3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
61 <em>02/07/2019</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 allows updates) used for Sequence Feature collections</li>
104 <!-- JAL-2808,JAL-2069,JAL-2820 -->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-3334 -->Use full Sequence Ontology (via BioJava) to
111 recognise variant features
114 <!-- JAL-2897 -->Show synonymous codon variants on peptide
118 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
122 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
123 algorithm (Z-sort/transparency and filter aware)
126 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
132 <!-- JAL-3205 -->Symmetric score matrices for faster
133 tree and PCA calculations
135 <li><strong>Principal Components Analysis Viewer</strong>
138 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
139 and Viewer state saved in Jalview Project
141 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
144 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
148 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
153 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
155 <li><strong>Speed and Efficiency</strong>
158 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
159 multiple groups when working with large alignments
162 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
166 <li><strong>User Interface</strong>
169 <!-- JAL-2933 -->Finder panel remembers last position in each
173 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
174 what is shown)<br />Only visible region of alignment is shown by
175 default (can be changed in user preferences)
178 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
179 to the Overwrite Dialog
182 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
186 <!-- JAL-1244 -->Status bar shows bounds when dragging a
187 selection region, and gap count when inserting or deleting gaps
190 <!-- JAL-3132 -->Status bar updates over sequence and annotation
194 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
198 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
202 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
205 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
209 <!-- JAL-3181 -->Consistent ordering of links in sequence id
213 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
215 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
219 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
220 <li><strong>Java 11 Support (not yet on general release)</strong>
223 <!-- -->OSX GUI integrations for App menu's 'About' entry and
228 <em>Deprecations</em>
231 <!-- JAL-3035 -->DAS sequence retrieval and annotation
232 capabilities removed from the Jalview Desktop
235 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
236 unmarshalling has been replaced by JAXB for Jalview projects
237 and XML based data retrieval clients</li>
238 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
239 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
240 </ul> <em>Documentation</em>
243 <!-- JAL-3003 -->Added remarks about transparent rendering effects
244 not supported in EPS figure export
246 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
247 </ul> <em>Development and Release Processes</em>
250 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
252 <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
254 <!-- JAL-3225 -->Eclipse project configuration managed with
257 <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
258 Atlassian Bamboo continuous integration for
259 unattended Test Suite execution</li>
261 <!-- JAL-2864 -->Memory test suite to detect leaks in common
263 <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
264 <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>
267 <td align="left" valign="top">
270 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
273 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
274 superposition in Jmol fail on Windows
277 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
278 structures for sequences with lots of PDB structures
281 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
285 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
286 project involving multiple views
289 <!-- JAL-3164 -->Overview for complementary view in a linked
290 CDS/Protein alignment is not updated when Hide Columns by
291 Annotation dialog hides columns
294 <!-- JAL-3158 -->Selection highlighting in the complement of a
295 CDS/Protein alignment stops working after making a selection in
296 one view, then making another selection in the other view
299 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
303 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
304 Settings and Jalview Preferences panels
307 <!-- JAL-2865 -->Jalview hangs when closing windows or the
308 overview updates with large alignments
311 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
312 region if columns were selected by dragging right-to-left and the
313 mouse moved to the left of the first column
316 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
317 hidden column marker via scale popup menu
320 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
321 doesn't tell users the invalid URL
324 <!-- JAL-2816 -->Tooltips displayed for features filtered by
328 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
329 show cross references or Fetch Database References are shown in
333 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
334 peptide sequence (computed variant shown as p.Res.null)
337 <!-- JAL-2060 -->'Graduated colour' option not offered for
338 manually created features (where if feature score is Float.NaN)
341 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
342 when columns are hidden
345 <!-- JAL-3082 -->Regular expression error for '(' in Select
346 Columns by Annotation description
349 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
350 out of Scale or Annotation Panel
353 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
357 <!-- JAL-3074 -->Left/right drag in annotation can scroll
361 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
365 <!-- JAL-3002 -->Column display is out by one after Page Down,
366 Page Up in wrapped mode
369 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
372 <!-- JAL-2932 -->Finder searches in minimised alignments
375 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
376 on opening an alignment
379 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
383 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
384 different groups in the alignment are selected
387 <!-- JAL-2717 -->Internationalised colour scheme names not shown
391 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
395 <!-- JAL-3125 -->Value input for graduated feature colour
396 threshold gets 'unrounded'
399 <!-- JAL-2982 -->PCA image export doesn't respect background
403 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
406 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
409 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
413 <!-- JAL-2964 -->Associate Tree with All Views not restored from
417 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
418 shown in complementary view
421 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
422 without normalisation
425 <!-- JAL-3021 -->Sequence Details report opens positioned to top
429 <!-- JAL-914 -->Help page can be opened twice
431 </ul> <em>Editing</em>
434 <!-- JAL-2822 -->Start and End should be updated when sequence
435 data at beginning or end of alignment added/removed via 'Edit'
439 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
440 relocate sequence features correctly when start of sequence is
441 removed (Known defect since 2.10)
444 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
445 dialog corrupts dataset sequence
448 <!-- JAL-868 -->Structure colours not updated when associated tree
449 repartitions the alignment view (Regression in 2.10.5)
455 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
456 sequence's End is greater than its length
458 </ul> <em>New Known Defects</em>
460 <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
463 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
464 regions of protein alignment.
467 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
468 is restored from a Jalview 2.11 project
471 <!-- JAL-3213 -->Alignment panel height can be too small after
475 <!-- JAL-3240 -->Display is incorrect after removing gapped
476 columns within hidden columns
479 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
480 window after dragging left to select columns to left of visible
484 <!-- JAL-2876 -->Features coloured according to their description
485 string and thresholded by score in earlier versions of Jalview are
486 not shown as thresholded features in 2.11. To workaround please
487 create a Score filter instead.
489 <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
491 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
493 <li><strong>Java 11 Specific defects</strong>
496 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
504 <td width="60" nowrap>
506 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
509 <td><div align="left">
513 <!-- JAL-3101 -->Default memory for Jalview webstart and
514 InstallAnywhere increased to 1G.
517 <!-- JAL-247 -->Hidden sequence markers and representative
518 sequence bolding included when exporting alignment as EPS,
519 SVG, PNG or HTML. <em>Display is configured via the
520 Format menu, or for command-line use via a jalview
521 properties file.</em>
524 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
525 API and sequence data now imported as JSON.
528 <!-- JAL-3065 -->Change in recommended way of starting
529 Jalview via a Java command line: add jars in lib directory
530 to CLASSPATH, rather than via the deprecated java.ext.dirs
537 <!-- JAL-3047 -->Support added to execute test suite
538 instrumented with <a href="http://openclover.org/">Open
543 <td><div align="left">
547 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
548 row shown in Feredoxin Structure alignment view of example
552 <!-- JAL-2854 -->Annotation obscures sequences if lots of
553 annotation displayed.
556 <!-- JAL-3107 -->Group conservation/consensus not shown
557 for newly created group when 'Apply to all groups'
561 <!-- JAL-3087 -->Corrupted display when switching to
562 wrapped mode when sequence panel's vertical scrollbar is
566 <!-- JAL-3003 -->Alignment is black in exported EPS file
567 when sequences are selected in exported view.</em>
570 <!-- JAL-3059 -->Groups with different coloured borders
571 aren't rendered with correct colour.
574 <!-- JAL-3092 -->Jalview could hang when importing certain
575 types of knotted RNA secondary structure.
578 <!-- JAL-3095 -->Sequence highlight and selection in
579 trimmed VARNA 2D structure is incorrect for sequences that
583 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
584 annotation when columns are inserted into an alignment,
585 and when exporting as Stockholm flatfile.
588 <!-- JAL-3053 -->Jalview annotation rows containing upper
589 and lower-case 'E' and 'H' do not automatically get
590 treated as RNA secondary structure.
593 <!-- JAL-3106 -->.jvp should be used as default extension
594 (not .jar) when saving a jalview project file.
597 <!-- JAL-3105 -->Mac Users: closing a window correctly
598 transfers focus to previous window on OSX
601 <em>Java 10 Issues Resolved</em>
604 <!-- JAL-2988 -->OSX - Can't save new files via the File
605 or export menus by typing in a name into the Save dialog
609 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
610 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
611 'look and feel' which has improved compatibility with the
612 latest version of OSX.
619 <td width="60" nowrap>
621 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
622 <em>7/06/2018</em></strong>
625 <td><div align="left">
629 <!-- JAL-2920 -->Use HGVS nomenclature for variant
630 annotation retrieved from Uniprot
633 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
634 onto the Jalview Desktop
638 <td><div align="left">
642 <!-- JAL-3017 -->Cannot import features with multiple
643 variant elements (blocks import of some Uniprot records)
646 <!-- JAL-2997 -->Clustal files with sequence positions in
647 right-hand column parsed correctly
650 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
651 not alignment area in exported graphic
654 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
655 window has input focus
658 <!-- JAL-2992 -->Annotation panel set too high when
659 annotation added to view (Windows)
662 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
663 network connectivity is poor
666 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
667 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
668 the currently open URL and links from a page viewed in
669 Firefox or Chrome on Windows is now fully supported. If
670 you are using Edge, only links in the page can be
671 dragged, and with Internet Explorer, only the currently
672 open URL in the browser can be dropped onto Jalview.</em>
675 <em>New Known Defects</em>
677 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
682 <td width="60" nowrap>
684 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
687 <td><div align="left">
691 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
692 for disabling automatic superposition of multiple
693 structures and open structures in existing views
696 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
697 ID and annotation area margins can be click-dragged to
701 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
705 <!-- JAL-2759 -->Improved performance for large alignments
706 and lots of hidden columns
709 <!-- JAL-2593 -->Improved performance when rendering lots
710 of features (particularly when transparency is disabled)
