3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.11">2.11</a><br />
74 <em>14/05/2019 (final due date !)</em></strong>
77 <td><div align="left">
80 <!-- JAL-3141 -->Optional automatic backups when saving
81 Jalview project or alignment files</li>
83 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
84 Viewer state is saved in Jalview Project<br />The 'Change
85 parameters' option has also been removed from the PCA viewer</li>
87 <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
89 <!-- JAL-2620 -->Alternative genetic code tables supported for
90 'Translate as cDNA'</li>
92 <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
94 <!-- JAL-3198 -->More efficient creation of selections and
95 multiple groups when working with large alignments</li>
97 <!-- JAL-3200 -->Speedier import of annotation rows when
98 parsing stockholm files</li>
100 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
102 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
103 shaded according to any associated attributes (e.g. variant
104 attributes from VCF file, or key-value pairs imported from
105 column 9 of GFF file)</li>
107 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
108 algorithm (Z-sort/transparency and filter aware)</li>
110 <!-- JAL-2527 -->Alignment Overview now by default shows
111 only visible region of alignment (this can be changed in
112 user preferences)</li>
114 <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
116 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
117 all sequences are hidden</li>
119 <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
120 region, and gap count when inserting or deleting gaps</li>
122 <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
124 <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
126 <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
128 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
130 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
132 <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
134 <!-- JAL-3203 -->Overview panel default changed to not show hidden regions</li>
136 <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
138 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
140 <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent
141 to a hidden column marker</li>
143 <em>Deprecations</em>
146 <!-- JAL-3035 -->DAS sequence retrieval and annotation
147 capabilities removed from the Jalview Desktop
150 <em>Release Processes</em>
153 Atlassian Bamboo continuous integration server for
154 unattended Test Suite execution</li>
156 <!-- JAL-2864 -->Memory test suite to detect leaks in common
159 <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
160 implementation) used for Sequence Feature collections</li>
162 <!-- JAL-3063 -->Castor library for XML marshalling and
163 unmarshalling has been replaced by JAXB for Jalview projects
164 and XML based data retrieval clients</li>
167 <td><div align="left">
171 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
173 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
174 Jalview project involving multiple views</li>
176 <!-- JAL-3164 -->Overview for complementary view in a linked
177 CDS/Protein alignment is not updated when Hide Columns by
178 Annotation dialog hides columns</li>
180 <!-- JAL-3158 -->Selection highlighting in the complement of
181 a CDS/Protein alignment stops working after making a
182 selection in one view, then making another selection in the
185 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
187 <!-- JAL-3154 -->Table Columns could be re-ordered in
188 Feature Settings and Jalview Preferences panels</li>
190 <!-- JAL-2865 -->Jalview hangs when closing windows
191 or the overview updates with large alignments</li>
193 <!-- JAL-2865 -->Tree and PCA calculation fails for selected
194 region if columns were selected by dragging right-to-left
195 and the mouse moved to the left of the first column</li>
197 <!-- JAL-2846 -->Error message for trying to load in invalid
198 URLs doesn't tell users the invalid URL</li>
200 <!-- JAL-3178 -->Nonpositional features lose feature group
201 on export as Jalview features file</li>
203 <!-- JAL-3161 -->Status bar updates beyond visible columns</li>
205 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
206 printed when columns are hidden</li>
208 <!-- JAL-3082 -->Regular expression error in Select Columns by Annotation description</li>
210 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
211 dragging out of Scale or Annotation Panel</li>
213 <!-- JAL-3002 -->Display is incorrect after Page Down and Up in wrapped mode</li>
215 <!-- JAL-914 -->Help page can be opened twice</li>
217 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
219 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
221 <!-- JAL-2750 -->Tree calculation fails on a selection dragged to left of alignment</li>
223 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
224 opening an alignment</li>
226 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
228 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
229 different groups in the alignment are selected</li>
231 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
236 <!-- JAL-2822 -->Start and End should be updated when
237 sequence data at beginning or end of alignment added/removed
238 via 'Edit' sequence</li>
240 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
241 sequence features correctly when start of sequence is
242 removed (Known defect since 2.10)</li>
244 <em>New Known Defects</em>
247 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
249 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
254 <td width="60" nowrap>
256 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
259 <td><div align="left">
263 <!-- JAL-3101 -->Default memory for Jalview webstart and
264 InstallAnywhere increased to 1G.
267 <!-- JAL-247 -->Hidden sequence markers and representative
268 sequence bolding included when exporting alignment as EPS,
269 SVG, PNG or HTML. <em>Display is configured via the
270 Format menu, or for command-line use via a jalview
271 properties file.</em>
274 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
275 API and sequence data now imported as JSON.
278 <!-- JAL-3065 -->Change in recommended way of starting
279 Jalview via a Java command line: add jars in lib directory
280 to CLASSPATH, rather than via the deprecated java.ext.dirs
287 <!-- JAL-3047 -->Support added to execute test suite
288 instrumented with <a href="http://openclover.org/">Open
293 <td><div align="left">
297 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
298 row shown in Feredoxin Structure alignment view of example
302 <!-- JAL-2854 -->Annotation obscures sequences if lots of
303 annotation displayed.
306 <!-- JAL-3107 -->Group conservation/consensus not shown
307 for newly created group when 'Apply to all groups'
311 <!-- JAL-3087 -->Corrupted display when switching to
312 wrapped mode when sequence panel's vertical scrollbar is
316 <!-- JAL-3003 -->Alignment is black in exported EPS file
317 when sequences are selected in exported view.</em>
320 <!-- JAL-3059 -->Groups with different coloured borders
321 aren't rendered with correct colour.
324 <!-- JAL-3092 -->Jalview could hang when importing certain
325 types of knotted RNA secondary structure.
328 <!-- JAL-3095 -->Sequence highlight and selection in
329 trimmed VARNA 2D structure is incorrect for sequences that
333 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
334 annotation when columns are inserted into an alignment,
335 and when exporting as Stockholm flatfile.
338 <!-- JAL-3053 -->Jalview annotation rows containing upper
339 and lower-case 'E' and 'H' do not automatically get
340 treated as RNA secondary structure.
343 <!-- JAL-3106 -->.jvp should be used as default extension
344 (not .jar) when saving a jalview project file.
347 <!-- JAL-3105 -->Mac Users: closing a window correctly
348 transfers focus to previous window on OSX
351 <em>Java 10 Issues Resolved</em>
354 <!-- JAL-2988 -->OSX - Can't save new files via the File
355 or export menus by typing in a name into the Save dialog
359 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
360 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
361 'look and feel' which has improved compatibility with the
362 latest version of OSX.
369 <td width="60" nowrap>
371 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
372 <em>7/06/2018</em></strong>
375 <td><div align="left">
379 <!-- JAL-2920 -->Use HGVS nomenclature for variant
380 annotation retrieved from Uniprot
383 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
384 onto the Jalview Desktop
388 <td><div align="left">
392 <!-- JAL-3017 -->Cannot import features with multiple
393 variant elements (blocks import of some Uniprot records)
396 <!-- JAL-2997 -->Clustal files with sequence positions in
397 right-hand column parsed correctly
400 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
401 not alignment area in exported graphic
404 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
405 window has input focus
408 <!-- JAL-2992 -->Annotation panel set too high when
409 annotation added to view (Windows)
412 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
413 network connectivity is poor
416 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
417 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
418 the currently open URL and links from a page viewed in
419 Firefox or Chrome on Windows is now fully supported. If
420 you are using Edge, only links in the page can be
421 dragged, and with Internet Explorer, only the currently
422 open URL in the browser can be dropped onto Jalview.</em>
428 <td width="60" nowrap>
430 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
433 <td><div align="left">
437 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
438 for disabling automatic superposition of multiple
439 structures and open structures in existing views
442 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
443 ID and annotation area margins can be click-dragged to
447 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
451 <!-- JAL-2759 -->Improved performance for large alignments
452 and lots of hidden columns
455 <!-- JAL-2593 -->Improved performance when rendering lots
456 of features (particularly when transparency is disabled)
461 <td><div align="left">
464 <!-- JAL-2899 -->Structure and Overview aren't updated
465 when Colour By Annotation threshold slider is adjusted
468 <!-- JAL-2778 -->Slow redraw when Overview panel shown
469 overlapping alignment panel
472 <!-- JAL-2929 -->Overview doesn't show end of unpadded
476 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
477 improved: CDS not handled correctly if transcript has no
481 <!-- JAL-2321 -->Secondary structure and temperature
482 factor annotation not added to sequence when local PDB
483 file associated with it by drag'n'drop or structure
487 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
488 dialog doesn't import PDB files dropped on an alignment
491 <!-- JAL-2666 -->Linked scrolling via protein horizontal
492 scroll bar doesn't work for some CDS/Protein views
495 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
496 Java 1.8u153 onwards and Java 1.9u4+.
499 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
500 columns in annotation row
503 <!-- JAL-2913 -->Preferences panel's ID Width control is not
504 honored in batch mode
507 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
508 for structures added to existing Jmol view
511 <!-- JAL-2223 -->'View Mappings' includes duplicate
512 entries after importing project with multiple views
515 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
516 protein sequences via SIFTS from associated PDB entries
517 with negative residue numbers or missing residues fails
520 <!-- JAL-2952 -->Exception when shading sequence with negative
521 Temperature Factor values from annotated PDB files (e.g.
522 as generated by CONSURF)
525 <!-- JAL-2920 -->Uniprot 'sequence variant' features
526 tooltip doesn't include a text description of mutation
529 <!-- JAL-2922 -->Invert displayed features very slow when
530 structure and/or overview windows are also shown
533 <!-- JAL-2954 -->Selecting columns from highlighted regions
534 very slow for alignments with large numbers of sequences
537 <!-- JAL-2925 -->Copy Consensus fails for group consensus
538 with 'StringIndexOutOfBounds'
541 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
542 platforms running Java 10
545 <!-- JAL-2960 -->Adding a structure to existing structure
546 view appears to do nothing because the view is hidden behind the alignment view
552 <!-- JAL-2926 -->Copy consensus sequence option in applet
553 should copy the group consensus when popup is opened on it
559 <!-- JAL-2913 -->Fixed ID width preference is not respected
562 <em>New Known Defects</em>
565 <!-- JAL-2973 --> Exceptions occasionally raised when
566 editing a large alignment and overview is displayed
569 <!-- JAL-2974 -->'Overview updating' progress bar is shown
570 repeatedly after a series of edits even when the overview
571 is no longer reflecting updates
574 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
575 structures for protein subsequence (if 'Trim Retrieved
576 Sequences' enabled) or Ensembl isoforms (Workaround in
577 2.10.4 is to fail back to N&W mapping)
584 <td width="60" nowrap>
586 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
589 <td><div align="left">
590 <ul><li>Updated Certum Codesigning Certificate
591 (Valid till 30th November 2018)</li></ul></div></td>
592 <td><div align="left">
595 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
596 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
597 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
598 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
599 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
600 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
601 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
607 <td width="60" nowrap>
609 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
612 <td><div align="left">
616 <!-- JAL-2446 -->Faster and more efficient management and
617 rendering of sequence features
620 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
621 429 rate limit request hander
624 <!-- JAL-2773 -->Structure views don't get updated unless
625 their colours have changed
628 <!-- JAL-2495 -->All linked sequences are highlighted for
629 a structure mousover (Jmol) or selection (Chimera)
632 <!-- JAL-2790 -->'Cancel' button in progress bar for
633 JABAWS AACon, RNAAliFold and Disorder prediction jobs
636 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
637 view from Ensembl locus cross-references
640 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
644 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
645 feature can be disabled
648 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
649 PDB easier retrieval of sequences for lists of IDs
652 <!-- JAL-2758 -->Short names for sequences retrieved from
658 <li>Groovy interpreter updated to 2.4.12</li>
659 <li>Example groovy script for generating a matrix of
660 percent identity scores for current alignment.</li>
662 <em>Testing and Deployment</em>
665 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
669 <td><div align="left">
673 <!-- JAL-2643 -->Pressing tab after updating the colour
674 threshold text field doesn't trigger an update to the
678 <!-- JAL-2682 -->Race condition when parsing sequence ID
682 <!-- JAL-2608 -->Overview windows are also closed when
683 alignment window is closed
686 <!-- JAL-2548 -->Export of features doesn't always respect
690 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
691 takes a long time in Cursor mode
697 <!-- JAL-2777 -->Structures with whitespace chainCode
698 cannot be viewed in Chimera
701 <!-- JAL-2728 -->Protein annotation panel too high in
705 <!-- JAL-2757 -->Can't edit the query after the server
706 error warning icon is shown in Uniprot and PDB Free Text
710 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
713 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
716 <!-- JAL-2739 -->Hidden column marker in last column not
717 rendered when switching back from Wrapped to normal view
720 <!-- JAL-2768 -->Annotation display corrupted when
721 scrolling right in unwapped alignment view
724 <!-- JAL-2542 -->Existing features on subsequence
725 incorrectly relocated when full sequence retrieved from
729 <!-- JAL-2733 -->Last reported memory still shown when
730 Desktop->Show Memory is unticked (OSX only)
733 <!-- JAL-2658 -->Amend Features dialog doesn't allow
734 features of same type and group to be selected for
738 <!-- JAL-2524 -->Jalview becomes sluggish in wide
739 alignments when hidden columns are present
742 <!-- JAL-2392 -->Jalview freezes when loading and
743 displaying several structures
746 <!-- JAL-2732 -->Black outlines left after resizing or
750 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
751 within the Jalview desktop on OSX
754 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
755 when in wrapped alignment mode
758 <!-- JAL-2636 -->Scale mark not shown when close to right
759 hand end of alignment
762 <!-- JAL-2684 -->Pairwise alignment of selected regions of
763 each selected sequence do not have correct start/end
767 <!-- JAL-2793 -->Alignment ruler height set incorrectly
768 after canceling the Alignment Window's Font dialog
771 <!-- JAL-2036 -->Show cross-references not enabled after
772 restoring project until a new view is created
775 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
776 URL links appears when only default EMBL-EBI link is
777 configured (since 2.10.2b2)
780 <!-- JAL-2775 -->Overview redraws whole window when box
784 <!-- JAL-2225 -->Structure viewer doesn't map all chains
785 in a multi-chain structure when viewing alignment
786 involving more than one chain (since 2.10)
789 <!-- JAL-2811 -->Double residue highlights in cursor mode
790 if new selection moves alignment window
793 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
794 arrow key in cursor mode to pass hidden column marker
797 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
798 that produces correctly annotated transcripts and products
801 <!-- JAL-2776 -->Toggling a feature group after first time
802 doesn't update associated structure view
805 <em>Applet</em><br />
808 <!-- JAL-2687 -->Concurrent modification exception when
809 closing alignment panel
812 <em>BioJSON</em><br />
815 <!-- JAL-2546 -->BioJSON export does not preserve
816 non-positional features
819 <em>New Known Issues</em>
822 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
823 sequence features correctly (for many previous versions of
827 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
828 using cursor in wrapped panel other than top
831 <!-- JAL-2791 -->Select columns containing feature ignores
832 graduated colour threshold
835 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
836 always preserve numbering and sequence features
839 <em>Known Java 9 Issues</em>
842 <!-- JAL-2902 -->Groovy Console very slow to open and is
843 not responsive when entering characters (Webstart, Java
850 <td width="60" nowrap>
852 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
853 <em>2/10/2017</em></strong>
856 <td><div align="left">
857 <em>New features in Jalview Desktop</em>
860 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
862 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
866 <td><div align="left">
870 <td width="60" nowrap>
872 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
873 <em>7/9/2017</em></strong>
876 <td><div align="left">
880 <!-- JAL-2588 -->Show gaps in overview window by colouring
881 in grey (sequences used to be coloured grey, and gaps were
885 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
889 <!-- JAL-2587 -->Overview updates immediately on increase
890 in size and progress bar shown as higher resolution
891 overview is recalculated
896 <td><div align="left">
900 <!-- JAL-2664 -->Overview window redraws every hidden
901 column region row by row
904 <!-- JAL-2681 -->duplicate protein sequences shown after
905 retrieving Ensembl crossrefs for sequences from Uniprot
908 <!-- JAL-2603 -->Overview window throws NPE if show boxes
909 format setting is unticked
912 <!-- JAL-2610 -->Groups are coloured wrongly in overview
913 if group has show boxes format setting unticked
916 <!-- JAL-2672,JAL-2665 -->Redraw problems when
917 autoscrolling whilst dragging current selection group to
918 include sequences and columns not currently displayed
921 <!-- JAL-2691 -->Not all chains are mapped when multimeric
922 assemblies are imported via CIF file
925 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
926 displayed when threshold or conservation colouring is also
930 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
934 <!-- JAL-2673 -->Jalview continues to scroll after
935 dragging a selected region off the visible region of the
939 <!-- JAL-2724 -->Cannot apply annotation based
940 colourscheme to all groups in a view
943 <!-- JAL-2511 -->IDs don't line up with sequences
944 initially after font size change using the Font chooser or
951 <td width="60" nowrap>
953 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
956 <td><div align="left">
957 <em>Calculations</em>
961 <!-- JAL-1933 -->Occupancy annotation row shows number of
962 ungapped positions in each column of the alignment.
