>Jalview privacy settings (user preferences and docs).</li>
3906 <li>Race condition in applet preventing startup in
3908 <li>Exception when feature created from selection beyond
3909 length of sequence.</li>
3910 <li>Allow synthetic PDB files to be imported gracefully</li>
3911 <li>Sequence associated annotation rows associate with
3912 all sequences with a given id</li>
3913 <li>Find function matches case-insensitively for sequence
3914 ID string searches</li>
3915 <li>Non-standard characters do not cause pairwise
3916 alignment to fail with exception</li>
3917 </ul> <em>Application Issues</em>
3919 <li>Sequences are now validated against EMBL database</li>
3920 <li>Sequence fetcher fetches multiple records for all
3922 </ul> <em>InstallAnywhere Issues</em>
3924 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3925 issue with installAnywhere mechanism)</li>
3926 <li>Command line launching of JARs from InstallAnywhere
3927 version (java class versioning error fixed)</li>
3934 <div align="center">
3935 <strong>2.4</strong><br> 27/8/2008
3938 <td><em>User Interface</em>
3940 <li>Linked highlighting of codon and amino acid from
3941 translation and protein products</li>
3942 <li>Linked highlighting of structure associated with
3943 residue mapping to codon position</li>
3944 <li>Sequence Fetcher provides example accession numbers
3945 and 'clear' button</li>
3946 <li>MemoryMonitor added as an option under Desktop's
3948 <li>Extract score function to parse whitespace separated
3949 numeric data in description line</li>
3950 <li>Column labels in alignment annotation can be centred.</li>
3951 <li>Tooltip for sequence associated annotation give name
3953 </ul> <em>Web Services and URL fetching</em>
3955 <li>JPred3 web service</li>
3956 <li>Prototype sequence search client (no public services
3958 <li>Fetch either seed alignment or full alignment from
3960 <li>URL Links created for matching database cross
3961 references as well as sequence ID</li>
3962 <li>URL Links can be created using regular-expressions</li>
3963 </ul> <em>Sequence Database Connectivity</em>
3965 <li>Retrieval of cross-referenced sequences from other
3967 <li>Generalised database reference retrieval and
3968 validation to all fetchable databases</li>
3969 <li>Fetch sequences from DAS sources supporting the
3970 sequence command</li>
3971 </ul> <em>Import and Export</em>
3972 <li>export annotation rows as CSV for spreadsheet import</li>
3973 <li>Jalview projects record alignment dataset associations,
3974 EMBL products, and cDNA sequence mappings</li>
3975 <li>Sequence Group colour can be specified in Annotation
3977 <li>Ad-hoc colouring of group in Annotation File using RGB
3978 triplet as name of colourscheme</li>
3979 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3981 <li>treenode binding for VAMSAS tree exchange</li>
3982 <li>local editing and update of sequences in VAMSAS
3983 alignments (experimental)</li>
3984 <li>Create new or select existing session to join</li>
3985 <li>load and save of vamsas documents</li>
3986 </ul> <em>Application command line</em>
3988 <li>-tree parameter to open trees (introduced for passing
3990 <li>-fetchfrom command line argument to specify nicknames
3991 of DAS servers to query for alignment features</li>
3992 <li>-dasserver command line argument to add new servers
3993 that are also automatically queried for features</li>
3994 <li>-groovy command line argument executes a given groovy
3995 script after all input data has been loaded and parsed</li>
3996 </ul> <em>Applet-Application data exchange</em>
3998 <li>Trees passed as applet parameters can be passed to
3999 application (when using "View in full
4000 application")</li>
4001 </ul> <em>Applet Parameters</em>
4003 <li>feature group display control parameter</li>
4004 <li>debug parameter</li>
4005 <li>showbutton parameter</li>
4006 </ul> <em>Applet API methods</em>
4008 <li>newView public method</li>
4009 <li>Window (current view) specific get/set public methods</li>
4010 <li>Feature display control methods</li>
4011 <li>get list of currently selected sequences</li>
4012 </ul> <em>New Jalview distribution features</em>