713 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
714 exchange of Jalview features and Chimera attributes made
720 <td><div align="left">
723 <!-- JAL-2899 -->Structure and Overview aren't updated
724 when Colour By Annotation threshold slider is adjusted
727 <!-- JAL-2778 -->Slow redraw when Overview panel shown
728 overlapping alignment panel
731 <!-- JAL-2929 -->Overview doesn't show end of unpadded
735 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
736 improved: CDS not handled correctly if transcript has no
740 <!-- JAL-2321 -->Secondary structure and temperature
741 factor annotation not added to sequence when local PDB
742 file associated with it by drag'n'drop or structure
746 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
747 dialog doesn't import PDB files dropped on an alignment
750 <!-- JAL-2666 -->Linked scrolling via protein horizontal
751 scroll bar doesn't work for some CDS/Protein views
754 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
755 Java 1.8u153 onwards and Java 1.9u4+.
758 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
759 columns in annotation row
762 <!-- JAL-2913 -->Preferences panel's ID Width control is not
763 honored in batch mode
766 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
767 for structures added to existing Jmol view
770 <!-- JAL-2223 -->'View Mappings' includes duplicate
771 entries after importing project with multiple views
774 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
775 protein sequences via SIFTS from associated PDB entries
776 with negative residue numbers or missing residues fails
779 <!-- JAL-2952 -->Exception when shading sequence with negative
780 Temperature Factor values from annotated PDB files (e.g.
781 as generated by CONSURF)
784 <!-- JAL-2920 -->Uniprot 'sequence variant' features
785 tooltip doesn't include a text description of mutation
788 <!-- JAL-2922 -->Invert displayed features very slow when
789 structure and/or overview windows are also shown
792 <!-- JAL-2954 -->Selecting columns from highlighted regions
793 very slow for alignments with large numbers of sequences
796 <!-- JAL-2925 -->Copy Consensus fails for group consensus
797 with 'StringIndexOutOfBounds'
800 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
801 platforms running Java 10
804 <!-- JAL-2960 -->Adding a structure to existing structure
805 view appears to do nothing because the view is hidden behind the alignment view
811 <!-- JAL-2926 -->Copy consensus sequence option in applet
812 should copy the group consensus when popup is opened on it
818 <!-- JAL-2913 -->Fixed ID width preference is not respected
821 <em>New Known Defects</em>
824 <!-- JAL-2973 --> Exceptions occasionally raised when
825 editing a large alignment and overview is displayed
828 <!-- JAL-2974 -->'Overview updating' progress bar is shown
829 repeatedly after a series of edits even when the overview
830 is no longer reflecting updates
833 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
834 structures for protein subsequence (if 'Trim Retrieved
835 Sequences' enabled) or Ensembl isoforms (Workaround in
836 2.10.4 is to fail back to N&W mapping)
839 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
840 option gives blank output
847 <td width="60" nowrap>
849 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
852 <td><div align="left">
853 <ul><li>Updated Certum Codesigning Certificate
854 (Valid till 30th November 2018)</li></ul></div></td>
855 <td><div align="left">
858 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
859 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
860 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
861 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
862 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
863 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
864 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
870 <td width="60" nowrap>
872 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
875 <td><div align="left">
879 <!-- JAL-2446 -->Faster and more efficient management and
880 rendering of sequence features
883 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
884 429 rate limit request hander
887 <!-- JAL-2773 -->Structure views don't get updated unless
888 their colours have changed
891 <!-- JAL-2495 -->All linked sequences are highlighted for
892 a structure mousover (Jmol) or selection (Chimera)
895 <!-- JAL-2790 -->'Cancel' button in progress bar for
896 JABAWS AACon, RNAAliFold and Disorder prediction jobs
899 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
900 view from Ensembl locus cross-references
903 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
907 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
908 feature can be disabled
911 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
912 PDB easier retrieval of sequences for lists of IDs
915 <!-- JAL-2758 -->Short names for sequences retrieved from
921 <li>Groovy interpreter updated to 2.4.12</li>
922 <li>Example groovy script for generating a matrix of
923 percent identity scores for current alignment.</li>
925 <em>Testing and Deployment</em>
928 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
932 <td><div align="left">
936 <!-- JAL-2643 -->Pressing tab after updating the colour
937 threshold text field doesn't trigger an update to the
941 <!-- JAL-2682 -->Race condition when parsing sequence ID
945 <!-- JAL-2608 -->Overview windows are also closed when
946 alignment window is closed
949 <!-- JAL-2548 -->Export of features doesn't always respect
953 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
954 takes a long time in Cursor mode
960 <!-- JAL-2777 -->Structures with whitespace chainCode
961 cannot be viewed in Chimera
964 <!-- JAL-2728 -->Protein annotation panel too high in
968 <!-- JAL-2757 -->Can't edit the query after the server
969 error warning icon is shown in Uniprot and PDB Free Text
973 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
976 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
979 <!-- JAL-2739 -->Hidden column marker in last column not
980 rendered when switching back from Wrapped to normal view
983 <!-- JAL-2768 -->Annotation display corrupted when
984 scrolling right in unwapped alignment view
987 <!-- JAL-2542 -->Existing features on subsequence
988 incorrectly relocated when full sequence retrieved from
992 <!-- JAL-2733 -->Last reported memory still shown when
993 Desktop->Show Memory is unticked (OSX only)
996 <!-- JAL-2658 -->Amend Features dialog doesn't allow
997 features of same type and group to be selected for
1001 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1002 alignments when hidden columns are present
1005 <!-- JAL-2392 -->Jalview freezes when loading and
1006 displaying several structures
1009 <!-- JAL-2732 -->Black outlines left after resizing or
1013 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1014 within the Jalview desktop on OSX
1017 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1018 when in wrapped alignment mode
1021 <!-- JAL-2636 -->Scale mark not shown when close to right
1022 hand end of alignment
1025 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1026 each selected sequence do not have correct start/end
1030 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1031 after canceling the Alignment Window's Font dialog
1034 <!-- JAL-2036 -->Show cross-references not enabled after
1035 restoring project until a new view is created
1038 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1039 URL links appears when only default EMBL-EBI link is
1040 configured (since 2.10.2b2)
1043 <!-- JAL-2775 -->Overview redraws whole window when box
1044 position is adjusted
1047 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1048 in a multi-chain structure when viewing alignment
1049 involving more than one chain (since 2.10)
1052 <!-- JAL-2811 -->Double residue highlights in cursor mode
1053 if new selection moves alignment window
1056 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1057 arrow key in cursor mode to pass hidden column marker
1060 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1061 that produces correctly annotated transcripts and products
1064 <!-- JAL-2776 -->Toggling a feature group after first time
1065 doesn't update associated structure view
1068 <em>Applet</em><br />
1071 <!-- JAL-2687 -->Concurrent modification exception when
1072 closing alignment panel
1075 <em>BioJSON</em><br />
1078 <!-- JAL-2546 -->BioJSON export does not preserve
1079 non-positional features
1082 <em>New Known Issues</em>
1085 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1086 sequence features correctly (for many previous versions of
1090 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1091 using cursor in wrapped panel other than top
1094 <!-- JAL-2791 -->Select columns containing feature ignores
1095 graduated colour threshold
1098 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1099 always preserve numbering and sequence features
1102 <em>Known Java 9 Issues</em>
1105 <!-- JAL-2902 -->Groovy Console very slow to open and is
1106 not responsive when entering characters (Webstart, Java
1113 <td width="60" nowrap>
1114 <div align="center">
1115 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1116 <em>2/10/2017</em></strong>
1119 <td><div align="left">
1120 <em>New features in Jalview Desktop</em>
1123 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1125 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1129 <td><div align="left">
1133 <td width="60" nowrap>
1134 <div align="center">
1135 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1136 <em>7/9/2017</em></strong>
1139 <td><div align="left">
1143 <!-- JAL-2588 -->Show gaps in overview window by colouring
1144 in grey (sequences used to be coloured grey, and gaps were
1148 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1152 <!-- JAL-2587 -->Overview updates immediately on increase
1153 in size and progress bar shown as higher resolution
1154 overview is recalculated
1159 <td><div align="left">
1163 <!-- JAL-2664 -->Overview window redraws every hidden
1164 column region row by row
1167 <!-- JAL-2681 -->duplicate protein sequences shown after
1168 retrieving Ensembl crossrefs for sequences from Uniprot
1171 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1172 format setting is unticked
1175 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1176 if group has show boxes format setting unticked
1179 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1180 autoscrolling whilst dragging current selection group to
1181 include sequences and columns not currently displayed
1184 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1185 assemblies are imported via CIF file
1188 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1189 displayed when threshold or conservation colouring is also
1193 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1197 <!-- JAL-2673 -->Jalview continues to scroll after
1198 dragging a selected region off the visible region of the
1202 <!-- JAL-2724 -->Cannot apply annotation based
1203 colourscheme to all groups in a view
1206 <!-- JAL-2511 -->IDs don't line up with sequences
1207 initially after font size change using the Font chooser or
1214 <td width="60" nowrap>
1215 <div align="center">
1216 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1219 <td><div align="left">
1220 <em>Calculations</em>
1224 <!-- JAL-1933 -->Occupancy annotation row shows number of
1225 ungapped positions in each column of the alignment.
1228 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1229 a calculation dialog box
1232 <!-- JAL-2379 -->Revised implementation of PCA for speed
1233 and memory efficiency (~30x faster)
1236 <!-- JAL-2403 -->Revised implementation of sequence
1237 similarity scores as used by Tree, PCA, Shading Consensus
1238 and other calculations
1241 <!-- JAL-2416 -->Score matrices are stored as resource
1242 files within the Jalview codebase
1245 <!-- JAL-2500 -->Trees computed on Sequence Feature
1246 Similarity may have different topology due to increased
1253 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1254 model for alignments and groups
1257 <!-- JAL-384 -->Custom shading schemes created via groovy
1264 <!-- JAL-2526 -->Efficiency improvements for interacting
1265 with alignment and overview windows
1268 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1272 <!-- JAL-2388 -->Hidden columns and sequences can be
1276 <!-- JAL-2611 -->Click-drag in visible area allows fine
1277 adjustment of visible position
1281 <em>Data import/export</em>
1284 <!-- JAL-2535 -->Posterior probability annotation from
1285 Stockholm files imported as sequence associated annotation
1288 <!-- JAL-2507 -->More robust per-sequence positional
1289 annotation input/output via stockholm flatfile
1292 <!-- JAL-2533 -->Sequence names don't include file
1293 extension when importing structure files without embedded
1294 names or PDB accessions
1297 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1298 format sequence substitution matrices
1301 <em>User Interface</em>
1304 <!-- JAL-2447 --> Experimental Features Checkbox in
1305 Desktop's Tools menu to hide or show untested features in
1309 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1310 via Overview or sequence motif search operations
1313 <!-- JAL-2547 -->Amend sequence features dialog box can be
1314 opened by double clicking gaps within sequence feature
1318 <!-- JAL-1476 -->Status bar message shown when not enough
1319 aligned positions were available to create a 3D structure
1323 <em>3D Structure</em>
1326 <!-- JAL-2430 -->Hidden regions in alignment views are not
1327 coloured in linked structure views
1330 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1331 file-based command exchange
1334 <!-- JAL-2375 -->Structure chooser automatically shows
1335 Cached Structures rather than querying the PDBe if
1336 structures are already available for sequences
1339 <!-- JAL-2520 -->Structures imported via URL are cached in
1340 the Jalview project rather than downloaded again when the
1341 project is reopened.
1344 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1345 to transfer Chimera's structure attributes as Jalview
1346 features, and vice-versa (<strong>Experimental
1350 <em>Web Services</em>
1353 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1356 <!-- JAL-2335 -->Filter non-standard amino acids and
1357 nucleotides when submitting to AACon and other MSA
1361 <!-- JAL-2316, -->URLs for viewing database
1362 cross-references provided by identifiers.org and the
1363 EMBL-EBI's MIRIAM DB
1370 <!-- JAL-2344 -->FileFormatI interface for describing and
1371 identifying file formats (instead of String constants)
1374 <!-- JAL-2228 -->FeatureCounter script refactored for
1375 efficiency when counting all displayed features (not
1376 backwards compatible with 2.10.1)
1379 <em>Example files</em>
1382 <!-- JAL-2631 -->Graduated feature colour style example
1383 included in the example feature file
1386 <em>Documentation</em>
1389 <!-- JAL-2339 -->Release notes reformatted for readability
1390 with the built-in Java help viewer
1393 <!-- JAL-1644 -->Find documentation updated with 'search
1394 sequence description' option
1400 <!-- JAL-2485, -->External service integration tests for
1401 Uniprot REST Free Text Search Client
1404 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1407 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1412 <td><div align="left">
1413 <em>Calculations</em>
1416 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1417 matrix - C->R should be '-3'<br />Old matrix restored
1418 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1420 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1421 Jalview's treatment of gaps in PCA and substitution matrix
1422 based Tree calculations.<br /> <br />In earlier versions
1423 of Jalview, gaps matching gaps were penalised, and gaps
1424 matching non-gaps penalised even more. In the PCA
1425 calculation, gaps were actually treated as non-gaps - so
1426 different costs were applied, which meant Jalview's PCAs
1427 were different to those produced by SeqSpace.<br />Jalview
1428 now treats gaps in the same way as SeqSpace (ie it scores
1429 them as 0). <br /> <br />Enter the following in the
1430 Groovy console to restore pre-2.10.2 behaviour:<br />
1431 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1432 // for 2.10.1 mode <br />
1433 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1434 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1435 these settings will affect all subsequent tree and PCA
1436 calculations (not recommended)</em></li>
1438 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1439 scaling of branch lengths for trees computed using
1440 Sequence Feature Similarity.
1443 <!-- JAL-2377 -->PCA calculation could hang when
1444 generating output report when working with highly
1445 redundant alignments
1448 <!-- JAL-2544 --> Sort by features includes features to
1449 right of selected region when gaps present on right-hand
1453 <em>User Interface</em>
1456 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1457 doesn't reselect a specific sequence's associated
1458 annotation after it was used for colouring a view
1461 <!-- JAL-2419 -->Current selection lost if popup menu
1462 opened on a region of alignment without groups
1465 <!-- JAL-2374 -->Popup menu not always shown for regions
1466 of an alignment with overlapping groups
1469 <!-- JAL-2310 -->Finder double counts if both a sequence's
1470 name and description match
1473 <!-- JAL-2370 -->Hiding column selection containing two
1474 hidden regions results in incorrect hidden regions
1477 <!-- JAL-2386 -->'Apply to all groups' setting when
1478 changing colour does not apply Conservation slider value
1482 <!-- JAL-2373 -->Percentage identity and conservation menu
1483 items do not show a tick or allow shading to be disabled
1486 <!-- JAL-2385 -->Conservation shading or PID threshold
1487 lost when base colourscheme changed if slider not visible
1490 <!-- JAL-2547 -->Sequence features shown in tooltip for
1491 gaps before start of features
1494 <!-- JAL-2623 -->Graduated feature colour threshold not
1495 restored to UI when feature colour is edited
1498 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1499 a time when scrolling vertically in wrapped mode.
1502 <!-- JAL-2630 -->Structure and alignment overview update
1503 as graduate feature colour settings are modified via the
1507 <!-- JAL-2034 -->Overview window doesn't always update
1508 when a group defined on the alignment is resized
1511 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1512 wrapped view result in positional status updates
1516 <!-- JAL-2563 -->Status bar doesn't show position for
1517 ambiguous amino acid and nucleotide symbols
1520 <!-- JAL-2602 -->Copy consensus sequence failed if
1521 alignment included gapped columns
1524 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1525 widgets don't permanently disappear
1528 <!-- JAL-2503 -->Cannot select or filter quantitative
1529 annotation that are shown only as column labels (e.g.
1530 T-Coffee column reliability scores)
1533 <!-- JAL-2594 -->Exception thrown if trying to create a
1534 sequence feature on gaps only
1537 <!-- JAL-2504 -->Features created with 'New feature'
1538 button from a Find inherit previously defined feature type
1539 rather than the Find query string
1542 <!-- JAL-2423 -->incorrect title in output window when
1543 exporting tree calculated in Jalview
1546 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1547 and then revealing them reorders sequences on the
1551 <!-- JAL-964 -->Group panel in sequence feature settings
1552 doesn't update to reflect available set of groups after
1553 interactively adding or modifying features
1556 <!-- JAL-2225 -->Sequence Database chooser unusable on
1560 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1561 only excluded gaps in current sequence and ignored
1568 <!-- JAL-2421 -->Overview window visible region moves
1569 erratically when hidden rows or columns are present
1572 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1573 Structure Viewer's colour menu don't correspond to
1577 <!-- JAL-2405 -->Protein specific colours only offered in
1578 colour and group colour menu for protein alignments
1581 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1582 reflect currently selected view or group's shading
1586 <!-- JAL-2624 -->Feature colour thresholds not respected
1587 when rendered on overview and structures when opacity at
1591 <!-- JAL-2589 -->User defined gap colour not shown in
1592 overview when features overlaid on alignment
1595 <!-- JAL-2567 -->Feature settings for different views not
1596 recovered correctly from Jalview project file
1599 <!-- JAL-2256 -->Feature colours in overview when first opened
1600 (automatically via preferences) are different to the main
1604 <em>Data import/export</em>
1607 <!-- JAL-2576 -->Very large alignments take a long time to
1611 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1612 added after a sequence was imported are not written to
1616 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1617 when importing RNA secondary structure via Stockholm
1620 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1621 not shown in correct direction for simple pseudoknots
1624 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1625 with lightGray or darkGray via features file (but can
1629 <!-- JAL-2383 -->Above PID colour threshold not recovered
1630 when alignment view imported from project
1633 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1634 structure and sequences extracted from structure files
1635 imported via URL and viewed in Jmol
1638 <!-- JAL-2520 -->Structures loaded via URL are saved in
1639 Jalview Projects rather than fetched via URL again when
1640 the project is loaded and the structure viewed
1643 <em>Web Services</em>
1646 <!-- JAL-2519 -->EnsemblGenomes example failing after
1647 release of Ensembl v.88
1650 <!-- JAL-2366 -->Proxy server address and port always
1651 appear enabled in Preferences->Connections
1654 <!-- JAL-2461 -->DAS registry not found exceptions
1655 removed from console output
1658 <!-- JAL-2582 -->Cannot retrieve protein products from
1659 Ensembl by Peptide ID
1662 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1663 created from SIFTs, and spurious 'Couldn't open structure
1664 in Chimera' errors raised after April 2017 update (problem
1665 due to 'null' string rather than empty string used for
1666 residues with no corresponding PDB mapping).