965 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
966 a calculation dialog box
969 <!-- JAL-2379 -->Revised implementation of PCA for speed
970 and memory efficiency (~30x faster)
973 <!-- JAL-2403 -->Revised implementation of sequence
974 similarity scores as used by Tree, PCA, Shading Consensus
975 and other calculations
978 <!-- JAL-2416 -->Score matrices are stored as resource
979 files within the Jalview codebase
982 <!-- JAL-2500 -->Trees computed on Sequence Feature
983 Similarity may have different topology due to increased
990 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
991 model for alignments and groups
994 <!-- JAL-384 -->Custom shading schemes created via groovy
1001 <!-- JAL-2526 -->Efficiency improvements for interacting
1002 with alignment and overview windows
1005 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1009 <!-- JAL-2388 -->Hidden columns and sequences can be
1013 <!-- JAL-2611 -->Click-drag in visible area allows fine
1014 adjustment of visible position
1018 <em>Data import/export</em>
1021 <!-- JAL-2535 -->Posterior probability annotation from
1022 Stockholm files imported as sequence associated annotation
1025 <!-- JAL-2507 -->More robust per-sequence positional
1026 annotation input/output via stockholm flatfile
1029 <!-- JAL-2533 -->Sequence names don't include file
1030 extension when importing structure files without embedded
1031 names or PDB accessions
1034 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1035 format sequence substitution matrices
1038 <em>User Interface</em>
1041 <!-- JAL-2447 --> Experimental Features Checkbox in
1042 Desktop's Tools menu to hide or show untested features in
1046 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1047 via Overview or sequence motif search operations
1050 <!-- JAL-2547 -->Amend sequence features dialog box can be
1051 opened by double clicking gaps within sequence feature
1055 <!-- JAL-1476 -->Status bar message shown when not enough
1056 aligned positions were available to create a 3D structure
1060 <em>3D Structure</em>
1063 <!-- JAL-2430 -->Hidden regions in alignment views are not
1064 coloured in linked structure views
1067 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1068 file-based command exchange
1071 <!-- JAL-2375 -->Structure chooser automatically shows
1072 Cached Structures rather than querying the PDBe if
1073 structures are already available for sequences
1076 <!-- JAL-2520 -->Structures imported via URL are cached in
1077 the Jalview project rather than downloaded again when the
1078 project is reopened.
1081 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1082 to transfer Chimera's structure attributes as Jalview
1083 features, and vice-versa (<strong>Experimental
1087 <em>Web Services</em>
1090 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1093 <!-- JAL-2335 -->Filter non-standard amino acids and
1094 nucleotides when submitting to AACon and other MSA
1098 <!-- JAL-2316, -->URLs for viewing database
1099 cross-references provided by identifiers.org and the
1100 EMBL-EBI's MIRIAM DB
1107 <!-- JAL-2344 -->FileFormatI interface for describing and
1108 identifying file formats (instead of String constants)
1111 <!-- JAL-2228 -->FeatureCounter script refactored for
1112 efficiency when counting all displayed features (not
1113 backwards compatible with 2.10.1)
1116 <em>Example files</em>
1119 <!-- JAL-2631 -->Graduated feature colour style example
1120 included in the example feature file
1123 <em>Documentation</em>
1126 <!-- JAL-2339 -->Release notes reformatted for readability
1127 with the built-in Java help viewer
1130 <!-- JAL-1644 -->Find documentation updated with 'search
1131 sequence description' option
1137 <!-- JAL-2485, -->External service integration tests for
1138 Uniprot REST Free Text Search Client
1141 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1144 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1149 <td><div align="left">
1150 <em>Calculations</em>
1153 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1154 matrix - C->R should be '-3'<br />Old matrix restored
1155 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1157 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1158 Jalview's treatment of gaps in PCA and substitution matrix
1159 based Tree calculations.<br /> <br />In earlier versions
1160 of Jalview, gaps matching gaps were penalised, and gaps
1161 matching non-gaps penalised even more. In the PCA
1162 calculation, gaps were actually treated as non-gaps - so
1163 different costs were applied, which meant Jalview's PCAs
1164 were different to those produced by SeqSpace.<br />Jalview
1165 now treats gaps in the same way as SeqSpace (ie it scores
1166 them as 0). <br /> <br />Enter the following in the
1167 Groovy console to restore pre-2.10.2 behaviour:<br />
1168 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1169 // for 2.10.1 mode <br />
1170 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1171 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1172 these settings will affect all subsequent tree and PCA
1173 calculations (not recommended)</em></li>
1175 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1176 scaling of branch lengths for trees computed using
1177 Sequence Feature Similarity.
1180 <!-- JAL-2377 -->PCA calculation could hang when
1181 generating output report when working with highly
1182 redundant alignments
1185 <!-- JAL-2544 --> Sort by features includes features to
1186 right of selected region when gaps present on right-hand
1190 <em>User Interface</em>
1193 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1194 doesn't reselect a specific sequence's associated
1195 annotation after it was used for colouring a view
1198 <!-- JAL-2419 -->Current selection lost if popup menu
1199 opened on a region of alignment without groups
1202 <!-- JAL-2374 -->Popup menu not always shown for regions
1203 of an alignment with overlapping groups
1206 <!-- JAL-2310 -->Finder double counts if both a sequence's
1207 name and description match
1210 <!-- JAL-2370 -->Hiding column selection containing two
1211 hidden regions results in incorrect hidden regions
1214 <!-- JAL-2386 -->'Apply to all groups' setting when
1215 changing colour does not apply Conservation slider value
1219 <!-- JAL-2373 -->Percentage identity and conservation menu
1220 items do not show a tick or allow shading to be disabled
1223 <!-- JAL-2385 -->Conservation shading or PID threshold
1224 lost when base colourscheme changed if slider not visible
1227 <!-- JAL-2547 -->Sequence features shown in tooltip for
1228 gaps before start of features
1231 <!-- JAL-2623 -->Graduated feature colour threshold not
1232 restored to UI when feature colour is edited
1235 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1236 a time when scrolling vertically in wrapped mode.
1239 <!-- JAL-2630 -->Structure and alignment overview update
1240 as graduate feature colour settings are modified via the
1244 <!-- JAL-2034 -->Overview window doesn't always update
1245 when a group defined on the alignment is resized
1248 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1249 wrapped view result in positional status updates
1253 <!-- JAL-2563 -->Status bar doesn't show position for
1254 ambiguous amino acid and nucleotide symbols
1257 <!-- JAL-2602 -->Copy consensus sequence failed if
1258 alignment included gapped columns
1261 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1262 widgets don't permanently disappear
1265 <!-- JAL-2503 -->Cannot select or filter quantitative
1266 annotation that are shown only as column labels (e.g.
1267 T-Coffee column reliability scores)
1270 <!-- JAL-2594 -->Exception thrown if trying to create a
1271 sequence feature on gaps only
1274 <!-- JAL-2504 -->Features created with 'New feature'
1275 button from a Find inherit previously defined feature type
1276 rather than the Find query string
1279 <!-- JAL-2423 -->incorrect title in output window when
1280 exporting tree calculated in Jalview
1283 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1284 and then revealing them reorders sequences on the
1288 <!-- JAL-964 -->Group panel in sequence feature settings
1289 doesn't update to reflect available set of groups after
1290 interactively adding or modifying features
1293 <!-- JAL-2225 -->Sequence Database chooser unusable on
1297 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1298 only excluded gaps in current sequence and ignored
1305 <!-- JAL-2421 -->Overview window visible region moves
1306 erratically when hidden rows or columns are present
1309 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1310 Structure Viewer's colour menu don't correspond to
1314 <!-- JAL-2405 -->Protein specific colours only offered in
1315 colour and group colour menu for protein alignments
1318 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1319 reflect currently selected view or group's shading
1323 <!-- JAL-2624 -->Feature colour thresholds not respected
1324 when rendered on overview and structures when opacity at
1328 <!-- JAL-2589 -->User defined gap colour not shown in
1329 overview when features overlaid on alignment
1332 <em>Data import/export</em>
1335 <!-- JAL-2576 -->Very large alignments take a long time to
1339 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1340 added after a sequence was imported are not written to
1344 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1345 when importing RNA secondary structure via Stockholm
1348 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1349 not shown in correct direction for simple pseudoknots
1352 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1353 with lightGray or darkGray via features file (but can
1357 <!-- JAL-2383 -->Above PID colour threshold not recovered
1358 when alignment view imported from project
1361 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1362 structure and sequences extracted from structure files
1363 imported via URL and viewed in Jmol
1366 <!-- JAL-2520 -->Structures loaded via URL are saved in
1367 Jalview Projects rather than fetched via URL again when
1368 the project is loaded and the structure viewed
1371 <em>Web Services</em>
1374 <!-- JAL-2519 -->EnsemblGenomes example failing after
1375 release of Ensembl v.88
1378 <!-- JAL-2366 -->Proxy server address and port always
1379 appear enabled in Preferences->Connections
1382 <!-- JAL-2461 -->DAS registry not found exceptions
1383 removed from console output
1386 <!-- JAL-2582 -->Cannot retrieve protein products from
1387 Ensembl by Peptide ID
1390 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1391 created from SIFTs, and spurious 'Couldn't open structure
1392 in Chimera' errors raised after April 2017 update (problem
1393 due to 'null' string rather than empty string used for
1394 residues with no corresponding PDB mapping).