4014 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4015 <li>RELEASE file gives build properties for the latest
4016 Jalview release.</li>
4017 <li>Java 1.1 Applet build made easier and donotobfuscate
4018 property controls execution of obfuscator</li>
4019 <li>Build target for generating source distribution</li>
4020 <li>Debug flag for javacc</li>
4021 <li>.jalview_properties file is documented (slightly) in
4022 jalview.bin.Cache</li>
4023 <li>Continuous Build Integration for stable and
4024 development version of Application, Applet and source
4029 <li>selected region output includes visible annotations
4030 (for certain formats)</li>
4031 <li>edit label/displaychar contains existing label/char
4033 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4034 <li>shorter peptide product names from EMBL records</li>
4035 <li>Newick string generator makes compact representations</li>
4036 <li>bootstrap values parsed correctly for tree files with
4038 <li>pathological filechooser bug avoided by not allowing
4039 filenames containing a ':'</li>
4040 <li>Fixed exception when parsing GFF files containing
4041 global sequence features</li>
4042 <li>Alignment datasets are finalized only when number of
4043 references from alignment sequences goes to zero</li>
4044 <li>Close of tree branch colour box without colour
4045 selection causes cascading exceptions</li>
4046 <li>occasional negative imgwidth exceptions</li>
4047 <li>better reporting of non-fatal warnings to user when
4048 file parsing fails.</li>
4049 <li>Save works when Jalview project is default format</li>
4050 <li>Save as dialog opened if current alignment format is
4051 not a valid output format</li>
4052 <li>UniProt canonical names introduced for both das and
4054 <li>Histidine should be midblue (not pink!) in Zappo</li>
4055 <li>error messages passed up and output when data read
4057 <li>edit undo recovers previous dataset sequence when
4058 sequence is edited</li>
4059 <li>allow PDB files without pdb ID HEADER lines (like
4060 those generated by MODELLER) to be read in properly</li>
4061 <li>allow reading of JPred concise files as a normal
4063 <li>Stockholm annotation parsing and alignment properties
4064 import fixed for PFAM records</li>
4065 <li>Structure view windows have correct name in Desktop
4067 <li>annotation consisting of sequence associated scores
4068 can be read and written correctly to annotation file</li>
4069 <li>Aligned cDNA translation to aligned peptide works
4071 <li>Fixed display of hidden sequence markers and
4072 non-italic font for representatives in Applet</li>
4073 <li>Applet Menus are always embedded in applet window on
4075 <li>Newly shown features appear at top of stack (in
4077 <li>Annotations added via parameter not drawn properly
4078 due to null pointer exceptions</li>
4079 <li>Secondary structure lines are drawn starting from
4080 first column of alignment</li>
4081 <li>UniProt XML import updated for new schema release in
4083 <li>Sequence feature to sequence ID match for Features
4084 file is case-insensitive</li>
4085 <li>Sequence features read from Features file appended to
4086 all sequences with matching IDs</li>
4087 <li>PDB structure coloured correctly for associated views
4088 containing a sub-sequence</li>
4089 <li>PDB files can be retrieved by applet from Jar files</li>
4090 <li>feature and annotation file applet parameters
4091 referring to different directories are retrieved correctly</li>
4092 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4093 <li>Fixed application hang whilst waiting for
4094 splash-screen version check to complete</li>
4095 <li>Applet properly URLencodes input parameter values
4096 when passing them to the launchApp service</li>
4097 <li>display name and local features preserved in results
4098 retrieved from web service</li>
4099 <li>Visual delay indication for sequence retrieval and
4100 sequence fetcher initialisation</li>
4101 <li>updated Application to use DAS 1.53e version of
4102 dasobert DAS client</li>
4103 <li>Re-instated Full AMSA support and .amsa file
4105 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4113 <div align="center">
4114 <strong>2.3</strong><br> 9/5/07
4119 <li>Jmol 11.0.2 integration</li>