1669 <em>Application UI</em>
1672 <!-- JAL-2361 -->User Defined Colours not added to Colour
1676 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1677 case' residues (button in colourscheme editor debugged and
1678 new documentation and tooltips added)
1681 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1682 doesn't restore group-specific text colour thresholds
1685 <!-- JAL-2243 -->Feature settings panel does not update as
1686 new features are added to alignment
1689 <!-- JAL-2532 -->Cancel in feature settings reverts
1690 changes to feature colours via the Amend features dialog
1693 <!-- JAL-2506 -->Null pointer exception when attempting to
1694 edit graduated feature colour via amend features dialog
1698 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1699 selection menu changes colours of alignment views
1702 <!-- JAL-2426 -->Spurious exceptions in console raised
1703 from alignment calculation workers after alignment has
1707 <!-- JAL-1608 -->Typo in selection popup menu - Create
1708 groups now 'Create Group'
1711 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1712 Create/Undefine group doesn't always work
1715 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1716 shown again after pressing 'Cancel'
1719 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1720 adjusts start position in wrap mode
1723 <!-- JAL-2563 -->Status bar doesn't show positions for
1724 ambiguous amino acids
1727 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1728 CDS/Protein view after CDS sequences added for aligned
1732 <!-- JAL-2592 -->User defined colourschemes called 'User
1733 Defined' don't appear in Colours menu
1739 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1740 score models doesn't always result in an updated PCA plot
1743 <!-- JAL-2442 -->Features not rendered as transparent on
1744 overview or linked structure view
1747 <!-- JAL-2372 -->Colour group by conservation doesn't
1751 <!-- JAL-2517 -->Hitting Cancel after applying
1752 user-defined colourscheme doesn't restore original
1759 <!-- JAL-2314 -->Unit test failure:
1760 jalview.ws.jabaws.RNAStructExportImport setup fails
1763 <!-- JAL-2307 -->Unit test failure:
1764 jalview.ws.sifts.SiftsClientTest due to compatibility
1765 problems with deep array comparison equality asserts in
1766 successive versions of TestNG
1769 <!-- JAL-2479 -->Relocated StructureChooserTest and
1770 ParameterUtilsTest Unit tests to Network suite
1773 <em>New Known Issues</em>
1776 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1777 phase after a sequence motif find operation
1780 <!-- JAL-2550 -->Importing annotation file with rows
1781 containing just upper and lower case letters are
1782 interpreted as WUSS RNA secondary structure symbols
1785 <!-- JAL-2590 -->Cannot load and display Newick trees
1786 reliably from eggnog Ortholog database
1789 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1790 containing features of type Highlight' when 'B' is pressed
1791 to mark columns containing highlighted regions.
1794 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1795 doesn't always add secondary structure annotation.
1800 <td width="60" nowrap>
1801 <div align="center">
1802 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1805 <td><div align="left">
1809 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1810 for all consensus calculations
1813 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1816 <li>Updated Jalview's Certum code signing certificate
1819 <em>Application</em>
1822 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1823 set of database cross-references, sorted alphabetically
1826 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1827 from database cross references. Users with custom links
1828 will receive a <a href="webServices/urllinks.html#warning">warning
1829 dialog</a> asking them to update their preferences.
1832 <!-- JAL-2287-->Cancel button and escape listener on
1833 dialog warning user about disconnecting Jalview from a
1837 <!-- JAL-2320-->Jalview's Chimera control window closes if
1838 the Chimera it is connected to is shut down
1841 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1842 columns menu item to mark columns containing highlighted
1843 regions (e.g. from structure selections or results of a
1847 <!-- JAL-2284-->Command line option for batch-generation
1848 of HTML pages rendering alignment data with the BioJS
1858 <!-- JAL-2286 -->Columns with more than one modal residue
1859 are not coloured or thresholded according to percent
1860 identity (first observed in Jalview 2.8.2)
1863 <!-- JAL-2301 -->Threonine incorrectly reported as not
1867 <!-- JAL-2318 -->Updates to documentation pages (above PID
1868 threshold, amino acid properties)
1871 <!-- JAL-2292 -->Lower case residues in sequences are not
1872 reported as mapped to residues in a structure file in the
1876 <!--JAL-2324 -->Identical features with non-numeric scores
1877 could be added multiple times to a sequence
1880 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1881 bond features shown as two highlighted residues rather
1882 than a range in linked structure views, and treated
1883 correctly when selecting and computing trees from features
1886 <!-- JAL-2281-->Custom URL links for database
1887 cross-references are matched to database name regardless
1892 <em>Application</em>
1895 <!-- JAL-2282-->Custom URL links for specific database
1896 names without regular expressions also offer links from
1900 <!-- JAL-2315-->Removing a single configured link in the
1901 URL links pane in Connections preferences doesn't actually
1902 update Jalview configuration
1905 <!-- JAL-2272-->CTRL-Click on a selected region to open
1906 the alignment area popup menu doesn't work on El-Capitan
1909 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1910 files with similarly named sequences if dropped onto the
1914 <!-- JAL-2312 -->Additional mappings are shown for PDB
1915 entries where more chains exist in the PDB accession than
1916 are reported in the SIFTS file
1919 <!-- JAL-2317-->Certain structures do not get mapped to
1920 the structure view when displayed with Chimera
1923 <!-- JAL-2317-->No chains shown in the Chimera view
1924 panel's View->Show Chains submenu
1927 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1928 work for wrapped alignment views
1931 <!--JAL-2197 -->Rename UI components for running JPred
1932 predictions from 'JNet' to 'JPred'
1935 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1936 corrupted when annotation panel vertical scroll is not at
1937 first annotation row
1940 <!--JAL-2332 -->Attempting to view structure for Hen
1941 lysozyme results in a PDB Client error dialog box
1944 <!-- JAL-2319 -->Structure View's mapping report switched
1945 ranges for PDB and sequence for SIFTS
1948 SIFTS 'Not_Observed' residues mapped to non-existant
1952 <!-- <em>New Known Issues</em>
1959 <td width="60" nowrap>
1960 <div align="center">
1961 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1962 <em>25/10/2016</em></strong>
1965 <td><em>Application</em>
1967 <li>3D Structure chooser opens with 'Cached structures'
1968 view if structures already loaded</li>
1969 <li>Progress bar reports models as they are loaded to
1970 structure views</li>
1976 <li>Colour by conservation always enabled and no tick
1977 shown in menu when BLOSUM or PID shading applied</li>
1978 <li>FER1_ARATH and FER2_ARATH labels were switched in
1979 example sequences/projects/trees</li>
1981 <em>Application</em>
1983 <li>Jalview projects with views of local PDB structure
1984 files saved on Windows cannot be opened on OSX</li>
1985 <li>Multiple structure views can be opened and superposed
1986 without timeout for structures with multiple models or
1987 multiple sequences in alignment</li>
1988 <li>Cannot import or associated local PDB files without a
1989 PDB ID HEADER line</li>
1990 <li>RMSD is not output in Jmol console when superposition
1992 <li>Drag and drop of URL from Browser fails for Linux and
1993 OSX versions earlier than El Capitan</li>
1994 <li>ENA client ignores invalid content from ENA server</li>
1995 <li>Exceptions are not raised in console when ENA client
1996 attempts to fetch non-existent IDs via Fetch DB Refs UI
1998 <li>Exceptions are not raised in console when a new view
1999 is created on the alignment</li>
2000 <li>OSX right-click fixed for group selections: CMD-click
2001 to insert/remove gaps in groups and CTRL-click to open group
2004 <em>Build and deployment</em>
2006 <li>URL link checker now copes with multi-line anchor
2009 <em>New Known Issues</em>
2011 <li>Drag and drop from URL links in browsers do not work
2018 <td width="60" nowrap>
2019 <div align="center">
2020 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2023 <td><em>General</em>
2026 <!-- JAL-2124 -->Updated Spanish translations.
2029 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2030 for importing structure data to Jalview. Enables mmCIF and
2034 <!-- JAL-192 --->Alignment ruler shows positions relative to
2038 <!-- JAL-2202 -->Position/residue shown in status bar when
2039 mousing over sequence associated annotation
2042 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2046 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2047 '()', canonical '[]' and invalid '{}' base pair populations
2051 <!-- JAL-2092 -->Feature settings popup menu options for
2052 showing or hiding columns containing a feature
2055 <!-- JAL-1557 -->Edit selected group by double clicking on
2056 group and sequence associated annotation labels
2059 <!-- JAL-2236 -->Sequence name added to annotation label in
2060 select/hide columns by annotation and colour by annotation
2064 </ul> <em>Application</em>
2067 <!-- JAL-2050-->Automatically hide introns when opening a
2068 gene/transcript view
2071 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2075 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2076 structure mappings with the EMBL-EBI PDBe SIFTS database
2079 <!-- JAL-2079 -->Updated download sites used for Rfam and
2080 Pfam sources to xfam.org
2083 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2086 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2087 over sequences in Jalview
2090 <!-- JAL-2027-->Support for reverse-complement coding
2091 regions in ENA and EMBL
2094 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2095 for record retrieval via ENA rest API
2098 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2102 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2103 groovy script execution
2106 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2107 alignment window's Calculate menu
2110 <!-- JAL-1812 -->Allow groovy scripts that call
2111 Jalview.getAlignFrames() to run in headless mode
2114 <!-- JAL-2068 -->Support for creating new alignment
2115 calculation workers from groovy scripts
2118 <!-- JAL-1369 --->Store/restore reference sequence in
2122 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2123 associations are now saved/restored from project
2126 <!-- JAL-1993 -->Database selection dialog always shown
2127 before sequence fetcher is opened
2130 <!-- JAL-2183 -->Double click on an entry in Jalview's
2131 database chooser opens a sequence fetcher
2134 <!-- JAL-1563 -->Free-text search client for UniProt using
2135 the UniProt REST API
2138 <!-- JAL-2168 -->-nonews command line parameter to prevent
2139 the news reader opening
2142 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2143 querying stored in preferences
2146 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2150 <!-- JAL-1977-->Tooltips shown on database chooser
2153 <!-- JAL-391 -->Reverse complement function in calculate
2154 menu for nucleotide sequences
2157 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2158 and feature counts preserves alignment ordering (and
2159 debugged for complex feature sets).
2162 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2163 viewing structures with Jalview 2.10
2166 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2167 genome, transcript CCDS and gene ids via the Ensembl and
2168 Ensembl Genomes REST API
2171 <!-- JAL-2049 -->Protein sequence variant annotation
2172 computed for 'sequence_variant' annotation on CDS regions
2176 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2180 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2181 Ref Fetcher fails to match, or otherwise updates sequence
2182 data from external database records.
2185 <!-- JAL-2154 -->Revised Jalview Project format for
2186 efficient recovery of sequence coding and alignment
2187 annotation relationships.
2189 </ul> <!-- <em>Applet</em>
2200 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2204 <!-- JAL-2018-->Export features in Jalview format (again)
2205 includes graduated colourschemes
2208 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2209 working with big alignments and lots of hidden columns
2212 <!-- JAL-2053-->Hidden column markers not always rendered
2213 at right of alignment window
2216 <!-- JAL-2067 -->Tidied up links in help file table of
2220 <!-- JAL-2072 -->Feature based tree calculation not shown
2224 <!-- JAL-2075 -->Hidden columns ignored during feature
2225 based tree calculation
2228 <!-- JAL-2065 -->Alignment view stops updating when show
2229 unconserved enabled for group on alignment
2232 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2236 <!-- JAL-2146 -->Alignment column in status incorrectly
2237 shown as "Sequence position" when mousing over
2241 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2242 hidden columns present
2245 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2246 user created annotation added to alignment
2249 <!-- JAL-1841 -->RNA Structure consensus only computed for
2250 '()' base pair annotation
2253 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2254 in zero scores for all base pairs in RNA Structure
2258 <!-- JAL-2174-->Extend selection with columns containing
2262 <!-- JAL-2275 -->Pfam format writer puts extra space at
2263 beginning of sequence
2266 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2270 <!-- JAL-2238 -->Cannot create groups on an alignment from
2271 from a tree when t-coffee scores are shown
2274 <!-- JAL-1836,1967 -->Cannot import and view PDB
2275 structures with chains containing negative resnums (4q4h)
2278 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2282 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2283 to Clustal, PIR and PileUp output
2286 <!-- JAL-2008 -->Reordering sequence features that are
2287 not visible causes alignment window to repaint
2290 <!-- JAL-2006 -->Threshold sliders don't work in
2291 graduated colour and colour by annotation row for e-value
2292 scores associated with features and annotation rows
2295 <!-- JAL-1797 -->amino acid physicochemical conservation
2296 calculation should be case independent
2299 <!-- JAL-2173 -->Remove annotation also updates hidden
2303 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2304 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2305 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2308 <!-- JAL-2065 -->Null pointer exceptions and redraw
2309 problems when reference sequence defined and 'show
2310 non-conserved' enabled
2313 <!-- JAL-1306 -->Quality and Conservation are now shown on
2314 load even when Consensus calculation is disabled
2317 <!-- JAL-1932 -->Remove right on penultimate column of
2318 alignment does nothing
2321 <em>Application</em>
2324 <!-- JAL-1552-->URLs and links can't be imported by
2325 drag'n'drop on OSX when launched via webstart (note - not
2326 yet fixed for El Capitan)
2329 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2330 output when running on non-gb/us i18n platforms
2333 <!-- JAL-1944 -->Error thrown when exporting a view with
2334 hidden sequences as flat-file alignment
2337 <!-- JAL-2030-->InstallAnywhere distribution fails when
2341 <!-- JAL-2080-->Jalview very slow to launch via webstart
2342 (also hotfix for 2.9.0b2)
2345 <!-- JAL-2085 -->Cannot save project when view has a
2346 reference sequence defined
2349 <!-- JAL-1011 -->Columns are suddenly selected in other
2350 alignments and views when revealing hidden columns
2353 <!-- JAL-1989 -->Hide columns not mirrored in complement
2354 view in a cDNA/Protein splitframe
2357 <!-- JAL-1369 -->Cannot save/restore representative
2358 sequence from project when only one sequence is
2362 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2363 in Structure Chooser
2366 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2367 structure consensus didn't refresh annotation panel
2370 <!-- JAL-1962 -->View mapping in structure view shows
2371 mappings between sequence and all chains in a PDB file
2374 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2375 dialogs format columns correctly, don't display array
2376 data, sort columns according to type
2379 <!-- JAL-1975 -->Export complete shown after destination
2380 file chooser is cancelled during an image export
2383 <!-- JAL-2025 -->Error when querying PDB Service with
2384 sequence name containing special characters
2387 <!-- JAL-2024 -->Manual PDB structure querying should be
2391 <!-- JAL-2104 -->Large tooltips with broken HTML
2392 formatting don't wrap
2395 <!-- JAL-1128 -->Figures exported from wrapped view are
2396 truncated so L looks like I in consensus annotation
2399 <!-- JAL-2003 -->Export features should only export the
2400 currently displayed features for the current selection or
2404 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2405 after fetching cross-references, and restoring from
2409 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2410 followed in the structure viewer
2413 <!-- JAL-2163 -->Titles for individual alignments in
2414 splitframe not restored from project
2417 <!-- JAL-2145 -->missing autocalculated annotation at
2418 trailing end of protein alignment in transcript/product
2419 splitview when pad-gaps not enabled by default
2422 <!-- JAL-1797 -->amino acid physicochemical conservation
2426 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2427 article has been read (reopened issue due to
2428 internationalisation problems)
2431 <!-- JAL-1960 -->Only offer PDB structures in structure
2432 viewer based on sequence name, PDB and UniProt
2437 <!-- JAL-1976 -->No progress bar shown during export of
2441 <!-- JAL-2213 -->Structures not always superimposed after
2442 multiple structures are shown for one or more sequences.