1397 <em>Application UI</em>
1400 <!-- JAL-2361 -->User Defined Colours not added to Colour
1404 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1405 case' residues (button in colourscheme editor debugged and
1406 new documentation and tooltips added)
1409 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1410 doesn't restore group-specific text colour thresholds
1413 <!-- JAL-2243 -->Feature settings panel does not update as
1414 new features are added to alignment
1417 <!-- JAL-2532 -->Cancel in feature settings reverts
1418 changes to feature colours via the Amend features dialog
1421 <!-- JAL-2506 -->Null pointer exception when attempting to
1422 edit graduated feature colour via amend features dialog
1426 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1427 selection menu changes colours of alignment views
1430 <!-- JAL-2426 -->Spurious exceptions in console raised
1431 from alignment calculation workers after alignment has
1435 <!-- JAL-1608 -->Typo in selection popup menu - Create
1436 groups now 'Create Group'
1439 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1440 Create/Undefine group doesn't always work
1443 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1444 shown again after pressing 'Cancel'
1447 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1448 adjusts start position in wrap mode
1451 <!-- JAL-2563 -->Status bar doesn't show positions for
1452 ambiguous amino acids
1455 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1456 CDS/Protein view after CDS sequences added for aligned
1460 <!-- JAL-2592 -->User defined colourschemes called 'User
1461 Defined' don't appear in Colours menu
1467 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1468 score models doesn't always result in an updated PCA plot
1471 <!-- JAL-2442 -->Features not rendered as transparent on
1472 overview or linked structure view
1475 <!-- JAL-2372 -->Colour group by conservation doesn't
1479 <!-- JAL-2517 -->Hitting Cancel after applying
1480 user-defined colourscheme doesn't restore original
1487 <!-- JAL-2314 -->Unit test failure:
1488 jalview.ws.jabaws.RNAStructExportImport setup fails
1491 <!-- JAL-2307 -->Unit test failure:
1492 jalview.ws.sifts.SiftsClientTest due to compatibility
1493 problems with deep array comparison equality asserts in
1494 successive versions of TestNG
1497 <!-- JAL-2479 -->Relocated StructureChooserTest and
1498 ParameterUtilsTest Unit tests to Network suite
1501 <em>New Known Issues</em>
1504 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1505 phase after a sequence motif find operation
1508 <!-- JAL-2550 -->Importing annotation file with rows
1509 containing just upper and lower case letters are
1510 interpreted as WUSS RNA secondary structure symbols
1513 <!-- JAL-2590 -->Cannot load and display Newick trees
1514 reliably from eggnog Ortholog database
1517 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1518 containing features of type Highlight' when 'B' is pressed
1519 to mark columns containing highlighted regions.
1522 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1523 doesn't always add secondary structure annotation.
1528 <td width="60" nowrap>
1529 <div align="center">
1530 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1533 <td><div align="left">
1537 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1538 for all consensus calculations
1541 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1544 <li>Updated Jalview's Certum code signing certificate
1547 <em>Application</em>
1550 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1551 set of database cross-references, sorted alphabetically
1554 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1555 from database cross references. Users with custom links
1556 will receive a <a href="webServices/urllinks.html#warning">warning
1557 dialog</a> asking them to update their preferences.
1560 <!-- JAL-2287-->Cancel button and escape listener on
1561 dialog warning user about disconnecting Jalview from a
1565 <!-- JAL-2320-->Jalview's Chimera control window closes if
1566 the Chimera it is connected to is shut down
1569 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1570 columns menu item to mark columns containing highlighted
1571 regions (e.g. from structure selections or results of a
1575 <!-- JAL-2284-->Command line option for batch-generation
1576 of HTML pages rendering alignment data with the BioJS
1586 <!-- JAL-2286 -->Columns with more than one modal residue
1587 are not coloured or thresholded according to percent
1588 identity (first observed in Jalview 2.8.2)
1591 <!-- JAL-2301 -->Threonine incorrectly reported as not
1595 <!-- JAL-2318 -->Updates to documentation pages (above PID
1596 threshold, amino acid properties)
1599 <!-- JAL-2292 -->Lower case residues in sequences are not
1600 reported as mapped to residues in a structure file in the
1604 <!--JAL-2324 -->Identical features with non-numeric scores
1605 could be added multiple times to a sequence
1608 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1609 bond features shown as two highlighted residues rather
1610 than a range in linked structure views, and treated
1611 correctly when selecting and computing trees from features
1614 <!-- JAL-2281-->Custom URL links for database
1615 cross-references are matched to database name regardless
1620 <em>Application</em>
1623 <!-- JAL-2282-->Custom URL links for specific database
1624 names without regular expressions also offer links from
1628 <!-- JAL-2315-->Removing a single configured link in the
1629 URL links pane in Connections preferences doesn't actually
1630 update Jalview configuration
1633 <!-- JAL-2272-->CTRL-Click on a selected region to open
1634 the alignment area popup menu doesn't work on El-Capitan
1637 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1638 files with similarly named sequences if dropped onto the
1642 <!-- JAL-2312 -->Additional mappings are shown for PDB
1643 entries where more chains exist in the PDB accession than
1644 are reported in the SIFTS file
1647 <!-- JAL-2317-->Certain structures do not get mapped to
1648 the structure view when displayed with Chimera
1651 <!-- JAL-2317-->No chains shown in the Chimera view
1652 panel's View->Show Chains submenu
1655 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1656 work for wrapped alignment views
1659 <!--JAL-2197 -->Rename UI components for running JPred
1660 predictions from 'JNet' to 'JPred'
1663 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1664 corrupted when annotation panel vertical scroll is not at
1665 first annotation row
1668 <!--JAL-2332 -->Attempting to view structure for Hen
1669 lysozyme results in a PDB Client error dialog box
1672 <!-- JAL-2319 -->Structure View's mapping report switched
1673 ranges for PDB and sequence for SIFTS
1676 SIFTS 'Not_Observed' residues mapped to non-existant
1680 <!-- <em>New Known Issues</em>
1687 <td width="60" nowrap>
1688 <div align="center">
1689 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1690 <em>25/10/2016</em></strong>
1693 <td><em>Application</em>
1695 <li>3D Structure chooser opens with 'Cached structures'
1696 view if structures already loaded</li>
1697 <li>Progress bar reports models as they are loaded to
1698 structure views</li>
1704 <li>Colour by conservation always enabled and no tick
1705 shown in menu when BLOSUM or PID shading applied</li>
1706 <li>FER1_ARATH and FER2_ARATH labels were switched in
1707 example sequences/projects/trees</li>
1709 <em>Application</em>
1711 <li>Jalview projects with views of local PDB structure
1712 files saved on Windows cannot be opened on OSX</li>
1713 <li>Multiple structure views can be opened and superposed
1714 without timeout for structures with multiple models or
1715 multiple sequences in alignment</li>
1716 <li>Cannot import or associated local PDB files without a
1717 PDB ID HEADER line</li>
1718 <li>RMSD is not output in Jmol console when superposition
1720 <li>Drag and drop of URL from Browser fails for Linux and
1721 OSX versions earlier than El Capitan</li>
1722 <li>ENA client ignores invalid content from ENA server</li>
1723 <li>Exceptions are not raised in console when ENA client
1724 attempts to fetch non-existent IDs via Fetch DB Refs UI
1726 <li>Exceptions are not raised in console when a new view
1727 is created on the alignment</li>
1728 <li>OSX right-click fixed for group selections: CMD-click
1729 to insert/remove gaps in groups and CTRL-click to open group
1732 <em>Build and deployment</em>
1734 <li>URL link checker now copes with multi-line anchor
1737 <em>New Known Issues</em>
1739 <li>Drag and drop from URL links in browsers do not work
1746 <td width="60" nowrap>
1747 <div align="center">
1748 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1751 <td><em>General</em>
1754 <!-- JAL-2124 -->Updated Spanish translations.
1757 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1758 for importing structure data to Jalview. Enables mmCIF and
1762 <!-- JAL-192 --->Alignment ruler shows positions relative to
1766 <!-- JAL-2202 -->Position/residue shown in status bar when
1767 mousing over sequence associated annotation
1770 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1774 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1775 '()', canonical '[]' and invalid '{}' base pair populations
1779 <!-- JAL-2092 -->Feature settings popup menu options for
1780 showing or hiding columns containing a feature
1783 <!-- JAL-1557 -->Edit selected group by double clicking on
1784 group and sequence associated annotation labels
1787 <!-- JAL-2236 -->Sequence name added to annotation label in
1788 select/hide columns by annotation and colour by annotation
1792 </ul> <em>Application</em>
1795 <!-- JAL-2050-->Automatically hide introns when opening a
1796 gene/transcript view
1799 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1803 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1804 structure mappings with the EMBL-EBI PDBe SIFTS database
1807 <!-- JAL-2079 -->Updated download sites used for Rfam and
1808 Pfam sources to xfam.org
1811 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1814 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1815 over sequences in Jalview
1818 <!-- JAL-2027-->Support for reverse-complement coding
1819 regions in ENA and EMBL
1822 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1823 for record retrieval via ENA rest API
1826 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1830 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1831 groovy script execution
1834 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1835 alignment window's Calculate menu
1838 <!-- JAL-1812 -->Allow groovy scripts that call
1839 Jalview.getAlignFrames() to run in headless mode
1842 <!-- JAL-2068 -->Support for creating new alignment
1843 calculation workers from groovy scripts
1846 <!-- JAL-1369 --->Store/restore reference sequence in
1850 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1851 associations are now saved/restored from project
1854 <!-- JAL-1993 -->Database selection dialog always shown
1855 before sequence fetcher is opened
1858 <!-- JAL-2183 -->Double click on an entry in Jalview's
1859 database chooser opens a sequence fetcher
1862 <!-- JAL-1563 -->Free-text search client for UniProt using
1863 the UniProt REST API
1866 <!-- JAL-2168 -->-nonews command line parameter to prevent
1867 the news reader opening
1870 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1871 querying stored in preferences
1874 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1878 <!-- JAL-1977-->Tooltips shown on database chooser
1881 <!-- JAL-391 -->Reverse complement function in calculate
1882 menu for nucleotide sequences
1885 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1886 and feature counts preserves alignment ordering (and
1887 debugged for complex feature sets).
1890 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1891 viewing structures with Jalview 2.10
1894 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1895 genome, transcript CCDS and gene ids via the Ensembl and
1896 Ensembl Genomes REST API
1899 <!-- JAL-2049 -->Protein sequence variant annotation
1900 computed for 'sequence_variant' annotation on CDS regions
1904 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1908 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1909 Ref Fetcher fails to match, or otherwise updates sequence
1910 data from external database records.
1913 <!-- JAL-2154 -->Revised Jalview Project format for
1914 efficient recovery of sequence coding and alignment
1915 annotation relationships.
1917 </ul> <!-- <em>Applet</em>
1928 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1932 <!-- JAL-2018-->Export features in Jalview format (again)
1933 includes graduated colourschemes
1936 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1937 working with big alignments and lots of hidden columns
1940 <!-- JAL-2053-->Hidden column markers not always rendered
1941 at right of alignment window
1944 <!-- JAL-2067 -->Tidied up links in help file table of
1948 <!-- JAL-2072 -->Feature based tree calculation not shown
1952 <!-- JAL-2075 -->Hidden columns ignored during feature
1953 based tree calculation
1956 <!-- JAL-2065 -->Alignment view stops updating when show
1957 unconserved enabled for group on alignment
1960 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1964 <!-- JAL-2146 -->Alignment column in status incorrectly
1965 shown as "Sequence position" when mousing over
1969 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1970 hidden columns present
1973 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1974 user created annotation added to alignment
1977 <!-- JAL-1841 -->RNA Structure consensus only computed for
1978 '()' base pair annotation
1981 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1982 in zero scores for all base pairs in RNA Structure
1986 <!-- JAL-2174-->Extend selection with columns containing
1990 <!-- JAL-2275 -->Pfam format writer puts extra space at
1991 beginning of sequence
1994 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1998 <!-- JAL-2238 -->Cannot create groups on an alignment from
1999 from a tree when t-coffee scores are shown
2002 <!-- JAL-1836,1967 -->Cannot import and view PDB
2003 structures with chains containing negative resnums (4q4h)
2006 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2010 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2011 to Clustal, PIR and PileUp output
2014 <!-- JAL-2008 -->Reordering sequence features that are
2015 not visible causes alignment window to repaint
2018 <!-- JAL-2006 -->Threshold sliders don't work in
2019 graduated colour and colour by annotation row for e-value
2020 scores associated with features and annotation rows
2023 <!-- JAL-1797 -->amino acid physicochemical conservation
2024 calculation should be case independent
2027 <!-- JAL-2173 -->Remove annotation also updates hidden
2031 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2032 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2033 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2036 <!-- JAL-2065 -->Null pointer exceptions and redraw
2037 problems when reference sequence defined and 'show
2038 non-conserved' enabled
2041 <!-- JAL-1306 -->Quality and Conservation are now shown on
2042 load even when Consensus calculation is disabled
2045 <!-- JAL-1932 -->Remove right on penultimate column of
2046 alignment does nothing
2049 <em>Application</em>
2052 <!-- JAL-1552-->URLs and links can't be imported by
2053 drag'n'drop on OSX when launched via webstart (note - not
2054 yet fixed for El Capitan)
2057 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2058 output when running on non-gb/us i18n platforms
2061 <!-- JAL-1944 -->Error thrown when exporting a view with
2062 hidden sequences as flat-file alignment
2065 <!-- JAL-2030-->InstallAnywhere distribution fails when
2069 <!-- JAL-2080-->Jalview very slow to launch via webstart
2070 (also hotfix for 2.9.0b2)
2073 <!-- JAL-2085 -->Cannot save project when view has a
2074 reference sequence defined
2077 <!-- JAL-1011 -->Columns are suddenly selected in other
2078 alignments and views when revealing hidden columns
2081 <!-- JAL-1989 -->Hide columns not mirrored in complement
2082 view in a cDNA/Protein splitframe
2085 <!-- JAL-1369 -->Cannot save/restore representative
2086 sequence from project when only one sequence is
2090 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2091 in Structure Chooser
2094 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2095 structure consensus didn't refresh annotation panel
2098 <!-- JAL-1962 -->View mapping in structure view shows
2099 mappings between sequence and all chains in a PDB file
2102 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2103 dialogs format columns correctly, don't display array
2104 data, sort columns according to type
2107 <!-- JAL-1975 -->Export complete shown after destination
2108 file chooser is cancelled during an image export
2111 <!-- JAL-2025 -->Error when querying PDB Service with
2112 sequence name containing special characters
2115 <!-- JAL-2024 -->Manual PDB structure querying should be
2119 <!-- JAL-2104 -->Large tooltips with broken HTML
2120 formatting don't wrap
2123 <!-- JAL-1128 -->Figures exported from wrapped view are
2124 truncated so L looks like I in consensus annotation
2127 <!-- JAL-2003 -->Export features should only export the
2128 currently displayed features for the current selection or
2132 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2133 after fetching cross-references, and restoring from
2137 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2138 followed in the structure viewer
2141 <!-- JAL-2163 -->Titles for individual alignments in
2142 splitframe not restored from project
2145 <!-- JAL-2145 -->missing autocalculated annotation at
2146 trailing end of protein alignment in transcript/product
2147 splitview when pad-gaps not enabled by default
2150 <!-- JAL-1797 -->amino acid physicochemical conservation
2154 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2155 article has been read (reopened issue due to
2156 internationalisation problems)
2159 <!-- JAL-1960 -->Only offer PDB structures in structure
2160 viewer based on sequence name, PDB and UniProt
2165 <!-- JAL-1976 -->No progress bar shown during export of
2169 <!-- JAL-2213 -->Structures not always superimposed after
2170 multiple structures are shown for one or more sequences.