4120 <li>PDB views stored in Jalview XML files</li>
4121 <li>Slide sequences</li>
4122 <li>Edit sequence in place</li>
4123 <li>EMBL CDS features</li>
4124 <li>DAS Feature mapping</li>
4125 <li>Feature ordering</li>
4126 <li>Alignment Properties</li>
4127 <li>Annotation Scores</li>
4128 <li>Sort by scores</li>
4129 <li>Feature/annotation editing in applet</li>
4134 <li>Headless state operation in 2.2.1</li>
4135 <li>Incorrect and unstable DNA pairwise alignment</li>
4136 <li>Cut and paste of sequences with annotation</li>
4137 <li>Feature group display state in XML</li>
4138 <li>Feature ordering in XML</li>
4139 <li>blc file iteration selection using filename # suffix</li>
4140 <li>Stockholm alignment properties</li>
4141 <li>Stockhom alignment secondary structure annotation</li>
4142 <li>2.2.1 applet had no feature transparency</li>
4143 <li>Number pad keys can be used in cursor mode</li>
4144 <li>Structure Viewer mirror image resolved</li>
4151 <div align="center">
4152 <strong>2.2.1</strong><br> 12/2/07
4157 <li>Non standard characters can be read and displayed
4158 <li>Annotations/Features can be imported/exported to the
4160 <li>Applet allows editing of sequence/annotation/group
4161 name & description
4162 <li>Preference setting to display sequence name in
4164 <li>Annotation file format extended to allow
4165 Sequence_groups to be defined
4166 <li>Default opening of alignment overview panel can be
4167 specified in preferences
4168 <li>PDB residue numbering annotation added to associated
4174 <li>Applet crash under certain Linux OS with Java 1.6
4176 <li>Annotation file export / import bugs fixed
4177 <li>PNG / EPS image output bugs fixed
4183 <div align="center">
4184 <strong>2.2</strong><br> 27/11/06
4189 <li>Multiple views on alignment
4190 <li>Sequence feature editing
4191 <li>"Reload" alignment
4192 <li>"Save" to current filename
4193 <li>Background dependent text colour
4194 <li>Right align sequence ids
4195 <li>User-defined lower case residue colours
4198 <li>Menu item accelerator keys
4199 <li>Control-V pastes to current alignment
4200 <li>Cancel button for DAS Feature Fetching
4201 <li>PCA and PDB Viewers zoom via mouse roller
4202 <li>User-defined sub-tree colours and sub-tree selection
4204 <li>'New Window' button on the 'Output to Text box'
4209 <li>New memory efficient Undo/Redo System
4210 <li>Optimised symbol lookups and conservation/consensus
4212 <li>Region Conservation/Consensus recalculated after
4214 <li>Fixed Remove Empty Columns Bug (empty columns at end
4216 <li>Slowed DAS Feature Fetching for increased robustness.
4218 <li>Made angle brackets in ASCII feature descriptions
4220 <li>Re-instated Zoom function for PCA
4221 <li>Sequence descriptions conserved in web service
4223 <li>UniProt ID discoverer uses any word separated by
4225 <li>WsDbFetch query/result association resolved
4226 <li>Tree leaf to sequence mapping improved
4227 <li>Smooth fonts switch moved to FontChooser dialog box.
4234 <div align="center">
4235 <strong>2.1.1</strong><br> 12/9/06
4240 <li>Copy consensus sequence to clipboard</li>
4245 <li>Image output - rightmost residues are rendered if
4246 sequence id panel has been resized</li>
4247 <li>Image output - all offscreen group boundaries are
4249 <li>Annotation files with sequence references - all
4250 elements in file are relative to sequence position</li>
4251 <li>Mac Applet users can use Alt key for group editing</li>
4257 <div align="center">
4258 <strong>2.1</strong><br> 22/8/06
4263 <li>MAFFT Multiple Alignment in default Web Service list</li>
4264 <li>DAS Feature fetching</li>
4265 <li>Hide sequences and columns</li>
4266 <li>Export Annotations and Features</li>
4267 <li>GFF file reading / writing</li>
4268 <li>Associate structures with sequences from local PDB
4270 <li>Add sequences to exisiting alignment</li>
4271 <li>Recently opened files / URL lists</li>
4272 <li>Applet can launch the full application</li>
4273 <li>Applet has transparency for features (Java 1.2
4275 <li>Applet has user defined colours parameter</li>
4276 <li>Applet can load sequences from parameter
4277 "sequence<em>x</em>"
4283 <li>Redundancy Panel reinstalled in the Applet</li>