2445 <!-- JAL-1370 -->Reference sequence characters should not
2446 be replaced with '.' when 'Show unconserved' format option
2450 <!-- JAL-1823 -->Cannot specify chain code when entering
2451 specific PDB id for sequence
2454 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2455 'Export hidden sequences' is enabled, but 'export hidden
2456 columns' is disabled.
2459 <!--JAL-2026-->Best Quality option in structure chooser
2460 selects lowest rather than highest resolution structures
2464 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2465 to sequence mapping in 'View Mappings' report
2468 <!-- JAL-2284 -->Unable to read old Jalview projects that
2469 contain non-XML data added after Jalvew wrote project.
2472 <!-- JAL-2118 -->Newly created annotation row reorders
2473 after clicking on it to create new annotation for a
2477 <!-- JAL-1980 -->Null Pointer Exception raised when
2478 pressing Add on an orphaned cut'n'paste window.
2480 <!-- may exclude, this is an external service stability issue JAL-1941
2481 -- > RNA 3D structure not added via DSSR service</li> -->
2486 <!-- JAL-2151 -->Incorrect columns are selected when
2487 hidden columns present before start of sequence
2490 <!-- JAL-1986 -->Missing dependencies on applet pages
2494 <!-- JAL-1947 -->Overview pixel size changes when
2495 sequences are hidden in applet
2498 <!-- JAL-1996 -->Updated instructions for applet
2499 deployment on examples pages.
2506 <td width="60" nowrap>
2507 <div align="center">
2508 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2509 <em>16/10/2015</em></strong>
2512 <td><em>General</em>
2514 <li>Time stamps for signed Jalview application and applet
2519 <em>Application</em>
2521 <li>Duplicate group consensus and conservation rows
2522 shown when tree is partitioned</li>
2523 <li>Erratic behaviour when tree partitions made with
2524 multiple cDNA/Protein split views</li>
2530 <td width="60" nowrap>
2531 <div align="center">
2532 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2533 <em>8/10/2015</em></strong>
2536 <td><em>General</em>
2538 <li>Updated Spanish translations of localized text for
2540 </ul> <em>Application</em>
2542 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2543 <li>Signed OSX InstallAnywhere installer<br></li>
2544 <li>Support for per-sequence based annotations in BioJSON</li>
2545 </ul> <em>Applet</em>
2547 <li>Split frame example added to applet examples page</li>
2548 </ul> <em>Build and Deployment</em>
2551 <!-- JAL-1888 -->New ant target for running Jalview's test
2559 <li>Mapping of cDNA to protein in split frames
2560 incorrect when sequence start > 1</li>
2561 <li>Broken images in filter column by annotation dialog
2563 <li>Feature colours not parsed from features file</li>
2564 <li>Exceptions and incomplete link URLs recovered when
2565 loading a features file containing HTML tags in feature
2569 <em>Application</em>
2571 <li>Annotations corrupted after BioJS export and
2573 <li>Incorrect sequence limits after Fetch DB References
2574 with 'trim retrieved sequences'</li>
2575 <li>Incorrect warning about deleting all data when
2576 deleting selected columns</li>
2577 <li>Patch to build system for shipping properly signed
2578 JNLP templates for webstart launch</li>
2579 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2580 unreleased structures for download or viewing</li>
2581 <li>Tab/space/return keystroke operation of EMBL-PDBe
2582 fetcher/viewer dialogs works correctly</li>
2583 <li>Disabled 'minimise' button on Jalview windows
2584 running on OSX to workaround redraw hang bug</li>
2585 <li>Split cDNA/Protein view position and geometry not
2586 recovered from jalview project</li>
2587 <li>Initial enabled/disabled state of annotation menu
2588 sorter 'show autocalculated first/last' corresponds to
2590 <li>Restoring of Clustal, RNA Helices and T-Coffee
2591 color schemes from BioJSON</li>
2595 <li>Reorder sequences mirrored in cDNA/Protein split
2597 <li>Applet with Jmol examples not loading correctly</li>
2603 <td><div align="center">
2604 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2606 <td><em>General</em>
2608 <li>Linked visualisation and analysis of DNA and Protein
2611 <li>Translated cDNA alignments shown as split protein
2612 and DNA alignment views</li>
2613 <li>Codon consensus annotation for linked protein and
2614 cDNA alignment views</li>
2615 <li>Link cDNA or Protein product sequences by loading
2616 them onto Protein or cDNA alignments</li>
2617 <li>Reconstruct linked cDNA alignment from aligned
2618 protein sequences</li>
2621 <li>Jmol integration updated to Jmol v14.2.14</li>
2622 <li>Import and export of Jalview alignment views as <a
2623 href="features/bioJsonFormat.html">BioJSON</a></li>
2624 <li>New alignment annotation file statements for
2625 reference sequences and marking hidden columns</li>
2626 <li>Reference sequence based alignment shading to
2627 highlight variation</li>
2628 <li>Select or hide columns according to alignment
2630 <li>Find option for locating sequences by description</li>
2631 <li>Conserved physicochemical properties shown in amino
2632 acid conservation row</li>
2633 <li>Alignments can be sorted by number of RNA helices</li>
2634 </ul> <em>Application</em>
2636 <li>New cDNA/Protein analysis capabilities
2638 <li>Get Cross-References should open a Split Frame
2639 view with cDNA/Protein</li>
2640 <li>Detect when nucleotide sequences and protein
2641 sequences are placed in the same alignment</li>
2642 <li>Split cDNA/Protein views are saved in Jalview
2647 <li>Use REST API to talk to Chimera</li>
2648 <li>Selected regions in Chimera are highlighted in linked
2649 Jalview windows</li>
2651 <li>VARNA RNA viewer updated to v3.93</li>
2652 <li>VARNA views are saved in Jalview Projects</li>
2653 <li>Pseudoknots displayed as Jalview RNA annotation can
2654 be shown in VARNA</li>
2656 <li>Make groups for selection uses marked columns as well
2657 as the active selected region</li>
2659 <li>Calculate UPGMA and NJ trees using sequence feature
2661 <li>New Export options
2663 <li>New Export Settings dialog to control hidden
2664 region export in flat file generation</li>
2666 <li>Export alignment views for display with the <a
2667 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2669 <li>Export scrollable SVG in HTML page</li>
2670 <li>Optional embedding of BioJSON data when exporting
2671 alignment figures to HTML</li>
2673 <li>3D structure retrieval and display
2675 <li>Free text and structured queries with the PDBe
2677 <li>PDBe Search API based discovery and selection of
2678 PDB structures for a sequence set</li>
2682 <li>JPred4 employed for protein secondary structure
2684 <li>Hide Insertions menu option to hide unaligned columns
2685 for one or a group of sequences</li>
2686 <li>Automatically hide insertions in alignments imported
2687 from the JPred4 web server</li>
2688 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2689 system on OSX<br />LGPL libraries courtesy of <a
2690 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2692 <li>changed 'View nucleotide structure' submenu to 'View
2693 VARNA 2D Structure'</li>
2694 <li>change "View protein structure" menu option to "3D
2697 </ul> <em>Applet</em>
2699 <li>New layout for applet example pages</li>
2700 <li>New parameters to enable SplitFrame view
2701 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2702 <li>New example demonstrating linked viewing of cDNA and
2703 Protein alignments</li>
2704 </ul> <em>Development and deployment</em>
2706 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2707 <li>Include installation type and git revision in build
2708 properties and console log output</li>
2709 <li>Jalview Github organisation, and new github site for
2710 storing BioJsMSA Templates</li>
2711 <li>Jalview's unit tests now managed with TestNG</li>
2714 <!-- <em>General</em>
2716 </ul> --> <!-- issues resolved --> <em>Application</em>
2718 <li>Escape should close any open find dialogs</li>
2719 <li>Typo in select-by-features status report</li>
2720 <li>Consensus RNA secondary secondary structure
2721 predictions are not highlighted in amber</li>
2722 <li>Missing gap character in v2.7 example file means
2723 alignment appears unaligned when pad-gaps is not enabled</li>
2724 <li>First switch to RNA Helices colouring doesn't colour
2725 associated structure views</li>
2726 <li>ID width preference option is greyed out when auto
2727 width checkbox not enabled</li>
2728 <li>Stopped a warning dialog from being shown when
2729 creating user defined colours</li>
2730 <li>'View Mapping' in structure viewer shows sequence
2731 mappings for just that viewer's sequences</li>
2732 <li>Workaround for superposing PDB files containing
2733 multiple models in Chimera</li>
2734 <li>Report sequence position in status bar when hovering
2735 over Jmol structure</li>
2736 <li>Cannot output gaps as '.' symbols with Selection ->
2737 output to text box</li>
2738 <li>Flat file exports of alignments with hidden columns
2739 have incorrect sequence start/end</li>
2740 <li>'Aligning' a second chain to a Chimera structure from
2742 <li>Colour schemes applied to structure viewers don't
2743 work for nucleotide</li>
2744 <li>Loading/cut'n'pasting an empty or invalid file leads
2745 to a grey/invisible alignment window</li>
2746 <li>Exported Jpred annotation from a sequence region
2747 imports to different position</li>
2748 <li>Space at beginning of sequence feature tooltips shown
2749 on some platforms</li>
2750 <li>Chimera viewer 'View | Show Chain' menu is not
2752 <li>'New View' fails with a Null Pointer Exception in
2753 console if Chimera has been opened</li>
2754 <li>Mouseover to Chimera not working</li>
2755 <li>Miscellaneous ENA XML feature qualifiers not
2757 <li>NPE in annotation renderer after 'Extract Scores'</li>
2758 <li>If two structures in one Chimera window, mouseover of
2759 either sequence shows on first structure</li>
2760 <li>'Show annotations' options should not make
2761 non-positional annotations visible</li>
2762 <li>Subsequence secondary structure annotation not shown
2763 in right place after 'view flanking regions'</li>
2764 <li>File Save As type unset when current file format is
2766 <li>Save as '.jar' option removed for saving Jalview
2768 <li>Colour by Sequence colouring in Chimera more
2770 <li>Cannot 'add reference annotation' for a sequence in
2771 several views on same alignment</li>
2772 <li>Cannot show linked products for EMBL / ENA records</li>
2773 <li>Jalview's tooltip wraps long texts containing no
2775 </ul> <em>Applet</em>
2777 <li>Jmol to JalviewLite mouseover/link not working</li>
2778 <li>JalviewLite can't import sequences with ID
2779 descriptions containing angle brackets</li>
2780 </ul> <em>General</em>
2782 <li>Cannot export and reimport RNA secondary structure
2783 via jalview annotation file</li>
2784 <li>Random helix colour palette for colour by annotation
2785 with RNA secondary structure</li>
2786 <li>Mouseover to cDNA from STOP residue in protein
2787 translation doesn't work.</li>
2788 <li>hints when using the select by annotation dialog box</li>
2789 <li>Jmol alignment incorrect if PDB file has alternate CA
2791 <li>FontChooser message dialog appears to hang after
2792 choosing 1pt font</li>
2793 <li>Peptide secondary structure incorrectly imported from
2794 annotation file when annotation display text includes 'e' or
2796 <li>Cannot set colour of new feature type whilst creating
2798 <li>cDNA translation alignment should not be sequence
2799 order dependent</li>
2800 <li>'Show unconserved' doesn't work for lower case
2802 <li>Nucleotide ambiguity codes involving R not recognised</li>
2803 </ul> <em>Deployment and Documentation</em>
2805 <li>Applet example pages appear different to the rest of
2806 www.jalview.org</li>