2173 <!-- JAL-1370 -->Reference sequence characters should not
2174 be replaced with '.' when 'Show unconserved' format option
2178 <!-- JAL-1823 -->Cannot specify chain code when entering
2179 specific PDB id for sequence
2182 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2183 'Export hidden sequences' is enabled, but 'export hidden
2184 columns' is disabled.
2187 <!--JAL-2026-->Best Quality option in structure chooser
2188 selects lowest rather than highest resolution structures
2192 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2193 to sequence mapping in 'View Mappings' report
2196 <!-- JAL-2284 -->Unable to read old Jalview projects that
2197 contain non-XML data added after Jalvew wrote project.
2200 <!-- JAL-2118 -->Newly created annotation row reorders
2201 after clicking on it to create new annotation for a
2205 <!-- JAL-1980 -->Null Pointer Exception raised when
2206 pressing Add on an orphaned cut'n'paste window.
2208 <!-- may exclude, this is an external service stability issue JAL-1941
2209 -- > RNA 3D structure not added via DSSR service</li> -->
2214 <!-- JAL-2151 -->Incorrect columns are selected when
2215 hidden columns present before start of sequence
2218 <!-- JAL-1986 -->Missing dependencies on applet pages
2222 <!-- JAL-1947 -->Overview pixel size changes when
2223 sequences are hidden in applet
2226 <!-- JAL-1996 -->Updated instructions for applet
2227 deployment on examples pages.
2234 <td width="60" nowrap>
2235 <div align="center">
2236 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2237 <em>16/10/2015</em></strong>
2240 <td><em>General</em>
2242 <li>Time stamps for signed Jalview application and applet
2247 <em>Application</em>
2249 <li>Duplicate group consensus and conservation rows
2250 shown when tree is partitioned</li>
2251 <li>Erratic behaviour when tree partitions made with
2252 multiple cDNA/Protein split views</li>
2258 <td width="60" nowrap>
2259 <div align="center">
2260 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2261 <em>8/10/2015</em></strong>
2264 <td><em>General</em>
2266 <li>Updated Spanish translations of localized text for
2268 </ul> <em>Application</em>
2270 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2271 <li>Signed OSX InstallAnywhere installer<br></li>
2272 <li>Support for per-sequence based annotations in BioJSON</li>
2273 </ul> <em>Applet</em>
2275 <li>Split frame example added to applet examples page</li>
2276 </ul> <em>Build and Deployment</em>
2279 <!-- JAL-1888 -->New ant target for running Jalview's test
2287 <li>Mapping of cDNA to protein in split frames
2288 incorrect when sequence start > 1</li>
2289 <li>Broken images in filter column by annotation dialog
2291 <li>Feature colours not parsed from features file</li>
2292 <li>Exceptions and incomplete link URLs recovered when
2293 loading a features file containing HTML tags in feature
2297 <em>Application</em>
2299 <li>Annotations corrupted after BioJS export and
2301 <li>Incorrect sequence limits after Fetch DB References
2302 with 'trim retrieved sequences'</li>
2303 <li>Incorrect warning about deleting all data when
2304 deleting selected columns</li>
2305 <li>Patch to build system for shipping properly signed
2306 JNLP templates for webstart launch</li>
2307 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2308 unreleased structures for download or viewing</li>
2309 <li>Tab/space/return keystroke operation of EMBL-PDBe
2310 fetcher/viewer dialogs works correctly</li>
2311 <li>Disabled 'minimise' button on Jalview windows
2312 running on OSX to workaround redraw hang bug</li>
2313 <li>Split cDNA/Protein view position and geometry not
2314 recovered from jalview project</li>
2315 <li>Initial enabled/disabled state of annotation menu
2316 sorter 'show autocalculated first/last' corresponds to
2318 <li>Restoring of Clustal, RNA Helices and T-Coffee
2319 color schemes from BioJSON</li>
2323 <li>Reorder sequences mirrored in cDNA/Protein split
2325 <li>Applet with Jmol examples not loading correctly</li>
2331 <td><div align="center">
2332 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2334 <td><em>General</em>
2336 <li>Linked visualisation and analysis of DNA and Protein
2339 <li>Translated cDNA alignments shown as split protein
2340 and DNA alignment views</li>
2341 <li>Codon consensus annotation for linked protein and
2342 cDNA alignment views</li>
2343 <li>Link cDNA or Protein product sequences by loading
2344 them onto Protein or cDNA alignments</li>
2345 <li>Reconstruct linked cDNA alignment from aligned
2346 protein sequences</li>
2349 <li>Jmol integration updated to Jmol v14.2.14</li>
2350 <li>Import and export of Jalview alignment views as <a
2351 href="features/bioJsonFormat.html">BioJSON</a></li>
2352 <li>New alignment annotation file statements for
2353 reference sequences and marking hidden columns</li>
2354 <li>Reference sequence based alignment shading to
2355 highlight variation</li>
2356 <li>Select or hide columns according to alignment
2358 <li>Find option for locating sequences by description</li>
2359 <li>Conserved physicochemical properties shown in amino
2360 acid conservation row</li>
2361 <li>Alignments can be sorted by number of RNA helices</li>
2362 </ul> <em>Application</em>
2364 <li>New cDNA/Protein analysis capabilities
2366 <li>Get Cross-References should open a Split Frame
2367 view with cDNA/Protein</li>
2368 <li>Detect when nucleotide sequences and protein
2369 sequences are placed in the same alignment</li>
2370 <li>Split cDNA/Protein views are saved in Jalview
2375 <li>Use REST API to talk to Chimera</li>
2376 <li>Selected regions in Chimera are highlighted in linked
2377 Jalview windows</li>
2379 <li>VARNA RNA viewer updated to v3.93</li>
2380 <li>VARNA views are saved in Jalview Projects</li>
2381 <li>Pseudoknots displayed as Jalview RNA annotation can
2382 be shown in VARNA</li>
2384 <li>Make groups for selection uses marked columns as well
2385 as the active selected region</li>
2387 <li>Calculate UPGMA and NJ trees using sequence feature
2389 <li>New Export options
2391 <li>New Export Settings dialog to control hidden
2392 region export in flat file generation</li>
2394 <li>Export alignment views for display with the <a
2395 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2397 <li>Export scrollable SVG in HTML page</li>
2398 <li>Optional embedding of BioJSON data when exporting
2399 alignment figures to HTML</li>
2401 <li>3D structure retrieval and display
2403 <li>Free text and structured queries with the PDBe
2405 <li>PDBe Search API based discovery and selection of
2406 PDB structures for a sequence set</li>
2410 <li>JPred4 employed for protein secondary structure
2412 <li>Hide Insertions menu option to hide unaligned columns
2413 for one or a group of sequences</li>
2414 <li>Automatically hide insertions in alignments imported
2415 from the JPred4 web server</li>
2416 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2417 system on OSX<br />LGPL libraries courtesy of <a
2418 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2420 <li>changed 'View nucleotide structure' submenu to 'View
2421 VARNA 2D Structure'</li>
2422 <li>change "View protein structure" menu option to "3D
2425 </ul> <em>Applet</em>
2427 <li>New layout for applet example pages</li>
2428 <li>New parameters to enable SplitFrame view
2429 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2430 <li>New example demonstrating linked viewing of cDNA and
2431 Protein alignments</li>
2432 </ul> <em>Development and deployment</em>
2434 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2435 <li>Include installation type and git revision in build
2436 properties and console log output</li>
2437 <li>Jalview Github organisation, and new github site for
2438 storing BioJsMSA Templates</li>
2439 <li>Jalview's unit tests now managed with TestNG</li>
2442 <!-- <em>General</em>
2444 </ul> --> <!-- issues resolved --> <em>Application</em>
2446 <li>Escape should close any open find dialogs</li>
2447 <li>Typo in select-by-features status report</li>
2448 <li>Consensus RNA secondary secondary structure
2449 predictions are not highlighted in amber</li>
2450 <li>Missing gap character in v2.7 example file means
2451 alignment appears unaligned when pad-gaps is not enabled</li>
2452 <li>First switch to RNA Helices colouring doesn't colour
2453 associated structure views</li>
2454 <li>ID width preference option is greyed out when auto
2455 width checkbox not enabled</li>
2456 <li>Stopped a warning dialog from being shown when
2457 creating user defined colours</li>
2458 <li>'View Mapping' in structure viewer shows sequence
2459 mappings for just that viewer's sequences</li>
2460 <li>Workaround for superposing PDB files containing
2461 multiple models in Chimera</li>
2462 <li>Report sequence position in status bar when hovering
2463 over Jmol structure</li>
2464 <li>Cannot output gaps as '.' symbols with Selection ->
2465 output to text box</li>
2466 <li>Flat file exports of alignments with hidden columns
2467 have incorrect sequence start/end</li>
2468 <li>'Aligning' a second chain to a Chimera structure from
2470 <li>Colour schemes applied to structure viewers don't
2471 work for nucleotide</li>
2472 <li>Loading/cut'n'pasting an empty or invalid file leads
2473 to a grey/invisible alignment window</li>
2474 <li>Exported Jpred annotation from a sequence region
2475 imports to different position</li>
2476 <li>Space at beginning of sequence feature tooltips shown
2477 on some platforms</li>
2478 <li>Chimera viewer 'View | Show Chain' menu is not
2480 <li>'New View' fails with a Null Pointer Exception in
2481 console if Chimera has been opened</li>
2482 <li>Mouseover to Chimera not working</li>
2483 <li>Miscellaneous ENA XML feature qualifiers not
2485 <li>NPE in annotation renderer after 'Extract Scores'</li>
2486 <li>If two structures in one Chimera window, mouseover of
2487 either sequence shows on first structure</li>
2488 <li>'Show annotations' options should not make
2489 non-positional annotations visible</li>
2490 <li>Subsequence secondary structure annotation not shown
2491 in right place after 'view flanking regions'</li>
2492 <li>File Save As type unset when current file format is
2494 <li>Save as '.jar' option removed for saving Jalview
2496 <li>Colour by Sequence colouring in Chimera more
2498 <li>Cannot 'add reference annotation' for a sequence in
2499 several views on same alignment</li>
2500 <li>Cannot show linked products for EMBL / ENA records</li>
2501 <li>Jalview's tooltip wraps long texts containing no
2503 </ul> <em>Applet</em>
2505 <li>Jmol to JalviewLite mouseover/link not working</li>
2506 <li>JalviewLite can't import sequences with ID
2507 descriptions containing angle brackets</li>
2508 </ul> <em>General</em>
2510 <li>Cannot export and reimport RNA secondary structure
2511 via jalview annotation file</li>
2512 <li>Random helix colour palette for colour by annotation
2513 with RNA secondary structure</li>
2514 <li>Mouseover to cDNA from STOP residue in protein
2515 translation doesn't work.</li>
2516 <li>hints when using the select by annotation dialog box</li>
2517 <li>Jmol alignment incorrect if PDB file has alternate CA
2519 <li>FontChooser message dialog appears to hang after
2520 choosing 1pt font</li>
2521 <li>Peptide secondary structure incorrectly imported from
2522 annotation file when annotation display text includes 'e' or
2524 <li>Cannot set colour of new feature type whilst creating
2526 <li>cDNA translation alignment should not be sequence
2527 order dependent</li>
2528 <li>'Show unconserved' doesn't work for lower case
2530 <li>Nucleotide ambiguity codes involving R not recognised</li>
2531 </ul> <em>Deployment and Documentation</em>
2533 <li>Applet example pages appear different to the rest of
2534 www.jalview.org</li>