4284 <li>Monospaced font - EPS / rescaling bug fixed</li>
4285 <li>Annotation files with sequence references bug fixed</li>
4291 <div align="center">
4292 <strong>2.08.1</strong><br> 2/5/06
4297 <li>Change case of selected region from Popup menu</li>
4298 <li>Choose to match case when searching</li>
4299 <li>Middle mouse button and mouse movement can compress /
4300 expand the visible width and height of the alignment</li>
4305 <li>Annotation Panel displays complete JNet results</li>
4311 <div align="center">
4312 <strong>2.08b</strong><br> 18/4/06
4318 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4319 <li>Righthand label on wrapped alignments shows correct
4326 <div align="center">
4327 <strong>2.08</strong><br> 10/4/06
4332 <li>Editing can be locked to the selection area</li>
4333 <li>Keyboard editing</li>
4334 <li>Create sequence features from searches</li>
4335 <li>Precalculated annotations can be loaded onto
4337 <li>Features file allows grouping of features</li>
4338 <li>Annotation Colouring scheme added</li>
4339 <li>Smooth fonts off by default - Faster rendering</li>
4340 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4345 <li>Drag & Drop fixed on Linux</li>
4346 <li>Jalview Archive file faster to load/save, sequence
4347 descriptions saved.</li>
4353 <div align="center">
4354 <strong>2.07</strong><br> 12/12/05
4359 <li>PDB Structure Viewer enhanced</li>
4360 <li>Sequence Feature retrieval and display enhanced</li>
4361 <li>Choose to output sequence start-end after sequence
4362 name for file output</li>
4363 <li>Sequence Fetcher WSDBFetch@EBI</li>
4364 <li>Applet can read feature files, PDB files and can be
4365 used for HTML form input</li>
4370 <li>HTML output writes groups and features</li>
4371 <li>Group editing is Control and mouse click</li>
4372 <li>File IO bugs</li>
4378 <div align="center">
4379 <strong>2.06</strong><br> 28/9/05
4384 <li>View annotations in wrapped mode</li>
4385 <li>More options for PCA viewer</li>
4390 <li>GUI bugs resolved</li>
4391 <li>Runs with -nodisplay from command line</li>
4397 <div align="center">
4398 <strong>2.05b</strong><br> 15/9/05
4403 <li>Choose EPS export as lineart or text</li>
4404 <li>Jar files are executable</li>
4405 <li>Can read in Uracil - maps to unknown residue</li>
4410 <li>Known OutOfMemory errors give warning message</li>
4411 <li>Overview window calculated more efficiently</li>
4412 <li>Several GUI bugs resolved</li>
4418 <div align="center">
4419 <strong>2.05</strong><br> 30/8/05
4424 <li>Edit and annotate in "Wrapped" view</li>
4429 <li>Several GUI bugs resolved</li>
4435 <div align="center">
4436 <strong>2.04</strong><br> 24/8/05
4441 <li>Hold down mouse wheel & scroll to change font
4447 <li>Improved JPred client reliability</li>
4448 <li>Improved loading of Jalview files</li>
4454 <div align="center">
4455 <strong>2.03</strong><br> 18/8/05
4460 <li>Set Proxy server name and port in preferences</li>
4461 <li>Multiple URL links from sequence ids</li>
4462 <li>User Defined Colours can have a scheme name and added
4464 <li>Choose to ignore gaps in consensus calculation</li>
4465 <li>Unix users can set default web browser</li>
4466 <li>Runs without GUI for batch processing</li>
4467 <li>Dynamically generated Web Service Menus</li>
4472 <li>InstallAnywhere download for Sparc Solaris</li>
4478 <div align="center">
4479 <strong>2.02</strong><br> 18/7/05
4485 <li>Copy & Paste order of sequences maintains
4486 alignment order.</li>
4492 <div align="center">
4493 <strong>2.01</strong><br> 12/7/05
4498 <li>Use delete key for deleting selection.</li>
4499 <li>Use Mouse wheel to scroll sequences.</li>
4500 <li>Help file updated to describe how to add alignment
4502 <li>Version and build date written to build properties
4504 <li>InstallAnywhere installation will check for updates
4505 at launch of Jalview.</li>
4510 <li>Delete gaps bug fixed.</li>
4511 <li>FileChooser sorts columns.</li>
4512 <li>Can remove groups one by one.</li>
4513 <li>Filechooser icons installed.</li>
4514 <li>Finder ignores return character when searching.
4515 Return key will initiate a search.<br>
4522 <div align="center">
4523 <strong>2.0</strong><br> 20/6/05
4528 <li>New codebase</li>