2807 </ul> <em>Application Known issues</em>
2809 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2810 <li>Misleading message appears after trying to delete
2812 <li>Jalview icon not shown in dock after InstallAnywhere
2813 version launches</li>
2814 <li>Fetching EMBL reference for an RNA sequence results
2815 fails with a sequence mismatch</li>
2816 <li>Corrupted or unreadable alignment display when
2817 scrolling alignment to right</li>
2818 <li>ArrayIndexOutOfBoundsException thrown when remove
2819 empty columns called on alignment with ragged gapped ends</li>
2820 <li>auto calculated alignment annotation rows do not get
2821 placed above or below non-autocalculated rows</li>
2822 <li>Jalview dekstop becomes sluggish at full screen in
2823 ultra-high resolution</li>
2824 <li>Cannot disable consensus calculation independently of
2825 quality and conservation</li>
2826 <li>Mouseover highlighting between cDNA and protein can
2827 become sluggish with more than one splitframe shown</li>
2828 </ul> <em>Applet Known Issues</em>
2830 <li>Core PDB parsing code requires Jmol</li>
2831 <li>Sequence canvas panel goes white when alignment
2832 window is being resized</li>
2838 <td><div align="center">
2839 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2841 <td><em>General</em>
2843 <li>Updated Java code signing certificate donated by
2845 <li>Features and annotation preserved when performing
2846 pairwise alignment</li>
2847 <li>RNA pseudoknot annotation can be
2848 imported/exported/displayed</li>
2849 <li>'colour by annotation' can colour by RNA and
2850 protein secondary structure</li>
2851 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2852 post-hoc with 2.9 release</em>)
2855 </ul> <em>Application</em>
2857 <li>Extract and display secondary structure for sequences
2858 with 3D structures</li>
2859 <li>Support for parsing RNAML</li>
2860 <li>Annotations menu for layout
2862 <li>sort sequence annotation rows by alignment</li>
2863 <li>place sequence annotation above/below alignment
2866 <li>Output in Stockholm format</li>
2867 <li>Internationalisation: improved Spanish (es)
2869 <li>Structure viewer preferences tab</li>
2870 <li>Disorder and Secondary Structure annotation tracks
2871 shared between alignments</li>
2872 <li>UCSF Chimera launch and linked highlighting from
2874 <li>Show/hide all sequence associated annotation rows for
2875 all or current selection</li>
2876 <li>disorder and secondary structure predictions
2877 available as dataset annotation</li>
2878 <li>Per-sequence rna helices colouring</li>
2881 <li>Sequence database accessions imported when fetching
2882 alignments from Rfam</li>
2883 <li>update VARNA version to 3.91</li>
2885 <li>New groovy scripts for exporting aligned positions,
2886 conservation values, and calculating sum of pairs scores.</li>
2887 <li>Command line argument to set default JABAWS server</li>
2888 <li>include installation type in build properties and
2889 console log output</li>
2890 <li>Updated Jalview project format to preserve dataset
2894 <!-- issues resolved --> <em>Application</em>
2896 <li>Distinguish alignment and sequence associated RNA
2897 structure in structure->view->VARNA</li>
2898 <li>Raise dialog box if user deletes all sequences in an
2900 <li>Pressing F1 results in documentation opening twice</li>
2901 <li>Sequence feature tooltip is wrapped</li>
2902 <li>Double click on sequence associated annotation
2903 selects only first column</li>
2904 <li>Redundancy removal doesn't result in unlinked
2905 leaves shown in tree</li>
2906 <li>Undos after several redundancy removals don't undo
2908 <li>Hide sequence doesn't hide associated annotation</li>
2909 <li>User defined colours dialog box too big to fit on
2910 screen and buttons not visible</li>
2911 <li>author list isn't updated if already written to
2912 Jalview properties</li>
2913 <li>Popup menu won't open after retrieving sequence
2915 <li>File open window for associate PDB doesn't open</li>
2916 <li>Left-then-right click on a sequence id opens a
2917 browser search window</li>
2918 <li>Cannot open sequence feature shading/sort popup menu
2919 in feature settings dialog</li>
2920 <li>better tooltip placement for some areas of Jalview
2922 <li>Allow addition of JABAWS Server which doesn't
2923 pass validation</li>
2924 <li>Web services parameters dialog box is too large to
2926 <li>Muscle nucleotide alignment preset obscured by
2928 <li>JABAWS preset submenus don't contain newly
2929 defined user preset</li>
2930 <li>MSA web services warns user if they were launched
2931 with invalid input</li>
2932 <li>Jalview cannot contact DAS Registy when running on
2935 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2936 'Superpose with' submenu not shown when new view
2940 </ul> <!-- <em>Applet</em>
2942 </ul> <em>General</em>
2944 </ul>--> <em>Deployment and Documentation</em>
2946 <li>2G and 1G options in launchApp have no effect on
2947 memory allocation</li>
2948 <li>launchApp service doesn't automatically open
2949 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2951 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2952 InstallAnywhere reports cannot find valid JVM when Java
2953 1.7_055 is available
2955 </ul> <em>Application Known issues</em>
2958 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2959 corrupted or unreadable alignment display when scrolling
2963 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2964 retrieval fails but progress bar continues for DAS retrieval
2965 with large number of ID
2968 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2969 flatfile output of visible region has incorrect sequence
2973 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2974 rna structure consensus doesn't update when secondary
2975 structure tracks are rearranged
2978 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2979 invalid rna structure positional highlighting does not
2980 highlight position of invalid base pairs
2983 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2984 out of memory errors are not raised when saving Jalview
2985 project from alignment window file menu
2988 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2989 Switching to RNA Helices colouring doesn't propagate to
2993 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2994 colour by RNA Helices not enabled when user created
2995 annotation added to alignment
2998 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2999 Jalview icon not shown on dock in Mountain Lion/Webstart
3001 </ul> <em>Applet Known Issues</em>
3004 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3005 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3008 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3009 Jalview and Jmol example not compatible with IE9
3012 <li>Sort by annotation score doesn't reverse order
3018 <td><div align="center">
3019 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3022 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3025 <li>Internationalisation of user interface (usually
3026 called i18n support) and translation for Spanish locale</li>
3027 <li>Define/Undefine group on current selection with
3028 Ctrl-G/Shift Ctrl-G</li>
3029 <li>Improved group creation/removal options in
3030 alignment/sequence Popup menu</li>
3031 <li>Sensible precision for symbol distribution
3032 percentages shown in logo tooltip.</li>
3033 <li>Annotation panel height set according to amount of
3034 annotation when alignment first opened</li>
3035 </ul> <em>Application</em>
3037 <li>Interactive consensus RNA secondary structure
3038 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3039 <li>Select columns containing particular features from
3040 Feature Settings dialog</li>
3041 <li>View all 'representative' PDB structures for selected
3043 <li>Update Jalview project format:
3045 <li>New file extension for Jalview projects '.jvp'</li>
3046 <li>Preserve sequence and annotation dataset (to
3047 store secondary structure annotation,etc)</li>
3048 <li>Per group and alignment annotation and RNA helix
3052 <li>New similarity measures for PCA and Tree calculation
3054 <li>Experimental support for retrieval and viewing of
3055 flanking regions for an alignment</li>
3059 <!-- issues resolved --> <em>Application</em>
3061 <li>logo keeps spinning and status remains at queued or
3062 running after job is cancelled</li>
3063 <li>cannot export features from alignments imported from
3064 Jalview/VAMSAS projects</li>
3065 <li>Buggy slider for web service parameters that take
3067 <li>Newly created RNA secondary structure line doesn't
3068 have 'display all symbols' flag set</li>
3069 <li>T-COFFEE alignment score shading scheme and other
3070 annotation shading not saved in Jalview project</li>
3071 <li>Local file cannot be loaded in freshly downloaded
3073 <li>Jalview icon not shown on dock in Mountain
3075 <li>Load file from desktop file browser fails</li>
3076 <li>Occasional NPE thrown when calculating large trees</li>
3077 <li>Cannot reorder or slide sequences after dragging an
3078 alignment onto desktop</li>
3079 <li>Colour by annotation dialog throws NPE after using
3080 'extract scores' function</li>
3081 <li>Loading/cut'n'pasting an empty file leads to a grey
3082 alignment window</li>
3083 <li>Disorder thresholds rendered incorrectly after
3084 performing IUPred disorder prediction</li>
3085 <li>Multiple group annotated consensus rows shown when
3086 changing 'normalise logo' display setting</li>
3087 <li>Find shows blank dialog after 'finished searching' if
3088 nothing matches query</li>
3089 <li>Null Pointer Exceptions raised when sorting by
3090 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3092 <li>Errors in Jmol console when structures in alignment
3093 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3095 <li>Not all working JABAWS services are shown in
3097 <li>JAVAWS version of Jalview fails to launch with
3098 'invalid literal/length code'</li>
3099 <li>Annotation/RNA Helix colourschemes cannot be applied
3100 to alignment with groups (actually fixed in 2.8.0b1)</li>
3101 <li>RNA Helices and T-Coffee Scores available as default
3104 </ul> <em>Applet</em>
3106 <li>Remove group option is shown even when selection is
3108 <li>Apply to all groups ticked but colourscheme changes
3109 don't affect groups</li>
3110 <li>Documented RNA Helices and T-Coffee Scores as valid
3111 colourscheme name</li>
3112 <li>Annotation labels drawn on sequence IDs when
3113 Annotation panel is not displayed</li>
3114 <li>Increased font size for dropdown menus on OSX and
3115 embedded windows</li>
3116 </ul> <em>Other</em>
3118 <li>Consensus sequence for alignments/groups with a
3119 single sequence were not calculated</li>
3120 <li>annotation files that contain only groups imported as
3121 annotation and junk sequences</li>
3122 <li>Fasta files with sequences containing '*' incorrectly
3123 recognised as PFAM or BLC</li>
3124 <li>conservation/PID slider apply all groups option
3125 doesn't affect background (2.8.0b1)
3127 <li>redundancy highlighting is erratic at 0% and 100%</li>
3128 <li>Remove gapped columns fails for sequences with ragged
3130 <li>AMSA annotation row with leading spaces is not
3131 registered correctly on import</li>
3132 <li>Jalview crashes when selecting PCA analysis for
3133 certain alignments</li>
3134 <li>Opening the colour by annotation dialog for an
3135 existing annotation based 'use original colours'
3136 colourscheme loses original colours setting</li>
3141 <td><div align="center">
3142 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3143 <em>30/1/2014</em></strong>
3147 <li>Trusted certificates for JalviewLite applet and
3148 Jalview Desktop application<br />Certificate was donated by
3149 <a href="https://www.certum.eu">Certum</a> to the Jalview
3150 open source project).