2535 </ul> <em>Application Known issues</em>
2537 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2538 <li>Misleading message appears after trying to delete
2540 <li>Jalview icon not shown in dock after InstallAnywhere
2541 version launches</li>
2542 <li>Fetching EMBL reference for an RNA sequence results
2543 fails with a sequence mismatch</li>
2544 <li>Corrupted or unreadable alignment display when
2545 scrolling alignment to right</li>
2546 <li>ArrayIndexOutOfBoundsException thrown when remove
2547 empty columns called on alignment with ragged gapped ends</li>
2548 <li>auto calculated alignment annotation rows do not get
2549 placed above or below non-autocalculated rows</li>
2550 <li>Jalview dekstop becomes sluggish at full screen in
2551 ultra-high resolution</li>
2552 <li>Cannot disable consensus calculation independently of
2553 quality and conservation</li>
2554 <li>Mouseover highlighting between cDNA and protein can
2555 become sluggish with more than one splitframe shown</li>
2556 </ul> <em>Applet Known Issues</em>
2558 <li>Core PDB parsing code requires Jmol</li>
2559 <li>Sequence canvas panel goes white when alignment
2560 window is being resized</li>
2566 <td><div align="center">
2567 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2569 <td><em>General</em>
2571 <li>Updated Java code signing certificate donated by
2573 <li>Features and annotation preserved when performing
2574 pairwise alignment</li>
2575 <li>RNA pseudoknot annotation can be
2576 imported/exported/displayed</li>
2577 <li>'colour by annotation' can colour by RNA and
2578 protein secondary structure</li>
2579 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2580 post-hoc with 2.9 release</em>)
2583 </ul> <em>Application</em>
2585 <li>Extract and display secondary structure for sequences
2586 with 3D structures</li>
2587 <li>Support for parsing RNAML</li>
2588 <li>Annotations menu for layout
2590 <li>sort sequence annotation rows by alignment</li>
2591 <li>place sequence annotation above/below alignment
2594 <li>Output in Stockholm format</li>
2595 <li>Internationalisation: improved Spanish (es)
2597 <li>Structure viewer preferences tab</li>
2598 <li>Disorder and Secondary Structure annotation tracks
2599 shared between alignments</li>
2600 <li>UCSF Chimera launch and linked highlighting from
2602 <li>Show/hide all sequence associated annotation rows for
2603 all or current selection</li>
2604 <li>disorder and secondary structure predictions
2605 available as dataset annotation</li>
2606 <li>Per-sequence rna helices colouring</li>
2609 <li>Sequence database accessions imported when fetching
2610 alignments from Rfam</li>
2611 <li>update VARNA version to 3.91</li>
2613 <li>New groovy scripts for exporting aligned positions,
2614 conservation values, and calculating sum of pairs scores.</li>
2615 <li>Command line argument to set default JABAWS server</li>
2616 <li>include installation type in build properties and
2617 console log output</li>
2618 <li>Updated Jalview project format to preserve dataset
2622 <!-- issues resolved --> <em>Application</em>
2624 <li>Distinguish alignment and sequence associated RNA
2625 structure in structure->view->VARNA</li>
2626 <li>Raise dialog box if user deletes all sequences in an
2628 <li>Pressing F1 results in documentation opening twice</li>
2629 <li>Sequence feature tooltip is wrapped</li>
2630 <li>Double click on sequence associated annotation
2631 selects only first column</li>
2632 <li>Redundancy removal doesn't result in unlinked
2633 leaves shown in tree</li>
2634 <li>Undos after several redundancy removals don't undo
2636 <li>Hide sequence doesn't hide associated annotation</li>
2637 <li>User defined colours dialog box too big to fit on
2638 screen and buttons not visible</li>
2639 <li>author list isn't updated if already written to
2640 Jalview properties</li>
2641 <li>Popup menu won't open after retrieving sequence
2643 <li>File open window for associate PDB doesn't open</li>
2644 <li>Left-then-right click on a sequence id opens a
2645 browser search window</li>
2646 <li>Cannot open sequence feature shading/sort popup menu
2647 in feature settings dialog</li>
2648 <li>better tooltip placement for some areas of Jalview
2650 <li>Allow addition of JABAWS Server which doesn't
2651 pass validation</li>
2652 <li>Web services parameters dialog box is too large to
2654 <li>Muscle nucleotide alignment preset obscured by
2656 <li>JABAWS preset submenus don't contain newly
2657 defined user preset</li>
2658 <li>MSA web services warns user if they were launched
2659 with invalid input</li>
2660 <li>Jalview cannot contact DAS Registy when running on
2663 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2664 'Superpose with' submenu not shown when new view
2668 </ul> <!-- <em>Applet</em>
2670 </ul> <em>General</em>
2672 </ul>--> <em>Deployment and Documentation</em>
2674 <li>2G and 1G options in launchApp have no effect on
2675 memory allocation</li>
2676 <li>launchApp service doesn't automatically open
2677 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2679 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2680 InstallAnywhere reports cannot find valid JVM when Java
2681 1.7_055 is available
2683 </ul> <em>Application Known issues</em>
2686 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2687 corrupted or unreadable alignment display when scrolling
2691 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2692 retrieval fails but progress bar continues for DAS retrieval
2693 with large number of ID
2696 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2697 flatfile output of visible region has incorrect sequence
2701 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2702 rna structure consensus doesn't update when secondary
2703 structure tracks are rearranged
2706 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2707 invalid rna structure positional highlighting does not
2708 highlight position of invalid base pairs
2711 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2712 out of memory errors are not raised when saving Jalview
2713 project from alignment window file menu
2716 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2717 Switching to RNA Helices colouring doesn't propagate to
2721 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2722 colour by RNA Helices not enabled when user created
2723 annotation added to alignment
2726 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2727 Jalview icon not shown on dock in Mountain Lion/Webstart
2729 </ul> <em>Applet Known Issues</em>
2732 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2733 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2736 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2737 Jalview and Jmol example not compatible with IE9
2740 <li>Sort by annotation score doesn't reverse order
2746 <td><div align="center">
2747 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2750 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2753 <li>Internationalisation of user interface (usually
2754 called i18n support) and translation for Spanish locale</li>
2755 <li>Define/Undefine group on current selection with
2756 Ctrl-G/Shift Ctrl-G</li>
2757 <li>Improved group creation/removal options in
2758 alignment/sequence Popup menu</li>
2759 <li>Sensible precision for symbol distribution
2760 percentages shown in logo tooltip.</li>
2761 <li>Annotation panel height set according to amount of
2762 annotation when alignment first opened</li>
2763 </ul> <em>Application</em>
2765 <li>Interactive consensus RNA secondary structure
2766 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2767 <li>Select columns containing particular features from
2768 Feature Settings dialog</li>
2769 <li>View all 'representative' PDB structures for selected
2771 <li>Update Jalview project format:
2773 <li>New file extension for Jalview projects '.jvp'</li>
2774 <li>Preserve sequence and annotation dataset (to
2775 store secondary structure annotation,etc)</li>
2776 <li>Per group and alignment annotation and RNA helix
2780 <li>New similarity measures for PCA and Tree calculation
2782 <li>Experimental support for retrieval and viewing of
2783 flanking regions for an alignment</li>
2787 <!-- issues resolved --> <em>Application</em>
2789 <li>logo keeps spinning and status remains at queued or
2790 running after job is cancelled</li>
2791 <li>cannot export features from alignments imported from
2792 Jalview/VAMSAS projects</li>
2793 <li>Buggy slider for web service parameters that take
2795 <li>Newly created RNA secondary structure line doesn't
2796 have 'display all symbols' flag set</li>
2797 <li>T-COFFEE alignment score shading scheme and other
2798 annotation shading not saved in Jalview project</li>
2799 <li>Local file cannot be loaded in freshly downloaded
2801 <li>Jalview icon not shown on dock in Mountain
2803 <li>Load file from desktop file browser fails</li>
2804 <li>Occasional NPE thrown when calculating large trees</li>
2805 <li>Cannot reorder or slide sequences after dragging an
2806 alignment onto desktop</li>
2807 <li>Colour by annotation dialog throws NPE after using
2808 'extract scores' function</li>
2809 <li>Loading/cut'n'pasting an empty file leads to a grey
2810 alignment window</li>
2811 <li>Disorder thresholds rendered incorrectly after
2812 performing IUPred disorder prediction</li>
2813 <li>Multiple group annotated consensus rows shown when
2814 changing 'normalise logo' display setting</li>
2815 <li>Find shows blank dialog after 'finished searching' if
2816 nothing matches query</li>
2817 <li>Null Pointer Exceptions raised when sorting by
2818 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2820 <li>Errors in Jmol console when structures in alignment
2821 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2823 <li>Not all working JABAWS services are shown in
2825 <li>JAVAWS version of Jalview fails to launch with
2826 'invalid literal/length code'</li>
2827 <li>Annotation/RNA Helix colourschemes cannot be applied
2828 to alignment with groups (actually fixed in 2.8.0b1)</li>
2829 <li>RNA Helices and T-Coffee Scores available as default
2832 </ul> <em>Applet</em>
2834 <li>Remove group option is shown even when selection is
2836 <li>Apply to all groups ticked but colourscheme changes
2837 don't affect groups</li>
2838 <li>Documented RNA Helices and T-Coffee Scores as valid
2839 colourscheme name</li>
2840 <li>Annotation labels drawn on sequence IDs when
2841 Annotation panel is not displayed</li>
2842 <li>Increased font size for dropdown menus on OSX and
2843 embedded windows</li>
2844 </ul> <em>Other</em>
2846 <li>Consensus sequence for alignments/groups with a
2847 single sequence were not calculated</li>
2848 <li>annotation files that contain only groups imported as
2849 annotation and junk sequences</li>
2850 <li>Fasta files with sequences containing '*' incorrectly
2851 recognised as PFAM or BLC</li>
2852 <li>conservation/PID slider apply all groups option
2853 doesn't affect background (2.8.0b1)
2855 <li>redundancy highlighting is erratic at 0% and 100%</li>
2856 <li>Remove gapped columns fails for sequences with ragged
2858 <li>AMSA annotation row with leading spaces is not
2859 registered correctly on import</li>
2860 <li>Jalview crashes when selecting PCA analysis for
2861 certain alignments</li>
2862 <li>Opening the colour by annotation dialog for an
2863 existing annotation based 'use original colours'
2864 colourscheme loses original colours setting</li>
2869 <td><div align="center">
2870 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2871 <em>30/1/2014</em></strong>
2875 <li>Trusted certificates for JalviewLite applet and
2876 Jalview Desktop application<br />Certificate was donated by
2877 <a href="https://www.certum.eu">Certum</a> to the Jalview
2878 open source project).
2880 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2881 <li>Output in Stockholm format</li>
2882 <li>Allow import of data from gzipped files</li>
2883 <li>Export/import group and sequence associated line
2884 graph thresholds</li>
2885 <li>Nucleotide substitution matrix that supports RNA and
2886 ambiguity codes</li>
2887 <li>Allow disorder predictions to be made on the current
2888 selection (or visible selection) in the same way that JPred
2890 <li>Groovy scripting for headless Jalview operation</li>
2891 </ul> <em>Other improvements</em>
2893 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2894 <li>COMBINE statement uses current SEQUENCE_REF and
2895 GROUP_REF scope to group annotation rows</li>
2896 <li>Support '' style escaping of quotes in Newick
2898 <li>Group options for JABAWS service by command line name</li>
2899 <li>Empty tooltip shown for JABA service options with a
2900 link but no description</li>
2901 <li>Select primary source when selecting authority in
2902 database fetcher GUI</li>
2903 <li>Add .mfa to FASTA file extensions recognised by
2905 <li>Annotation label tooltip text wrap</li>
2910 <li>Slow scrolling when lots of annotation rows are
2912 <li>Lots of NPE (and slowness) after creating RNA
2913 secondary structure annotation line</li>
2914 <li>Sequence database accessions not imported when
2915 fetching alignments from Rfam</li>
2916 <li>Incorrect SHMR submission for sequences with
2918 <li>View all structures does not always superpose
2920 <li>Option widgets in service parameters not updated to
2921 reflect user or preset settings</li>
2922 <li>Null pointer exceptions for some services without
2923 presets or adjustable parameters</li>
2924 <li>Discover PDB IDs entry in structure menu doesn't
2925 discover PDB xRefs</li>
2926 <li>Exception encountered while trying to retrieve
2927 features with DAS</li>
2928 <li>Lowest value in annotation row isn't coloured
2929 when colour by annotation (per sequence) is coloured</li>
2930 <li>Keyboard mode P jumps to start of gapped region when
2931 residue follows a gap</li>
2932 <li>Jalview appears to hang importing an alignment with
2933 Wrap as default or after enabling Wrap</li>
2934 <li>'Right click to add annotations' message
2935 shown in wrap mode when no annotations present</li>
2936 <li>Disorder predictions fail with NPE if no automatic
2937 annotation already exists on alignment</li>
2938 <li>oninit javascript function should be called after
2939 initialisation completes</li>
2940 <li>Remove redundancy after disorder prediction corrupts
2941 alignment window display</li>
2942 <li>Example annotation file in documentation is invalid</li>
2943 <li>Grouped line graph annotation rows are not exported
2944 to annotation file</li>
2945 <li>Multi-harmony analysis cannot be run when only two
2947 <li>Cannot create multiple groups of line graphs with
2948 several 'combine' statements in annotation file</li>
2949 <li>Pressing return several times causes Number Format
2950 exceptions in keyboard mode</li>
2951 <li>Multi-harmony (SHMMR) method doesn't submit
2952 correct partitions for input data</li>
2953 <li>Translation from DNA to Amino Acids fails</li>
2954 <li>Jalview fail to load newick tree with quoted label</li>
2955 <li>--headless flag isn't understood</li>
2956 <li>ClassCastException when generating EPS in headless
2958 <li>Adjusting sequence-associated shading threshold only
2959 changes one row's threshold</li>
2960 <li>Preferences and Feature settings panel panel
2961 doesn't open</li>
2962 <li>hide consensus histogram also hides conservation and
2963 quality histograms</li>
2968 <td><div align="center">
2969 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2971 <td><em>Application</em>
2973 <li>Support for JABAWS 2.0 Services (AACon alignment
2974 conservation, protein disorder and Clustal Omega)</li>
2975 <li>JABAWS server status indicator in Web Services
2977 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2978 in Jalview alignment window</li>
2979 <li>Updated Jalview build and deploy framework for OSX
2980 mountain lion, windows 7, and 8</li>
2981 <li>Nucleotide substitution matrix for PCA that supports
2982 RNA and ambiguity codes</li>
2984 <li>Improved sequence database retrieval GUI</li>
2985 <li>Support fetching and database reference look up
2986 against multiple DAS sources (Fetch all from in 'fetch db
2988 <li>Jalview project improvements
2990 <li>Store and retrieve the 'belowAlignment'
2991 flag for annotation</li>
2992 <li>calcId attribute to group annotation rows on the
2994 <li>Store AACon calculation settings for a view in
2995 Jalview project</li>
2999 <li>horizontal scrolling gesture support</li>
3000 <li>Visual progress indicator when PCA calculation is
3002 <li>Simpler JABA web services menus</li>
3003 <li>visual indication that web service results are still
3004 being retrieved from server</li>
3005 <li>Serialise the dialogs that are shown when Jalview
3006 starts up for first time</li>
3007 <li>Jalview user agent string for interacting with HTTP
3009 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3011 <li>Examples directory and Groovy library included in
3012 InstallAnywhere distribution</li>
3013 </ul> <em>Applet</em>
3015 <li>RNA alignment and secondary structure annotation
3016 visualization applet example</li>
3017 </ul> <em>General</em>
3019 <li>Normalise option for consensus sequence logo</li>
3020 <li>Reset button in PCA window to return dimensions to
3022 <li>Allow seqspace or Jalview variant of alignment PCA
3024 <li>PCA with either nucleic acid and protein substitution
3026 <li>Allow windows containing HTML reports to be exported
3028 <li>Interactive display and editing of RNA secondary
3029 structure contacts</li>
3030 <li>RNA Helix Alignment Colouring</li>
3031 <li>RNA base pair logo consensus</li>
3032 <li>Parse sequence associated secondary structure
3033 information in Stockholm files</li>
3034 <li>HTML Export database accessions and annotation
3035 information presented in tooltip for sequences</li>
3036 <li>Import secondary structure from LOCARNA clustalw
3037 style RNA alignment files</li>
3038 <li>import and visualise T-COFFEE quality scores for an
3040 <li>'colour by annotation' per sequence option to
3041 shade each sequence according to its associated alignment
3043 <li>New Jalview Logo</li>
3044 </ul> <em>Documentation and Development</em>
3046 <li>documentation for score matrices used in Jalview</li>
3047 <li>New Website!</li>
3049 <td><em>Application</em>
3051 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3052 wsdbfetch REST service</li>
3053 <li>Stop windows being moved outside desktop on OSX</li>
3054 <li>Filetype associations not installed for webstart
3056 <li>Jalview does not always retrieve progress of a JABAWS
3057 job execution in full once it is complete</li>
3058 <li>revise SHMR RSBS definition to ensure alignment is
3059 uploaded via ali_file parameter</li>
3060 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3061 <li>View all structures superposed fails with exception</li>
3062 <li>Jnet job queues forever if a very short sequence is
3063 submitted for prediction</li>
3064 <li>Cut and paste menu not opened when mouse clicked on
3066 <li>Putting fractional value into integer text box in
3067 alignment parameter dialog causes Jalview to hang</li>
3068 <li>Structure view highlighting doesn't work on
3070 <li>View all structures fails with exception shown in
3072 <li>Characters in filename associated with PDBEntry not
3073 escaped in a platform independent way</li>
3074 <li>Jalview desktop fails to launch with exception when
3076 <li>Tree calculation reports 'you must have 2 or more
3077 sequences selected' when selection is empty</li>
3078 <li>Jalview desktop fails to launch with jar signature
3079 failure when java web start temporary file caching is
3081 <li>DAS Sequence retrieval with range qualification
3082 results in sequence xref which includes range qualification</li>
3083 <li>Errors during processing of command line arguments
3084 cause progress bar (JAL-898) to be removed</li>
3085 <li>Replace comma for semi-colon option not disabled for
3086 DAS sources in sequence fetcher</li>
3087 <li>Cannot close news reader when JABAWS server warning
3088 dialog is shown</li>
3089 <li>Option widgets not updated to reflect user settings</li>
3090 <li>Edited sequence not submitted to web service</li>
3091 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3092 <li>InstallAnywhere installer doesn't unpack and run
3093 on OSX Mountain Lion</li>
3094 <li>Annotation panel not given a scroll bar when
3095 sequences with alignment annotation are pasted into the
3097 <li>Sequence associated annotation rows not associated
3098 when loaded from Jalview project</li>
3099 <li>Browser launch fails with NPE on java 1.7</li>
3100 <li>JABAWS alignment marked as finished when job was
3101 cancelled or job failed due to invalid input</li>
3102 <li>NPE with v2.7 example when clicking on Tree
3103 associated with all views</li>
3104 <li>Exceptions when copy/paste sequences with grouped
3105 annotation rows to new window</li>
3106 </ul> <em>Applet</em>
3108 <li>Sequence features are momentarily displayed before
3109 they are hidden using hidefeaturegroups applet parameter</li>
3110 <li>loading features via javascript API automatically
3111 enables feature display</li>
3112 <li>scrollToColumnIn javascript API method doesn't
3114 </ul> <em>General</em>
3116 <li>Redundancy removal fails for rna alignment</li>
3117 <li>PCA calculation fails when sequence has been selected
3118 and then deselected</li>
3119 <li>PCA window shows grey box when first opened on OSX</li>
3120 <li>Letters coloured pink in sequence logo when alignment
3121 coloured with clustalx</li>
3122 <li>Choosing fonts without letter symbols defined causes
3123 exceptions and redraw errors</li>
3124 <li>Initial PCA plot view is not same as manually
3125 reconfigured view</li>
3126 <li>Grouped annotation graph label has incorrect line
3128 <li>Grouped annotation graph label display is corrupted
3129 for lots of labels</li>
3134 <div align="center">
3135 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3138 <td><em>Application</em>
3140 <li>Jalview Desktop News Reader</li>
3141 <li>Tweaked default layout of web services menu</li>
3142 <li>View/alignment association menu to enable user to
3143 easily specify which alignment a multi-structure view takes
3144 its colours/correspondences from</li>
3145 <li>Allow properties file location to be specified as URL</li>
3146 <li>Extend Jalview project to preserve associations
3147 between many alignment views and a single Jmol display</li>
3148 <li>Store annotation row height in Jalview project file</li>
3149 <li>Annotation row column label formatting attributes
3150 stored in project file</li>
3151 <li>Annotation row order for auto-calculated annotation
3152 rows preserved in Jalview project file</li>
3153 <li>Visual progress indication when Jalview state is
3154 saved using Desktop window menu</li>
3155 <li>Visual indication that command line arguments are
3156 still being processed</li>
3157 <li>Groovy script execution from URL</li>
3158 <li>Colour by annotation default min and max colours in
3160 <li>Automatically associate PDB files dragged onto an
3161 alignment with sequences that have high similarity and
3163 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3164 <li>'view structures' option to open many
3165 structures in same window</li>
3166 <li>Sort associated views menu option for tree panel</li>
3167 <li>Group all JABA and non-JABA services for a particular
3168 analysis function in its own submenu</li>
3169 </ul> <em>Applet</em>
3171 <li>Userdefined and autogenerated annotation rows for
3173 <li>Adjustment of alignment annotation pane height</li>
3174 <li>Annotation scrollbar for annotation panel</li>
3175 <li>Drag to reorder annotation rows in annotation panel</li>
3176 <li>'automaticScrolling' parameter</li>
3177 <li>Allow sequences with partial ID string matches to be
3178 annotated from GFF/Jalview features files</li>
3179 <li>Sequence logo annotation row in applet</li>
3180 <li>Absolute paths relative to host server in applet
3181 parameters are treated as such</li>
3182 <li>New in the JalviewLite javascript API:
3184 <li>JalviewLite.js javascript library</li>
3185 <li>Javascript callbacks for
3187 <li>Applet initialisation</li>
3188 <li>Sequence/alignment mouse-overs and selections</li>
3191 <li>scrollTo row and column alignment scrolling
3193 <li>Select sequence/alignment regions from javascript</li>
3194 <li>javascript structure viewer harness to pass
3195 messages between Jmol and Jalview when running as
3196 distinct applets</li>
3197 <li>sortBy method</li>
3198 <li>Set of applet and application examples shipped
3199 with documentation</li>
3200 <li>New example to demonstrate JalviewLite and Jmol
3201 javascript message exchange</li>
3203 </ul> <em>General</em>
3205 <li>Enable Jmol displays to be associated with multiple
3206 multiple alignments</li>
3207 <li>Option to automatically sort alignment with new tree</li>
3208 <li>User configurable link to enable redirects to a
3209 www.Jalview.org mirror</li>
3210 <li>Jmol colours option for Jmol displays</li>
3211 <li>Configurable newline string when writing alignment
3212 and other flat files</li>
3213 <li>Allow alignment annotation description lines to
3214 contain html tags</li>
3215 </ul> <em>Documentation and Development</em>
3217 <li>Add groovy test harness for bulk load testing to
3219 <li>Groovy script to load and align a set of sequences
3220 using a web service before displaying the result in the
3221 Jalview desktop</li>
3222 <li>Restructured javascript and applet api documentation</li>
3223 <li>Ant target to publish example html files with applet
3225 <li>Netbeans project for building Jalview from source</li>
3226 <li>ant task to create online javadoc for Jalview source</li>
3228 <td><em>Application</em>
3230 <li>User defined colourscheme throws exception when
3231 current built in colourscheme is saved as new scheme</li>
3232 <li>AlignFrame->Save in application pops up save
3233 dialog for valid filename/format</li>
3234 <li>Cannot view associated structure for UniProt sequence</li>
3235 <li>PDB file association breaks for UniProt sequence
3237 <li>Associate PDB from file dialog does not tell you
3238 which sequence is to be associated with the file</li>
3239 <li>Find All raises null pointer exception when query
3240 only matches sequence IDs</li>
3241 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3242 <li>Jalview project with Jmol views created with Jalview
3243 2.4 cannot be loaded</li>
3244 <li>Filetype associations not installed for webstart
3246 <li>Two or more chains in a single PDB file associated
3247 with sequences in different alignments do not get coloured
3248 by their associated sequence</li>
3249 <li>Visibility status of autocalculated annotation row
3250 not preserved when project is loaded</li>
3251 <li>Annotation row height and visibility attributes not
3252 stored in Jalview project</li>
3253 <li>Tree bootstraps are not preserved when saved as a
3254 Jalview project</li>
3255 <li>Envision2 workflow tooltips are corrupted</li>
3256 <li>Enabling show group conservation also enables colour
3257 by conservation</li>
3258 <li>Duplicate group associated conservation or consensus
3259 created on new view</li>
3260 <li>Annotation scrollbar not displayed after 'show
3261 all hidden annotation rows' option selected</li>