3152 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3153 <li>Output in Stockholm format</li>
3154 <li>Allow import of data from gzipped files</li>
3155 <li>Export/import group and sequence associated line
3156 graph thresholds</li>
3157 <li>Nucleotide substitution matrix that supports RNA and
3158 ambiguity codes</li>
3159 <li>Allow disorder predictions to be made on the current
3160 selection (or visible selection) in the same way that JPred
3162 <li>Groovy scripting for headless Jalview operation</li>
3163 </ul> <em>Other improvements</em>
3165 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3166 <li>COMBINE statement uses current SEQUENCE_REF and
3167 GROUP_REF scope to group annotation rows</li>
3168 <li>Support '' style escaping of quotes in Newick
3170 <li>Group options for JABAWS service by command line name</li>
3171 <li>Empty tooltip shown for JABA service options with a
3172 link but no description</li>
3173 <li>Select primary source when selecting authority in
3174 database fetcher GUI</li>
3175 <li>Add .mfa to FASTA file extensions recognised by
3177 <li>Annotation label tooltip text wrap</li>
3182 <li>Slow scrolling when lots of annotation rows are
3184 <li>Lots of NPE (and slowness) after creating RNA
3185 secondary structure annotation line</li>
3186 <li>Sequence database accessions not imported when
3187 fetching alignments from Rfam</li>
3188 <li>Incorrect SHMR submission for sequences with
3190 <li>View all structures does not always superpose
3192 <li>Option widgets in service parameters not updated to
3193 reflect user or preset settings</li>
3194 <li>Null pointer exceptions for some services without
3195 presets or adjustable parameters</li>
3196 <li>Discover PDB IDs entry in structure menu doesn't
3197 discover PDB xRefs</li>
3198 <li>Exception encountered while trying to retrieve
3199 features with DAS</li>
3200 <li>Lowest value in annotation row isn't coloured
3201 when colour by annotation (per sequence) is coloured</li>
3202 <li>Keyboard mode P jumps to start of gapped region when
3203 residue follows a gap</li>
3204 <li>Jalview appears to hang importing an alignment with
3205 Wrap as default or after enabling Wrap</li>
3206 <li>'Right click to add annotations' message
3207 shown in wrap mode when no annotations present</li>
3208 <li>Disorder predictions fail with NPE if no automatic
3209 annotation already exists on alignment</li>
3210 <li>oninit javascript function should be called after
3211 initialisation completes</li>
3212 <li>Remove redundancy after disorder prediction corrupts
3213 alignment window display</li>
3214 <li>Example annotation file in documentation is invalid</li>
3215 <li>Grouped line graph annotation rows are not exported
3216 to annotation file</li>
3217 <li>Multi-harmony analysis cannot be run when only two
3219 <li>Cannot create multiple groups of line graphs with
3220 several 'combine' statements in annotation file</li>
3221 <li>Pressing return several times causes Number Format
3222 exceptions in keyboard mode</li>
3223 <li>Multi-harmony (SHMMR) method doesn't submit
3224 correct partitions for input data</li>
3225 <li>Translation from DNA to Amino Acids fails</li>
3226 <li>Jalview fail to load newick tree with quoted label</li>
3227 <li>--headless flag isn't understood</li>
3228 <li>ClassCastException when generating EPS in headless
3230 <li>Adjusting sequence-associated shading threshold only
3231 changes one row's threshold</li>
3232 <li>Preferences and Feature settings panel panel
3233 doesn't open</li>
3234 <li>hide consensus histogram also hides conservation and
3235 quality histograms</li>
3240 <td><div align="center">
3241 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3243 <td><em>Application</em>
3245 <li>Support for JABAWS 2.0 Services (AACon alignment
3246 conservation, protein disorder and Clustal Omega)</li>
3247 <li>JABAWS server status indicator in Web Services
3249 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3250 in Jalview alignment window</li>
3251 <li>Updated Jalview build and deploy framework for OSX
3252 mountain lion, windows 7, and 8</li>
3253 <li>Nucleotide substitution matrix for PCA that supports
3254 RNA and ambiguity codes</li>
3256 <li>Improved sequence database retrieval GUI</li>
3257 <li>Support fetching and database reference look up
3258 against multiple DAS sources (Fetch all from in 'fetch db
3260 <li>Jalview project improvements
3262 <li>Store and retrieve the 'belowAlignment'
3263 flag for annotation</li>
3264 <li>calcId attribute to group annotation rows on the
3266 <li>Store AACon calculation settings for a view in
3267 Jalview project</li>
3271 <li>horizontal scrolling gesture support</li>
3272 <li>Visual progress indicator when PCA calculation is
3274 <li>Simpler JABA web services menus</li>
3275 <li>visual indication that web service results are still
3276 being retrieved from server</li>
3277 <li>Serialise the dialogs that are shown when Jalview
3278 starts up for first time</li>
3279 <li>Jalview user agent string for interacting with HTTP
3281 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3283 <li>Examples directory and Groovy library included in
3284 InstallAnywhere distribution</li>
3285 </ul> <em>Applet</em>
3287 <li>RNA alignment and secondary structure annotation
3288 visualization applet example</li>
3289 </ul> <em>General</em>
3291 <li>Normalise option for consensus sequence logo</li>
3292 <li>Reset button in PCA window to return dimensions to
3294 <li>Allow seqspace or Jalview variant of alignment PCA
3296 <li>PCA with either nucleic acid and protein substitution
3298 <li>Allow windows containing HTML reports to be exported
3300 <li>Interactive display and editing of RNA secondary
3301 structure contacts</li>
3302 <li>RNA Helix Alignment Colouring</li>
3303 <li>RNA base pair logo consensus</li>
3304 <li>Parse sequence associated secondary structure
3305 information in Stockholm files</li>
3306 <li>HTML Export database accessions and annotation
3307 information presented in tooltip for sequences</li>
3308 <li>Import secondary structure from LOCARNA clustalw
3309 style RNA alignment files</li>
3310 <li>import and visualise T-COFFEE quality scores for an
3312 <li>'colour by annotation' per sequence option to
3313 shade each sequence according to its associated alignment
3315 <li>New Jalview Logo</li>
3316 </ul> <em>Documentation and Development</em>
3318 <li>documentation for score matrices used in Jalview</li>
3319 <li>New Website!</li>
3321 <td><em>Application</em>
3323 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3324 wsdbfetch REST service</li>
3325 <li>Stop windows being moved outside desktop on OSX</li>
3326 <li>Filetype associations not installed for webstart
3328 <li>Jalview does not always retrieve progress of a JABAWS
3329 job execution in full once it is complete</li>
3330 <li>revise SHMR RSBS definition to ensure alignment is
3331 uploaded via ali_file parameter</li>
3332 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3333 <li>View all structures superposed fails with exception</li>
3334 <li>Jnet job queues forever if a very short sequence is
3335 submitted for prediction</li>
3336 <li>Cut and paste menu not opened when mouse clicked on
3338 <li>Putting fractional value into integer text box in
3339 alignment parameter dialog causes Jalview to hang</li>
3340 <li>Structure view highlighting doesn't work on
3342 <li>View all structures fails with exception shown in
3344 <li>Characters in filename associated with PDBEntry not
3345 escaped in a platform independent way</li>
3346 <li>Jalview desktop fails to launch with exception when
3348 <li>Tree calculation reports 'you must have 2 or more
3349 sequences selected' when selection is empty</li>
3350 <li>Jalview desktop fails to launch with jar signature
3351 failure when java web start temporary file caching is
3353 <li>DAS Sequence retrieval with range qualification
3354 results in sequence xref which includes range qualification</li>
3355 <li>Errors during processing of command line arguments
3356 cause progress bar (JAL-898) to be removed</li>
3357 <li>Replace comma for semi-colon option not disabled for
3358 DAS sources in sequence fetcher</li>
3359 <li>Cannot close news reader when JABAWS server warning
3360 dialog is shown</li>
3361 <li>Option widgets not updated to reflect user settings</li>
3362 <li>Edited sequence not submitted to web service</li>
3363 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3364 <li>InstallAnywhere installer doesn't unpack and run
3365 on OSX Mountain Lion</li>
3366 <li>Annotation panel not given a scroll bar when
3367 sequences with alignment annotation are pasted into the
3369 <li>Sequence associated annotation rows not associated
3370 when loaded from Jalview project</li>
3371 <li>Browser launch fails with NPE on java 1.7</li>
3372 <li>JABAWS alignment marked as finished when job was
3373 cancelled or job failed due to invalid input</li>
3374 <li>NPE with v2.7 example when clicking on Tree
3375 associated with all views</li>
3376 <li>Exceptions when copy/paste sequences with grouped
3377 annotation rows to new window</li>
3378 </ul> <em>Applet</em>
3380 <li>Sequence features are momentarily displayed before
3381 they are hidden using hidefeaturegroups applet parameter</li>
3382 <li>loading features via javascript API automatically
3383 enables feature display</li>
3384 <li>scrollToColumnIn javascript API method doesn't
3386 </ul> <em>General</em>
3388 <li>Redundancy removal fails for rna alignment</li>
3389 <li>PCA calculation fails when sequence has been selected
3390 and then deselected</li>
3391 <li>PCA window shows grey box when first opened on OSX</li>
3392 <li>Letters coloured pink in sequence logo when alignment
3393 coloured with clustalx</li>
3394 <li>Choosing fonts without letter symbols defined causes
3395 exceptions and redraw errors</li>
3396 <li>Initial PCA plot view is not same as manually
3397 reconfigured view</li>
3398 <li>Grouped annotation graph label has incorrect line
3400 <li>Grouped annotation graph label display is corrupted
3401 for lots of labels</li>
3406 <div align="center">
3407 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3410 <td><em>Application</em>
3412 <li>Jalview Desktop News Reader</li>
3413 <li>Tweaked default layout of web services menu</li>
3414 <li>View/alignment association menu to enable user to
3415 easily specify which alignment a multi-structure view takes
3416 its colours/correspondences from</li>
3417 <li>Allow properties file location to be specified as URL</li>
3418 <li>Extend Jalview project to preserve associations
3419 between many alignment views and a single Jmol display</li>
3420 <li>Store annotation row height in Jalview project file</li>
3421 <li>Annotation row column label formatting attributes
3422 stored in project file</li>
3423 <li>Annotation row order for auto-calculated annotation
3424 rows preserved in Jalview project file</li>
3425 <li>Visual progress indication when Jalview state is
3426 saved using Desktop window menu</li>
3427 <li>Visual indication that command line arguments are
3428 still being processed</li>
3429 <li>Groovy script execution from URL</li>
3430 <li>Colour by annotation default min and max colours in
3432 <li>Automatically associate PDB files dragged onto an
3433 alignment with sequences that have high similarity and
3435 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3436 <li>'view structures' option to open many
3437 structures in same window</li>
3438 <li>Sort associated views menu option for tree panel</li>
3439 <li>Group all JABA and non-JABA services for a particular
3440 analysis function in its own submenu</li>
3441 </ul> <em>Applet</em>
3443 <li>Userdefined and autogenerated annotation rows for
3445 <li>Adjustment of alignment annotation pane height</li>
3446 <li>Annotation scrollbar for annotation panel</li>
3447 <li>Drag to reorder annotation rows in annotation panel</li>
3448 <li>'automaticScrolling' parameter</li>
3449 <li>Allow sequences with partial ID string matches to be
3450 annotated from GFF/Jalview features files</li>
3451 <li>Sequence logo annotation row in applet</li>
3452 <li>Absolute paths relative to host server in applet
3453 parameters are treated as such</li>
3454 <li>New in the JalviewLite javascript API:
3456 <li>JalviewLite.js javascript library</li>
3457 <li>Javascript callbacks for
3459 <li>Applet initialisation</li>
3460 <li>Sequence/alignment mouse-overs and selections</li>
3463 <li>scrollTo row and column alignment scrolling
3465 <li>Select sequence/alignment regions from javascript</li>
3466 <li>javascript structure viewer harness to pass
3467 messages between Jmol and Jalview when running as
3468 distinct applets</li>
3469 <li>sortBy method</li>
3470 <li>Set of applet and application examples shipped
3471 with documentation</li>
3472 <li>New example to demonstrate JalviewLite and Jmol
3473 javascript message exchange</li>
3475 </ul> <em>General</em>
3477 <li>Enable Jmol displays to be associated with multiple
3478 multiple alignments</li>
3479 <li>Option to automatically sort alignment with new tree</li>
3480 <li>User configurable link to enable redirects to a
3481 www.Jalview.org mirror</li>
3482 <li>Jmol colours option for Jmol displays</li>
3483 <li>Configurable newline string when writing alignment
3484 and other flat files</li>
3485 <li>Allow alignment annotation description lines to
3486 contain html tags</li>
3487 </ul> <em>Documentation and Development</em>
3489 <li>Add groovy test harness for bulk load testing to
3491 <li>Groovy script to load and align a set of sequences
3492 using a web service before displaying the result in the
3493 Jalview desktop</li>
3494 <li>Restructured javascript and applet api documentation</li>
3495 <li>Ant target to publish example html files with applet
3497 <li>Netbeans project for building Jalview from source</li>
3498 <li>ant task to create online javadoc for Jalview source</li>
3500 <td><em>Application</em>
3502 <li>User defined colourscheme throws exception when
3503 current built in colourscheme is saved as new scheme</li>
3504 <li>AlignFrame->Save in application pops up save
3505 dialog for valid filename/format</li>
3506 <li>Cannot view associated structure for UniProt sequence</li>
3507 <li>PDB file association breaks for UniProt sequence
3509 <li>Associate PDB from file dialog does not tell you
3510 which sequence is to be associated with the file</li>
3511 <li>Find All raises null pointer exception when query
3512 only matches sequence IDs</li>
3513 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3514 <li>Jalview project with Jmol views created with Jalview
3515 2.4 cannot be loaded</li>
3516 <li>Filetype associations not installed for webstart
3518 <li>Two or more chains in a single PDB file associated
3519 with sequences in different alignments do not get coloured
3520 by their associated sequence</li>
3521 <li>Visibility status of autocalculated annotation row
3522 not preserved when project is loaded</li>
3523 <li>Annotation row height and visibility attributes not
3524 stored in Jalview project</li>
3525 <li>Tree bootstraps are not preserved when saved as a
3526 Jalview project</li>
3527 <li>Envision2 workflow tooltips are corrupted</li>
3528 <li>Enabling show group conservation also enables colour
3529 by conservation</li>
3530 <li>Duplicate group associated conservation or consensus
3531 created on new view</li>
3532 <li>Annotation scrollbar not displayed after 'show
3533 all hidden annotation rows' option selected</li>