3262 <li>Alignment quality not updated after alignment
3263 annotation row is hidden then shown</li>
3264 <li>Preserve colouring of structures coloured by
3265 sequences in pre Jalview 2.7 projects</li>
3266 <li>Web service job parameter dialog is not laid out
3268 <li>Web services menu not refreshed after 'reset
3269 services' button is pressed in preferences</li>
3270 <li>Annotation off by one in Jalview v2_3 example project</li>
3271 <li>Structures imported from file and saved in project
3272 get name like jalview_pdb1234.txt when reloaded</li>
3273 <li>Jalview does not always retrieve progress of a JABAWS
3274 job execution in full once it is complete</li>
3275 </ul> <em>Applet</em>
3277 <li>Alignment height set incorrectly when lots of
3278 annotation rows are displayed</li>
3279 <li>Relative URLs in feature HTML text not resolved to
3281 <li>View follows highlighting does not work for positions
3283 <li><= shown as = in tooltip</li>
3284 <li>Export features raises exception when no features
3286 <li>Separator string used for serialising lists of IDs
3287 for javascript api is modified when separator string
3288 provided as parameter</li>
3289 <li>Null pointer exception when selecting tree leaves for
3290 alignment with no existing selection</li>
3291 <li>Relative URLs for datasources assumed to be relative
3292 to applet's codebase</li>
3293 <li>Status bar not updated after finished searching and
3294 search wraps around to first result</li>
3295 <li>StructureSelectionManager instance shared between
3296 several Jalview applets causes race conditions and memory
3298 <li>Hover tooltip and mouseover of position on structure
3299 not sent from Jmol in applet</li>
3300 <li>Certain sequences of javascript method calls to
3301 applet API fatally hang browser</li>
3302 </ul> <em>General</em>
3304 <li>View follows structure mouseover scrolls beyond
3305 position with wrapped view and hidden regions</li>
3306 <li>Find sequence position moves to wrong residue
3307 with/without hidden columns</li>
3308 <li>Sequence length given in alignment properties window
3310 <li>InvalidNumberFormat exceptions thrown when trying to
3311 import PDB like structure files</li>
3312 <li>Positional search results are only highlighted
3313 between user-supplied sequence start/end bounds</li>
3314 <li>End attribute of sequence is not validated</li>
3315 <li>Find dialog only finds first sequence containing a
3316 given sequence position</li>
3317 <li>Sequence numbering not preserved in MSF alignment
3319 <li>Jalview PDB file reader does not extract sequence
3320 from nucleotide chains correctly</li>
3321 <li>Structure colours not updated when tree partition
3322 changed in alignment</li>
3323 <li>Sequence associated secondary structure not correctly
3324 parsed in interleaved stockholm</li>
3325 <li>Colour by annotation dialog does not restore current
3327 <li>Hiding (nearly) all sequences doesn't work
3329 <li>Sequences containing lowercase letters are not
3330 properly associated with their pdb files</li>
3331 </ul> <em>Documentation and Development</em>
3333 <li>schemas/JalviewWsParamSet.xsd corrupted by
3334 ApplyCopyright tool</li>
3339 <div align="center">
3340 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3343 <td><em>Application</em>
3345 <li>New warning dialog when the Jalview Desktop cannot
3346 contact web services</li>
3347 <li>JABA service parameters for a preset are shown in
3348 service job window</li>
3349 <li>JABA Service menu entries reworded</li>
3353 <li>Modeller PIR IO broken - cannot correctly import a
3354 pir file emitted by Jalview</li>
3355 <li>Existing feature settings transferred to new
3356 alignment view created from cut'n'paste</li>
3357 <li>Improved test for mixed amino/nucleotide chains when
3358 parsing PDB files</li>
3359 <li>Consensus and conservation annotation rows
3360 occasionally become blank for all new windows</li>
3361 <li>Exception raised when right clicking above sequences
3362 in wrapped view mode</li>
3363 </ul> <em>Application</em>
3365 <li>multiple multiply aligned structure views cause cpu
3366 usage to hit 100% and computer to hang</li>
3367 <li>Web Service parameter layout breaks for long user
3368 parameter names</li>
3369 <li>Jaba service discovery hangs desktop if Jaba server
3376 <div align="center">
3377 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3380 <td><em>Application</em>
3382 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3383 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3386 <li>Web Services preference tab</li>
3387 <li>Analysis parameters dialog box and user defined
3389 <li>Improved speed and layout of Envision2 service menu</li>
3390 <li>Superpose structures using associated sequence
3392 <li>Export coordinates and projection as CSV from PCA
3394 </ul> <em>Applet</em>
3396 <li>enable javascript: execution by the applet via the
3397 link out mechanism</li>
3398 </ul> <em>Other</em>
3400 <li>Updated the Jmol Jalview interface to work with Jmol
3402 <li>The Jalview Desktop and JalviewLite applet now
3403 require Java 1.5</li>
3404 <li>Allow Jalview feature colour specification for GFF
3405 sequence annotation files</li>
3406 <li>New 'colour by label' keword in Jalview feature file
3407 type colour specification</li>
3408 <li>New Jalview Desktop Groovy API method that allows a
3409 script to check if it being run in an interactive session or
3410 in a batch operation from the Jalview command line</li>
3414 <li>clustalx colourscheme colours Ds preferentially when
3415 both D+E are present in over 50% of the column</li>
3416 </ul> <em>Application</em>
3418 <li>typo in AlignmentFrame->View->Hide->all but
3419 selected Regions menu item</li>
3420 <li>sequence fetcher replaces ',' for ';' when the ',' is
3421 part of a valid accession ID</li>
3422 <li>fatal OOM if object retrieved by sequence fetcher
3423 runs out of memory</li>
3424 <li>unhandled Out of Memory Error when viewing pca
3425 analysis results</li>
3426 <li>InstallAnywhere builds fail to launch on OS X java
3427 10.5 update 4 (due to apple Java 1.6 update)</li>
3428 <li>Installanywhere Jalview silently fails to launch</li>
3429 </ul> <em>Applet</em>
3431 <li>Jalview.getFeatureGroups() raises an
3432 ArrayIndexOutOfBoundsException if no feature groups are
3439 <div align="center">
3440 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3446 <li>Alignment prettyprinter doesn't cope with long
3448 <li>clustalx colourscheme colours Ds preferentially when
3449 both D+E are present in over 50% of the column</li>
3450 <li>nucleic acid structures retrieved from PDB do not
3451 import correctly</li>
3452 <li>More columns get selected than were clicked on when a
3453 number of columns are hidden</li>
3454 <li>annotation label popup menu not providing correct
3455 add/hide/show options when rows are hidden or none are
3457 <li>Stockholm format shown in list of readable formats,
3458 and parser copes better with alignments from RFAM.</li>
3459 <li>CSV output of consensus only includes the percentage
3460 of all symbols if sequence logo display is enabled</li>
3462 </ul> <em>Applet</em>
3464 <li>annotation panel disappears when annotation is
3466 </ul> <em>Application</em>
3468 <li>Alignment view not redrawn properly when new
3469 alignment opened where annotation panel is visible but no
3470 annotations are present on alignment</li>
3471 <li>pasted region containing hidden columns is
3472 incorrectly displayed in new alignment window</li>
3473 <li>Jalview slow to complete operations when stdout is
3474 flooded (fix is to close the Jalview console)</li>
3475 <li>typo in AlignmentFrame->View->Hide->all but
3476 selected Rregions menu item.</li>
3477 <li>inconsistent group submenu and Format submenu entry
3478 'Un' or 'Non'conserved</li>
3479 <li>Sequence feature settings are being shared by
3480 multiple distinct alignments</li>
3481 <li>group annotation not recreated when tree partition is
3483 <li>double click on group annotation to select sequences
3484 does not propagate to associated trees</li>
3485 <li>Mac OSX specific issues:
3487 <li>exception raised when mouse clicked on desktop
3488 window background</li>
3489 <li>Desktop menu placed on menu bar and application
3490 name set correctly</li>
3491 <li>sequence feature settings not wide enough for the
3492 save feature colourscheme button</li>
3501 <div align="center">
3502 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3505 <td><em>New Capabilities</em>
3507 <li>URL links generated from description line for
3508 regular-expression based URL links (applet and application)
3510 <li>Non-positional feature URL links are shown in link
3512 <li>Linked viewing of nucleic acid sequences and
3514 <li>Automatic Scrolling option in View menu to display
3515 the currently highlighted region of an alignment.</li>
3516 <li>Order an alignment by sequence length, or using the
3517 average score or total feature count for each sequence.</li>
3518 <li>Shading features by score or associated description</li>
3519 <li>Subdivide alignment and groups based on identity of
3520 selected subsequence (Make Groups from Selection).</li>
3521 <li>New hide/show options including Shift+Control+H to
3522 hide everything but the currently selected region.</li>
3523 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3524 </ul> <em>Application</em>
3526 <li>Fetch DB References capabilities and UI expanded to
3527 support retrieval from DAS sequence sources</li>
3528 <li>Local DAS Sequence sources can be added via the
3529 command line or via the Add local source dialog box.</li>
3530 <li>DAS Dbref and DbxRef feature types are parsed as
3531 database references and protein_name is parsed as
3532 description line (BioSapiens terms).</li>
3533 <li>Enable or disable non-positional feature and database
3534 references in sequence ID tooltip from View menu in
3536 <!-- <li>New hidden columns and rows and representatives capabilities
3537 in annotations file (in progress - not yet fully implemented)</li> -->
3538 <li>Group-associated consensus, sequence logos and
3539 conservation plots</li>
3540 <li>Symbol distributions for each column can be exported
3541 and visualized as sequence logos</li>
3542 <li>Optionally scale multi-character column labels to fit
3543 within each column of annotation row<!-- todo for applet -->
3545 <li>Optional automatic sort of associated alignment view
3546 when a new tree is opened.</li>
3547 <li>Jalview Java Console</li>
3548 <li>Better placement of desktop window when moving
3549 between different screens.</li>
3550 <li>New preference items for sequence ID tooltip and
3551 consensus annotation</li>
3552 <li>Client to submit sequences and IDs to Envision2
3554 <li><em>Vamsas Capabilities</em>
3556 <li>Improved VAMSAS synchronization (Jalview archive
3557 used to preserve views, structures, and tree display
3559 <li>Import of vamsas documents from disk or URL via
3561 <li>Sharing of selected regions between views and
3562 with other VAMSAS applications (Experimental feature!)</li>
3563 <li>Updated API to VAMSAS version 0.2</li>
3565 </ul> <em>Applet</em>
3567 <li>Middle button resizes annotation row height</li>
3570 <li>sortByTree (true/false) - automatically sort the
3571 associated alignment view by the tree when a new tree is
3573 <li>showTreeBootstraps (true/false) - show or hide
3574 branch bootstraps (default is to show them if available)</li>
3575 <li>showTreeDistances (true/false) - show or hide
3576 branch lengths (default is to show them if available)</li>
3577 <li>showUnlinkedTreeNodes (true/false) - indicate if
3578 unassociated nodes should be highlighted in the tree
3580 <li>heightScale and widthScale (1.0 or more) -
3581 increase the height or width of a cell in the alignment
3582 grid relative to the current font size.</li>
3585 <li>Non-positional features displayed in sequence ID
3587 </ul> <em>Other</em>
3589 <li>Features format: graduated colour definitions and
3590 specification of feature scores</li>
3591 <li>Alignment Annotations format: new keywords for group
3592 associated annotation (GROUP_REF) and annotation row display
3593 properties (ROW_PROPERTIES)</li>
3594 <li>XML formats extended to support graduated feature
3595 colourschemes, group associated annotation, and profile
3596 visualization settings.</li></td>
3599 <li>Source field in GFF files parsed as feature source
3600 rather than description</li>
3601 <li>Non-positional features are now included in sequence
3602 feature and gff files (controlled via non-positional feature
3603 visibility in tooltip).</li>
3604 <li>URL links generated for all feature links (bugfix)</li>
3605 <li>Added URL embedding instructions to features file
3607 <li>Codons containing ambiguous nucleotides translated as
3608 'X' in peptide product</li>
3609 <li>Match case switch in find dialog box works for both
3610 sequence ID and sequence string and query strings do not
3611 have to be in upper case to match case-insensitively.</li>
3612 <li>AMSA files only contain first column of
3613 multi-character column annotation labels</li>
3614 <li>Jalview Annotation File generation/parsing consistent
3615 with documentation (e.g. Stockholm annotation can be
3616 exported and re-imported)</li>
3617 <li>PDB files without embedded PDB IDs given a friendly
3619 <li>Find incrementally searches ID string matches as well
3620 as subsequence matches, and correctly reports total number
3624 <li>Better handling of exceptions during sequence
3626 <li>Dasobert generated non-positional feature URL
3627 link text excludes the start_end suffix</li>
3628 <li>DAS feature and source retrieval buttons disabled
3629 when fetch or registry operations in progress.</li>
3630 <li>PDB files retrieved from URLs are cached properly</li>
3631 <li>Sequence description lines properly shared via
3633 <li>Sequence fetcher fetches multiple records for all
3635 <li>Ensured that command line das feature retrieval
3636 completes before alignment figures are generated.</li>
3637 <li>Reduced time taken when opening file browser for
3639 <li>isAligned check prior to calculating tree, PCA or
3640 submitting an MSA to JNet now excludes hidden sequences.</li>
3641 <li>User defined group colours properly recovered
3642 from Jalview projects.</li>
3651 <div align="center">
3652 <strong>2.4.0.b2</strong><br> 28/10/2009
3657 <li>Experimental support for google analytics usage
3659 <li>Jalview privacy settings (user preferences and docs).</li>
3664 <li>Race condition in applet preventing startup in
3666 <li>Exception when feature created from selection beyond
3667 length of sequence.</li>
3668 <li>Allow synthetic PDB files to be imported gracefully</li>
3669 <li>Sequence associated annotation rows associate with
3670 all sequences with a given id</li>
3671 <li>Find function matches case-insensitively for sequence
3672 ID string searches</li>
3673 <li>Non-standard characters do not cause pairwise
3674 alignment to fail with exception</li>
3675 </ul> <em>Application Issues</em>
3677 <li>Sequences are now validated against EMBL database</li>
3678 <li>Sequence fetcher fetches multiple records for all
3680 </ul> <em>InstallAnywhere Issues</em>
3682 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3683 issue with installAnywhere mechanism)</li>
3684 <li>Command line launching of JARs from InstallAnywhere
3685 version (java class versioning error fixed)</li>
3692 <div align="center">
3693 <strong>2.4</strong><br> 27/8/2008
3696 <td><em>User Interface</em>
3698 <li>Linked highlighting of codon and amino acid from
3699 translation and protein products</li>
3700 <li>Linked highlighting of structure associated with
3701 residue mapping to codon position</li>
3702 <li>Sequence Fetcher provides example accession numbers
3703 and 'clear' button</li>
3704 <li>MemoryMonitor added as an option under Desktop's
3706 <li>Extract score function to parse whitespace separated
3707 numeric data in description line</li>
3708 <li>Column labels in alignment annotation can be centred.</li>
3709 <li>Tooltip for sequence associated annotation give name
3711 </ul> <em>Web Services and URL fetching</em>
3713 <li>JPred3 web service</li>
3714 <li>Prototype sequence search client (no public services
3716 <li>Fetch either seed alignment or full alignment from
3718 <li>URL Links created for matching database cross
3719 references as well as sequence ID</li>
3720 <li>URL Links can be created using regular-expressions</li>
3721 </ul> <em>Sequence Database Connectivity</em>
3723 <li>Retrieval of cross-referenced sequences from other
3725 <li>Generalised database reference retrieval and
3726 validation to all fetchable databases</li>
3727 <li>Fetch sequences from DAS sources supporting the
3728 sequence command</li>
3729 </ul> <em>Import and Export</em>
3730 <li>export annotation rows as CSV for spreadsheet import</li>
3731 <li>Jalview projects record alignment dataset associations,
3732 EMBL products, and cDNA sequence mappings</li>
3733 <li>Sequence Group colour can be specified in Annotation
3735 <li>Ad-hoc colouring of group in Annotation File using RGB
3736 triplet as name of colourscheme</li>
3737 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3739 <li>treenode binding for VAMSAS tree exchange</li>
3740 <li>local editing and update of sequences in VAMSAS
3741 alignments (experimental)</li>
3742 <li>Create new or select existing session to join</li>
3743 <li>load and save of vamsas documents</li>
3744 </ul> <em>Application command line</em>
3746 <li>-tree parameter to open trees (introduced for passing
3748 <li>-fetchfrom command line argument to specify nicknames
3749 of DAS servers to query for alignment features</li>
3750 <li>-dasserver command line argument to add new servers
3751 that are also automatically queried for features</li>
3752 <li>-groovy command line argument executes a given groovy
3753 script after all input data has been loaded and parsed</li>
3754 </ul> <em>Applet-Application data exchange</em>
3756 <li>Trees passed as applet parameters can be passed to
3757 application (when using "View in full
3758 application")</li>
3759 </ul> <em>Applet Parameters</em>
3761 <li>feature group display control parameter</li>
3762 <li>debug parameter</li>
3763 <li>showbutton parameter</li>
3764 </ul> <em>Applet API methods</em>
3766 <li>newView public method</li>
3767 <li>Window (current view) specific get/set public methods</li>
3768 <li>Feature display control methods</li>
3769 <li>get list of currently selected sequences</li>
3770 </ul> <em>New Jalview distribution features</em>
3772 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3773 <li>RELEASE file gives build properties for the latest
3774 Jalview release.</li>
3775 <li>Java 1.1 Applet build made easier and donotobfuscate
3776 property controls execution of obfuscator</li>
3777 <li>Build target for generating source distribution</li>
3778 <li>Debug flag for javacc</li>
3779 <li>.jalview_properties file is documented (slightly) in
3780 jalview.bin.Cache</li>
3781 <li>Continuous Build Integration for stable and
3782 development version of Application, Applet and source
3787 <li>selected region output includes visible annotations
3788 (for certain formats)</li>
3789 <li>edit label/displaychar contains existing label/char
3791 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3792 <li>shorter peptide product names from EMBL records</li>
3793 <li>Newick string generator makes compact representations</li>
3794 <li>bootstrap values parsed correctly for tree files with
3796 <li>pathological filechooser bug avoided by not allowing
3797 filenames containing a ':'</li>
3798 <li>Fixed exception when parsing GFF files containing
3799 global sequence features</li>
3800 <li>Alignment datasets are finalized only when number of
3801 references from alignment sequences goes to zero</li>
3802 <li>Close of tree branch colour box without colour
3803 selection causes cascading exceptions</li>
3804 <li>occasional negative imgwidth exceptions</li>
3805 <li>better reporting of non-fatal warnings to user when
3806 file parsing fails.</li>
3807 <li>Save works when Jalview project is default format</li>
3808 <li>Save as dialog opened if current alignment format is
3809 not a valid output format</li>
3810 <li>UniProt canonical names introduced for both das and
3812 <li>Histidine should be midblue (not pink!) in Zappo</li>
3813 <li>error messages passed up and output when data read
3815 <li>edit undo recovers previous dataset sequence when
3816 sequence is edited</li>
3817 <li>allow PDB files without pdb ID HEADER lines (like
3818 those generated by MODELLER) to be read in properly</li>
3819 <li>allow reading of JPred concise files as a normal
3821 <li>Stockholm annotation parsing and alignment properties
3822 import fixed for PFAM records</li>
3823 <li>Structure view windows have correct name in Desktop
3825 <li>annotation consisting of sequence associated scores
3826 can be read and written correctly to annotation file</li>
3827 <li>Aligned cDNA translation to aligned peptide works
3829 <li>Fixed display of hidden sequence markers and
3830 non-italic font for representatives in Applet</li>
3831 <li>Applet Menus are always embedded in applet window on
3833 <li>Newly shown features appear at top of stack (in
3835 <li>Annotations added via parameter not drawn properly
3836 due to null pointer exceptions</li>
3837 <li>Secondary structure lines are drawn starting from
3838 first column of alignment</li>
3839 <li>UniProt XML import updated for new schema release in
3841 <li>Sequence feature to sequence ID match for Features
3842 file is case-insensitive</li>
3843 <li>Sequence features read from Features file appended to
3844 all sequences with matching IDs</li>
3845 <li>PDB structure coloured correctly for associated views
3846 containing a sub-sequence</li>
3847 <li>PDB files can be retrieved by applet from Jar files</li>
3848 <li>feature and annotation file applet parameters
3849 referring to different directories are retrieved correctly</li>
3850 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3851 <li>Fixed application hang whilst waiting for
3852 splash-screen version check to complete</li>
3853 <li>Applet properly URLencodes input parameter values
3854 when passing them to the launchApp service</li>
3855 <li>display name and local features preserved in results
3856 retrieved from web service</li>
3857 <li>Visual delay indication for sequence retrieval and
3858 sequence fetcher initialisation</li>
3859 <li>updated Application to use DAS 1.53e version of
3860 dasobert DAS client</li>
3861 <li>Re-instated Full AMSA support and .amsa file
3863 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3871 <div align="center">
3872 <strong>2.3</strong><br> 9/5/07
3877 <li>Jmol 11.0.2 integration</li>
3878 <li>PDB views stored in Jalview XML files</li>
3879 <li>Slide sequences</li>
3880 <li>Edit sequence in place</li>
3881 <li>EMBL CDS features</li>
3882 <li>DAS Feature mapping</li>
3883 <li>Feature ordering</li>
3884 <li>Alignment Properties</li>
3885 <li>Annotation Scores</li>
3886 <li>Sort by scores</li>
3887 <li>Feature/annotation editing in applet</li>
3892 <li>Headless state operation in 2.2.1</li>
3893 <li>Incorrect and unstable DNA pairwise alignment</li>
3894 <li>Cut and paste of sequences with annotation</li>
3895 <li>Feature group display state in XML</li>
3896 <li>Feature ordering in XML</li>
3897 <li>blc file iteration selection using filename # suffix</li>
3898 <li>Stockholm alignment properties</li>
3899 <li>Stockhom alignment secondary structure annotation</li>
3900 <li>2.2.1 applet had no feature transparency</li>
3901 <li>Number pad keys can be used in cursor mode</li>
3902 <li>Structure Viewer mirror image resolved</li>
3909 <div align="center">
3910 <strong>2.2.1</strong><br> 12/2/07
3915 <li>Non standard characters can be read and displayed
3916 <li>Annotations/Features can be imported/exported to the
3918 <li>Applet allows editing of sequence/annotation/group
3919 name & description
3920 <li>Preference setting to display sequence name in
3922 <li>Annotation file format extended to allow
3923 Sequence_groups to be defined
3924 <li>Default opening of alignment overview panel can be
3925 specified in preferences
3926 <li>PDB residue numbering annotation added to associated
3932 <li>Applet crash under certain Linux OS with Java 1.6
3934 <li>Annotation file export / import bugs fixed
3935 <li>PNG / EPS image output bugs fixed
3941 <div align="center">
3942 <strong>2.2</strong><br> 27/11/06
3947 <li>Multiple views on alignment
3948 <li>Sequence feature editing
3949 <li>"Reload" alignment
3950 <li>"Save" to current filename
3951 <li>Background dependent text colour
3952 <li>Right align sequence ids
3953 <li>User-defined lower case residue colours
3956 <li>Menu item accelerator keys
3957 <li>Control-V pastes to current alignment
3958 <li>Cancel button for DAS Feature Fetching
3959 <li>PCA and PDB Viewers zoom via mouse roller
3960 <li>User-defined sub-tree colours and sub-tree selection
3962 <li>'New Window' button on the 'Output to Text box'
3967 <li>New memory efficient Undo/Redo System
3968 <li>Optimised symbol lookups and conservation/consensus
3970 <li>Region Conservation/Consensus recalculated after
3972 <li>Fixed Remove Empty Columns Bug (empty columns at end
3974 <li>Slowed DAS Feature Fetching for increased robustness.
3976 <li>Made angle brackets in ASCII feature descriptions
3978 <li>Re-instated Zoom function for PCA
3979 <li>Sequence descriptions conserved in web service
3981 <li>UniProt ID discoverer uses any word separated by
3983 <li>WsDbFetch query/result association resolved
3984 <li>Tree leaf to sequence mapping improved
3985 <li>Smooth fonts switch moved to FontChooser dialog box.
3992 <div align="center">
3993 <strong>2.1.1</strong><br> 12/9/06
3998 <li>Copy consensus sequence to clipboard</li>
4003 <li>Image output - rightmost residues are rendered if
4004 sequence id panel has been resized</li>
4005 <li>Image output - all offscreen group boundaries are
4007 <li>Annotation files with sequence references - all
4008 elements in file are relative to sequence position</li>
4009 <li>Mac Applet users can use Alt key for group editing</li>
4015 <div align="center">
4016 <strong>2.1</strong><br> 22/8/06
4021 <li>MAFFT Multiple Alignment in default Web Service list</li>
4022 <li>DAS Feature fetching</li>
4023 <li>Hide sequences and columns</li>
4024 <li>Export Annotations and Features</li>
4025 <li>GFF file reading / writing</li>
4026 <li>Associate structures with sequences from local PDB
4028 <li>Add sequences to exisiting alignment</li>
4029 <li>Recently opened files / URL lists</li>
4030 <li>Applet can launch the full application</li>
4031 <li>Applet has transparency for features (Java 1.2
4033 <li>Applet has user defined colours parameter</li>
4034 <li>Applet can load sequences from parameter
4035 "sequence<em>x</em>"
4041 <li>Redundancy Panel reinstalled in the Applet</li>
4042 <li>Monospaced font - EPS / rescaling bug fixed</li>
4043 <li>Annotation files with sequence references bug fixed</li>
4049 <div align="center">
4050 <strong>2.08.1</strong><br> 2/5/06
4055 <li>Change case of selected region from Popup menu</li>
4056 <li>Choose to match case when searching</li>
4057 <li>Middle mouse button and mouse movement can compress /
4058 expand the visible width and height of the alignment</li>
4063 <li>Annotation Panel displays complete JNet results</li>
4069 <div align="center">
4070 <strong>2.08b</strong><br> 18/4/06
4076 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4077 <li>Righthand label on wrapped alignments shows correct
4084 <div align="center">
4085 <strong>2.08</strong><br> 10/4/06
4090 <li>Editing can be locked to the selection area</li>
4091 <li>Keyboard editing</li>
4092 <li>Create sequence features from searches</li>
4093 <li>Precalculated annotations can be loaded onto
4095 <li>Features file allows grouping of features</li>
4096 <li>Annotation Colouring scheme added</li>
4097 <li>Smooth fonts off by default - Faster rendering</li>
4098 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4103 <li>Drag & Drop fixed on Linux</li>
4104 <li>Jalview Archive file faster to load/save, sequence
4105 descriptions saved.</li>
4111 <div align="center">
4112 <strong>2.07</strong><br> 12/12/05
4117 <li>PDB Structure Viewer enhanced</li>
4118 <li>Sequence Feature retrieval and display enhanced</li>
4119 <li>Choose to output sequence start-end after sequence
4120 name for file output</li>
4121 <li>Sequence Fetcher WSDBFetch@EBI</li>
4122 <li>Applet can read feature files, PDB files and can be
4123 used for HTML form input</li>
4128 <li>HTML output writes groups and features</li>
4129 <li>Group editing is Control and mouse click</li>
4130 <li>File IO bugs</li>
4136 <div align="center">
4137 <strong>2.06</strong><br> 28/9/05
4142 <li>View annotations in wrapped mode</li>
4143 <li>More options for PCA viewer</li>
4148 <li>GUI bugs resolved</li>
4149 <li>Runs with -nodisplay from command line</li>
4155 <div align="center">
4156 <strong>2.05b</strong><br> 15/9/05
4161 <li>Choose EPS export as lineart or text</li>
4162 <li>Jar files are executable</li>
4163 <li>Can read in Uracil - maps to unknown residue</li>
4168 <li>Known OutOfMemory errors give warning message</li>
4169 <li>Overview window calculated more efficiently</li>
4170 <li>Several GUI bugs resolved</li>
4176 <div align="center">
4177 <strong>2.05</strong><br> 30/8/05
4182 <li>Edit and annotate in "Wrapped" view</li>
4187 <li>Several GUI bugs resolved</li>
4193 <div align="center">
4194 <strong>2.04</strong><br> 24/8/05
4199 <li>Hold down mouse wheel & scroll to change font
4205 <li>Improved JPred client reliability</li>
4206 <li>Improved loading of Jalview files</li>
4212 <div align="center">
4213 <strong>2.03</strong><br> 18/8/05
4218 <li>Set Proxy server name and port in preferences</li>
4219 <li>Multiple URL links from sequence ids</li>
4220 <li>User Defined Colours can have a scheme name and added
4222 <li>Choose to ignore gaps in consensus calculation</li>
4223 <li>Unix users can set default web browser</li>
4224 <li>Runs without GUI for batch processing</li>
4225 <li>Dynamically generated Web Service Menus</li>
4230 <li>InstallAnywhere download for Sparc Solaris</li>
4236 <div align="center">
4237 <strong>2.02</strong><br> 18/7/05
4243 <li>Copy & Paste order of sequences maintains
4244 alignment order.</li>
4250 <div align="center">
4251 <strong>2.01</strong><br> 12/7/05
4256 <li>Use delete key for deleting selection.</li>
4257 <li>Use Mouse wheel to scroll sequences.</li>
4258 <li>Help file updated to describe how to add alignment
4260 <li>Version and build date written to build properties
4262 <li>InstallAnywhere installation will check for updates
4263 at launch of Jalview.</li>
4268 <li>Delete gaps bug fixed.</li>
4269 <li>FileChooser sorts columns.</li>
4270 <li>Can remove groups one by one.</li>
4271 <li>Filechooser icons installed.</li>
4272 <li>Finder ignores return character when searching.
4273 Return key will initiate a search.<br>
4280 <div align="center">
4281 <strong>2.0</strong><br> 20/6/05
4286 <li>New codebase</li>