3534 <li>Alignment quality not updated after alignment
3535 annotation row is hidden then shown</li>
3536 <li>Preserve colouring of structures coloured by
3537 sequences in pre Jalview 2.7 projects</li>
3538 <li>Web service job parameter dialog is not laid out
3540 <li>Web services menu not refreshed after 'reset
3541 services' button is pressed in preferences</li>
3542 <li>Annotation off by one in Jalview v2_3 example project</li>
3543 <li>Structures imported from file and saved in project
3544 get name like jalview_pdb1234.txt when reloaded</li>
3545 <li>Jalview does not always retrieve progress of a JABAWS
3546 job execution in full once it is complete</li>
3547 </ul> <em>Applet</em>
3549 <li>Alignment height set incorrectly when lots of
3550 annotation rows are displayed</li>
3551 <li>Relative URLs in feature HTML text not resolved to
3553 <li>View follows highlighting does not work for positions
3555 <li><= shown as = in tooltip</li>
3556 <li>Export features raises exception when no features
3558 <li>Separator string used for serialising lists of IDs
3559 for javascript api is modified when separator string
3560 provided as parameter</li>
3561 <li>Null pointer exception when selecting tree leaves for
3562 alignment with no existing selection</li>
3563 <li>Relative URLs for datasources assumed to be relative
3564 to applet's codebase</li>
3565 <li>Status bar not updated after finished searching and
3566 search wraps around to first result</li>
3567 <li>StructureSelectionManager instance shared between
3568 several Jalview applets causes race conditions and memory
3570 <li>Hover tooltip and mouseover of position on structure
3571 not sent from Jmol in applet</li>
3572 <li>Certain sequences of javascript method calls to
3573 applet API fatally hang browser</li>
3574 </ul> <em>General</em>
3576 <li>View follows structure mouseover scrolls beyond
3577 position with wrapped view and hidden regions</li>
3578 <li>Find sequence position moves to wrong residue
3579 with/without hidden columns</li>
3580 <li>Sequence length given in alignment properties window
3582 <li>InvalidNumberFormat exceptions thrown when trying to
3583 import PDB like structure files</li>
3584 <li>Positional search results are only highlighted
3585 between user-supplied sequence start/end bounds</li>
3586 <li>End attribute of sequence is not validated</li>
3587 <li>Find dialog only finds first sequence containing a
3588 given sequence position</li>
3589 <li>Sequence numbering not preserved in MSF alignment
3591 <li>Jalview PDB file reader does not extract sequence
3592 from nucleotide chains correctly</li>
3593 <li>Structure colours not updated when tree partition
3594 changed in alignment</li>
3595 <li>Sequence associated secondary structure not correctly
3596 parsed in interleaved stockholm</li>
3597 <li>Colour by annotation dialog does not restore current
3599 <li>Hiding (nearly) all sequences doesn't work
3601 <li>Sequences containing lowercase letters are not
3602 properly associated with their pdb files</li>
3603 </ul> <em>Documentation and Development</em>
3605 <li>schemas/JalviewWsParamSet.xsd corrupted by
3606 ApplyCopyright tool</li>
3611 <div align="center">
3612 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3615 <td><em>Application</em>
3617 <li>New warning dialog when the Jalview Desktop cannot
3618 contact web services</li>
3619 <li>JABA service parameters for a preset are shown in
3620 service job window</li>
3621 <li>JABA Service menu entries reworded</li>
3625 <li>Modeller PIR IO broken - cannot correctly import a
3626 pir file emitted by Jalview</li>
3627 <li>Existing feature settings transferred to new
3628 alignment view created from cut'n'paste</li>
3629 <li>Improved test for mixed amino/nucleotide chains when
3630 parsing PDB files</li>
3631 <li>Consensus and conservation annotation rows
3632 occasionally become blank for all new windows</li>
3633 <li>Exception raised when right clicking above sequences
3634 in wrapped view mode</li>
3635 </ul> <em>Application</em>
3637 <li>multiple multiply aligned structure views cause cpu
3638 usage to hit 100% and computer to hang</li>
3639 <li>Web Service parameter layout breaks for long user
3640 parameter names</li>
3641 <li>Jaba service discovery hangs desktop if Jaba server
3648 <div align="center">
3649 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3652 <td><em>Application</em>
3654 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3655 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3658 <li>Web Services preference tab</li>
3659 <li>Analysis parameters dialog box and user defined
3661 <li>Improved speed and layout of Envision2 service menu</li>
3662 <li>Superpose structures using associated sequence
3664 <li>Export coordinates and projection as CSV from PCA
3666 </ul> <em>Applet</em>
3668 <li>enable javascript: execution by the applet via the
3669 link out mechanism</li>
3670 </ul> <em>Other</em>
3672 <li>Updated the Jmol Jalview interface to work with Jmol
3674 <li>The Jalview Desktop and JalviewLite applet now
3675 require Java 1.5</li>
3676 <li>Allow Jalview feature colour specification for GFF
3677 sequence annotation files</li>
3678 <li>New 'colour by label' keword in Jalview feature file
3679 type colour specification</li>
3680 <li>New Jalview Desktop Groovy API method that allows a
3681 script to check if it being run in an interactive session or
3682 in a batch operation from the Jalview command line</li>
3686 <li>clustalx colourscheme colours Ds preferentially when
3687 both D+E are present in over 50% of the column</li>
3688 </ul> <em>Application</em>
3690 <li>typo in AlignmentFrame->View->Hide->all but
3691 selected Regions menu item</li>
3692 <li>sequence fetcher replaces ',' for ';' when the ',' is
3693 part of a valid accession ID</li>
3694 <li>fatal OOM if object retrieved by sequence fetcher
3695 runs out of memory</li>
3696 <li>unhandled Out of Memory Error when viewing pca
3697 analysis results</li>
3698 <li>InstallAnywhere builds fail to launch on OS X java
3699 10.5 update 4 (due to apple Java 1.6 update)</li>
3700 <li>Installanywhere Jalview silently fails to launch</li>
3701 </ul> <em>Applet</em>
3703 <li>Jalview.getFeatureGroups() raises an
3704 ArrayIndexOutOfBoundsException if no feature groups are
3711 <div align="center">
3712 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3718 <li>Alignment prettyprinter doesn't cope with long
3720 <li>clustalx colourscheme colours Ds preferentially when
3721 both D+E are present in over 50% of the column</li>
3722 <li>nucleic acid structures retrieved from PDB do not
3723 import correctly</li>
3724 <li>More columns get selected than were clicked on when a
3725 number of columns are hidden</li>
3726 <li>annotation label popup menu not providing correct
3727 add/hide/show options when rows are hidden or none are
3729 <li>Stockholm format shown in list of readable formats,
3730 and parser copes better with alignments from RFAM.</li>
3731 <li>CSV output of consensus only includes the percentage
3732 of all symbols if sequence logo display is enabled</li>
3734 </ul> <em>Applet</em>
3736 <li>annotation panel disappears when annotation is
3738 </ul> <em>Application</em>
3740 <li>Alignment view not redrawn properly when new
3741 alignment opened where annotation panel is visible but no
3742 annotations are present on alignment</li>
3743 <li>pasted region containing hidden columns is
3744 incorrectly displayed in new alignment window</li>
3745 <li>Jalview slow to complete operations when stdout is
3746 flooded (fix is to close the Jalview console)</li>
3747 <li>typo in AlignmentFrame->View->Hide->all but
3748 selected Rregions menu item.</li>
3749 <li>inconsistent group submenu and Format submenu entry
3750 'Un' or 'Non'conserved</li>
3751 <li>Sequence feature settings are being shared by
3752 multiple distinct alignments</li>
3753 <li>group annotation not recreated when tree partition is
3755 <li>double click on group annotation to select sequences
3756 does not propagate to associated trees</li>
3757 <li>Mac OSX specific issues:
3759 <li>exception raised when mouse clicked on desktop
3760 window background</li>
3761 <li>Desktop menu placed on menu bar and application
3762 name set correctly</li>
3763 <li>sequence feature settings not wide enough for the
3764 save feature colourscheme button</li>
3773 <div align="center">
3774 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3777 <td><em>New Capabilities</em>
3779 <li>URL links generated from description line for
3780 regular-expression based URL links (applet and application)
3782 <li>Non-positional feature URL links are shown in link
3784 <li>Linked viewing of nucleic acid sequences and
3786 <li>Automatic Scrolling option in View menu to display
3787 the currently highlighted region of an alignment.</li>
3788 <li>Order an alignment by sequence length, or using the
3789 average score or total feature count for each sequence.</li>
3790 <li>Shading features by score or associated description</li>
3791 <li>Subdivide alignment and groups based on identity of
3792 selected subsequence (Make Groups from Selection).</li>
3793 <li>New hide/show options including Shift+Control+H to
3794 hide everything but the currently selected region.</li>
3795 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3796 </ul> <em>Application</em>
3798 <li>Fetch DB References capabilities and UI expanded to
3799 support retrieval from DAS sequence sources</li>
3800 <li>Local DAS Sequence sources can be added via the
3801 command line or via the Add local source dialog box.</li>
3802 <li>DAS Dbref and DbxRef feature types are parsed as
3803 database references and protein_name is parsed as
3804 description line (BioSapiens terms).</li>
3805 <li>Enable or disable non-positional feature and database
3806 references in sequence ID tooltip from View menu in
3808 <!-- <li>New hidden columns and rows and representatives capabilities
3809 in annotations file (in progress - not yet fully implemented)</li> -->
3810 <li>Group-associated consensus, sequence logos and
3811 conservation plots</li>
3812 <li>Symbol distributions for each column can be exported
3813 and visualized as sequence logos</li>
3814 <li>Optionally scale multi-character column labels to fit
3815 within each column of annotation row<!-- todo for applet -->
3817 <li>Optional automatic sort of associated alignment view
3818 when a new tree is opened.</li>
3819 <li>Jalview Java Console</li>
3820 <li>Better placement of desktop window when moving
3821 between different screens.</li>
3822 <li>New preference items for sequence ID tooltip and
3823 consensus annotation</li>
3824 <li>Client to submit sequences and IDs to Envision2
3826 <li><em>Vamsas Capabilities</em>
3828 <li>Improved VAMSAS synchronization (Jalview archive
3829 used to preserve views, structures, and tree display
3831 <li>Import of vamsas documents from disk or URL via
3833 <li>Sharing of selected regions between views and
3834 with other VAMSAS applications (Experimental feature!)</li>
3835 <li>Updated API to VAMSAS version 0.2</li>
3837 </ul> <em>Applet</em>
3839 <li>Middle button resizes annotation row height</li>
3842 <li>sortByTree (true/false) - automatically sort the
3843 associated alignment view by the tree when a new tree is
3845 <li>showTreeBootstraps (true/false) - show or hide
3846 branch bootstraps (default is to show them if available)</li>
3847 <li>showTreeDistances (true/false) - show or hide
3848 branch lengths (default is to show them if available)</li>
3849 <li>showUnlinkedTreeNodes (true/false) - indicate if
3850 unassociated nodes should be highlighted in the tree
3852 <li>heightScale and widthScale (1.0 or more) -
3853 increase the height or width of a cell in the alignment
3854 grid relative to the current font size.</li>
3857 <li>Non-positional features displayed in sequence ID
3859 </ul> <em>Other</em>
3861 <li>Features format: graduated colour definitions and
3862 specification of feature scores</li>
3863 <li>Alignment Annotations format: new keywords for group
3864 associated annotation (GROUP_REF) and annotation row display
3865 properties (ROW_PROPERTIES)</li>
3866 <li>XML formats extended to support graduated feature
3867 colourschemes, group associated annotation, and profile
3868 visualization settings.</li></td>
3871 <li>Source field in GFF files parsed as feature source
3872 rather than description</li>
3873 <li>Non-positional features are now included in sequence
3874 feature and gff files (controlled via non-positional feature
3875 visibility in tooltip).</li>
3876 <li>URL links generated for all feature links (bugfix)</li>
3877 <li>Added URL embedding instructions to features file
3879 <li>Codons containing ambiguous nucleotides translated as
3880 'X' in peptide product</li>
3881 <li>Match case switch in find dialog box works for both
3882 sequence ID and sequence string and query strings do not
3883 have to be in upper case to match case-insensitively.</li>
3884 <li>AMSA files only contain first column of
3885 multi-character column annotation labels</li>
3886 <li>Jalview Annotation File generation/parsing consistent
3887 with documentation (e.g. Stockholm annotation can be
3888 exported and re-imported)</li>
3889 <li>PDB files without embedded PDB IDs given a friendly
3891 <li>Find incrementally searches ID string matches as well
3892 as subsequence matches, and correctly reports total number
3896 <li>Better handling of exceptions during sequence
3898 <li>Dasobert generated non-positional feature URL
3899 link text excludes the start_end suffix</li>
3900 <li>DAS feature and source retrieval buttons disabled
3901 when fetch or registry operations in progress.</li>
3902 <li>PDB files retrieved from URLs are cached properly</li>
3903 <li>Sequence description lines properly shared via
3905 <li>Sequence fetcher fetches multiple records for all
3907 <li>Ensured that command line das feature retrieval
3908 completes before alignment figures are generated.</li>
3909 <li>Reduced time taken when opening file browser for
3911 <li>isAligned check prior to calculating tree, PCA or
3912 submitting an MSA to JNet now excludes hidden sequences.</li>
3913 <li>User defined group colours properly recovered
3914 from Jalview projects.</li>
3923 <div align="center">
3924 <strong>2.4.0.b2</strong><br> 28/10/2009
3929 <li>Experimental support for google analytics usage
3931 <li>Jalview privacy settings (user preferences and docs).</li>
3936 <li>Race condition in applet preventing startup in
3938 <li>Exception when feature created from selection beyond
3939 length of sequence.</li>
3940 <li>Allow synthetic PDB files to be imported gracefully</li>
3941 <li>Sequence associated annotation rows associate with
3942 all sequences with a given id</li>
3943 <li>Find function matches case-insensitively for sequence
3944 ID string searches</li>
3945 <li>Non-standard characters do not cause pairwise
3946 alignment to fail with exception</li>
3947 </ul> <em>Application Issues</em>
3949 <li>Sequences are now validated against EMBL database</li>
3950 <li>Sequence fetcher fetches multiple records for all
3952 </ul> <em>InstallAnywhere Issues</em>
3954 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3955 issue with installAnywhere mechanism)</li>
3956 <li>Command line launching of JARs from InstallAnywhere
3957 version (java class versioning error fixed)</li>
3964 <div align="center">
3965 <strong>2.4</strong><br> 27/8/2008
3968 <td><em>User Interface</em>
3970 <li>Linked highlighting of codon and amino acid from
3971 translation and protein products</li>
3972 <li>Linked highlighting of structure associated with
3973 residue mapping to codon position</li>
3974 <li>Sequence Fetcher provides example accession numbers
3975 and 'clear' button</li>
3976 <li>MemoryMonitor added as an option under Desktop's
3978 <li>Extract score function to parse whitespace separated
3979 numeric data in description line</li>
3980 <li>Column labels in alignment annotation can be centred.</li>
3981 <li>Tooltip for sequence associated annotation give name
3983 </ul> <em>Web Services and URL fetching</em>
3985 <li>JPred3 web service</li>
3986 <li>Prototype sequence search client (no public services
3988 <li>Fetch either seed alignment or full alignment from
3990 <li>URL Links created for matching database cross
3991 references as well as sequence ID</li>
3992 <li>URL Links can be created using regular-expressions</li>
3993 </ul> <em>Sequence Database Connectivity</em>
3995 <li>Retrieval of cross-referenced sequences from other
3997 <li>Generalised database reference retrieval and
3998 validation to all fetchable databases</li>
3999 <li>Fetch sequences from DAS sources supporting the
4000 sequence command</li>
4001 </ul> <em>Import and Export</em>
4002 <li>export annotation rows as CSV for spreadsheet import</li>
4003 <li>Jalview projects record alignment dataset associations,
4004 EMBL products, and cDNA sequence mappings</li>
4005 <li>Sequence Group colour can be specified in Annotation
4007 <li>Ad-hoc colouring of group in Annotation File using RGB
4008 triplet as name of colourscheme</li>
4009 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4011 <li>treenode binding for VAMSAS tree exchange</li>
4012 <li>local editing and update of sequences in VAMSAS
4013 alignments (experimental)</li>
4014 <li>Create new or select existing session to join</li>
4015 <li>load and save of vamsas documents</li>
4016 </ul> <em>Application command line</em>
4018 <li>-tree parameter to open trees (introduced for passing
4020 <li>-fetchfrom command line argument to specify nicknames
4021 of DAS servers to query for alignment features</li>
4022 <li>-dasserver command line argument to add new servers
4023 that are also automatically queried for features</li>
4024 <li>-groovy command line argument executes a given groovy
4025 script after all input data has been loaded and parsed</li>
4026 </ul> <em>Applet-Application data exchange</em>
4028 <li>Trees passed as applet parameters can be passed to
4029 application (when using "View in full
4030 application")</li>
4031 </ul> <em>Applet Parameters</em>
4033 <li>feature group display control parameter</li>
4034 <li>debug parameter</li>
4035 <li>showbutton parameter</li>
4036 </ul> <em>Applet API methods</em>
4038 <li>newView public method</li>
4039 <li>Window (current view) specific get/set public methods</li>
4040 <li>Feature display control methods</li>
4041 <li>get list of currently selected sequences</li>
4042 </ul> <em>New Jalview distribution features</em>
4044 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4045 <li>RELEASE file gives build properties for the latest
4046 Jalview release.</li>
4047 <li>Java 1.1 Applet build made easier and donotobfuscate
4048 property controls execution of obfuscator</li>
4049 <li>Build target for generating source distribution</li>
4050 <li>Debug flag for javacc</li>
4051 <li>.jalview_properties file is documented (slightly) in
4052 jalview.bin.Cache</li>
4053 <li>Continuous Build Integration for stable and
4054 development version of Application, Applet and source
4059 <li>selected region output includes visible annotations
4060 (for certain formats)</li>
4061 <li>edit label/displaychar contains existing label/char
4063 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4064 <li>shorter peptide product names from EMBL records</li>
4065 <li>Newick string generator makes compact representations</li>
4066 <li>bootstrap values parsed correctly for tree files with
4068 <li>pathological filechooser bug avoided by not allowing
4069 filenames containing a ':'</li>
4070 <li>Fixed exception when parsing GFF files containing
4071 global sequence features</li>
4072 <li>Alignment datasets are finalized only when number of
4073 references from alignment sequences goes to zero</li>
4074 <li>Close of tree branch colour box without colour
4075 selection causes cascading exceptions</li>
4076 <li>occasional negative imgwidth exceptions</li>
4077 <li>better reporting of non-fatal warnings to user when
4078 file parsing fails.</li>
4079 <li>Save works when Jalview project is default format</li>
4080 <li>Save as dialog opened if current alignment format is
4081 not a valid output format</li>
4082 <li>UniProt canonical names introduced for both das and
4084 <li>Histidine should be midblue (not pink!) in Zappo</li>
4085 <li>error messages passed up and output when data read
4087 <li>edit undo recovers previous dataset sequence when
4088 sequence is edited</li>
4089 <li>allow PDB files without pdb ID HEADER lines (like
4090 those generated by MODELLER) to be read in properly</li>
4091 <li>allow reading of JPred concise files as a normal
4093 <li>Stockholm annotation parsing and alignment properties
4094 import fixed for PFAM records</li>
4095 <li>Structure view windows have correct name in Desktop
4097 <li>annotation consisting of sequence associated scores
4098 can be read and written correctly to annotation file</li>
4099 <li>Aligned cDNA translation to aligned peptide works
4101 <li>Fixed display of hidden sequence markers and
4102 non-italic font for representatives in Applet</li>
4103 <li>Applet Menus are always embedded in applet window on
4105 <li>Newly shown features appear at top of stack (in
4107 <li>Annotations added via parameter not drawn properly
4108 due to null pointer exceptions</li>
4109 <li>Secondary structure lines are drawn starting from
4110 first column of alignment</li>
4111 <li>UniProt XML import updated for new schema release in
4113 <li>Sequence feature to sequence ID match for Features
4114 file is case-insensitive</li>
4115 <li>Sequence features read from Features file appended to
4116 all sequences with matching IDs</li>
4117 <li>PDB structure coloured correctly for associated views
4118 containing a sub-sequence</li>
4119 <li>PDB files can be retrieved by applet from Jar files</li>
4120 <li>feature and annotation file applet parameters
4121 referring to different directories are retrieved correctly</li>
4122 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4123 <li>Fixed application hang whilst waiting for
4124 splash-screen version check to complete</li>
4125 <li>Applet properly URLencodes input parameter values
4126 when passing them to the launchApp service</li>
4127 <li>display name and local features preserved in results
4128 retrieved from web service</li>
4129 <li>Visual delay indication for sequence retrieval and
4130 sequence fetcher initialisation</li>
4131 <li>updated Application to use DAS 1.53e version of
4132 dasobert DAS client</li>
4133 <li>Re-instated Full AMSA support and .amsa file
4135 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4143 <div align="center">
4144 <strong>2.3</strong><br> 9/5/07
4149 <li>Jmol 11.0.2 integration</li>
4150 <li>PDB views stored in Jalview XML files</li>
4151 <li>Slide sequences</li>
4152 <li>Edit sequence in place</li>
4153 <li>EMBL CDS features</li>
4154 <li>DAS Feature mapping</li>
4155 <li>Feature ordering</li>
4156 <li>Alignment Properties</li>
4157 <li>Annotation Scores</li>
4158 <li>Sort by scores</li>
4159 <li>Feature/annotation editing in applet</li>
4164 <li>Headless state operation in 2.2.1</li>
4165 <li>Incorrect and unstable DNA pairwise alignment</li>
4166 <li>Cut and paste of sequences with annotation</li>
4167 <li>Feature group display state in XML</li>
4168 <li>Feature ordering in XML</li>
4169 <li>blc file iteration selection using filename # suffix</li>
4170 <li>Stockholm alignment properties</li>
4171 <li>Stockhom alignment secondary structure annotation</li>
4172 <li>2.2.1 applet had no feature transparency</li>
4173 <li>Number pad keys can be used in cursor mode</li>
4174 <li>Structure Viewer mirror image resolved</li>
4181 <div align="center">
4182 <strong>2.2.1</strong><br> 12/2/07
4187 <li>Non standard characters can be read and displayed
4188 <li>Annotations/Features can be imported/exported to the
4190 <li>Applet allows editing of sequence/annotation/group
4191 name & description
4192 <li>Preference setting to display sequence name in
4194 <li>Annotation file format extended to allow
4195 Sequence_groups to be defined
4196 <li>Default opening of alignment overview panel can be
4197 specified in preferences
4198 <li>PDB residue numbering annotation added to associated
4204 <li>Applet crash under certain Linux OS with Java 1.6
4206 <li>Annotation file export / import bugs fixed
4207 <li>PNG / EPS image output bugs fixed
4213 <div align="center">
4214 <strong>2.2</strong><br> 27/11/06
4219 <li>Multiple views on alignment
4220 <li>Sequence feature editing
4221 <li>"Reload" alignment
4222 <li>"Save" to current filename
4223 <li>Background dependent text colour
4224 <li>Right align sequence ids
4225 <li>User-defined lower case residue colours
4228 <li>Menu item accelerator keys
4229 <li>Control-V pastes to current alignment
4230 <li>Cancel button for DAS Feature Fetching
4231 <li>PCA and PDB Viewers zoom via mouse roller
4232 <li>User-defined sub-tree colours and sub-tree selection
4234 <li>'New Window' button on the 'Output to Text box'
4239 <li>New memory efficient Undo/Redo System
4240 <li>Optimised symbol lookups and conservation/consensus
4242 <li>Region Conservation/Consensus recalculated after
4244 <li>Fixed Remove Empty Columns Bug (empty columns at end
4246 <li>Slowed DAS Feature Fetching for increased robustness.
4248 <li>Made angle brackets in ASCII feature descriptions
4250 <li>Re-instated Zoom function for PCA
4251 <li>Sequence descriptions conserved in web service
4253 <li>UniProt ID discoverer uses any word separated by
4255 <li>WsDbFetch query/result association resolved
4256 <li>Tree leaf to sequence mapping improved
4257 <li>Smooth fonts switch moved to FontChooser dialog box.
4264 <div align="center">
4265 <strong>2.1.1</strong><br> 12/9/06
4270 <li>Copy consensus sequence to clipboard</li>
4275 <li>Image output - rightmost residues are rendered if
4276 sequence id panel has been resized</li>
4277 <li>Image output - all offscreen group boundaries are
4279 <li>Annotation files with sequence references - all
4280 elements in file are relative to sequence position</li>
4281 <li>Mac Applet users can use Alt key for group editing</li>
4287 <div align="center">
4288 <strong>2.1</strong><br> 22/8/06
4293 <li>MAFFT Multiple Alignment in default Web Service list</li>
4294 <li>DAS Feature fetching</li>
4295 <li>Hide sequences and columns</li>
4296 <li>Export Annotations and Features</li>
4297 <li>GFF file reading / writing</li>
4298 <li>Associate structures with sequences from local PDB
4300 <li>Add sequences to exisiting alignment</li>
4301 <li>Recently opened files / URL lists</li>
4302 <li>Applet can launch the full application</li>
4303 <li>Applet has transparency for features (Java 1.2
4305 <li>Applet has user defined colours parameter</li>
4306 <li>Applet can load sequences from parameter
4307 "sequence<em>x</em>"
4313 <li>Redundancy Panel reinstalled in the Applet</li>
4314 <li>Monospaced font - EPS / rescaling bug fixed</li>
4315 <li>Annotation files with sequence references bug fixed</li>
4321 <div align="center">
4322 <strong>2.08.1</strong><br> 2/5/06
4327 <li>Change case of selected region from Popup menu</li>
4328 <li>Choose to match case when searching</li>
4329 <li>Middle mouse button and mouse movement can compress /
4330 expand the visible width and height of the alignment</li>
4335 <li>Annotation Panel displays complete JNet results</li>
4341 <div align="center">
4342 <strong>2.08b</strong><br> 18/4/06
4348 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4349 <li>Righthand label on wrapped alignments shows correct
4356 <div align="center">
4357 <strong>2.08</strong><br> 10/4/06
4362 <li>Editing can be locked to the selection area</li>
4363 <li>Keyboard editing</li>
4364 <li>Create sequence features from searches</li>
4365 <li>Precalculated annotations can be loaded onto
4367 <li>Features file allows grouping of features</li>
4368 <li>Annotation Colouring scheme added</li>
4369 <li>Smooth fonts off by default - Faster rendering</li>
4370 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4375 <li>Drag & Drop fixed on Linux</li>
4376 <li>Jalview Archive file faster to load/save, sequence
4377 descriptions saved.</li>
4383 <div align="center">
4384 <strong>2.07</strong><br> 12/12/05
4389 <li>PDB Structure Viewer enhanced</li>
4390 <li>Sequence Feature retrieval and display enhanced</li>
4391 <li>Choose to output sequence start-end after sequence
4392 name for file output</li>
4393 <li>Sequence Fetcher WSDBFetch@EBI</li>
4394 <li>Applet can read feature files, PDB files and can be
4395 used for HTML form input</li>
4400 <li>HTML output writes groups and features</li>
4401 <li>Group editing is Control and mouse click</li>
4402 <li>File IO bugs</li>
4408 <div align="center">
4409 <strong>2.06</strong><br> 28/9/05
4414 <li>View annotations in wrapped mode</li>
4415 <li>More options for PCA viewer</li>
4420 <li>GUI bugs resolved</li>
4421 <li>Runs with -nodisplay from command line</li>
4427 <div align="center">
4428 <strong>2.05b</strong><br> 15/9/05
4433 <li>Choose EPS export as lineart or text</li>
4434 <li>Jar files are executable</li>
4435 <li>Can read in Uracil - maps to unknown residue</li>
4440 <li>Known OutOfMemory errors give warning message</li>
4441 <li>Overview window calculated more efficiently</li>
4442 <li>Several GUI bugs resolved</li>
4448 <div align="center">
4449 <strong>2.05</strong><br> 30/8/05
4454 <li>Edit and annotate in "Wrapped" view</li>
4459 <li>Several GUI bugs resolved</li>
4465 <div align="center">
4466 <strong>2.04</strong><br> 24/8/05
4471 <li>Hold down mouse wheel & scroll to change font
4477 <li>Improved JPred client reliability</li>
4478 <li>Improved loading of Jalview files</li>
4484 <div align="center">
4485 <strong>2.03</strong><br> 18/8/05
4490 <li>Set Proxy server name and port in preferences</li>
4491 <li>Multiple URL links from sequence ids</li>
4492 <li>User Defined Colours can have a scheme name and added
4494 <li>Choose to ignore gaps in consensus calculation</li>
4495 <li>Unix users can set default web browser</li>
4496 <li>Runs without GUI for batch processing</li>
4497 <li>Dynamically generated Web Service Menus</li>
4502 <li>InstallAnywhere download for Sparc Solaris</li>
4508 <div align="center">
4509 <strong>2.02</strong><br> 18/7/05
4515 <li>Copy & Paste order of sequences maintains
4516 alignment order.</li>
4522 <div align="center">
4523 <strong>2.01</strong><br> 12/7/05
4528 <li>Use delete key for deleting selection.</li>
4529 <li>Use Mouse wheel to scroll sequences.</li>
4530 <li>Help file updated to describe how to add alignment
4532 <li>Version and build date written to build properties
4534 <li>InstallAnywhere installation will check for updates
4535 at launch of Jalview.</li>
4540 <li>Delete gaps bug fixed.</li>
4541 <li>FileChooser sorts columns.</li>
4542 <li>Can remove groups one by one.</li>
4543 <li>Filechooser icons installed.</li>
4544 <li>Finder ignores return character when searching.
4545 Return key will initiate a search.<br>
4552 <div align="center">
4553 <strong>2.0</strong><br> 20/6/05
4558 <li>New codebase</li>